bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning of representations for transcriptomics-based phenotype prediction
Authors: Smith Aaron M. , Walsh Jonathan R. , Long John , Davis Craig B. , Henstock Peter , Hodge Martin R. , Maciejewski Mateusz , Mu Xinmeng Jasmine , Ra Stephen , Zhao Shanrong , Ziemek Daniel , Fisher Charles K. 
Published: March 2019

AbstractThe ability to predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. This task is complicated because expression data are high dimensional whereas each experiment is usually small (e.g.,∼20,000 genes may be measured for∼100 subjects). However, thousands of transcriptomics experiments with hundreds of thousands of samples are available in public repositories. Can representation learning techniques leverage these public data to improve predictive performance on other tasks? Here, we report a comprehensive analysis using different gene sets, normalization schemes, and machine learning methods on a set of 24 binary and multiclass prediction problems and 26 survival analysis tasks. Methods that combine large numbers of genes outperformed single gene methods, but neither unsupervised nor semi-supervised representation learning techniques yielded consistent improvements in out-of-sample performance across datasets. Our findings suggest that usingl2-regularized regression methods applied to centered log-ratio transformed transcript abundances provide the best predictive analyses.
Integrating natural history-derived phenomics with comparative genomics to study the genetic architecture of convergent evolution
Authors: Lamichhaney Sangeet , Card Daren C. , Grayson Phil , Tonini João F.R. , Bravo Gustavo A. , Näpflin Kathrin , Termignoni-Garcia Flavia , Torres Christopher , Burbrink Frank , Clarke Julia A. , Sackton Timothy B. , Edwards Scott V. 
Published: March 2019

AbstractEvolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part due to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.
WinnerTakeAlmostAll: A parsimony approach integrating multi-targets improves marker gene profiling
Authors: Song Zewei , Sun Xiaohuan , Xia Zhongkui , Jia Yangyang , Jie Zhu , Fang Chao , Yang Huanming , Wang Jian 
Published: March 2019

AbstractAmplicon sequencing need to go from using single region to multiple region, one for higher resolution, one for technical replicates. WinnerTakeAlmostAll is an algorithm to calculate a minimum set of references based on the reference-query graph. We showed that this algorithm is superior in resolving species, as well as average out the run effect using technical replicates.
The ubiquitin-conjugating enzyme Ubc13-Mms2 cooperates with a family of FYVE-type-RING ubiquitin protein ligases in K63-polyubiquitylation at internal membranes
Authors: Renz Christian , Tröster Vera , Albert Thomas K. , Santt Olivier , Jacobs Susan C. , Khmelinskii Anton , Ulrich Helle D. 
Published: March 2019

AbstractThe heterodimeric ubiquitin-conjugating enzyme (E2), Ubc13-Mms2, catalyses K63-specific polyubiquitylation in genome maintenance and inflammatory signalling. In budding yeast, the only ubiquitin protein ligase (E3) known to cooperate with Ubc13-Mms2 so far is a nuclear RING finger protein, Rad5, involved in the replication of damaged DNA. We have now identified a family of membrane-associated FYVE-(type)-RING finger proteins as cognate E3s for Ubc13-Mms2 in several species. We show that budding yeast Pib1, a FYVE-RING finger E3 associated with internal membranes, exhibits exquisite selectivity for Ubc13-Mms2 and cooperates with the E2 in the multivesicular body pathway. Phenotypic analysis indicates that the contribution of Ubc13-Mms2 to membrane trafficking goes beyond its cooperation with Pib1, suggesting an involvement with additional E3s in the endocytic compartment. These results widely implicate Ubc13-Mms2 in the regulation of membrane protein sorting.
A Probabilistic Programming Approach to Protein Structure Superposition
Authors: Sanz Moreta Lys , Al-Sibahi Ahmad Salim , Theobald Douglas , Bullock William , Rommes Basile Nicolas , Manoukian Andreas , Hamelryck Thomas 
Published: March 2019

AbstractOptimal superposition of protein structures is crucial for understanding their structure, function, dynamics and evolution. We investigate the use of probabilistic programming to superimpose protein structures guided by a Bayesian model. Our model THESEUS-PP is based on the THESEUS model, a probabilistic model of protein superposition based on rotation, translation and perturbation of an underlying, latent mean structure. The model was implemented in the deep probabilistic programming language Pyro. Unlike conventional methods that minimize the sum of the squared distances, THESEUS takes into account correlated atom positions and heteroscedasticity (i.e., atom positions can feature different variances). THESEUS performs maximum likelihood estimation using iterative expectation-maximization. In contrast, THESEUS-PP allows automated maximum a-posteriori (MAP) estimation using suitable priors over rotation, translation, variances and latent mean structure. The results indicate that probabilistic programming is a powerful new paradigm for the formulation of Bayesian probabilistic models concerning biomolecular structure. Specifically, we envision the use of the THESEUS-PP model as a suitable error model or likelihood in Bayesian protein structure prediction using deep probabilistic programming.
Impact of Direct Acting Antivirals on Survival in Patients with Chronic Hepatitis C and Hepatocellular Carcinoma
Authors: Kamp William M. , Sellers Cortlandt M. , Stein Stacey M. , Lim Joseph K. , Kim Hyun S. 
Published: March 2019

AbstractBackgroundTo investigate the impact of direct-acting antivirals (DAA) and 12-week sustained viral response (SVR12) in patients with hepatocellular carcinoma (HCC) and chronic hepatitis C virus (HCV) infection.MethodsRetrospective analysis of HCC patients diagnosed from 2005 to 2016 at an urban tertiary-care hospital. Kaplan-Meier curves and multivariable Cox proportional hazards models were used to assess survival.Results969 patients met inclusion criteria. 478 patients received interventional oncology treatment (catheter-based therapies, ablation or combination locoregional therapies), 141 received supportive care (palliative or no treatment), 125 underwent liver transplantation, 112 had tumor resection and 94 received chemotherapy or radiation as their primary treatment. Median overall survival of the cohort was 24.2 months (95% CI: 20.9-27.9). 470 patients had HCV (56%). 123 patients received DAA therapies for HCV (26.2%), 83 of whom achieved SVR12 (68%). HCV-positive and HCV-negative patients had similar survival (20.7 months vs 17.4 months, p=0.22). Patients receiving DAA therapy had an overall survival of 71.8 months (CI: 39.5-not reached) vs 11.6 months (CI: 9.8-14.5) for patients without DAA therapy (p<0.0001). DAA patients who achieved SVR12 had an overall survival of 75.6 months (CI: 49.2-not reached) vs the non-SVR12 group (26.7 months, CI: 13.7-31.1, p<0.0001). Multivariable analysis revealed AJCC, Child-Pugh Score, MELD, tumor size, tumor location and treatment type had independent influence on survival (p<0.05). In HCV-positive patients, AJCC, MELD, tumor location, treatment allocation and DAA were significant (p<0.05). In patients receiving DAA therapy, only MELD and SVR12 were predictive of overall survival (p<0.05).ConclusionsDAA therapy and achieving SVR12 is associated with increased overall survival in HCV patients with HCC.SummaryDirect-acting antiviral use is associated with increased survival in hepatitis C-related hepatocellular carcinoma patients. Patients treated with direct-acting antiviral who achieved hepatitis C cure had additionally increased survival versus those treated with direct-acting antiviral who did not achieve hepatitis C cure. This study supports the use of direct-acting antiviral for hepatitis C treatment in hepatocellular carcinoma patients.
Corporate governance and evolution of trust in entrepreneurial networks
Authors: Wang Shiquan , Shang Guoyin , Zhang Shuang 
Published: March 2019

PurposeConcerning that limited explanation exists examining the function of corporate governance in trust processing within entrepreneurial network development, the purpose of this paper is to explore trust evolution and the role of corporate governance in an entrepreneurial network.Design/methodology/approachThis paper makes an innovative exploration based on the case study of NVC Lighting Holding Limited.FindingsIt proposes that in the initial period of network relationship which is based on entrepreneur’s individual social network and embodies sole social network embeddness, entrepreneurial network relies more on affective trust than contractual trust. When stepping into extending period of network relationship which reflects separate embeddedness of social and market network, however, entrepreneurial network has an equal reliance on both affective trust and contractual trust. With further development, when ushering in the phase of maturity which undergoes superimposing embeddedness of both social and market network, entrepreneur network inclines to rely more heavily on affective trust than contractual trust. During the whole process, it can be found that the reliance of entrepreneurial network on trust has the tendency to transfer from affective trust to contractual trust. Furthermore, decreasing of equity ratio of founders and strengthening of controlling right heterogeneity in the corporate governance have facilitated the transfer process and the entrepreneurs’ authority has restraining effect on the evolution of the process.Originality/valueThrough case study, this paper presents the trust evolution process in different stages of entrepreneurial network. Another important theoretic contribution of this paper is that it reveals the function of corporate governance in trust processing within entrepreneurial network development.
Testing the stationarity and convergence of CO2emissions series in MENA countries
Authors: Magazzino Cosimo 
Published: March 2019

PurposeThis study aims to investigate the stationarity and convergence of CO2emissions series in MENA countries. The stationarity and unit root properties of per capita carbon dioxide (CO2) emissions series are explored by an increasing amount of studies, which use different methodologies. Examining the time series properties of energy and environmental series is crucial for both researchers and the policymakers, given the close link between energy, environment and the real economy. In fact, if energy exhibits the presence of a unit root, this suggests that this series does not revert to its equilibrium level after being hit by a shock.Design/methodology/approachThe contribution of this work is twofold. First, to the author’s knowledge, a very little attention has been paid to the topics of stationarity and convergence of CO2emissions in the case of Middle East and North Africa (MENA) member states, especially in a panel context. Convergence analyses of CO2emissions for MENA countries can improve the knowledge of energy and environmental scenario of the area, giving some ideas for appropriate future policies. Second, this is the first study that jointly analyzed time series and panel data properties of emissions series for these countries.FindingsThe author finds that relative per capita CO2emissions in the 19 MENA countries are a mixture of I(0) and I(1) processes and there is a weak evidence to support the stationarity of CO2emissions. After having verified the presence of cross-sectional dependence in the series, the panel unit root tests in presence of cross-section dependence show strong evidence in favor of non-stationarity. In addition, after performing tests forß-convergence, it is also found that per capita CO2emissions are converging on average in 11 out of 19 sample’s countries, whiles-convergence analysis reveals that the variance of per capita CO2emissions decreased over time, which is an indication of convergence.Originality/valueImportant policy implications emerge from the empirical results. Sustainable environmental and energy policies rely heavily on the CO2series’ properties. In this regard, determining whether shocks to CO2emissions are permanent or transitory is important for setting feasible goals for sustainable environmental policies. Given that per capita CO2emissions are essentially associated with a quality of life, the issues of their reduction have been the leading agenda in energy and environmental management over the past two decades.
The efficacy of gender-based federal procurement policies in the United States
Authors: Orser Barbara , Riding Allan , Weeks Julie 
Published: March 2019

Purpose
Because procurement policies are one of the means of redressing discrimination and economic exclusion, the US Government has targeted 23 per cent of its annual half-trillion dollar spend to small- and medium-sized enterprises (SMEs) and 5 per cent of its spend to women-owned businesses.

Design/methodology/approach
The research framework is informed by two theoretical paradigms, feminist empiricism and entrepreneurial feminism, and uses a secondary analysis of survey data of active federal contractors.

Findings
Empirical findings inform the extent to which certifications are associated with bid frequency and bid success. The results indicate that none of the various certifications increase either bid frequency or bid success. The findings are consistent with entrepreneurial feminism and call for federal accountability in contracting with women-owned supplier firms.

Research limitations/implications
The findings are consistent with entrepreneurial feminism and call for federal accountability in contracting with women-owned supplier firms.

Practical implications
Recommendations include the need to review the impact of consolidated tenders on designated (as certified) SME vendors and to train procurement personnel about the economic contributions of women-owned businesses.

Originality/value
This research studies the efficacy of various certifications, with particular reference to that of women-owned, on the frequency with which SMEs bid on, and succeed in obtaining, US federal procurement contracts.
Self-reflective mentoring: perspectives of peer mentors in an education doctoral program
Authors: McConnell Kat , Geesa Rachel Louise , Lowery Kendra 
Published: March 2019

Purpose
The purpose of this paper is to discover peer mentors’ perspectives of an education doctoral (Doctorate of Education) peer mentoring program implemented in a mid-sized public institution.

Design/methodology/approach
Data from one focus group and an interview collected from peer mentors as part of a larger case study of mentors and mentees in a peer mentoring program for education doctoral students are presented. Four (n=4) peer mentors participated in a focus group (n=3) and an interview (n=1). Participants were asked about their perceptions of the program and their experiences as mentors.

Findings
Four themes were discovered within the data: mentors relate to social, emotional and academic life balances of mentees, mentors provide support and reassurance to mentees, mentors guide mentees to focus on the future, and mentors gain personal and professional growth from the peer mentoring program. Results indicated that mentors believed that the program was helpful for their mentees and beneficial to their own personal and professional development.

Research limitations/implications
Limitations of this study include the small sample size (n=4) and the short period of time in which participants were asked to be a part of the mentoring program and reflect in focus groups and interview (one academic year). Implications of this study include the benefits of peer mentoring for both mentors and mentees alike.

Originality/value
In contrast to many other studies of peer mentoring programs, this peer mentoring program targeted scholar-practitioner students who were balancing full-time careers with their coursework and family lives. Thus, peer mentors focused more on career and work-life balance with mentees than mentors may in other programs, as well as finding benefit to their own professional development.
An extension of the improving and embedding project management practice framework
Authors: Fernandes Gabriela , Araújo Madalena , Pinto Eduardo B. , Machado Ricardo J. 
Published: March 2019

Purpose
The purpose of this paper is to develop and test an extension of a previously conceived framework for improving and embedding project management (PM) practice in organisations. The framework identifies the most useful project management improvement initiatives (PMIIs) and the key factors for embedding PM practice. However, professionals need guidance on how to operationalise such framework in their organisations, therefore a method for applying the framework is developed.

Design/methodology/approach
The method being proposed for applying the framework is demonstrated and tested with a large University–Industry consortium case study. During the case study analysis three research methods were applied: participant observation, document analysis and focus groups.

Findings
In what concerns both the PMIIs and key embedding factors in the framework, the proposed method comprises their acknowledgement, scoring, relevance analysis, selection and planning. The detailed report on how the framework was applied in the particular case study also sheds light on how University–Industry consortiums can make use of PM to become more successful.

Research limitations/implications
The research was performed using only one case study which limits the generalisability of its findings.

Practical implications
Detailed guidance is provided for applying the framework’s both constructs, “improving” and “embedding”, through a set of clear steps.

Originality/value
The paper shows the explanatory power of the framework for improving and embedding PM practice in a case study, demonstrating that the method for its application is practical and suitable.
Mapping of scientific coverage on education for Entrepreneurship in Higher Education
Authors: Durán-Sánchez Amador , Del Río-Rama María de la Cruz , Álvarez-García José , García-Vélez Diego Fernando 
Published: March 2019

PurposeThe purpose of this paper is to present an in-depth analysis of the current state of research related to Education for Entrepreneurship in Higher Education. Education for entrepreneurship is one of the fastest growing fields within academic training worldwide, which is a good indicator of the importance that entrepreneurship and the creation of companies have for the economic development of any society. Education for entrepreneurship is essential, not only to promote an entrepreneurial spirit among young people but also to provide the basic skills, knowledge and innovative attitudes to carry out new business models successfully.Design/methodology/approachA descriptive bibliometric study was carried out with analysis of citations of 164 articles included in the multidisciplinary database Scopus (Elsevier) until 2017.FindingsThe results obtained show a growing interest of the scientific community in its study, as shown by the significant increase both in the number of articles and their citations in recent years.Research limitations/implicationsIn any bibliometric study, the limitation involved when analysing the results, the choice of a specific database and a specific search equation must be taken into account. With respect to the search terms, those used in this research may not be possible, the inclusion of new terms will alter the results. On the other hand, the aim was not to evaluate the quality of the content of the selected articles at any time, an objective that can be considered in a subsequent investigation, but a descriptive-quantitative analysis of the works and citations related to Education for Entrepreneurship in Higher Education, present in Scopus. To expand the present study, it would be interesting to examine the documents indexed in other databases (Redalyc, Scielo, ProQuest, Directory of Open Access Journals[DOAJ]), together with the possibility of including comparative and overlapping studies between them.Originality/valueThe purpose of this work is to serve as a reference for researchers who are developing their studies in the general field of education for entrepreneurship and more specifically in the field of higher education, to improve their knowledge on the most relevant articles, the most productive authors or the key scientific journals that address this topic.