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Find video protocols related to scientific articles indexed in Pubmed.
Corticosterone Mediates the Inhibitory Effect of Restraint Stress on the Migration of Mesenchymal Stem Cell to Carbon Tetrachloride-Induced Fibrotic Liver by Downregulating CXCR4/7 Expression.
Stem Cells Dev.
PUBLISHED: 10-01-2014
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Recent studies have revealed that mesenchymal stem cells (MSCs) have a great potential in therapeutic applications. The low efficiency of MSC recruitment and homing to sites of diseased organ tissue, however, remains a major hurdle in their application for treatment of diseases. Stress is commonly associated with various diseases. At the present time, little information is available about the effect of stress on MSC function. Here, we employed a carbon tetrachloride (CCl4)-induced mouse liver fibrosis model to investigate whether constraint stress affects the migration of MSCs to fibrotic liver. MSC homing to the fibrotic liver was significantly inhibited in mice with restraint stress. Restraint stress induced an elevation of corticosterone level in the serum. Blocking glucocorticoid signaling with either corticosterone-synthesis inhibitor metyrapone (MET) or glucocorticoid receptor antagonist RU486 attenuated restraint stress-induced inhibition of MSCs migration. The serum concentration of stromal cell-derived factor-1 (SDF-1) increased in mice treated with CCl4. Restraint stress had no influence on expression of SDF-1 and hepatocyte growth factor (HGF) in the fibrotic liver. Culture with the serum of CCl4-treated mice or SDF-1 promoted MSC migration, which was suppressed by corticosterone. Exposure of MSCs to corticosterone decreased their expression of C-X-C chemokine receptor type 4 (CXCR4) and C-X-C chemokine receptor type 7 (CXCR7). These results demonstrate that the inhibitory effect of corticosterone on MSC migration might be mediated via decreasing the expression of CXCR4 and CXCR7 in MSCs. Interventions targeting the interaction between corticosterone and its receptor improve migration and homing of MSCs in hosts receiving transplantation of these cells.
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[Early complications of intra-operative radiotherapy in locally advanced pancreatic cancer].
Zhonghua Zhong Liu Za Zhi
PUBLISHED: 09-23-2014
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To investigate the complications in intra-operative radiotherapy (IORT) for patients with local advanced pancreatic cancer.
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EBV-driven LMP1 and IFN-? up-regulate PD-L1 in nasopharyngeal carcinoma: Implications for oncotargeted therapy.
Oncotarget
PUBLISHED: 07-20-2014
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PD-L1 expression is a feature of Epstein-Barr virus (EBV) associated malignancies such as nasopharyngeal carcinoma (NPC). Here, we found that EBV-induced latent membrane protein 1 (LMP1) and IFN-? pathways cooperate to regulate programmed cell death protein 1 ligand (PD-L1). Expression of PD-L1 was higher in EBV positive NPC cell lines compared with EBV negative cell lines. PD-L1 expression could be increased by exogenous and endogenous induction of LMP1 induced PD-L1. In agreement, expression of PD-L1 was suppressed by knocking down LMP1 in EBV positive cell lines. We further demonstrated that LMP1 up-regulated PD-L1 through STAT3, AP-1, and NF-?B pathways. Besides, IFN-? was independent of but synergetic with LMP1 in up-regulating PD-L1 in  NPC. Furthermore, we showed that PD-L1 was associated with worse disease-free survival in NPC patients. These results imply that blocking both the LMP1 oncogenic pathway and PD-1/PD-L1 checkpoints may be a promising therapeutic approach for EBV positive NPC patients.
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Functional expression, characterization and application of the human S100A4 protein.
Mol Med Rep
PUBLISHED: 07-09-2014
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Preparations utilizing monoclonal antibodies against S100A4 provide useful tools for functional studies to investigate the clinical applications of the human S100A4 protein. In the present study, human S100A4 protein was expressed in Escherichia coli (E. coli) BL21 (DE3), successfully purified by diethylaminoethyl cellulose anion-exchange chromatography and identified by western blot analysis. Soluble S100A4 bioactivity was confirmed by Transwell migration and invasion assays in the human HeLa cell line. Monoclonal antibodies (mAbs) were generated utilizing the standard hybridoma method and were validated by enzyme-linked immunosorbent assay and western blot analysis. The antibody was then used to examine human gastric carcinoma specimens by immunohistochemistry. Recombinant S100A4 was functionally expressed in E. coli and promoted the migration and invasion of HeLa cells. Four hybridoma cell lines, which secreted mAbs specifically against human S100A4 protein, were obtained. One of the four mAbs, namely 2A12D10B2, recognized human S100A4 as indicated by immunohistochemical staining of human gastric carcinoma specimens and recombinant S100A4 was functionally expressed in E. coli. The mAbs of recombinant S100A4 were suitable for detecting S100A4 expression in human tissues and for investigating the subsequent clinical applications of the protein.
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Synthesis and biological evaluation of a novel class of coumarin derivatives.
Bioorg. Med. Chem. Lett.
PUBLISHED: 06-08-2014
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In this study, several novel coumarin derivatives, 7-hydroxy-2-oxo-2H-chromene-3-carboxyl-Trp-Trp-AA-OBzl compounds, were designed and synthesized as potential anticancer agents. Their in vitro cytotoxic activities were evaluated using methylthiazoltetrazolium (MTT) assay. The anti-tumor activity of the newly coumarin derivatives was determined in a S180 bearing mouse model and some of the compounds demonstrated tumor growth inhibition similar to the positive control, doxorubicin. Compared to doxorubicin, most of the compounds exhibited enhanced immunologic function suggesting a relatively minor toxic effect. The intercalation of the coumarin derivatives synthesized with calf thymus (CT) DNA was also studied.
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Prognostic Significance of Metastatic Lymph Node Number, Ratio and Station in Gastric Neuroendocrine Carcinoma.
J. Gastrointest. Surg.
PUBLISHED: 05-23-2014
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The objective of this study was to analyze the prognostic significance of metastatic lymph node status in gastric neuroendocrine carcinoma (GNEC) patients following radical gastrectomy. A consecutive series of 73 patients who underwent gastrectomy between 1999 and 2011 for GNEC was retrospectively reviewed. Indexes of lymph node involvement (the pN classification, metastatic lymph node number [MLNn], ratio [MLNr], and station [MLNs]) and other clinicopathological data were analyzed. Fifty-four patients met the inclusion criteria and were enrolled in the study. Among them, 44 patients (81 %) were found to have lymph node metastases. The median survival time of the entire cohort was 63.2 (range, 14-153) months with 3- and 5-year survival rates of 88.9 and 47.9 %, respectively. The median total number of lymph nodes, MLNn, and MLNr were 19 (range, 10-56), 5 (range, 1-21), and 25 % (6-100 %), respectively. Cox regression analysis revealed pN classification?=?1, MLNn >2, MLNr >0.1, and MLNs?=?2, and distant metastases influenced prognosis independently (P?=?0.0266, 0.0091, 0.0031, 0.0119, and 0.0021, respectively). In addition to the pN classification, indexes of metastatic lymph node involvement, including MLNn, MLNr, and MLNs, were all significant predictors of survival in GNEC patients. Distant metastasis was also a significant prognostic factor. These indexes proved to be accurate and important supplements to survival factors, which may improve risk classification of GNEC patients.
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A survey on CPG-inspired control models and system implementation.
IEEE Trans Neural Netw Learn Syst
PUBLISHED: 05-09-2014
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This paper surveys the developments of the last 20 years in the field of central pattern generator (CPG) inspired locomotion control, with particular emphasis on the fast emerging robotics-related applications. Functioning as a biological neural network, CPGs can be considered as a group of coupled neurons that generate rhythmic signals without sensory feedback; however, sensory feedback is needed to shape the CPG signals. The basic idea in engineering endeavors is to replicate this intrinsic, computationally efficient, distributed control mechanism for multiple articulated joints, or multi-DOF control cases. In terms of various abstraction levels, existing CPG control models and their extensions are reviewed with a focus on the relative advantages and disadvantages of the models, including ease of design and implementation. The main issues arising from design, optimization, and implementation of the CPG-based control as well as possible alternatives are further discussed, with an attempt to shed more light on locomotion control-oriented theories and applications. The design challenges and trends associated with the further advancement of this area are also summarized.
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[Pancreatic cystic neoplasms: a report of 139 cases].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 04-24-2014
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To review our experience in the diagnosis and treatment of pancreatic cystic neoplasms (PCN).
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?-Glucosidase inhibitory activity of polyphenols from the burs of Castanea mollissima Blume.
Molecules
PUBLISHED: 04-15-2014
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Polyphenol extracts from the burs of Castanea mollissima Blume (CMPE) exhibited potential antioxidant and hypoglycemic activities. The ?-glucosidase inhibitory activities of CMPE were assessed as a means of elucidating the mechanism behind its hypoglycemic activities. In vitro studies showed that CMPE significantly inhibited both yeast ?-glucosidase, through a noncompetitive mode with an IC50 of 0.33 ?g/mL, and rat intestinal ?-glucosidase. In vivo studies revealed that oral administration of CMPE at doses of 600 mg/kg significantly reduced postprandial blood glucose levels by 27.2% in normal rats following sucrose challenges. Gel permeation chromatography revealed that CMPE exhibited typical characteristics of high-molecular-mass polymers with mean (Mn) and weight (Mw) average molecular weights of 35.4 and 50.7 kDa, respectively, and a polydispersity (Mw/Mn) of 1.432. Acid hydrolysis analysis indicated the presence of ellagitannins. These data suggest that CMPE, enriched with ellagitannins, would be an efficacious dietary supplement for diabetes management through the inhibition of alpha-glucosidase.
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[Diagnosis and treatment of solid-pseudopapillary carcinoma of the pancreas].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 04-12-2014
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To summarize the institutional experiences of diagnosis, treatment and prognosis for solid-pseudopapillary carcinoma of the pancreas (SPCP).
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The Change in Suicide Rates between 2002 and 2011 in China.
Suicide Life Threat Behav
PUBLISHED: 04-01-2014
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Chinese suicide rates have been reported in various studies in the past two decades, but few of them were based on national data. The most recent mortality data (2002-2011) provided by the China Ministry of Health and the detailed census data provided by the National Population Census were used in this study. We calculated the age-, gender-, and region-specific suicide rates and their trends in the past 10 years between 2002 and 2011. The overall suicide rates in China decreased during the study period. The rural/urban ratio of the suicide rates has been significantly reduced from the ratio in the 1990s, and male suicide rates have exceeded those of females. Age was positively associated with suicide rates without the two peaks found in the suicide rates over 20 years ago. The Chinese suicide rates have significantly declined in the past decade, with withering of the unique suicide rate patterns previously found in Chinese suicides about 20 years ago.
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Automatic segmentation for brain MR images via a convex optimized segmentation and bias field correction coupled model.
Magn Reson Imaging
PUBLISHED: 03-26-2014
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Accurate segmentation of magnetic resonance (MR) images remains challenging mainly due to the intensity inhomogeneity, which is also commonly known as bias field. Recently active contour models with geometric information constraint have been applied, however, most of them deal with the bias field by using a necessary pre-processing step before segmentation of MR data. This paper presents a novel automatic variational method, which can segment brain MR images meanwhile correcting the bias field when segmenting images with high intensity inhomogeneities. We first define a function for clustering the image pixels in a smaller neighborhood. The cluster centers in this objective function have a multiplicative factor that estimates the bias within the neighborhood. In order to reduce the effect of the noise, the local intensity variations are described by the Gaussian distributions with different means and variances. Then, the objective functions are integrated over the entire domain. In order to obtain the global optimal and make the results independent of the initialization of the algorithm, we reconstructed the energy function to be convex and calculated it by using the Split Bregman theory. A salient advantage of our method is that its result is independent of initialization, which allows robust and fully automated application. Our method is able to estimate the bias of quite general profiles, even in 7T MR images. Moreover, our model can also distinguish regions with similar intensity distribution with different variances. The proposed method has been rigorously validated with images acquired on variety of imaging modalities with promising results.
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Hierarchical mergence approach to cell detection in phase contrast microscopy images.
Comput Math Methods Med
PUBLISHED: 03-25-2014
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Phase contrast microscope is one of the most universally used instruments to observe long-term cell movements in different solutions. Most of classic segmentation methods consider a homogeneous patch as an object, while the recorded cell images have rich details and a lot of small inhomogeneous patches, as well as some artifacts, which can impede the applications. To tackle these challenges, this paper presents a hierarchical mergence approach (HMA) to extract homogeneous patches out and heuristically add them up. Initially, the maximum region of interest (ROI), in which only cell events exist, is drawn by using gradient information as a mask. Then, different levels of blurring based on kernel or grayscale morphological operations are applied to the whole image to produce reference images. Next, each of unconnected regions in the mask is applied with Otsu method independently according to different reference images. Consequently, the segmentation result is generated by the combination of usable patches in all informative layers. The proposed approach is more than simply a fusion of the basic segmentation methods, but a well-organized strategy that integrates these basic methods. Experiments demonstrate that the proposed method outperforms previous methods within our datasets.
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Functionally active rat S100A4 from a polymerase chain reaction-synthesized gene expressed in soluble form in Escherichia coli.
Oncol Lett
PUBLISHED: 02-11-2014
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S100A4 protein is associated with Ca(2+)-dependent regulation of intracellular activities and is significant in the invasion, growth and metastasis of cancer. In order to express rat S100A4 functionally and identify its biological activity following purification, an S100A4 gene fragment was optimized and fully synthesized via overlapping polymerase chain reaction. The gene was inserted into the prokaryotic expression vector, pBV220, with phage ? PRPL promoters following confirmation by DNA sequencing. The pBV220-S100A4 plasmid was constructed and transformed into Escherichia coli DH5?. Following temperature induction, rat S100A4 was overexpressed and the protein was observed to be located in the supernatant of the lysates, which was ~30-40% of the total protein within the host. The protein was isolated and purified by metal-chelate affinity chromatography. High purity protein (>98% purity) was obtained and in vitro western blot analysis identified that the recombinant S100A4 was able to bind to the antibody against wild-type S100A4. The bioactivity of the recombinant protein was detected via Transwell migration and invasion assays. The polyclonal antibody of rat S100A4 protein was prepared for rabbit immunization and exhibited similar efficacies when compared with commercial S100A4. Therefore, rat S100A4 was functionally expressed in E. coli; thus, the production of active recombinant S100A4 protein in E. coli may further aid with the investigation and application of S100A4.
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Effect of trimetazidine on recurrent angina pectoris and left ventricular structure in elderly multivessel coronary heart disease patients with diabetes mellitus after drug-eluting stent implantation: a single-centre, prospective, randomized, double-blind study at 2-yea
Clin Drug Investig
PUBLISHED: 01-29-2014
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Trimetazidine has been shown to improve angina pectoris and left ventricular (LV) function in diabetic patients with ischaemic cardiomyopathy. The objective of this study was to evaluate the effects of trimetazidine on recurrent angina pectoris and LV structure after drug-eluting stent (DES) implantation in elderly multivessel coronary heart disease (CHD) patients with diabetes mellitus (DM) and a left ventricular ejection fraction (LVEF) of ? 50 %.
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Nano-engineering thermal transport performance of carbon nanotube networks with polymer intercalation: a molecular dynamics study.
Phys Chem Chem Phys
PUBLISHED: 01-25-2014
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Based on polymer perfusion behaviour inside carbon nanotube (CNT) networks, the thermal transport performances of the CNT networks with various extents of polymer intercalation are studied by dividing them into two parts: thermal transport at the tube contact interfaces of CNT junctions and along the tube axis. The thermal transport performance at the tube contact interfaces of CNT junctions is similar to that in the transverse direction of graphene layers. Hence, to obtain a fundamental understanding of thermal transport performance at the tube contact interfaces, thermal conductance along the z-axis direction of graphene layers with and without polymer intercalation is investigated using a non-equilibrium molecular dynamics (MD) simulation method. Thermal conductivity along the tube axis direction of the polymer wrapped CNT is also calculated using the same method. The simulation results show that a low extent of polymer aggregation at the tube contact interfaces can significantly improve the interfacial thermal conductance. However, when the polymer content at the tube contact interfaces exceeds a critical fraction, the interfacial thermal conductance is decreased. The results also indicate that the polymer molecules wrapping around the CNT walls have a strong negative influence on the bulk thermal conductivity of the CNT along its axis direction.
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Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping.
Genetics
PUBLISHED: 01-14-2014
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Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html).
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Synergistic effect of smoking with genetic variants in the AMPK?1 gene on the risk of coronary artery disease in type 2 diabetes.
Diabetes Metab. Res. Rev.
PUBLISHED: 01-08-2014
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Increasing evidence suggests that adenosine monophosphate-activated protein kinase (AMPK) plays a critical physiological role in the cardiovascular system. The objective of this study was to assess the possible correlation between the genetic variability of the AMPK?1 (PRKAA1) gene and the risk of cardiovascular disease, as well as the interactive effects of the genetic variations and environmental factors, on the risk in Chinese patients with type 2 diabetes.
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Design and control of an embedded vision guided robotic fish with multiple control surfaces.
ScientificWorldJournal
PUBLISHED: 01-01-2014
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This paper focuses on the development and control issues of a self-propelled robotic fish with multiple artificial control surfaces and an embedded vision system. By virtue of the hybrid propulsion capability in the body plus the caudal fin and the complementary maneuverability in accessory fins, a synthesized propulsion scheme including a caudal fin, a pair of pectoral fins, and a pelvic fin is proposed. To achieve flexible yet stable motions in aquatic environments, a central pattern generator- (CPG-) based control method is employed. Meanwhile, a monocular underwater vision serves as sensory feedback that modifies the control parameters. The integration of the CPG-based motion control and the visual processing in an embedded microcontroller allows the robotic fish to navigate online. Aquatic tests demonstrate the efficacy of the proposed mechatronic design and swimming control methods. Particularly, a pelvic fin actuated sideward swimming gait was first implemented. It is also found that the speeds and maneuverability of the robotic fish with coordinated control surfaces were largely superior to that of the swimming robot propelled by a single control surface.
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Preparation of colloidal gold immunochromatographic strip for detection of Paragonimiasis skrjabini.
PLoS ONE
PUBLISHED: 01-01-2014
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Paragonimiasis is a food-borne trematodiasis, a serious public health issue and a neglected tropical disease. Paragonimus skrjabini is a unique species found in China. Unlike paragonimiasis westermani, it is nearly impossible to make a definitive diagnosis for paragonimiasis skrjabini by finding eggs in sputum or feces. Immunodiagnosis is the best choice to detect paragonimiasis skrjabini. There is an urgent need to develop a novel, rapid and simple immunoassay for large-scale screening patients in endemic areas.
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Network meta-analysis of erlotinib, gefitinib, afatinib and icotinib in patients with advanced non-small-cell lung cancer harboring EGFR mutations.
PLoS ONE
PUBLISHED: 01-01-2014
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Several EGFR-tyrosine kinase inhibitors (EGFR-TKIs) including erlotinib, gefitinib, afatinib and icotinib are currently available as treatment for patients with advanced non-small-cell lung cancer (NSCLC) who harbor EGFR mutations. However, no head to head trials between these TKIs in mutated populations have been reported, which provides room for indirect and integrated comparisons.
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Genetic variants in PCSK1 gene are associated with the risk of coronary artery disease in type 2 diabetes in a Chinese Han population: a case control study.
PLoS ONE
PUBLISHED: 01-01-2014
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Insulin and glucagon-like peptide 1 (GLP-1), converted by proprotein convertase 1 (PC1/3) from proinsulin and proglucagon, are associated with type 2 diabetes (T2DM) and coronary artery disease (CAD). The aim of this study is to investigate the association of PCSK1 gene, which encodes PC1/3, with the risk of CAD in Chinese patients with T2DM.
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Sparsity-regularized HMAX for visual recognition.
PLoS ONE
PUBLISHED: 01-01-2014
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About ten years ago, HMAX was proposed as a simple and biologically feasible model for object recognition, based on how the visual cortex processes information. However, the model does not encompass sparse firing, which is a hallmark of neurons at all stages of the visual pathway. The current paper presents an improved model, called sparse HMAX, which integrates sparse firing. This model is able to learn higher-level features of objects on unlabeled training images. Unlike most other deep learning models that explicitly address global structure of images in every layer, sparse HMAX addresses local to global structure gradually along the hierarchy by applying patch-based learning to the output of the previous layer. As a consequence, the learning method can be standard sparse coding (SSC) or independent component analysis (ICA), two techniques deeply rooted in neuroscience. What makes SSC and ICA applicable at higher levels is the introduction of linear higher-order statistical regularities by max pooling. After training, high-level units display sparse, invariant selectivity for particular individuals or for image categories like those observed in human inferior temporal cortex (ITC) and medial temporal lobe (MTL). Finally, on an image classification benchmark, sparse HMAX outperforms the original HMAX by a large margin, suggesting its great potential for computer vision.
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Effect of Remote Ischemic Preconditioning in the Elderly Patients With Coronary Artery Disease With Diabetes Mellitus Undergoing Elective Drug-Eluting Stent Implantation.
Angiology
PUBLISHED: 10-24-2013
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There is conflicting evidence regarding the effectiveness of remote ischemic preconditioning (RIPC) in patients undergoing elective percutaneous coronary intervention (PCI). Therefore, we prospectively enrolled elderly patients with coronary heart disease (CHD) with diabetes mellitus (DM) undergoing elective drug-eluting stent (DES) implantation. They were randomized to receive RIPC within 2 hours before PCI (n = 102) or not (controls, n = 98). Baseline clinical characteristics were similar between the 2 groups. Despite a trend toward decline, the median high-sensitivity cardiac troponin I (hscTnI) level (P = .256) and the incidence of myocardial infarction (MI) type 4a (P = .106) in the RIPC group 16 hours after PCI procedure was not significantly different from the control group. The RIPC could attenuate the release of a myocardial biomarker but failed to show a significant effect on hscTnI level or MI type 4a incidence after PCI procedure in elderly patients with CHD having DM undergoing elective DES implantation.
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Efficacy of epidermal growth factor receptor-tyrosine kinase inhibitors for Chinese patients with squamous cell carcinoma of lung harboring EGFR mutation.
J Thorac Dis
PUBLISHED: 09-24-2013
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Epidermal growth factor receptor (EGFR) mutation mostly occurred in lung adenocarcinoma, rarely in squamous cell carcinoma (SQCC). EGFR mutation rate in SQCC varied in previous reports, and the efficacy of EGFR tyrosine kinase inhibitors (TKIs) in SQCC harboring EGFR mutation has not yet been fully evaluated. The aim of this study was to investigate the efficacy EGFR-TKIs for Chinese patients with SQCC of lung harboring EGFR mutation.
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Heterogeneity-related anticancer therapy response differences in metastatic colon carcinoma: new hints to tumor-site-based personalized cancer therapy.
Hepatogastroenterology
PUBLISHED: 09-13-2013
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Heterogeneity in primary tumor and related metastases may result in different response to anticancer therapy. Previous work revealed that there were heterogeneity in primary colon carcinoma and matched lymphatic and hepatic metastases. Subsequent study further ascertained the different expression of some functional genes in primary colon carcinoma and paired hepatic metastases in a larger group of patients with metastatic colon carcinoma. However, whether such heterogeneity in primary colon carcinoma and corresponding lymphatic and hepatic metastases would result in different response to anticancer therapy is unknown.METHODOLOGY: To investigate whether the heterogeneity in primary colon carcinoma and matched lymphatic and hepatic metastases would result in different response to anticancer therapy, patient-derived tumor tissue (PDTT) xenograft models of colon carcinoma with lymphatic and hepatic metastases were used to evaluate the response to VEGF-targeted therapy (bevacizumab) in combination with chemotherapy (capecitabine).RESULTS: All xenografts of primary colon carcinoma and corresponding lymphatic and hepatic metastases in nude mice responded to VEGF-targeted therapy (bevacizumab) in combination with chemotherapy (capecitabine). However, chemotherapy (capecitabine) alone resulted in significantly higher tumor growth inhibition rate in xenogfafts of primary colon carcinoma than that of corresponding lymphatic and hepatic metastasis (P < 0.01). VEGF-targeted therapy (bevacizumab) in combination with chemotherapy (capecitabine) resulted in significantly higher tumor growth inhibition rate in xenogfafts of colon carcinoma lymphatic metastasis than that of corresponding primary colon carcinoma and hepatic metastasis (P < 0.001).CONCLUSION: Our results demonstrate that primary colon carcinoma and its corresponding lymphatic and hepatic metastases have different response rate to chemotherapy (capecitabine) and to VEGF-targeted therapy (bevacizumab) in combination with chemotherapy (capecitabine). This study provides us new hints to tumor-site-based personalized cancer therapy in metastatic colon carcinoma.
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Analgesic effect of acupuncture at hegu (LI 4) on transvaginal oocyte retrieval with ultrasonography.
J Tradit Chin Med
PUBLISHED: 09-13-2013
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To observe the analgesic effect of acupuncture at Hegu (LI 4) in vitro fertilization-embryo transfer (IVF-ET) transvaginal oocyte retrieval using ultrasonography and explore its mechanism.
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Effect of tensile strain on thermal conductivity in monolayer graphene nanoribbons: a molecular dynamics study.
Sensors (Basel)
PUBLISHED: 05-14-2013
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The thermal conductivity of monolayer graphene nanoribbons (GNRs) with different tensile strain is investigated by using a nonequilibrium molecular dynamics method. Significant increasing amplitude of the molecular thermal vibration, molecular potential energy vibration and thermal conductivity vibration of stretching GNRs were detected. Some 20%~30% thermal conductivity decay is found in 9%~15% tensile strain of GNR cases. It is explained by the fact that GNR structural ridges scatter some low-frequency phonons which pass in the direction perpendicular to the direction of GNR stretching which was indicated by a phonon density of state investigation.
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Effect of strain on the evolution of magnetic multi-vortices in ferromagnetic nano-platelets.
J Phys Condens Matter
PUBLISHED: 05-10-2013
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The effect of external strain on the evolution of magnetic multi-vortices in nanoscale ferromagnetic platelets is investigated by a phase field model that explicitly includes the coupling between the magnetization and deformation. Phase field simulations show that a compressive strain makes the magnetic vortex-antivortex pair stable in rectangular ferromagnetic platelets, which is unstable in the absence of an external magnetic field and strain. The magnetic clockwise (CW) and counterclockwise (CCW) vortex pairs disappear in ferromagnetic platelets under an external magnetic field through the annihilation of the vortex and antivortex, or through expulsion when external strain is absent. In the presence of tensile strain, the expulsion of CW and CCW vortices is suppressed in ferromagnetic platelets. However, external strain has less effect on the annihilation of CW and CCW vortices. For ferromagnetic platelets with triple vortices, both tensile strain and a magnetic field induce the annihilation and expulsion of vortices. The effect of strain on the evolution of magnetic vortices suggests a new way to control them by strain engineering.
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Overexpression of S100A4 is closely associated with the progression and prognosis of gastric cancer in young patients.
Oncol Lett
PUBLISHED: 02-13-2013
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The aim of this study was to determine the correlation of S100A4 expression with the progression, prognosis and clinical pathology of gastric cancer (GC) in young pateints. A total of 85 tumor tissues with corresponding adjacent normal tissues and 62 non-metastatic lymph nodes (LNs) with corresponding metastatic LNs were obtained from young GC patients (<40 years old) who underwent surgery between January 2001 and December 2006. The expression of S100A4 was detected by RT-PCR and immunohistochemistry. Differences in the expression of S100A4 mRNA or protein were observed among the GC tissues, matched normal gastric mucosa, non-metastatic LNs and metastatic LNs. The expression of S100A4 mRNA and protein in GC tissues and metastatic LNs was significantly higher compared with that in the matched normal gastric mucosa and non-metastatic LNs, respectively (P<0.05). The overexpression of S100A4 was significantly associated with parameters involved in tumor progression and poor prognosis, including tumor size (P=0.017), Lauren classification (P=0.002), histological classification (P= 0.010), histological differentiation (P= 0.000), Borrmann classification (P=0.020), tumor-node-metastasis (TNM) stage (P=0.000), LN metastasis (P=0.000) and distant metastasis (P=0.024). Multivariate analysis suggested that patient age (P=0.035), tumor size (P=0.002), TNM stage (P=0.001) and S100A4 upregulation (P=0.000) were independent prognostic indicators for the disease. The overexpression of S100A4 in young GC patients is significantly associated with the clinicopathological characteristics. S100A4 may be used as a biomarker to predict the progression and poor prognosis of GC in young patients.
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An acupuncture research protocol developed from historical writings by mathematical reflections: a rational individualized acupoint selection method for immediate pain relief.
Evid Based Complement Alternat Med
PUBLISHED: 01-29-2013
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While balancing yin and yang is one basic principle of Chinese medicine, balancing methods for combination of meridians and acupoints had been described throughout the history of Chinese medicine. We have identified six historical systems for combinations of acupuncture points in historical writings. All of them represent symmetrical combinations which are defined by the steps in the Chinese Clock. Taking the historical systems as a basis, we calculated the possible combinations that fit into these systems they revealed, leading to a total of 19 systems offering new balancing combinations. Merging the data of these 19 systems, there are 7 combinatorial options for every meridian. On the basis of this data, we calculated 4-meridian combinations with an ideal balance pattern, which is given when all meridians balance each other. We identified 5 of these patterns for every meridian, so we end up with 60 patterns for all the 12 meridians but we find multiple overlapping. Finally, 15 distinct patterns remain. By combining this theoretical concept with the Image and Mirror Concept, we developed an acupuncture research protocol. This protocol potentially solves some problems of acupuncture trials because it represents a rational reproducible procedure independent of examiner experience, but the resulting treatment is individualized.
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Ma-PbFRET: multiple acceptors FRET measurement based on partial acceptor photobleaching.
Microsc. Microanal.
PUBLISHED: 01-25-2013
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Fluorescence resonance energy transfer (FRET) measurement based on partial acceptor photobleaching (PbFRET) is easy to implement without external references. However, the current PbFRET methods are inapplicable to the construct with multiple acceptors, which largely increase the Förster distance. Here, we proposed a linear theory for the dependence of the acceptor photobleaching probability of construct with multiple acceptors on the photobleaching degree (x) and developed a multiple acceptors PbFRET method (Ma-PbFRET) to measure the FRET efficiency of construct with multiple acceptors (n) by measuring the fluorescence intensities of both donor and acceptor channels before and after acceptor photobleaching. The Ma-PbFRET method was validated by measuring the FRET efficiency of construct with two or three acceptors under different x in living cells. Our experimental results demonstrate that the Ma-PbFRET method is capable of exactly quantifying the FRET efficiency of construct with multiple acceptors, providing a simple and powerful tool to investigate the assembly/disassembly of biomolecular complexes with larger distance in living cells.
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A Literature Analysis on 14 Cases of Allergic Shock Caused by Safflower Injection.
Afr J Tradit Complement Altern Med
PUBLISHED: 01-01-2013
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The objective of this paper was to investigate the characteristics and general rules of domestic safflower injection causing allergic shock, to retrieve the medical journals published domestically, and to make statistical analysis on the cases of allergic shock caused by safflower injection. Results showed that the incidence of allergic shock caused by safflower injection in patients above 40 years old was high: females were more than males. It occurred within 30min after medication, and no patient died after emergency treatment. The study concluded that allergic shock caused by safflower injection is related to many factors, and clinical care personnel should pay more attention to it.
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Serum proteomic study on EGFR-TKIs target treatment for patients with NSCLC.
Onco Targets Ther
PUBLISHED: 01-01-2013
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Although epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) are widely used for EGFR mutated non-small-cell lung cancer (NSCLC) patients, tumor sample availability and heterogeneity of the tumor remain challenging for physicians selection of these patients. Here, we developed a serum proteomic classifier based on matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) to predict the clinical outcome of patients treated with EGFR-TKIs.
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Motion analysis of live objects by super-resolution fluorescence microscopy.
Comput Math Methods Med
PUBLISHED: 09-01-2011
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Motion analysis plays an important role in studing activities or behaviors of live objects in medicine, biotechnology, chemistry, physics, spectroscopy, nanotechnology, enzymology, and biological engineering. This paper briefly reviews the developments in this area mostly in the recent three years, especially for cellular analysis in fluorescence microscopy. The topic has received much attention with the increasing demands in biomedical applications. The tasks of motion analysis include detection and tracking of objects, as well as analysis of motion behavior, living activity, events, motion statistics, and so forth. In the last decades, hundreds of papers have been published in this research topic. They cover a wide area, such as investigation of cell, cancer, virus, sperm, microbe, karyogram, and so forth. These contributions are summarized in this review. Developed methods and practical examples are also introduced. The review is useful to people in the related field for easy referral of the state of the art.
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Conservation and purifying selection of transcribed genes located in a rice centromere.
Plant Cell
PUBLISHED: 08-19-2011
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Recombination is strongly suppressed in centromeric regions. In chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. Surprisingly, the centromere of chromosome8 (Cen8) of rice (Oryza sativa) contains several transcribed genes. However, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in Cen8. Sequencing of orthologous Cen8 regions from two additional Oryza species, Oryza glaberrima and Oryza brachyantha, which diverged from O. sativa 1 and 10 million years ago, respectively, revealed a set of seven transcribed Cen8 genes conserved across all three species. Chromatin immunoprecipitation analysis with the centromere-specific histone CENH3 confirmed that the sequenced orthologous regions are part of the functional centromere. All seven Cen8 genes have undergone purifying selection, representing a striking phenomenon of active gene survival within a recombination-free zone over a long evolutionary time. The coding sequences of the Cen8 genes showed sequence divergence and mutation rates that were significantly reduced from those of genes located on the chromosome arms. This suggests that Oryza has a mechanism to maintain the fidelity and functionality of Cen8 genes, even when embedded in a sea of repetitive sequences and transposable elements.
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[Five-layer realistic finite element head models based on segmented computer tomography data].
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi
PUBLISHED: 07-22-2011
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This paper is focused on head modeling using the sophisticated realistic finite element method (FEM) with five-layer tissues based on segmented data. First, the location of every pixel of the FEM head model was fixed on according to the registration method based on the magnetic resonance imaging (MRI) and computer tomography (CT) images. Then the location information was rebuilt with the hexahedron pattern in the ANSYS FEM software. Finally, the forward problem numerical computation was performed on this FEM head model. The simulation results verified the rationality and reliability of the model applied on the electroencephalograph (EEG)/magnetoencephalograph (MEG) study. The hexahedron meshing realistic head model combined with the MRI scanner information has potential in the future research of EEG/MEG.
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Design and comparison of GaAs, GaAsP and InGaAlAs quantum-well active regions for 808-nm VCSELs.
Opt Express
PUBLISHED: 07-01-2011
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Vertical-cavity surface-emitting lasers emitting at 808 nm with unstrained GaAs/Al0.3Ga0.7As, tensilely strained GaAs(x)P(1-x)/Al0.3Ga0.7As and compressively strained In(1-x-y)Ga(x)Al(y)As/Al0.3Ga0.7As quantum-well active regions have been investigated. A comprehensive model is presented to determine the composition and width of these quantum wells. The numerical simulation shows that the gain peak wavelength is near 800 nm at room temperature for GaAs well with width of 4 nm, GaAs0.87P0.13 well with width of 13 nm and In0.14Ga0.74Al0.12As well with width of 6 nm. Furthermore, the output characteristics of the three designed quantum-well VCSELs are studied and compared. The results indicate that In0.14Ga0.74Al0.12As is the most appropriate candidate for the quantum well of 808-nm VCSELs.
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Analyzing image deblurring through three paradigms.
IEEE Trans Image Process
PUBLISHED: 06-20-2011
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To recover a sharp version from a blurred image is a long-standing inverse problem. In this paper, we analyze the research on this topic both theoretically and experimentally through three paradigms: 1) the deterministic filter; 2) Bayesian estimation; and 3) the conjunctive deblurring algorithm (CODA), which performs the deterministic filter and Bayesian estimation in a conjunctive manner. We point out the weaknesses of the deterministic filter and unify the limitation latent in two kinds of Bayesian estimators. We further explain why the CODA is able to handle quite large blurs beyond Bayesian estimation. Finally, we propose a novel method to overcome several unreported limitations of the CODA. Although extensive experiments demonstrate that our method outperforms state-of-the-art methods with a large margin, some common problems of image deblurring still remain unsolved and should attract further research efforts.
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Target contour recovering for tracking people in complex environments.
Comput Math Methods Med
PUBLISHED: 06-13-2011
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Recovering people contours from partial occlusion is a challenging problem in a visual tracking system. Partial occlusions would bring about unreasonable contour changes of the target object. In this paper, a novel method is presented to detect partial occlusion on people contours and recover occluded portions. Unlike other occlusion detection methods, the proposed method is only based on contours, which makes itself more flexible to be extended for further applications. Experiments with synthetic images demonstrate the accuracy of the method for detecting partial occlusions, and experiments on real-world video sequence are also carried out to prove that the method is also good enough to be used to recover target contours.
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Hepatic artery thrombosis after orthotopic liver transplant: a review of the same institute 5 years later.
Exp Clin Transplant
PUBLISHED: 06-09-2011
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Summarize the experience of managing patients with hepatic artery thrombosis after orthotopic liver transplant in a single center.
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An anisotropic images segmentation and bias correction method.
Magn Reson Imaging
PUBLISHED: 05-23-2011
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Intensity inhomogeneities cause considerable difficulty in the quantitative analysis of magnetic resonance (MR) images. Thus, bias field correction is a necessary step before quantitative analysis of MR data can be undertaken. This paper presents an anisotropic approach to bias correction and segmentation for images with intensity inhomogeneities and noise. Intensity-based methods are usually applied to estimate the bias field; however, most of them only concern the intensity information. When the images have noise or slender topological objects, these methods cannot obtain accurate results or bias fields. We use structure information to construct an anisotropic Gibbs field and combine the anisotropic Gibbs field with the Bayesian framework to segment images while estimating the bias fields. Our method is able to capture bias of quite general profiles. Moreover, it is robust to noise and slender topological objects. The proposed method has been used for images of various modalities with promising results.
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Diagnosis and treatment of acute appendicitis after orthotopic liver transplant in adults.
Exp Clin Transplant
PUBLISHED: 04-02-2011
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The incidence of acute appendicitis after orthotopic liver transplant is low but difficult to differentiate from other posttransplant complications. We sought to summarize the clinical characteristics, diagnosis, and treatment of acute appendicitis during the early posttransplant stage.
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Synthesis of mimetic peptides containing glucosamine.
Carbohydr. Res.
PUBLISHED: 03-10-2011
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A convenient synthesis of 2-amino-3,4,6-tri-O-benzyl-2-deoxy-?-d-glucopyranoside was described from the readily available starting material 2-acetamido-2-deoxy-d-glucose (N-acetyl-d-glucosamine). Herein, the coupling of different lipophilic amino acids with 2-amino-3,4,6-tri-O-benzyl-2-deoxy-?-d-glucose was reported via an amide linkage as useful building blocks for the synthesis of glycopeptides. Of particular interest, bioactive peptide Arg-Gly-Asp (RGD) was incorporated into the building block containing valine was also reported. The 15 examples of corresponding di-, tri- and tetra-peptides were obtained as single ?anomers.
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Effect of G-rich oligonucleotides on the proliferation of leukemia cells and its relationship with p53 expression.
Oligonucleotides
PUBLISHED: 01-19-2011
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G-rich oligonucleotides (GROs) can inhibit cell proliferation by inducing cell cycle arrest at S phase in tumor cell lines. GROs bind specific cellular proteins, such as nucleolin, a crucial protein interacting with P53; however, little is known about the relationship between GROs and P53. In this study, we have shown that GROs inhibited the proliferation of U937 cells (a human monocytic leukemia cell line without P53 expression) by inducing S-phase arrest. We also showed that GRO colocalized with nucleolin in U937 cells. GRO treatment induced alteration of a series of cell cycle regulatory proteins in U937 cells. Increased Cdk2 expression might promote the cells to enter S phase and subsequent decrease of Cdk2 might induce cell cycle arrest in S phase. Transfection of U937 cells with a wild-type p53 gene caused the formation of nucleolin-P53 complex, which alleviated the effect of GRO on leukemia cells. This alleviated effect is probably due to the decreased uptake of GRO.
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Localization of receptor site on insect sodium channel for depressant ?-toxin BmK IT2.
PLoS ONE
PUBLISHED: 01-14-2011
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BmK IT2 is regarded as a receptor site-4 modulator of sodium channels with depressant insect toxicity. It also displays anti-nociceptive and anti-convulsant activities in rat models. In this study, the potency and efficacy of BmK IT2 were for the first time assessed and compared among four sodium channel isoforms expressed in Xenopus oocytes. Combined with molecular approach, the receptor site of BmK IT2 was further localized.
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Novel Cu(II)-RGD-octapeptides: Synthesis, coordination mode, in vitro anti-platelet aggregation/in vivo anti-thrombotic evaluation and correlation of sequence with nano-structure.
Nanomedicine
PUBLISHED: 01-05-2011
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The synthesis, bioassays and nano-structure characterization of Cu(II)-RGD-octapeptide complexes Cu(II)-Arg-Gly-Asp-Ser-Arg-Gly-Asp-Ser [Cu(II)-4a], Cu(II)-Arg-Gly-Asp-Val-Arg-Gly-Asp-Val [Cu(II)-4b] and Cu(II)-Arg-Gly-Asp-Phe-Arg-Gly-Asp-Phe [Cu(II)-4c] were investigated. UV-vis, CD and CD/ESI-MS spectra suggested that the coordination of Cu(II)-4a-c met a 3 N mode. In the in vitro anti-platelet aggregation assay the IC(50) values of Cu(II)-RGD-octapeptide complexes were 10 - 110 folds lower than that of RGD-octapeptides. In the in vivo anti-thrombotic assay the effective dose of Cu(II)-RGD-octapeptide complexes was 5000 folds lower than that of RGD-octapeptides. In transmission electron microscopy measurement Cu(II)-4a-c offered distinct nano-images. The effect of the sequence on the in vitro anti-platelet aggregation/in vivo anti-thrombotic activity and the nano-structure of Cu(II)-4a-c was discussed.
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Multimodal cognitive interface for robot navigation.
Cogn Process
PUBLISHED: 01-04-2011
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To build effective interactions between humans and robots, they should have common ground of understanding that creates realistic expectations and forms the basis communications. An emerging approach to doing this is to create cognitive models of human reasoning and behavior selection. We have developed a robot navigation system that uses both spatial language and graphical representation to describe route-based navigation tasks for a mobile robot. Our proposed route instruction language (RIL) is intended as a semi-formal language for instructing the robot to execute a route in an indoor environment. We implemented an instruction interpreter to process the route description and generate its equivalent symbolic and topological map representations. A topological map is generated to describe relationships among features of the environment in a more abstract form without any absolute reference system to treat the ambiguity which can occur when the robot cannot recognize the current landmark. The symbolic and topological map representations are supplied to other system components as an initial path estimation to guide the robot while it plans its navigation task. We conducted some experiments to evaluate the routes which are written by using the RIL instructions.
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Leaf age affects the responses of foliar injury and gas exchange to tropospheric ozone in Prunus serotina seedlings.
Environ. Pollut.
PUBLISHED: 04-14-2010
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We investigated the effect of leaf age on the response of net photosynthesis (A), stomatal conductance (g(wv)), foliar injury, and leaf nitrogen concentration (N(L)) to tropospheric ozone (O(3)) on Prunus serotina seedlings grown in open-plots (AA) and open-top chambers, supplied with either carbon-filtered or non-filtered air. We found significant variation in A, g(wv), foliar injury, and N(L) (P < 0.05) among O(3) treatments. Seedlings in AA showed the highest A and g(wv) due to relatively low vapor pressure deficit (VPD). Older leaves showed significantly lower A, g(wv), N(L), and higher foliar injury (P < 0.001) than younger leaves. Leaf age affected the response of A, g(wv), and foliar injury to O(3). Both VPD and N(L) had a strong influence on leaf gas exchange. Foliar O(3)-induced injury appeared when cumulative O(3) uptake reached 8-12 mmol m(-2), depending on soil water availability. The mechanistic assessment of O(3)-induced injury is a valuable approach for a biologically relevant O(3) risk assessment for forest trees.
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The B73 maize genome: complexity, diversity, and dynamics.
Patrick S Schnable, Doreen Ware, Robert S Fulton, Joshua C Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A Graves, Patrick Minx, Amy Denise Reily, Laura Courtney, Scott S Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M Rock, Eddie Belter, Feiyu Du, Kyung Kim, Rachel M Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, Hyeran Kim, Seunghee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim, Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Müller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael J Levy, Linda McMahan, Peter Van Buren, Matthew W Vaughn, Kai Ying, Cheng-Ting Yeh, Scott J Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, W Brad Barbazuk, Regina S Baucom, Thomas P Brutnell, Nicholas C Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C Estill, Yan Fu, Jeffrey A Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C McCann, Phillip SanMiguel, Alan M Myers, Dan Nettleton, John Nguyen, Bryan W Penning, Lalit Ponnala, Kevin L Schneider, David C Schwartz, Anupma Sharma, Carol Soderlund, Nathan M Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L Bennetzen, R Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G Presting, Susan R Wessler, Srinivas Aluru, Robert A Martienssen, Sandra W Clifton, W Richard McCombie, Rod A Wing, Richard K Wilson.
Science
PUBLISHED: 12-08-2009
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We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
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Detailed analysis of a contiguous 22-Mb region of the maize genome.
PLoS Genet.
PUBLISHED: 08-21-2009
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Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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The physical and genetic framework of the maize B73 genome.
PLoS Genet.
PUBLISHED: 07-14-2009
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Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map ( approximately 1,993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1).
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Single feature polymorphisms between two rice cultivars detected using a median polish method.
Theor. Appl. Genet.
PUBLISHED: 03-20-2009
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Expression levels measured in microarrays of oligonucleotide probes have now been adapted as a high throughput approach for identifying DNA sequence variation between genotypes, referred to as single feature polymorphisms (SFPs). Although there have been increasing interests in this approach, there is still need for improving the algorithm in order to achieve high sensitivity and specificity especially with complex genome and large datasets, while maintaining optimal computational performance. We obtained microarray datasets for expression profiles of two rice cultivars and adapted a median polish method to detect SFPs. The analysis identified 6,655 SFPs between two the rice varieties representing 3,131 rice unique genes. We showed that the median polish method has the advantage of avoiding fitting complex linear models thus can be used to analyze complex transcriptome datasets like the ones in this study. The method is also superior in sensitivity, accuracy and computing time requirement compared with two previously used methods. A comparison with data from a resequencing project indicated that 75.6% of the SFPs had SNP supports in the probe regions. Further comparison revealed that SNPs in sequences immediately flanking the probes also had contributions to the detection of SFPs in cases where the probes and the targets had perfectly matched sequences. It was shown that differences in minimum free energies caused by flanking SNPs, which may change the stability of RNA secondary structure, may partly explain the SFPs as detected. These SFPs may facilitate gene discovery in future studies.
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An improved level set method for brain MR images segmentation and bias correction.
Comput Med Imaging Graph
PUBLISHED: 03-06-2009
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Intensity inhomogeneities cause considerable difficulty in the quantitative analysis of magnetic resonance (MR) images. Thus, bias field estimation is a necessary step before quantitative analysis of MR data can be undertaken. This paper presents a variational level set approach to bias correction and segmentation for images with intensity inhomogeneities. Our method is based on an observation that intensities in a relatively small local region are separable, despite of the inseparability of the intensities in the whole image caused by the overall intensity inhomogeneity. We first define a localized K-means-type clustering objective function for image intensities in a neighborhood around each point. The cluster centers in this objective function have a multiplicative factor that estimates the bias within the neighborhood. The objective function is then integrated over the entire domain to define the data term into the level set framework. Our method is able to capture bias of quite general profiles. Moreover, it is robust to initialization, and thereby allows fully automated applications. The proposed method has been used for images of various modalities with promising results.
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Analysis of mathematical models of Pseudomonas spp. growth in pallet-package pork stored at different temperatures.
Meat Sci.
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Pseudomonas of pallet-packaged raw pork grown at 0, 5, 10, 15, 20 and 25°C has been studied in this paper. The modified Gompertz, Baranyi and Huang models were used for data fitting. Statistical criteria such as residual sum of squares, mean square error, Akaikes information criterion, and pseudo-R(2) were used to evaluate model performance. Results showed that there was an apparent decline in Pseudomonas growth at initial-storage phase at low temperatures. The modified Gompertz model outperformed the others at 5, 15, and 20°C, while Baranyi model was appropriate for 0 and 25°C. The Huang model was optimal at 10°C. No single model can give a consistently preferable goodness-of-fit for all growth data. The Gompertz model, with the smallest average values of RSS, AIC, MSE and the biggest pseudo-R(2) at all temperatures, is the most appropriate model to describe the growth of Pseudomonas of raw pork under pallet packaging.
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Effects of surface and morphological properties of zeolite on impedance spectroscopy-based sensing performance.
Sensors (Basel)
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Measurement by impedance spectroscopy of the changes in intrazeolitic cation motion of pressed pellets of zeolite particles upon adsorption of dimethylmethylphosphonate (DMMP) provides a strategy for sensing DMMP, a commonly used simulant for highly toxic organophosphate nerve agents. In this work, two strategies for improving the impedance spectroscopy based sensing of DMMP on zeolites were investigated. The first one is the use of cerium oxide (CeO(2)) coated on the zeolite surface to neutralize acidic groups that may cause the decomposition of DMMP, and results in better sensor recovery. The second strategy was to explore the use of zeolite Y membrane. Compared to pressed pellets, the membranes have connected supercages of much longer length scales. The zeolite membranes resulted in higher sensitivity to DMMP, but recovery of the device was significantly slower as compared to pressed zeolite pellets.
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The impact of tumor size change after target therapy on survival: analysis of patients enrolled onto three clinical trials of advanced NSCLC from one institution.
Onco Targets Ther
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To explore whether changes in tumor size impact survival in advanced non-small-cell lung cancer (NSCLC) after target therapy, especially in patients with evaluation of stable disease (SD), and to review the applicability of the Response Evaluation Criteria in Solid Tumors (RECIST) criteria in target therapy.
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Abnormal amplitude low-frequency oscillations in medication-naive, first-episode patients with major depressive disorder: a resting-state fMRI study.
J Affect Disord
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Recent resting-state fMRI studies on major depressive disorder (MDD) have found altered temporal correlation between low-frequency oscillations (LFOs). However, changes on the amplitudes of these LFOs remain largely unknown.
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4-1BB protects dendritic cells from prostate cancer-induced apoptosis.
Pathol. Oncol. Res.
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It has been shown that human prostate cancer (PCa) cells induced apoptotic death of the most potent antigen-presenting cells, dendritic cells (DCs), which are responsible for the induction of specific antitumor immune responses. Here, we investigated the function of 4-1BB on protecting DCs from prostate cancer-induced apoptosis with an agonistic mAb to 4-1BB. RM-1 cells and DCs were co-incubated for 48 h and DC apoptosis was assessed by Annexin Vassay. TNF-? and IL-12 production were assessed by enzyme-linked immunosorbent assay (ELISA) and Bcl-2 and Bcl-xL on DCs were analyzed by Western blot. We have shown that co-incubation of RM-1 cells with DCs is accompanied by an increased level of DCs apoptosis. Triggering 4-1BB on DCs resulted in increased resistance of DCs to RM-1 cells-induced apoptosis, which was owing to the up-regulated expression of Bcl-2 and Bcl-xL, and increased secretion of TNF-?and IL-12. These results demonstrate that triggering 4-1BB on DCs could increased resistance of DCs to PCa-induced apoptosis.
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Synergistic effect of retinoic acid and vitamin D analog EB1089-induced apoptosis of hepatocellular cancer cells.
Cytotechnology
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Previous report showed that leukemia cells differentiation could be induced by retinoic acid (RA), and prostate cancer cells proliferation could be inhibited by Vitamin D or its analog. This study aimed to examine whether RA and vitamin D analog EB1089 have synergistic effect on hepatocellular cancer cells apoptosis. The hepatocellular cancer cell lines viability was determined by MTT method after treating by RA and EB1089 alone or in combination, cell cycle of SSMC-7721 cell analyzed by FACS, mitochondrial membrane potential of SSMC-7721 under different treatments were detected using MitoTracker Red CMXRos. TUNEL analysis was also used for cell apoptosis detection. Real time-PCR and Western Blot assay were used to detect the expression of Bcl-2 and Bax. Moreover, hepatocellular cancer model was developed by subcutaneously (S.C.) challenging H22 cells to nude mice. In the combination group (10 ?mol/L RA, 10 nmol/L EB1089), the viability of hepatocellular cancer cells decreased significantly compared with drugs used alone (P < 0.05). From the TUNEL analysis, SSMC-7721 cells have a higher apoptotic ratio in the combined drug group than in the groups for which the drugs were used separately. In a hepatocellular cancer model, the tumor weight of H22 tumor bearing mice was more reduced in the combined drug treated group when compared to the groups for which the drugs were used alone (P < 0.05), in addition, significantly prolonged survival was observed. Combination of RA and EB1089 exert synergistic growth inhibition and apoptosis induction on hepatocellular cancers cells.
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Salvage liver transplantation for patients with recurrent hepatocellular carcinoma after curative resection.
PLoS ONE
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To summarize the experience with salvage liver transplantation (SLT) for patients with recurrent hepatocellular carcinoma (HCC) after primary hepatic resection in a single center.
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Classification of different therapeutic responses of major depressive disorder with multivariate pattern analysis method based on structural MR scans.
PLoS ONE
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Previous studies have found numerous brain changes in patients with major depressive disorder (MDD), but no neurological biomarker has been developed to diagnose depression or to predict responses to antidepressants. In the present study, we used multivariate pattern analysis (MVPA) to classify MDD patients with different therapeutic responses and healthy controls and to explore the diagnostic and prognostic value of structural neuroimaging data of MDD.
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Abnormal regional spontaneous neural activity in first-episode, treatment-naive patients with late-life depression: a resting-state fMRI study.
Prog. Neuropsychopharmacol. Biol. Psychiatry
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The previous resting perfusion or task-based studies have provided evidence of functional changes in the brains of patients with late-life depression (LLD). Little is known, so far, about the changes in the spontaneous brain activity in LLD during the resting state. The aim of this study was to investigate the spontaneous neural activity in first-episode, treatment-naive patients with LLD by using resting-state functional magnetic resonance imaging (fMRI).
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Mathematical reflections on acupoint combinations in the traditional meridian systems.
Evid Based Complement Alternat Med
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The meridian system is a systematic order of empirical knowledge functioning as a rational ground for a balanced treatment by combining meridians. In TCM theory, a continuous circulation of Qi through 12 meridians is postulated, described as the Chinese clock (CC). On this basis, combinations of meridians and acupoints had been described in historical writings. The most common is the interior/exterior system beside the neighbouring system, the opposite clock system, and three systems, developed out of the theory of the six stages. All of these represent symmetrical combinations, which were defined by the steps in the CC. We calculated the possible combinations that fit into the systematics of the historical descriptions, leading to 19 systems. Merging the data of the 19 systems, possible steps in the CC clock for balancing a meridian are 1, 2, 3, and 6. Step 4 is not possible. Step 5 is a combinatory possibility but has no widespread tradition except for activating the yin extraordinary vessels. These possibilities can be plotted on the CC as a powerful tool for daily practice. Only two meridians might be excluded as potentially balancing meridians, so it seems almost impossible to define noneffective acupuncture points as controls in clinical trials.
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Design, synthesis, and evaluation of a novel class of 2,3-disubstituted-tetrahydro-?-carboline derivatives.
Bioorg. Med. Chem. Lett.
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Several novel tetrahydro-?-carboline derivatives with amino acid residues at the 2-position and a glucosamine group at the 3-position of the tetrahydro-?-carboline nucleus were synthesized from a readily available starting material, tryptophane, and were evaluated for their anti-inflammatory activity in the present study. Our results showed that all of the derivatives tested exhibited a significant inhibition of xylene-induced inflammation in mice.
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Recent advances in morphological cell image analysis.
Comput Math Methods Med
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This paper summarizes the recent advances in image processing methods for morphological cell analysis. The topic of morphological analysis has received much attention with the increasing demands in both bioinformatics and biomedical applications. Among many factors that affect the diagnosis of a disease, morphological cell analysis and statistics have made great contributions to results and effects for a doctor. Morphological cell analysis finds the cellar shape, cellar regularity, classification, statistics, diagnosis, and so forth. In the last 20 years, about 1000 publications have reported the use of morphological cell analysis in biomedical research. Relevant solutions encompass a rather wide application area, such as cell clumps segmentation, morphological characteristics extraction, 3D reconstruction, abnormal cells identification, and statistical analysis. These reports are summarized in this paper to enable easy referral to suitable methods for practical solutions. Representative contributions and future research trends are also addressed.
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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.

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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.