bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early vocal production and functional flexibility in wild infant chimpanzees
Authors: Dezecache Guillaume , Zuberbühler Klaus , Davila-Ross Marina , Dahl Christoph D. 
Published: November 2019

ABSTRACTHow did human language evolve from earlier forms of communication? One way to address this question is to compare prelinguistic human vocal behavior with nonhuman primate calls. Here, an important finding has been that, prior to speech, human infant vocal behavior exhibits functional flexibility, the capacity of producing protophones that are not tied to one specific function. Nonhuman primate vocal behavior, by contrast, is comparably inflexible, with different call types tied to specific functions. Our research challenges the generality of this claim, with new findings of flexible vocal behavior in infant chimpanzees. We used artificial intelligence consisting of automated feature extraction and supervised learning algorithms to analyze grunt and whimper vocalizations from free-ranging infants during their first year of life. We found that grunt production was highly flexible occurring in positive, neutral and negative circumstances, as already shown in human infants. We also found acoustic variants of grunts produced in different affective contexts, suggesting gradation within this vocal category. By contrast, the second most common call type of infant chimpanzees, the whimpers, was produced in only one affective context in line with standard models of nonhuman primate vocal behavior. We concluded that the most common chimpanzee vocalization, the grunt, qualifies as functionally flexible, suggesting that evolution of vocal functional flexibility occurred before the split between the Homo and Pan lineages.
Cryptic, solo acylhomoserine lactone synthase from predatory myxobacterium suggests beneficial contribution to prey quorum signaling
Authors: Albataineh Hanan , Duke Maya , Misra Sandeep K. , Sharp Joshua S. , Stevens D. Cole 
Published: November 2019

AbstractConsidered a key taxon in microbial communities, myxobacteria exist as coordinated swarms that utilize an excreted combination of lytic enzymes and specialized metabolites to facilitate predation of numerous microbial phyla. This capacity to produce biologically active metabolites and the associated abundance of natural product biosynthetic pathways contained within their genomes have motivated continued drug discovery efforts from myxobacteria. Of all the biosynthetic gene clusters associated with myxobacteria deposited in the antiSMASH database (∼1,000 total), only one putative acylhomoserine lactone synthase, agpI, was observed in genome data from the myxobacterium Archangium gephyra. Without an acylhomoserine lactone (AHL) receptor also apparent in the genome of A. gephyra, we sought to determine if AgpI was the first example of an orphaned AHL synthase. Herein we report the bioinformatic assessment of AgpI and discovery of a second myxobacterial AHL synthase from Vitiosangium sp. strain GDMCC 1.1324. During axenic cultivation conditions, no detectible AHL metabolites were observed in A. gephyra extracts. However, heterologous expression of each synthase in Escherichia coli provided detectible quantities of 3 AHL signals including 2 known AHLs, C8-AHL and C9-AHL. These results suggest that A. gephyra AHL production is dormant during axenic cultivation conditions and requires an unknown external cue for activation. The orphaned AHL synthase, AgpI, is the first to be reported from a predatory myxobacterium, and predator production of prey quorum signals provides unique insight into interspecies crosstalk within polymicrobial communities.ImportanceThe presence of orphaned quorum signal receptors and associated recognition and response to exogenous acylhomoserine lactone quorum signals observed in microbial communities provides evidence for small molecule-mediated interspecies interactions. While the high occurrence of orphaned AHL receptors from bacteria that do not produce cognate AHL signals suggests the involvement of AHL signals as a shared chemical resource in polymicrobial communities, no orphaned AHL synthases have been determined to be functional in a species without an associated AHL receptor. An orphan signal synthase from a predatory myxobacterium provides an alternative perspective on the evolution and benefits of quorum signaling systems within these communities.
IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
Authors: Minh Bui Quang , Schmidt Heiko , Chernomor Olga , Schrempf Dominik , Woodhams Michael , von Haeseler Arndt , Lanfear Robert 
Published: November 2019

AbstractIQ-TREE (http://www.iqtree.org) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
Midgut aminopeptidase N expression profile in Castor semilooper during sublethal Cry toxin exposure
Authors: Chauhan Vinod K. , Dhania Narender K. , Lokya Vadthya , Bhuvanachandra Bhoopal , Padmasree Kollipara , Dutta-Gupta Aparna 
Published: November 2019

AbstractMidgut of lepidopteran larvae is a multifunctional tissue, which performs roles in digestion, absorption, immunity; transmission of pathogens and interaction with ingested various molecules. The proteins localized at the inner apical brush border membrane are primarily digestive proteases but some of them like aminopeptidase N, alkaline phosphatase, cadherins, ABC transporter C2 etc. interact with Crystal (Cry) toxins produced by Bacillus thuringiensis (Bt). In the present study aminopeptidase N (APN) was characterized as Cry toxin interacting protein in larval midgut of castor semilooper, Achaea janata. Transcriptomic and proteomic analyses revealed the presence of multiple isoforms of APNs (APN1, 2, 4, 6 and 9) which have less than 40% sequence similarity but show the presence of characteristic “GAMENEG” and zinc-binding motifs. Feeding of sublethal dose of Cry toxin caused differential expression of various APN isoform. Further, 6th generation Cry toxin exposed larvae showed reduced expression of APN2. This report suggests that A. janata larvae exploit altered expression of APNs to overcome the deleterious effects of Cry toxicity, which might facilitate toxin tolerance in long run.
Role of microRNA-21 in hypertrophic cardiac remodeling
Authors: Watanabe Ken , Narumi Taro , Watanabe Tetsu , Otaki Yoichiro , Takahashi Tetsuya , Aono Tomonori , Goto Jun , Toshima Taku , Sugai Takayuki , Wanezaki Masahiro , Kutsuzawa Daisuke , Kato Shigehiko , Tamura Harutoshi , Nishiyama Satoshi , Takahashi Hiroki , Arimoto Takanori , Shishido Tetsuro , Watanabe Masafumi 
Published: November 2019

AbstractHypertension is a major public health problem among with aging population worldwide. It causes cardiac remodeling, including hypertrophy and interstitial fibrosis, which leads to development of hypertensive heart disease (HHD). Although microRNA-21 (miR-21) is associated with fibrogenesis in multiple organs, its impact on hypertrophic cardiac remodeling in hypertension is not known. Circulating miR-21 level was higher in patients with HHD than that in the control subjects. It also positively correlated with serum myocardial fibrotic markers. MiR-21 expression levels were significantly upregulated in the mice hearts after angiotensin II (Ang II) infusion or transverse aortic constriction (TAC) compared with control mice. Expression level of programmed cell death 4 (PDCD4), a main target of miR-21, was significantly decreased in Ang II infused mice and TAC mice compared with control mice. Expression levels of transcriptional activator protein 1 (AP-1) and transforming growth factor-β1 (TGF-β1), which were downstream targets of PDCD4, were increased in Ang II infused mice and TAC mice compared with control mice. In vitro, mirVana-miR-21-specific inhibitor attenuated Ang II-induced PDCD4 downregulation and contributed to subsequent deactivation of AP-1/TGF-β1 signaling pathway in neonatal rat cardiomyocytes. Thus, suppression of miR-21 prevents hypertrophic cardiac remodeling by regulating PDCD4, AP-1, and TGF-β1 signaling pathway.
Estrogen receptor β exerts tumor suppressive effects in prostate cancer through repression of androgen receptor activity
Authors: Chaurasiya Surendra , Widmann Scott , Botero Cindy , Lin Chin-Yo , Strom Anders M. , Gustafsson Jan-Åke 
Published: November 2019

AbstractEstrogen receptor β (ERβ) was first identified in the rodent prostate and is abundantly expressed in human and rodent prostate epithelium, stroma, immune cells and endothelium of the blood vessels. In the prostates of mice with inactivated ERβ, mutant phenotypes include epithelial hyperplasia and increased expression of androgen receptor (AR)-regulated genes, most of which are also upregulated in prostate cancer (PCa). ERβ is expressed in both basal and luminal cells in the prostate while AR is expressed in luminal but not in the basal cell layer which harbors the prostate stem cells. To investigate the mechanisms of action of ERβ and its potential cross-talk with AR, we used RNA-seq to study the effects of estradiol or the synthetic ligand, LY3201, in AR-positive LNCaP PCa cells which had been engineered to express ERβ. Transcriptomic analysis indicated relatively few changes in gene expression with ERβ overexpression, but robust responses following ligand treatments. There is significant overlap of responsive genes between the two ligands, as well as ligand-specific alterations. Gene set analysis of down-regulated genes identified an enrichment of androgen-responsive genes, such as FKBP5, CAMKK2, and TBC1D4. Consistently, AR transcript, protein levels, and transcriptional activity were down-regulated following ERβ activation. In agreement with this, we find that the phosphorylation of the CAMKK2 target, AMPK, was repressed by ligand-activated ERβ. Down-regulation of TBC1D4, a major regulator of glucose uptake in prostate, indicates that ERβ is changing glucose metabolism in the prostate. These findings suggest that ERβ-mediated signaling pathways are involved in the negative regulation of AR expression and activity, thus supporting a tumor suppressive role for ERβ in PCa.
alignparse: A Python package for parsing complex features from high-throughput long-read sequencing
Authors: Crawford Katharine H.D. , Bloom Jesse D. 
Published: November 2019

Summary & PurposeAdvances in sequencing technology have made it possible to generate large numbers of long, high-accuracy sequencing reads. For instance, the new PacBio Sequel platform can generate hundreds of thousands of high-quality circular consensus sequences in a single run (Rhoads and F. 2015; Hebert et al. 2018). Good programs exist for aligning these reads for genome assembly (Chaisson and Tesler 2012; Li 2018). However, these long reads can also be used for other purposes, such as sequencing PCR amplicons that contain various features of interest. For instance, PacBio circular consensus sequences have been used to identify the mutations in influenza viruses in single cells (Russell et al. 2019), or to link barcodes to gene mutants in deep mutational scanning (Matreyek et al. 2018). For such applications, the alignment of the sequences to the targets may be fairly trivial, but it is not trivial to then parse specific features of interest (such as mutations, unique molecular identifiers, cell barcodes, and flanking sequences) from these alignments.Here we describe alignparse, a Python package for parsing complex sets of features from long sequences that map to known targets. Specifically, it allows the user to provide complex target sequences in Genbank format that contain an arbitrary number of user-defined sub-sequence features. It then aligns the sequencing reads to these targets and filters alignments based on whether the user-specified features are present with the desired identities (which can be set to different thresholds for different features). Finally, it parses out the sequences, mutations, and/or accuracy of these features as specified by the user. The flexibility of this package therefore fulfills the need for a tool to extract and analyze complex sets of features in large numbers of long sequencing reads.
A short commentary on indents and edges of β-sheets
Authors: Khare Harshavardhan , Ramakumar Suryanarayanarao 
Published: November 2019

Abstractβ-sheets in proteins are formed by extended polypeptide chains, called β-strands. While there is a general consensus on two types of β-strands, viz. ‘edge strands’ (or ‘edges’) and ‘inner strands’ (or ‘central strands’), the possibility of distinguishing between different regions of inner strands remains less explored. In this paper, we address the portions of inner strands of β-sheets that stick out on either or both sides. We call these portions the ‘indent strands’ or ‘indents’ because they give the typical indented appearance to β-sheets. Similar to the edge strands, the indent strands also have β-bridge partner residues on one side while the other side is still open for backbone hydrogen bonds. Despite this similarity, the indent strands differ from the edge strands in terms of various properties such as β-bulges and amino acid composition due to their localization within β-sheets and therefore within folded proteins to certain extent. The localization of indents and edges within folded proteins seems to govern the strategies deployed to deter unhindered β-sheet propagation through β-strand stacking interactions. Our findings suggest that, edges and indents differ in their strategies to avoid further β-strand stacking. Short length itself is a good strategy to avoid stacking and a majority of indents are two residue or shorter in length. Edge strands on the other hand are overall longer. While long edges are known to use various negative design strategies like β-bulges, prolines, strategically placed charges, inward-pointing charged side chains and loop coverage to avoid further β-strand stacking, long indents seem to favor mechanisms such as enrichment in flexible residues with high solvation potential and depletion in hydrophobic residues in response to their less solvent exposed nature. Such subtle differences between indents and edges could be leveraged for designing novel β-sheet architectures.
Is learning anytime, anywhere a good strategy for success? Identifying successful spatial-temporal patterns of on-the-job and full-time students
Authors: Du Xu , Yang Juan , Shelton Brett , Hung Jui-Long 
Published: November 2019

Purpose
Online learning is well-known by its flexibility of learning anytime and anywhere. However, how behavioral patterns tied to learning anytime and anywhere influence learning outcomes are still unknown.

Design/methodology/approach
This study proposed concepts of time and location entropy to depict students’ spatial-temporal patterns. A total of 5,221 students with 1,797,677 logs, including 485 on-the-job students and 4,736 full-time students, were analyzed to depict their spatial-temporal learning patterns, including the relationships between identified patterns and students’ learning performance.

Findings
Analysis results indicate on-the-job students took more advantage of anytime, anywhere than full-time students. Students with a higher tendency for learning anytime and a lower level of learning anywhere were more likely to have better outcomes. Gender did not show consistent findings on students’ spatial-temporal patterns, but partial findings could be supported by evidence in neural science or by cultural and geographical differences.

Research limitations/implications
A more accurate approach for categorizing position and location might be considered. Some findings need more studies for further validation. Finally, future research can consider connections between other well-known performance predictors (such as financial situation, motivation, personality and major) and the type of learning patterns.

Practical implications
The findings gained from this study can help improve the understandings of students’ learning behavioral patterns and design as well as implement better online education programs.

Originality/value
This study proposed concepts of time and location entropy to identify successful spatial-temporal patterns of on-the-job and full-time students.
Examining similarities and differences of citation patterns between monographs and papers: a case in biology and computer science
Authors: Wang Yuzhuo , Zhang Chengzhi 
Published: November 2019

Purpose
Citation content in academic papers and academic monographs promotes the knowledge flow among different publications. However, existing citation content analysis (CCA) focuses on academic papers and monographs have not received much research attention. We want to know if monographs are appropriate objects of CCA and whether existing methods of analyzing citation in papers are suitable for citation in monographs. Therefore, this paper aims to learn more about features of cited references and citation content in monographs and compare the characteristic of citation pattern between monographs and papers.

Design/methodology/approach
The authors manually annotate the references and syntactic citation content in academic monographs published by Morgan & Claypool and automatically extracted the references and citation content from academic papers published by Public Library of Science. Five features in two types citation pattern, namely, pattern of cited reference (including year, source and mention frequency of reference) and pattern of citation content (including location, length of citation content) are used to examine similarities and differences between monographs and papers.

Findings
The results indicate that between monographs and papers, differences are shown in location, length of citation content and year, source of reference, whereas frequency of mention of reference is similar.

Originality/value
Previous studies have explored the patter of citation content in academic papers. However, none of the existing literature, as far as the authors know, has considered the citation content in academic monographs and the similarities or differences among academic documents when studying the citation pattern.
Fraud triangle in public procurement: evidence from Indonesia
Authors: Rustiarini Ni Wayan , Sutrisno Sutrisno , Nurkholis Nurkholis , Andayani Wuryan 
Published: November 2019

Purpose
This study aims to examine the effects of fraud triangle (pressure, opportunity and rationalization) on individual fraudulent behavior in Indonesian public procurement. Empirical research in this area is relatively sparse.

Design/methodology/approach
Data were collected using laboratory experiments.

Findings
The results revealed that fraudulent behavior is higher when an individual has high pressure and high opportunity. These factors play an important role in determining individual rationalization. Most of participants used “displacing responsibility” to rationalize their actions. This study also demonstrated that negative affect mediates the relationship between fraudulent behavior and rationalization.

Research limitations/implications
First, fraudulent behavior research cannot be separated from social desirability bias. Second, the experiments only involved individual decision-making, not in groups. Finally, this study did not examine the effectiveness of rationalization in reducing negative affect.

Practical implications
Over the years, the government has only focused on the identification of pressure and reduction of opportunities, but ignored individual psychological reasons. Considering that procurement fraud is always increasing, the government must more focus on individual reasons to design an effective prevention and detection system.

Social implications
There are various conflicts of interest in public procurement budgeting. These conflicts can distort resource allocation and causes budget leakage. As a result, the government is incapacitated to achieve social and economic goals of the community.

Originality/value
There is limited research about fraud in public procurement budgeting, especially in developing countries. In addition, the fraud triangle research, which focuses on rationalization is still limited.
China’s poverty alleviation over the last 40 years: successes and challenges
Authors: Liu Mingyue , Feng Xiaolong , Wang Sangui , Qiu Huanguang 
Published: November 2019

Over the past 40 years, China has made significant progress towards its poverty alleviation goals. The rural population under the current poverty line has decreased by 739.9 million. China has contributed to more than 70 per cent of world poverty reduction. To better promote the new anti‐poverty strategy and to serve as a reference for poverty alleviation in other developing countries, this paper summarises the main experiences of China’s poverty alleviation over the past 40 years and then discusses the challenges associated with implementing the targeted poverty alleviation policy in the new era. China’s experience with poverty alleviation includes development‐oriented poverty alleviation, improving self‐development capabilities of the poor population, encouraging multiple subjects to participate in poverty alleviation and focusing on innovation and ways to improve poverty alleviation. Although China’s poverty alleviation initiatives have achieved significant successes, there are still several challenges that should be of concern in the coming years, such as the diminishing marginal effect of financial inputs on poverty alleviation, the resulting negative incentives for the poor to improve their internal motivations and the insufficient participation of markets and social forces in poverty alleviation. Given these challenges, this paper provides suggestions for anti‐poverty policies beyond 2020.
Overruling uncertainty about preventative medications: the social organisation of healthcare professionals’ knowledge and practices
Authors: Cupit Caroline , Rankin Janet , Armstrong Natalie , Martin Graham P. 
Published: November 2019

AbstractIn this article, we draw on an institutional ethnographic (IE) study of cardiovascular disease prevention in general practice, exploring the work of healthcare professionals who introduce a discussion of risk and preventative medications into consultations with patients. Our aim is to explicate, using IE's theoretical ontology and analytical tools, how troubling patient experiences in this clinical context are coordinated institutionally. We focus our attention on the social organisation of healthcare professionals’ knowledge and front‐line practices, highlighting the textual processes through which they overrule patients’ concerns and uncertainties about taking preventative medication, such that some patients feel unable to openly discuss their health needs in preventative consultations. We show how healthcare professionals activate knowledge of ‘evidence‐based risk reduction’ to frame patients’ queries as ‘barriers’ to be overcome. Our analysis points not to deficiencies of healthcare professionals who lack the expertise or inclination to adequately ‘share decisions’ with patients, but to the ways in which their work is institutionally orientated towards performance measures which will demonstrate to local and national policymakers that they are tackling the ‘burden of (cardiovascular) disease’.