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Find video protocols related to scientific articles indexed in Pubmed.
Draft Genome Sequence of Penicillium expansum Strain R19, Which Causes Postharvest Decay of Apple Fruit.
Genome Announc
PUBLISHED: 06-21-2014
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Among the species that cause blue mold, isolates of Penicillium expansum are the most prevalent and virulent species, causing more than 50 percent of postharvest decay. We report the draft genome sequence of P. expansum R19 in order to identify fungal virulence factors and to understand the mechanism of infection.
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Genome Sequences of Nine Bordetella holmesii Strains Isolated in the United States.
Genome Announc
PUBLISHED: 06-21-2014
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An increasing number of pertussis-like cases are attributed to the emergent pathogen Bordetella holmesii. The genomes of 9 clinical isolates show that they are clonal, lack the virulence factors encoded by B. pertussis, and are more similar to nonpertussis bordetellae. New markers for B. holmesii can be developed using these sequences.
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Monitoring tectonic uplift and paleoenvironmental reconstruction for marine terraces near Ma?aracik and Samanda?, Hatay Province, Turkey.
Radiat Prot Dosimetry
PUBLISHED: 06-18-2014
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Near Hatay, the Antakya-Samanda?-Cyprus Fault (ASCF), East Anatolian and Dead Sea Fault Zones, the large faults that form the edges of the African, Anatolian, Cyprus and Arabian Plates, all produce large earthquakes, which have decimated Hatay repeatedly. Near Samanda?, Hatay, differential vertical displacement on the ASCF has uplifted the southeastern side relative to northwestern side, producing large fault scarps that parallel the Asi (Orontes) River. Tectonic uplift coupled with Quaternary sealevel fluctuations has produced several stacked marine terraces stranded above current sealevel. This study dated 24 mollusc samples from 10 outcrops on six marine terraces near Samanda? electron spin resonance (ESR). Ages were calculated using time-averaged and volumetrically averaged external dose rates, modelled by assuming typical water depths for the individual species and sediment thicknesses estimated from geological criteria. Uplift rates were then calculated for each fault block. At all the Ma?arac?k terraces, the dates suggest that many shells were likely reworked. On the 30 m terrace at Ma?arac?k IV (UTM 766588-3999880), Lithophagus burrows with in situ shells cross the unconformity. One such shell dated to 62 ± 6 ka, setting the minimum possible age for the terrace. For all the Ma?arac?k terraces at ?30 m above mean sealevel (amsl), the youngest ages for the reworked shells, which averaged 60 ± 3 ka for six separate analyses, sets the maximum possible age for this unit. Thus, the terrace must date to 60-62 ± 3 ka, at the MIS 3/4 boundary when temperatures and sealevels were fluctuating rapidly. Older units dating to MIS 7, 6, and 5 likely were being eroded to supply some fossils found in this terrace. At Ma?arac?k Dump (UTM 765391-4001048), ?103 m amsl, Ostrea and other shells were found cemented in growth position to the limestone boulders outcropping there <2.0 m above a wave-eroded notch. If the oysters grew at the same time as the wave-cut notch and the related terrace, the date, 91 ± 13 ka, for the oysters, this fault block has been uplifted at 1.19 ± 0.15 m ky(-1), since MIS 5c. At Samanda? Kurt Stream at 38 m amsl, molluscs were deposited fine sandy gravel, which was likely formed in a large tidal channel. Four molluscs averaged 116 ± 5 ka. If these molluscs have not been reworked, this fault block has uplifted at 0.34 ± 0.05 m ky(-1) since the MIS 5d/5e boundary. The differences in these uplift rates suggests that at least one, and possibly two, hitherto undiscovered faults may separate the Ma?arac?k Dump site from the other Ma?arac?k sites and from the Samanda? Kurt Stream site.
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Prevalence of depression and validation of the Beck Depression Inventory-II and the Children's Depression Inventory-Short amongst HIV-positive adolescents in Malawi.
J Int AIDS Soc
PUBLISHED: 01-01-2014
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There is a remarkable dearth of evidence on mental illness in adolescents living with HIV/AIDS, particularly in the African setting. Furthermore, there are few studies in sub-Saharan Africa validating the psychometric properties of diagnostic and screening tools for depression amongst adolescents. The primary aim of this cross-sectional study was to estimate the prevalence of depression amongst a sample of HIV-positive adolescents in Malawi. The secondary aim was to develop culturally adapted Chichewa versions of the Beck Depression Inventory-II (BDI-II) and Children's Depression Inventory-II-Short (CDI-II-S) and conduct a psychometric evaluation of these measures by evaluating their performance against a structured depression assessment using the Children's Rating Scale, Revised (CDRS-R).
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Beyond early infant diagnosis: case finding strategies for identification of HIV-infected infants and children.
AIDS
PUBLISHED: 12-24-2013
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There are 3.4 million children infected with HIV worldwide, with up to 2.6 million eligible for treatment under current guidelines. However, roughly 70% of infected children are not receiving live-saving HIV care and treatment. Strengthening case finding through improved diagnosis strategies, and actively linking identified HIV-infected children to care and treatment is essential to ensuring that these children benefit from the care and treatment available to them. Without attention or advocacy, the majority of these children will remain undiagnosed and die from complications of HIV. In this article, we summarize the challenges of identifying HIV-infected infants and children, review currently available evidence and guidance, describe promising new strategies for case finding, and make recommendations for future research and interventions to improve identification of HIV-infected infants and children.
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Beyond prevention of mother-to-child transmission: keeping HIV-exposed and HIV-positive children healthy and alive.
AIDS
PUBLISHED: 12-24-2013
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In 2011, Joint United Nations Programme on HIV/AIDS announced a plan to eliminate new HIV infections among children by 2015. This increased focus on the elimination of maternal to child transmission (MTCT) is most welcome but is insufficient, as access to prevention of MTCT (PMTCT) programming is neither uniform nor universal. A new and more expansive agenda must be articulated to ensure that those infants and children who will never feel the impact of the current elimination agenda are reached and linked to appropriate care and treatment. This agenda must addresses challenges around both reducing vertical transmission through PMTCT and ensuring access to appropriate HIV testing, care, and treatment for all affected children who were never able to access PMTCT programming. Option B+, or universal test and treat for HIV-infected pregnant women is an excellent start, but it may be time to rethink our current approaches to delivering PMTCT services. New strategies will reduce vertical transmission to less than 1% for those mother-infant pairs who can access them allowing for the contemplation of not just PMTCT, but actual elimination of MTCT. But expanded thinking is needed to ensure elimination of pediatric HIV.
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Linkage, initiation and retention of children in the antiretroviral therapy cascade: an overview.
AIDS
PUBLISHED: 12-24-2013
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In 2012, there were an estimated 2 million children in need of antiretroviral therapy (ART) in the world, but ART is still reaching fewer than 3 in 10 children in need of treatment. [1, 7] As more HIV-infected children are identified early and universal treatment is initiated in children under 5 regardless of CD4, the success of pediatric HIV programs will depend on our ability to link children into care and treatment programs, and retain them in those services over time. In this review, we summarize key individual, institutional, and systems barriers to diagnosing children with HIV, linking them to care and treatment, and reducing loss to follow-up (LTFU). We also explore how linkage and retention can be optimally measured so as to maximize the impact of available pediatric HIV care and treatment services.
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HIV-exposed infants: rethinking care for a lifelong condition.
AIDS
PUBLISHED: 12-24-2013
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Each year over a million infants are born to HIV-infected mothers. With scale up of prevention of mother-to-child transmission (PMTCT) interventions, only 210?000 of the 1.3 million infants born to mothers with HIV/AIDS in 2012 became infected. Current programmatic efforts directed at infants born to HIV-infected mothers are primarily focused on decreasing their risk of infection, but an emphasis on maternal interventions has meant follow-up of exposed infants has been poor. Programs are struggling to retain this population in care until the end of exposure, typically at the cessation of breastfeeding, between 12 and 24 months of age. But HIV exposure is a life-long condition that continues to impact the health and well being of a child long after exposure has ended. A better understanding of the impact of HIV on exposed infants is needed and new programs and interventions must take into consideration the long-term health needs of this growing population. The introduction of lifelong treatment for all HIV-infected pregnant women is an opportunity to rethink how we provide services adapted for the long-term retention of mother-infant pairs.
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Challenges in infant and young child nutrition in the context of HIV.
AIDS
PUBLISHED: 12-24-2013
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There is consensus on the benefits for all infants of exclusive breastfeeding for 6 months and introduction of appropriate complementary foods at 6 months, followed by continued breastfeeding. However, guidelines on infant and young child feeding (IYCF) for HIV-positive mothers have changed continually since 2000. This article explores issues and evidence related to IYCF for the prevention and care of paediatric HIV in resource-limited settings in light of new HIV treatment guidelines, implementation challenges and knowledge gaps.In 2010 the impact of antiretroviral drugs (ARVs) on reducing the risk of mother-to-child transmission of HIV moved WHO to urge countries to endorse either avoidance of all breastfeeding or exclusive breastfeeding for the first 6 months while taking ARVs, depending on which strategy could give their infants the greatest chance of HIV-free survival. Implementation of the 2010 recommendations is challenged by lack of healthcare provider training, weak clinic-community linkages to support mother/infant pairs and lack of national monitoring and reporting on infant feeding indicators.More evidence is needed to inform prevention and treatment of malnutrition among HIV-exposed and HIV-infected children. Knowledge gaps include the effects of prolonged ARV exposure, the cause of HIV-associated growth faltering, the effects of early infant testing on continuation of breastfeeding and specific nutrition interventions needed for HIV-infected children.Significant progress has been made toward keeping mothers alive and reducing paediatric HIV infection, but sustained political, financial and scientific commitment are required to ensure meaningful interventions to eliminate postnatal transmission and meet the nutritional needs of HIV-exposed and HIV-infected children.
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Genome Sequences of 28 Bordetella pertussis U.S. Outbreak Strains Dating from 2010 to 2012.
Genome Announc
PUBLISHED: 12-21-2013
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Despite the availability of highly effective vaccines, Bordetella pertussis incidence has been rapidly rising in highly vaccinated populations. Recent outbreaks have received media attention, feeding concerns about the emergence of dangerous new strains with increased virulence or that escape vaccine-induced immunity. To accelerate the study of this reemerging pathogen, we sequenced the genomes of 28 B. pertussis strains isolated during outbreaks from 2010 through 2012, making both strains and sequence data available to the scientific community.
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Draft Genome Sequences of Burkholderia cenocepacia ET12 Lineage Strains K56-2 and BC7.
Genome Announc
PUBLISHED: 10-19-2013
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The Burkholderia cepacia complex (BCC) is a group of closely related bacteria that are responsible for respiratory infections in immunocompromised humans, most notably those with cystic fibrosis (CF). We report the genome sequences for Burkholderia cenocepacia ET12 lineage CF isolates K56-2 and BC7.
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Risks and benefits of lifelong antiretroviral treatment for pregnant and breastfeeding women: a review of the evidence for the Option B+ approach.
Curr Opin HIV AIDS
PUBLISHED: 08-09-2013
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Considerable debate has emerged on whether Option B+ (B+), initiation of lifelong antiretroviral therapy (ART) for all pregnant and breastfeeding women, is the best approach to achieving elimination of mother-to-child-transmission. However, direct evidence and experience with B+ is limited. We review the current evidence informing the proposed benefits and potential risks of the B+ approach, distinguishing individual health concerns for mother and child from program delivery and public health issues.
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Targeting of Painting of fourth to roX1 and roX2 proximal sites suggests evolutionary links between dosage compensation and the regulation of the fourth chromosome in Drosophila melanogaster.
G3 (Bethesda)
PUBLISHED: 06-05-2013
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In Drosophila melanogaster, two chromosome-specific targeting and regulatory systems have been described. The male-specific lethal (MSL) complex supports dosage compensation by stimulating gene expression from the male X-chromosome, and the protein Painting of fourth (POF) specifically targets and stimulates expression from the heterochromatic 4(th) chromosome. The targeting sites of both systems are well characterized, but the principles underlying the targeting mechanisms have remained elusive. Here we present an original observation, namely that POF specifically targets two loci on the X-chromosome, PoX1 and PoX2 (POF-on-X). PoX1 and PoX2 are located close to the roX1 and roX2 genes, which encode noncoding RNAs important for the correct targeting and spreading of the MSL-complex. We also found that the targeting of POF to PoX1 and PoX2 is largely dependent on roX expression and identified a high-affinity target region that ectopically recruits POF. The results presented support a model linking the MSL-complex to POF and dosage compensation to regulation of heterochromatin.
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Low rates of mother-to-child HIV transmission in a routine programmatic setting in Lilongwe, Malawi.
PLoS ONE
PUBLISHED: 01-01-2013
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The Tingathe program utilizes community health workers to improve prevention of mother-to-child transmission (PMTCT) service delivery. We evaluated the impact of antiretroviral (ARV) regimen and maternal CD4+ count on HIV transmission within the Tingathe program in Lilongwe, Malawi.
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A new powerful method for site-specific transgene stabilization based on chromosomal double-strand break repair.
PLoS ONE
PUBLISHED: 06-29-2011
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Transgenic insects are a promising tool in sterile insect techniques and population replacement strategies. Such transgenic insects can be created using nonautonomous transposons, which cannot be transferred without a transposase source. In biocontrol procedures where large numbers of insects are released, there is increased risk of transgene remobilization caused by external transposase sources that can alter the characteristics of the transgenic organisms lead horizontal transgene transfer to other species. Here we describe a novel, effective method for transgene stabilization based on the introduction of directed double-strand breaks (DSB) into a genome-integrated sequence and their subsequent repair by the single-strand annealing (SSA) pathway. Due to the constructs organization, the repair pathway is predictable, such that all transposon and marker sequences can be deleted, while preserving integration of exogenous DNA in the genome. The exceptional conservation of DNA repair pathways makes this method suitable for a broad range of organisms.
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Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche.
Genome Biol Evol
PUBLISHED: 06-21-2011
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Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth-death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA.
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Going deeper: metagenome of a hadopelagic microbial community.
PLoS ONE
PUBLISHED: 02-02-2011
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The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.
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Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation.
PLoS ONE
PUBLISHED: 01-13-2011
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Yersinia pestis is the causative agent of the plague. Y. pestis KIM 10+ strain was passaged and selected for loss of the 102 kb pgm locus, resulting in an attenuated strain, KIM D27. In this study, whole genome sequencing was performed on KIM D27 in order to identify any additional differences. Initial assemblies of 454 data were highly fragmented, and various bioinformatic tools detected between 15 and 465 SNPs and INDELs when comparing both strains, the vast majority associated with A or T homopolymer sequences. Consequently, Illumina sequencing was performed to improve the quality of the assembly. Hybrid sequence assemblies were performed and a total of 56 validated SNP/INDELs and 5 repeat differences were identified in the D27 strain relative to published KIM 10+ sequence. However, further analysis showed that 55 of these SNP/INDELs and 3 repeats were errors in the KIM 10+ reference sequence. We conclude that both 454 and Illumina sequencing were required to obtain the most accurate and rapid sequence results for Y. pestis KIMD27. SNP and INDELS calls were most accurate when both Newbler and CLC Genomics Workbench were employed. For purposes of obtaining high quality genome sequence differences between strains, any identified differences should be verified in both the new and reference genomes.
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Inadequate coordination of maternal and infant HIV services detrimentally affects early infant diagnosis outcomes in Lilongwe, Malawi.
J. Acquir. Immune Defic. Syndr.
PUBLISHED: 01-13-2011
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To assess the continuity of care and outcome of pediatric HIV prevention, testing, and treatment services, focusing on early infant diagnosis with DNA polymerase chain reaction (PCR).
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Genomic and functional adaptation in surface ocean planktonic prokaryotes.
Nature
PUBLISHED: 09-22-2010
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The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0??m size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.
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Therapy of percutaneous infection around craniofacial implants.
Int J Prosthodont
PUBLISHED: 11-18-2009
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This study sought to develop treatment strategies for managing percutaneous infection around craniofacial implants. The present general pathogen situation together with a bacterial resistance were determined in 57 infected peri-implant sites. Forty-four implants were randomly assigned for wound cleaning and split into three groups-two with local antibiotics of proven efficacy and one with 3% hydrogen peroxide (H2O2). The pathogen spectrum differed depending on the severity of the infection, with Staphylococcus aureus clearly correlated with the degree of inflammation (positive correlation: R = 0.72). It was observed that the use of additional local antibiotics was not superior to conventional wound cleaning with 3% H2O2. It is suggested that sulcus fluid flow rate measurements could serve as a simple and reliable objective parameter for recall examinations.
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The Tingathe programme: a pilot intervention using community health workers to create a continuum of care in the prevention of mother to child transmission of HIV (PMTCT) cascade of services in Malawi.
J Int AIDS Soc
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Loss to follow-up is a major challenge in the prevention of mother to child transmission of HIV (PMTCT) programme in Malawi with reported loss to follow-up of greater than 70%. Tingathe-PMTCT is a pilot intervention that utilizes dedicated community health workers (CHWs) to create a complete continuum of care within the PMTCT cascade, improving service utilization and retention of mothers and infants. We describe the impact of the intervention on longitudinal care starting with diagnosis of the mother at antenatal care (ANC) through final diagnosis of the infant.
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Nature and function of insulator protein binding sites in the Drosophila genome.
Genome Res.
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Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes.
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Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary.
J. Bacteriol.
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Ammonia-oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the ammonia-oxidizing archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.
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Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary.
J. Bacteriol.
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Here, we present the draft genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, an ammonia-oxidizing archaeon enriched in culture from low-salinity sediments of the San Francisco Bay estuary. The genome sequence revealed many similarities to the previously sequenced genome of "Ca. Nitrosoarchaeum limnia" SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of a clade of ammonia-oxidizing archaea (AOA) found in low-salinity habitats worldwide.
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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.