bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution
Authors: Spill Yannick G. , Castillo David , Vidal Enrique , Marti-Renom Marc A. 
Published: April 2019

AbstractChromosome conformation capture techniques, such as Hi-C, are fundamental in characterizing genome organization. These methods have revealed several genomic features, such as chromatin loops, whose disruption can have dramatic effects in gene regulation. Unfortunately, their detection is difficult; current methods require that the users choose the resolution of interaction maps based on dataset quality and sequencing depth. Here, we introduce Binless, a resolution-agnostic method that adapts to the quality and quantity of available data, to detect both interactions and differences. Binless relies on an alternate representation of Hi-C data, which leads to a more detailed classification of paired-end reads. Using a large-scale benchmark, we demonstrate that Binless is able to call interactions with higher reproducibility than other existing methods. Binless, which is freely available, can thus reliably be used to identify chromatin loops as well as for differential analysis of chromatin interaction maps.
Dynamic gene regulation by nuclear colony-stimulating factor 1 receptor in human monocytes and macrophages
Authors: Bencheikh Laura , Diop M’Boyba Khadija , Rivière Julie , Imanci Aygun , Pierron Gerard , Souquere Sylvie , Naimo Audrey , Morabito Margot , Dussiot Michaël , De Leeuw Frédéric , Lobry Camille , Solary Eric , Droin Nathalie 
Published: April 2019

AbstractDespite their location at the cell surface, several receptor tyrosine kinases (RTK) are also found in the nucleus, as either intracellular domains or full length proteins. However, their potential nuclear functions remain poorly understood. Here we find that a fraction of full length Colony Stimulating Factor-1 Receptor (CSF-1R), an RTK involved in monocyte/macrophage generation, migrates to the nucleus upon CSF-1 stimulation in human primary monocytes. Chromatin-immunoprecipitation identifies the preferential recruitment of CSF-1R to intergenic regions, where it co-localizes with H3K4me1 and interacts with the transcription factor EGR1. When monocytes are differentiated into macrophages with CSF-1, CSF-1R is redirected to transcription starting sites, colocalizes with H3K4me3, and interacts with ELK and YY1 transcription factors. CSF-1R expression and chromatin recruitment is modulated by small molecule CSF-1R inhibitors and altered in monocytes from chronic myelomonocytic leukemia patients. Unraveling this dynamic non-canonical CSF-1R function suggests new avenues to explore the poorly understood functions of this receptor and its ligands.
A genetic variant rs13293512 in the promoter of let-7 is associated with an increased risk of breast cancer in Chinese women
Authors: Sun Ruifen , Gong Jianyu , Li Ju , Ruan Zhiguo , Yang Xiaomi , Zheng Yongren , Qing Lili , He Xiaoshan , Jiang Jike , Peng Yanxia , Zou Haijian 
Published: April 2019

Abstract
Growing evidence has demonstrated that single-nucleotide polymorphisms (SNPs) in the promoter of miRNA may influence individuals’ susceptibility to human diseases. We examined two SNPs rs10877887 and rs13293512 in the promoters of let-7 family to determine if the two SNPs were related to the occurrence of breast cancer (BC). Genotyping of the two SNPs was performed by PCR and restriction fragment length polymorphism analysis or TaqMan assay in 301 BC patients and 310 age matched controls. We found a higher frequency of rs13293512 CC genotype and rs13293512 C allele amongst BC patients (CC vs TT: adjusted odds ratio (OR) = 1.78; 95% CI: 1.14–2.80; P=0.012; C vs T: adjusted OR = 1.33; 95% CI: 1.06–1.67; P=0.013). Stratification analysis showed that rs13293512 CC genotype was associated with an increased risk of BC in patients with negative estrogen receptor (adjusted OR = 2.39; 95% CI: 1.32–4.30; P=0.004), patients with negative progesterone receptor (adjusted OR = 1.92; 95% CI: 1.11–3.33; P=0.02), patients with T1-2 stage cancer (adjusted OR = 1.77; 95% CI: 1.07–2.93; P=0.03), and patients with N1-3 stage cancer (adjusted OR = 1.89; 95% CI: 1.13–3.17; P=0.015). These findings suggest that rs13293512 in the promoter of let-7a-1/let-7f-1/let-7d cluster may be a possible biomarker for the development of BC in Chinese women.
Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: structural genomics approach
Authors: Amir Mohd. , Kumar Vijay , Mohammad Taj , Dohare Ravins , Rehman Md. Tabish , Alajmi Mohamed F. , Hussain Afzal , Ahmad Faizan , Hassan Md. Imtaiyaz 
Published: April 2019

Abstract
TEN1 protein is a key component of CST complex, implicated in maintaining the telomere homeostasis, and provides stability to the eukaryotic genome. Mutations in TEN1 gene have higher chances of deleterious impact; thus, interpreting the number of mutations and their consequential impact on the structure, stability, and function is essentially important. Here, we have investigated the structural and functional consequences of nsSNPs in the TEN1 gene. A wide array of sequence- and structure-based computational prediction tools were employed to identify the effects of 78 nsSNPs on the structure and function of TEN1 protein and to identify the deleterious nsSNPs. These deleterious or destabilizing nsSNPs are scattered throughout the structure of TEN1. However, major mutations were observed in the α1-helix (12–16 residues) and β5-strand (88–96 residues). We further observed that mutations at the C-terminal region were having higher tendency to form aggregate. In-depth structural analysis of these mutations reveals that the pathogenicity of these mutations are driven mainly through larger structural changes because of alterations in non-covalent interactions. This work provides a blueprint to pinpoint the possible consequences of pathogenic mutations in the CST complex subunit TEN1.
Effects of Eugenol on Haemoproteus columbae in domestic pigeons (Columba livia domestica) from Riyadh, Saudi Arabia
Authors: Metwally Dina M. , Al-Talhi Razan A. , Barakat Ibrahim A.H. , ElKhadragy Manal F. 
Published: April 2019

Abstract
Eugenol was investigated for the treatment of Haemoproteus columbae (H. columbae) infected squabs (young domestic pigeons, Columba domestica). Thirty naturally-infected squabs were divided into three groups of 10 each. One group was treated with Eugenol, while the positive and negative control groups were administered buparvaquone (Butalex®) and distilled water, respectively. The number of infected red blood cells (RBCs) was calculated in all groups before and after treatment at 4-day intervals for 16 days. The results showed a significant therapeutic effect of Eugenol, with a progressive decrease in the number of infected RBCs from 89.20 ± 2.11 before treatment to 0.90 ± 0.31 at the end of treatment (P≤0.05). Butalex® was able to suppress the number of infected RBCs from 93.70 ± 1.72 before treatment to 0.90 ± 0.35 at the end of the experiment (P≤0.05). Eugenol showed therapeutic effects against H. columbae and may be regarded as a candidate for further studies to develop new drugs against blood parasites, in both animals and humans.
Longitudinal Relationships Between Decline in Speech-in-Noise Recognition Ability and Cognitive Functioning: The Longitudinal Aging Study Amsterdam
Authors: Pronk Marieke , Lissenberg-Witte Birgit I. , van der Aa Hilde P. A. , Comijs Hannie C. , Smits Cas , Lemke Ulrike , Zekveld Adriana A. , Kramer Sophia E. 
Published: April 2019

Purpose
Various directional hypotheses for the observed links between aging, hearing, and cognition have been proposed: (a) cognitive load on perception hypothesis, (b) information degradation hypothesis, (c) sensory deprivation hypothesis, and (d) common cause hypothesis. Supporting evidence for all 4 hypotheses has been reported. No studies have modeled the corresponding 4 causal pathways into 1 single model, which would be required to evidence that multiple directional hypotheses apply. The aim of the current study was to tease out which pathways apply for 5 different cognitive measures.

Method
Data from 1,029 respondents of the Longitudinal Aging Study Amsterdam were used spanning a maximum follow-up of 7 years (3 measurements). Speech-in-noise recognition ability (digit triplet speech-in-noise test) was included as a measure of auditory function. Cognitive measures included global cognitive functioning, fluid intelligence, information processing speed, and verbal memory (immediate recall and retention). Bivariate dual change score modeling was used to model the causal pathways between hearing, cognition, and baseline age.

Results
For information processing speed, global cognitive functioning, fluid intelligence, and memory-immediate recall, all pathways except for the sensory deprivation pathway were supported. For memory-retention, only the common cause and the sensory deprivation pathways were supported.

Conclusions
Causal pathways corresponding to all 4 hypotheses were supported. Support for the common cause hypothesis, the information degradation hypothesis, and the cognitive load on perception hypotheses was found for 4 of 5 cognitive measures. This was unexpected in some cases (e.g., support for the information degradation pathway for cognitive measures that do not rely on auditory stimuli). The sensory deprivation pathway that emerged for memory-retention might point toward processes related to early stages of dementia. In summary, the results show that the links between decline in auditory function, cognition, and aging are complex and most likely are captured by pathways belonging to various directional hypotheses.
Different Responses to Altered Auditory Feedback in Younger and Older Adults Reflect Differences in Lexical Bias
Authors: Colby Sarah , Shiller Douglas M. , Clayards Meghan , Baum Shari 
Published: April 2019

Purpose
Previous work has found that both young and older adults exhibit a lexical bias in categorizing speech stimuli. In young adults, this has been argued to be an automatic influence of the lexicon on perceptual category boundaries. Older adults exhibit more top-down biases than younger adults, including an increased lexical bias. We investigated the nature of the increased lexical bias using a sensorimotor adaptation task designed to evaluate whether automatic processes drive this bias in older adults.

Method

A group of older adults (
n
= 27) and younger adults (
n
= 35) participated in an altered auditory feedback production task. Participants produced target words and nonwords under altered feedback that affected the 1st formant of the vowel. There were 2 feedback conditions that affected the lexical status of the target, such that target words were shifted to sound more like nonwords (e.g.,
less-liss
) and target nonwords to sound more like words (e.g.,
kess-kiss
).

Results

A mixed-effects linear regression was used to investigate the magnitude of compensation to altered auditory feedback between age groups and lexical conditions. Over the course of the experiment, older adults compensated (by shifting their production of 1st formant) more to altered auditory feedback when producing words that were shifted toward nonwords (
less-liss
) than when producing nonwords that were shifted toward words (
kess-kiss
). This is in contrast to younger adults who compensated more to nonwords that were shifted toward words compared to words that were shifted toward nonwords.

Conclusion
We found no evidence that the increased lexical bias previously observed in older adults is driven by a greater sensitivity to top-down lexical influence on perceptual category boundaries. We suggest the increased lexical bias in older adults is driven by postperceptual processes that arise as a result of age-related cognitive and sensory changes.
Age-Related Differences in the Perception of Emotion in Spoken Language: The Relative Roles of Prosody and Semantics
Authors: Ben-David Boaz M. , Gal-Rosenblum Sarah , van Lieshout Pascal H. H. M. , Shakuf Vered 
Published: April 2019

Purpose
We aim to identify the possible sources for age-related differences in the perception of emotion in speech, focusing on the distinct roles of semantics (words) and prosody (tone of speech) and their interaction.

Method

We implement the Test for Rating of Emotions in Speech (
Ben-David, Multani, Shakuf, Rudzicz, & van Lieshout, 2016
). Forty older and 40 younger adults were presented with spoken sentences made of different combinations of 5 emotional categories (anger, fear, happiness, sadness, and neutral) presented in the prosody and semantics. In separate tasks, listeners were asked to attend to the sentence as a whole, integrating both speech channels, or to focus on 1 channel only (prosody/semantics). Their task was to rate how much they agree the sentence is conveying a predefined emotion.

Results
(a) Identification of emotions: both age groups identified presented emotions. (b) Failure of selective attention: both age groups were unable to selectively attend to 1 channel when instructed, with slightly larger failures for older adults. (c) Integration of channels: younger adults showed a bias toward prosody, whereas older adults showed a slight bias toward semantics.

Conclusions
Three possible sources are suggested for age-related differences: (a) underestimation of the emotional content of speech, (b) slightly larger failures to selectively attend to 1 channel, and (c) different weights assigned to the 2 speech channels.
Personalentwicklung in der Notaufnahme
Authors: Wasser Christoph , Riessen Reimer 
Published: April 2019

AbstractIn the last years, the number of patients in German emergency department (ED) is rising continously. At the same time, it is diffcult to find enough physicians to occupy the positions in the ED. Therefore human resources development is critical for the success of any ED. This article describes human resources development and recruitment in the context of current health policy trends in Germany.
Point of Care Ultrasound in Geriatric Patients: Prospective Evaluation of a Portable Handheld Ultrasound Device
Authors: Fröhlich Eckhart , Beller Katharina , Muller Reinhold , Herrmann Maria , Debove Ines , Klinger Christoph , Pauluschke-Fröhlich Jan , Hoffmann Tatjana , Kreppenhofer Sorina , Dietrich Christoph F. 
Published: April 2019

Abstract
Purpose The aim of the current study was to evaluate point of care ultrasound (POCUS) in geriatric patients by echoscopy using a handheld ultrasound device (HHUSD, VScan) at bedside in comparison to a high-end ultrasound system (HEUS) as the gold standard.
Materials and Methods Prospective observational study with a total of 112 geriatric patients. The ultrasound examinations were independently performed by two experienced blinded examiners with a portable handheld device and a high-end ultrasound device. The findings were compared with respect to diagnostic findings and therapeutic implications.
Results The main indications for the ultrasound examinations were dyspnea (44.6 %), fall (frailty) (24.1 %) and fever (21.4 %). The most frequently found diagnoses were cystic lesions 32.1 % (35/109), hepatic vein congestion 19.3 % (21/109) and ascites 13.6 % (15/110). HHUSD delivered 13 false-negative findings in the abdomen resulting in an “overall sensitivity” of 89.5 %. The respective “overall specificity” was 99.6 % (7 false-positive diagnoses). HHUSD (versus HEUS data) resulted in 13.6 % (17.3 %) diagnostically relevant procedures in the abdomen and 0.9 % (0.9 %) in the thorax. Without HHUSD (HEUS) 95.7 % (100 %) of important pathological findings would have been missed.
Conclusion The small HHUSD tool improves clinical decision-making in immobile geriatric patients at the point of care (geriatric ward). In most cases, HHUSD allows sufficiently accurate yes/no diagnoses already at the bedside, thereby clarifying the leading symptoms for early clinical decision-making.
中文社交问答网络社区中的情境学习 (Situated learning in a Chinese question-and-answer online community)
Authors: Zeng Zhini 
Published: April 2019

摘要“知乎”是使用频率最高 (7.6%) 的中文社交问答网络社区 (CNNIC, 2017)。本文从中级汉语媒体课中运用“知乎”开展教学活动的案例入手，以“情境学习”理论 (Lave & Wenger, 1991) 的视角，揭示了学生在目的语社会中的网络平台上参与集体知识构建取得的收获及遇到的挑战，并以此为契机，介绍一种将社交问答网络平台运用于中高级对外汉语教学的思路。本文共有三个部分：首先，在充分参考前人研究的基础上，本文通过介绍三种围绕“知乎”展开的教学活动，提出了一个将网络社交问答社区运用于对外汉语教学的模型。其次，通过一项针对十名在中文课内、外使用“知乎”的学生的前导型调查，以及分析学生在“知乎”平台上创作的文本，本文进一步检测了该教学模型在实际应用中的收效与阻碍。最后，基于对现有案例的分析结果，本文总结了将网络社交问答社区引入对外汉语课堂的五个优势，并为未来的教学实践提出了两点建议。
Register in English for Academic Purposes and English for Specific Purposes
Authors: Conrad Susan 
Published: April 2019

AbstractSusan Conrad, Professor of Applied Linguistics at Portland State University (USA), contributes this article on the applications of register research to English for Academic Purposes (EAP) and English for Specific Purposes (ESP). Her research focuses on topics including academic register variation, discipline-specific language, student and workplace writing, and grammar and writing pedagogy. Since the 1990s, her work has advocated for and exemplified the ways in which register-based descriptions can facilitate language teaching, including building awareness of register variation in learners and novice writers themselves. This focus is illustrated in her bookReal Grammar: A Corpus-Based Approach to English(Conrad & Biber 2009, Pearson Longman), which takes many of the major register-based patterns of variation in English grammar (described in theLongman Grammar of Spoken and Written English,Biber et al. 1999) and translates them into practical grammar lessons for language learners, making explicit how grammar use is mediated by register. Her applied focus is also evident in her work as Principal Investigator for the Civil Engineering Writing Project <http://www.cewriting.org/>. The project, funded by the National Science Foundation, addresses the writing needs of Civil Engineering students through corpus-based register comparisons (of university student writing, practitioner workplace writing, and published academic writing), applying the results to the development and evaluation of pedagogical materials that improve students’ preparation for writing in the workplace.
Acer L.
Authors: Savill P. 
Published: April 2019

Abstract

This chapter describes the origin and introduction; climatic and site requirements, and other silvicultural characteristics; pests and diseases; natural regeneration; flowering, seed production and nursery conditions; conservation; provenance; timber and uses; area and yield; and place of the following maple species in British forestry: Acer campestre, A. macrophyllum, A. platanoides, and A. pseudoplatanus. The chapter also provides details on other species of Acer that might be useful in a changing climate.
Chamaecyparis Spach.
Authors: Savill P. 
Published: April 2019

Abstract

This chapter describes the origin and introduction; climatic and site requirements, and other silvicultural characteristics; pests and diseases; natural regeneration; flowering, seed production and nursery conditions; provenance and cultivars; area and yield; timber and uses; and place of Lawson cypress (Chamaecyparis lawsoniana) in British forestry.
Global status of the regulation of genome editing technologies.
Authors: Smyth S. J. 
Published: April 2019

Abstract

Innovations affect societies in various ways. For example, the latest innovations in cell phones and electronics are readily adopted without hesitation. However, many innovations regarding the breeding of plants, the production of food crops and the processing of food products, can be met with fear and trepidation by some societies. Europe, the foundation of the Industrial Revolution, has developed strong adversity to agricultural innovations that involve innovative genome editing methods in general and to genetically modified (GM) crops in particular. While much of the industrial world models their regulatory frameworks for plant agriculture on the science-based risk assessment framework developed through the efforts of the Organisation for Economic Cooperation and Development, the European Union's regulatory framework for GM crops is based on the precautionary principle, approving but a single GM crop variety for production in the twenty-first century. As any field of science and technology advances, so has the breeding of GM crops. GM crop varieties were developed through the insertion of a gene or genes from a different species, such as the insertion of the trait for insect resistance in plants that originally came from a soil bacterium. Crop varieties are now being developed through a group of targeted, site-directed mutation technologies, known as genome editing, where some of this group of technologies results in no foreign genes being transferred into new varieties. While technologically viewed as a significant advancement in the development of new plant varieties, some jurisdictions have chosen to regulate genome editing as equivalent to GM crops, thereby establishing a
de facto
ban on the application of the technology. Yet other jurisdictions have chosen to embrace the technology, announcing that some applications of genome editing will face no regulatory oversight. This paper provides a global overview of the various regulatory frameworks for genome editing.
Moving beyond size and phosphatidylserine exposure: evidence for a diversity of apoptotic cell‐derived extracellular vesicles in vitro
Authors: Poon Ivan K. H. , Parkes Michael A. F. , Jiang Lanzhou , Atkin‐Smith Georgia K. , Tixeira Rochelle , Gregory Christopher D. , Ozkocak Dilara C. , Rutter Stephanie F. , Caruso Sarah , Santavanond Jascinta P. , Paone Stephanie , Shi Bo , Hodge Amy L. , Hulett Mark D. , Chow Jenny D. Y. , Phan Thanh Kha , Baxter Amy A. 
Published: April 2019

ABSTRACTApoptosis is a form of programmed cell death that occurs throughout life as part of normal development as well as pathologic processes including chronic inflammation and infection. Although the death of a cell is often considered as the only biological outcome of a cell committed to apoptosis, it is becoming increasingly clear that the dying cell can actively communicate with other cells via soluble factors as well as membrane‐bound extracellular vesicles (EVs) to regulate processes including cell clearance, immunity and tissue repair. Compared to EVs generated from viable cells such as exosomes and microvesicles, apoptotic cell‐derived EVs (ApoEVs) are less well defined and the basic criteria for ApoEV characterization have not been established in the field. In this study, we will examine the current understanding of ApoEVs, in particular, the ApoEV subtype called apoptotic bodies (ApoBDs). We described that a subset of ApoBDs can be larger than 5 μm and smaller than 1 μm based on flow cytometry and live time‐lapse microscopy analysis, respectively. We also described that a subset of ApoBDs can expose a relatively low level of phosphatidylserine on its surface based on annexin A5 staining. Furthermore, we characterized the presence of caspase‐cleaved proteins (in particular plasma membrane‐associated or cytoplasmic proteins) in samples enriched in ApoBDs. Lastly, using a combination of biochemical‐, live imaging‐ and flow cytometry‐based approaches, we characterized the progressive lysis of ApoBDs. Taken together, these results extended our understanding of ApoBDs.