bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Variable and Joining germline genes and alleles for Rhesus macaque from B-cell receptor repertoires
Authors: Zhang Wei , Li Xinyue , Wang Longlong , Deng Jianxiang , Lin Liya , Tian Lei , Wu Jinghua , Yang Huanming , Wang Jian , Qiu Ping , Fu Tong-Ming , Saksena Nitin K. , Wang I-Ming , Liu Xiao 
Published: January 2018

AbstractThe Rhesus macaque is a valuable preclinical animal model to estimate vaccine effectiveness, and is also important for understanding antibody maturation and B-cell repertoire evolution responding to vaccination; however, incomplete mapping of rhesus immunoglobulin germline genes hinders the research efforts. To address this deficiency, we sequenced B-cell receptor (BCR) repertoires of 75 India Rhesus macaques. Using a bioinformatic method that has been validated with BCR repertoire analysis of three human donors, we were able to infer rhesus Variable (V) and Joint(J) germline alleles, identifying a total of 122 V and 20 J germline alleles. Importantly, 91 V and 13 J alleles were novel, and 40 V and 13 J genes were found at a novel genome region that has not been previously recorded. The novelty of these newly identified alleles was supported by two observations. Firstly, 50 V and 5 J novel alleles were observed in whole genome sequencing data of 10 Rhesus macaques. Secondly, using alignment reference including the novel alleles, the mutation rate of rearranged repertoires was significant declined in 9 other irrelevant samples, and all our identified novel V and J alleles were 100% identity mapped by rearranged repertoire data. These newly identified novel alleles, along with previous reported alleles, provide an important reference for future investigations of rhesus immune repertoire evolution, in response to vaccination or infection. In addition, the method outlined in our study offered an example to future efforts in identifying novel immunoglobulin alleles.
The primacy model and the structure of olfactory space
Authors: Giaffar Hamza , Shuvaev Sergey , Rinberg Dmitry , Koulakov Alexei A. 
Published: January 2018

SUMMARYUnderstanding sensory processing relies on establishing a consistent relationship between the stimulus space, its neural representation, and perceptual quality. In olfaction, the difficulty in establishing these links lies partly in the complexity of the underlying odor input space and perceptual responses. Based on the recently proposed primacy code for concentration invariant odor identity representation and a few assumptions, we have developed a theoretical framework for mapping the odor input space to the response properties of olfactory receptors. We analyze a geometrical structure containing odor representations in a multidimensional space of receptor affinities and describe its low-dimensional implementation, the primacy hull. We propose the implications of the primacy hull for the structure of feedforward connectivity in early olfactory networks. We test the predictions of our theory by comparing the existing receptor-ligand affinity and connectivity data obtained in the fruit fly olfactory system. We find that the Kenyon cells of the insect mushroom body integrate inputs from the high-affinity (primacy) sets of olfactory receptors in agreement with the primacy theory.
Investigating the shared genetics of non-syndromic cleft lip/palate and facial morphology
Authors: Howe Laurence J , Lee Myoung Keun , Sharp Gemma C , Smith George Davey , Pourcain Beate St , Shaffer John R , Marazita Mary L , Feingold Eleanor , Zhurov Alexei , Stergiakouli Evie , Sandy Jonathan , Richmond Stephen , Weinberg Seth M , Hemani Gibran , Lewis Sarah J 
Published: January 2018

AbstractThere is increasing evidence that genetic risk variants for non-syndromic cleft lip/palate (nsCL/P) are also associated with normal-range variation in facial morphology. However, previous analyses are mostly limited to candidate SNPs and findings have not been consistently replicated. Here, we used polygenic risk scores (PRS) to test for genetic overlap between nsCL/P and seven biologically relevant facial phenotypes. Where evidence was found of genetic overlap, we used bidirectional Mendelian randomization (MR) to test the hypothesis that genetic liability to nsCL/P is causally related to implicated facial phenotypes. Across 5,804 individuals of European ancestry from two studies, we found strong evidence, using PRS, of genetic overlap between nsCL/P and philtrum width; a 1 S.D. increase in nsCL/P PRS was associated with a 0.10 mm decrease in philtrum width (95% C.I. 0.054, 0.146; P = 0.00002). Follow-up MR analyses supported a causal relationship; genetic variants for nsCL/P homogeneously cause decreased philtrum width. In addition to the primary analysis, we also identified two novel risk loci for philtrum width at 5q22.2 and 7p15.2 in our Genome-wide Association Study (GWAS) of 6,136 individuals. Our results support a liability threshold model of inheritance for nsCL/P, related to abnormalities in development of the philtrum.
Assessment of an organ-specific de novo transcriptome of the nematode trap-crop, Solanum sisymbriifolium
Authors: Wixom Alexander Q , Casavant N Carol , Kuhl Joseph C , Xiao Fangming , Dandurand Louise-Marie , Caplan Allan B 
Published: January 2018

AbstractSolanum sisymbriifolium, also known as “Litchi Tomato” or “Sticky Nightshade,” is an undomesticated and poorly researched plant related to potato and tomato. Unlike the latter species, S. sisymbriifolium induces eggs of the cyst nematode, Globodera pallida, to hatch and migrate into its roots, but then arrests further nematode maturation. In order to provide researchers with a partial blueprint of its genetic make-up so that the mechanism of this response might be identified, we used single molecule real time (SMRT) sequencing to compile a high quality de novo transcriptome of 41,189 unigenes drawn from individually sequenced bud, root, stem, and leaf RNA populations. Functional annotation and BUSCO analysis showed that this transcriptome was surprisingly complete, even though it represented genes expressed at a single time point. By sequencing the 4 organ libraries separately, we found we could get a reliable snapshot of transcript distributions in each organ. A divergent site analysis of the merged transcriptome indicated that this species might have undergone a recent genome duplication and re-diploidization. Further analysis indicated that the plant then retained a disproportionate number of genes associated with photosynthesis and amino acid metabolism in comparison to genes with characteristics of R-proteins or involved in secondary metabolism. The former processes may have given S. sisymbriifolium a bigger competitive advantage than the latter did.
An infodemiology study on breast cancer in Iran
Authors: SeyyedHosseini Shohreh , Asemi Asefeh , Shabani Ahmad , CheshmehSohrabi Mozafar 
Published: January 2018

Purpose
According to the studies conducted in Iran, the breast cancer is the most frequent type of cancer among women. This study aimed to explore the state of health information supply and demand on breast cancer among Iranian medical researchers and Iranian Web users from 2011 to 2015.

Design/methodology/approach
A mixed method research is conducted in this study. In qualitative part, a focus group interview is applied to the users to identify their selected keywords searched for breast cancer in Google. The collected data are analyzed using Open Code software. In quantitative part, data are synthesized using the R software in two parts. First, users’ internet information-seeking behavior (ISB) is analyzed using the Google Trends outputs from 2011 to 2015. Second, the scientific publication behavior of Iranian breast cancer specialists are surveyed using PubMed during the period of the study.

Findings
The results show that the search volume index of preferred keywords on breast cancer has increased from 4,119 in 2011 to 4,772 in 2015. Also, the findings reveal that Iranian scholars had 873 scientific papers on breast cancer in PubMed from 2011 to 2015. There was a significant and positive relationship between Iranian ISB in the Google Trends and SPB of Iranian scholars on breast cancer in PubMed.

Research limitations/implications
This study investigates only the state of health information supply and demand in PubMed and Google Trends and not additional databases often used for medical studies and treatment.

Originality/value
This study provides a road map for health policymakers in Iran to direct the breast cancer studies.
Analysis and optimization of PDF-to-EPUB in the digital publishing process
Authors: Pu Qian , Zhu Xiaomin , Chen Donghua , Zhang Runtong 
Published: January 2018

PurposeThis paper aims to provide an optimization method of workflow for publishing houses and electronic book (e-book) studies in the field of digital publishing.Design/methodology/approachBased on the studies of publishing houses in Beijing, the present conversion workflow is illustrated using a functional modeling methodology. Then, the workflow is analyzed using 5W1H (why, who, what, where, when, how) methodology and optimized using ECRSI (eliminate, combine, rearrange, simplify and increase) principles. To validate the optimization effect, the workflow before and after optimization are generated and implemented by the ExtendSim® simulation software.FindingsThe simulation results show that under similar circumstances, both quantity and quality of the products are improved after optimization, which indicate that the optimization method is effective.Practical implicationsElectronic PUBlication (EPUB) has significant requirements to satisfy the needs of the mobile reading market and to earn increased profits, whereas some e-books are still preserved in a portable document format (PDF). This study results in the enhanced EPUB quality and production efficiency of the PDF-to-EPUB format conversion workflow in publishing houses. Publishing houses around the world can refer to this study to make a similar optimization when handling PDF-to-EPUB.Originality/valueThis research introduces the traditional industrial engineering analytical techniques to the workflow optimization of e-book conversion. Compared with the most of other methods used to optimize workflow, this method is simpler, more efficient and more suitable for e-book format conversion.
A utilitarian re-examination of enterprise-scale information security management
Authors: Stewart Andrew 
Published: January 2018

Purpose
An action is utilitarian when it is both useful and practical. This paper aims to examine a number of traditional information security management practices to ascertain their utility. That analysis is performed according to the particular set of challenges and requirements experienced by very large organizations. Examples of such organizations include multinational corporations, the governments of large nations and global investment banks.

Design/methodology/approach
The author performs a gap analysis of a number of security management practices. The examination is focused on the question of whether these practices are both useful and practical when used within very large organizations.

Findings
The author identifies a number of information security management practices that are considered to be “best practice” in the general case but that are suboptimal at the margin represented by very large organizations. A number of alternative management practices are proposed that compensate for the identified weaknesses.

Originality/value
Quoting from the conclusion of the paper: We have seen in our analysis within this paper that some best practices can experience what economists refer to as diminishing marginal utility. As the target organization drifts from the typical use-case the amount of value-added declines and can potentially enter negative territory. We have also examined the degree of innovation in the practice of security management and the extent to which the literature can support practical, real-world activities. In both the areas, we have identified a number of opportunities to perform further work.
Clinicians’ perception of the preventability of inpatient mortality
Authors: Nash Robert , Srinivasan Ramya , Kenway Bruno , Quinn James 
Published: January 2018

Purpose
The purpose of this paper is to assess whether clinicians have an accurate perception of the preventability of their patients’ mortality. Case note review estimates that approximately 5 percent of inpatient deaths are preventable.

Design/methodology/approach
The design involved in the study is a prospective audit of inpatient mortality in a single NHS hospital trust. The case study includes 979 inpatient mortalities. A number of outcome measures were recorded, including a Likert scale of the preventability of death- and NCEPOD-based grading of care quality.

Findings
Clinicians assessed only 1.4 percent of deaths as likely to be preventable. This is significantly lower than previously published values (p<0.0001). Clinicians were also more likely to rate the quality of care as “good,” and less likely to identify areas of substandard clinical or organizational management.

Research limitations/implications
The implications of objective assessment of the preventability of mortality are essential to drive quality improvement in this area.

Practical implications
There is a wide disparity between independent case note review and clinicians assessing the care of their own patients. This may be due to a “knowledge gap” between reviewers and treating clinicians, or an “objectivity gap” meaning clinicians may not recognize preventability of death of patients under their care.

Social implications
This study gives some insight into deficiencies in clinical governance processes.

Originality/value
No similar study has been performed. This has significant implications for the idea of the preventability of mortality.
Multi-disciplinary decision making in general practice
Authors: Kirby Ann , Murphy Aileen , Bradley Colin 
Published: January 2018

Purpose
Internationally, healthcare systems are moving towards delivering care in an integrated manner which advocates a multi-disciplinary approach to decision making. Such an approach is formally encouraged in the management of Atrial Fibrillation patients through the European Society of Cardiology guidelines. Since the emergence of new oral anticoagulants switching between oral anticoagulants (OACs) has become prevalent. This case study considers the role of multi-disciplinary decision making, given the complex nature of the agents. The purpose of this paper is to explore Irish General Practitioners’ (GPs) experience of switching between all OACs for Arial Fibrillation (AF) patients; prevalence of multi-disciplinary decision making in OAC switching decisions and seeks to determine the GP characteristics that appear to influence the likelihood of multi-disciplinary decision making.

Design/methodology/approach
A probit model is used to determine the factors influencing multi-disciplinary decision making and a multinomial logit is used to examine the factors influencing who is involved in the multi-disciplinary decisions.

Findings
Results reveal that while some multi-disciplinary decision-making is occurring (64 per cent), it is not standard practice despite international guidelines on integrated care. Moreover, there is a lack of patient participation in the decision-making process. Female GPs and GPs who have initiated prescriptions for OACs are more likely to engage in multi-disciplinary decision-making surrounding switching OACs amongst AF patients. GPs with training practices were less likely to engage with cardiac consultants and those in urban areas were more likely to engage with other (non-cardiac) consultants.

Originality/value
For optimal decision making under uncertainty multi-disciplinary decision-making is needed to make a more informed judgement and to improve treatment decisions and reduce the opportunity cost of making the wrong decision.
An examination of ecopreneurs’ incentives through a combination between institutional and resource-based approach
Authors: Nikolaou Ioannis E. , Tsagarakis Konstantinos P. , Tasopoulou Kyriaki 
Published: January 2018

PurposeThe purpose of this paper is to address two research questions: which are the key factors that stimulate entrepreneurs to invest in ecopreneurship, and how ecopreneurhsip contributes to environmental sustainability.Design/methodology/approachTo answer these questions, a framework has been developed to identify the incentives that lead entrepreneurs to invest in firms in the ecopreneurship through institutional and resource-based thinking.FindingsFrom a survey of 91 Greek firms from the green service sector, it is shown that some specific institutional and resource-based view factors play a critical role in green entrepreneurs’ decisions, as well as some certain environmental practices that are frequently used by entrepreneurs to address environmental issues.Research limitations/implicationsFirst, the answer of the second research question through data collected by a questionnaire survey may be faced with skepticism by some authors, as it could be seen that entrepreneurs and managers of firms could have overstated their company's environmental activities. Second, although the sample selection of 91 firms is a representative sample (response rate 12.35 percent) of the total population of Greek green firms (761) and equal to other relative studies, a higher number of firms and a wider variety of green entrepreneurship ventures is necessary in future research.Practical implicationsThe findings are useful for scholars, practitioners and policy makers since it provide information regarding the behavior of green entrepreneurs.Originality/valueThe paper analyze the types of green entrepreneurs in relation to the different features and strategies which are emerged from two theories, such as institutional and resource-based theory.
Does financial development improve environmental quality in Turkey? An application of endogenous structural breaks based cointegration approach
Authors: Dar Javaid Ahmad , Asif Mohammad 
Published: January 2018

PurposeThe purpose of this paper is to investigate the long-run effect of financial sector development, energy use and economic growth on carbon emissions for Turkey, in presence of possible regime shifts over a period of 1960-2013.Design/methodology/approachAlong with the conventional unit root tests, Zivot-Andrews unit root test with structural break has been employed to check the stationarity of variables. The cointegrating relationship between variables is investigated by using the autoregressive distributed lag bounds test and Hatemi-J threshold cointegration test.FindingsThe results confirm a cointegrating relationship between the variables. The long-run relationship between the variables has gone through two endogenous structural breaks in 1976 and 1986. Development of financial sector improves environmental quality whereas energy use and economic growth degrade it. The results challenge the validity of environmental Kuznets curve hypothesis in Turkish economy.Research limitations/implicationsThe study uses domestic credit to private sector as a proxy for development of financial sector. The model can be improved by constructing an index of financial development instead of using a single determinant as a proxy for financial development.Practical implicationsThe study may pave the way for policy makers to capture important environmental pollutants in better way and develop effective and efficient energy and economic policies. This may make significant contribution to curbing CO2emissions while sustaining economic growth.Originality/valueThis is the only study to examine long-run impact of financial sector development on carbon emissions, using the threshold cointegration approach. Hence, the study is a gentle request to reduce the possible omitted variable econometric estimation bias and fill the gap in the existing literature.
Assessing sustainable supply chain enablers using total interpretive structural modeling approach and fuzzy-MICMAC analysis
Authors: Mohanty Mahamaya 
Published: January 2018

PurposeThe purpose of this paper is to model the enablers of an integrated logistics. The integration is accounted for incorporating sustainability, thereby aiming in its theory building. Existing models have focused on enablers of sustainable supply chain independently which lacks a holistic view in understanding the integrated logistics for sustainable supply chain.Design/methodology/approachAn extensive literature review, expert opinion from both industry and academia based on questionnaire survey, is conducted to find the relevant enablers. The modeling of these enablers is done using total interpretive structural modeling (TISM). Finally, TISM along with its respective fuzzy-matriced impact croises multiplication applique (fuzzy-MICMAC) analysis is depicted.FindingsThe result of the survey and TISM model with its respective fuzzy-MICMAC has been used to evolve the mutual relationships among the important enablers of integrated logistics of consumer durables. The strategic factors obtained from TISM are integration and collaboration in the supply chain, vehicle type, and capacity; reduction in average length of haul; and real-time information system. Route selection and scheduling, reduction of fuel consumption, customer relationship management, green technology, cost reduction, etc., are some of the operational factors. Sustainable environment performance is obtained as the performance factor. Fuzzy-MICMAC is more responsive than the traditional MICMAC analysis.Research limitations/implicationsThe study has limitation for the development of a conceptual framework for integrated logistics in uncertain environments. So it can be extended by combining soft computing methodologies. There is a lack of mathematical quantification of the proposed model where the enablers of sustainability can be measured.Practical implicationsThe study on integrated logistics for sustainable supply chain is itself a new area to be explored, as very few studies on this relevant topic exist. The research concentrates on TISM for the integrated logistics and the movement of consumer durables through different distribution channels of a supply chain. The study has implications for practitioners, academicians, and policy makers. For practitioners, it provides a list of strategic factors, operational factors, and performance factors. For academicians, this methodology can be opted to conduct an exploratory study by identifying the essential enablers. For policy makers, the regulations can be developed using the above model.Originality/valueIt is an effort to model the important enablers and establish sustainability in integrated logistics of consumer durables.