bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating natural language processing to improve classification of axial spondyloarthritis using electronic health records
Authors: Zhao Sizheng Steven , Hong Chuan , Cai Tianrun , Xu Chang , Huang Jie , Ermann Joerg , Goodson Nicola J , Solomon Daniel H , Cai Tianxi , Liao Katherine P 
Published: July 2019

AbstractObjectivesTo develop classification algorithms that accurately identify axial SpA (axSpA) patients in electronic health records, and compare the performance of algorithms incorporating free-text data against approaches using only International Classification of Diseases (ICD) codes.MethodsAn enriched cohort of 7853 eligible patients was created from electronic health records of two large hospitals using automated searches (⩾1 ICD codes combined with simple text searches). Key disease concepts from free-text data were extracted using NLP and combined with ICD codes to develop algorithms. We created both supervised regression-based algorithms—on a training set of 127 axSpA cases and 423 non-cases—and unsupervised algorithms to identify patients with high probability of having axSpA from the enriched cohort. Their performance was compared against classifications using ICD codes only.ResultsNLP extracted four disease concepts of high predictive value: ankylosing spondylitis, sacroiliitis, HLA-B27 and spondylitis. The unsupervised algorithm, incorporating both the NLP concept and ICD code for AS, identified the greatest number of patients. By setting the probability threshold to attain 80% positive predictive value, it identified 1509 axSpA patients (mean age 53 years, 71% male). Sensitivity was 0.78, specificity 0.94 and area under the curve 0.93. The two supervised algorithms performed similarly but identified fewer patients. All three outperformed traditional approaches using ICD codes alone (area under the curve 0.80–0.87).ConclusionAlgorithms incorporating free-text data can accurately identify axSpA patients in electronic health records. Large cohorts identified using these novel methods offer exciting opportunities for future clinical research.
The Enduring Influence of Cohort Characteristics on Race-Specific Homicide Rates
Authors: Vogel Matt , Thompson Kristina J , Messner Steven F 
Published: July 2019

AbstractThis study extends research on cohort effects and crime by considering how bifurcated population dynamics and institutional constraints explain variation in homicide rates across racial groups in the United States. Drawing upon the extensive research on racial residential segregation and institutional segmentation, we theorize how the criminogenic influences of cohort characteristics elucidated in prior work will be greater for Black cohorts than for White cohorts. We assess our hypothesis by estimating Age-Period-Cohort Characteristic models with data for the total population and separately for the Black and White populations over the 1975–2014 period. The results reveal persistent effects of relative cohort size and nonmarital births on Black cohort-specific homicide rates but null effects among the White population. These effects follow Black birth cohorts across the life course, leading to higher rates of both homicide arrest and homicide victimization.
Late Medieval Jewish Physicians and their Manuscripts
Authors: Kozodoy Maud 
Published: July 2019

Abstract
Most medieval Hebrew manuscripts in late medieval Iberia, especially those containing non-religious texts, were copied by individuals for their personal use. Hebrew medical codices were thus very often both written and used by Jewish physicians. Considering these manuscripts as material objects opens a new window onto medical practice among the Jewish community. This article uses two case studies—one exploring a single manuscript (Vatican Biblioteca Apostolica ebr. 362) and the various medical texts it contains and the other following the transmission of a single medical text (Bernard de Gordon’s Lilium medicinae) through a number of different manuscripts—to inquire into what can be learned from the scribal practices of the Jewish doctors who wrote, owned and used these manuscripts.
Impact of a phytogenic feed additive on growth performance, feed intake, and carcass traits of finishing steers
Authors: Brand Tassilo , Hünerberg Martin , McAllister Tim A , He Maolong , Saleem Atef M , Shen Yizhao , Miller Bryan , Yang Wenzhu 
Published: July 2019

Abstact:
The purpose of this study was to evaluate the effect of a phytogenic feed additive (Digestarom [DA]; Biomin, Getzersdorf, Austria) on growth performance, feed intake, carcass traits, fatty acid composition, and liver abscesses of finishing steers. One hundred twenty Angus × Charolais crossbred steers (488 ± 26.5 kg) were used in a 110-d feeding experiment. Steers were blocked by weight and randomly assigned to 12 pens with 10 steers per pen. Each pen was allocated to one of three diets. Each diet contained 86.5% barley, 10.0% barley silage, and 3.5% vitamin and mineral supplement on a dry matter (DM) basis. The diets contained 0, 0.05, and 0.1 g DA/kg complete diet (DM basis), to achieve average daily DA intakes of 0 (control), 0.5 (LowDA), and 1.0 g (HighDA) per steer. Diets were prepared once daily and provided ad libitum. Two pens per treatment were equipped to record individual feed intake behavior. Steers were weighed every 28 d and carcass traits and liver scores were recorded at slaughter. Dry matter intake (average: 9.34 kg/d) did not differ (P &gt; 0.05) among diets. Average daily gain tended to increase linearly as DA increased (control: 1.82; LowDA: 1.87; and HighDA: 1.95 kg/d; P &lt; 0.09), but gain:feed ratio was not affected. Supplementation of DA affected longissimus muscle area quadratically (P = 0.05) with the largest area observed for LowDA. However, dressing percentage decreased linearly in response to increasing level of DA (P &lt; 0.01). Total abscessed livers were not affected, whereas proportion of severe liver abscesses was numerically lower with DA (30.8% and 42.5% for LowDA and HighDA) compared to the control (50%).
Designing a text messaging program to increase adherence to medication for the secondary prevention of cardiovascular disease
Authors: Uribe-Rodríguez Ana , Pérez-Rivero Paula , Free Caroline , Perel Pablo , Murray Elizabeth , Serrano Díaz Norma , Horne Robert , Atkins Louise , Casas Juan Pablo , Bermon Angarita Anderson 
Published: July 2019

AbstractBackgroundCardiovascular medication for secondary prevention has been shown to be effective. However, cardiovascular patients have poor medication adherence, the consequences of which include premature death, recurrence risk, hospitalization, and high financial cost for the healthcare system. Behavioral interventions based on text messaging technology are a promising strategy to improving adherence in medications. In low-middle income settings there is no high-quality evidence of a behavioral program delivered by SMS; hence we describe the development, message content, and the program design of the intervention for improving adherence to cardiovascular medication.MethodsWe used the model reported by Abroms and colleagues’ for developing and evaluating text messages-based interventions. This model describes a process in which the intervention created is based on theory and evidence, the target audience is involved to ensure the intervention is engaging and useful, and there is a focus on implementation from the outset.ResultsOur main result was the design of the program, which consisted of a twelve-month structured intervention based on Transtheoretical Model of Behavior Change. We wrote and validated clusters of texts messages targeting each stage of the model. Each message went through an examination process including the evaluation of former cardiovascular patients, experts and the team research personnel. Another important result was an understanding of patients’ perceptions of their experience of cardiovascular disease, barriers to accessing healthcare in Colombia and the use of mobile technology for health.ConclusionsAn SMS intervention has the potential to be an acceptable and effective way of improving adherence to medication in patients with cardiovascular disease. This paper describes the development and content of one such intervention.
Esophageal Cooling For Protection During Left Atrial Ablation: A Systematic Review And Meta- Analysis
Authors: Leung Lisa , Gallagher Mark , Santangeli Pasquale , Tschabrunn Cory , Guerra Jose , Campos Bieito , Hayat Jamal , Atem Folefac , Mickelsen Steven , Kulstad Erik 
Published: July 2019

ABSTRACTBackgroundThermal damage to the esophagus is a risk from radiofrequency (RF) ablation of the left atrium for the treatment of atrial fibrillation (AF), with the most extreme type of thermal injury resulting in atrio-esophageal fistula (AEF), with a correspondingly high mortality rate. Various approaches have been developed to reduce esophageal injury, including power reduction, avoidance of greater contact-force, esophageal deviation, and esophageal cooling. One method of esophageal cooling involves direct instillation of cold water or saline into the esophagus during RF ablation. Although this method provides limited heat-extraction capacity, studies of it have suggested potential benefit.ObjectiveWe sought to perform a meta-analysis of existing studies evaluating esophageal cooling via direct liquid instillation for the reduction of thermal injury.MethodsWe reviewed Medline for existing studies involving esophageal cooling for protection of thermal injury during RF ablation. A meta-analysis was then performed using random effects model to calculate estimated effect size with 95% confidence intervals, with outcome of esophageal lesions, stratified by severity, as determined by post-procedure endoscopy.ResultsA total of 9 studies were identified and reviewed. After excluding pre-clinical and mathematical model studies, 3 were included in the meta-analysis, totaling 494 patients. Esophageal cooling showed a tendency to shift lesion severity downward, such that total lesions did not show a statistically significant change (OR 0.6, 95% CI 0.15 to 2.38). For high grade lesions, a significant OR of 0.39 (95% CI 0.17 to 0.89) in favor of esophageal cooling was found, suggesting that esophageal cooling, even utilizing a low-capacity thermal extraction technique, reduces lesion severity from RF ablation.ConclusionsEsophageal cooling reduces lesion severity encountered during RF ablation, even when using relatively low heat extraction methods such as direct instillation of cold liquid. Further investigation of this approach is warranted.
Scarabaeidae larvae are neglected greenhouse gas sources in soils
Authors: Görres Carolyn-Monika , Kammann Claudia 
Published: July 2019

AbstractA precise knowledge of the sink and source distributions of greenhouse gases (GHG) in regional and global carbon and nitrogen budgets, and of the processes governing them, is a necessary prerequisite for the development and assessment of climate change adaptation and mitigation strategies1-3. Certain soil-inhabiting Arthropoda groups are known producers of GHG, namely methane (CH4), but apart from termites, their emissions have never been studied in the field and quantified at different scales4,5. Here we report the first field GHG emission data of soil-dwelling Scarabaeidae larvae, focusing on pest insects in a temperate climate region (Melolontha melolontha and M. hippocastani). Variations in larval biomass explained variations in larval field CO2 and CH4 emissions well at the individual and site level. This correlation disappeared after transferring larvae from the field to a laboratory setting. We show that GHG emissions of soil-inhabiting Scarabaeidae larvae are comparable to those from termites, thus questioning the neglect of Scarabaeidae larvae in GHG flux research, and we demonstrate the importance of field-based emission estimates for soil biota.
Female Assamese macaques bias their affiliation to paternal and maternal kin
Authors: De Moor Delphine , Roos Christian , Ostner Julia , Schülke Oliver 
Published: July 2019

ABSTRACTForming strong social bonds leads to higher reproductive success, increased longevity and/or increased infant survival in several mammal species. Given these adaptive benefits, understanding what determines partner preferences in social bonding is important. Maternal relatedness strongly predicts partner preference across many mammalian taxa. Although paternal and maternal kin share the same number of genes, and theoretically similar preferences would therefore be expected for paternal kin, the role of paternal relatedness has received relatively little attention. Here, we investigate the role of maternal and paternal relatedness for female bonding in Assamese macaques (Macaca assamensis), a species characterized by a relatively low male reproductive skew. We studied a wild population under natural conditions using extensive behavioural data and relatedness analyses based on pedigree reconstruction. We found stronger social bonds and more time spent grooming between maternal kin and paternal half-sisters compared to non-kin, with no preference of maternal over paternal kin. Paternally related and non-related dyads did not form stronger bonds when they had less close maternal kin available, however we would need a bigger sample size to confirm this. As expected given the low reproductive skew, bonds between paternal half-sisters closer in age were not stronger than between paternal half-sisters with larger age differences, suggesting that age similarity was not the mechanism by which paternally related individuals recognized each other. An alternative way through which paternal kin could get familiarized is mother- and/or father-mediated familiarity.
Targeting USP9x/SOX2 axis contributes to the anti-osteosarcoma effect of neogambogic acid
Authors: Chen Xiangyun , Zhang Xingming , Cai Haiyan , Yang Wupeng , Lei Hu , Xu Hanzhang , Wang Weiwei , Zhu Qi , Kang Jingwu , Yin Tong , Gu Wenli , Wu Ying-Li 
Published: July 2019

AbstractSOX2 has been viewed as a critical oncoprotein in osteosarcoma. Emerging evidence show that inducing the degradation of transcription factors such as SOX2 is a promising strategy to make them druggable. Here, we show that neogambogic acid (NGA), an active ingredients in garcinia, significantly inhibited the proliferation of osteosarcoma cells with ubiquitin proteasome-mediated degradation of SOX2 in vitro and in vivo. We further identified USP9x as a bona fide deubiquitinase for SOX2 and NGA directly interacts with USP9x in cells. Moreover, knockdown of USP9x inhibited the proliferation and colony formation of osteosarcoma cells, which could be rescued by overexpression of SOX2. Consistent with this, knockdown of USP9x inhibited the proliferation of osteosarcoma cells in a xenograft mouse model. Collectively, we identify USP9x as the first deubiquitinating enzyme for controlling the stability of SOX2 and USP9x is a direct target for NGA. We propose that targeting the USP9x/SOX2 axis represents a novel strategy for the therapeutic of osteosarcoma and other SOX2 related cancers.
Regional oceanographic features and hydrothermal activity influence protist diversity and biogeography in the Okinawa Trough
Authors: Brisbin Margaret Mars , Conover Asa E. , Mitarai Satoshi 
Published: July 2019

AbstractMicrobial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but factors shaping protist diversity, such as dispersal barriers and environmental selection, remain difficult to parse. Deep-sea water masses, which form geographic barriers, and hydrothermal vents, which represent isolated productivity hotspots, are ideal opportunities for studying the effects of dispersal barriers and environmental selection on protist communities. The Okinawa Trough, a deep, back-arc spreading basin, contains distinct water masses in the bottom waters of northern and southern regions and at least twenty-five active hydrothermal vents. In this study, we used metabarcoding to characterize protist communities from fourteen stations spanning the length of the Okinawa Trough, including three hydrothermal vent sites. Significant differences in community structure reflecting regional oceanography and water mass composition were present, indicating the importance of geographic factors in shaping protist communities. Protist communities in bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.
Polyanions provide selective control of APC/C interactions with the activator subunit
Authors: Mizrak Arda , Morgan David O. 
Published: July 2019

ABSTRACTTransient interactions between the Anaphase-Promoting Complex/Cyclosome (APC/C) and its activator subunit Cdc20 or Cdh1 generate oscillations in ubiquitination activity necessary to maintain the order of cell cycle events. Activator binds the APC/C with high affinity and exhibits negligible dissociation kinetics in vitro, and it is not clear how the rapid turnover of APC/C-activator complexes is achieved in vivo. Here, we describe a mechanism that controls APC/C-activator interactions based on the availability of substrates. We find that APC/C-activator dissociation is stimulated by abundant cellular polyanions such as nucleic acids and polyphosphate. Polyanions also interfere with the ubiquitination of low-affinity substrates. However, engagement with high-affinity substrates blocks the inhibitory effects of polyanions on activator binding and APC/C activity. This mechanism amplifies the effects of substrate affinity on APC/C function, stimulating processive ubiquitination of high-affinity substrates and suppressing ubiquitination of low-affinity substrates.
ΔSCOPE: A new method to quantify 3D biological structures and identify differences in zebrafish forebrain development
Authors: Schwartz Morgan S , Schnabl Jake , Litz Mackenzie P.H. , Baumer Benjamin S , Barresi Michael 
Published: July 2019

AbstractResearch in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called ΔSCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination). Our approach uses the fluorescent signal distribution within a 3D data set and reorients the fluorescent signal to a relative biological reference structure. This approach enables quantification and statistical analysis of spatial relationships and signal density in 3D multichannel signals that are positioned around a well-defined structure contained in a reference channel. We validated the application of ΔSCOPE by analyzing normal axon and glial cell guidance in the zebrafish forebrain and by quantifying the commissural phenotypes associated with abnormal Slit guidance cue expression in the forebrain. Despite commissural phenotypes which display disruptions to the reference structure, ΔSCOPE was able to detect subtle, previously uncharacterized changes in zebrafish forebrain midline crossing axons and glia. This method has been developed as a user-friendly, open source program. We propose that ΔSCOPE is an innovative approach to advancing the state of image quantification in the field of high resolution microscopy, and that the techniques presented here are of broad applications to the life science field.
Autonomous emergence of connectivity assemblies via spike triplet interactions
Authors: Montangie Lisandro , Gjorgjieva Julijana 
Published: July 2019

AbstractNon-random connectivity can emerge without structured external input driven by activity-dependent mechanisms of synaptic plasticity based on precise spiking patterns. Here we analyze the emergence of global structures in recurrent networks based on a triplet model of spike timing dependent plasticity (STDP) which depends on the interactions of three precisely-timed spikes and can describe plasticity experiments with varying spike frequency better than the classical pair-based STDP rule. We describe synaptic changes arising from emergent higher-order correlations, and investigate their influence on different connectivity motifs in the network. Our motif expansion framework reveals novel motif structures under the triplet STDP rule, which support the formation of bidirectional connections and loops in contrast to the classical pair-based STDP rule. Therefore, triplet STDP drives the spontaneous emergence of self-connected groups of neurons, or assemblies, proposed to represent functional units in neural circuits. Assembly formation has often been associated with plasticity driven by firing rates or external stimuli. We propose that assembly structure can emerge without the need for externally patterned inputs or assuming a symmetric pair-based STDP rule commonly assumed in previous studies. The emergence of non-random network structure under triplet STDP occurs through internally-generated higher-order correlations, which are ubiquitous in natural stimuli and neuronal spiking activity, and important for coding. We further demonstrate how neuromodulatory mechanisms that modulate the shape of triplet STDP or the synaptic transmission function differentially promote connectivity motifs underlying the emergence of assemblies, and quantify the differences using graph theoretic measures.