bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression inference with deep learning
Authors: Chen Yifei , Li Yi , Narayan Rajiv , Subramanian Aravind , Xie Xiaohui 
Published: February 2016

Abstract
Motivation: Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes.
Results: We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes.
Availability and implementation: D-GEX is available at https://github.com/uci-cbcl/D-GEX.
Contact: xhx@ics.uci.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data
Authors: Kahles André , Ong Cheng Soon , Zhong Yi , Rätsch Gunnar 
Published: February 2016

Abstract
Motivation: Understanding the occurrence and regulation of alternative splicing (AS) is a key task towards explaining the regulatory processes that shape the complex transcriptomes of higher eukaryotes. With the advent of high-throughput sequencing of RNA (RNA-Seq), the diversity of AS transcripts could be measured at an unprecedented depth. Although the catalog of known AS events has grown ever since, novel transcripts are commonly observed when working with less well annotated organisms, in the context of disease, or within large populations. Whereas an identification of complete transcripts is technically challenging and computationally expensive, focusing on single splicing events as a proxy for transcriptome characteristics is fruitful and sufficient for a wide range of analyses.
Results: We present SplAdder, an alternative splicing toolbox, that takes RNA-Seq alignments and an annotation file as input to (i) augment the annotation based on RNA-Seq evidence, (ii) identify alternative splicing events present in the augmented annotation graph, (iii) quantify and confirm these events based on the RNA-Seq data and (iv) test for significant quantitative differences between samples. Thereby, our main focus lies on performance, accuracy and usability.
Availability: Source code and documentation are available for download at http://github.com/ratschlab/spladder. Example data, introductory information and a small tutorial are accessible via http://bioweb.me/spladder.
Contacts: andre.kahles@ratschlab.org or gunnar.ratsch@ratschlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
The Effects of Youth Employment: Evidence from New York City Lotteries
*
Authors: Gelber Alexander , Isen Adam , Kessler Judd B. 
Published: February 2016

Abstract
Programs to encourage labor market activity among youth, including public employment programs and wage subsidies like the Work Opportunity Tax Credit, can be supported by three broad rationales. They may (i) provide contemporaneous income support to participants; (ii) encourage work experience that improves future employment and/or educational outcomes of participants; and/or (iii) keep participants “out of trouble.” We study randomized lotteries for access to the New York City (NYC) Summer Youth Employment Program (SYEP), the largest summer youth employment program in the United States, by merging SYEP administrative data on 294,100 lottery participants to IRS data on the universe of U.S. tax records; to New York State administrative incarceration data; and to NYC administrative cause of death data. In assessing the three rationales, we find that (i) SYEP participation causes average earnings and the probability of employment to increase in the year of program participation, with modest contemporaneous crowdout of other earnings and employment; (ii) SYEP participation causes a modest decrease in average earnings for three years following the program and has no impact on college enrollment; and (iii) SYEP participation decreases the probability of incarceration and decreases the probability of mortality, which has important and potentially pivotal implications for analyzing the net benefits of the program.
Undertaking individual transdisciplinary PhD research for sustainable development
Authors: van Breda John , Musango Josephine , Brent Alan 
Published: February 2016

Purpose– This paper aims to improve the understanding of individual transdisciplinary PhD research in a developing country context, focusing on three individual PhD case studies in South Africa.Design/methodology/approach– Multiple-case method was used, and three completed transdisciplinary PhD research efforts undertaken at the Stellenbosch University were selected. They were coordinated through the TsamaHub, an inter-faculty platform at the University which organises educational modules for transdisciplinary research. Using actual research experiences and reflections of the three individual PhDs, the paper evaluates their work in terms of ontological, epistemological, methodological and methodical/methods aspects.Findings– The central challenge to individual PhD researchers is engagement with non-academic actors to enable joint problem formulation, analysis and transformation. To overcome this, the paper suggests that developing individual epistemic relationships to build “transdisciplinary epistemic communities” should be considered for inclusion as an intentional aspect of transdisciplinary research design.Research limitations/implications– “Transdisciplinary epistemic communities” is still a concept in its infancy and needs more work before it may be theoretically and practically useful.Practical implications– Continuously guiding the individual transdisciplinary research process in a reflexive, recursive, transparent and equal manner is absolutely critical because transdisciplinary research cannot be done successfully if dominated by overly methods-driven approaches.Originality/value– The discourse around transdisciplinary methodology has major implications for the design of individual PhD research. The paper provides recommendations to enhance the theory and practice of individual transdisciplinary PhD research.
Data networks and sustainability education in African universities
Authors: Bothun Gregory D 
Published: February 2016

Purpose
– The purpose of this paper is to provide a case study report of the development of data networks and initial connectivity in the Sub-Saharan African (SSA) region and how that development evolved into the formation of research and education (R
&
E) networks that enable new collaborations and curriculum potential.

Design/methodology/approach
– This case study is presented through the past 20 year’s operations and field activities of the Network Startup Resource Center (NSRC) at the University of Oregon, who in partnership with the National Science Foundation has worked together to significantly train network engineers in Africa on how to develop regional R
&
E networks that can link together the various research universities in SSA.

Findings
– The author shows how the development of these networks have fostered improved collaboration between African and US scientists, particularly around issues that relate to climate change. This paper contains testimonials from both scientists and on-the-ground key directors in Africa about the value of these improved networks. The expansion of regional R
&
E networks has allowed the Association of African Universities (AAU) to launch sustainable development as one of its new core programs over the period 2013-2017. Within this new core AAU program are four sub-themes: agriculture and food security, water resources management, climate change and energy. All of these themes will benefit directly from these new, network-enabled, data-sharing abilities.

Practical implications
– The current state of network-driven curriculum and curriculum exchange between African universities is assessed and compared that to that in the early days of academic network penetration (1990-2000) in the USA to find similar rates of evolution. Since 2015, SSA has sufficient network access and connectivity to now enable a wide variety of new collaborative research and collaborative academic programs.

Originality/value
– The experience and operational competence of the NSRC at the University of Oregon needs to be detailed and espoused. No other American university has had such an impact on Africa in terms of improving its overall network infrastructure enabling new kinds of collaborative research on real-world problems, such as climate change and resource depletion in Africa.
Cigarette advertising in Cold War Bulgaria
Authors: Neuburger Mary Catherine 
Published: February 2016

Purpose– This paper aims to explore the parameters of Bulgarian cigarette advertising in the Cold War period. It contrasts the evolution of cigarette marketing in Bulgaria and the USA in the context of contrasting communist and capitalist notions of the “good life” versus the “common good”.Design/methodology/approach– The paper is informed by a growing literature on advertising under communism, but also new work on consumption in the Soviet Union and Cold War Eastern Europe. It draws upon archival and printed Bulgarian, and some American, sources, and the memoir of a key player in the Bulgarian tobacco industry.Findings– The paper concludes that marketing of cigarettes in communist Bulgaria gained momentum in the same period that cigarette advertising in the USA was severely curtailed. In Bulgaria, the notion that cigarettes were key to the promised “good life” and “building socialism”, out-weighed any notion of harm to the “common good”.Originality/value– This study casts doubt on the common notion that there was no advertising under communism, by offering an in-depth study of an industry that was allowed to market and develop a quality product to an unusual degree. It undermines assumptions about “command” economy, industry behavior, contributing to a re-thinking of Eastern Bloc consumer culture. In addition, it sheds light on changes in the acceptability of cigarette advertising within the Cold War context, namely, how the process of advertising regulation in the West, and increased marketing in the East, fit into Cold War debates and interactions.
The fashion gap: the Cold War politics of American and Soviet fashion, 1945-1959
Authors: Amerian Stephanie M. 
Published: February 2016

Purpose– The purpose of this paper is to examine the role that fashion played in the Cold War competition between the USA and the Soviet Union during the period from 1945 to 1959.Design/methodology/approach– This paper begins by situating fashion within the larger American efforts of cultural diplomacy. It then examines the American and Soviet approaches to fashion. Finally, it focuses on the fashion show at the 1959 American National Exhibition in Moscow. This paper utilizes primary sources, including archival sources and period newspapers and magazines.Findings– Both American and Soviet leaders tried to use fashion to embody the ideological values of each political and economic system. Both also acknowledged a “fashion gap”, whereby Americans enjoyed clear superiority thanks to a well-developed mass production system of ready-made, stylish clothing, that some termed the American Look. Americans hoped the fashion gap would demonstrate that only capitalism could provide women with an abundance of the necessary – but also desirable – consumer goods that enhanced their feminine beauty. Thus, fashion played an important part in the Cold War cultural struggle, in which American and Soviet women were key participants.Originality/value– Much has been written about the Cold War cultural diplomacy, especially the Moscow exhibition, but fashion is often left out of the analyses. Meanwhile, both the American Look and Soviet efforts to create socialist fashion have been examined, but no work has been done to look at the two together to understand fashion’s larger implications for the Cold War.
Forgotten classics:Advertising in a Free Society, by Ralph Harris and Arthur Seldon (1959)
Authors: Pressey Andrew D 
Published: February 2016

Purpose– The purpose of this paper is to reviewAdvertising in a Free Society– a defence of the advertising industry – by Ralph Harris and Arthur Seldon, and to evaluate its status as a justifiable forgotten classic of the marketing literature.Design/Methodology/Approach–Advertising in a Free Societyis placed in historical context (the Cold War), summarised and reviewed.Findings– During the 1950s, as the UK experienced a period of affluence and growing consumerism, the advertising industry was again subject to the criticisms that had been levelled at it by influential scholars in the late nineteenth and early twentieth centuries. Against this context,Advertising in a Free Societydeserves to be remembered as one of the earliest defences of advertising and remains highly relevant. Harris and Seldon were leading figures in the Institute of Economic Affairs (IEA), joining shortly after its inception, which became an influential group both in the UK and abroad, influencing policy on free markets.Originality/Value– AlthoughAdvertising in a Free Societyattracted few citations (going out of print between its publication in 1959 and 2014 when it was republished by the IEA), and largely forgotten by marketing scholars, it provides a significant source for marketing historians interested in advertising criticism, the growth of the British advertising industry and the role of advertising in democratic societies. A reanalysis of the text situated in its historical context – the height of the Cold War – reveals that the text can be viewed as an artefact of the conflict, deploying the rhetoric of the period in defending the advertising industry and highlighting the positive role that advertising could make in free societies.
Eosinophilic pustular folliculitis: A published work‐based comprehensive analysis of therapeutic responsiveness
Authors: Nomura Takashi , Katoh Mayumi , Yamamoto Yosuke , Miyachi Yoshiki , Kabashima Kenji 
Published: February 2016

AbstractEosinophilic pustular folliculitis (EPF) is a non‐infectious inflammatory dermatosis of unknown etiology that principally affects the hair follicles. There are three variants of EPF: (i) classic EPF; (ii) immunosuppression‐associated EPF, which is subdivided into HIV‐associated (IS/HIV) and non‐HIV‐associated (IS/non‐HIV); and (iii) infancy‐associated EPF. Oral indomethacin is efficacious, especially for classic EPF. No comprehensive information on the efficacies of other medical management regimens is currently available. In this study, we surveyed regimens for EPF that were described in articles published between 1965 and 2013. In total, there were 1171 regimens; 874, 137, 45 and 115 of which were applied to classic, IS/HIV, IS/non‐HIV and infancy‐associated EPF, respectively. Classic EPF was preferentially treated with oral indomethacin with efficacy of 84% whereas topical steroids were preferred for IS/HIV, IS/non‐HIV and infancy‐associated EPF with efficacy of 47%, 73% and 82%, respectively. Other regimens such as oral Sairei‐to (a Chinese–Japanese herbal medicine), diaminodiphenyl sulfone, cyclosporin and topical tacrolimus were effective for indomethacin‐resistant cases. Although the preclusion of direct comparison among cases was one limitation, this study provides a dataset that is applicable to the construction of therapeutic algorithms for EPF.
Angiotensin receptor‐1A knockout leads to hydronephrosis not associated with a loss of pyeloureteric peristalsis in the mouse renal pelvis
Authors: Nguyen Michael J , Hashitani Hikaru , Lang Richard J 
Published: February 2016

SummaryThe action of angiotensin II (AngII) on the Ca2+ signals driving pyeloureteric peristalsis was investigated using both conventional and angiotensin receptor (ATr) ATr1A and ATr2 knockout (−/−) mice. Contractility in the renal pelvis of adult ATr1A−/− and ATr2−/− mice was compared to their respective wildtype (ATr1A+/+ and ATr2+/+) controls of the same genetic background (FVB/N and C57Bl/6 respectively) using video microscopy. The effects of AngII on the Ca2+ signals in typical and atypical smooth muscle cells (TSMCs and ASMCs, respectively) within the pelvic wall of conventional mice were recorded using Fluo‐4 Ca2+ imaging. Compared to ATr1A+/+, ATr2+/+ and ATr2−/− mice, kidneys of the ATr1A−/− mouse were mildly‐to‐severely hydronephrotic, associated with an enlarged calyx, an atrophic papilla and a hypoplastic renal pelvis. Contraction frequencies in the renal pelvis of moderately hydronephrotic ATr1A−/− and unaffected ATr2−/− mice were not significantly different from their ATr1A+/+, ATr2+/+ controls. No contractions were observed in severely‐hydronephrotic ATr1A−/− kidneys. AngII increased the spontaneous contraction frequency of the renal pelvis in ATr1A+/+, ATr2+/+ and ATr2−/− mice, but had little effect on the contractions in the mildly‐hydronephrotic ATr1A−/− renal pelvis. The ATr1 blocker, candesartan prevented the positive chronotropic effects of AngII. AngII increased the frequency and synchronicity of Ca2+ transients in both TSMCs and ASMCs. It was concluded that the hydronephrosis observed in ATr1A−/− mouse kidneys does not arise from a failure in the development of the essential pacemaker and contractile machinery driving pyeloureteric peristalsis.
The unaccountable risks of LIBOR
Authors: Bryan Dick , Rafferty Michael 
Published: February 2016

AbstractOne of the on‐going consequences of recent financial crises seems to be that the conventional ‘anchor’ measures of global finance (such as the US dollar, treasury bonds and AAA rated securities) are no longer playing the anchoring role once believed of them. LIBOR now needs to be added to this list and not just because it has been tarnished by illegal practices, but because it is looking increasingly surpassed by financial market practices. LIBOR was believed to provide a risk‐free rate of interest, but has been revealed to be risk‐laden. Moreover, LIBOR is a measure of the costs of borrowing, whilst market concern is increasingly with measures of interest rate volatility.This paper looks at why, in the context of crisis, financial market focus on interest rates is turning towards other benchmarks, notably the overnight indexed swap (OIS) market, and what this shift might be telling us about the anchoring requirements of global financial markets.
Party competition over decentralisation: The influence of ideology and electoral incentives on issue emphasis
Authors: TOUBEAU SIMON , WAGNER MARKUS 
Published: February 2016

AbstractUnder what conditions is decentralisation a salient issue for state‐wide political parties? It is argued in this article that the extent to which state‐wide parties emphasise decentralisation depends on their strategic considerations: on their overall ideology, on the electoral incentives created by the context in which they compete, and on the interaction between the two. The results of the analysis of party manifestos in 31 countries since 1945 are as follows. First, parties that pay greater attention to cultural matters relative to economic matters tend to talk more about decentralisation. Second, the systemic salience of decentralisation also encourages parties to talk more about decentralisation. Third, the larger the regionally based ethnic groups within a country, the more salience all state‐wide political parties will attach to decentralisation. Finally, only parties that put greater relative emphasis on cultural matters tend to respond to the electoral threat of regionalist parties. The influence of territorial diversity on the salience of decentralisation thus works through two channels and is partly conditioned by political parties’ ideological profile.
Do the media set the parliamentary agenda? A comparative study in seven countries
Authors: VLIEGENTHART RENS , WALGRAVE STEFAAN , BAUMGARTNER FRANK R. , BEVAN SHAUN , BREUNIG CHRISTIAN , BROUARD SYLVAIN , BONAFONT LAURA CHAQUÉS , GROSSMAN EMILIANO , JENNINGS WILL , MORTENSEN PETER B. , PALAU ANNA M. , SCIARINI PASCAL , TRESCH ANKE 
Published: February 2016

AbstractA growing body of work has examined the relationship between media and politics from an agenda‐setting perspective: Is attention for issues initiated by political elites with the media following suit, or is the reverse relation stronger? A long series of single‐country studies has suggested a number of general agenda‐setting patterns but these have never been confirmed in a comparative approach. In a comparative, longitudinal design including comparable media and politics evidence for seven European countries (Belgium, Denmark, France, Netherlands, Spain, Switzerland and the United Kingdom), this study highlights a number of generic patterns. Additionally, it shows how the political system matters. Overall, the media are a stronger inspirer of political action in countries with single‐party governments compared to those with multiple‐party governments for opposition parties. But, government parties are more reactive to media under multiparty governments.
Banks’ Financial Reporting and Financial System Stability
Authors: ACHARYA VIRAL V. , RYAN STEPHEN G. 
Published: February 2016

ABSTRACTThe use of accounting measures and disclosures in banks’ contracts and regulation suggests that the quality of banks’ financial reporting is central to the efficacy of market discipline and nonmarket mechanisms in limiting banks’ development of debt and risk overhangs in economic good times and in mitigating the adverse consequences of those overhangs for the stability of the financial system in downturns. This essay examines how research on banks’ financial reporting, informed by the financial economics literature on banking, can generate insights about how to enhance the stability of the financial system. We begin with a foundational discussion of how aspects of banks’ accounting and disclosures may affect stability. We then evaluate representative papers in the empirical literature on banks’ financial reporting and stability, pointing out the research design issues that empirical accounting researchers need to confront to develop well‐specified tests able to generate reliably interpretable findings. To this end, we provide examples of settings amenable to addressing these issues. We conclude with considerations for accounting standard setters and financial system policy makers.