bluuebunny/crossref_metadata_2025_split huggingface dataset:
Operating Room Efficiency: Examining the Impact of Personnel Handoffs
Authors: Geynisman-Tan Julia , Brown Oluwateniola , Mueller Margaret , Bochenska Katarzyna , Collins Sarah , Lewicky-Gaupp Christina , Kenton Kimberly 
Published: February 2018

Objectives
This study aimed to determine if personnel handoffs or number of learners in the operating room (OR) are associated with longer OR times in women having pelvic organ prolapse surgery.

Methods
A retrospective review of women undergoing prolapse surgery in 2016 was conducted. Demographics; procedure; OR, anesthetic, and surgical time; number of handoffs between anesthesia members, circulators, and surgical technologies; and number of learners were abstracted.

Results
One hundred forty-eight women underwent pelvic organ prolapse surgery. Mean age was 54 ± 14 years, and most women were healthy and white. Procedures performed were as follows: 31% laparoscopic sacrocolpoexies (LASCs), 28% robotic sacrocolpopexies (RASCs), 19% colpocleises, and 22% native tissue reconstructions. For minimally invasive sacrocolpopexies (LASC + RASC), mean OR time was 270 ± 65 minutes. Median anesthesia, surgical technology, and circulator handoffs for sacrocolpopexies were 2 (interquartile range, 0–4), 1 (0–3), and 2 (2–6). Median number of learners in the OR for sacrocolpopexies was 4 (interquartile range, 1–7). Patient comorbidities and American Society of Anesthesiologists class were not associated with longer OR times (P = 0.9 and P = 0.4). Longer OR times were positively correlated with increasing numbers of anesthesia, surgical technology, and circulator handoffs, but not with the number of learners (Spearman ρ = 0.34, P = 0.001; ρ = 0.34, P < 0.001; ρ = 0.59, P < 0.001, and ρ = 0.16, P = 0.43). For LASC, every technology handoff was associated with 23 additional minutes of OR time (P = 0.004). For RASC, every technology handoff was associated with 31 additional minutes of OR time (P = 0.007), and each circulator handoff was associated with 15 additional minutes (P = 0.05).

Conclusion
Handoffs between OR personnel are associated with longer OR times, independent of patient factors.
Dextromethorphan/Quinidine in Migraine Prophylaxis: An Open-label Observational Clinical Study
Authors: Berkovich Regina R. , Sokolov Alexey Y. , Togasaki Daniel M. , Yakupova Aida A. , Cesar Paul-Henry , Sahai-Srivastava Soma 
Published: February 2018

Objective
This study aimed to assess potential efficacy and safety of dextromethorphan/quinidine (DMQ) in prophylactic treatment of migraine in patients with multiple sclerosis (MS) with superimposed pseudobulbar affect (PBA).

Methods
Multiple sclerosis patients with superimposed PBA and comorbid migraine were enrolled into this open-label observational study at the University of Southern California Comprehensive MS Center. The baseline characteristics included, among other data, frequency and severity of acute migraine attacks and use of migraine relievers. The DMQ was used exclusively per its primary indication — PBA symptoms control — 20/10 mg orally, twice a day for the mean of 4.5 months (the shortest exposure registered was 3 months and the longest, 6 months). To determine whether treatment caused an effect on migraine frequency and severity, the baseline and posttreatment values were compared using nonparametric sign test.

Results
Thirty-three MS subjects with PBA, who also suffered from migraines, were identified. Twenty-nine subjects had improvement in headache frequency, 4 had no change, and none had worsening (P < 0.001 as compared with the baseline). Twenty-eight subjects had improvement in headache severity, 5 had no change, and none had worsening (P < 0.001).

Conclusions
Our pilot study results provide evidence that DMQ shows promise as a candidate for larger clinical studies evaluating its efficacy for the prevention of migraine headaches.
The hemodynamic initial-dip consists of both volumetric and oxymetric changes correlated to localized spiking activity
Authors: Zaidi Ali Danish , Birbaumer Niels , Fetz Eberhard , Logothetis Nikos , Sitaram Ranganatha 
Published: February 2018

AbstractThe “initial-dip” is a transient decrease frequently observed in functional neuroimaging signals, immediately after stimulus onset, and is believed to originate from a rise in deoxy-hemoglobin (HbR) caused by local neural activity. It has been shown to be more spatially specific than the hemodynamic response, and is believed to represent focal neuronal activity. However, despite being observed in various neuroimaging modalities (such as fMRI, fNIRS, etc), its origins are disputed and its neuronal correlates unknown. Here, we show that the initial-dip is dominated by a decrease in total-hemoglobin (HbT). We also find a biphasic response in HbR, with an early decrease and later rebound. However, HbT decreases were always large enough to counter spiking-induced increases in HbR. Moreover, the HbT-dip and HbR-rebound were strongly coupled to highly localized spiking activity. Our results suggest that the HbT-dip helps prevent accumulation of spiking-induced HbR-concentration in capillaries by flushing out HbT, probably by active venule dilation.
Epigenetic Profiling for the Molecular Classification of Metastatic Brain Tumors
Authors: Orozco Javier I. J. , Knijnenburg Theo A. , Manughian-Peter Ayla O. , Salomon Matthew P. , Barkhoudarian Garni , Jalas John R. , Wilmott James S. , Hothi Parvinder , Wang Xiaowen , Takasumi Yuki , Buckland Michael E. , Thompson John F. , Long Georgina V. , Cobbs Charles S. , Shmulevich Ilya , Kelly Daniel F. , Scolyer Richard A. , Hoon Dave S. B. , Marzese Diego M. 
Published: February 2018

AbstractOptimal treatment of brain metastases is often hindered by limitations in diagnostic capabilities. To meet these challenges, we generated genome-scale DNA methylomes of the three most frequent types of brain metastases: melanoma, breast, and lung cancers (n=96). Using supervised machine learning and integration of multiple DNA methylomes from normal, primary, and metastatic tumor specimens (n=1,860), we unraveled epigenetic signatures specific to each type of metastatic brain tumor and constructed a three-step DNA methylation-based classifier (BrainMETH) that categorizes brain metastases according to the tissue of origin and therapeutically-relevant subtypes. BrainMETH predictions were supported by routine histopathologic evaluation. We further characterized and validated the most predictive genomic regions in a large cohort of brain tumors (n=165) using quantitative methylation-specific PCR. Our study highlights the importance of brain tumor-defining epigenetic alterations, which can be utilized to further develop DNA methylation profiling as a critical tool in the histomolecular stratification of patients with brain metastases.
EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins
Authors: Ghosh Pritha , Guita Niang , Offmann Bernard , Sowdhamini R. 
Published: February 2018

AbstractBackgroundThe repertoire of RNA-binding proteins (RBPs) in bacteria play crucial role for their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome.ResultsEcRBPome contains RBPs recorded from 166 complete E. coli proteomes available in the RefSeq database (as of May 2016). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download.ConclusionTo the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community. Database URL: http://caps.ncbs.res.in/ecrbpome
Genie: An interactive real-time simulation for teaching genetic drift
Authors: Castillo Andreina I. , Roos Ben H. , Rosenberg Michael S. , Cartwright Reed A. , Wilson Melissa A. 
Published: February 2018

AbstractNeutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is specially challenging. Here we present Genie, a browser-based educational tool that facilitates demonstration of concepts such as genetic drift, population isolation, gene flow, and genetic mutation. Because it does not need to be downloaded and installed, Genie can scale to large groups of students and is useful for both in-person and online instruction. Genie was used to teach genetic drift to Evolution students at Arizona State University during Spring 2016 and Spring 2017. The effectiveness of Genie to teach key genetic drift concepts and misconceptions was assessed with the Genetic Drift Inventory developed by Price et al. (2014). Overall, Genie performed comparably to that of traditional static methods across all evaluated classes. We have empirically demonstrated that Genie can be successfully integrated with traditional instruction to reduce misconceptions about genetic drift.
eTumorMetastasis, a network-based algorithm predicts clinical outcomes using whole-exome sequencing data of cancer patients
Authors: Milanese Jean-Sébastien , Tibiche Chabane , Zaman Naif , Zou Jinfeng , Han Pengyong , Meng Zhiganag , Nantel Andre , Droit Arnaud , Wang Edwin 
Published: February 2018

AbstractContinual reduction in sequencing cost is expanding the accessibility of genome sequencing data for routine clinical applications. However, the lack of methods to construct machine learning-based predictive models using these datasets has become a crucial bottleneck for the application of sequencing technology in clinics. Here we developed a new algorithm, eTumorMetastasis, which transforms tumor functional mutations into network-based profiles, and identify network operational gene signatures (NOG signatures) which model the tipping point at which a tumor cell shifts from a state that doesn’t favor recurrences to one that does. We showed that NOG signatures derived from genomic mutations of tumor founding clones (i.e., the ‘most recent common ancestor’ of the cells within a tumor) significantly distinguished recurred and non-recurred breast tumors. These results imply that somatic mutations of tumor founders are association with tumor recurrence and can be used to predict clinical outcomes. Finally, the concepts underlying the eTumorMetastasis pave the way for the application of genome sequencing in predictions for other complex genetic diseases.
Influenza A virus environmental persistence is driven by the hemagglutinin and the neuraminidase
Authors: Labadie Thomas , Batéjat Christophe , Manuguerra Jean-Claude , Leclercq India 
Published: February 2018

AbstractThe transmission routes of Influenza A viruses (IAVs) submit virus particles to a wide range of environmental conditions that affect their transmission. In water, temperature, salinity and pH are important factors modulating viral persistence in a strain-dependant manner, and the viral factors driving IAV persistence remained to be described. We used an innovative method based on a real-time cell system analysis to quantify viral decay in an environmental model. Thus, we identified the viral hemagglutinin (HA) and neuraminidase (NA) as the main proteins driving the environmental persistence by comparing the inactivation slopes of several reassortant viruses. We also introduced synonymous and non-synonymous mutations in the HA or in the NA that modulated IAV persistence. Our results demonstrate that HA stability and expression level, as well as calcium-binding sites of the NA protein are molecular determinants of viral persistence.Finally, IAV particles could not trigger membrane fusion after environmental exposure, stressing the importance of the HA and the NA for environmental persistence.
Adaptive planning in human search
Authors: Krusche Moritz J. F. , Schulz Eric , Guez Arthur , Speekenbrink Maarten 
Published: February 2018

AbstractHow do people plan ahead when searching for rewards? We investigate planning in a foraging task in which participants search for rewards on an infinite two-dimensional grid. Our results show that their search is best-described by a model which searches at least 3 steps ahead. Furthermore, participants do not seem to update their beliefs during planning, but rather treat their initial beliefs as given, a strategy similar to a heuristic called root-sampling. This planning algorithm corresponds well with participants’ behavior in test problems with restricted movement and varying degrees of information, outperforming more complex models. These results enrich our understanding of adaptive planning in complex environments.
GLUE: A flexible software system for virus sequence data
Authors: Singer Joshua B , Thomson Emma C , McLauchlan John , Hughes Joseph , Gifford Robert J 
Published: February 2018

AbstractBackgroundVirus genome sequences, generated in ever-higher volumes, can provide new scientific insights and inform our responses to epidemics and outbreaks. To facilitate interpretation, such data must be organised and processed within scalable computing resources that encapsulate virology expertise. GLUE (Genes Linked by Underlying Evolution) is a data-centric bioinformatics environment for building such resources. The GLUE core data schema organises sequence data along evolutionary lines, capturing not only nucleotide data but associated items such as alignments, genotype definitions, genome annotations and motifs. Its flexible design emphasises applicability to different viruses and to diverse needs within research, clinical or public health contexts.ResultsHCV-GLUE is a case study GLUE resource for hepatitis C virus (HCV). It includes an interactive public web application providing sequence analysis in the form of a maximum-likelihood-based genotyping method, antiviral resistance detection and graphical sequence visualisation. HCV sequence data from GenBank is categorised and stored in a large-scale sequence alignment which is accessible via web-based queries. Whereas this web resource provides a range of basic functionality, the underlying GLUE project can also be downloaded and extended by bioinformaticians addressing more advanced questions.ConclusionGLUE can be used to rapidly develop virus sequence data resources with public health, research and clinical applications. This streamlined approach, with its focus on reuse, will help realise the full value of virus sequence data.
Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant—fungus networks
Authors: Toju Hirokazu , Sato Hirotoshi , Yamamoto Satoshi , Tanabe Akifumi S. 
Published: February 2018

AbstractBackgroundBelow-ground linkage between plant and fungal communities is one of the major drivers of terrestrial ecosystem dynamics. However, we still have limited knowledge of how such plant–fungus associations vary in their community-scale properties depending on fungal functional groups and geographic locations.MethodsBased on high-throughput sequencing of root-associated fungi in eight forests along the Japanese Archipelago, we performed a comparative analysis of arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic associations across a latitudinal gradient from cool-temperate to subtropical regions.ResultsIn most of the plant–fungus networks analyzed, host–symbiont associations were significantly specialized but lacked “nested” architecture, which has been commonly reported in plant–pollinator and plant–seed disperser networks. Meanwhile, the structure of arbuscular mycorrhizal networks was differentiated from that of ectomycorrhizal and saprotrophic/endophytic networks, characterized by high connectance. Our data also suggested that geographic factors affected the organization of plant–fungus network structure. For example, the southernmost subtropical site analyzed in this study displayed lower network-level specificity of host–symbiont associations and higher (but still low) nestedness than northern localities.ConclusionsOur comparative analyses suggest that arbuscular mycorrhizal, ectomycorrhizal, and saprotrophic/endophytic plant–fungus associations often lack nested network architecture, while those associations can vary, to some extent, in their community-scale properties along a latitudinal gradient. Overall, this study provides a basis for future studies that will examine how different types of plant–fungus associations collectively structure terrestrial ecosystems.
Big and Small Cerebral Asymmetries
Authors: Eckert Mark A. , Vaden Kenneth I. ,   Dyslexia Data Consortium
Published: February 2018

Letter HighlightsDeformation-based asymmetries replicate previously observed grey matter asymmetries and characterize white matter asymmetries.Increased sensitivity to structural asymmetries in some brain regions depends on smaller-scale normalization or deformation parameters.Tuning deformation parameters can provide more precise asymmetry measures for understanding the mechanisms and functional significance of cerebral asymmetries.
Sound induces change in orientation preference of V1 neurons: Audio-visual cross-influence
Authors: Chanauria Nayan , Bharmauria Vishal , Bachatene Lyes , Cattan Sarah , Rouat Jean , Molotchnikoff Stéphane 
Published: February 2018

AbstractIn the cortex, demarcated unimodal sensory regions often respond to unforeseen sensory stimuli and exhibit plasticity. The goal of the current investigation was to test evoked responses of primary visual cortex (V1) neurons when an adapting auditory stimulus is applied in isolation. Using extracellular recordings in anesthetized cats, we demonstrate that, unlike the prevailing observation of only slight modulations in the firing rates of the neurons, sound imposition in isolation entirely shifted the peaks of orientation tuning curves of neurons in both supra- and infragranular layers of V1. Our results suggest that neurons specific to either layer dynamically integrate features of sound and modify the organization of the orientation map of V1. Intriguingly, these experiments present novel findings that the mere presentation of a prolonged auditory stimulus may drastically recalibrate the tuning properties of the visual neurons and highlight the phenomenal neuroplasticity of V1 neurons.HighlightsProlonged application of sound shifts preferred orientation of neurons in area 17 of cats.Orientation tuning shifts in the individual neurons in supra- and infragranular layers of V1.Supra- and infragranular layers of V1 operate together but also as distinct compartments following sound adaptation.Visual cortex is specifically and dynamically impacted by non-visual stimuli.Sound adaptation certainly modifies the organization of orientation maps in V1.
AlignmentViewer: Sequence Analysis of Large Protein Families
Authors: Reguant Roc , Antipin Yevgeniy , Sheridan Rob , Luna Augustin , Sander Chris 
Published: February 2018

AbstractSummaryAlignmentViewer is multiple sequence alignment viewer for protein families with flexible visualization, analysis tools and links to protein family databases. It is directly accessible in web browsers without the need for software installation, as it is implemented in JavaScript, and does not require an internet connection to function. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, facilitating the computation of protein 3D structures and the detection of functionally constrained interactions.Availability and ImplementationAlignmentViewer is open source software under the MIT license. The viewer is at http://alignmentviewer.org and the source code, documentation and issue tracking, for co-development, are at https://github.com/dfci/alignmentviewerContactalignment.viewer@gmail.com, reaches all authors
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity
Authors: Zhu Houxiang , Liang Chun 
Published: February 2018

AbstractThe CRISPR-Cpf1 system has been successfully applied in genome editing. However, target efficiency of the CRISPR-Cpf1 system varies among different gRNA sequences. We reanalyzed the published CRISPR-Cpf1 gRNAs data and found many sequence and structural features related to their target efficiency. Using machine learning technology, a SVM model was created to predict target efficiency for any given gRNAs. We have developed the first web service application, CRISPR-DT (CRISPR DNA Targeting), to help users design optimal gRNAs for the CRISPR-Cpf1 system by considering both target efficiency and specificity. CRISPR-DT is available athttp://bioinfolab.miamioh.edu/CRISPR-DT.
Survey of human chromosome 21 gene expression effects on early development in Danio rerio
Authors: McGuire Edie Sarah , Zaghloul Norann A , Leitch Carmen C , Klinedinst Donna K , Lebron Janette , Thole Joey F , McCallion Andrew S , Katsanis Nicholas , Reeves Roger H. 
Published: February 2018

ABSTRACT:Trisomy for human chromosome 21 (Hsa21) results in Down syndrome (DS), one of the most genetically complex conditions compatible with human survival. Assessment of the physiological consequences of dosage-driven overexpression of individual Hsa21 genes during early embryogenesis and the resulting contributions to DS pathology in mammals are not tractable in a systematic way. A recent study looked loss-of-function of C. elegans orthologues of Hsa21 genes and identified ten candidates with behavioral phenotypes, but the equivalent over-expression experiment has not been done. We turned to zebrafish as a developmental model and, using a number of surrogate phenotypes, we screened Hsa21 genes for dosage sensitive effects on early embyrogenesis. We prepared a library of 164 cDNAs of conserved protein coding genes, injected mRNA into early embryos and evaluated up to 5 days post-fertilization (dpf). Twenty-four genes produced a gross morphological phenotype, 11 of which could be reproduced reliably. Seven of these gave a phenotype consistent with down regulation of the sonic hedgehog (Shh) pathway; two showed defects indicative of defective neural crest migration; one resulted consistently in pericardial edema; and one was embryonic lethal. Combinatorial injections of multiple Hsa21 genes revealed both additive and compensatory effects, supporting the notion that complex genetic relationships underlie end phenotypes of trisomy that produce DS. Together, our data suggest that this system is useful in the genetic dissection of dosage-sensitive gene effects on early development and can inform the contribution of both individual loci and their combinatorial effects to phenotypes relevant to the etiopathology of DS.