bluuebunny/crossref_metadata_2025_split huggingface dataset:
Should T-Tube Drainage be Performed for Choledocholithiasis after Laparoscopic Common Bile Duct Exploration? A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Zhang Woods , Li Ge , Chen Yan-ling 
Published: October 2017

Background:
Laparoscopic common bile duct exploration (LCBDE) has been verified to be a comparatively effective treatment approach for uncomplicated choledocholithiasis, and it has been previously proposed that the primary duct closure (PDC) technique, in which the bile duct can directly be sutured in only 1 step compared with the T-tube drainage (TTD), can be deemed a choice after LCBDE; however, the conventional TTD performance is controversial in the minimally invasive surgery era. On the basis of the above-mentioned point, this meta-analysis was conducted to assess the different effects between TTD and PDC after LCBDE.

Materials and Methods:
In PubMed, EMBASE, and the Cochrane Library, literature search was conducted to screen out randomized controlled trials (RCTs) to compare PDC with TTD. The analyzed outcome variables included overall morbidity, biliary-specific morbidity (retained stones, biliary leak, biliary peritonitis), other morbidities, operating time, postoperative hospital stay, reintervention (surgery, endoscopy/radiology), and median hospital expenses.

Results:
In this meta-analysis, there are 4 RCTs qualifying for inclusion, including 396 patients in all (222 in PDC and 214 in TTD). With respect to postoperative overall morbidity (P<0.05), biliary peritonitis (P<0.05), surgery time (P<0.05), length of stay (P<0.05), and median hospital expenses (P<0.05), PDC presented remarkably better results than TTD (P<0.05). Statistically, no remarkable distinction was found between the 2 groups as to biliary-specific morbidity, retained stones, biliary leak, other morbidities, or reintervention (radiology/endoscopy, surgery).

Conclusions:
In this meta-analysis, there was no evidence provided for clinical benefits of using TTD after LCBDE. Therefore, TTD should not routinely be performed after LCBDE. However, multicenter, large sample size, RCTs should be conducted to clarify this issue.
Monitoring modalities and assessment of fluid status: A practice management guideline from the Eastern Association for the Surgery of Trauma
Authors: Plurad David S. , Chiu William , Raja Ali S. , Galvagno Samuel M. , Khan Uzer , Kim Dennis Y. , Tisherman Samuel A. , Ward Jeremy , Hamill Mark E. , Bennett Vicki , Williams Brian , Robinson Bryce 
Published: October 2017

BACKGROUND
Fluid administration in critically ill surgical patients must be closely monitored to avoid complications. Resuscitation guided by invasive methods are not consistently associated with improved outcomes. As such, there has been increased use of focused ultrasound and Arterial Pulse Waveform Analysis (APWA) to monitor and aid resuscitation. An assessment of these methods using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) framework is presented.

METHODS
A subsection of the Surgical Critical Care Task Force of the Practice Management Guideline Committee of EAST conducted two systematic reviews to address the use of focused ultrasound and APWA in surgical patients being evaluated for shock. Six population, intervention, comparator, and outcome (PICO) questions were generated. Critical outcomes were prediction of fluid responsiveness, reductions in organ failures or complications and mortality. Forest plots were generated for summary data and GRADE methodology was used to assess for quality of the evidence. Reviews are registered in PROSPERO, the International Prospective Register of Systematic Reviews (42015032402 and 42015032530).

RESULTS
Twelve focused ultrasound studies and 20 APWA investigations met inclusion criteria. The appropriateness of focused ultrasound or APWA-based protocols to predict fluid responsiveness varied widely by study groups. Results were mixed in the one focused ultrasound study and 9 APWA studies addressing reductions in organ failures or complications. There was no mortality advantage of either modality versus standard care. Quality of the evidence was considered very low to low across all PICO questions.

CONCLUSION
Focused ultrasound and APWA compare favorably to standard methods of evaluation but only in specific clinical settings. Therefore, conditional recommendations are made for the use of these modalities in surgical patients being evaluated for shock.

LEVEL OF EVIDENCE
Systematic Review, level II.
Neural Correlates of Motor Imagery, Action Observation, and Movement Execution: A Comparison Across Quantitative Meta-Analyses
Authors: Hardwick Robert M , Caspers Svenja , Eickhoff Simon B , Swinnen Stephan P 
Published: October 2017

AbstractThere is longstanding interest in the relationship between motor imagery, action observation, and movement execution. Several models propose that these tasks recruit the same brain regions in a similar manner; however, there is no quantitative synthesis of the literature that compares their respective networks. Here we summarized data from neuroimaging experiments examining Motor Imagery (303 experiments, 4,902 participants), Action Observation (595 experiments, 11,032 participants), and related control tasks involving Movement Execution (142 experiments, 2,302 participants). Motor Imagery recruited a network of premotor-parietal cortical regions, alongside the thalamus, putamen, and cerebellum. Action Observation involved a cortical premotor-parietal and occipital network, with no consistent subcortical contributions. Movement Execution engaged sensorimotor-premotor areas, and the thalamus, putamen, and cerebellum. Comparisons across these networks highlighted key differences in their recruitment of motor cortex,and parietal cortex, and subcortical structures. Conjunction across all three tasks identified a consistent premotor-parietal and somatosensory network. These data amend previous models of the relationships between motor imagery, action observation, and movement execution, and quantify the relationships between their respective networks.HighlightsWe compared quantitative meta-analyses of movement imagery, observation, and executionSubcortical structures were most commonly associated with imagery and executionConjunctions identified a consistent premotor-parietal-somatosensory networkThese data can inform basic and translational work using imagery and observation
Predicting division planes of three-dimensional cells by soap-film minimization
Authors: Martinez Pablo , Allsman Lindy A. , Brakke Kenneth A. , Hoyt Christopher , Hayes Jordan , Liang Hong , Neher Wesley , Rui Yue , Roberts Allyson M. , Moradifam Amir , Goldstein Bob , Anderson Charles T. , Rasmussen Carolyn G. 
Published: October 2017

AbstractOne key aspect of cell division in multicellular organisms is the orientation of the division plane. Proper division plane establishment contributes to normal organization of the plant body. To determine the importance of cell geometry in division plane orientation, we designed a threedimensional probabilistic mathematical modeling approach to directly test the century-old hypothesis that cell divisions mimic “soap-film minima” or that daughter cells have equal volume and the resulting division plane is a local surface area minimum. Predicted division planes were compared to a plant microtubule array that marks the division site, the preprophase band (PPB). PPB location typically matched one of the predicted divisions. Predicted divisions offset from the PPB occurred when a neighboring cell wall or PPB was observed directly adjacent to the predicted division site, to avoid creating a potentially structurally unfavorable four-way junction. By comparing divisions of differently shaped plant and animal cells to divisions simulated in silico, we demonstrate the generality of this model to accurately predict in vivo division. This powerful model can be used to separate the contribution of geometry from mechanical stresses or developmental regulation in predicting division plane orientation.
A common molecular logic determines embryonic stem cell self-renewal and reprogramming
Authors: Dunn Sara-Jane , Li Meng Amy , Carbognin Elena , Smith Austin , Martello Graziano 
Published: October 2017

AbstractDuring differentiation and reprogramming new cell identities are generated by reconfiguration of gene regulatory networks. Here we combined automated formal reasoning with experimentation to expose the logic of network activation during induction of naïve pluripotency. We find that a Boolean network architecture defined for maintenance of naïve state embryonic stem cells (ESC) also explains transcription factor behaviour and potency during resetting from primed pluripotency. Computationally identified gene activation trajectories were experimentally substantiated at single cell resolution. Contingency of factor availability explains the counterintuitive observation that Klf2, which is dispensable for ESC maintenance, is required during resetting. We tested 136 predictions formulated by the dynamic network, finding a predictive accuracy of 78.7%. Finally, we show that this network explains and predicts experimental observations of somatic cell reprogramming. We conclude that a common deterministic program of gene regulation is sufficient to govern maintenance and induction of naïve pluripotency. The tools exemplified here could be broadly applied to delineate dynamic networks underlying cell fate transitions.
Diverse laboratory colonies ofAedes aegyptiharbor the same adult midgut bacterial microbiome
Authors: Dickson Laura B. , Ghozlane Amine , Volant Stevenn , Bouchier Christiane , Ma Laurence , Vega-Rúa Anubis , Dusfour Isabelle , Jiolle Davy , Paupy Christophe , Mayanja Martin N. , Kohl Alain , Lutwama Julius J. , Duong Veasna , Lambrechts Louis 
Published: October 2017

AbstractBackgroundHost-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six recent laboratory colonies ofAedes aegyptirepresenting the geographical range and genetic diversity of the species.ResultsWe found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies ofAe. aegypti, regardless of their geographic origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.ConclusionsOur finding that geographically diverse colonies ofAe. aegyptireared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.
Characterization of Thylakoid Division Using Chloroplast Dividing Mutants inArabidopsis
Authors: Ho Jonathan , Kwan Warren , Li Vivian , Theg Steven M. 
Published: October 2017

AbstractChloroplasts are double membrane bound organelles that are found in plants and algae. Their division requires a number of proteins to assemble into rings along the center of the organelle and to constrict in synchrony. Chloroplasts possess a third membrane system, the thylakoids, which house the majority of proteins responsible for the light-dependent reactions. The mechanism that allows chloroplasts to sort out and separate the intricate thylakoid membrane structures during organelle division remain unknown. By characterizing the sizes of thylakoids found in a number of different chloroplast division mutants inArabidopsis, we show that thylakoids do not divide independently of the chloroplast division cycle. More specifically, we show that thylakoid division requires the formation of both the inner and the outer contractile rings of the chloroplast.
Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms
Authors: Costello Maura , Fleharty Mark , Abreu Justin , Farjoun Yossi , Ferriera Steven , Holmes Laurie , Howd Tom , Mason Tamara , Vicente Gina , Dasilva Michael , Brodeur Wendy , DeSmet Timothy , Dodge Sheila , Lennon Niall J. , Gabriel Stacey 
Published: October 2017

ABSTRACTHere, we present an in-depth characterization of the index swapping mechanism on Illumina instruments that employ the ExAmp chemistry for cluster generation (HiSeqX, HiSeq4000, and NovaSeq). We discuss best practices for eliminating the effects of index swapping on data integrity by utilizing unique dual indexing for complete filtering of index swapped reads. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different methods can have vastly different swap rates, and show that even non-ExAmp chemistry instruments display trace levels of index swapping. Finally, using computational methods we provide a greater insight into the mechanism of index swapping.
Restoring p53 Function and Silencing REV3L Suppresses the Cancerous Metabolic Phenotype in Cisplatin Treated Human Non-Small Lung Carcinoma Cells
Authors: Kong Linghao , Murata Michael M. , Digman Michelle A. 
Published: October 2017

AbstractLung cancer is one of the deadliest cancers in the world accounting for over one-quarter of all cancer-related deaths, but in many cases, the cancer can develop a resistance to the cisplatin-based chemotherapies. It is well known that cancer cells exhibit the Warburg effect and some studies have suggested that cancer cell metabolism may be linked to cisplatin resistance. In this study, the effects of tumor suppressor protein p53 and translesional synthesis protein REV3L are studied to relate DNA damage signaling and repair to cellular metabolism by using the fluorescence lifetime of the metabolic coenzyme NADH. It was found that simultaneously restoring function to p53 and silencing REV3L suppressed the cancerous metabolic phenotype and resulted in the greatest amount of cancer cell death. This study demonstrates a previously unrecognized relationship between p53 and REV3L in cellular metabolism and may lead to improvements in chemotherapy treatment plans that reduce cisplatin resistance in cancer cells.
Population-scale organization of cerebellar granule neuron signaling during a visuomotor behavior
Authors: Sylvester Sherika J.G. , Lee Melanie M. , Ramirez Alexandro , Lim Sukbin , Goldman Mark S. , Aksay Emre R.F. 
Published: October 2017

ABSTRACTGranule cells at the input layer of the cerebellum comprise over half the neurons in the human brain and are thought to be critical for learning. However, little is known about granule neuron signaling at the population scale during behavior. We used calcium imaging in awake zebrafish during optokinetic behavior to record transgenically identified granule neurons throughout a cerebellar population. A significant fraction of the population was responsive at any given time. In contrast to core precerebellar populations, granule neuron responses were relatively heterogeneous, with variation in the degree of rectification and the balance of excitation versus inhibition. Functional correlations were strongest for nearby cells, with weak spatial gradients in the degree of rectification and excitation. These data open a new window upon cerebellar function and suggest granule layer signals represent elementary building blocks underrepresented in core sensorimotor pathways, thereby enabling the construction of novel patterns of activity for learning.SIGNIFICANCE STATEMENTCerebellar processing is important for a variety of fine motor tasks and sensorimotor adaptations, and a growing body of evidence indicates a prominent role in cognitive control. However, it has been challenging to understand cerebellar function during behavior because of difficulties in recording from cerebellar granule neurons, the most populous neuron type in the brain. We use population-scale optical imaging in the larval zebrafish to compare precerebellar activity to granule cell signaling. Our results suggest a behaviorally relevant expansion of precerebellar signaling representations at the granule layer of the cerebellum.
Dilated Convolutions for Modeling Long-Distance Genomic Dependencies
Authors: Gupta Ankit , Rush Alexander M. 
Published: October 2017

AbstractWe consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA’s 3-dimensional conformation. In order to study long-distance dependencies, we develop and release a novel dataset for a larger-context modeling task. Using this new data set we model long-distance interactions using dilated convolutional neural networks, and compare them to standard convolutions and recurrent neural networks. We show that dilated convolutions are effective at modeling the locations of regulatory markers in the human genome, such as transcription factor binding sites, histone modifications, and DNAse hypersensitivity sites.
SSEalign: accurate function prediction of bacterial unannotated protein, based on effective training dataset
Authors: Yang Zhiyuan , Tsui Stephen Kwok-Wing 
Published: October 2017

AbstractThe functions of numerous bacterial proteins remain unknown because of the variety of their sequences. The performances of existing prediction methods are highly weak toward these proteins, leading to the annotation of “hypothetical protein” deposited in NCBI database. Elucidating the functions of these unannotated proteins is an urgent task in computational biology. We report a method about secondary structure element alignment called SSEalign based on an effective training dataset extracting from 20 well-studied bacterial genomes. The experimentally validated same genes in different species were selected as training positives, while different genes in different species were selected as training negatives. Moreover, SSEalign used a set of well-defined basic alignment elements with the backtracking line search algorithm to derive the best parameters for accurate prediction. Experimental results showed that SSEalign achieved 91.2% test accuracy, better than existing prediction methods. SSEalign was subsequently applied to identify the functions of those unannotated proteins in the latest published minimal bacteria genome JCVI-syn3.0. Results indicated that At least 99 proteins out of 149 unannotated proteins in the JCVI-syn3.0 genome could be annotated by SSEalign. In conclusion, our method is effective for the identification of protein homology and the annotation of uncharacterized proteins in the genome.
Measurement of leaf day respiration using a new isotopic disequilibrium method compared with the Laisk method
Authors: Gong Xiao Ying , Tcherkez Guillaume , Wenig Johannes , Schäufele Rudi , Schnyder Hans 
Published: October 2017

SummaryQuantification of leaf respiration is of great importance for the understanding of plant physiology and ecosystem biogeochemical processes. Leaf respiration continues in light (RL) but supposedly at a lower rate compared to the dark (RD). Yet, there is no method for direct measurement ofRLand most available methods require unphysiological measurement conditions.A method based on isotopic disequilibrium quantifiedRL(RL 13C) and mesophyll conductance of young and old fully-expanded leaves of six species comparedRL 13CtoRLvalues determined by the Laisk method (RL Laisk).RL 13CandRL Laiskwere consistently lower thanRD. Leaf ageing negatively affected photosynthetic performance, but had no significant effect onRLorRL/RDas determined by both methods.RL LaiskandRL 13Cwere measured successively on the same leaves and correlated positively (r2=0.38), but averageRL Laiskwas 28% lower thanRL13C. UsingA/Cccurves instead ofA/Cicurves, a higher photocompensation point Γ* (by 5 μmol mol-1) was found but the correction had no influence onRL Laiskestimates.The results suggest that the Laisk method underestimatedRL. The isotopic disequilibrium method is useful for assessing responses ofRLto irradiance and CO2, improving our mechanistic understanding ofRL.
Touching proteins with virtual bare hands: how to visualize protein-drug complexes and their dynamics in virtual reality
Authors: Martins Ratamero Erick , Bellini Dom , Dowson Christopher G. , Röemer Rudolf A. 
Published: October 2017

AbstractThe ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more precise visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). In this work, we present a freely available software pipeline for visualising protein structures through VR. New customer hardware, such as the HTC VIVEand the OCULUSRIFTutilized in this study, are available at reasonable prices. Moreover, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-lead drug design by exposing molecular interactions that might be hidden in the less informative static models.
Biopipe: A Lightweight System Enabling Comparison of Bioinformatics Tools and Workflows
Authors: Tithi Saima Sultana , Lee Jiyoung , Zhang Liqing , Li Song , Meng Na 
Published: October 2017

AbstractAnalyzing next generation sequencing data always requires researchers to install many tools, prepare input data compliant to the required data format, and execute the tools in specific orders. Such tool installation and workflow execution process is tedious and error-prone, and becomes very challenging when researchers need to compare multiple alternative tool chains. To mitigate this problem, we developed a new lightweight and portable system, Biopipe, to simplify the creation and execution of bioinformatics tools and workflows, and to further enable the comparison between alternative tools or workflows. Biopipe allows users to create and edit workflows with user-friendly web interfaces, and automates tool installation as well as workflow synthesis by downloading and executing predefined Docker images. With Biopipe, biologists can easily experiment with and compare different bioinformatics tools and workflows without much computer science knowledge. There are mainly two parts in Biopipe: a web application and a standalone Java application. They are freely available athttp://bench.cs.vt.edu:8282/Biopipe-Workflow-Editor-0.0.1/index.xhtmlandhttps://code.vt.edu/saima5/Biopipe-Run-WorkflowContactnm8247@cs.vt.eduSupplementary informationSupplementary data are available online.