bluuebunny/crossref_metadata_2025 huggingface dataset:
Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting
Authors: Lu Alex X , Kraus Oren Z , Cooper Sam , Moses Alan M
Published: August 2018

Cellular microscopy images contain rich insights about biology. To extract this information, researchers use features, or measurements of the patterns of interest in the images. Here, we introduce a convolutional neural network (CNN) to automatically design features for fluorescence microscopy. We use a self-supervised method to learn feature representations of single cells in microscopy images without labelled training data. We train CNNs on a simple task that leverages the inherent structure of microscopy images and controls for variation in cell morphology and imaging: given one cell from an image, the CNN is asked to predict the fluorescence pattern in a second different cell from the same image. We show that our method learns high-quality features that describe protein expression patterns in single cells both yeast and human microscopy datasets. Moreover, we demonstrate that our features are useful for exploratory biological analysis, by capturing high-resolution cellular components in a proteome-wide cluster analysis of human proteins, and by quantifying multi-localized proteins and single-cell variability. We believe paired cell inpainting is a generalizable method to obtain feature representations of single cells in multichannel microscopy images.

Author Summary

To understand the cell biology captured by microscopy images, researchers use features, or measurements of relevant properties of cells, such as the shape or size of cells, or the intensity of fluorescent markers. Features are the starting point of most image analysis pipelines, so their quality in representing cells is fundamental to the success of an analysis. Classically, researchers have relied on features manually defined by imaging experts. In contrast, deep learning techniques based on convolutional neural networks (CNNs) automatically learn features, which can outperform manually-defined features at image analysis tasks. However, most CNN methods require large manually-annotated training datasets to learn useful features, limiting their practical application. Here, we developed a new CNN method that learns high-quality features for single cells in microscopy images, without the need for any labeled training data. We show that our features surpass other comparable features in identifying protein localization from images, and that our method can generalize to diverse datasets. By exploiting our method, researchers will be able to automatically obtain high-quality features customized to their own image datasets, facilitating many downstream analyses, as we highlight by demonstrating many possible use cases of our features in this study.
Endogenous viral elements are widespread in arthropod genomes and commonly give rise to piRNAs
Authors: ter Horst Anneliek M. , Nigg Jared C. , Falk Bryce W.
Published: August 2018

Arthropod genomes contain sequences derived from integrations of DNA and non-retroviral RNA viruses. These sequences, known as endogenous viral elements (EVEs), have been acquired over the course of evolution and have been proposed to serve as a record of past viral infection. Recent evidence indicates that EVEs can function as templates for the biogenesis of PIWI-interacting RNAs (piRNAs) in some mosquito species and cell lines, raising the possibility that EVEs may function as a source of immunological memory in these organisms. However, whether EVEs are capable of acting as templates for piRNA production in other arthropod species is unknown. Here we used publically available genome assemblies and small RNA sequencing datasets to characterize the repertoire and function of EVEs across 48 arthropod genomes. We found that EVEs are widespread in arthropod genomes and primarily correspond to unclassified ssRNA viruses and viruses belonging to the Rhabdoviridae and Parvoviridae families. Additionally, EVEs were enriched in piRNA clusters in a majority of species and we found that production of primary piRNAs from EVEs is common, particularly for EVEs located within piRNA clusters. While we found evidence suggesting that piRNAs mapping to a number of EVEs are produced via the ping-pong cycle, potentially pointing towards a role for EVE-derived piRNAs during viral infection, limited nucleotide identity between currently described viruses and EVEs identified here likely limits the extent to which this process plays a role during infection with known viruses.
New human chromosomal safe harbor sites for genome engineering with CRISPR/Cas9, TAL effector and homing endonucleases
Authors: Pellenz Stefan , Phelps Michael , Tang Weiliang , Hovde Blake T. , Sinit Ryan B. , Fu Wenqing , Li Hui , Chen Eleanor , Monnat Raymond J.
Published: August 2018

Safe Harbor Sites (SHS) are genomic locations where new genes or genetic elements can be introduced without disrupting the expression or regulation of adjacent genes. We have identified 35 potential new human SHS in order to substantially expand SHS options beyond the three widely used canonical human SHS,AAVS1, CCR5andhROSA26. All 35 potential new human SHS and the three canonical sites were assessed for SHS potential using 9 different criteria weighted to emphasize safety that were broader and more genomics-based than previous efforts to assess SHS potential. We then systematically compared and rank-ordered our 35 new sites and the widely used humanAAVS1, hROSA26andCCR5sites, then experimentally validated a subset of the highly ranked new SHS together versus the canonicalAAVS1site. These characterizations includedin vitroandin vivocleavage-sensitivity tests; the assessment of population-level sequence variants that might confound SHS targeting or use for genome engineering; homology–dependent and –independent, SHS-targeted transgene integration in different human cell lines; and comparative transgene integration efficiencies at two new SHS versus the canonicalAAVS1site. Stable expression and function of new SHS-integrated transgenes were demonstrated for transgene-encoded fluorescent proteins, selection cassettes and Cas9 variants including a transcription transactivator protein that were shown to drive large deletions in aPAX3/FOXO1fusion oncogene and induce expression of theMYF5gene that is normally silent in human rhabdomyosarcoma cells. We also developed a SHS genome engineering ‘toolkit’ to enable facile use of the most extensively characterized of our new human SHS located on chromosome 4p. We anticipate our newly identified human SHS, located on 16 chromosomes including both arms of the human X chromosome, will be useful in enabling a wide range of basic and more clinically-oriented human gene editing and engineering.
Loan delinquency and macroeconomic conditions
Authors: Abaidoo Rexford
Published: August 2018

Purpose

The purpose of this paper is to examine how specific macroeconomic indicators and conditions impact short- and long-run loan delinquency rates among US commercial banks under various economic episodes.

Design/methodology/approach

The study employs an autoregressive distributed lag framework (ARDL) and error correction model in its examination of how loan delinquency rates are impacted by specific macroeconomic variables and conditions.

Findings

This study finds that in both the short and long run, a percentage growth in macroeconomic indicators, such as industrial productivity and private domestic investments, reduces loan delinquency rates among commercial banks, given all things being equal. Additionally, this study also finds that adverse macroeconomic conditions, such as inflation, economic policy uncertainty and volatility, associated with specific macroeconomic variables, such as investment growth, etc., tend to worsen loan delinquency rates. Empirical results further suggest that among the various macroeconomic conditions examined, inflationary pressures tend to have the most significant heightening impact on loan delinquency rates among commercial banks.

Originality/value

The uniqueness of this study, compared to similar studies found in the literature, has to do with its verification of potential association between loan delinquency rates and specific hitherto unexamined macroeconomic conditions. Compared to similar studies on loan delinquency, this study collectively examines how conditions of uncertainty, volatility and expectations of macroeconomic conditions shape loan delinquency rates among commercial banks.
Food without sun: price and life-saving potential
Authors: Denkenberger David , Pearce Joshua , Taylor Andrew Ray , Black Ryan
Published: August 2018

Purpose

The purpose of this study is to estimate the price and life-saving potential of alternate foods. The sun could be blocked by asteroid impact, supervolcanic eruption or nuclear winter caused by burning of cities during a nuclear war. The primary problem in these scenarios is loss of food production. Previous work has shown that alternate foods not dependent on sunlight, such as bacteria grown on natural gas and cellulose turned into sugar enzymatically, could feed everyone in these catastrophes, and preparation for these foods would save lives in a manner that is highly cost-effective.

Design/methodology/approach

This study estimates the price of alternate foods during a catastrophe in line with global trade and information sharing, but factors such as migration, loans, aid or conflict are not taken into consideration.

Findings

Without alternate foods, for a five-year winter, only approximately 10 per cent of the population would survive. The price of dry food would rise to approximately $100/kg, and the expenditure on this food would be approximately $100tn. If alternate foods were $8/kg, the surviving global population increases to approximately 70 per cent, saving >4billion lives.

Research limitations/implications

A nongovernmental mechanism for coordinating the investments of rich people may be possible. Identifying companies whose interests align with alternate food preparations may save lives at a negative cost.

Practical implications

The probability of loss of civilization and its impact on future generations would be lower in this scenario, and the total expenditure on food would be halved.

Originality/value

Preparation for alternate foods is a good investment even for wealthy people who would survive without alternate foods.
The last possible resort: Latin American migrants’ rapport with Spanish healthcare
Authors: Lamarque Muriel , Moro-Gutiérrez Lourdes
Published: August 2018

Purpose

The purpose of this paper is to analyze the relationship between Latin American migrants and the Spanish healthcare system, from the users’ perspective, in order to examine the socio-cultural determinants for access and attention, as well as the possible difficulties faced when attending institutional facilities.

Design/methodology/approach

This work is based on qualitative ethnographic research with the Latin American community established in the region of Castile and León, Spain. Analysis was established through a thematic approach and illustrated with the testimonies of participants involved, to inspect personal meanings and interpretations, as well as specific practices regarding healthcare.

Findings

The encounter between foreigners and health services is frequently expressed with negative emotions, such as feelings of fear facing a system that is perceived as designed “for others.” For many Latin American immigrants in Spain, institutional healthcare is not considered their first choice for treating illness. This has been related to economic, bureaucratic, ideological and emotional factors.

Originality/value

Most of the existing literature about immigrant healthcare in Spain has focused on sanitary conditions or patterns of service use from an institutional perspective and a quantitative approach. This paper highlights the perceptions of users to enrich comprehension of the rapport between migrants and medical care.
Variables affecting positive faculty-student relationships in an Ecuadorian university
Authors: Cabezas Christian Benjamin , Acurio Carlos Vidal , Merlyn Marie-France , Orbe Cristina Elizabeth , Riera Wilma Leonila
Published: August 2018

Purpose

The purpose of this paper is to identify the main variables that affect the establishment of a good faculty-student pedagogical relationship in representative samples from a main university in Ecuador.

Design/methodology/approach

In the first phase of this exploratory mixed methods study, focus groups were conducted to identify the variables of interest, and in a second phase, these variables were rated in relevance by applying the “pile-sort” method.

Findings

Results showed that for students, the variable that most affects the establishment of a good relationship with their faculty is the “faculty’s knowledge,” while the variable that showed the least effect is the “number of students in the classroom.” On the other hand, faculty members responded that the variables that most affect the establishment of a good pedagogical relationship are “empathy with students,” “vocation” and “faculty’s knowledge,” while they considered that the least relevant variables were “context” variables such as “the number of students in the classroom” and “the physical conditions of the classroom.”

Practical implications

These results provide relevant insights into the importance that students place on the theoretical resources that faculty members show as a foundation for establishing positive relationships. In the same way, the relevance that faculty members place on the elements “empathy,” “vocation” and “knowledge” as key variables needed to establish positive interactions.

Originality/value

Previous research had underlined the importance that positive faculty-students relationships have on achieving learning goals. However, the variables that would affect the establishment of these relationships were not clearly recognized.
Office space: Australian advertising agencies in the twentieth century
Authors: Crawford Robert
Published: August 2018

Purpose

This paper aims to examine the evolution of the advertising agency and its offices in Australia over the course of the twentieth century. Historical accounts of advertising have paid scant attention to agencies’ attempts to organise and manage their offices, as well as the impact that these efforts has had on the work undertaken by agency staff.

Design/methodology/approach

This study draws on reports in the advertising industry press, as well as oral history testimony to examine the agencies’ changing layout and interior design. It identifies three distinct periods, which reveal the impact of modernist and post-industrialist ideas on the organisation and functions of the advertising agency’s offices and, indeed, their impact on the agency’s outputs.

Findings

This examination of the office space within the agency setting not only offers a new perspective of the advertising agency business as a whole but also demonstrates the importance of material culture for historians working across management, business and marketing fields.

Originality/value

The originality of this study lies in its use of material culture and space as a tool for examining management history and understanding its impact on everyday work practices. By charting the changes reflected in advertising agency office spaces, this study also offers a unique overview of the ways that management practices have historically interacted with business work spaces.
Trend analysis of co-authorship network in Library Hi Tech
Authors: Cheng Fei-Fei , Huang Yu-Wen , Tsaih Der-Chian , Wu Chin-Shan
Published: August 2018

Purpose

The purpose of this paper is to examine the evolution of collaboration among researchers in Library Hi Tech based on the co-authorship network analysis.

Design/methodology/approach

The Library Hi Tech publications were retrieved from Web of Science database between 2006 and 2017. Social network analysis based on co-authorship was analyzed by using BibExcel software and a visual knowledge map was generated by Pajek. Three important social capital indicators: degree centrality, closeness centrality and betweenness centrality were calculated to indicate the co-authorship. Cohesive subgroup analysis which includes components and k-core was then applied to show the connectivity of co-authorship network of Library Hi Tech.

Findings

The results indicated that around 42 percent of the articles were written by single author, while an increasing trend of multi-authored articles suggesting the collaboration among researchers in librarian research field becomes popular. Furthermore, the social network analysis identified authorship network with three core authors – Markey, K., Fourie, I. and Li, X. Finally, six core subgroups each included six or seven tightly connected researchers were also identified.

Originality/value

This study contributed to the existing literature by revealing the co-authorship network in librarian research field. Key researchers in the major subgroup were identified. This is one of the limited studies that describe the collaboration network among authors from different perspectives showing a more comprehensive co-authorship network.
Social media users’ share intention and subjective well-being
Authors: Ma Liang , Zhang Xin , Yan Ding Xiao
Published: August 2018

Purpose

The rise of social media has gained increasing attention in recent years; however, few studies have focused on social media users’ specific behavior and subjective well-being. To fill this research gap, the purpose of this paper is to develop an integrated model to investigate factors that affect social media user’s share intention and the relationship between user’s share intention and subjective well-being.

Design/methodology/approach

Structural equation model is used in this study. A field survey with 398 WeChat users is conducted to test the research model and hypotheses.

Findings

The empirical results show that: utilitarian value, hedonic value, user satisfaction and information source credibility are important factors affecting users’ share intention; users’ share intention positively affects user’s subjective well-being; moderating effects show that relative significance positively moderates the relationship between utilitarian value and users’ share intention; and users’ demographic characteristics differences actually exist in users’ share intention.

Originality/value

First, the authors clear that factors affect social media users’ share intention from the perspective of customer-perceived value. The results deepen our understanding about the factors that affect WeChat users’ share intention. Second, the authors focus on the effect of users’ specific behavior on users’ subjective well-being and found that users’ share intention is one of the important aspects that affect user’s subjective well-being. More importantly, the authors tested users’ characteristic differences in social media users’ share intention, which have previously received limited attention.
Challenges to open peer review
Authors: Teixeira da Silva Jaime A.
Published: August 2018

Purpose

The purpose of this paper is to assess what the challenges to open peer review (OPR) are, relative to traditional peer review (TPR).

Design/methodology/approach

By examining select issues within peer review, more broadly, and challenges within TPR, the effectiveness of OPR is questioned.

Findings

Although OPR brings an aspect of transparency, by partially eliminating biases, fear of reprisals and of professional blow-back, either by authors who may be criticized or by competitors, limits the expansion of this peer review model, or its adoption as an industry-wide standard.

Originality/value

Open Science 2.0 boasts of greater openness and transparency and OPR is touted as one tool to achieve this. However, that potential is limited. This limitation needs to be recognized.
Does social capital constrain firms’ tax avoidance?
Authors: Chircop Justin , Fabrizi Michele , Ipino Elisabetta , Parbonetti Antonio
Published: August 2018

Purpose

This paper aims to investigate whether the level of social capital of the region in which a firm is headquartered affects its tax avoidance activities. Social capital can be defined as the mutual trust in society and literature shows that firms headquartered in high social capital regions exhibit higher level of corporate social responsibility. Recent research suggests that some stakeholders consider tax avoidance as a socially irresponsible and illegitimate activity, whereas others deem corporate tax payments as detrimental to social welfare because they hurt economic development. Building on this debate, the relationship between social capital and tax avoidance is empirically investigated.

Design/methodology/approach

A sample of 52,962 firm-year observations over the period 1990-2014 was used to empirically investigate the relationship between social capital and tax avoidance.

Findings

Consistent with the idea that managers consider corporate tax payments as a socially responsible action, evidence was found that firms headquartered in areas with high social capital engage significantly less in tax avoidance activities. It was also documented that the negative impact of social capital on tax avoidance is stronger in the presence of high religiosity, high corporate performance and lower sensitivity of CEO’s compensation to stock volatility.

Originality/value

This paper extends research on social capital and improves the understanding of the effect of the social environment on managerial decision. Importantly, by studying the relationship between social capital and tax avoidance, the authors add to the recent debate on companies’ perception of the desirability of tax avoidance activities from a social viewpoint.
MiR‐873 inhibition enhances gefitinib resistance in non‐small cell lung cancer cells by targeting glioma‐associated oncogene homolog 1
Authors: Jin Shidai , He Jing , Li Jun , Guo Renhua , Shu Yongqian , Liu Ping
Published: August 2018

Background

The five‐year survival rate of non‐small cell lung cancer (NSCLC) patients is very low. MiR‐873 is involved in the growth, metastasis, and differentiation of tumors. Herein, we determined the target gene and influence of miR‐873 in NSCLC.

Methods

MiRanda and Targetscan websites were used to predict the target gene of miR‐873 in NSCLC. Luciferase activity was examined using a dual luciferase reporter gene assay kit. The viability, tube formation, and proliferation of cells were analyzed by cell counting kit‐8, angiogenic analysis, and flow cytometry, respectively. The levels of miR‐873 and GLI1 were evaluated using quantitative real‐time PCR and Western blot assays.

Results

Low levels of GLI1 and high levels of miR‐873 were observed in an NSCLC cell line (PC9) highly sensitive to EGFR‐tyrosine kinase inhibitors. There was a negative correlation between miR‐873 and GLI1 expression in PC9 and PC9/GR cells. The inhibition of miR‐873 enhanced GLI1 levels. MiR‐873 expression was inhibited by gefitinib. Gefitinib markedly reduced the viability, tube formation, and cell number in PC9 cells. However, suppression of miR‐873 enhanced the resistance and knockdown of GLI1 enhanced the sensitivity of PC9 cells to gefitinib.

Conclusions

GLI1 is a target gene of miR‐873 in NSCLC. The inhibition of miR‐873 increased gefitinib resistance of NSCLC cells via the upregulation of GLI1. These results indicate that miR‐873‐GLI1 signaling is involved in gefitinib resistance in NSCLC.
Tau protein aggregation is associated with cellular senescence in the brain
Authors: Musi Nicolas , Valentine Joseph M. , Sickora Kathryn R. , Baeuerle Eric , Thompson Cody S. , Shen Qiang , Orr Miranda E.
Published: August 2018

Tau protein accumulation is the most common pathology among degenerative brain diseases, including Alzheimer's disease (AD), progressive supranuclear palsy (PSP), traumatic brain injury (TBI), and over twenty others. Tau‐containing neurofibrillary tangle (NFT) accumulation is the closest correlate with cognitive decline and cell loss (Arriagada, Growdon, Hedley‐Whyte, & Hyman, ), yet mechanisms mediating tau toxicity are poorly understood. NFT formation does not induce apoptosis (de Calignon, Spires‐Jones, Pitstick, Carlson, & Hyman, 2009), which suggests that secondary mechanisms are driving toxicity. Transcriptomic analyses of NFT‐containing neurons microdissected from postmortem AD brain revealed an expression profile consistent with cellular senescence. This complex stress response induces aberrant cell cycle activity, adaptations to maintain survival, cellular remodeling, and metabolic dysfunction. Using four AD transgenic mouse models, we found that NFTs, but not Aβ plaques, display a senescence‐like phenotype. Cdkn2a transcript level, a hallmark measure of senescence, directly correlated with brain atrophy and NFT burden in mice. This relationship extended to postmortem brain tissue from humans with PSP to indicate a phenomenon common to tau toxicity. Tau transgenic mice with late‐stage pathology were treated with senolytics to remove senescent cells. Despite the advanced age and disease progression, MRI brain imaging and histopathological analyses indicated a reduction in total NFT density, neuron loss, and ventricular enlargement. Collectively, these findings indicate a strong association between the presence of NFTs and cellular senescence in the brain, which contributes to neurodegeneration. Given the prevalence of tau protein deposition among neurodegenerative diseases, these findings have broad implications for understanding, and potentially treating, dozens of brain diseases.
A comparison of the risk of postoperative recurrence between African‐American and Caucasian patients with Crohn's disease
Authors: Anyane‐Yeboa Adjoa , Yamada Akihiro , Haider Haider , Wang Yunwei , Komaki Yuga , Komaki Fukiko , Pekow Joel , Dalal Sushila , Cohen Russell D. , Cannon Lisa , Umanskiy Konstantin , Smith Radhika , Hurst Roger , Hyman Neil , Rubin David T. , Sakuraba Atsushi
Published: August 2018

Background

Many patients with Crohn's disease will develop complications that require surgery. Recurrence after surgery is common.

Aim

To assess racial differences in postoperative recurrence between African‐Americans and Caucasians.

Methods

Medical records of Crohn's disease patients who underwent surgery (ileal, colonic, or ileocolonic resection) between June 2014 and June 2016 were reviewed. The primary endpoints were clinical and endoscopic remission at 6‐12 months after a Crohn's disease surgery. Secondary outcomes included biological and histologic remission. Risks of recurrence were assessed by univariate, multivariate, and propensity score‐matched analysis.

Results

Thirty‐six African‐American and 167 Caucasian patients with Crohn's disease were included for analysis. There was no difference in disease location, disease behaviour, type of surgery performed, and pre‐ or postoperative medication use between the two groups. The rate of endoscopic remission did not differ between African‐American and Caucasian patients (50% vs 42%, P = 0.76), and race did not influence the risk of endoscopic recurrence on univariate, multivariate, or propensity score‐matched analysis. The rate of clinical remission was significantly lower in African‐American patients compared to Caucasian patients (36% vs. 63%, P = 0.008). African‐American race was significantly associated with clinical recurrence on univariate (odds ratio (OR) 6.76, 95% CI 1.50‐30.40; P = 0.01), multivariate (OR 5.02, 95% CI 1.60‐15.80; P = 0.006), and propensity‐matched analysis (68% vs. 32% in Caucasians, P = 0.005). Rates of biologic and histologic remission were similar between the two groups on all analyses.

Conclusions

We found that African‐American patients with Crohn's disease have a similar degree of objective measures of mucosal inflammation after surgery including endoscopic recurrence as compared to Caucasian patients. However, African‐American race was significantly associated with clinical recurrence, suggesting the presence of ethnic variation in postoperative presentation in Crohn's disease.
Proteomic analysis of the hypothalamus of broiler‐type Taiwan country chickens in response to acute heat stress
Authors: Tu Wei‐Lin , Cheng Chuen‐Yu , Chen Chao‐Jung , Chan Hong‐Lin , Wang Shih‐Han , Tang Pin‐Chi , Chen Chih‐Feng , Chen Hsin‐Hsin , Lee Yen‐Pai , Chen Shuen‐Ei , Huang San‐Yuan
Published: August 2018

The hypothalamus is a critical center for regulating heat retention or dissipation. This study investigated global protein changes in the hypothalamus of broiler‐type Taiwan country chickens (TCCs) after acute heat stress. Twelve TCC hens aged 30 weeks were allocated to groups subjected to acute heat stress at 38°C for 2 hr without recovery, with 2 hr of recovery, and with 6 hr of recovery; a control group was maintained at 25°C. Hypothalami were collected for protein expression analysis at the end of each time point. The results showed 114 protein spots differentially expressed after acute heat stress. Most of the differentially expressed proteins were involved in cellular processes, metabolism, transport, and cellular component organization. Functional annotation analysis suggested that these proteins were related to cellular defensive responses against heat and oxidative stress, detoxification and toxin export/delivery, cytoskeleton integrity, oxygen transport, and neural development. The results of this study suggest that acute heat stress damages the hypothalamus of broiler‐type TCCs through oxidative stress and provokes a series of responses to stabilize protein structures, degrade misfolded proteins, and remodel cytoskeletons for attenuating the detrimental effects by acute heat stress.
Postpartum oestrous cycling resumption of yak cows following different calf weaning strategies under range conditions
Authors: Liu Peipei , Dong Quanmin , Liu Shujie , Degen Allan , Zhang Jiaojiao , Qiu Qiang , Jing Xiaoping , Shang Zhanhuan , Zheng Wenming , Ding Luming
Published: August 2018

Early weaning can improve body condition and reproductive performance of cows. The objectives of this study were to examine and compare oestrous cycling resumption, behaviour and blood parameters of yak cows following four different strategies of calf weaning. Twenty‐six yak cows (4–8 years) and their calves (94.3 ± 2.4 days) were studied in which calves were: weaned naturally with free access to their mothers (NW;n = 13); weaned abruptly and separated permanently from their mothers (PW;n = 5); separated temporarily from their mothers for 15 days (TW;n = 5); and fitted with nose plates for 15 days, but allowed free access to their mothers (NP;n = 3). Yak cows with sucking calves (NW) spent more time grazing in the cold season (from d 39 to 84). Based on serum progesterone concentrations, none of nineNWyak cows resumed oestrous cycling during the study, while seven of nine yak cows with weaned calves resumed cycling (3/3 forPW; 2/3 forTW; and 2/3 forNPyaks). We concluded that early weaning improved postpartum reproductive performance of yak cows on the Qinghai‐Tibetan plateau and that abrupt and permanent weaning was an appropriate strategy.
Bayesian Negative Binomial Mixture Regression Models for the Analysis of Sequence Count and Methylation Data
Authors: Li Qiwei , Cassese Alberto , Guindani Michele , Vannucci Marina
Published: August 2018

In this article, we develop a Bayesian hierarchical mixture regression model for studying the association between a multivariate response, measured as counts on a set of features, and a set of covariates. We have available RNA-Seq and DNA methylation data measured on breast cancer patients at different stages of the disease. We account for the heterogeneity and over-dispersion of count data (here, RNA-Seq data) by considering a mixture of negative binomial distributions and incorporate the covariates (here, methylation data) into the model via a linear modeling construction on the mean components. Our modeling construction includes several innovative characteristics. First, it employs selection techniques that allow the identification of a small subset of features that best discriminate the samples while simultaneously selecting a set of covariates associated to each feature. Second, it incorporates known dependencies into the feature selection process via the use of Markov random field (MRF) priors. On simulated data, we show how incorporating existing information via the prior model can improve the accuracy of feature selection. In the analysis of RNA-Seq and DNA methylation data on breast cancer, we incorporate knowledge on relationships among genes via a gene-gene network, which we extract from the KEGG database. Our data analysis identifies genes which are discriminatory of cancer stages and simultaneously selects significant associations between those genes and DNA methylation sites. A biological interpretation of our findings reveals several biomarkers that can help understanding the effect of DNA methylation on gene expression transcription across cancer stages.
COLLABORATE OR CONSOLIDATE: ASSESSING THE COMPETITIVE EFFECTS OF PRODUCTION JOINT VENTURES
Authors: Aguelakakis Nicolas , Yankelevich Aleksandr
Published: August 2018

We analyze collaborations in which two firms facing external competition reorganize to form an input joint venture as an alternative to horizontal merger. Under standard regularity conditions, the collaboration can lead to higher profits than a horizontal merger, though the effect on prices, quantities, and welfare depends on the form of downstream competition. In light of our results regarding profits, we provide reasons why firms might still wish to merge: imperfect information, cost synergies, and organizational asymmetries. We further consider how our comparisons change with the managerial structure of the joint venture (i.e., by delegation of input pricing). (JEL L13, L23, L42)
Does government R&D stimulate or crowd out firm R&D spending? Evidence from Chinese manufacturing industries
Authors: Hu Albert G.Z. , Yongxu Deng
Published: August 2018

We examine whether receiving a government R&D grant stimulates or crowds out a firm’s own R&D spending in Chinese manufacturing industries. Using a database that spans the population of large and medium size privately owned Chinese manufacturing firms for the period from 2007 to 2011, a matching estimator and a matching and difference in‐differences estimator, we find a large firm R&D promoting effect of government R&D: receiving a government R&D grant led to a 4 to 9‐million‐yuan increase in a firm’s own R&D expenditures. This is a significant effect since the average R&D expenditures ranged from 5 to 9 million yuan in the year before receiving the grant. To understand the mechanisms behind this effect, we compare the before‐ and after‐treatment performance and behaviour of the treated and the control firms. We find that the government R&D receiving firms became more profitable following their receipt of the grant. We also find that receiving a government R&D grant increases the likelihood of a firm continuing its R&D performance after receiving the initial grant.
The need to educate future dental professionals on E‐cigarette effects
Authors: Martín Carreras‐Presas C. , Naeim M. , Hsiou D. , Somacarrera Pérez M. L. , Messadi D. V.
Published: August 2018

Objective

To compare knowledge and attitude of dental students in two countries towards E‐cigarettes and their long‐term effects.

Material and Methods

An anonymous cross‐sectional survey, using self‐administered questionnaires, was conducted amongst dental students from the University of California, Los Angeles School of Dentistry (UCLA) and Universidad Europea of Madrid (UE).

Results

There were significant differences in knowledge and perception of E‐cigarettes between dental students from both countries. Three (3%) of the participants from UE sample smoked E‐cigarettes every day, compared to none of the students from UCLA. Almost 54 (80%) students from UCLA claimed that they had never experimented with an E‐cigarette, whereas 61 (65%) of UE sample reported not having experimented with E‐cigarettes in the past. More than 15% of students in both populations were unsure of the potentially harmful effects of E‐cigarette usage. A significantly higher proportion of the Spanish sample used conventional cigarettes compared to the US sample 53 (56%) compared to 36 (24%), P < 0.001). In addition, when compared to the UE sample, UCLA students rated E‐cigarettes as being less harmful overall than tobacco P < 0.001. Furthermore, more than 86% of both populations indicated interest in learning more about the potential risks associated with E‐cigarettes.

Conclusions

This survey indicated that students from one dental school in the United States of America (USA) and one in Spain lacked the knowledge to address the rising E‐cigarette population usage and provide information regarding them to patients. Specific educational programmes on E‐cigarette hazards and long‐term effects on oral and systemic health should be implemented in dental curricula in both of these schools in order to stay receptive to the changing field of tobacco education.
Mature students’ access to higher education: A critical analysis of the impact of the 23+ policy in Portugal
Authors: Amorim José Pedro
Published: August 2018

Increasing mature students’ access to higher education (HE) is a worldwide priority. In Portugal, the 23+ policy which was launched ten years ago opened HE to these students. A critical analysis of eight years’ data on the universe of mature candidates in HE in Portugal shows that this “opening” varies in inverse ratio to the social prestige of institutions and subject areas. The private polytechnics and the soft sciences display a greater receptiveness than the public universities and the hard sciences. This article demonstrates that mature students save the HEIs that are less sought‐after by “traditional” students and argues for fairer access to the most prestigious HEIs and programmes.
Bioinformatics for immunologists
Authors: Altmann Daniel M.
Published: August 2018

Immunology was once a specialty prone to cause dismay or even scepticism among outsiders for its struggles to visualize poorly understood, complex interactions through descriptive models integrating cell types, their factors and functions. This was the age of ‘too many soft ideas propped up by too little hard data’. Twenty‐first century immunologists have the advantage of being able to marry this rich conceptual legacy to a contemporary toolkit offering such depth of hard data across different ‘omics’ platforms, that they are faced by the opposite dilemma: ‘too much hard data to comprehend or synthesize into a meaningful narrative’. Approaches including next‐generation sequencing of host and pathogen genomes and transcriptomes, metagenomics of the microbiota, creative strategies for receptor repertoire sequencing, and then for proteomics and metabolomics, encompass all that is needed to tell the entire story, if only we are creative enough, not only to evaluate the message from any given omics platform, but to derive the tools that enable us to integrate the answers from diverse omics platforms in a meaningful way. To achieve this goal, there is an urgent need to ensure we train the next generation of bioinformatically literate researchers.
First report on a pupping area of the tope shark Galeorhinus galeus (Carcharhiniformes, Triakidae) in the south‐west Atlantic
Authors: Bovcon Nelson D. , Cochia Pablo D. , Navoa Ximena , Ledesma Pablo , Caille Guillermo M. , Baigun Claudio R. M.
Published: August 2018

Neonates of the tope shark Galeorhinus galeus are captured in sport and recreational coastal fisheries from January to April each year in Engaño Bay (42° 58′–43° 41′ S), Chubut, Argentina. The presence of these neonates is the first evidence of a pupping area for this shark in the south‐west Atlantic Ocean. Knowledge of the pupping areas of chondrichthyans is important for establishing conservation measures and appropriate fishing regulations.
Multiple factors contribute to bimodal toxin gene expression in Clostridioides (Clostridium) difficile
Authors: Ransom Eric M. , Kaus Gabriela M. , Tran Phuong M. , Ellermeier Craig D. , Weiss David S.
Published: August 2018

Clostridioides (formerly Clostridium) difficile produces two major toxins, TcdA and TcdB, upon entry into stationary phase. Transcription of tcdA and tcdB requires the specialized sigma factor, σTcdR, which also directs RNA Polymerase to transcribe tcdR itself. We fused a gene for a red fluorescent protein to the tcdA promoter to study toxin gene expression at the level of individual C. difficile cells. Surprisingly, only a subset of cells became red fluorescent upon entry into stationary phase. Breaking the positive feedback loop that controls σTcdR production by engineering cells to express tcdR from a tetracycline‐inducible promoter resulted in uniform fluorescence across the population. Experiments with two regulators of tcdR expression, σD and CodY, revealed neither is required for bimodal toxin gene expression. However, σD biased cells toward the Toxin‐ON state, while CodY biased cells toward the Toxin‐OFF state. Finally, toxin gene expression was observed in sporulating cells. We conclude that (i) toxin production is regulated by a bistable switch governed by σTcdR, which only accumulates to high enough levels to trigger toxin gene expression in a subset of cells, and (ii) toxin production and sporulation are not mutually exclusive developmental programs.
Biological parameters of the triatomine,Meccus phyllosomus pallidipennis, fed on two bloodmeal sources under laboratory conditions
Authors: Martínez‐Ibarra J. A. , Grant‐Guillén Y. , Nogueda‐Torres B. , Villagrán‐Herrera M. E. , de Diego‐Cabrera J. A. , Bustos‐Saldaña R.
Published: August 2018

Chagas disease is one of the most important vector‐borne diseases in Latin America, including Mexico.Meccus phyllosomus pallidipennis(Stål), 1872 (Hemiptera: Reduviidae) is a Mexican triatomine vector that is commonly associated with hens and rabbits. The biological parameters of two cohorts fed on hens (H) and on rabbits (R) were evaluated. The median lifecycles of the two cohorts were 198 days (H) and 180 days (R). Moreover, mortality was around 30% in both cohorts. Time lapse for beginning of feeding was 0.5–1.9 (H) and 1.1–2.4 min (R). Feeding times of each instar in both cohorts were over 10 min. Most specimens fed on hens defecated immediately after feeding, whereas those that fed on rabbits defecated within 1–5 min post‐feeding. Similar numbers of males and females (50%) were obtained in both cohorts. An average of 2.1–2.3 eggs per female per day was noted in both cohorts, with eclosion rates of 95.4 (H) and 88.8% (R). Thus, it can be concluded thatM. phyllosomus pallidipennismay take advantage of feeding in hens, as in rabbits, which could imply a higher risk ofTrypanosoma cruzitransmission to humans and animals in its distribution area.
Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model
Authors: Puttick Mark N. , O'Reilly Joseph E. , Pisani Davide , Donoghue Philip C. J.
Published: August 2018

To understand patterns and processes of the diversification of life, we require an accurate understanding of taxon interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and maximum likelihood Mk model provide phylogenies of higher accuracy compared to parsimony methods. This has proved controversial, particularly studies simulating morphology‐data under Markov models that assume shared branch lengths for characters, as it is claimed this leads to bias favouring the Bayesian or maximum likelihood Mk model over parsimony models which do not explicitly make this assumption. We avoid these potential issues by employing a simulation protocol in which character states are randomly assigned to tips, but datasets are constrained to an empirically realistic distribution of homoplasy as measured by the consistency index. Datasets were analysed with equal weights and implied weights parsimony, and the maximum likelihood and Bayesian Mk model. We find that consistent (low homoplasy) datasets render method choice largely irrelevant, as all methods perform well with high consistency (low homoplasy) datasets, but the largest discrepancies in accuracy occur with low consistency datasets (high homoplasy). In such cases, the Bayesian Mk model is significantly more accurate than alternative models and implied weights parsimony never significantly outperforms the Bayesian Mk model. When poorly supported branches are collapsed, the Bayesian Mk model recovers trees with higher resolution compared to other methods. As it is not possible to assess homoplasy independently of a tree estimate, the Bayesian Mk model emerges as the most reliable approach for categorical morphological analyses.
Contrast‐enhanced computed tomography may be helpful for characterizing and staging canine gastric tumors
Authors: Tanaka Toshiyuki , Akiyoshi Hideo , Mie Keiichiro , Okamoto Mari , Yoshida Yuuki , Kurokawa Shohei
Published: August 2018

In humans, computed tomography (CT) is a widely performed technique for the diagnosis and staging of gastric tumors. The purpose of this retrospective case series study was to describe CT findings in a group of dogs with confirmed gastric tumors. For each included dog, the following CT parameters were recorded: gastric tumor location, tumor shape, gastric involvement pattern, tumor enhancement pattern in early and late phases, presence and location of lymphadenopathy, gastric tumor attenuation values, attenuation values of enlarged lymph nodes, maximum short‐axis diameter (mm) of enlarged lymph node, maximum long‐axis diameter (mm) of enlarged lymph node, and short‐axis diameter to long‐axis diameter ratio (short axis/long axis). A total of 16 dogs met inclusion criteria and had the following final diagnoses: five lymphoma, six adenocarcinoma, three inflammatory polyps, and two leiomyoma. In the early‐ and delayed‐phase postcontrast images, the mean CT attenuation value for lymphoma was lower than that of other gastric tumors. Lymphadenopathy was widespread in lymphomas and regional in adenocarcinomas. Lymphadenopathy was not detected in leiomyomas. Lymph node measurements in lymphoma were larger than lymph node measurements in adenocarcinoma. Although there were overlapping findings for the different types of gastric tumors, contrast‐enhanced CT provided helpful information for characterizing gastric tumors based on the following criteria: early and late enhancement patterns, the site of origin of the mass lesion, and extent of local invasion and distant metastases. Lymphoma should be considered for canine gastric tumors with low mean attenuation values during early‐ and delayed‐phase postcontrast images, and widespread, bulky, and rounded lymphadenopathy.
Doping Solar Field Heat Transfer Fluid With Nanoparticles
Authors: Abutayeh Mohammad , Addad Yacine , Abu-Nada Eiyad , Alazzam Anas
Published: August 2018

A previously developed model of a concentrating solar power plant has been modified to accommodate doping the heat transfer fluid (HTF) with nanoparticles. The model with its unalloyed HTF has been validated with actual operating data beforehand. The thermo-physical properties of the HTF were modified to account for the nanoparticle doping. The nanoparticle content in the HTF was then varied to evaluate its influence on solar power generation. The model was run to simulate plant operation on four different days representing the four different seasons. As the nanoparticle concentration was increased, heat losses were slightly reduced, transient warm up heat was increased, transient cool down heat was reduced, and the overall impact on power generation was trivial. Doping HTFs with nanoparticles does not seem promising for solar thermal power generation from a performance perspective. Moreover, doping HTFs with nanoparticles involves many other operational challenges such as sedimentation and abrasion.