bluuebunny/crossref_metadata_2025_split huggingface dataset:
TIFA as a crucial mediator for NLRP3 inflammasome
Authors: Lin Ting-Yang , Wei Tong-You Wade , Li Shuai , Wang Shen-Chih , He Ming , Martin Marcy , Zhang Jiao , Shentu Tzu-Pin , Xiao Han , Kang Jian , Wang Kuei-Chun , Chen Zhen , Chien Shu , Tsai Ming-Daw , Shyy John Y.-J. 
Published: December 2016

Significance
Oxidative and inflammatory stresses (e.g., atheroprone flow and hyperlipidemia) induce innate immune responses in vascular endothelium, of which the assembly and activation of nucleotide oligomerization domain-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome constitute a core mechanism. We show that TNF-α receptor-associated factor-interacting protein with a forkhead-associated domain (TIFA) is a mediator of NLRP3 inflammasome in endothelium. The involved regulations include that sterol regulatory element-binding protein 2 transcriptionally induces TIFA (signal 1) and that phosphorylated TIFA causes higher-order assembly of NLRP3 inflammasome (signal 2). Given that sustained innate immune response/activation in endothelium is common to a variety of vascular impairments, TIFA-mediated NLRP3 inflammasome constitutes a pathway by which sustained oxidative and inflammatory stresses lead to dysfunctional endothelium.
PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice
Authors: Fan Yourong , Yang Jiangyi , Mathioni Sandra M. , Yu Jinsheng , Shen Jianqiang , Yang Xuefei , Wang Lei , Zhang Qinghua , Cai Zhaoxia , Xu Caiguo , Li Xianghua , Xiao Jinghua , Meyers Blake C. , Zhang Qifa 
Published: December 2016

SignificanceNew discoveries have been continuously made in recent years on the roles of noncoding RNAs in regulating biological processes. Phased small-interfering RNAs (phasiRNAs) may be the newest member discovered in recent years. The photoperiod-sensitive male sterility (PSMS) rice is a very valuable germplasm that started the era of two-line hybrid rice. Here we show that phasiRNAs generated by a long-noncoding RNAPMS1Tencoded by thePms1locus regulates PSMS in rice. This work provides a case associating the phasiRNAs with a biological trait, especially an agriculturally highly important trait, thus confirming that the phasiRNAs indeed have biological functions.
Phrasal and clausal comparatives in Dutch
Authors: Lindenbergh Charlotte G. 
Published: December 2016

AbstractThis paper presents a new analysis of Dutch comparatives and argues that they should be classified intophrasalandclausalcomparatives (as e.g.Hankamer (1973)argues for English). Arguments for this classification come from differences in case marking and island effects.Merchant (2009)notes the same island effects in Greek comparatives, and by applying his analysis to Dutch we can explain the differences between the Dutch phrasal and clausal comparatives. Crucial in this analysis is the ellipsis of underlying structure, not only in the reduced clausal comparative, but also in the phrasal comparative, which reflects the similarity in their interpretation.
Fragment answers with infinitives in a Flemish dialect
Authors: Rys Kathy , Oosterhof Albert 
Published: December 2016

AbstractThis paper is devoted to a construction in a specific Flemish dialect, in which infinitives are used in fragment answers in contexts where this would be unacceptable in other varieties. Questions such asWaar is mijn boek?‘Where is my book?’ can be answered with constructions such asOp tafel liggen‘lay.INFon the table’. We apply an analysis in terms of ellipsis to these infinitival constructions. However, we find fragment answers with infinitives in contexts where the assumption of ellipsis is problematic, since there is no plausible underlying structure available. We show that the use of this construction has extended to contexts in which the infinitive independently expresses the clausal tense features. Our description of the construction is based on a questionnaire study in which around thirty speakers were tested.
Voicing distinctions in the Dutch-German dialect continuum
Authors: Ouddeken Nina 
Published: December 2016

Abstract
This study investigates the phonetics and phonology of voicing distinctions in the Dutch-German dialect continuum, which forms a transition zone between voicing and aspiration systems. Two phonological approaches to represent this contrast exist in the literature: a [±voice] approach and Laryngeal Realism. The implementation of the change between the two language types in the transition zone will provide new insights in the nature of the phonological representation of the contrast. In this paper I will locate the transition zone by looking at phonetic overlap between VOT values of fortis and lenis plosives, and I will compare the two phonological approaches, showing that both face analytical problems as they cannot explain the variation observed in word-initial plosives and plosive clusters.
Conditional use of prepositional phrases in Dutch
Authors: Reuneker Alex 
Published: December 2016

Abstract
Conditionality can be expressed using a variety of grammatical constructions, ranging from the prototypical lexical marker if to other grammatical patterns. This corpus study investigates the expression of conditionality using prepositional phrases introduced by Dutch zonder (‘without’) compared to their non-conditional use and the use of als (‘if’). The conditional use of zonder-phrases is discussed with respect to complement type, modal marking and negation. A regression analysis was performed to analyse the contribution of these factors to a conditional interpretation.
Object relative clauses in Dutch-speaking children with High-Functioning Autism (HFA)
Authors: Schaeffer Jeannette , Siekman Bart 
Published: December 2016

Abstract
Previous studies show that Direct Object Scrambling (DOS) is impaired in Dutch-speaking children with High-Functioning Autism (HFA). However, as DOS can be considered a syntax-pragmatics interface phenomenon, it is unclear whether DOS errors are due to impaired syntax or impaired pragmatics. In order to shed light on this question, the current study investigates Object Relative Clauses (ORC), assumed to involve syntactic object placement (as in DOS), but not pragmatics, in children with HFA.
We examine the elicited production, comprehension and judgment of ORCs in 25 Dutch-speaking children with HFA (age 6–14) and 25 TD matches with comparable non-verbal reasoning scores. Results reveal no differences between groups, but show that, similar to TD children (and adults), children with HFA use passives and animacy to disambiguate ORCs. The TD-HFA similarity indicates that the syntactic part of DOS is unimpaired in children with HFA and suggests problems with the pragmatic part.
The role of suspiciousness in understanding others’ goals
Authors: Palomares Nicholas A. , Grasso Katherine , Li Siyue , Li Na 
Published: December 2016

Abstract
An experiment examined goal understanding and how perceivers’ suspiciousness was associated with the accuracy, valence, and certainty of their inferences about a pursuer’s goal. In initial interactions, one dyad member was randomly assigned as the pursuer, and the other was the perceiver. The congruency of the perceiver’s and the pursuer’s conversation goals (i.e., discordant, identical, or concordant) and the perceiver’s cognitive busyness were manipulated. Results confirmed that accuracy decreased as perceivers’ suspiciousness increased only for not-busy perceivers in the goal-discord condition because perceivers’ inferences were negatively valenced. Results also supported the hypotheses that certainty decreased as perceivers’ suspiciousness increased only for not-busy perceivers in the goal-discord condition and that certainty increased as perceivers’ suspiciousness increased both for not-busy perceivers in the identical-goal condition and for busy perceivers in the goal-discord condition.
Multi-modal referring expressions in human-human task descriptions and their implications for human-robot interaction
Authors: Gross Stephanie , Krenn Brigitte , Scheutz Matthias 
Published: December 2016

AbstractHuman instructors often refer to objects and actions involved in a task description using both linguistic and non-linguistic means of communication. Hence, for robots to engage in natural human-robot interactions, we need to better understand the various relevant aspects of human multi-modal task descriptions. We analyse reference resolution to objects in a data collection comprising two object manipulation tasks (22 teacher student interactions in Task 1 and 16 in Task 2) and find that 78.76% of all referring expressions to the objects relevant in Task 1 are verbally underspecified and 88.64% of all referring expressions are verbally underspecified in Task 2. The data strongly suggests that a language processing module for robots must be genuinely multi-modal, allowing for seamless integration of information transmitted in the verbal and the visual channel, whereby tracking the speaker’s eye gaze and gestures as well as object recognition are necessary preconditions.
Now you feel it, now you don’t
Authors: Quadflieg Susanne , Ul-Haq Israr , Mavridis Nikolaos 
Published: December 2016

Abstract
Robots seemingly in possession of an experiential mind, as well as humans allegedly incapable thereof, have been reported to elicit feelings of eeriness in their perceivers. The current work re-examined this claim, asking participants to rate both robots and humans in various social situations regarding their mind capacities (e.g., emotional capability, intelligence), non-mind qualities (e.g., animacy, usefulness), and overall appeal (e.g., eeriness, likeability). It was found that feelings of eeriness towards both targets formed a distinct emotional response that was separable from simple dislike. Yet, unexpectedly, eeriness towards both targets intensified, the less they were seen as possessing a typical human mind. For robots, however, this association was less consistent. Moreover, eeriness towards robots, but not towards humans, was most strongly predicted by a lack of perceived usefulness. These results indicate that mind attributions affect people’s attitudes towards each other more strongly than their attitudes towards humanoid robots.
Bilateral comparison of 1 Ω and 10 kΩ standards (ongoing BIPM key comparisons BIPM.EM-K13.a and 13.b) between the NSAI NML (Ireland) and the BIPM
Authors: Rolland B , Fletcher N , Power O 
Published: December 2016

This report gives the result of a bilateral comparison of resistance between the NSAI NML (Ireland) and the BIPM carried out in 2014-2015. Two 1 Ω and two 10 kΩ travelling standards belonging to the BIPM were used. The comparison was carried out with an 'A-B-A' pattern of measurements; the standards were measured first at the BIPM for a period of about one month, then for a similar period at the NSAI-NML, and finally again at the BIPM. The measurand was the 4 terminal dc resistance at low power. The BIPM was the pilot laboratory, and the comparison forms part of the ongoing BIPM key comparisons BIPM.EM-K13.a (for 1 Ω) and BIPM.EM-K13b (for 10 kΩ).
The results from the NSAI NML and the BIPM were found to be in good agreement, with a difference smaller than the relative expanded uncertainties (95% confidence, k = 2) of 0.16 × 10-6 for 1 Ω and 0.42 × 10-6 for 10 kΩ.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification
Authors: Huang Xiao-Tai , Zhu Yuan , Chan Lai Hang Leanne , Zhao Zhongying , Yan Hong 
Published: December 2016

Abstract

Motivation
Cell fate specification plays a key role to generate distinct cell types during metazoan development. However, most of the underlying signaling networks at cellular level are not well understood. Availability of time lapse single-cell gene expression data collected throughout Caenorhabditis elegans embryogenesis provides an excellent opportunity for investigating signaling networks underlying cell fate specification at systems, cellular and molecular levels.

Results
We propose a framework to infer signaling networks at cellular level by exploring the single-cell gene expression data. Through analyzing the expression data of nhr-25, a hypodermis-specific transcription factor, in every cells of both wild-type and mutant C.elegans embryos through RNAi against 55 genes, we have inferred a total of 23 genes that regulate (activate or inhibit) nhr-25 expression in cell-specific fashion. We also infer the signaling pathways consisting of each of these genes and nhr-25 based on a probabilistic graphical model for the selected five founder cells, ‘ABarp’, ‘ABpla’, ‘ABpra’, ‘Caa’ and ‘Cpa’, which express nhr-25 and mostly develop into hypodermis. By integrating the inferred pathways, we reconstruct five signaling networks with one each for the five founder cells. Using RNAi gene knockdown as a validation method, the inferred networks are able to predict the effects of the knockdown genes. These signaling networks in the five founder cells are likely to ensure faithful hypodermis cell fate specification in C.elegans at cellular level.

Availability and Implementation
All source codes and data are available at the github repository https://github.com/xthuang226/Worm_Single_Cell_Data_and_Codes.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
switchde: inference of switch-like differential expression along single-cell trajectories
Authors: Campbell Kieran R , Yau Christopher 
Published: December 2016

Abstract

Motivation
Pseudotime analyses of single-cell RNA-seq data have become increasingly common. Typically, a latent trajectory corresponding to a biological process of interest—such as differentiation or cell cycle—is discovered. However, relatively little attention has been paid to modelling the differential expression of genes along such trajectories.

Results
We present switchde, a statistical framework and accompanying R package for identifying switch-like differential expression of genes along pseudotemporal trajectories. Our method includes fast model fitting that provides interpretable parameter estimates corresponding to how quickly a gene is up or down regulated as well as where in the trajectory such regulation occurs. It also reports a P-value in favour of rejecting a constant-expression model for switch-like differential expression and optionally models the zero-inflation prevalent in single-cell data.

Availability and Implementation
The R package switchde is available through the Bioconductor project at https://bioconductor.org/packages/switchde.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estuarine retention and production of striped bass larvae: a mark-recapture experiment
Authors: Secor David H. , Houde Edward D. , Kellogg Loren L. 
Published: December 2016

AbstractMark-recapture experiments were conducted in the tidal Nanticoke River (Chesapeake Bay) to determine how the salt front retains striped bass larvae and controls nursery production. During two spring spawning seasons, 25.1 million hatchery-produced, first-feeding larvae (5–12 days post-hatch) were released with chemically marked otoliths at selected locations and times. Surveys tracked the spatial and demographic fates of released and naturally spawned larvae. Released larvae dispersed rapidly within the freshwater tidal portion of the estuary and were retained above the salt front. Their distributions overlapped with natural larvae. Growth and mortality rates did not differ with respect to release location, but did vary with day of release, influenced by storm events and seasonal changes in temperature. In 1993, a group released during a storm event did not yield any recaptured larvae. Zooplankton concentrations in both years were likely sufficient for successful larval feeding. In spring 1993, a season of relatively high freshwater flow, nursery volume was 2.1-fold larger and juvenile production from larval releases was fourfold higher than in 1992. We propose that increased nursery volume reduces variance in water quality, enhances retention of larvae within the nursery, thus increasing production of larval striped bass.
Evaluating the Impact of the Medical Education Partnership Initiative at the University of Zimbabwe College of Health Sciences Using the Most Significant Change Technique
Authors: Connors Susan C. , Nyaude Shemiah , Challender Amelia , Aagaard Eva , Velez Christine , Hakim James 
Published: December 2016

Problem
In medical education, evaluating outcomes from programs intended to transform attitudes or influence career trajectories using conventional methods of monitoring is often difficult. To address this problem, the authors adapted the most significant change (MSC) technique to gain a more comprehensive understanding of the impact of the Medical Education Partnership Initiative (MEPI) program at the University of Zimbabwe College of Health Sciences.

Approach
In 2014–2015, the authors applied the MSC to systematically examine the personal significance and level of positive transformation that individuals attributed to their MEPI participation. Interviews were conducted with 28 participants nominated by program leaders. The authors coded results inductively for prevalent themes in participants’ stories and prepared profiles with representative quotes to place the stories in context. Stakeholders selected 9 themes and 18 stories to illustrate the most significant changes.

Outcomes
Six themes (or outcomes) were expected, as they aligned with MEPI goals—becoming a better teacher, becoming a better clinician, increased interest in teaching, increased interest in research, new career pathways (including commitment to practice in Zimbabwe), and improved research skills. Three themes were unexpected—increased confidence, expanded interprofessional networks, and improved interpersonal interactions.

Next Steps
The authors found the MSC to be a useful and systematic evaluation approach for large, complex, and transformative initiatives like MEPI. The MSC seemed to encourage participant reflection, support values inquiry by program leaders, and provide insights into the personal and cultural impacts of MEPI. Additional trial applications of the MSC technique in academic medicine are warranted.
Perioperative Outcomes and Management in Pediatric Complex Cranial Vault Reconstruction
Authors: Stricker Paul A. , Goobie Susan M. , Cladis Franklyn P. , Haberkern Charles M. , Meier Petra M. , Reddy Srijaya K. , Nguyen Thanh T. , Cai Lingyu , Polansky Marcia , Szmuk Peter ,   the Pediatric Craniofacial Collaborative Group
Published: December 2016

Abstract

Background
The Pediatric Craniofacial Collaborative Group established the Pediatric Craniofacial Surgery Perioperative Registry to elucidate practices and outcomes in children with craniosynostosis undergoing complex cranial vault reconstruction and inform quality improvement efforts. The aim of this study is to determine perioperative management, outcomes, and complications in children undergoing complex cranial vault reconstruction across North America and to delineate salient features of current practices.

Methods
Thirty-one institutions contributed data from June 2012 to September 2015. Data extracted included demographics, perioperative management, length of stay, laboratory results, and blood management techniques employed. Complications and outlier events were described. Outcomes analyzed included total blood donor exposures, intraoperative and perioperative transfusion volumes, and length of stay outcomes.

Results
One thousand two hundred twenty-three cases were analyzed: 935 children aged less than or equal to 24 months and 288 children aged more than 24 months. Ninety-five percent of children aged less than or equal to 24 months and 79% of children aged more than 24 months received at least one transfusion. There were no deaths. Notable complications included cardiac arrest, postoperative seizures, unplanned postoperative mechanical ventilation, large-volume transfusion, and unplanned second surgeries. Utilization of blood conservation techniques was highly variable.

Conclusions
The authors present a comprehensive description of perioperative management, outcomes, and complications from a large group of North American children undergoing complex cranial vault reconstruction. Transfusion remains the rule for the vast majority of patients. The occurrence of numerous significant complications together with large variability in perioperative management and outcomes suggest targets for improvement.
Economic Impact of Nonmodifiable Risk Factors in Orthopaedic Fracture Care: Is Bundled Payment Feasible?
Authors: Mahure Siddharth A. , Hutzler Lorraine , Yoon Richard S. , Bosco Joseph A. 
Published: December 2016

Objectives:
To determine whether bundled payments are feasible in the orthopaedic fracture setting, and the potential economic implications of this reimbursement structure.

Design:
Prospective.

Setting:
Multicenter.

Patients/Participants:
Between 2004 and 2014, a total of 23,643 operatively treated patients with fracture and 544,067 patients with total joint arthroplasty (TJA) were identified using the New York State Statewide Planning and Research Cooperative System database.

Interventions:
Severity of illness (SOI), hospital charges ($USD), length of stay (LOS; days), and discharge disposition (homebound vs. not) were collected.

Main Outcome Measurements:
Patients were subdivided into groups of minor and severe SOI. Differences in hospital charges, LOS, and discharge disposition were analyzed. Differences in charges, LOS, and discharges were further analyzed based on minor and severe SOI.

Results:
The difference in hospital charge between patients with minor or severe SOI undergoing elective TJA ranged between 153% and 211%. In contrast, patients undergoing fracture surgery exhibited differences ranging from 314% to 489% between minor and severe SOI levels. Similar differences were observed regarding mean hospital LOS and homebound discharge disposition, with patients with fracture demonstrating greater sensitivity to increasing SOI.

Conclusions:
Although bundled payments may be a viable option for patients undergoing elective TJA, this payment model requires particular attention when applied to fracture care.