bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of diagnostic accuracy for nonocclusive mesenteric ischemia in models with biomarkers including intestinal fatty acid–binding protein in addition to clinical findings
Authors: Matsumoto Shokei , Shiraishi Atsushi , Kojima Mitsuaki , Funaoka Hiroyuki , Funabiki Tomohiro , Saida Takafumi , Kitano Mitsuhide 
Published: October 2018

BACKGROUND
Nonocclusive mesenteric ischemia (NOMI) is an acute and life-threatening gastrointestinal disorder, requiring rapid therapeutic intervention for ischemic bowel. However, its rapid detection remains challenging. This retrospective, observational study was aimed at comparing the diagnostic accuracy for NOMI in models of biomarkers, including intestinal fatty acid–binding protein (I-FABP), and clinical findings.

METHODS
All consecutive patients who presented to the emergency department of the study hospital with suspected NOMI were prospectively enrolled. Receiver operating characteristic analysis compared the diagnostic accuracy of I-FABP with traditional biomarkers (white blood cell count, C-reactive protein, lactate, creatine kinase, and D-dimer) alone and in combination with the baseline model established from clinical findings.

RESULTS
Of 96 patients with suspected NOMI, 25 (26.0%) were clinically diagnosed with NOMI. In-hospital mortality was higher in patients with NOMI than those with other conditions (56.0% vs. 4.2%, p < 0.001). Receiver operating characteristic analyses revealed that the I-FABP model had the highest area under the curve (0.805) in the diagnosis of NOMI, compared with other biomarkers. The diagnostic model of clinical findings including age, cardiovascular disease history, undergoing hemodialysis, hypotension, and consciousness disturbance in combination with I-FABP showed the best discrimination (area under the curve, 0.883), compared with other biomarkers. The bootstrap optimism estimate showed the lowest discrimination among the other models with other biomarkers (0.006).

CONCLUSION
The usefulness of I-FABP for final diagnosis of NOMI in patients with clinically suspected NOMI at the emergency department was internally validated. Further external validation study is warranted.

LEVEL OF EVIDENCE
Diagnostic test, level III.
An introduction to patient-reported outcome measures (PROMs) in trauma
Authors: Turner Grace M. , Slade Anita , Retzer Ameeta , McMullan Christel , Kyte Derek , Belli Antonio , Calvert Melanie 
Published: October 2018

ABSTRACT
Increased survival rates from traumatic injury have resulted in more people living with disability and reduced quality of life. To understand how peoples' quality of life is affected following a traumatic injury and the effects of that injury on their health and well-being, it is important to capture patients' perspectives of their own health. Patient-reported outcome measures (PROMs) are questionnaires, completed by patients, which can be used to measure the symptom burden associated with trauma and its treatment, and impact on quality of life. Patient-reported outcome measures have a wide variety of uses that are relevant to trauma. In a research setting, PROMs can be used to assess the effectiveness of treatment and burden of disease. In a clinical setting, PROMs have the potential to inform and guide patient-centered care and clinical decision making. Collected as part of trauma registries, PROMs can be used at an aggregate level to inform improvements and uphold the quality of trauma care. This literature review explores and summarizes the key current and potential future uses of PROMs in trauma research, routine clinical practice, and registries.
Ketamine infusion for pain control in adult patients with multiple rib fractures: Results of a randomized control trial
Authors: Carver Thomas W. , Kugler Nathan W. , Juul Janelle , Peppard William J. , Drescher Karin Madsen , Somberg Lewis B. , Szabo Aniko , Yin Ziyan , Paul Jasmeet S. 
Published: October 2018

BACKGROUND
Rib fractures occur in up to 40% of trauma patients and are associated with increased mortality. Opiate-based pain regimens remain the cornerstone of rib fracture management; however, concerns around opioids have fostered interest in alternative analgesics. Ketamine is currently being used in lieu of opioids, but little evidence exists supporting its use within the trauma population.

METHODS
A prospective, randomized, double-blind placebo-controlled trial of adult patients with three or more rib fractures admitted to a Level I trauma center was conducted. Exclusion criteria included age older than 64 years, Glasgow Coma Scale score less than 13, and chronic opiate use. The experimental arm received low-dose ketamine (LDK) at 2.5 μg·kg−1·min−1 while the placebo cohort received an equivalent rate of 0.9% normal saline. All infusions were continued for 48 hours. The primary outcome was reduction in numeric pain score (NPS) during the first 24 hours. Secondary outcomes studied included oral morphine equivalent (OME) utilization, length of stay, epidural rates, pulmonary complications, and adverse events.

RESULTS
Forty-five (49%) of 91 patients were randomized to the experimental arm. Both groups were similar in makeup. Overall, 74.7% were male, had a median age of 49 years, and an Injury Severity Score (ISS) of 14. Low-dose ketamine was not associated with a significant reduction in 24-hour NPS or OME totals. Subgroup analysis of 45 severely injured patients (ISS, >15) demonstrated that LDK was associated with a significant reduction in OME utilization during the first 24 hours (35.7 vs. 68, p = 0.03), 24 hours to 48 hours (64.2 vs. 96, p = 0.03), and overall (152.1 vs. 198, p = 0.048). No difference in other secondary outcomes or adverse events was noted.

CONCLUSION
Low-dose ketamine failed to decrease NPS or OME within the overall cohort, but a decrease in OME was observed among patients with an ISS greater than 15. Confirmatory studies are necessary to determine if LDK is a useful adjunct among severely injured patients.

LEVEL OF EVIDENCE
Therapeutic study, level II.
Self-reported Lifestyle Activities in Relation to Longitudinal Cognitive Trajectories
Authors: Pettigrew Corinne , Shao Yi , Zhu Yuxin , Grega Maura , Brichko Rostislav , Wang Mei-Cheng , Carlson Michelle C. , Albert Marilyn , Soldan Anja 
Published: October 2018

Background:
Few studies have examined the relationship between lifestyle activity engagement and cognitive trajectories among individuals who were cognitively normal at baseline.

Objective:
To examine the relationship of current engagement in lifestyle activities to previous cognitive performance among individuals who were cognitively normal at baseline, and whether this relationship differed for individuals who subsequently developed mild cognitive impairment (MCI), or by APOE-4 genotype, age, and level of cognitive reserve.

Methods:
Participants (N=189) were primarily middle-aged (M=56.6 y) at baseline and have been prospectively followed with annual assessments (M follow-up=14.3 y). Engagement in physical, cognitive, and social activities was measured by the CHAMPS activity questionnaire. Longitudinal cognitive performance was measured by a global composite score.

Results:
Among individuals who progressed to MCI (n=27), higher lifestyle activity engagement was associated with less decline in prior cognitive performance. In contrast, among individuals who remained cognitively normal, lifestyle activity engagement was not associated with prior cognitive trajectories. These effects were largely independent of APOE-4 genotype, age, and cognitive reserve.

Conclusions:
Greater engagement in lifestyle activities may modify the rate of cognitive decline among those who develop symptoms of MCI, but these findings need to be confirmed in prospective studies.
Neurotrauma as a big-data problem
Authors: Huie J. Russell , Almeida Carlos A. , Ferguson Adam R. 
Published: October 2018

Purpose of review
The field of neurotrauma research faces a reproducibility crisis. In response, research leaders in traumatic brain injury (TBI) and spinal cord injury (SCI) are leveraging data curation and analytics methods to encourage transparency, and improve the rigor and reproducibility. Here we review the current challenges and opportunities that come from efforts to transform neurotrauma's big data to knowledge.

Recent findings
Three parallel movements are driving data-driven-discovery in neurotrauma. First, large multicenter consortia are collecting large quantities of neurotrauma data, refining common data elements (CDEs) that can be used across studies. Investigators are now testing the validity of CDEs in diverse research settings. Second, data sharing initiatives are working to make neurotrauma data findable, accessible, interoperable, and reusable (FAIR). These efforts are reflected by recent open data repository projects for preclinical and clinical neurotrauma. Third, machine learning analytics are allowing researchers to uncover novel data-driven-hypotheses and test new therapeutics in multidimensional outcome space.

Summary:
We are on the threshold of a new era in data collection, curation, and analysis. The next phase of big data in neurotrauma research will require responsible data stewardship, a culture of data-sharing, and the illumination of ‘dark data’.
Retrospective Evaluation of Cyclosporine in the Treatment of Chronic Hepatitis in Dogs: 2010-2017
Authors: Tarini Ullal , Yoko Ambrosini , Sangeeta Rao , Cynthia RL Webster , David Twedt 
Published: October 2018

BackgroundIdiopathic chronic hepatitis (CH) in dogs is a prevalent hepatic disorder. The etiology is poorly understood; however, there is evidence to support an immune-mediated pathogenesis. No literature exists investigating the efficacy of cyclosporine (CsA) therapy for CH in dogs.ObjectivesTo retrospectively evaluate the efficacy and adverse side effects of CsA in the treatment of CH in dogs, and to identify factors that impact response to CsA therapy.Animals48 client-owned dogs diagnosed with CH treated with CsA for at least 2 weeks.MethodsRetrospective review of medical records between the years 2010-2017.ResultsTwenty-two breeds of dogs were included of which 54% were spayed females, 42% neutered males and 4% intact males. Median age was 8.5 years (range, 0.7-14 years). Complete remission (normalization of alanine aminotransferase [ALT]) in response to CsA was attained in 79% of dogs (38/48). Median dose of CsA at the time of remission was 7.9 mg/kg/day (range, 2.5-12.7mg/kg/day) and median time to remission was 2.5 months (range, 0.75-18 months). None of the factors evaluated including clinical score, presence of ascites, hypoalbuminemia, hyperbilirubinemia, prolonged coagulation times, dose, or duration of therapy influenced remission. Common side effects were gastrointestinal signs in 38% (18/48) and gingival hyperplasia in 25% (12/48) of dogs.Conclusion and Clinical ImportanceCsA proved to be a tolerated and effective medication in attaining remission in dogs with idiopathic CH based on normalization of serum ALT. None of the evaluated factors were shown to negatively impact response to CsA or remission of disease.
Charting a tissue from single-cell transcriptomes
Authors: Nitzan Mor , Karaiskos Nikos , Friedman Nir , Rajewsky Nikolaus 
Published: October 2018

AbstractMassively multiplexed sequencing of RNA in individual cells is transforming basic and clinical life sciences. However, in standard experiments, tissues must first be dissociated. Thus, after sequencing, information about the spatial relationships between cells is lost although this knowledge is crucial for understanding cellular and tissue-level function. Recent attempts to overcome this fundamental challenge rely on employing additional in situ gene expression imaging data which can guide spatial mapping of sequenced cells. Here we present a conceptually different approach that allows to reconstruct spatial positions of cells in a variety of tissues without using reference imaging data. We first show for several complex biological systems that distances of single cells in expression space monotonically increase with their physical distances across tissues. We therefore seek to map cells to tissue space such that this principle is optimally preserved, while matching existing imaging data when available. We show that this optimization problem can be cast as a generalized optimal transport problem and solved efficiently. We apply our approach successfully to reconstruct the mammalian liver and intestinal epithelium as well as fly and zebrafish embryos. Our results demonstrate a simple spatial expression organization principle and that this principle (or future refined principles) can be used to infer, for individual cells, meaningful spatial position probabilities from the sequencing data alone.
The essential role of feedback processing for figure-ground perception in mice
Authors: Kirchberger Lisa , Mukherjee Sreedeep , Schnabel Ulf H. , van Beest Enny H. , Barsegyan Areg , Levelt Christiaan N. , Heimel J. Alexander , Lorteije Jeannette A. M. , van der Togt Chris , Self Matthew W. , Roelfsema Pieter R. 
Published: October 2018

AbstractThe segregation of figures from the background is an important step in visual perception. In primary visual cortex, figures evoke stronger activity than backgrounds during a delayed phase of the neuronal responses, but it is unknown how this figure-ground modulation (FGM) arises and whether it is necessary for perception. Here we show, using optogenetic silencing in mice, that the delayed V1 response phase is necessary for figure-ground segregation. Neurons in higher visual areas also exhibit FGM and optogenetic silencing of higher areas reduced FGM in V1. In V1, figures elicited higher activity of vasoactive intestinal peptide-expressing (VIP) interneurons than the background, whereas figures suppressed somatostatin-positive interneurons, resulting in an increased activation of pyramidal cells. Optogenetic silencing of VIP neurons reduced FGM in V1, indicating that disinhibitory circuits contribute to FGM. Our results provide new insight in how lower and higher areas of the visual cortex interact to shape visual perception.
Precise optical probing of perceptual detection
Authors: Lerman Gilad M. , Gill Jonathan V. , Rinberg Dmitry , Shoham Shy 
Published: October 2018

SummaryEstablishing causal links between patterns of neuronal activity and perception is crucial for understanding brain function. Electrical and optogenetic stimulation experiments demonstrated that animals can detect activation of a few neurons. However, these methodologies offer very limited control of ensemble activity and yielded highly divergent thresholds. Here, we use holographic two-photon (2P) optogenetic stimulation to probe the detection of evoked neuronal activity at cellular and single action potential resolution, with millisecond precision. We find that mice can detect single action potentials evoked synchronously across <20 olfactory bulb neurons, while ruling out detection of indirect effects using a novel optical sham-photostimulation technique. Our results demonstrate that mice are acutely attuned to sparse, synchronous ensemble activity signals, introducing order-of-magnitude revisions to earlier estimates of perceptual thresholds.
SIP: An Interchangeable Pipeline for scRNA-seq Data Processing
Authors: Chen Sijie , Wei Zheng , Chen Yang , Hua Kui , Zhang Wei , Liu Changyi , Gao Haoxiang , Sun Hao , Wang Zhenyi , Yin Qijin , Chen Shengquan , Song Shaoming , Feng Chen , Lu Hairong , Jiang Rui , Wang Xiaowo , Gu Jin , Zhang Xuegong 
Published: October 2018

AbstractMultiple steps of bioinformatics processing are needed to convert the raw scRNA-seq data to information that can be used in downstream analyses and in building cell atlases. Dozens of software packages have been developed and different labs tend to have different preferences on choices of the workflow. Such diversity can cause difficulties in future efforts of aggregating data from multiple labs, and also difficulties for new labs to start in this field. A few pipelines have been developed to help integrating multiple steps into a whole, but the fixed software architecture makes it hard for developers to add new features or exchange parts in the pipeline.We presented SIP, a Single-cell Interchangeable Pipeline. It is a one-stop platform for the processing of scRNA-seq data from multiple platforms, and will also support for other types of data like scATAC-seq data. SIP utilizes container technology to solve the deployment dilemma when handling multiple packages and provides an easy-to-use interface for users to conduct the complicated multi-step process from raw data to final results with a single command. It also allows advanced users to assemble different versions of the pipeline by interchanging parts or adding new modules. SIP is available at https://github.com/XuegongLab/SIP under the GPL-3.0 license.
Mapping native R-loops genome-wide using a targeted nuclease approach
Authors: Yan Qingqing , Shields Emily J. , Bonasio Roberto , Sarma Kavitha 
Published: October 2018

AbstractR-loops are three-stranded DNA:RNA hybrids that are pervasive in the eukaryotic and prokaryotic genomes and have been implicated in a variety of nuclear processes, including transcription, replication, DNA repair, and chromosome segregation. While R-loops may have physiological roles, the formation of stable, aberrant R-loops has been observed in disease, particularly neurological disorders and cancer. Despite the importance of these structures, methods to assess their distribution in the genome invariably rely on affinity purification, which requires large amounts of input material, is plagued by high level of noise, and is poorly suited to capture dynamic and unstable R-loops. Here, we present a new method that leverages the affinity of RNase H for DNA:RNA hybrids to target micrococcal nuclease to genomic sites that contain R-loops, which are subsequently cleaved, released, and sequenced. Our R-loop mapping method, MapR, is as specific as existing techniques, less prone to recover non-specific repetitive sequences, and more sensitive, allowing for genome-wide coverage with low input material and read numbers, in a fraction of the time.
Robust methods for detecting convergent shifts in evolutionary rates
Authors: Partha Raghavendran , Kowalczyk Amanda , Clark Nathan , Chikina Maria 
Published: October 2018

AbstractIdentifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree datasets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.
Biodiversity trends are stronger in marine than terrestrial assemblages
Authors: Blowes Shane , Supp Sarah , Antão Laura , Bates Amanda , Bruelheide Helge , Chase Jon , Moyes Faye , Magurran Anne , McGill Brian , Myers-Smith Isla , Winter Marten , Bjorkman Anne , Bowler Diana , Byrnes Jarrett E.K. , Gonzalez Andrew , Hines Jes , Isbell Forest , Jones Holly , Navarro Laetitia M. , Thompson Patrick , Vellend Mark , Waldock Conor , Dornelas Maria 
Published: October 2018

SummaryHuman activities have fundamentally altered biodiversity. Extinction rates are elevated and model projections suggest drastic biodiversity declines. Yet, observed temporal trends in recent decades are highly variable, despite consistent change in species composition. Here, we uncover clear spatial patterns within this variation. We estimated trends in the richness and composition of assemblages in over 50,000 time-series, to provide the most comprehensive assessment of temporal change in biodiversity across the planet to date. The strongest, most consistent pattern shows compositional change dominated by species turnover, with marine taxa experiencing up to fourfold the variation in rates of change of terrestrial taxa. Richness change ranged from no change to richness gains or losses of ~10% per year, with tropical marine biomes experiencing the most extreme changes. Earth is undergoing a process of spatial reorganisation of species and, while few areas are unaffected, biodiversity change is consistently strongest in the oceans.
Choice-Related Activity during Visual Slant Discrimination in Macaque CIP but Not V3A
Authors: Elmore L. Caitlin , Rosenberg Ari , DeAngelis Gregory C. , Angelaki Dora E. 
Published: October 2018

AbstractCreating three-dimensional (3D) representations of the world from two-dimensional retinal images is fundamental to many visual guided behaviors including reaching and grasping. A critical component of this process is determining the 3D orientation of objects. Previous studies have shown that neurons in the caudal intraparietal area (CIP) of the macaque monkey represent 3D planar surface orientation (i.e., slant and tilt). Here we compare the responses of neurons in areas V3A (which is implicated in 3D visual processing and which precedes CIP in the visual hierarchy) and CIP to 3D oriented planar surfaces. We then examine whether activity in these areas correlates with perception during a fine slant discrimination task in which monkeys report if the top of a surface is slanted towards or away from them. Although we find that V3A and CIP neurons show similar sensitivity to planar surface orientation, significant choice-related activity during the slant discrimination task is rare in V3A but prominent in CIP. These results implicate both V3A and CIP in the representation of 3D surface orientation, and suggest a functional dissociation between the areas based on slant-related decision signals.Significance StatementSurface orientation perception is fundamental to visually guided behaviors such as reaching, grasping, and navigation. Previous studies implicate the caudal intraparietal area (CIP) in the representation of 3D surface orientation. Here we show that responses to 3D oriented planar surfaces are similar in CIP and V3A, which precedes CIP in the cortical hierarchy. However, we also find a qualitative distinction between the two areas: only CIP neurons show robust choice-related activity during a fine visual orientation discrimination task.