bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix metalloproteinases cleave membrane-bound PD-L1 on CD90+ (myo-)fibroblasts in Crohn’s disease and regulate Th1/Th17 cell responses
Authors: Aguirre Jose E , Beswick Ellen J , Grim Carl , Uribe Gabriela , Tafoya Marissa , Chacon Palma Gabriela , Samedi Von , McKee Rohini , Villeger Romain , Fofanov Yuriy , Cong Yingzi , Yochum Gregory , Koltun Walter , Powell Don , Pinchuk Irina V 
Published: October 2019

AbstractIncreased T helper (Th)1/Th17 immune responses are a hallmark of Crohn’s disease (CD) immunopathogenesis. CD90+ (myo-)fibroblasts (MFs) are abundant cells in the normal (N) intestinal mucosa contributing to mucosal tolerance via suppression of Th1 cell activity through cell surface membrane-bound PD-L1 (mPD-L1). CD-MFs have a decreased level of mPD-L1. Consequently, mPD-L1-mediated suppression of Th1 cells by CD-MFs is decreased, yet the mechanism responsible for the reduction in mPDL-1 is unknown. Increased expression of matrix metalloproteinases (MMPs) has been reported in CD. Herein we observed that when compared to N- and ulcerative colitis (UC)-MFs, CD-MFs increase in LPS-inducible levels of MMP-7 and -9 with a significant increase in both basal and inducible MMP-10. A similar pattern of MMP expression was observed in the CD-inflamed mucosa. Treatment of N-MFs with a combination of recombinant human MMP-7, -9 and -10 significantly decreased mPD-L1. In contrast, inhibition of MMP activity with MMP inhibitors or anti-MMP-10 neutralizing antibodies restores mPD-L1 on CD-MFs. CD-MFs demonstrated reduced capacity to suppress Th1 and Th17 responses from activated CD4+ T cells. By contrast, supplementation of the CD-MF:T-cell co-cultures with MMP inhibitors or anti-MMP neutralizing antibodies restored the CD-MF-mediated suppression. Our data suggest that (i) increased MMP-10 expression by CD-MFs and concomitant cleavage of PD-L1 from the surface of CD-MFs are likely to be one of the factors contributing to the decrease of mPD-L1-mediated suppression of Th1/Th17 cells in CD; and (ii) MMPs are likely to have a significant role in the intestinal mucosal immune responses.
Gentamicin, azithromycin and ceftriaxone in the treatment of gonorrhoea: the relationship between antibiotic MIC and clinical outcome
Authors: Cole Michelle J , Tan Wei , Fifer Helen , Brittain Clare , Duley Lelia , Hepburn Trish , Lawrence Tessa , Montgomery Alan A , Sprange Kirsty , Thandi Sukhwinder , Churchward Colin , Tripodo Francesco , Woodford Neil , Ross Jonathan D C 
Published: October 2019

AbstractObjectivesTo investigate the relationship between MIC and clinical outcome in a randomized controlled trial that compared gentamicin 240 mg plus azithromycin 1 g with ceftriaxone 500 mg plus azithromycin 1 g. MIC analysis was performed on Neisseria gonorrhoeae isolates from all participants who were culture positive before they received treatment.MethodsViable gonococcal cultures were available from 279 participants, of whom 145 received ceftriaxone/azithromycin and 134 received gentamicin/azithromycin. Four participants (6 isolates) and 14 participants (17 isolates) did not clear infection in the ceftriaxone/azithromycin and gentamicin/azithromycin arms, respectively. MICs were determined by Etest on GC agar base with 1% Vitox. The geometric mean MICs of azithromycin, ceftriaxone and gentamicin were compared using logistic and linear regression according to treatment received and N. gonorrhoeae clearance.ResultsAs the azithromycin MIC increased, gentamicin/azithromycin treatment was less effective than ceftriaxone/azithromycin at clearing N. gonorrhoeae. There was a higher geometric mean MIC of azithromycin for isolates from participants who had received gentamicin/azithromycin and did not clear infection compared with those who did clear infection [ratio 1.95 (95% CI 1.28–2.97)], but the use of categorical MIC breakpoints did not accurately predict the treatment response. The geometric mean MIC of azithromycin was higher in isolates from the pharynx compared with genital isolates.ConclusionsWe found that categorical resistance to azithromycin or ceftriaxone in vitro, and higher gentamicin MICs in the absence of breakpoints, were poorly predictive of treatment failure.
Abductive reasoning: let’s Find Out some models
Authors: Żyluk Natalia , Urbański Mariusz , Żelechowska Dorota 
Published: October 2019

Abstract
We present preliminary results on modelling structure of solutions to a task involving abductive reasoning. Research data were gathered using our new tool—Find Out, which has been designed in order to account empirically for abduction relatively close to everyday reasoning processes, with the necessary level of procedure standardization. The tool enables to capture abduction as a compound form of reasoning, from both product and process perspective. Find Out is set up as a game that requires playing the role of an investigator seeking an explanation of what has happened in the presented enigmatic situation. The task consists of three time-limited stages that require different reasoning activities (forming and evaluating of hypotheses, devising final explanations). In the paper, we present quantitative models of structures of solutions to the task proposed by the subjects in the form of situational graphs. We present also some ideas concerning qualitative characteristics of these solutions.
Why and How Does Participatory Governance Affect Policy Outcomes? Theory and Evidence from the Electric Sector
Authors: Baldwin Elizabeth 
Published: October 2019

AbstractIn many policy arenas, decision makers have supplemented or even replaced traditional forms of bureaucratic decision making with more participatory approaches to governance. While theory suggests that participatory governance can have an instrumental effect on policy outcomes, there have been few efforts to systematically test these theories across multiple jurisdictions. This study asks whether and how participatory governance in electric sector regulation affects utilities’ energy savings. Using a mixed-methods research design, this study develops hypotheses drawn from participatory governance theory, analyzes regulatory documents to operationalize a set of participatory governance variables, and uses a multilevel fixed effects model to test whether these participatory governance variables have an effect on electricity consumption by customers of 250 utilities across 42 states between 2000 and 2015. Model results show that deliberation among stakeholders has a significant decrease in electricity use by consumers, but that this effect must be realized over time as stakeholders gain experience with the deliberative process. To explore why deliberation produces this effect, the study presents qualitative evidence from Connecticut and Maryland, two states that have used participatory governance to regulate utilities’ energy efficiency plans. Results suggest that information exchange among participants has a direct effect on utilities’ energy efficiency plans. Participatory governance also contributes to a network of engaged stakeholders who can help hold utilities accountable for achieving their savings goals.
Familial sliding hiatus hernia in four siblings with uncommon features: a case series report
Authors: Kakaje Ameer , Al Khoury Firas , Alfarroukh Ammar , Khouri Lina 
Published: October 2019

AbstractThis case report shows a very rare case series of one family with four children who had severe congenital sliding hiatus hernia (HH) with uncommon presentations, and they had one parent with sliding hernia and the other with reflux symptoms. It is rarely described in the literature a direct link to a familial type that might refer to a common genetic factor. Hiatus hernia is protrusion of abdominal viscera through the oesophagus opening in the diaphragm into the thoracic cavity with sliding hernia being the most common. It can be either asymptomatic or accompanied by a variety of symptoms. We present a case series of one family in which four siblings had congenital sliding diaphragmatic hernia with atypical symptoms and gastro-oesophageal reflux disease (GORD). It is a rare case that suggests a common factor that can cause such a common disease. All four had uncommon presentations which all required surgical repair. Few cases reported on the medical literature, and they were discussed and compared with our case. However, we need further studies in families that might have this phenomenon.
Trade in Runaway Peasants and “The Chichikov Phenomenon” in Eighteenth-Century Russia
Authors: Gornostaev Andrey V 
Published: October 2019

Abstract
This article examines the trade in fugitive serfs in eighteenth-century Russia. This trade emerged from two interrelated phenomena—the sale of individual serfs and peasant flight—and was practiced by nobles, merchants, factory owners, and government officials. The acquisition of absent peasants, although seemingly absurd, represented a risky investment from which the new owners could profit upon discovery and reclamation of the fugitives. According to several eighteenth-century decrees, individuals found guilty of accepting fugitives were required to pay monetary compensation to the peasants’ legal owners for each year of harboring. In some instances, the sum of compensation reached staggering amounts of several thousand rubles. Exploiting this legal opportunity, eighteenth-century nobles or “Chichikovs”—named after the protagonist of Nikolai Gogol’s novel Dead Souls—purchased serfs on the run for the specific purpose of making a significant profit by collecting compensation. This article argues that the trade in runaways and “Chichikov schemes” reveals a yet unexplored dimension of Russian serfdom and its influence, both beneficial and ruinous, on the interactions between nobles, and between nobles and other members of imperial society. The article additionally advances the understanding of serfdom as a social framework based on practices and customs rather than on legislation alone.
The Verb *√L(-)Đ ‘To Remove’ in Early Aramaic Curses and the Evolution of Aramaic Interdental Orthography and Phonology
Authors: Richey Madadh 
Published: October 2019

Abstract
Several verbal morphologies including the core orthography {ld} are attested in ninth- and eighth-century bce Aramaic texts from Sefire and Tell Fekheriyeh. From their similar contexts, all can be demon-strated to have the semantics ‘to remove’, but scholars are divided as to the root source and precise phonology of these verbs. The present paper demonstrates that these {ld} verbs belong to a cognate set descendant from proto-Semitic . The representation of the reflex of the interdental by {d} is a precocious development only attested broadly in later Aramaic, but its surfacing here can be ration-alized by appeal to diachronic phonology, phonotactics and linguistic typology. The consistent employment of developed orthography for this root is perhaps related to the existence of a broad and consistent early Aramaic curse tradition.
Requiem for the STAT Test: Automation and Point of Care Testing
Authors: Singh Gurmukh , Savage Natasha M , Gunsolus Brandy , Foss Kellie A 
Published: October 2019

AbstractObjectiveQuick turnaround of laboratory test results is needed for medical and administrative reasons. Historically, laboratory tests have been requested as routine or STAT. With a few exceptions, a total turnaround time of 90 minutes has been the usually acceptable turnaround time for STAT tests.MethodsWe implemented front-end automation and autoverification and eliminated batch testing for routine tests. We instituted on-site intraoperative testing for selected analytes and employed point of care (POC) testing judiciously. The pneumatic tube system for specimen transport was expanded.ResultsThe in-laboratory turnaround time was reduced to 45 minutes for more than 90% of tests that could reasonably be ordered STAT. With rare exceptions, the laboratory no longer differentiates between routine and STAT testing. Having a single queue for all tests has improved the efficiency of the laboratory.ConclusionIt has been recognized in manufacturing that batch processing and having multiple queues for products are inefficient. The same principles were applied to laboratory testing, which resulted in improvement in operational efficiency and elimination of STAT tests. We propose that the target for in-laboratory turnaround time for STAT tests, if not all tests, be 45 minutes or less for more than 90% of specimens.
De-biasing role induced bias using Bayesian networks
Authors: Schweizer Mark 
Published: October 2019

AbstractThe merits of using subjective probability theory as a normative standard for evidence evaluation by legal fact-finders have been hotly debated for decades. Critics argue that formal mathematical models only lead to an apparent precision that obfuscates the ad-hoc nature of the many assumptions that underlie the model. Proponents of using subjective probability theory as normative standard for legal decision makers, specifically proponents of using Bayesian networks as decision aids in complex evaluations of evidence, must show that formal models have tangible benefits over the more natural, holistic assessment of evidence by explanatory coherence. This article demonstrates that the assessment of evidence using a Bayesian network parametrized with values obtained from the decision makers reduces role-induced bias, a bias that has been largely resistant to de-biasing attempts so far.
Modelling differential rotation of red giants: the case of the evolved sun
Authors: Kitchatinov Leonid , Nepomnyashchikh Alexander 
Published: October 2019

ABSTRACT
Asteroseismology has revealed that cores of red giants rotate about one order of magnitude faster than their convective envelopes. This paper attempts an explanation for this rotational state in terms of the theory of angular momentum transport in stellar convection zones. A differential rotation model based on the theory is applied to a sequence of evolutionary states of a red giant of one solar mass. The model computations show a rotation of about ten times faster in the cores compared to the stellar surface. This rotational state is caused by the non-diffusive downward convective transport of angular momentum. The contrast in rotational rates between core and envelope increases with the radius (age) of the star. Seismologically detected scaling for the spin-down of the giants’ cores is also reproduced.
Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily
Authors: Iwasaki Watal M , Kijima T E , Innan Hideki 
Published: October 2019

AbstractIn order to understand how DNA sequences of transposable elements (TEs) evolve, extensive simulations were carried out. We first used our previous model, in which the copy number of TEs is mainly controlled by selection against ectopic recombination. It was found that along a simulation run, the shape of phylogeny changes quite much, from monophyletic trees to dimorphic trees with two clusters. Our results demonstrated that the change of the phase is usually slow from a monomorphic phase to a dimorphic phase, accompanied with a growth of an internal branch by accumulation of variation between two types. Then, the phase immediately changes back to a monomorphic phase when one group gets extinct. Under this condition, monomorphic and dimorphic phases arise repeatedly, and it is very difficult to maintain two or more different types of TEs for a long time. Then, how a new subfamily can evolve? To solve this, we developed a new model, in which ectopic recombination is restricted between two types under some condition, for example, accumulation of mutations between them. Under this model, because selection works on the copy number of each types separately, two types can be maintained for a long time. As expected, our simulations demonstrated that a new type arises and persists quite stably, and that it will be recognized as a new subfamily followed by further accumulation of mutations. It is indicated that how ectopic recombination is regulated in a genome is an important factor for the evolution of a new subfamily.
Heliosciurus rufobrachium (Rodentia: Sciuridae)
Authors: Thomas Howard H , Best Troy L , Agwanda Bernard 
Published: October 2019

AbstractHeliosciurus rufobrachium (Waterhouse, 1842), one of six species of Heliosciurus, is a sciurid commonly called red-legged sun squirrel. It is a medium-sized diurnally adapted tree squirrel occurring at ground-level to upper heights of the canopy of mature forests. It ranges from the west coast of Africa to Garissa County, Kenya. Adapted to an arboreal life, its frugivorous diet makes it a seed disperser for forest plants. In portions of West Africa, it serves as a source of bushmeat and it is a reservoir for human monkey-pox virus and Trypanosoma brucei, which causes African sleeping sickness. H. rufobrachium is listed as “Least Concern” by the International Union for Conservation of Nature and Natural Resources.
The International Genome Sample Resource (IGSR) collection of open human genomic variation resources
Authors: Fairley Susan , Lowy-Gallego Ernesto , Perry Emily , Flicek Paul 
Published: October 2019

Abstract
To sustain and develop the largest fully open human genomic resources the International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on the foundation of the 1000 Genomes Project, which created the largest openly accessible catalogue of human genomic variation developed from samples spanning five continents. IGSR (i) maintains access to 1000 Genomes Project resources, (ii) updates 1000 Genomes Project resources to the GRCh38 human reference assembly, (iii) adds new data generated on 1000 Genomes Project cell lines, (iv) shares data from samples with a similarly open consent to increase the number of samples and populations represented in the resources and (v) provides support to users of these resources. Among recent updates are the release of variation calls from 1000 Genomes Project data calculated directly on GRCh38 and the addition of high coverage sequence data for the 2504 samples in the 1000 Genomes Project phase three panel. The data portal, which facilitates web-based exploration of the IGSR resources, has been updated to include samples which were not part of the 1000 Genomes Project and now presents a unified view of data and samples across almost 5000 samples from multiple studies. All data is fully open and publicly accessible.
MirGeneDB 2.0: the metazoan microRNA complement
Authors: Fromm Bastian , Domanska Diana , Høye Eirik , Ovchinnikov Vladimir , Kang Wenjing , Aparicio-Puerta Ernesto , Johansen Morten , Flatmark Kjersti , Mathelier Anthony , Hovig Eivind , Hackenberg Michael , Friedländer Marc R , Peterson Kevin J 
Published: October 2019

AbstractSmall non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked &gt;2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
Role of Gamma Knife Radiosurgery in Small Cell Lung Cancer: A Multi-Institutional Retrospective Study of the International Radiosurgery Research Foundation (IRRF)
Authors: Cifarelli Christopher P , Vargo John A , Fang Wei , Liscak Roman , Guseynova Khumar , Warnick Ronald E , Lee Cheng-chia , Yang Huai-che , Borghei-Razavi Hamid , Maiti Tonmoy , Siddiqui Zaid A , Yuan Justin C , Grills Inga S , Mathieu David , Touchette Charles J , Cordeiro Diogo , Chiang Veronica , Hess Judith , Tien Christopher J , Faramand Andrew , Kano Hideyuki , Barnett Gene H , Sheehan Jason P , Lunsford L Dade 
Published: October 2019

Abstract

BACKGROUND
Despite a high incidence of brain metastases in patients with small-cell lung cancer (SCLC), limited data exist on the use of stereotactic radiosurgery (SRS), specifically Gamma Knife™ radiosurgery (Elekta AB), for SCLC brain metastases.

OBJECTIVE
To provide a detailed analysis of SCLC patients treated with SRS, focusing on local failure, distant brain failure, and overall survival (OS).

METHODS
A multi-institutional retrospective review was performed on 293 patients undergoing SRS for SCLC brain metastases at 10 medical centers from 1991 to 2017. Data collection was performed according to individual institutional review boards, and analyses were performed using binary logistic regression, Cox-proportional hazard models, Kaplan-Meier survival analysis, and competing risks analysis.

RESULTS
Two hundred thirty-two (79%) patients received SRS as salvage following prior whole-brain irradiation (WBRT) or prophylactic cranial irradiation, with a median marginal dose of 18 Gy. At median follow-up after SRS of 6.4 and 18.0 mo for surviving patients, the 1-yr local failure, distant brain failure, and OS were 31%, 49%, and 28%. The interval between WBRT and SRS was predictive of improved OS for patients receiving SRS more than 1 yr after initial treatment (21%, <1 yr vs 36%, >1 yr, P = .01). On multivariate analysis, older age was the only significant predictor for OS (hazard ratio 1.63, 95% CI 1.16-2.29, P = .005).

CONCLUSION
SRS plays an important role in the management of brain metastases from SCLC, especially in salvage therapy following WBRT. Ongoing prospective trials will better assess the value of radiosurgery in the primary management of SCLC brain metastases and potentially challenge the standard application of WBRT in SCLC patients.