bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lithophagy Prolongs Voluntary Dives in American alligators (Alligator mississippiensis)
Authors: Uriona T J , Lyon M , Farmer C G 
Published: January 2019

AbstractMany vertebrates ingest stones, but the function of this behavior is not fully understood. We tested the hypothesis that lithophagy increases the duration of voluntary dives in juvenile American alligators (Alligator mississippiensis). After ingestion of granite stones equivalent to 2.5% of body weight, the average duration of dives increased by 88% and the maximum duration increased by 117%. These data are consistent with the hypothesis that gastroliths serve to increase specific gravity, and that the animals compensate by increasing lung volume, thereby diving with larger stores of pulmonary oxygen.
Novel displays of patient information in critical care settings: a systematic review
Authors: Waller Rosalie G , Wright Melanie C , Segall Noa , Nesbitt Paige , Reese Thomas , Borbolla Damian , Del Fiol Guilherme 
Published: January 2019

Abstract

Objective
Clinician information overload is prevalent in critical care settings. Improved visualization of patient information may help clinicians cope with information overload, increase efficiency, and improve quality. We compared the effect of information display interventions with usual care on patient care outcomes.

Materials and Methods
We conducted a systematic review including experimental and quasi-experimental studies of information display interventions conducted in critical care and anesthesiology settings. Citations from January 1990 to June 2018 were searched in PubMed and IEEE Xplore. Reviewers worked independently to screen articles, evaluate quality, and abstract primary outcomes and display features.

Results
Of 6742 studies identified, 22 studies evaluating 17 information displays met the study inclusion criteria. Information display categories included comprehensive integrated displays (3 displays), multipatient dashboards (7 displays), physiologic and laboratory monitoring (5 displays), and expert systems (2 displays). Significant improvement on primary outcomes over usual care was reported in 12 studies for 9 unique displays. Improvement was found mostly with comprehensive integrated displays (4 of 6 studies) and multipatient dashboards (5 of 7 studies). Only 1 of 5 randomized controlled trials had a positive effect in the primary outcome.

Conclusion
We found weak evidence suggesting comprehensive integrated displays improve provider efficiency and process outcomes, and multipatient dashboards improve compliance with care protocols and patient outcomes. Randomized controlled trials of physiologic and laboratory monitoring displays did not show improvement in primary outcomes, despite positive results in simulated settings. Important research translation gaps from laboratory to actual critical care settings exist.
The Role of the Canadian Association of Chiefs of Police in Supporting the Professionalization of Police in Canada
Authors: Montgomery Ruth 
Published: January 2019

Abstract
The public deserves and expects professional and accountable policing. The need and desire to maintain and build public trust and respect in policing in dynamic, complex, and constantly evolving political, socio-economic, technological, and demographic contexts has driven increased discussion and examination of professionalization of policing. Effective and efficient policing today requires police leaders who are innovative, have political acumen and agile decision-making capacity, and can engage with a variety of actors at multiple levels to address public safety and security issues. Police leaders are also charged with ensuring that police officers at all levels have the education, knowledge, skills and competencies, and supports needed to solve crimes and problems, enforce laws, and prevent crime. The Commonwealth countries of England, Wales, Australia, and New Zealand have established professional bodies to regulate policing and address these requirements. This review uses identified characteristics of professions as a framework for comparing the work of these associations with contributions the Canadian Association of Chiefs has made in supporting, preparing, and professionalizing policing in Canada. It concludes by comparing the approaches to police professionalization in England, Wales, Australia, New Zealand, and Canada.
Sequencing of Chemotherapy and Radiotherapy for Newly Diagnosed Anaplastic Oligodendroglioma and Oligoastrocytoma
Authors: Ryckman Jeffrey M. , Surkar Swati M. , Haque Waqar , Butler E. Brian , Teh Bin S. , Verma Vivek 
Published: January 2019

Introduction:
Adjuvant management of anaplastic oligodendrogliomas (AOs) and anaplastic oligoastrocytomas (AOAs) is guided by 2 seminal phase III trials, one of which utilized radiotherapy (RT) followed by chemotherapy (CT) (RT-CT), and the other in which CT was followed by RT (CT-RT). Both paradigms are endorsed by the National Comprehensive Cancer Network because no direct comparison in the first-line (nonprogressive) setting has been performed to date. This study of a contemporary national database sought to evaluate practice patterns and outcomes between both approaches.

Materials and Methods:
The National Cancer Database (NCDB) was queried for newly diagnosed AO/AOA treated with postoperative sequential CT-RT or RT-CT. Multivariable logistic regression ascertained factors independently associated with delivery of a particular paradigm. Overall survival (OS) between cohorts was compared using Kaplan-Meier methodology. Univariate and multivariate Cox proportional hazards modeling evaluated factors associated with OS.

Results:
Of 225 patients, 19 (8.4%) received CT-RT and 206 (91.6%) underwent RT-CT. Groups were well-balanced, although CT-RT was more often administered to men (P=0.009) and AOs (P=0.037). Median follow-up was 58 months. Median OS in the CT-RT cohort was 93 months (95% confidence interval, 37-150 mo), and 107 months (95% confidence interval, 72-142 mo) in the RT-CT group (P=0.709). Therapy sequence was not associated with OS on univariate (P=0.709) or multivariate (P=0.257) assessment.

Conclusions:
In the United States, most AO/AOA patients receiving sequential therapy undergo RT followed by CT. No differences in survival were observed with either approach; this addresses a knowledge gap and confirms that both paradigms are appropriate in the first-line setting.
Increased signal diversity/complexity of spontaneous EEG, but not evoked EEG responses, in ketamine-induced psychedelic state in humans
Authors: Farnes Nadine , Juel Bjørn E. , Nilsen André S. , Romundstad Luis G. , Storm Johan F. 
Published: January 2019

AbstractObjectiveHow and to what extent electrical brain activity is affected in pharmacologically altered states of consciousness, where it is mainly the phenomenological content rather than the level of consciousness that is altered, is not well understood. An example is the moderately psychedelic state caused by low doses of ketamine. Therefore, we investigated whether and how measures of evoked and spontaneous electroencephalographic (EEG) signal diversity are altered by sub-anaesthetic levels of ketamine compared to normal wakefulness, and how these measures relate to subjective assessments of consciousness.MethodsHigh-density electroencephalography (EEG, 62 channels) was used to record spontaneous brain activity and responses evoked by transcranial magnetic stimulation (TMS) in 10 healthy volunteers before and after administration of sub-anaesthetic doses of ketamine in an open-label within-subject design. Evoked signal diversity was assessed using the perturbational complexity index (PCI), calculated from the global EEG responses to local TMS perturbations. Signal diversity of spontaneous EEG, with eyes open and eyes closed, was assessed by Lempel Ziv complexity (LZc), amplitude coalition entropy (ACE), and synchrony coalition entropy (SCE).ResultsAlthough no significant difference was found in the index of TMS-evoked complexity (PCI) between the sub-anaesthetic ketamine condition and normal wakefulness, all the three measures of spontaneous EEG signal diversity showed significantly increased values in the sub-anaesthetic ketamine condition. This increase in signal diversity also correlated with subjective assessment of altered states of consciousness. Moreover, spontaneous signal diversity was significantly higher when participants had eyes open compared to eyes closed, both during normal wakefulness and during influence of sub-anaesthetic ketamine doses.ConclusionThe results suggest that PCI and spontaneous signal diversity may be complementary and potentially measure different aspects of consciousness. Thus, our results seem compatible with PCI being indicative of the brain’s ability to sustain consciousness, as indicated by previous research, while it is possible that spontaneous EEG signal diversity may be indicative of the complexity of conscious content. The observed sensitivity of the latter measures to visual input seems to support such an interpretation. Thus, sub-anaesthetic ketamine may increase the complexity of both the conscious content (experience) and the brain activity underlying it, while the level, degree, or general capacity of consciousness remains largely unaffected.
Kinetic Analysis of Bacteriophage Sf6 Binding to Outer Membrane Protein A Using Whole Virions
Authors: Hubbs Natalia B. , Whisby-Pitts Mareena M. , McMurry Jonathan L. 
Published: January 2019

AbstractFor successful infection, viruses must recognize their respective host cells. A common mechanism of host recognition by viruses is to utilize a portion of the host cell as a receptor. Bacteriophage Sf6, which infects Shigella flexneri, uses lipopolysaccharide as a primary receptor and then requires interaction with a secondary receptor, a role that can be fulfilled by either outer membrane proteins (Omp) A or C. Our previous work showed that specific residues in the loops of OmpA mediate Sf6 infection. To better understand Sf6 interactions with OmpA loop variants, we determined the kinetics of these interactions through the use of biolayer interferometry, an optical biosensing technique that yields data similar to surface plasmon resonance. Here, we successfully tethered whole Sf6 virions, determined the binding constant of Sf6 to OmpA to be 36 nM. Additionally, we showed that Sf6 bound to five variant OmpAs and the resulting kinetic parameters varied only slightly. Based on these data, we propose a model in which Sf6: Omp receptor recognition is not solely based on kinetics, but likely also on the ability of an Omp to induce a conformational change that results in productive infection.
Intermittent hormonal therapy shows similar outcome than SOC in ER+ breast cancer preclinical model
Authors: Enriquez-Navas Pedro M. , Garcia Libia , Abdalah Mahmoud , Stringfield Olya , Luddy Kimberly , Hassan Sabrina , Gillies Robert J. , Gatenby. Robert A. 
Published: January 2019

AbstractClinical breast cancers in which at least 10% of cells express the estrogen receptor are labeled as “ER positive.” First line therapy for these patients is typically continuous administration of anti-estrogen drugs at maximum tolerated dose (MTD) until progression. In the vast majority of patients, resistance to hormone therapy evolves in the breast cancer cells within 2 years leading to treatment failure and tumor progression. In prior studies, we have demonstrated continuous application of MTD chemotherapy results in evolutionary dynamics (termed “competitive release”) that accelerates proliferation of treatment-resistance populations. In contrast, evolution-informed application of treatment reduces drug administration to maintain substantial populations of therapy-sensitive cells to reduce proliferation of resistant phenotypes. Prior pre-clinical and clinical studies have shown this strategy can delay or prevent proliferation of resistant cells and prolong time to progression (TTP). We hypothesize that similar dynamics may be observed in hormonal therapy of ER+ breast cancers. Here we address two important dynamics. First, we consider a clinical scenario in which symptoms are sufficiently severe or life-threatening to require rapid and substantial tumor reduction. Can this be achieved while retaining evolutionary dynamics to subsequently delay proliferation of resistance? A second, related question is defining the cost of resistance to anti-estrogen therapy. Here, we investigated the evolutionary dynamics of resistance to anti-estrogen therapy using ER+ MCF-7 orthotropic xenografts treated with both continuous Tamoxifen as well as cycles in which estrogen stimulation is combined with estrogen suppression. As expected, continuous administration of anti-estrogen drugs successfully suppressed tumor growth. However we found that brief interruptions in drug administration permitted equal tumor control while administering up to 50% less drug and maintaining cell phenotypes that retained high levels of ER expression and lower levels of MDR1 expression. In follow-on experiments combining hormonal and chemo-therapies; we obtained similar tumor control to hormonal therapy alone but with more necrosis and significantly lower ER expression in the surviving population.
Spatial organization of the transcriptional regulatory network of Saccharomyces cerevisiae
Authors: Sun Dong-Qing , Tian Liu , Ma Bin-Guang 
Published: January 2019

AbstractTranscriptional regulatory network (TRN) is a directed complex network composed of all regulatory interactions between transcription factors and corresponding target genes. Recently, the three-dimensional (3D) genomics studies have shown that the 3D structure of the genome makes a difference to the regulation of gene transcription, which provides us with a novel perspective. In this study, we constructed the TRN of the budding yeast Saccharomyces cerevisiae and placed it in the context of 3D genome model. We analyzed the spatial organization of the yeast TRN on four levels: global feature, central nodes, hierarchical structure and network motifs. Our results suggested that the TRN of S. cerevisiae presents an optimized structure in space to adapt to functional requirement.
Knock-knock, who’s there: Sex-coding, competition and the energetics of tapping communication in the tok-tok beetle,Psammodes striatus(Coleoptera: Tenebrionidae)
Authors: Lighton John R.B. 
Published: January 2019

ABSTRACTI describe the abdomino-substratal tapping communication system of a Southern African tenebrionid beetle,Psammodes striatus(Fabricius, 1775) (Coleoptera: Tenebrionidae: Molurini), using computer simulation of tapping signals and computer-assisted acquisition of precise response timing data, augmented with data from natural beetle-beetle communication. Communication consists of trains of 5 - 7 Hz taps in groups or trains separated by 2-3 sec intervals. Male beetles spontaneously produce groups of tap-trains with 8 - 18 taps per train. If other beetles reply, an alternating duet commences. Solitary female beetles do not tap spontaneously but respond to male tapping with short, distinctive tap-trains containing 4 – 6 taps; they ignore female signals. In contrast, extensive communication occurs between male beetles, the nature of which changes significantly if the stimulus call is typical of male or of female beetles. Inter-male communication consists of long tap-trains, but males interacting with females produce shorter tap-trains and engage in phonotactic behavior that is absent in inter-male communication. Females respond highly preferentially to inter-male communication, rather than to the signals produced spontaneously by single males. Finally, I propose a simple model of the selective advantages of this unusual communication system, and calculate its approximate energetic leverage over random locomotion (∼13x).
Protein Fold Determination by Assembling Extended Super-Secondary Structure Motifs Using Limited NMR Data
Authors: Pilla Kala Bharath 
Published: January 2019

AbstractThe 3D fold determination of proteins by computational algorithms guided by experimental restraints is a reliable and efficient approach. However, the current algorithms struggle with sampling the conformational space and scaling in performance with the increase in the size of the proteins. This paper demonstrates a new data-driven, time-efficient, heuristics algorithm that assembles the 3D structure of a protein from its elemental super-secondary structure motifs (Smotifs) using a limited number of nuclear magnetic resonance (NMR) derived restraints. The DINGO-NOE-RDC algorithm (3D assembly of Individual smotifs to Near-native Geometry as Orchestrated by limited nuclear Overhauser effects (NOE) and residual dipolar couplings (RDC)) leverages on the distance restraints recorded on methyl-methyl (CH3-CH3), methyl-amide (CH3-HN), and amide-amide (HN–HN) NOE contacts, and orientation restraints recorded via RDC on the backbone amide protons, to assemble the target’s Smotifs. Two conceptual advancements were made to bootstrap the structure determination from limited NMR restraints; first, expand the basic definition of a ‘Smotif’ and, second, employ a data driven approach for selection, scoring, ranking and clustering of Smotif assemblies. In contrast to existing methods, the DINGO-NOE-RDC algorithm does not use any force-fields, physical/empirical scoring functions or the target’s amino-acid sequence makeup. Additionally, the algorithm employs a universal Smotif library that applies to any target protein and, can generate numerically reproducible results. For a benchmark set of ten different targets with different topologies, ranging from 100-200 residues, the algorithm identified near-native Smotifs in all of them.
Gain-of-function mutations in the UNC-2/CaV2α channel lead to hyperactivity and excitation-dominant synaptic transmission in Caenorhabditis elegans
Authors: Huang Yung-Chi , Pirri Jennifer K. , Rayes Diego , Gao Shangbang , Mulcahy Ben , Grant Jeff , Saheki Yasunori , Francis Michael M. , Zhen Mei , Alkema Mark J. 
Published: January 2019

AbstractMutations in pre-synaptic voltage gated calcium channels can lead to familial hemiplegic migraine type 1 (FHM1). While mammalian studies indicate that the migraine brain is hyperexcitable due to enhanced excitation or reduced inhibition, the molecular and cellular mechanisms underlying this excitatory/inhibitory (E/I) imbalance are poorly understood. We identified a gain-of-function (gf) mutation in the Caenorhabditis elegans CaV2 channel α1 subunit, UNC-2, which leads to increased calcium currents. unc-2(gf) mutants exhibit hyperactivity and seizure-like motor behaviors. Expression of the unc-2 gene with FHM1 substitutions R192Q and S218L leads to hyperactivity similar to that of unc-2(gf) mutants unc-2(gf) mutants display increased cholinergic- and decreased GABAergic-transmission. Moreover, we reveal that and increased cholinergic transmission in unc-2(gf) mutants leads to reduction of GABA synapses in a TAX-6/calcineurin dependent manner. Our studies provide mechanistic insight into how CaV2 gain-of-function mutations disrupt excitation-inhibition balance in the nervous system.
BioSAILs: versatile workflow management for high-throughput data analysis
Authors: Rowe Jillian , Drou Nizar , Youssef Ayman , Gunsalus Kristin C. 
Published: January 2019

AbstractMotivationHigh-throughput analysis in the current era of systems biology encompasses a range of analysis workflows for different applications, such as transcriptomics, epigenetics, variant discovery, de novo genome assembly, etc. Many research institutes house a genomics core facility that is responsible for generating high-throughput sequencing data and often includes a core bioinformatics team that carries out data analysis. Core teams must both keep track of data and maintain numerous software packages and databases – which must be scalable according to ever-changing research needs – and they must allocate computational resources to them. Typical data analysis pipelines involve multiple software packages and require the ability to install, execute, and maintain software stacks on a variety of hardware/operating system configurations, including high-performance computing (HPC) facilities, stand-alone servers, and Cloud services. At the same time, individual researchers need to analyze their data and share their analysis steps with collaborators. Having to rely on ad hoc scripts and rigid internally developed pipelines is inefficient, difficult to track and maintain, and ultimately, limits the ability to adapt and evolve as research methods progress.ResultsHere, we present BioSAILs (Bioinformatics Standardized Analysis Information Layers), a scientific workflow management system (WMS) developed by the Core Bioinformatics team at NYU Abu Dhabi. BioSAILs comprises two central components, BioX command and HPCRunner command, supported by BioStacks software stacks. BioX structures executable workflows that may be either run directly on a desktop or lab server, or submitted by HPCRunner to HPC infrastructure or the Cloud. BioSAILs is supported by a range of pre-configured, customizable BioStacks software stacks for various applications (e.g. RNA-seq, de novo genome/transcriptome assembly, variant discovery, etc.) Software stacks are built using Conda and BioConda (6), have been pre-packaged into modules using EasyBuild, and can be deployed with or without BioSAILs. Within the BioSAILs WMS, users can also invoke commands that take advantage of containerized software in Docker (10) and Singularity (8). Finally, the BioSAILs web resource provides documentation, blog posts related to various BioSAILs analysis tasks, forums, knowledge base & FAQs, as well as an interactive web-based workflow editor/creator. BioSAILs is production-level software that has been in use as the main WMS at NYU Abu Dhabi for the past 2 years and is continuously developed and maintained by the core bioinformatics team.AvailabilityBioSAILs is open source software, available under the GNU license. Online documentation, support and guides can be found at biosails.abudhabi.nyu.edu. The public Github project is available at Github – BioSAILs. HPC-Runner and BioX-Workflow can be installed through Conda using the BioConda channel.
The green autofluorescence intensity and asymmetry of older men is significantly higher than those of older women in their fingernails and certain regions of skin
Authors: Tao Yue , Zhang Mingchao , Wu Danhong , Li Yujia , Ying Weihai 
Published: January 2019

AbstractOur recent studies have suggested that the patients of multiple diseases have characteristic Pattern of Autofluorescence (AF) in their skin and fingernails, which may become novel biomarkers for both disease diagnosis and evaluation of health state. Since male populations may have higher levels of oxidative stress and inflammation than female population, in our current study we tested our hypothesis that the green AF intensity of older men is higher than that of older women in their fingernails and skin. We found that in both left and right Index Fingernails, the green AF intensity of the men of both the age group of 61 - 70 years of old and the age group of 71 - 80 years of old is significantly higher than that of the women of the same age groups. At both left Dorsal Centremetacarpus and left Centremetacarpus, the green AF intensity of the men at the age between 71 - 80 years of old is also significantly higher than that of the women of the same age group. Moreover, in Index Fingernails, Dorsal Centremetacarpus and Centremetacarpus, the green AF asymmetry of the older men of certain age groups is significantly higher than that of the women of the same age groups. Collectively, our study has provided the first evidence indicating the gender difference between the green AF intensity and asymmetry of older men and those of older women in their fingernails and certain regions of skin, which is valuable for establishing the AF-based diagnostic method.