bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjutant: an R-based tool to support topic discovery for systematic and literature reviews
Authors: Crisan Anamaria , Munzner Tamara , Gardy Jennifer L 
Published: August 2018

AbstractSummaryAdjutant is an open-source, interactive and R-based application to support mining PubMed for literature reviews. Given a PubMed-compatible search query, Adjutant downloads the relevant articles and allows the user to perform an unsupervised clustering analysis to identify data-driven topic clusters. Following clustering, users can also sample documents using different strategies to obtain a more manageable dataset for further analysis. Adjutant makes explicit trade-offs between speed and accuracy, which are modifiable by the user, such that a complete analysis of several thousand documents can take a few minutes. All analytic datasets generated by Adjutant are saved, allowing users to easily conduct other downstream analyses that Adjutant does not explicitly support.Availability and implementationAdjutant is implemented in R, using Shiny, and is available at https://github.com/amcrisan/Adjutant.Supplementary informationSupplementary data are available at Bioinformatics online.
SpaRC: scalable sequence clustering using Apache Spark
Authors: Shi Lizhen , Meng Xiandong , Tseng Elizabeth , Mascagni Michael , Wang Zhong 
Published: August 2018

Abstract

Motivation
Whole genome shotgun based next-generation transcriptomics and metagenomics studies often generate 100–1000 GB sequence data derived from tens of thousands of different genes or microbial species. Assembly of these data sets requires tradeoffs between scalability and accuracy. Current assembly methods optimized for scalability often sacrifice accuracy and vice versa. An ideal solution would both scale and produce optimal accuracy for individual genes or genomes.

Results
Here we describe an Apache Spark-based scalable sequence clustering application, SparkReadClust (SpaRC), that partitions reads based on their molecule of origin to enable downstream assembly optimization. SpaRC produces high clustering performance on transcriptomes and metagenomes from both short and long read sequencing technologies. It achieves near-linear scalability with input data size and number of compute nodes. SpaRC can run on both cloud computing and HPC environments without modification while delivering similar performance. Our results demonstrate that SpaRC provides a scalable solution for clustering billions of reads from next-generation sequencing experiments, and Apache Spark represents a cost-effective solution with rapid development/deployment cycles for similar large-scale sequence data analysis problems.

Availability and implementation
https://bitbucket.org/berkeleylab/jgi-sparc
The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models
Authors: Zhang Yuqing , Bernau Christoph , Parmigiani Giovanni , Waldron Levi 
Published: August 2018

SUMMARY
Cross-study validation (CSV) of prediction models is an alternative to traditional cross-validation (CV) in domains where multiple comparable datasets are available. Although many studies have noted potential sources of heterogeneity in genomic studies, to our knowledge none have systematically investigated their intertwined impacts on prediction accuracy across studies. We employ a hybrid parametric/non-parametric bootstrap method to realistically simulate publicly available compendia of microarray, RNA-seq, and whole metagenome shotgun microbiome studies of health outcomes. Three types of heterogeneity between studies are manipulated and studied: (i) imbalances in the prevalence of clinical and pathological covariates, (ii) differences in gene covariance that could be caused by batch, platform, or tumor purity effects, and (iii) differences in the “true” model that associates gene expression and clinical factors to outcome. We assess model accuracy, while altering these factors. Lower accuracy is seen in CSV than in CV. Surprisingly, heterogeneity in known clinical covariates and differences in gene covariance structure have very limited contributions in the loss of accuracy when validating in new studies. However, forcing identical generative models greatly reduces the within/across study difference. These results, observed consistently for multiple disease outcomes and omics platforms, suggest that the most easily identifiable sources of study heterogeneity are not necessarily the primary ones that undermine the ability to accurately replicate the accuracy of omics prediction models in new studies. Unidentified heterogeneity, such as could arise from unmeasured confounding, may be more important.
Iron overload is accompanied by mitochondrial and lysosomal dysfunction in WDR45 mutant cells
Authors: Seibler Philip , Burbulla Lena F , Dulovic Marija , Zittel Simone , Heine Johanne , Schmidt Thomas , Rudolph Franziska , Westenberger Ana , Rakovic Aleksandar , Münchau Alexander , Krainc Dimitri , Klein Christine 
Published: August 2018

Abstract
Beta-propeller protein-associated neurodegeneration is a subtype of monogenic neurodegeneration with brain iron accumulation caused by de novo mutations in WDR45. The WDR45 protein functions as a beta-propeller scaffold and plays a putative role in autophagy through its interaction with phospholipids and autophagy-related proteins. Loss of WDR45 function due to disease-causing mutations has been linked to defects in autophagic flux in patient and animal cells. However, the role of WDR45 in iron homeostasis remains elusive. Here we studied patient-specific WDR45 mutant fibroblasts and induced pluripotent stem cell-derived midbrain neurons. Our data demonstrated that loss of WDR45 increased cellular iron levels and oxidative stress, accompanied by mitochondrial abnormalities, autophagic defects, and diminished lysosomal function. Restoring WDR45 levels partially rescued oxidative stress and the susceptibility to iron treatment, and activation of autophagy reduced the observed iron overload in WDR45 mutant cells. Our data suggest that iron-containing macromolecules and organelles cannot effectively be degraded through the lysosomal pathway due to loss of WDR45 function.
Expression of Transcripts Selective for GABA Neuron Subpopulations across the Cortical Visuospatial Working Memory Network in the Healthy State and Schizophrenia
Authors: Tsubomoto Makoto , Kawabata Rika , Zhu Xiaonan , Minabe Yoshio , Chen Kehui , Lewis David A , Hashimoto Takanori 
Published: August 2018

Abstract
Visuospatial working memory (WM), which is impaired in schizophrenia, depends on a distributed network including visual, posterior parietal, and dorsolateral prefrontal cortical regions. Within each region, information processing is differentially regulated by subsets of γ-aminobutyric acid (GABA) neurons that express parvalbumin (PV), somatostatin (SST), or vasoactive intestinal peptide (VIP). In schizophrenia, WM impairments have been associated with alterations of PV and SST neurons in the dorsolateral prefrontal cortex. Here, we quantified transcripts selectively expressed in GABA neuron subsets across four cortical regions in the WM network from comparison and schizophrenia subjects. In comparison subjects, PV mRNA levels declined and SST mRNA levels increased from posterior to anterior regions, whereas VIP mRNA levels were comparable across regions except for the primary visual cortex (V1). In schizophrenia subjects, each transcript in PV and SST neurons exhibited similar alterations across all regions, whereas transcripts in VIP neurons were unaltered in any region except for V1. These findings suggest that the contribution of each GABA neuron subset to inhibitory regulation of local circuitry normally differs across cortical regions of the visuospatial WM network and that in schizophrenia alterations of PV and SST neurons are a shared feature across these regions, whereas VIP neurons are affected only in V1.
Software application profile: mrrobust—a tool for performing two-sample summary Mendelian randomization analyses
Authors: Spiller Wes , Davies Neil M , Palmer Tom M 
Published: August 2018

Abstract

Motivation
In recent years, Mendelian randomization analysis using summary data from genome-wide association studies has become a popular approach for investigating causal relationships in epidemiology. The mrrobust Stata package implements several of the recently developed methods.

Implementation
mrrobust is freely available as a Stata package.

General features
The package includes inverse variance weighted estimation, as well as a range of median, modal and MR-Egger estimation methods. Using mrrobust, plots can be constructed visualizing each estimate either individually or simultaneously. The package also provides statistics such as IGX2, which are useful in assessing attenuation bias in causal estimates.

Availability
The software is freely available from GitHub [https://raw.github.com/remlapmot/mrrobust/master/].
Shifted Symplectic Lie Algebroids
Authors: Pym Brent , Safronov Pavel 
Published: August 2018

AbstractShifted symplectic Lie and $L_{\infty }$ algebroids model formal neighborhoods of manifolds in shifted symplectic stacks and serve as target spaces for twisted variants of the classical topological field theory defined by Alexandrov--Kontsevich--Schwarz--Zaboronsky. In this paper, we classify zero-, one-, and two-shifted symplectic algebroids and their higher gauge symmetries, in terms of classical geometric “higher structures”, such as Courant algebroids twisted by $\Omega ^{2}$-gerbes. As applications, we produce new examples of twisted Courant algebroids from codimension-two cycles, and we give symplectic interpretations for several well-known features of higher structures (such as twists, Pontryagin classes, and tensor products). The proofs are valid in the $C^{\infty }$, holomorphic, and algebraic settings and are based on a number of technical results on the homotopy theory of $L_{\infty }$ algebroids and their differential forms, which may be of independent interest.
Macrophages in inflammation, repair and regeneration
Authors: Oishi Yumiko , Manabe Ichiro 
Published: August 2018

Abstract
Tissue injury triggers a complex series of cellular responses, starting from inflammation activated by tissue and cell damage and proceeding to healing. By clearing cell debris, activating and resolving inflammation and promoting fibrosis, macrophages play key roles in most, if not all, phases of the response to injury. Recent studies of the mechanisms underlying the initial inflammation and later tissue regeneration and repair revealed that macrophages bridge these processes in part by supporting and activating stem/progenitor cells, clearing damaged tissue, remodeling extracellular matrix to prepare scaffolding for regeneration and promoting angiogenesis. However, macrophages also have a central role in the development of pathology induced by failed resolution (e.g. chronic inflammation) and excessive scarring. In this review, we summarize the activities of macrophages in inflammation and healing in response to acute injury in tissues with differing regenerative capacities. While macrophages lead similar processes in response to tissue injury in these tissues, their priorities and the consequences of their activities differ among tissues. Moreover, the magnitude, nature and duration of injury also greatly affect cellular responses and healing processes. In particular, continuous injury and/or failed resolution of inflammation leads to chronic ailments in which macrophage activities may become detrimental.
Trading Old Masters in Florence 1890–1914: heritage protection and the Florentine art trade in Post-Unification Italy
Authors: Cappellini Patrizia 
Published: August 2018

Abstract
Between 1855 and 1873 many religious orders were abolished in Italy and the contents of convents, monasteries and churches found their way on to the art market. Meanwhile, economic troubles led many noble families to sell their estates, a situation that lasted until World War i. Focusing on the Florentine art market from 1890 to 1914, this paper seeks to shed new light on the roles of some Florentine merchants and their relationships with British antique dealers and German patrons and scholars (such as Wilhelm von Bode). It also reviews the evidence – anecdotal, archival and published – relating to the dealers in question.
Reliability of Oncology Value Framework Outputs: Concordance Between Independent Research Groups
Authors: Del Paggio Joseph C , Cheng Sierra , Booth Christopher M , Cheung Matthew C , Chan Kelvin K W 
Published: August 2018

Abstract
Research groups are increasingly utilizing value frameworks, but little is known of their reliability. To assess framework concordance and interrater reliability between two major value frameworks currently in use, we identified all previously published datasets containing both scores from the American Society of Clinical Oncology Value Framework (ASCO-VF) and grades from the European Society for Medical Oncology-Magnitude of Clinical Benefit Scale (ESMO-MCBS). The intraclass correlation coefficient (ICC) was used to assess interrater reliability. Four eligible studies contained drugs evaluated by both value frameworks, resulting in a dataset of 39 grades/scores for discrete drug indications. ICC was 0.82 (95% confidence interval = 0.70 to 0.90) for ASCO-VF and 0.88 (95% confidence interval = 0.80 to 0.93) for ESMO-MCBS. Absolute concordance was found to be 5% for ASCO-VF and 44% for ESMO-MCBS, increasing to 74% and 80% when deviations within 20 points and 1 grade were considered, respectively. Interrater reliability of ASCO-VF and ESMO-MCBS is, therefore, near perfect, while absolute concordance is poor. This has implications when considering framework outputs in drug funding or treatment decision making.
The black hole fundamental plane in low-excitation radio galaxies
Authors: Li Shuang-Liang , Gu Minfeng 
Published: August 2018

ABSTRACT
The radio–X-ray slope in the fundamental plane of radio-loud active galactic nuclei (AGNs) has been found to be steeper than that of radio-quiet AGNs in previous studies. In this paper, we reinvestigate the fundamental plane in radio-loud AGNs by compiling a sample of 13 low-excitation radio galaxies (LERGs) from the 3CR radio galaxies, for the reason that the accretion mode in LERGs is believed to be a radiatively inefficient accretion flow. All the sources in our sample have data available both at the 5-GHz core radio luminosity as detected by VLA/VLBI/VLBA and at the core X-ray luminosity as detected by Chandra/XMM–Newton. Surprisingly, we find that the slope in the fundamental plane (logLR = 0.52log LX + 0.84log MBH + 10.84) of LERGs is consistent with that reported by Merloni et al. However, the normalization is found to be shifted by about 0.7 dex, which could be due to the difference in the magnetic field strength in different objects. A shallower slope of the LR−LX relationship ($L_{\rm R}\sim L_{\rm X}^{0.63}$) is also found for our sample, which demonstrates that the X-ray emission in LERGs may come from the accretion disc, rather than jets suggested by previous works.
An Experimental Feasibility Study of a Hybrid Telephone Counseling/Text Messaging Intervention for Post-Discharge Cessation Support Among Hospitalized Smokers in Brazil
Authors: Cruvinel Erica , Richter Kimber P , Colugnati Fernando , Ronzani Telmo Mota 
Published: August 2018

AbstractObjectiveText messaging interventions are effective. Despite high utilization of smartphones, few studies evaluate text messaging for cessation in middle-/lower-income countries. Initiating tobacco treatment in hospitals is an effective but underutilized approach for reaching smokers. We evaluated a hybrid phone counseling/text messaging intervention for supporting cessation among hospitalized smokers in Brazil.MethodsWe used an experimental design to assess the feasibility and potential effect size of the intervention. Participants (N = 66) were recruited from a university hospital and randomized in a 2:1 ratio into TXT (one session of telephone counseling plus 2 weeks of text messaging; N = 44) or Standard Care control group (N = 22). Participants lost to follow-up were counted as smokers.ResultsCounselors sent 1186 texts, of which 924 (77.9%) were received by study participants. Participants rated the TXT content as “helpful” (80.4%) and the phone counseling length to be “just right” (95.1%). Although the study was not powered to evaluate abstinence rates, we did observe a higher prevalence of abstinence in the TXT compared to control group at both 1-month follow-up (25.0% vs. 9.1%) and 3-month follow-up (31.8% vs. 9.1%). Carbon monoxide-verified abstinence at month 3 was also higher in TXT (20.5% vs. 4.5%).ConclusionsThis hybrid telephone/text intervention should progress to full-scale effectiveness testing as it achieved favorable outcomes, was acceptable to participants, and was readily implemented. This type of intervention has strong potential for expanding the reach of hospital-initiated tobacco treatment in middle-/lower-income countries.ImplicationsThis study extends research on hospital-initiated smoking cessation by establishing the feasibility of a novel text-messaging approach for post-discharge follow-up. Text messaging is a low-cost alternative to proactive telephone counseling that could help overcome resource barriers in middle- and lower-income countries. This hybrid texting/counseling intervention identified smokers in hospitals, established rapport through a single telephone follow-up, and expanded acceptability and reach of later support by using text-messaging, which is free of charge in this and other low-income countries. The favorable cessation outcomes achieved by the hybrid intervention provide support for a fully powered effectiveness trial.
Semantics as Model-Based Science
Authors: Yalcin Seth 
Published: August 2018

AbstractThis chapter critiques a number of standard ways of understanding the role of the metalanguage in a semantic theory for natural language, including the idea that disquotation plays a nontrivial role in any explanatory natural language semantics. It then proposes that the best way to understand the role of a semantic metalanguage involves recognizing that semantics is a model-based science. The metalanguage of semantics is language for articulating features of the theorist’s model. Models are understood as mediating instruments—idealized structures used to represent select aspects of the world, aspects the theorist is seeking some theoretical understanding of. The aspect of reality we are seeking some understanding of in semantics is a dimension of human linguistic competence—informally, knowledge of meaning.
Palatal harmony
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis chapter applies the model that was developed in Chapters 2 and 3 to some well-known and well-studied cases of palatal vowel harmony. Palatal harmony is common in, and almost confined to, Finno-Ugric and Altaic languages. In the latter, palatal harmony often co-occurs with labial harmony. The chapter first discusses variation in the behavior of neutral vowels in Balto-Finnic languages and some special cases in this family. It then analyzes palatal harmony systems in Hungarian and considers the systems of several other languages. The focus is on asymmetries in vowel harmony involving disharmonic suffixes, anti-harmonic roots, disharmonic roots, and non-alternating suffixes.
Asian tongue root systems
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis chapter is devoted to tongue root (ATR or RTR) harmony in Tungusic languages (a.o. Classical Manchu) and Mongolian languages (Khalka and Buriat), which all belong the Altaic language group. In addition to TR-harmony, most Tungusic and Mongolian languages also have a limited form of labial harmony, especially among low vowels. After discussing the Tungusic and Mongolian systems the chapter will focus on the behavior of high vowels, which do not participate in labial harmony, and are either transparent or opaque. A notable difference between Tungusic and Mongolic regards the fact that whereas [i] is transparent to labial harmony in Mongolic, it is opaque in Tungusic. High round vowels are opaque in both groups.
Summary and areas for further research
Authors: van der Hulst Harry 
Published: August 2018

AbstractThis chapter summarizes the theory and the typology of the vowel harmony systems it predicts. The summary recaptures the simple idea that formed the beginning of the theory (including the use of variable elements and licensing) and then summarizes how the use of variable elements was extended to include both vowels that alternate harmonically and neutral vowels. A special section is devoted to the notion of system dependency which discusses cases of parasitic harmony, including approaches that extend this notion beyond the cases that have been analyzed in this book. The chapter concludes with suggestions for further research.
Aggregated neutrophil extracellular traps resolve inflammation by proteolysis of cytokines and chemokines and protection from antiproteases
Authors: Hahn Jonas , Schauer Christine , Czegley Christine , Kling Lasse , Petru Lenka , Schmid Benjamin , Weidner Daniela , Reinwald Christiane , Biermann Mona H. C. , Blunder Stefan , Ernst Jürgen , Lesner Adam , Bäuerle Tobias , Palmisano Ralf , Christiansen Silke , Herrmann Martin , Bozec Aline , Gruber Robert , Schett Georg , Hoffmann Markus H. 
Published: August 2018

ABSTRACTPapillon‐Lefèvre syndrome (PLS) is characterized by nonfunctional neutrophil serine proteases (NSPs) and fulminant periodontal inflammation of unknown cause. Here we investigated neutrophil extracellular trap (NET)‐associated aggregation and cytokine/chemokine‐release/degradation by normal and NSP‐deficient human and mouse granulocytes. Stimulated with solid or soluble NET inducers, normal neutrophils formed aggregates and both released and degraded cytokines/chemokines. With increasing cell density, proteolytic degradation outweighed release. Maximum output of cytokines/chemokines occurred mostly at densities between 2 × 107 and 4 × 107 neutrophils/cm3. Assessment of neutrophil density in vivo showed that these concentrations are surpassed during inflammation. Association with aggregated NETs conferred protection of neutrophil elastase against αl‐antitrypsin. In contrast, eosinophils did not influence cytokine/chemokine concentrations. The proteolytic degradation of inflammatory mediators seen in NETs was abrogated in Papillon–Lèfevre syndrome (PLS) neutrophils. In summary, neutrophil‐driven proteolysis of inflammatory mediators works as a built‐in safeguard for inflammation. The absence of this negative feedback mechanism might be responsible for the nonresolving periodontitis seen in PLS.—Hahn, J., Schauer, C., Czegley, C., Kling, L., Petru, L., Schmid, B., Weidner, D., Reinwald, C., Biermann, M. H. C., Blunder, S., Ernst, J., Lesner, A., Bäuerle, T., Palmisano, R., Christiansen, S., Herrmann, M., Bozec, A., Gruber, R., Schett, G., Hoffmann, M. H. Aggregated neutrophil extracellular traps resolve inflammation by proteolysis of cytokines and chemokines and protection from antiproteases. FASEB J. 33, 1401–1414 (2019). www.fasebj.org