bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concordant developmental expression profiles of orthologues in highly divergent Bilateria
Authors: Ferretti Luca , Krämer-Eis Andrea , Schiffer Philipp H. 
Published: October 2019

AbstractBilateria are the predominant clade of animals on earth. Despite having evolved a large variety of body-plans and developmental modes, they are characterized by common morphological traits. However, it is not clear if clade-specific genes can be linked to these traits, distinguishing bilaterians from non-bilaterians, with their less complex body morphology. Comparing proteomes of bilaterian and non-bilaterian species in an elaborate computational pipeline we aimed to find and define a set of of bilaterian-specific genes. Finding no high-confidence set of such genes, we nevertheless detected an evolutionary signal possibly uniting the highly diverse bilaterian taxa. Using a novel multi-species GO-enrichment method, we determined the functional repertoire of genes that are widely conserved among Bilateria. We found that these genes contribute to morphogenesis, neuronal-system and muscle development, processes that have been described as different between bilaterians and non-bilaterians. Analyzing gene expression profiles in three very distantly related bilaterina species, we find characteristic peaks at comparable stages of development and a delayed onset of expression in embryos. In particular, the expression of the conserved genes appears to peak at the phylotypic stage of different bilaterian phyla. In summary, our data underpin the orthologue conjecture and illustrate how development connects distantly related Bilateria after millions of years of divergence, pointing to processes potentially separating them from non-bilaterians.
SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction
Authors: Uddin Mostofa Rafid , Mahbub Sazan , Rahman M Saifur , Bayzid Md Shamsuzzoha 
Published: October 2019

AbstractMotivationProtein structures provide basic insight into how they can interact with other proteins, their functions and biological roles in an organism. Experimental methods (e.g., X-ray crystallography, nuclear magnetic resonance spectroscopy) for predicting the secondary structure (SS) of proteins are very expensive and time consuming. Therefore, developing efficient computational approaches for predicting the secondary structure of protein is of utmost importance. Advances in developing highly accurate SS prediction methods have mostly been focused on 3-class (Q3) structure prediction. However, 8-class (Q8) resolution of secondary structure contains more useful information and is much more challenging than the Q3 prediction.ResultsWe present SAINT, a highly accurate method for Q8 structure prediction, which incorporates self-attention mechanism (a concept from natural language processing) with the Deep Inception-Inside-Inception (Deep3I) network in order to effectively capture both theshort-rangeandlong-range interactionsamong the amino acid residues. SAINT offers a more interpretable framework than the typical black-box deep neural network methods. Through an extensive evaluation study, we report the performance of SAINT in comparison with the existing best methods on a collection of benchmark datasets, namely, TEST2016, TEST2018, CASP12 and CASP13. Our results suggest that self-attention mechanism improves the prediction accuracy and outperforms the existing best alternate methods. SAINT is the first of its kind and offers the best known Q8 accuracy. Thus, we believe SAINT represents a major step towards the accurate and reliable prediction of secondary structures of proteins.AvailabilitySAINT is freely available as an open source project athttps://github.com/SAINTProtein/SAINT.
Natural selection shapes variation in genome-wide recombination rate inDrosophila pseudoobscura
Authors: Samuk Kieran , Manzano-Winkler Brenda , Ritz Kathryn R. , Noor Mohamed A.F. 
Published: October 2019

AbstractWhile recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations ofDrosophila pseudoobscurafrom Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FSTanalysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations (2) interpopulation differences in recombination rate may be the result of local adaptation, and (3) the observed variation among individuals in recombination rate is primarily driven by global regulators of crossover rate, with little detected variation in recombination rate among strains across specific tracts of individual chromosomes.
EphB6 regulates social behavior through gut microbiota-mediated vitamin B6 metabolism and excitation/inhibition balance of medial prefrontal cortex in mice
Authors: Li Ying , Luo Zheng-Yi , Hu Yu-Ying , Bi Yue-Wei , Yang Jian-Ming , Liu Ming-An , Zou Wen-Jun , Li Shi , Shen Tong , Li Shu-Ji , Huang Lang , Zhou Ai-Jun , Song Yun-Long , Gao Tian-Ming , Li Jian-Ming 
Published: October 2019

AbstractAutism spectrum disorder (ASD) is a developmental disorder with no effective pharmacological treatments so far. Gut microbiota has been suggested to contribute to autistic symptoms. However, the key genes and the mechanisms linking gut microbiota and brain dysfunctions in ASD are still unclear. Here, we found deletion of EphB6, an ASD-associated candidate gene, induced dysregulated gut microbiota and autism-like behavior in mice. More importantly, transplanting fecal microbiota from EphB6-deficient mice resulted in disturbed gut microbiota and autism-like behavior in antibiotics-treated C57BL/6J mice. Meanwhile, transplanting fecal microbiota from wild-type mice ameliorated disturbed gut microbiota and autism-like behavior in mice with deletion of EphB6. At the metabolic levels, dysregulated gut microbiota led to vitamin B6 and dopamine defects in EphB6-deficient mice. At the cellular levels, excitation/inhibition (E/I) imbalance in medial prefrontal cortex was induced by gut microbiota-mediated defects of vitamin B6 metabolism in EphB6-deficient mice. Our study uncovers a key role for EphB6 in regulation of social behavior by gut microbiota-mediated vitamin B6 metabolism, dopamine synthesis and E/I balance, suggesting a new strategy for treatment of ASD patients.
Three-dimensional Genome Structure Reveals Distinct Chromatin Signatures of Mouse Female Germline Stem Cells During Development
Authors: Tian Geng G. , Zhao Xinyan , Xie Wenhai , Li Xiaoyong , Hou Changliang , Wang Yinjuan , Wang Lijuan , Zhao Xiaodong , Li Hua , Li Jing , Wu Ji 
Published: October 2019

SUMMARYThe three-dimensional configuration of the genome ensures cell-type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we revealed the distinct features of the chromatin architecture in female germline stem cells (FGSCs) by in situ high-throughput chromosome conformation analysis. We also showed that the X chromosome structures were similar in spermatogonial stem cells and FGSCs. Using integrative analysis of the three-dimensional chromatin structure, we observed that the TADs were attenuated in germinal vesicle oocytes and disappeared in metaphase II oocytes during FGSC development. Finally, we identified conserved compartments belonging to the paternal/maternal genomes during early embryonic development, which were related to imprinted genes. These results will provide a valuable resource for studying and further our understanding of the fundamental characteristics of oogenesis and early embryo development.
ISX-9 manipulates endocrine progenitor fate revealing conserved intestinal lineages in mouse and human
Authors: Tsakmaki Anastasia , Fonseca Pedro Patricia , Pavlidis Polychronis , Hayee Bu’Hussain , Bewick Gavin A 
Published: October 2019

AbstractEnteroendocrine cells (EECs) survey the gut luminal environment and co-ordinate hormonal, immune and neuronal responses to it. They exhibit well characterised physiological roles ranging from the control of local gut function to whole body metabolism, but little is known regarding the regulatory networks controlling their differentiation, especially in human gut.The small molecule Isoxazole-9 (ISX-9) stimulates neuronal and pancreatic beta-cell differentiation, both closely related to EEC differentiation. We used ISX-9 as a tool to explore EEC specification in mouse and human intestinal organoids. ISX-9 increased the number of neurogenin3 (Ngn3) positive endocrine progenitor cells and upregulated NeuroD1 and Pax4, transcription factors which play roles in mouse EEC specification. Single cell analysis revealed induction of Pax4 expression in a developmentally late Ngn3+ population of cells and potentiation of genes associated with progenitors biased towards serotonin-producing enterochromaffin (EC) cells. This coincided with enrichment of organoids with functional EC cells which was partly dependent on stimulation of calcium signalling in a population of cells residing outside the crypt base. Inducible Pax4 overexpression, in ileal organoids, uncovered its importance as a component of early human endocrine specification and highlighted the potential existence of two major endocrine lineages, the early appearing enterochromaffin lineage and the later developing peptidergic lineage which contains classical gut hormone cell types.Our data provide proof-of-concept for the controlled manipulation of specific endocrine lineages with small molecules, whilst also shedding new light on human EEC differentiation and its similarity to mouse. Given their diverse roles, understanding endocrine lineage plasticity and its control could have multiple therapeutic implications.
Natural variation in the contribution of microbial density to inducible immune dynamics
Authors: Jent Derrick , Perry Abby , Critchlow Justin , Tate Ann T. 
Published: October 2019

AbstractImmune responses evolve to balance the benefits of microbial killing against the costs of autoimmunity and energetic resource use. Models that explore the evolution of optimal immune responses generally include a term for constitutive immunity, or the level of immunological investment prior to microbial exposure, and for inducible immunity, or investment in immune function after microbial challenge. However, studies rarely consider the functional form of inducible immune responses with respect to microbial density, despite the theoretical dependence of immune system evolution on microbe-versus immune-mediated damage to the host. In this study, we analyze antimicrobial peptide (AMP) gene expression from seven wild-caught flour beetle populations (Tribolium spp.) during acute infection with the virulent bacteria Bacillus thuringiensis (Bt) and Photorhabdus luminescens (P.lum) to demonstrate that inducible immune responses mediated by the humoral IMD pathway exhibit natural variation in both microbe density-dependent and independent temporal dynamics. Beetle populations that exhibited greater AMP expression sensitivity to Bt density were also more likely to die from infection, while populations that exhibited higher microbe density-independent AMP expression were more likely to survive P. luminescens infection. Reduction in pathway signaling efficiency through RNAi-mediated knockdown of the imd gene reduced the magnitude of both microbe-independent and dependent responses and reduced host resistance to Bt growth, but had no net effect on host survival. This study provides a framework for understanding natural variation in the flexibility of investment in inducible immune responses and should inform theory on the contribution of non-equilibrium host-microbe dynamics to immune system evolution.
Thermal sensitivity of lizard embryos indicates a mismatch between oxygen supply and demand at near-lethal temperatures
Authors: Hall Joshua M. , Warner Daniel A. 
Published: October 2019

ABSTRACTAspects of global change (e.g. urbanization, climate change) result in novel, stressful thermal environments that threaten biodiversity. Though much research quantifies the thermal sensitivity of adult organisms, effects of global change on developing offspring (e.g. embryos) are also important. Oviparous, non-avian reptiles have received considerable attention because eggs are left to develop under prevailing environmental conditions, making them vulnerable to increases in ambient temperature. Though many studies assess embryo thermal tolerance and physiology in response to long-term (i.e. chronic), constant incubation temperatures, fewer assess responses to acute exposures which are more ecologically relevant for many species. We subjected eggs of the brown anole lizard (Anolis sagrei) to heat shocks, thermal ramps, and extreme diurnal fluctuations to determine the lethal temperature of embryos, measure the thermal sensitivity of embryo heart rate and metabolism, and quantify the effects of sub-lethal but stressful temperatures on embryo development and hatchling phenotypes and survival. Most embryos died at heat shocks of 45 or 46 °C, which is ∼12 °C warmer than the highest constant temperatures suitable for development. Heart rate and O2consumption increased with temperature; however, as embryos approached the lethal temperature, heart rate and CO2production continued rising while O2consumption plateaued. These data indicate a mismatch between oxygen supply and demand at high temperatures. Exposure to extreme, diurnal temperature fluctuations depressed embryo developmental rates and heart rates, and resulted in hatchlings with smaller body size, reduced growth rates, and lower survival in the laboratory. Thus, even brief exposure to extreme temperatures can have important effects on embryo development, and our study highlights the role of both immediate and cumulative effects of high temperatures on egg survival. Such effects must be considered to predict how populations will respond to global change.
The evolution of the monitoring board in Japan: how the board performs monitoring function in Japanese corporate governance
Authors: Miyamoto Kohei 
Published: October 2019

Purpose
The purpose of this paper is to trace a legal evolution of the monitoring board and to reveal what brought the evolution and what is expected to emerge. The paper points to unique complementarities in Japanese corporate governance institutions and norms which will affect how the monitoring board performs its functions.

Design/Methodology/Approach
Analysis is based on texts on corporate governance legislations in Japan from the revision of Commercial Code in 1950 to the revision of Companies Act in 2014. Other sources include Tokyo Stock Exchange regulations, White Paper on Corporate Governance and other academic literatures on Japanese corporate governance.

Findings
Changes of non-legal institutions and norms in Japanese corporate governance necessitated legal reforms toward the monitoring board. Persisting institutions and norms, in particular lifetime employment, influences how the monitoring board performs its functions in Japan.

Originality/Value
This paper explains how the evolution of the monitoring board in Japan emerged and what will cause different expected functions of the monitoring board in Japan and other jurisdictions.
An investigation of the digital literacy skills and knowledge-based competencies among librarians working in university libraries in Nigeria
Authors: Okeji Chukwuma Clement , Tralagba Eriye Chris , Obi Ifeyinwa Calista 
Published: October 2019

Purpose The purpose of this paper is to investigate the digital literacy skills possessed by librarians working in university libraries in Nigeria.

Design/methodology/approach An online questionnaire was developed using SurveyMonkey to collect data from 111 librarians working in both public and private universities in Nigeria.

Findings The study revealed the digital literacy skills that the librarians rated as very high and high, and those that they rated as moderate and low. The study also revealed the knowledge and competencies that they rated to be highly competent and competent, as well as also those that they rated to be neutral and not good. The librarians rated their knowledge of network and system security; ability to apply security software firewalls, filtering routers and ability to protect access to digital content by providing password or IP base access as neutral and not good. Overall, the study revealed that almost half of the librarians rated their level of digital literacy skills possessed to be moderate. Only few librarians rated their digital literacy skills to be excellent.

Practical implications The findings will be helpful to librarians, information professionals, libraries and library schools. The results will inform librarians on the skills and digital competencies that are essential for developing and managing digital resources and protecting digital contents.

Originality/value Findings will be helpful to explore the skills and competencies needed by information professionals and to act as a guideline for competency development and curriculum update in library schools in developing countries.
Enhanced authentication and key exchange for end to end security in mobile commerce using wireless public key infrastructure
Authors: Prakasha Krishna , Muniyal Balachandra , Acharya Vasundhara 
Published: October 2019

Purpose
The purpose of the study is to develop a secure, efficient, and enhanced user authentication mechanism to achieve reliable and authenticated connection. In online transactions, users and resources are located at different places, and the sensitive information is to be protected and transferred using the suitable, reliable mechanism.

Design/methodology/approach
One of the latest approach to handle the requirement is by a Public Key Infrastructure (PKI) or its variant Wireless Public Key Infrastructure (WPKI). Fundamental management techniques are required to be very secure and vital since they are one of the points of attack in public key cryptosystem. Entity authentication and key agreement (AKA) is a critical cryptographic problem in wireless communication, where a mutual entity authentication plays a vital role in the establishment of the secure and authentic connection. This paper proposes an efficient and enhanced AKA scheme (EAKA) with the end-to-end security and verifies the proposed system for protection using automated validation of internet security protocols and applications. An efficient way for the implementation of an enhanced version of the protocol is proposed using a lattice-based cryptographic algorithm.

Findings
The time consumed for the proposed research work shows that it is practical and acceptable.

Originality/value
The proposed research work is an efficient and enhanced user authentication mechanism.
Developing strategies for patient safety implementation: a national study in Iran
Authors: Maher Ali , Ayoubian Ali , Rafiei Sima , Sheibani Tehrani Donya , Mostofian Farnaz , Mazyar Pooneh 
Published: October 2019

Purpose
Today, healthcare organizations focus mainly on development and implementation of patient safety strategic plan to improve quality and ensure safety of provided services. The purpose of this paper is to recommend potential strategies for successful implementation of patient safety program in Iranian hospitals based on a strengths, weaknesses, opportunities, threats (SWOT) analysis.

Design/methodology/approach
In this qualitative study, key informant interviews and documentation review were done to identify strength and weakness points of Iranian hospitals in addition to opportunities and threats facing them in successful implementation of a patient safety program. Accordingly, the research team formulated main patient safety strategies and consequently prioritized them based on Quantitative Strategic Planning Matrix (QSPM) matrix.

Findings
The study recommended some of the potential patient safety strategies including provision of education for employees, promoting a safety culture in hospitals, managerial support and accountability, creating a safe and high-quality delivery environment, developing national legislations for hospital staff to comply with patient safety standards and developing a continuous monitoring system for quality improvement and patient safety activities to ensure the achievement of predetermined goals.

Practical implications
Developing a comprehensive and integrated strategic plan for patient safety based on accurate information about the health system’s weaknesses, strengths, opportunities and threats and trying to implement the plan in accordance with patient safety principles can help hospitals achieve great success.

Originality/value
Ministry of Health and Medical Education (MOHME) conducted a national study to recommend potential strategies for successful implementation of patient safety in Iranian hospitals based on a SWOT analysis and QSPM matrix.
Harmonizing and constructing an integrated maqāṣid al-Sharīʿah index for measuring the performance of Islamic banks
Authors: Hudaefi Fahmi Ali , Noordin Kamaruzaman 
Published: October 2019

Purpose
This paper aims to develop a performance measure for Islamic banks (IBs) by harmonizing related studies. Furthermore, this work uses the developed yardstick to analyze the performance of a sample of 11 IBs from across different countries.

Design/methodology/approach
This paper uses the mix-mode method. The qualitative approach is engaged first to construct the IBs performance yardstick. Following this, the quantitative approach is applied through the use of the performance yardstick to measure the sample’s performance.

Findings
This study develops a maqāṣid-based performance yardstick adapted from previous works. The developed model in this study is called an integrated maqāṣid al-Sharīʿah--based performance measure (IMSPM). By using this performance measure, the present paper finds that the sample performed highest on the objective of nafs (self) over the three-year period. In addition, this study identifies the information which best indicates the sample’s performance during the analysis.

Research limitations/implications
This paper uses the sample’s annual reports. The analysis is thus limited to informational disclosure.

Practical implications
Islamic banking and financial institutions may use the IMSPM to communicate a measurable report on their promotion of the maqāṣid al-Sharīʿah (objectives of Islamic law).

Social implications
The evidence from 11 IBs is indicative of their efforts to realize maqāṣid al-Sharīʿah in the banking industry. This point may best challenge the practice of stigmatizing IBs for not being in line with the Sharīʿah (Islamic law) or of imitating conventional banks.

Originality/value
The novelty of this study lies in two points. First, this study harmonizes previous works to integrate financial and religious measures in a single yardstick. Second, by using the developed standard, this study offers a fresh insight into the global IBs’ performance, represented by 11 IBs worldwide.