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Find video protocols related to scientific articles indexed in Pubmed.
Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation.
ACS Synth Biol
PUBLISHED: 11-20-2014
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In microbial communities, bacterial populations are commonly controlled using indiscriminate, broad range antibiotics. There are few ways to target specific strains effectively without disrupting the entire microbiome and local environment. Here we use conjugation, a natural DNA horizontal transfer process among bacterial species, to deliver an engineered CRISPR interference (CRISPRi) system for targeting specific genes in recipient Escherichia coli cells. We show that delivery of the CRISPRi system is successful and can specifically repress a reporter gene in recipient cells, thereby establishing a new tool for gene regulation across bacterial cells and potentially for bacterial population control.
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Sample-Averaged Biexciton Quantum Yield Measured by Solution-Phase Photon Correlation.
Nano Lett.
PUBLISHED: 11-20-2014
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The brightness of nanoscale optical materials such as semiconductor nanocrystals is currently limited in high excitation flux applications by inefficient multiexciton fluorescence. We have devised a solution-phase photon correlation measurement that can conveniently and reliably measure the average biexciton-to-exciton quantum yield ratio of an entire sample without user selection bias. This technique can be used to investigate the multiexciton recombination dynamics of a broad scope of synthetically underdeveloped materials, including those with low exciton quantum yields and poor fluorescence stability. Here, we have applied this method to measure weak biexciton fluorescence in samples of visible-emitting InP/ZnS and InAs/ZnS core/shell nanocrystals, and to demonstrate that a rapid CdS shell growth procedure can markedly increase the biexciton fluorescence of CdSe nanocrystals.
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Early versus On-Demand Nasoenteric Tube Feeding in Acute Pancreatitis.
N. Engl. J. Med.
PUBLISHED: 11-20-2014
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Background Early enteral feeding through a nasoenteric feeding tube is often used in patients with severe acute pancreatitis to prevent gut-derived infections, but evidence to support this strategy is limited. We conducted a multicenter, randomized trial comparing early nasoenteric tube feeding with an oral diet at 72 hours after presentation to the emergency department in patients with acute pancreatitis. Methods We enrolled patients with acute pancreatitis who were at high risk for complications on the basis of an Acute Physiology and Chronic Health Evaluation II score of 8 or higher (on a scale of 0 to 71, with higher scores indicating more severe disease), an Imrie or modified Glasgow score of 3 or higher (on a scale of 0 to 8, with higher scores indicating more severe disease), or a serum C-reactive protein level of more than 150 mg per liter. Patients were randomly assigned to nasoenteric tube feeding within 24 hours after randomization (early group) or to an oral diet initiated 72 hours after presentation (on-demand group), with tube feeding provided if the oral diet was not tolerated. The primary end point was a composite of major infection (infected pancreatic necrosis, bacteremia, or pneumonia) or death during 6 months of follow-up. Results A total of 208 patients were enrolled at 19 Dutch hospitals. The primary end point occurred in 30 of 101 patients (30%) in the early group and in 28 of 104 (27%) in the on-demand group (risk ratio, 1.07; 95% confidence interval, 0.79 to 1.44; P=0.76). There were no significant differences between the early group and the on-demand group in the rate of major infection (25% and 26%, respectively; P=0.87) or death (11% and 7%, respectively; P=0.33). In the on-demand group, 72 patients (69%) tolerated an oral diet and did not require tube feeding. Conclusions This trial did not show the superiority of early nasoenteric tube feeding, as compared with an oral diet after 72 hours, in reducing the rate of infection or death in patients with acute pancreatitis at high risk for complications. (Funded by the Netherlands Organization for Health Research and Development and others; PYTHON Current Controlled Trials number, ISRCTN18170985 .).
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Community-onset Gram-negative Surveillance Program annual report, 2012.
Commun Dis Intell Q Rep
PUBLISHED: 11-20-2014
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The Australian Group on Antimicrobial Resistance performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2012 survey focussed on community-onset infections, examining isolates from urinary tract infections from patients presenting to outpatient clinics, emergency departments or to community practitioners. In 2012, 2,025 Escherichia coli, 538 Klebsiella species and 239 Enterobacter species were tested using a commercial automated method (Vitek 2, BioMérieux) and results were analysed using Clinical and Laboratory Standards Institute breakpoints from January 2012. Of the key resistances, non-susceptibility to the third-generation cephalosporin, ceftriaxone, was found in 4.2% of E. coli and 4.6%-6.9% of Klebsiella spp. Non-susceptibility rates to ciprofloxacin were 6.9% for E. coli, 0.0%-3.5% for Klebsiella spp. and 0.8%-1.9% in Enterobacter spp, and resistance rates to piperacillin-tazobactam were 1.7%, 0.7%-9.2%, and 8.8%-11.4% for the same 3 groups respectively. Only 1 Enterobacter cloacae was shown to harbour a carbapenemase (IMP-4). Commun Dis Intell 2014;38(1):E54-E58.
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Hospital-onset Gram-negative Surveillance Program annual report, 2011.
Commun Dis Intell Q Rep
PUBLISHED: 11-20-2014
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The Australian Group on Antimicrobial Resistance performs regular period-prevalence studies to monitor changes in antimicrobial resistance in selected enteric Gram-negative pathogens. The 2011 survey focussed on hospital-onset infections, examining isolates from all specimens presumed to be causing disease. In 2011, 1,827 Escherichia coli, 537 Klebsiella species and 269 Enterobacter species were tested using a commercial automated method (Vitek 2, BioMérieux) and results were analysed using Clinical and Laboratory Standards Institute breakpoints from January 2012. Of the key resistances, non-susceptibilty to the third-generation cephalosporin, ceftriaxone, was found in 9.6% of E. coli and 9.5%-12.1% of Klebsiella spp. Non-susceptibility rates to ciprofloxacin were 10.6% for E. coli, 0.0%-8.3% for Klebsiella spp. and 0.0%-5.0% in Enterobacter spp. Resistance rates to gentamicin were 8.6%, 2.9%-10.9%, and 0.0%-15.6% for the same 3 groups respectively. Eight strains, 5 Klebsiella spp. and 3 Enterobacter spp. were shown to harbour a carbapenemase (IMP-4). Commun Dis Intell 2014;38 (1):E49-E53.
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Hepatitis A outbreak associated with kava drinking.
Commun Dis Intell Q Rep
PUBLISHED: 11-20-2014
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Hepatitis A is caused by the hepatitis A virus (HAV), with transmission occurring through the faecal-oral route. In May 2013, a case of hepatitis A infection was reported to a Western Australian regional public health unit, with infection acquired in Fiji. Following this, 2 further cases were linked to the index case by kava drinking and 1 further case was a household contact of a secondary case. This outbreak highlights that the preparation of kava drink and/or the use of a common drinking vessel could be a vehicle for the transmission of HAV.
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The Significance of Preoperative Impaired Sensorium on Surgical Outcomes in Nonemergent General Surgical Operations.
JAMA Surg
PUBLISHED: 11-20-2014
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With an aging population, preoperative assessment of the frail older adult requires evaluation beyond simply accounting for chronic diseases. Impaired cognition is a recognized characteristic of the frail older adult.
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Serological Evidence of Ongoing Transmission of Dengue Virus in Permanent Residents of Key West, Florida.
Vector Borne Zoonotic Dis.
PUBLISHED: 11-20-2014
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Abstract Introduction: Dengue fever is the most important mosquito-borne viral disease in the world, with 40% of the global population at risk of infection. Dengue virus is responsible for infections in over 100 countries, including the Americas and Caribbean Basin; however, it has been largely eradicated from the United States through the implementation of effective vector control programs. However, between 2009 and 2010, 27 permanent residents of Key West, Florida, were reported to have locally acquired infections, marking the first autochthonous cases detected in Florida since 1934. Despite this recent and unusual transmission, and the potential risk of serious illness associated with sequential infections, no active surveillance had been conducted since. Materials and Methods: A serosurvey of permanent residents of Key West, Florida, was conducted in March of 2012. After informed consent, enrolled participants (n=173) were given a dengue virus rapid diagnostic test and completed a corresponding questionnaire. Results: The presence of immunoglobulin G (IgG) antibodies was indicated in 12 participants (6.9%), all of whom reported travel to endemic countries within the past 2 years. Surprisingly, six participants (3.5%) without any recent travel outside the state of Florida gave positive results for IgM antibodies. The presence of birdbaths and bromeliads on the property and sleeping outdoors emerged as significant factors related to previous exposure, whereas home air conditioning without the use of open windows and the use of mosquito repellent were protective. Conclusions: These findings suggest local transmission occurred in Key West in early 2012, indicating that transmission may not have subsided in 2010.
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Australian enterococcal sepsis outcome progamme, 2011.
Commun Dis Intell Q Rep
PUBLISHED: 11-14-2014
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From 1 January to 31 December 2011, 29 institutions around Australia participated in the Australian Enterococcal Sepsis Outcome Programme (AESOP). The aim of AESOP 2011 was to determine the proportion of enterococcal bacteraemia isolates in Australia that are antimicrobial resistant, with particular emphasis on susceptibility to ampicillin and the glycopeptides, and to characterise the molecular epidemiology of the Enterococcus faecalis and E. faecium isolates. Of the 1,079 unique episodes of bacteraemia investigated, 95.8% were caused by either E. faecalis (61.0%) or E. faecium (34.8%). Ampicillin resistance was detected in 90.4% of E. faecium but not detected in E. faecalis. Using Clinical and Laboratory Standards Institute breakpoints (CLSI), vancomycin non-susceptibility was reported in 0.6% and 31.4% of E. faecalis and E. faecium respectively and was predominately due to the acquisition of the vanB operon. Approximately 1 in 6 vanB E. faecium isolates however, had an minimum inhibitory concentration at or below the CLSI vancomycin susceptible breakpoint of ? 4 mg/L. Overall, 37% of E. faecium harboured vanA or vanB genes. Although molecular typing identified 126 E. faecalis pulsed-field gel electrophoresis (PFGE) pulsotypes, more than 50% belonged to 2 pulsotypes that were isolated across Australia. E. faecium consisted of 73 PFGE pulsotypes from which 43 multilocus sequence types were identified. Almost 90% of the E. faecium were identified as clonal complex 17 clones, of which approximately half were characterised as sequence type 203, which was isolated Australia-wide. In conclusion, the AESOP 2011 has shown that although polyclonal, enterococcal bacteraemias in Australia are frequently caused by ampicillin-resistant vanB E. faecium.
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Evolution of invasion in a diverse set of fusobacterium species.
MBio
PUBLISHED: 11-06-2014
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The diverse Fusobacterium genus contains species implicated in multiple clinical pathologies, including periodontal disease, preterm birth, and colorectal cancer. The lack of genetic tools for manipulating these organisms leaves us with little understanding of the genes responsible for adherence to and invasion of host cells. Actively invading Fusobacterium species can enter host cells independently, whereas passively invading species need additional factors, such as compromise of mucosal integrity or coinfection with other microbes. We applied whole-genome sequencing and comparative analysis to study the evolution of active and passive invasion strategies and to infer factors associated with active forms of host cell invasion. The evolution of active invasion appears to have followed an adaptive radiation in which two of the three fusobacterial lineages acquired new genes and underwent expansions of ancestral genes that enable active forms of host cell invasion. Compared to passive invaders, active invaders have much larger genomes, encode FadA-related adhesins, and possess twice as many genes encoding membrane-related proteins, including a large expansion of surface-associated proteins containing the MORN2 domain of unknown function. We predict a role for proteins containing MORN2 domains in adhesion and active invasion. In the largest and most comprehensive comparison of sequenced Fusobacterium species to date, we have generated a testable model for the molecular pathogenesis of Fusobacterium infection and illuminate new therapeutic or diagnostic strategies.
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Interventions to Reduce Sedentary Behavior.
Med Sci Sports Exerc
PUBLISHED: 09-16-2014
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This paper reports on presentations and discussion from the working group on "Influences on Sedentary Behavior & Interventions" as part of the Sedentary Behavior: Identifying Research Priorities Workshop.
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Feasibility of the hydrogen sulfide test for the assessment of drinking water quality in post-earthquake Haiti.
Environ Monit Assess
PUBLISHED: 09-03-2014
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In 2010, a magnitude 7.0 earthquake struck Haiti, severely damaging the drinking and wastewater infrastructure and leaving millions homeless. Compounding this problem, the introduction of Vibrio cholerae resulted in a massive cholera outbreak that infected over 700,000 people and threatened the safety of Haiti's drinking water. To mitigate this public health crisis, non-government organizations installed thousands of wells to provide communities with safe drinking water. However, despite increased access, Haiti currently lacks the monitoring capacity to assure the microbial safety of any of its water resources. For these reasons, this study was designed to assess the feasibility of using a simple, low-cost method to detect indicators of fecal contamination of drinking water that could be implemented at the community level. Water samples from 358 sources of drinking water in the Léogâne flood basin were screened with a commercially available hydrogen sulfide test and a standard membrane method for the enumeration of thermotolerant coliforms. When compared with the gold standard method, the hydrogen sulfide test had a sensitivity of 65 % and a specificity of 93 %. While the sensitivity of the assay increased at higher fecal coliform concentrations, it never exceeded 88 %, even with fecal coliform concentrations greater than 100 colony-forming units per 100 ml. While its simplicity makes the hydrogen sulfide test attractive for assessing water quality in low-resource settings, the low sensitivity raises concerns about its use as the sole indicator of the presence or absence of fecal coliforms in individual or community water sources.
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Minimally invasive intervention for infected necrosis in acute pancreatitis.
Expert Rev Med Devices
PUBLISHED: 08-14-2014
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Infected necrosis is the main indication for invasive intervention in acute necrotizing pancreatitis. The 2013 IAP/APA guidelines state that percutaneous catheter drainage should be the first step in the treatment of infected necrosis. In 50-65% of patients, additional necrosectomy is required after catheter drainage, which was traditionally done by open necrosectomy. Driven by the perceived lower complication rate, there is an increasing trend toward minimally invasive percutaneous and endoscopic transluminal necrosectomy. The authors present an overview of current minimally invasive treatment options for necrotizing pancreatitis and review recent developments in clinical studies.
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Tryptophan supplementation and postoperative delirium--a randomized controlled trial.
J Am Geriatr Soc
PUBLISHED: 08-12-2014
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To determine whether the postoperative administration of tryptophan would be beneficial for elderly adults undergoing surgery who are at risk of developing postoperative delirium.
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Childhood florid follicular hyperplasia with immunoglobulin light-chain restriction in the gastrointestinal tract.
Histopathology
PUBLISHED: 08-11-2014
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Immunoglobulin light-chain expression is used routinely as an indirect marker of clonality for recognizing B cell lymphoproliferative disorders.
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The upside of failure: how regional student groups learn from their mistakes.
PLoS Comput. Biol.
PUBLISHED: 08-01-2014
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Success is the result of planning, hard work, determination, foresight, and a little bit of luck. Unfortunately, nobody has thought to pave the road to success. Although failure can be discouraging and time-consuming, it presents incredible learning opportunities-the biggest difference between those who succeed and those who abandon their projects lies in their response to adversity. This article reviews events undertaken by the Regional Student Groups (RSGs) in India and Argentina, the problems they encountered, and what can be learned from them. RSG-India attempted to organize an online scientific meeting (also known as a virtual conference) with geographically dispersed stakeholders, a totally new concept for them. RSG-Argentina tackled the challenge of organizing a two-day symposium, their first event ever. Some of the complications they faced were easy to fix, others led to the cancellation of activities, and all of them resulted in valuable lessons. The main goal of this article is to highlight, through their experiences, the universal importance of a healthy panel of contingency plans.
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How hemostatic agents interact with the coagulation cascade.
AORN J
PUBLISHED: 08-01-2014
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Hemostasis is a critical component of the preservation of hemodynamic stability and operative visibility during surgery. Initially, hemostasis is achieved via the careful application of direct pressure to allow time for the coagulation cascade to create a fibrin and platelet plug. Other first-line methods of hemostasis in surgery include repair or ligation of the bleeding vessel with sutures, clips, or staples and coagulation of the bleeding site with a thermal energy-based device. When these methods are insufficient to provide adequate hemostasis, topical hemostatic agents can be used to augment the creation of a clot during surgery. A basic understanding of how and where these products interact with the coagulation cascade is essential to achieving optimal hemostasis outcomes.
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Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction.
Genome Res.
PUBLISHED: 07-14-2014
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The comprehension of protein and DNA binding in vivo is essential to understand gene regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a global map of the regulatory binding network. Most ChIP-seq analysis tools focus on identifying binding regions from coverage enrichment. However, less work has been performed to infer the physical and regulatory details inside the enriched regions. This research extends a previous blind-deconvolution approach to develop a post-peak-calling algorithm that improves binding site resolution and predicts cooperative interactions. At the core of our new method is a physically motivated model that characterizes the binding signal as an extreme value distribution. This model suggests a mathematical framework to study physical properties of DNA shearing from the ChIP-seq coverage. The model explains the ChIP-seq coverage with two signals: The first considers DNA fragments with only a single binding event, whereas the second considers fragments with two binding events (a double-binding signal). The model incorporates motif discovery and is able to detect multiple sites in an enriched region with single-nucleotide resolution, high sensitivity, and high specificity. Our method improves peak caller sensitivity, from less than 45% up to 94%, at a false positive rate < 11% for a set of 47 experimentally validated prokaryotic sites. It also improves resolution of highly enriched regions of large-scale eukaryotic data sets. The double-binding signal provides a novel application in ChIP-seq analysis: the identification of cooperative interaction. Predictions of known cooperative binding sites show a 0.85 area under an ROC curve.
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Soft skills: an important asset acquired from organizing regional student group activities.
PLoS Comput. Biol.
PUBLISHED: 07-01-2014
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Contributing to a student organization, such as the International Society for Computational Biology Student Council (ISCB-SC) and its Regional Student Group (RSG) program, takes time and energy. Both are scarce commodities, especially when you are trying to find your place in the world of computational biology as a graduate student. It comes as no surprise that organizing ISCB-SC-related activities sometimes interferes with day-to-day research and shakes up your priority list. However, we unanimously agree that the rewards, both in the short as well as the long term, make the time spent on these extracurricular activities more than worth it. In this article, we will explain what makes this so worthwhile: soft skills.
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Dual acquisition of (18)F-FMISO and (18)F-FDOPA.
Phys Med Biol
PUBLISHED: 06-24-2014
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Metabolic imaging using positron emission tomography (PET) has found increasing clinical use for the management of infiltrating tumours such as glioma. However, the heterogeneous biological nature of tumours and intrinsic treatment resistance in some regions means that knowledge of multiple biological factors is needed for effective treatment planning. For example, the use of (18)F-FDOPA to identify infiltrative tumour and (18)F-FMISO for localizing hypoxic regions. Performing multiple PET acquisitions is impractical in many clinical settings, but previous studies suggest multiplexed PET imaging could be viable. The fidelity of the two signals is affected by the injection interval, scan timing and injected dose. The contribution of this work is to propose a framework to explicitly trade-off signal fidelity with logistical constraints when designing the imaging protocol. The particular case of estimating (18)F-FMISO from a single frame prior to injection of (18)F-FDOPA is considered. Theoretical experiments using simulations for typical biological scenarios in humans demonstrate that results comparable to a pair of single-tracer acquisitions can be obtained provided protocol timings are carefully selected. These results were validated using a pre-clinical data set that was synthetically multiplexed. The results indicate that the dual acquisition of (18)F-FMISO and (18)F-FDOPA could be feasible in the clinical setting. The proposed framework could also be used to design protocols for other tracers.
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Energy harvesting of non-emissive triplet excitons in tetracene by emissive PbS nanocrystals.
Nat Mater
PUBLISHED: 06-09-2014
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Triplet excitons are ubiquitous in organic optoelectronics, but they are often an undesirable energy sink because they are spin-forbidden from emitting light and their high binding energy hinders the generation of free electron-hole pairs. Harvesting their energy is consequently an important technological challenge. Here, we demonstrate direct excitonic energy transfer from 'dark' triplets in the organic semiconductor tetracene to colloidal PbS nanocrystals, thereby successfully harnessing molecular triplet excitons in the near infrared. Steady-state excitation spectra, supported by transient photoluminescence studies, demonstrate that the transfer efficiency is at least (90 ± 13)%. The mechanism is a Dexter hopping process consisting of the simultaneous exchange of two electrons. Triplet exciton transfer to nanocrystals is expected to be broadly applicable in solar and near-infrared light-emitting applications, where effective molecular phosphors are lacking at present. In particular, this route to 'brighten' low-energy molecular triplet excitons may permit singlet exciton fission sensitization of conventional silicon solar cells.
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Pacific freshening drives Pliocene cooling and Asian monsoon intensification.
Sci Rep
PUBLISHED: 06-05-2014
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The monsoon is a fundamental component of Earth's climate. The Pliocene warm period is characterized by long-term global cooling yet concurrent monsoon dynamics are poorly known. Here we present the first fully quantified and calibrated reconstructions of separate Pliocene air temperature and East Asian summer monsoon precipitation histories on the Chinese Loess Plateau through joint analysis of loess/red clay magnetic parameters with different sensitivities to air temperature and precipitation. East Asian summer monsoon precipitation shows an intensified trend, paradoxically at the same time that climate cooled. We propose a hitherto unrecognized feedback where persistently intensified East Asian summer monsoon during the late Pliocene, triggered by the gradual closure of the Panama Seaway, reinforced late Pliocene Pacific freshening, sea-ice development and ice volume increase, culminating in initiation of the extensive Northern Hemisphere glaciations of the Quaternary Ice Age. This feedback mechanism represents a fundamental reinterpretation of the origin of the Quaternary glaciations and the impact of the monsoon.
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Age-specific malaria seroprevalence rates: a cross-sectional analysis of malaria transmission in the Ouest and Sud-Est departments of Haiti.
Malar. J.
PUBLISHED: 06-03-2014
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Malaria transmission continues to occur in Haiti, with 25,423 confirmed cases of Plasmodium falciparum and 161,236 suspected infections reported in 2012. At low prevalence levels, passive surveillance measures, which rely primarily on reports from health systems, becomes less appropriate for capturing annual malaria incidence. To improve understanding of malaria transmission in Haiti, participants from the Ouest and Sud-Est departments were screened using a highly sensitive enzyme-linked immunosorbent assay (ELISA).
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Kappa and lambda light chain mRNA in situ hybridization compared to flow cytometry and immunohistochemistry in B cell lymphomas.
Diagn Pathol
PUBLISHED: 03-18-2014
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Detection of B cell clonality is useful for assisting in the diagnosis of B cell lymphomas. Clonality assessment can be accomplished through evaluation of KAPPA and LAMBDA light chain expression. Currently, only slide based methods are available for the majority of patient biopsies and do not detect light chain protein or mRNA in many B-cell lymphomas. Herein we evaluated a new method, known as colorimetric in situ hybridization (CISH), with improved sensitivity and multiplexing capacity, for its usefulness in clonality detection in mature B cell malignancies.
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Preoperative characteristics of patients with presumed pancreatic cancer but ultimately benign disease: a multicenter series of 344 pancreatoduodenectomies.
Ann. Surg. Oncol.
PUBLISHED: 02-28-2014
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Preoperative differentiation between malignant and benign pancreatic tumors can be difficult. Consequently, a proportion of patients undergoing pancreatoduodenectomy for suspected malignancy will ultimately have benign disease. The aim of this study was to compare preoperative clinical and diagnostic characteristics of patients with unexpected benign disease after pancreatoduodenectomy with those of patients with confirmed (pre)malignant disease.
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Dictyostelium discoideum Dgat2 can substitute for the essential function of Dgat1 in triglyceride production but not in ether lipid synthesis.
Eukaryotic Cell
PUBLISHED: 02-21-2014
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Triacylglycerol (TAG), the common energy storage molecule, is formed from diacylglycerol and a coenzyme A-activated fatty acid by the action of an acyl coenzyme A:diacylglycerol acyltransferase (DGAT). In order to conduct this step, most organisms rely on more than one enzyme. The two main candidates in Dictyostelium discoideum are Dgat1 and Dgat2. We show, by creating single and double knockout mutants, that the endoplasmic reticulum (ER)-localized Dgat1 enzyme provides the predominant activity, whereas the lipid droplet constituent Dgat2 contributes less activity. This situation may be opposite from what is seen in mammalian cells. Dictyostelium Dgat2 is specialized for the synthesis of TAG, as is the mammalian enzyme. In contrast, mammalian DGAT1 is more promiscuous regarding its substrates, producing diacylglycerol, retinyl esters, and waxes in addition to TAG. The Dictyostelium Dgat1, however, produces TAG, wax esters, and, most interestingly, also neutral ether lipids, which represent a significant constituent of lipid droplets. Ether lipids had also been found in mammalian lipid droplets, but the role of DGAT1 in their synthesis was unknown. The ability to form TAG through either Dgat1 or Dgat2 activity is essential for Dictyostelium to grow on bacteria, its natural food substrate.
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Effect of radiofrequency energy emitted from monopolar "Bovie" instruments on cardiac implantable electronic devices.
J. Am. Coll. Surg.
PUBLISHED: 01-31-2014
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The monopolar "Bovie" instrument emits radiofrequency energy that can disrupt the function of other implanted electronic devices through a phenomenon termed electromagnetic interference. The purpose of this study was to quantify the electromagnetic interference occurring on cardiac implantable devices (CIEDs) resulting from monopolar instrument use in common, modifiable clinical scenarios.
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Skin and soft tissue infections caused by nontuberculous mycobacteria.
Curr. Opin. Infect. Dis.
PUBLISHED: 01-28-2014
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Skin and soft tissues infections (SSTIs) caused by nontuberculous mycobacteria (NTM) are underrecognized and difficult to treat. Controversies exist for optimal medical management and the role of surgery. Defining the epidemiology in the environment, in animals and in healthcare aids disease prevention. This review focuses on recent advances in epidemiology, risk factors, diagnostics and therapy.
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A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification.
Plant Physiol.
PUBLISHED: 01-22-2014
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Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation, this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis (Arabidopsis thaliana) cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional chromatin immunoprecipitation and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and coexpression network analyses demonstrates the quality of the E2Fa TChAP sequencing data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency.
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ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development.
Plant Cell
PUBLISHED: 01-17-2014
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The transcriptional coactivator ANGUSTIFOLIA3 (AN3) stimulates cell proliferation during Arabidopsis thaliana leaf development, but the molecular mechanism is largely unknown. Here, we show that inducible nuclear localization of AN3 during initial leaf growth results in differential expression of important transcriptional regulators, including GROWTH REGULATING FACTORs (GRFs). Chromatin purification further revealed the presence of AN3 at the loci of GRF5, GRF6, CYTOKININ RESPONSE FACTOR2, CONSTANS-LIKE5 (COL5), HECATE1 (HEC1), and ARABIDOPSIS RESPONSE REGULATOR4 (ARR4). Tandem affinity purification of protein complexes using AN3 as bait identified plant SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complexes formed around the ATPases BRAHMA (BRM) or SPLAYED. Moreover, SWI/SNF ASSOCIATED PROTEIN 73B (SWP73B) is recruited by AN3 to the promoters of GRF5, GRF3, COL5, and ARR4, and both SWP73B and BRM occupy the HEC1 promoter. Furthermore, we show that AN3 and BRM genetically interact. The data indicate that AN3 associates with chromatin remodelers to regulate transcription. In addition, modification of SWI3C expression levels increases leaf size, underlining the importance of chromatin dynamics for growth regulation. Our results place the SWI/SNF-AN3 module as a major player at the transition from cell proliferation to cell differentiation in a developing leaf.
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BCL2 antibodies targeted at different epitopes detect varying levels of protein expression and correlate with frequent gene amplification in diffuse large B-cell lymphoma.
Hum. Pathol.
PUBLISHED: 01-06-2014
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Patients with aggressive, BCL2 protein-positive (+) diffuse large B-cell lymphoma (DLBCL) often experience rapid disease progression that is refractory to standard therapy. However, there is potential for false-negative staining of BCL2 using the standard monoclonal mouse 124 antibody that hinders the identification of these high-risk DLBCL patients. Herein, we compare 2 alternative rabbit monoclonal antibodies (E17 and SP66) to the 124 clone in staining for BCL2 in formalin-fixed, paraffin-embedded DLBCL tissues. Overall, in 2 independent DLBCL cohorts, E17 and SP66 detected BCL2 expression more frequently than 124. In the context of MYC expression, cases identified as BCL2 (+) with SP66 demonstrated the strongest correlation with worse overall survival. The 124 clone failed to detect BCL2 expression in the majority of translocation (+), amplification (+), and activated B-cell DLBCL cases in which high levels of BCL2 protein are expected. Using dual in situ hybridization as a new tool to detect BCL2 translocation and amplification, we observed similar results as previously reported for fluorescence in situ hybridization for translocation but a higher amplification frequency, indicating that BCL2 amplification may be underreported in DLBCL. Among the discrepant cases, phosphorylation of BCL2 at T69 and/or S70 was more common than in the concordant cases and may contribute to the 124 false negatives, in addition to previously associated mutations within the epitope region. The accurate detection of BCL2 expression is important in the prognosis and treatment of DLBCL particularly with new anti-BCL2 therapies.
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Molecular epidemiology of enterococcal bacteremia in Australia.
J. Clin. Microbiol.
PUBLISHED: 01-03-2014
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Enterococci are a major cause of health care-associated infections and account for approximately 10% of all bacteremias globally. The aim of this study was to determine the proportion of enterococcal bacteremia isolates in Australia that are antimicrobial resistant, with particular emphasis on susceptibility to ampicillin and the glycopeptides, and to characterize the molecular epidemiology of the Enterococcus faecalis and Enterococcus faecium isolates. From 1 January to 31 December 2011, 1,079 unique episodes of bacteremia were investigated, of which 95.8% were caused by either E. faecalis (61.0%) or E. faecium (34.8%). The majority of bacteremias were health care associated, and approximately one-third were polymicrobial. Ampicillin resistance was detected in 90.4% of E. faecium isolates but was not detected in E. faecalis isolates. Vancomycin nonsusceptibility was reported in 0.6% and 36.5% of E. faecalis and E. faecium isolates, respectively. Unlike Europe and the United States, where vancomycin resistance in E. faecium is predominately due to the acquisition of the vanA operon, 98.4% of E. faecium isolates harboring van genes carried the vanB operon, and 16.1% of the vanB E. faecium isolates had vancomycin MICs at or below the susceptible breakpoint of the CLSI. Although molecular typing identified 126 E. faecalis pulsed-field gel electrophoresis pulsotypes, >50% belonged to two pulsotypes that were isolated across Australia. E. faecium consisted of 73 pulsotypes from which 43 multilocus sequence types were identified. Almost 90% of the E. faecium isolates were identified as CC17 clones, of which approximately half were characterized as ST203, which was isolated Australia-wide. In conclusion, the Australian Enterococcal Sepsis Outcome Programme (AESOP) study has shown that although they are polyclonal, enterococcal bacteremias in Australia are frequently caused by ampicillin-resistant vanB E. faecium.
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Identification of Highly Conserved Putative Developmental Enhancers Bound by SOX3 in Neural Progenitors Using ChIP-Seq.
PLoS ONE
PUBLISHED: 01-01-2014
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The transcription factor SOX3 is expressed within most neural progenitor (NP) cells of the vertebrate central nervous system (CNS) and is essential for normal brain development in mice and humans. However, despite the widespread expression of Sox3, CNS defects in null mice are relatively mild due to functional redundancy with the other SOXB1 sub-group members Sox1 and Sox2. To further understand the molecular function of SOX3, we investigated the genome-wide binding profile of endogenous SOX3 in NP cells using ChIP-seq. SOX3 binding was identified at over 8,000 sites, most of which were intronic or intergeneic and were significantly associated with neurodevelopmental genes. The majority of binding sites were moderately or highly conserved (phastCons scores >0.1 and 0.5, respectively) and included the previously characterised, SOXB1-binding Nestin NP cell enhancer. Comparison of SOX3 and published ChIP-Seq data for the co-activator P300 in embryonic brain identified hundreds of highly conserved putative enhancer elements. In addition, we identified a subset of highly conserved putative enhancers for CNS development genes common to SOXB1 members in NP cells, all of which contained the SOX consensus motif (ACAAWR). Together these data implicate SOX3 in the direct regulation of hundreds of NP genes and provide molecular insight into the overlapping roles of SOXB1 proteins in CNS development.
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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement.
PLoS ONE
PUBLISHED: 01-01-2014
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Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3-5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.
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Immunohistochemistry of Colorectal Cancer Biomarker Phosphorylation Requires Controlled Tissue Fixation.
PLoS ONE
PUBLISHED: 01-01-2014
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Phosphorylated signaling molecules are biomarkers of cancer pathophysiology and resistance to therapy, but because phosphoprotein analytes are often labile, poorly controlled clinical laboratory practices could prevent translation of research findings in this area from the bench to the bedside. We therefore compared multiple biomarker and phosphoprotein immunohistochemistry (IHC) results in 23 clinical colorectal carcinoma samples after either a novel, rapid tissue fixation protocol or a standard tissue fixation protocol employed by clinical laboratories, and we also investigated the effect of a defined post-operative "cold" ischemia period on these IHC results. We found that a one-hour cold ischemia interval, allowed by ASCO/CAP guidelines for certain cancer biomarker assays, is highly deleterious to certain phosphoprotein analytes, specifically the phosphorylated epidermal growth factor receptor (pEGFR), but shorter ischemic intervals (less than 17 minutes) facilitate preservation of phosphoproteins. Second, we found that a rapid 4-hour, two temperature, formalin fixation yielded superior staining in several cases with select markers (pEGFR, pBAD, pAKT) compared to a standard overnight room temperature fixation protocol, despite taking less time. These findings indicate that the future research and clinical utilities of phosphoprotein IHC for assessing colorectal carcinoma pathophysiology absolutely depend upon attention to preanalytical factors and rigorously controlled tissue fixation protocols.
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High-Frequency Rugose Exopolysaccharide Production by Vibrio cholerae Strains Isolated in Haiti.
PLoS ONE
PUBLISHED: 01-01-2014
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In October, 2010, epidemic cholera was reported for the first time in Haiti in over 100 years. Establishment of cholera endemicity in Haiti will be dependent in large part on the continued presence of toxigenic V. cholerae O1 in aquatic reservoirs. The rugose phenotype of V. cholerae, characterized by exopolysaccharide production that confers resistance to environmental stress, is a potential contributor to environmental persistence. Using a microbiologic medium promoting high-frequency conversion of smooth to rugose (S-R) phenotype, 80 (46.5%) of 172 V. cholerae strains isolated from clinical and environmental sources in Haiti were able to convert to a rugose phenotype. Toxigenic V. cholerae O1 strains isolated at the beginning of the epidemic (2010) were significantly less likely to shift to a rugose phenotype than clinical strains isolated in 2012/2013, or environmental strains. Frequency of rugose conversion was influenced by incubation temperature and time. Appearance of the biofilm produced by a Haitian clinical rugose strain (altered biotype El Tor HC16R) differed from that of a typical El Tor rugose strain (N16961R) by confocal microscopy. On whole-genome SNP analysis, there was no phylogenetic clustering of strains showing an ability to shift to a rugose phenotype. Our data confirm the ability of Haitian clinical (and environmental) strains to shift to a protective rugose phenotype, and suggest that factors such as temperature influence the frequency of transition to this phenotype.
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Implementing hospital-based surveillance for severe acute respiratory infections caused by influenza and other respiratory pathogens in New Zealand.
Western Pac Surveill Response J
PUBLISHED: 01-01-2014
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Recent experience with pandemic influenza A(H1N1)pdm09 highlighted the importance of global surveillance for severe respiratory disease to support pandemic preparedness and seasonal influenza control. Improved surveillance in the southern hemisphere is needed to provide critical data on influenza epidemiology, disease burden, circulating strains and effectiveness of influenza prevention and control measures. Hospital-based surveillance for severe acute respiratory infection (SARI) cases was established in New Zealand on 30 April 2012. The aims were to measure incidence, prevalence, risk factors, clinical spectrum and outcomes for SARI and associated influenza and other respiratory pathogen cases as well as to understand influenza contribution to patients not meeting SARI case definition.
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Dbx1 is a direct target of SOX3 in the spinal cord.
PLoS ONE
PUBLISHED: 01-01-2014
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SoxB1 sub-family of transcriptional regulators are expressed in progenitor (NP) cells throughout the neuroaxis and are generally downregulated during neuronal differentiation. Gain- and loss-of-function studies indicate that Sox1, Sox2 and Sox3 are key regulators of NP differentiation and that their roles in CNS development are largely redundant. Nevertheless, mutation of each SoxB1 individually results in a different array of CNS defects, raising the possibility that SoxB1 proteins have subtly different functions in NP cells. To explore the mechanism of SOXB1 functional redundancy, and to identify genes that are most sensitive to loss of the Sox3 gene, we performed genome wide expression profiling of Sox3 null NP cells. Nineteen genes with abnormal expression were identified, including the homeobox gene Dbx1. Analysis of Sox3 null embryos revealed that Dbx1 was significantly reduced in the neural tube and developing brain and that SOX3 bound directly to conserved elements associated with this gene in cultured NP cells and in vivo. These data define Dbx1 as a direct SOX3 target gene whose expression, intriguingly, is not fully rescued by other SOXB1 transcription factors, suggesting that there are inherent differences in SOXB1 protein activity.
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Beware of false-negative CT scan for anastomotic leakage after colonic surgery.
Int J Colorectal Dis
PUBLISHED: 12-04-2013
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Anastomotic leakage is one of the most life-threatening complications after colonic surgery. Correct diagnosis and treatment is important to reduce morbidity and mortality. An abdominal CT scan is one of the main diagnostic tools in diagnosing anastomotic leaks. The aim of this study was to examine the accuracy of abdominal CT scanning to detect anastomotic leakage and to evaluate the consequences of a false-negative CT outcome.
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Mammalian sex determination and gonad development.
Curr. Top. Dev. Biol.
PUBLISHED: 12-03-2013
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From a developmental biology perspective, gonadogenesis is of particular interest because it provides a unique example of how distinct organs, the testis and ovary, can arise from a common bipotential primordium. Gonadogenesis is also highly relevant from a clinical perspective, as congenital disorders of sex development (DSDs) are not uncommon, occurring in approximately 1 in 4500 live births. In recent years, there has been significant progress in our understanding of the genes and pathways that control important aspects of gonadogenesis including the initial decision to develop as a testis or ovary (sex determination), elaboration and cross-repression of the testis and ovary developmental pathways, and maintenance of the gonadal phenotype after birth. In this chapter, we provide an overview of gonadal morphogenesis and cell lineage specification, focusing primarily on these processes in mice and humans. We also provide an update on the genetic mechanisms that control murine gonadogenesis and maintenance and, where possible, discuss new insights into the pathological mechanisms of DSDs associated with mutation of orthologous genes in mice and humans.
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The Spirit of Competition: To Win or Not To Win.
PLoS Comput. Biol.
PUBLISHED: 12-01-2013
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A competition is a contest between individuals or groups. The gain is often an award or recognition, which serves as a catalyst to motivate individuals to put forth their very best. Such events for recognition and success are part of many International Society for Computational Biology (ISCB) Student Council Regional Student Groups (RSGs) activities. These include a popular science article contest, a Wikipedia article competition, travel grants, poster and oral presentation awards during conferences, and quizzes at social events. Organizing competitions is no different than any other event; they require a lot of hard work to be successful. Each event gives remarkable organizational and social experience for students running it, while at the same time the participants of the competitions are rewarded by prizes and recognition. It gives everybody involved an opportunity to demonstrate their extraordinary talents and skills. Competitions are unique because they bring out both the best and worst in people.
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Relationship between asking an older adult about falls and surgical outcomes.
JAMA Surg
PUBLISHED: 10-11-2013
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IMPORTANCE More than one-third of all US inpatient operations are performed on patients aged 65 years and older. Existing preoperative risk assessment strategies are not adequate to meet the needs of the aging population. OBJECTIVES To evaluate the relationship of a history of falls (a geriatric syndrome) to postoperative outcomes in older adults undergoing major elective operations. DESIGN, SETTING, AND PARTICIPANTS This prospective, cohort study was conducted at a referral medical center. Persons aged 65 years and older undergoing elective colorectal and cardiac operations were enrolled. The predictor variable was having fallen in the 6 months prior to the operation. MAIN OUTCOMES AND MEASURES Postoperative outcomes measured included 30-day complications, the need for discharge institutionalization, and 30-day readmission. RESULTS There were 235 subjects with a mean (SD) age of 74 (6) years. Preoperative falls occurred in 33%. One or more postoperative complications occurred more frequently in the group with prior falls compared with the nonfallers following both colorectal (59% vs 25%; P?=?.004) and cardiac (39% vs 15%; P?=?.002) operations. These findings were independent of advancing chronologic age. The need for discharge to an institutional care facility occurred more frequently in the group that had fallen in comparison with the nonfallers in both the colorectal (52% vs 6%; P?<?.001) and cardiac (62% vs 32%; P?=?.001) groups. Similarly, 30-day readmission was higher in the group with prior falls following both colorectal (P?=?.04) and cardiac (P?=?.02) operations. CONCLUSIONS AND RELEVANCE A history of 1 or more falls in the 6 months prior to an operation forecasts increased postoperative complications, the need for discharge institutionalization, and 30-day readmission across surgical specialties. Using a history of prior falls in preoperative risk assessment for an older adult represents a shift from current preoperative assessment strategies.
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Transluminal endoscopic step-up approach versus minimally invasive surgical step-up approach in patients with infected necrotising pancreatitis (TENSION trial): design and rationale of a randomised controlled multicenter trial [ISRCTN09186711].
BMC Gastroenterol
PUBLISHED: 10-08-2013
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Infected necrotising pancreatitis is a potentially lethal disease that nearly always requires intervention. Traditionally, primary open necrosectomy has been the treatment of choice. In recent years, the surgical step-up approach, consisting of percutaneous catheter drainage followed, if necessary, by (minimally invasive) surgical necrosectomy has become the standard of care. A promising minimally invasive alternative is the endoscopic transluminal step-up approach. This approach consists of endoscopic transluminal drainage followed, if necessary, by endoscopic transluminal necrosectomy. We hypothesise that the less invasive endoscopic step-up approach is superior to the surgical step-up approach in terms of clinical and economic outcomes.
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Persistence of related bla-IMP-4 metallo-beta-lactamase producing Enterobacteriaceae from clinical and environmental specimens within a burns unit in Australia - a six-year retrospective study.
Antimicrob Resist Infect Control
PUBLISHED: 10-03-2013
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To describe the clinical epidemiology, environmental surveillance and infection control interventions undertaken in a six-year persistence of bla-IMP-4 metallo-beta-lactamase (MBL) producing Enterobacteriaceae within a separately confined hospital burns unit in a tertiary hospital in Sydney, Australia.
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The regional student group program of the ISCB student council: stories from the road.
PLoS Comput. Biol.
PUBLISHED: 09-01-2013
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The International Society for Computational Biology (ISCB) Student Council was launched in 2004 to facilitate interaction between young scientists in the fields of bioinformatics and computational biology. Since then, the Student Council has successfully run events and programs to promote the development of the next generation of computational biologists. However, in its early years, the Student Council faced a major challenge, in that students from different geographical regions had different needs; no single activity or event could address the needs of all students. To overcome this challenge, the Student Council created the Regional Student Group (RSG) program. The program consists of locally organised and run student groups that address the specific needs of students in their region. These groups usually encompass a given country, and, via affiliation with the international Student Council, are provided with financial support, organisational support, and the ability to share information with other RSGs. In the last five years, RSGs have been created all over the world and organised activities that have helped develop dynamic bioinformatics student communities. In this article series, we present common themes emerging from RSG initiatives, explain their goals, and highlight the challenges and rewards through specific examples. This article, the first in the series, introduces the Student Council and provides a high-level overview of RSG activities. Our hope is that the article series will be a valuable source of information and inspiration for initiating similar activities in other regions and scientific communities.
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Slower walking speed forecasts increased postoperative morbidity and 1-year mortality across surgical specialties.
Ann. Surg.
PUBLISHED: 08-28-2013
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The purpose of this study was to determine the relationship between the Timed Up and Go test and postoperative morbidity and 1-year mortality, and to compare the Timed Up and Go to the standard-of-care surgical risk calculators for prediction of postoperative complications.
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Advancing age and 30-day adverse outcomes after nonemergent general surgeries.
J Am Geriatr Soc
PUBLISHED: 08-08-2013
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To determine whether 30-day postoperative mortality, complications, failure-to-rescue (FTR) rates, and postoperative length of stay increase with advancing age.
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[Bone metastases or an insufficiency fracture? Oncology patients reporting pain or showing bone abnormalities on a scan].
Ned Tijdschr Geneeskd
PUBLISHED: 07-12-2013
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A 71-year-old patient reported pain in the left hip 14 months after treatment with radiotherapy for a ypT3N1M0 rectal carcinoma, and a 61-year-old patient reported pain in the lower back with radiation to the buttocks 8 months after radiotherapy for a ypT3N2M0 rectal carcinoma. In both patients the initial diagnosis considered was bone metastasis. After MRI and nuclear bone scans, however, diagnoses of insufficiency fractures of the acetabulum and sacroiliac (SI) joints, respectively, were made. Insufficiency fractures of the SI joints or acetabula are a frequent complication of radiotherapy and should be considered in all oncology patients who present with sudden onset of back pain or lower back pain after radiotherapy. A MRI scan is the initial investigation of choice. Treatment is conservative, with analgesia and physiotherapy. Prognosis is good; symptoms disappear within 1 year in almost all patients.
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Distance informed Track-Weighted Imaging (diTWI): A framework for sensitising streamline information to neuropathology.
Neuroimage
PUBLISHED: 07-11-2013
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Track-Weighted Imaging (TWI), where voxel intensity is based on image metrics encoded along streamline trajectories, provides a mechanism to study white matter disease. However, with generalised streamline weighting, it is difficult to localise the precise anatomical source and spread of injury or neuropathology. This limitation can be overcome by modulating the voxel weight based on the distance of the voxel from a given anatomical location along the tract, which we term diTWI: distance informed Track-Weighted Imaging. The location of known neuropathology can be delineated on any given imaging modality (e.g. MRI or PET). To demonstrate the clinical utility of this approach, we measured tumour cell infiltration along WM fibre tracts in 13 patients with newly diagnosed glioblastoma and 1 patient with Anaplastic Astrocytoma. TWI and diTWI maps were generated using information obtained from dynamic contrast enhanced MRI (area under the curve, AUC) and diffusivity maps (ADC and FA) with tumour boundaries automatically extracted using a logistic regression classifier. The accuracy of the derived tumour volumes was compared to those generated using 3,4-dihydroxy-6-[(18)F]-fluoro-l-phenylalanine (FDOPA) PET imaging. The accuracy of the tumour volumes generated from the diTWI maps was superior to volumes derived from the TWI, geometric distance or baseline AUC, FA and ADC maps. The relative overlap and relative dissimilarity rates for the diTWI generated tumour volumes after classification were found to be 82.3±15.3% (range 69.1-91.9) and 16.9±8.8% (range 7.9-37.5), respectively. These findings show that diTWI maps provide a useful framework for localising neuropathological processes occurring along WM pathways.
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New methods for ALK status diagnosis in non-small-cell lung cancer: an improved ALK immunohistochemical assay and a new, Brightfield, dual ALK IHC-in situ hybridization assay.
J Thorac Oncol
PUBLISHED: 07-03-2013
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The demonstration of anaplastic lymphoma kinase (ALK) positivity in non-small-cell lung cancer (NSCLC) has been hindered by the technical complexity and interpretative challenges of fluorescence in situ hybridization methods for detection of ALK gene rearrangement and by the inadequate sensitivity of existing immunohistochemistry (IHC) methods for ALK protein detection. In this study, we sought to increase the sensitivity of ALK IHC detection and to develop a brightfield assay for concurrent detection of ALK protein expression and ALK gene rearrangement.
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The microtubule end-binding protein EB2 is a central regulator of microtubule reorganisation in apico-basal epithelial differentiation.
J. Cell. Sci.
PUBLISHED: 06-26-2013
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Microtubule end-binding (EB) proteins influence microtubule dynamic instability, a process that is essential for microtubule reorganisation during apico-basal epithelial differentiation. Here, we establish for the first time that expression of EB2, but not that of EB1, is crucial for initial microtubule reorganisation during apico-basal epithelial differentiation, and that EB2 downregulation promotes bundle formation. EB2 siRNA knockdown during early stages of apico-basal differentiation prevented microtubule reorganisation, whereas its downregulation at later stages promoted microtubule stability and bundle formation. Interestingly, although EB1 is not essential for microtubule reorganisation, its knockdown prevented apico-basal bundle formation and epithelial elongation. siRNA depletion of EB2 in undifferentiated epithelial cells induced the formation of straight, less dynamic microtubules with EB1 and ACF7 lattice association and co-alignment with actin filaments, a phenotype that could be rescued by inhibition with formin. Importantly, in situ inner ear and intestinal crypt epithelial tissue revealed direct correlations between a low level of EB2 expression and the presence of apico-basal microtubule bundles, which were absent where EB2 was elevated. EB2 is evidently important for initial microtubule reorganisation during epithelial polarisation, whereas its downregulation facilitates EB1 and ACF7 microtubule lattice association, microtubule-actin filament co-alignment and bundle formation. The spatiotemporal expression of EB2 thus dramatically influences microtubule organisation, EB1 and ACF7 deployment and epithelial differentiation.
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Dientamoeba fragilis: a family cluster of disease associated with marked peripheral eosinophilia.
Clin. Infect. Dis.
PUBLISHED: 06-11-2013
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Dientamoeba fragilis has emerged as an important and underrecognized cause of gastrointestinal illness. We report a familial cluster of D. fragilis associated with marked peripheral eosinophilia and gastrointestinal symptoms. Dientamoeba fragilis infection should be considered in the setting of unexplained eosinophilia. If confirmed, screening of household members should be considered.
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The role of routine fine-needle aspiration in the diagnosis of infected necrotizing pancreatitis.
Surgery
PUBLISHED: 05-23-2013
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Diagnosing infected necrotizing pancreatitis (INP) may be challenging. The aim of this study was to determine the added value of routine fine-needle aspiration (FNA) in addition to clinical and imaging signs of infection in patients who underwent intervention for suspected INP.
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The Mycobacterium tuberculosis regulatory network and hypoxia.
Nature
PUBLISHED: 05-23-2013
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We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.
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Risk of major nonemergent inpatient general surgical procedures in patients on long-term dialysis.
JAMA Surg
PUBLISHED: 04-06-2013
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Patients on long-term dialysis undergoing major nonemergent general surgical procedures are thought to have high rates of postoperative complications and death.
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The new revised classification of acute pancreatitis 2012.
Surg. Clin. North Am.
PUBLISHED: 03-27-2013
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This study aims to update the 1991 Atlanta Classification of acute pancreatitis, to standardize the reporting of and terminology of the disease and its complications. Important features of this classification have incorporated new insights into the disease learned over the last 20 years, including the recognition that acute pancreatitis and its complications involve a dynamic process involving two phases, early and late. The accurate and consistent description of acute pancreatitis will help to improve the stratification and reporting of new methods of care of acute pancreatitis across different practices, geographic areas, and countries.
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Another look at follicular lymphoma: immunophenotypic and molecular analyses identify distinct follicular lymphoma subgroups.
Histopathology
PUBLISHED: 03-20-2013
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The aim of this study was to analyse the immunophenotypic and molecular features of a large series of follicular lymphomas, focusing in particular on atypical cases that fail to express CD10 and/or bcl-2. Such cases present diagnostic pitfalls, especially with regard to the differential diagnosis from follicular hyperplasia and marginal zone B-cell lymphoma. Therefore, we also included an immunohistochemical evaluation of stathmin, which is strongly expressed by germinal centre B cells, as a putative new marker for follicular lymphomas, particularly those with an atypical phenotype.
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Expression of the murine transcription factor SOX3 during embryonic and adult neurogenesis.
Gene Expr. Patterns
PUBLISHED: 03-11-2013
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Previous studies have shown that Sox3 is expressed in nascent neuroprogenitor cells and is functionally required in mammals for development of the dorsal telencephalon and hypothalamus. However, Sox3 expression during embryonic and adult neurogenesis has not been examined in detail. Using a SOX3-specific antibody, we show that murine SOX3 expression is maintained throughout telencephalic neurogenesis and is restricted to progenitor cells with neuroepithelial and radial glial morphologies. We also demonstrate that SOX3 is expressed within the adult neurogenic regions and is coexpressed extensively with the neural stem cell marker SOX2 indicating that it is a lifelong marker of neuroprogenitor cells. In contrast to the telencephalon, Sox3 expression within the developing hypothalamus is upregulated in developing neurons and is maintained in a subset of differentiated hypothalamic cells through to adulthood. Together, these data show that Sox3 regulation is region-specific, consistent with it playing distinct biological roles in the dorsal telencephalon and hypothalamus.
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Mechanistic insight into the pathology of polyalanine expansion disorders revealed by a mouse model for X linked hypopituitarism.
PLoS Genet.
PUBLISHED: 03-07-2013
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Polyalanine expansions in transcription factors have been associated with eight distinct congenital human diseases. It is thought that in each case the polyalanine expansion causes misfolding of the protein that abrogates protein function. Misfolded proteins form aggregates when expressed in vitro; however, it is less clear whether aggregation is of relevance to these diseases in vivo. To investigate this issue, we used targeted mutagenesis of embryonic stem (ES) cells to generate mice with a polyalanine expansion mutation in Sox3 (Sox3-26ala) that is associated with X-linked Hypopituitarism (XH) in humans. By investigating both ES cells and chimeric mice, we show that endogenous polyalanine expanded SOX3 does not form protein aggregates in vivo but rather is present at dramatically reduced levels within the nucleus of mutant cells. Importantly, the residual mutant protein of chimeric embryos is able to rescue a block in gastrulation but is not sufficient for normal development of the hypothalamus, a region that is functionally compromised in Sox3 null embryos and individuals with XH. Together, these data provide the first definitive example of a disease-relevant PA mutant protein that is both nuclear and functional, thereby manifesting as a partial loss-of-function allele.
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A randomized clinical trial of the efficacy of extended smoking cessation treatment for adolescent smokers.
Nicotine Tob. Res.
PUBLISHED: 03-04-2013
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Relatively few well-designed smoking cessation studies have been conducted with teen smokers. This study examined the efficacy of extended cognitive-behavioral treatment in promoting longer term smoking cessation among adolescents.
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Bright-field in situ hybridization methods to discover gene amplifications and rearrangements in clinical samples.
Methods Mol. Biol.
PUBLISHED: 02-26-2013
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Brightfield in situ hybridization (BISH) applications have significant advantages over traditional fluorescence in situ hybridization (FISH). BISH slides can be analyzed using a regular microscope while FISH slides require the use of a specialized fluorescence microscope. BISH slides allow observers for correlating the gene status (gene amplifications, gene rearrangements, and gene deletions) and tissue morphology better than FISH slides. Also, BISH slides are ideal for the permanent preservation of gene signals. Furthermore, BISH applications can be optimized using an automated tissue slide processing system. BISH applications are becoming a popular method for clinical examination of gene status for selecting cancer treatments.
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Autophagy and formation of tubulovesicular autophagosomes provide a barrier against nonviral gene delivery.
Autophagy
PUBLISHED: 02-19-2013
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Cationic liposome (lipoplex) and polymer (polyplex)-based vectors have been developed for nonviral gene delivery. These vectors bind DNA and enter cells via endosomes, but intracellular transfer of DNA to the nucleus is inefficient. Here we show that lipoplex and polyplex vectors enter cells in endosomes, activate autophagy and generate tubulovesicular autophagosomes. Activation of autophagy was dependent on ATG5, resulting in lipidation of LC3, but did not require the PtdIns 3-kinase activity of PIK3C3/VPS34. The autophagosomes generated by lipoplex fused with each other, and with endosomes, resulting in the delivery of vectors to large tubulovesicular autophagosomes, which accumulated next to the nucleus. The tubulovesicular autophagosomes contained autophagy receptor protein SQSTM1/p62 and ubiquitin, suggesting capture of autophagy cargoes, but fusion with lysosomes was slow. Gene delivery and expression from both lipoplex and polyplex increased 8-fold in atg5 (-/-) cells unable to generate tubulovesicular autophagosomes. Activation of autophagy and capture within tubulovesicular autophagosomes therefore provides a new cellular barrier against efficient gene transfer and should be considered when designing efficient nonviral gene delivery vectors.
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Mutation-specific antibody detects mutant BRAFV600E protein expression in human colon carcinomas.
Cancer
PUBLISHED: 02-13-2013
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A point mutation (V600E) in the BRAF oncogene is a prognostic biomarker and may predict for nonresponse to anti-EGFR antibody therapy in patients with colorectal carcinoma. BRAFV600E mutations are frequently detected in tumors with microsatellite instability and indicate a sporadic origin. We used a mutation-specific antibody to examine mutant BRAFV600E protein expression and its concordance with BRAFV600E mutation data.
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Limited diversity in the gene pool allows prediction of third-generation cephalosporin and aminoglycoside resistance in Escherichia coli and Klebsiella pneumoniae.
Int. J. Antimicrob. Agents
PUBLISHED: 02-06-2013
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Early appropriate antibiotic treatment reduces mortality in severe sepsis, but current methods to identify antibiotic resistance still generally rely on bacterial culture. Modern diagnostics promise rapid gene detection, but the apparent diversity of relevant resistance genes in Enterobacteriaceae is a problem. Local surveys and analysis of publicly available data sets suggested that the resistance gene pool is dominated by a relatively small subset of genes, with a very high positive predictive value for phenotype. In this study, 152 Escherichia coli and 115 Klebsiella pneumoniae consecutive isolates with a cefotaxime, ceftriaxone and/or ceftazidime minimum inhibitory concentration (MIC) of ? 2 ?g/mL were collected from seven major hospitals in Sydney (Australia) in 2008-2009. Nearly all of those with a MIC in excess of European Committee on Antimicrobial Susceptibility Testing (EUCAST) resistance breakpoints contained one or more representatives of only seven gene types capable of explaining this phenotype, and this included 96% of those with a MIC ? 2 ?g/mL to any one of these drugs. Similarly, 97% of associated gentamicin-non-susceptibility (MIC ? 8 ?g/mL) could be explained by three gene types. In a country like Australia, with a background prevalence of resistance to third-generation cephalosporins of 5-10%, this equates to a negative predictive value of >99.5% for non-susceptibility and is therefore suitable for diagnostic application. This is an important proof-of-principle that should be tested in other geographic locations.
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Simple frailty score predicts postoperative complications across surgical specialties.
Am. J. Surg.
PUBLISHED: 02-01-2013
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Our purpose was to determine the relationship between preoperative frailty and the occurrence of postoperative complications after colorectal and cardiac operations.
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Blend mode reduces unintended thermal injury by laparoscopic monopolar instruments: a randomized controlled trial.
Surg Endosc
PUBLISHED: 01-25-2013
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The purpose of this study was to compare histologic evidence of thermal injury at the epigastric and umbilical incisions after elective laparoscopic cholecystectomy performed using the monopolar "Bovie" instrument set on the higher voltage coag mode versus the lower voltage blend mode. We hypothesized that the higher voltage coag mode would create more unintended thermal tissue injury at the epigastric trocars incision.
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A photoinduced electron transfer-based nanoprobe as a marker of acidic organelles in mammalian cells.
Anal Bioanal Chem
PUBLISHED: 01-09-2013
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Photoinduced electron transfer (PET)-based molecular probes have been successfully used for the intracellular imaging of the pH of acidic organelles. In this study, we describe the synthesis and characterization of a novel PET-based pH nanoprobe and its biological application for the signaling of acidic organelles in mammalian cells. A fluorescent ligand sensitive to pH via the PET mechanism that incorporates a thiolated moiety was synthesized and used to stabilize gold nanoparticles (2.4 ± 0.6 nm), yielding a PET-based nanoprobe. The PET nanoprobe was unambiguously characterized by transmission electron microscopy, proton nuclear magnetic resonance, Fourier transform infrared, ultraviolet-visible absorption, and steady-state/time-resolved fluorescence spectroscopies which confirmed the functionalization of the gold nanoparticles with the PET-based ligand. Following a classic PET behavior, the fluorescence emission of the PET-based nanoprobe was quenched in alkaline conditions and enhanced in an acidic environment. The PET-based nanoprobe was used for the intracellular imaging of acidic environments within Chinese hamster ovary cells by confocal laser scanning microscopy. The internalization of the nanoparticles by the cells was confirmed by confocal fluorescence images and also by recording the fluorescence emission spectra of the intracellular PET-based nanoprobe from within the cells. Co-localization experiments using a marker of acidic organelles, LysoTracker Red DND-99, and a marker of autophagosomes, GFP-LC3, confirm that the PET-based nanoprobe acts as marker of acidic organelles and autophagosomes within mammalian cells.
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Compromised visceral circulation does not affect the outcome of colorectal surgery.
Surg. Today
PUBLISHED: 01-03-2013
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Anastomotic leakage is a serious complication after colorectal surgery, and many risk factors for this problem have so far been identified. The aim of this study was to assess the association between visceral arterial occlusive disease and anastomotic leakage.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.