bluuebunny/crossref_metadata_2025_split huggingface dataset:
Doppler ultrasound surveillance of TIPS-patency in the era of covered stents – retrospective analysis of a large single-center cohort
Authors: Klinger Christoph , Riecken Bettina , Müller Johannes , Westphal Anja , Löffler Joachim , Froehlich Eckhart , Caca Karel 
Published: September 2018

Abstract
Purpose The purpose of this study was to determine accuracy and necessity of long-term Doppler ultrasound (DU) surveillance of transjugular intrahepatic portosystemic shunt (TIPS) patency after implantation of an ePTFE-covered stent-graft (Viatorr).
Methods This single-center retrospective study includes 228 consecutive cirrhotic patients with TIPS implantation due to portal hypertensive complications. Standardized DU surveillance was scheduled 3 – 5 days, 3 months, and 6 months after TIPS implantation and every 6 months thereafter. Portal venography was performed in case of DU findings suspicious of TIPS dysfunction, clinical signs of recurrent portal hypertension, or refractory hepatic encephalopathy.
Results During a mean follow-up of 16.6 ± 23.4 months, 866 DU examinations were performed. Twenty-two cases of TIPS dysfunction were observed in 16 patients with no first dysfunction more than 4 years after implantation. Routine DU in asymptomatic patients had little therapeutic impact (0.75 %). DU and venography were concordant in 39/46 (84.8 %) paired examinations, and 1-, 2-, and 5-year primary TIPS patency was 87.4 %, 83.7 %, and 79.97 %, respectively. Patients with TIPS dysfunction and subsequent successful revision during the first 2 years of follow-up had a significantly higher risk (p = 0.001) of new dysfunction compared to those without TIPS dysfunction. Cumulative 1-, 2-, and 5-year survival was 68.7 %, 61.3 %, and 42.7 %, respectively.
Conclusions Despite acceptable accuracy, scheduled DU surveillance proved to have minor therapeutic impact. Thus, detailed DU surveillance is not useful in asymptomatic patients after 2 years of unremarkable follow-up. In contrast, long-term DU surveilleance should be performed in patients after successful revision of TIPS dysfunction and patients with prothrombotic states (e. g., portal vein thrombosis, Budd-Chiari syndrome).
Fibroblasts lacking nuclear lamins do not have nuclear blebs or protrusions but nevertheless have frequent nuclear membrane ruptures
Authors: Chen Natalie Y. , Kim Paul , Weston Thomas A. , Edillo Lovelyn , Tu Yiping , Fong Loren G. , Young Stephen G. 
Published: September 2018

Significance
Genetic defects in nuclear lamins or reduced expression of nuclear lamins is accompanied by nuclear blebs and an increased susceptibility for nuclear membrane ruptures. Nuclear membrane ruptures are exacerbated by subjecting cells to mechanical forces. Here, we demonstrate that cells lacking nuclear lamins have oblong nuclei, but no nuclear blebs and no protrusions of the chromatin beyond the bounds of the nuclear membranes. Nevertheless, the cells displayed frequent and prolonged nuclear membrane ruptures, associated with DNA damage and occasionally by cell death. Thus, the nuclear lamina is crucial for the integrity of the nuclear membranes and for limiting damage to DNA. We suspect that our observations could be relevant to disease caused by defects or deficiencies in the nuclear lamins.
Gender variation in signs of sexual behaviour in Hong Kong Sign Language
Authors: Wei Monica X. , Sze Felix Y. B. , Wong Aaron Y. L. 
Published: September 2018

Abstract
This paper discusses possible gender variation in the signs of sexual behaviour in Hong Kong Sign Language (HKSL). The data comes
from a research project that aims at documenting and analyzing sex-related signs in this sign language for the sake of producing
materials for sex education and interpreter training programs. Since sex is a highly taboo topic, euphemistic signs for the target
concepts were collected and analyzed. This paper presents evidence that linguistic variation of neutral and euphemistic
expressions of sex-related concepts exists in HKSL, and that gender plays a role in the choice of some but not all variants and
their euphemistic counterparts.
Tracing the evolutionary trajectory of verbal working memory with neuro-archaeology
Authors: Putt Shelby S. , Wijeakumar Sobanawartiny 
Published: September 2018

AbstractWe used optical neuroimaging to explore the extent of functional overlap between working memory (WM) networks involved in language and Early Stone Age toolmaking behaviors. Oldowan tool production activates two verbal WM areas, but the functions of these areas are indistinguishable from general auditory WM, suggesting that the first hominin toolmakers relied on early precursors of verbal WM to make simple flake tools. Early Acheulian toolmaking elicits activity in a region bordering on Broca’s area that is involved in both visual and verbal WM tasks. The sensorimotor and mirror neurons in this area, along with enhancement of general WM capabilities around 1.8 million years ago, may have provided the scaffolding upon which a WM network dedicated to processing exclusively linguistic information could evolve. In the road map going forward, neuro-archaeologists should investigate the trajectory of WM over the course of human evolution to better understand its contribution to language origins.
From actions to events
Authors: Pustejovsky James 
Published: September 2018

AbstractIn this paper, I argue that an important component of the language-ready brain is the ability to recognize and conceptualize events. By ‘event’, I mean any situation or activity in the world or our mental life, that we find salient enough to individuate as a thought or word. While this may sound either trivial or non-unique to humans, I hope to show that abstracting away events and their participants from the embodied flow of experience is a characteristic unique to humans. This ability is enabled, I will argue, by two critical competencies that act as scaffolds for language-ready thought in the prehuman brain. The first, as argued by Arbib (2006,2012,2016) and others, is a sophisticated system of gesture production and understanding in prehumans, which provided a template for schema-like sequencing and slot-filling of information units. The second involves the integration of multiple modalities of expression in the communicative act, in particular, the alignment of co-gestural speech and co-speech gesture. With such computational facilities, action-based gestures can be abstracted away from their associated objects and become full event representations. This view supports the MSH argument for the emergence of more complex linguistic expressions from initially holophrastic units. In particular, actions can be thought of as protoverbs, which through this process are abstracted to full event descriptions, i.e., verbs.
Introducing a special issue
Authors: Arbib Michael A. 
Published: September 2018

Abstract
The paper introduces a Special Issue of Interaction Studies which includes 21 papers based on presentations and discussion
at a workshop entitled “How the Brain Got Language: Towards a New Road Map.” Unifying themes include the comparative study of brain,
behavior and communication in monkeys, apes and humans, and an EvoDevoSocio framework for approaching biological and cultural evolution
within a shared perspective. The final article of the special issue builds on the previous papers to present “The Comparative
Neuroprimatology 2018 (CNP-2018) Road Map for Research on How the Brain Got Language.”
STatistical Inference Relief (STIR) feature selection
Authors: Le Trang T , Urbanowicz Ryan J , Moore Jason H , McKinney Brett A 
Published: September 2018

Abstract

Motivation
Relief is a family of machine learning algorithms that uses nearest-neighbors to select features whose association with an outcome may be due to epistasis or statistical interactions with other features in high-dimensional data. Relief-based estimators are non-parametric in the statistical sense that they do not have a parameterized model with an underlying probability distribution for the estimator, making it difficult to determine the statistical significance of Relief-based attribute estimates. Thus, a statistical inferential formalism is needed to avoid imposing arbitrary thresholds to select the most important features. We reconceptualize the Relief-based feature selection algorithm to create a new family of STatistical Inference Relief (STIR) estimators that retains the ability to identify interactions while incorporating sample variance of the nearest neighbor distances into the attribute importance estimation. This variance permits the calculation of statistical significance of features and adjustment for multiple testing of Relief-based scores. Specifically, we develop a pseudo t-test version of Relief-based algorithms for case-control data.

Results
We demonstrate the statistical power and control of type I error of the STIR family of feature selection methods on a panel of simulated data that exhibits properties reflected in real gene expression data, including main effects and network interaction effects. We compare the performance of STIR when the adaptive radius method is used as the nearest neighbor constructor with STIR when the fixed-k nearest neighbor constructor is used. We apply STIR to real RNA-Seq data from a study of major depressive disorder and discuss STIR’s straightforward extension to genome-wide association studies.

Availability and implementation
Code and data available at http://insilico.utulsa.edu/software/STIR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Contemporaneous and Granger causality among US corn cash and futures prices
Authors: Xu Xiaojie 
Published: September 2018

AbstractThis paper examines contemporaneous and Granger causality among US corn futures and seven cash prices from major producing states for January 2006–March 2011. Causal flows from futures to cash prices are identified with contemporaneous and in-sample Granger causality tests but not with the out-of-sample Granger causality test. While no interstate in-sample or out-of-sample Granger causality is found, contemporaneous causal linkages are revealed. No causality from cash to futures prices is determined.
Epigenetic changes in preterm birth placenta suggest a role for ADAMTS genes in spontaneous preterm birth
Authors: Mani Sneha , Ghosh Jayashri , Lan Yemin , Senapati Suneeta , Ord Teri , Sapienza Carmen , Coutifaris Christos , Mainigi Monica 
Published: September 2018

AbstractPreterm birth (PTB) affects approximately 1 in 10 pregnancies and contributes to approximately 50% of neonatal mortality. However, despite decades of research, little is understood about the etiology of PTB, likely due to the multifactorial nature of the disease. In this study, we examined preterm and term placentas, from unassisted conceptions and those conceived using in vitro fertilization (IVF). IVF increases the risk of PTB and causes epigenetic change in the placenta and fetus; therefore, we utilized these patients as a unique population with a potential common etiology. We investigated genome-wide DNA methylation in placentas from term IVF, preterm IVF, term control (unassisted conception) and preterm control pregnancies and discovered epigenetic dysregulation of multiple genes involved in cell migration, including members of the ADAMTS family, ADAMTS12 and ADAMTS16. These genes function in extracellular matrix regulation and tumor cell invasion, processes replicated by invasive trophoblasts (extravillous trophoblasts (EVTs)) during early placentation. Though expression was similar between term and preterm placentas, we found that both genes demonstrate high expression in first- and second-trimester placenta, specifically in EVTs and syncytiotrophoblasts. When we knocked down ADAMTS12 or ADAMTS16in vitro, there was poor EVT invasion and reduced matrix metalloproteinase activity, reinforcing their critical role in placentation. In conclusion, utilizing a population at high risk for PTB, we have identified a role for ADAMTS gene methylation in regulating early placentation and susceptibility to PTB.
GLS hyperactivity causes glutamate excess, infantile cataract and profound developmental delay
Authors: Rumping Lynne , Tessadori Federico , Pouwels Petra J W , Vringer Esmee , Wijnen Jannie P , Bhogal Alex A , Savelberg Sanne M C , Duran Karen J , Bakkers Mark J G , Ramos Rúben J J , Schellekens Peter A W , Kroes Hester Y , Klomp Dennis W J , Black Graeme C M , Taylor Rachel L , Bakkers Jeroen P W , Prinsen Hubertus C M T , van der Knaap Marjo S , Dansen Tobias B , Rehmann Holger , Zwartkruis Fried J T , Houwen Roderick H J , van Haaften Gijs , Verhoeven-Duif Nanda M , Jans Judith J M , van Hasselt Peter M 
Published: September 2018

Abstract
Loss-of-function mutations in glutaminase (GLS), the enzyme converting glutamine into glutamate, and the counteracting enzyme glutamine synthetase (GS) cause disturbed glutamate homeostasis and severe neonatal encephalopathy. We report a de novo Ser482Cys gain-of-function variant in GLS encoding GLS associated with profound developmental delay and infantile cataract. Functional analysis demonstrated that this variant causes hyperactivity and compensatory downregulation of GLS expression combined with upregulation of the counteracting enzyme GS, supporting pathogenicity. Ser482Cys-GLS likely improves the electrostatic environment of the GLS catalytic site, thereby intrinsically inducing hyperactivity. Alignment of +/−12.000 GLS protein sequences from >1000 genera revealed extreme conservation of Ser482 to the same degree as catalytic residues. Together with the hyperactivity, this indicates that Ser482 is evolutionarily preserved to achieve optimal—but submaximal—GLS activity. In line with GLS hyperactivity, increased glutamate and decreased glutamine concentrations were measured in urine and fibroblasts. In the brain (both grey and white matter), glutamate was also extremely high and glutamine was almost undetectable, demonstrated with magnetic resonance spectroscopic imaging at clinical field strength and subsequently supported at ultra-high field strength. Considering the neurotoxicity of glutamate when present in excess, the strikingly high glutamate concentrations measured in the brain provide an explanation for the developmental delay. Cataract, a known consequence of oxidative stress, was evoked in zebrafish expressing the hypermorphic Ser482Cys-GLS and could be alleviated by inhibition of GLS. The capacity to detoxify reactive oxygen species was reduced upon Ser482Cys-GLS expression, providing an explanation for cataract formation. In conclusion, we describe an inborn error of glutamate metabolism caused by a GLS hyperactivity variant, illustrating the importance of balanced GLS activity.
Development and Validation of a Risk Score for Febrile Neutropenia After Chemotherapy in Patients With Cancer: The FENCE Score
Authors: Aagaard Theis , Roen Ashley , Reekie Joanne , Daugaard Gedske , Brown Peter de Nully , Specht Lena , Sengeløv Henrik , Mocroft Amanda , Lundgren Jens , Helleberg Marie 
Published: September 2018

AbstractBackgroundFebrile neutropenia (FN) after chemotherapy causes a high burden of morbidity and mortality. We aimed to develop and validate a risk score to predict FN in the first cycle of chemotherapy.MethodsWe included patients with solid cancers and diffuse large B-cell lymphomas at Rigshospitalet, University of Copenhagen, 2010-2016. Predictors of FN were analyzed using Poisson regression and random split-sampling.ResultsAmong 6294 patients in the derivation cohort, 360 developed FN. Female sex, older age, cancer type, disease stage, low albumin, elevated bilirubin, low creatinine clearance, infection before chemotherapy, and number of and type of chemotherapy drugs predicted FN. Compared with those at low risk (n = 2520, 40.0%), the incidence rate ratio of developing FN was 4.8 (95% confidence interval [CI] = 2.9 to 8.1), 8.7 (95% CI = 5.3 to 14.1) and 24.0 (95% CI = 15.2 to 38.0) in the intermediate (n = 1294, 20.6%), high (n = 1249, 19.8%) and very high (n = 1231, 19.6%) risk groups, respectively, corresponding to a number needed to treat with granulocyte colony-stimulating factors to avoid one FN event in the first cycle of 284, 60, 34 and 14. The discriminatory ability (Harrell’s C-statistic = 0.80, 95% CI = 0.78 to 0.82) was similar in the validation cohort (n = 3163) (0.79, 95% CI = 0.75 to 0.82).ConclusionWe developed and internally validated a risk score for FN in the first cycle of chemotherapy. The FENCE score is available online and provides good differentiation of risk groups.
Evaluation of Intravenous Posaconazole Dosing and Pharmacokinetic Target Attainment in Pediatric Patients
Authors: Nickless Jenna R , Bridger Kathryn E , Vora Surabhi B , Brothers Adam W 
Published: September 2018

Abstract
Limited data exist on intravenous (IV) posaconazole dosing and the risk for hepatotoxicity it confers to children. In this study, we evaluated dosing and resulting trough levels in 10 pediatric patients on IV posaconazole. A therapeutic level in these patients was achieved 95% of the time. We found a median minimum effective dose of 6.55 mg/kg of body weight. No correlation was found between the duration or posaconazole trough level and an increased alanine transaminase level.
SDSS J0909+4449: A large-separation strongly lensed quasar at z ∼ 2.8 with three images
Authors: Shu Yiping , Marques-Chaves Rui , Evans N Wyn , Pérez-Fournon Ismael 
Published: September 2018

ABSTRACT
We report the discovery of SDSS J0909+4449, an exceptional system consisting of a quasar at z = 2.788 strongly lensed by a group of galaxies at z ∼ 0.9 into three images separated by up to 14 arcsec based on archival data collected by the Sloan Digital Sky Survey, extended Baryon Oscillation Spectroscopic Survey, Beijing–Arizona Sky Survey, the Mayall z-band Legacy Survey, and the Gemini Telescope. We discuss two hypotheses on the nature of SDSS J0909+4449, i.e. a rare triply imaged quasar in the naked cusp configuration and a typical quadruply imaged quasar with the fourth image undetected in this data. We find that simple lens models can provide excellent fits to the observed image positions and the non-detection under either hypothesis. Deeper imaging data, spectroscopic observations, and follow-up light-curve measurements will be helpful in determining which hypothesis is correct and provide better constraints on the lens mass distribution. Nevertheless, given its unusually large image separations, SDSS J0909+4449 will be a unique probe for the mass structure and the underlying cooling and stellar feedback processes on group or cluster scales.
Health and mass unemployment events—developing a framework for preparedness and response
Authors: Davies A R , Homolova L , Grey C N B , Bellis M A 
Published: September 2018

Abstract

Background
Mass unemployment events are not uncommon yet the impact on health is not well recognised. There is a need for a preparedness and response framework, as exists for other events that threaten population health.

Methods
Framework informed by a narrative review of the impact of mass unemployment on health (studies published in English from 1990 to 2016), and qualitative data from 23 semi-structured interviews with individuals connected to historical national and international events, addressing gaps in published literature on lessons learnt from past responses.

Results
Economic and employment shock triggered by mass unemployment events have a detrimental impact on workers, families and communities. We present a public health informed response framework which includes (i) identify areas at risk, (ii) develop an early warning system, (iii) mobilise multi-sector action including health and community, (iv) provision of support across employment, finance and health (v) proportionate to need, (vi) extend support to family members and (vii) communities and (viii) evaluate and learn.

Conclusion
Mass unemployment events have an adverse impact on the health, financial and social circumstances of workers, families, and communities. This is the first framework for action to mitigate and address the detrimental impact of mass unemployment events on population health.
Education Spillovers in Farm Productivity: Revisiting the Evidence
Authors: Gille Véronique 
Published: September 2018

Abstract
This paper exploits the social organization of India to revisit the question of education spillovers in farm productivity. The fact that social interactions mainly occur within castes in rural India provides tools to show that the observed correlation between farm productivity and neighbors’ education is likely to be a spillover effect. In particular, there are no cross-caste and no cross-occupation effects, which underlines that, under specific assumptions, which are stated and explored in the paper, the education of neighbors does not capture the effect of group unobservables. This evidence is complemented by separate estimations by crops, which show results that are consistent with education spillovers. The strategy used in this paper helps understand and interpret previous findings from the literature.
A survey on polynomial in momenta integrals for billiard problems
Authors: Bialy Misha , Mironov Andrey E. 
Published: September 2018

In this paper, we give a short survey of recent results on the algebraic version of the Birkhoff conjecture for integrable billiards on surfaces of constant curvature. We also discuss integrable magnetic billiards. As a new application of the algebraic technique, we study the existence of polynomial integrals for the two-sided magnetic billiards introduced by Kozlov and Polikarpov.
This article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’.
Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks
Authors: Rubin Adam J. , Parker Kevin R. , Satpathy Ansuman T. , Qi Yanyan , Wu Beijing , Ong Alvin J. , Mumbach Maxwell R. , Ji Andrew L. , Kim Daniel S. , Cho Seung Woo , Zarnegar Brian J. , Greenleaf William J. , Chang Howard Y. , Khavari Paul A. 
Published: September 2018

SummaryHere we present Perturb-ATAC, a method which combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells, based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 unique genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning, and identified a hierarchical organization of TFs that govern B cell state, variation, and disease-associatedcis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules ofcis-elements that specify keratinocyte fate, orchestrated by the TFs JUNB, KLF4, ZNF750, CEBPA, and EHF. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful and general strategy to dissect gene regulatory networks in development and disease.HighlightsA new method for simultaneous measurement of CRISPR perturbations and chromatin state in single cells.Perturb-ATAC reveals regulatory factors that controlcis-element accessibility,trans-factor occupancy, and nucleosome positioning.Perturb-ATAC reveals regulatory modules of coordinatedtrans-factor activity in B lymphoblasts.Keratinocyte differentiation is orchestrated by synergistic activities of co-binding TFs oncis-elements.