bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility and Acceptability of Health Communication Interventions Within a Combination Intervention Strategy for Improving Linkage and Retention in HIV Care in Mozambique
Authors: Sutton Roberta , Lahuerta Maria , Abacassamo Fatima , Ahoua Laurence , Tomo Maria , Lamb Matthew R. , Elul Batya 
Published: December 2016

Background:
Challenges to ensuring timely linkage to and retention in HIV care are well documented. Combination intervention strategies can be effective in improving the HIV care continuum. Data on feasibility and acceptability of intervention types within intervention packages are limited.

Methods:
The Engage4Health study assessed the effectiveness of a combination intervention strategy to increase linkage and retention among adults newly diagnosed with HIV in Mozambique. The study included 2 health communication interventions—modified delivery of pre-antiretroviral therapy (pre-ART) counseling sessions and SMS reminders—and 3 structural interventions—point-of-care CD4 testing after diagnosis, accelerated ART initiation, and noncash financial incentives. We used a process evaluation framework to assess dose delivered—extent each intervention was delivered as planned—and dose received—participant acceptability—of health communication versus structural interventions in the effectiveness study to understand associated benefits and challenges. Data sources included study records, participant interviews, and clinical data.

Results:
For dose delivered of health communication interventions, 98% of eligible clients received pre-ART counseling and 90% of participants received at least one SMS reminder. For structural interventions, 74% of clients received CD4 testing and 53% of eligible participants initiated ART within 1 month. Challenges for structural interventions included facility-level barriers, staffing limitations, and machine malfunctions. For dose received, participants reported pre-ART counseling and CD4 testing as the most useful interventions for linkage and financial incentives as the least useful for linkage and retention.

Discussion:
Findings demonstrate that health communication interventions can be feasibly and acceptably integrated with structural interventions to create combination intervention strategies.
A Pooled Analysis of Robotic Versus Laparoscopic Surgery for Colon Cancer
Authors: Duan Bo-Shi , Zhao Guo-Hua , Yang Helen , Wang Yue 
Published: December 2016

Objective:
An increasing number of studies have been reported since the “Da Vinci” Robotic System was used in gastrointestinal disease. Thus, we conducted this meta-analysis to evaluate the safety and efficacy of robotic colectomy (RC) compared with laparoscopic colectomy (LC) in the treatment of colon cancer.

Method:
A systematic search of Medline, Embase databases, and the Cochrane Library was performed to identify studies that compared RC and LC and were published up to February 2015. The methodological quality of the selected studies was assessed. Depending on statistical heterogeneity, the fixed or the random-effect model was used for the meta-analysis. Outcomes of interest included the operating time, blood loss, the length of hospital stay, conversion rates to open, postoperative complications, and related outcomes were evaluated.

Results:
Fourteen studies were included in the meta-analysis. These studies involved a total of 125,989 patients: 4924 of them underwent RC and 121,055 underwent LC. The meta-analysis showed that the RC group had a longer operating time (P<0.01), lower blood loss (P<0.01), lower intraoperative conversion to open rate (P<0.01), shorter hospital stay (P<0.01), lower postoperative complication rate (P<0.01), and significantly faster bowel function recovery (P<0.01). There were no differences in the number of lymph nodes harvested (P>0.05).

Conclusions:
Our data suggest that RC may be a safe, feasible, and minimally invasive alternative to its LC counterpart when performed by experienced surgeons in selected patients. However, the long-term outcomes between the 2 techniques need to be further examined.
Invasions and extinctions through the looking glass of evolutionary ecology
Authors: Colautti Robert I. , Alexander Jake M. , Dlugosch Katrina M. , Keller Stephen R. , Sultan Sonia E. 
Published: December 2016

Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
Adaptation to fragmentation: evolutionary dynamics driven by human influences
Authors: Cheptou Pierre-Olivier , Hargreaves Anna L. , Bonte Dries , Jacquemyn Hans 
Published: December 2016

Fragmentation—the process by which habitats are transformed into smaller patches isolated from each other—has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions. While species have adapted to natural fragmentation, adaptation to anthropogenic fragmentation has received little attention. In this review, we address how and whether organisms might adapt to anthropogenic fragmentation. Drawing on selected case studies and evolutionary ecology models, we show that anthropogenic fragmentation can generate selection on traits at both the patch and landscape scale, and affect the adaptive potential of populations. We suggest that dispersal traits are likely to experience especially strong selection, as dispersal both enables migration among patches and increases the risk of landing in the inhospitable matrix surrounding them. We highlight that suites of associated traits are likely to evolve together. Importantly, we show that adaptation will not necessarily rescue populations from the negative effects of fragmentation, and may even exacerbate them, endangering the entire metapopulation.
This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
Adaptive capabilities and fitness consequences associated with pollution exposure in fish
Authors: Hamilton Patrick B. , Rolshausen Gregor , Uren Webster Tamsyn M. , Tyler Charles R. 
Published: December 2016

Many fish populations are exposed to harmful levels of chemical pollution and selection pressures associated with these exposures have led to the evolution of tolerance. Our understanding of the physiological basis for these adaptations is limited, but they are likely to include processes involved with the absorption, distribution, metabolism and/or excretion of the target chemical. Other potential adaptive mechanisms include enhancements in antioxidant responses, an increased capacity for DNA and/or tissue repair and alterations to the life cycle of fish that enable earlier reproduction. Analysis of single-nucleotide polymorphism frequencies has shown that tolerance to hydrocarbon pollutants in both marine and estuarine fish species involves alteration in the expression of the xenobiotic metabolism enzyme CYP1A. In this review, we present novel data showing also that variants of the CYP1A gene have been under selection in guppies living in Trinidadian rivers heavily polluted with crude oil. Potential costs associated with these adaptations could reduce fitness in unpolluted water conditions. Integrating knowledge of local adaptation to pollution is an important future consideration in conservation practices such as for successful restocking, and improving connectivity within river systems.This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.
The Aquarius/EMB-4 helicase licenses co-transcriptional gene silencing
Authors: Akay Alper , Domenico Tomas Di , Suen Kin M. , Nabih Amena , Parada Guillermo E. , Larance Mark , Medhi Ragini , Berkyurek Ahmet C. , Zhang Xinlian , Wedeles Christopher J. , Ma Ping , Lamond Angus I. , Hemberg Martin , Claycomb Julie M. , Miska Eric A. 
Published: December 2016

SUMMARYSmall RNAs (sRNAs) play an ancient role in genome defence against transposable elements. In animals, plants and fungi small RNAs guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. In animals the link between small RNA pathways and the transcriptional machinery remains unclear. Here we show that theCaenorhabditis elegansgermline Argonaute HRDE-1 physically interacts with the conserved RNA helicase Aquarius/EMB-4. We demonstrate that the Aquarius/EMB-4 helicase activity is required to initiate small RNA-induced co-transcriptional gene silencing. HRDE-1 and Aquarius/EMB-4 are required to silence the transcription of overlapping sets of transposable elements. Surprisingly, removal of introns from a small RNA pathway target abolishes the requirement for Aquarius/EMB-4, but not HRDE-1, for gene silencing. We conclude that the Aquarius/EMB-4 helicase activity allows HRDE-1/sRNA complexes to efficiently engage nascent RNA transcripts - in competition with the general RNA processing machinery. We postulate that Aquarius/EMB-4 facilitates the surveillance of the nascent transcriptome to detect and silence transposable elements through small RNA pathways.
How Cancer Genomics Drives Cancer Biology: Does Synthetic Lethality Explain Mutually Exclusive Oncogenic Mutations?
Authors: Varmus Harold , Unni Arun M. , Lockwood William W. 
Published: December 2016

AbstractLarge-scale analyses of cancer genomes are revealing patterns of mutations that suggest biologically significant ideas about many aspects of cancer, including carcinogenesis, classification, and preventive and therapeutic strategies. Among those patterns is “mutual exclusivity”, a phenomenon observed when two or more mutations that are commonly observed in samples of a type of cancer are not found combined in individual tumors. We have been studying a striking example of mutual exclusivity: the absence of co-existing mutations in theKRASandEGFRproto-oncogenes in human lung adenocarcinomas, despite the high individual frequencies of such mutations in this common type of cancer. Multiple lines of evidence suggest that toxic effects of the joint expression ofKRASandEGFRmutant oncogenes, rather than loss of any selective advantages conferred by a second oncogene that operates through the same signaling pathway, are responsible for the observed mutational pattern. We discuss the potential for understanding the physiological basis of such toxicity, for exploiting it therapeutically, and for extending the studies to other examples of mutual exclusivity.
Bacterial genome reduction as a result of short read sequence assembly
Authors: Williamson Charles H.D. , Sanchez Andrew , Vazquez Adam , Gutman Joshua , Sahl Jason W. 
Published: December 2016

AbstractHigh-throughput comparative genomics has changed our view of bacterial evolution and relatedness. Many genomic comparisons, especially those regarding the accessory genome that is variably conserved across strains in a species, are performed using assembled genomes. For completed genomes, an assumption is made that the entire genome was incorporated into the genome assembly, while for draft assemblies, often constructed from short sequence reads, an assumption is made that genome assembly is an approximation of the entire genome. To understand the potential effects of short read assemblies on the estimation of the complete genome, we downloaded all completed bacterial genomes from GenBank, simulated short reads, assembled the simulated short reads and compared the resulting assembly to the completed assembly. Although most simulated assemblies demonstrated little reduction, others were reduced by as much as 25%, which was correlated with the repeat structure of the genome. A comparative analysis of lost coding region sequences demonstrated that up to 48 CDSs or up to ~112,000 bases of coding region sequence, were missing from some draft assemblies compared to their finished counterparts. Although this effect was observed to some extent in 32% of genomes, only minimal effects were observed on pan-genome statistics when using simulated draft genome assemblies. The benefits and limitations of using draft genome assemblies should be fully realized before interpreting data from assembly-based comparative analyses.
Monolayer-Crystal Streptavidin Support Films Provide an Internal Standard of cryo-EM Image Quality
Authors: Han Bong-Gyoon , Watson Zoe , Cate Jamie H. D. , Glaeser Robert M. 
Published: December 2016

ABSTRACTAnalysis of images of biotinylatedEscherichia coli70S ribosome particles, bound to streptavidin affinity grids, demonstrates that the image-quality of particles can be predicted by the image-quality of the monolayer crystalline support film. The quality of the Thon rings is also a good predictor of the image-quality of particles, but only when images of the streptavidin crystals extend to relatively high resolution. When the estimated resolution of streptavidin was 5 Å or worse, for example, the ribosomal density map obtained from 22,697 particles went to only 9.5 Å, while the resolution of the map reached 4.0 Å for the same number of particles, when the estimated resolution of streptavidin crystal was 4 Å or better. It thus is easy to tell which images in a data set ought to be retained for further work, based on the highest resolution seen for Bragg peaks in the computed Fourier transforms of the streptavidin component. The refined density map obtained from 57,826 particles obtained in this way extended to 3.6 Å, a marked improvement over the value of 3.9 Å obtained previously from a subset of 52,433 particles obtained from the same initial data set of 101,213 particles after 3-D classification. These results are consistent with the hypothesis that interaction with the air-water interface can damage particles when the sample becomes too thin. Streptavidin monolayer crystals appear to provide a good indication of when that is the case.
Similar evolutionary trajectories for retrotransposon accumulation in mammals
Authors: Buckley Reuben M , Kortschak R Daniel , Raison Joy M , Adelson David L 
Published: December 2016

AbstractThe factors guiding retrotransposon insertion site preference are not well understood. Different types of retrotransposons share common replication machinery and yet occupy distinct genomic domains. Autonomous long interspersed elements accumulate in gene-poor domains and their non-autonomous short interspersed elements accumulate in gene-rich domains. To determine genomic factors that contribute to this discrepancy we analysed the distribution of retrotransposons within the framework of chromosomal domains and regulatory elements. Using comparative genomics, we identified large-scale conserved patterns of retrotransposon accumulation across several mammalian genomes. Importantly, retrotransposons that were active after our sample-species diverged accumulated in orthologous regions. This suggested a similar evolutionary interaction between retrotransposon activity and conserved genome architecture across our species. In addition, we found that retrotransposons accumulated at regulatory element boundaries in open chromatin, where accumulation of particular retrotransposon types depended on insertion size and local regulatory element density. From our results, we propose a model where density and distribution of genes and regulatory elements canalise retrotransposon accumulation. Through conservation of synteny, gene regulation and nuclear organisation, mammalian genomes with dissimilar retrotransposons follow similar evolutionary trajectories.
Colonization and transmission of the gut microbiota of the burying beetle,Nicrophorus vespolloides, through development
Authors: Wang Yin , Rozen Daniel E. 
Published: December 2016

AbstractCarrion beetles in the genusNicrophorusrear their offspring on decomposing carcasses where larvae are exposed to a diverse microbiome of decomposer bacteria. Parents coat the carcass with antimicrobial secretions prior to egg hatch (defined as Pre-Hatch care) and also feed regurgitated food, and potentially bacteria, to larvae throughout development (defined as Full care). Here we partition the roles of pre- and post-hatch parental care in the transmission and persistence of culturable symbiotic bacteria to larvae. Using three treatment groups (Full-Care, Pre-Hatch care only, and No Care), we found that larvae receiving Full-Care are predominantly colonized by bacteria resident in the maternal gut, while larvae receiving No Care are colonized exclusively with bacteria from the carcass. More importantly, larvae receiving only Pre-Hatch care were also predominantly colonized by maternal bacteria; this result indicates that parental treatment of the carcass, including application of bacteria to the carcass surface, is sufficient to ensure symbiont transfer even in the absence of direct larval feeding. Later in development, we found striking evidence that pupae undergo a aposymbiotic stage, after which they are recolonized at eclosion with bacteria shed in the moulted larval cuticle and on the wall of the pupal chamber. Our results clarify the importance of pre-hatch parental care for symbiont transmission inNicrophorus vespilloides, and suggest that these bacteria successfully outcompete decomposer bacteria during larval and pupal gut colonization.ImportanceHere we examine the origin and persistence of the culturable gut microbiota of larvae in the burying beetleNicrophorus vespilloides.This insect is particularly interesting for this study because larvae are reared on decomposing vertebrate carcasses where they are exposed to high-densities of carrion-decomposing microbes. Larvae also receive extensive parental care in the form of carcass preservation and direct larval feeding. We find that parents transmit their gut bacteria to larvae both directly, through regurgitation, and indirectly via their effects on the carcass. In addition, we find that larvae become aposymbiotic during pupation, but are recolonized from bacteria shed onto the insect cuticle before adult eclosion. Our results highlight the diverse interactions between insect behavior and development on microbiota composition. They further indicate that strong competitive interactions mediate the bacterial composition ofNicrophoruslarvae, suggesting that the bacterial communities of these insects may be highly coevolved with their host species.
Adaptive evolution by spontaneous domain fusion and protein relocalisation
Authors: Farr Andrew D , Rainey Paul B 
Published: December 2016

AbstractKnowledge of adaptive processes encompasses understanding of the emergence of new genes. Computational analyses of genomes suggest that new genes can arise by domain swapping, however, empirical evidence has been lacking. Here we describe a set of nine independent deletion mutations that arose during the course of selection experiments with the bacteriumPseudomonas fluorescensin which the membrane-spanning domain of a fatty acid desaturase became translationally fused to a cytosolic di-guanylate cyclase (DGC) generating an adaptive phenotype. Detailed genetic analysis of one chimeric fusion protein showed that the DGC domain had become membrane-localised resulting in a new biological function. The relative ease by which this new gene arose along with its profound functional and regulatory effects provides a glimpse of mutational events and their consequences that are likely to play a significant role in the evolution of new genes.
Specific expression and function of the Six3optixin serially homologous organs
Authors: Khatib Amer Al , Siomava Natalia , Posnien Nico , Casares Fernando 
Published: December 2016

ABSTRACTOrgan size and pattern results from the integration of two positional information systems. One global, encoded by the Hox genes, links organ type with position along the main body axis. Within specific organs, local information is conveyed by signaling molecules that regulate organ growth and pattern. The mesothoracic (T2) wing and the metathoracic (T3) haltere ofDrosophilarepresent a paradigmatic example of this coordination. The Hox geneUltrabithorax (Ubx), expressed in the developing T3, selects haltere identity by, among other processes, modulating the production and signaling efficiency of Dpp, a BMP2-like molecule that acts as a major regulator of size and pattern. Still, the mechanisms of the Hox-signal integration even in this well-studied system, are incomplete. Here we have investigated this issue by studying the expression and function of the Six3 transcription factoroptixduring the development of theDrosophilawing and haltere development. We find that in both organs Dpp defines the expression domain ofoptixthrough repression, and that the specific position of this domain in wing and haltere seems to reflect the differential signaling profile among these organs. We show thatoptixexpression in wing and haltere primordia is conserved beyondDrosophilain other higher diptera. Despite the similar expression pattern,optixplays different roles in wing and haltere. In the wing,optixis required for the growth of the most anterior/proximal region (the “marginal cell”) and for the correct formation of sensory structures along the proximal anterior wing margin. In contrast, in the haltereoptixis necessary for the suppression of sensory bristles without any noticeable effect on organ growth. Therefore,optixshows an organ-specific function. Beyond dipterans,optixexpression in the anterior wing has been shown also in butterflies. We propose that the ancestral role ofoptixmight have been structural in the anterior wing. Once expressed in the wing,optixexpression had been re-deployed for wing spot formation in other parts of the wing of Heliconius butterflies.