bluuebunny/crossref_metadata_2025_split huggingface dataset:
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins
Authors: Makrodimitris Stavros , Reinders Marcel , van Ham Roeland 
Published: November 2019

AbstractPhysical interaction between two proteins is strong evidence that the proteins are involved in the same biological process, making Protein-Protein Interaction (PPI) networks a valuable data resource for predicting the cellular functions of proteins. However, PPI networks are largely incomplete for non-model species. Here, we tested to what extened these incomplete networks are still useful for genome-wide function prediction. We used two network-based classifiers to predict Biological Process Gene Ontology terms from protein interaction data in four species: Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana and Solanum lycopersicum (tomato). The classifiers had reasonable performance in the well-studied yeast, but performed poorly in the other species. We showed that this poor performance can be considerably improved by adding edges predicted from various data sources, such as text mining, and that associations from the STRING database are more useful than interactions predicted by a neural network from sequence-based features.
The diet and feeding behaviour of the black-and-white colobus (Colobus guereza) in the Kalinzu Forest, Uganda
Authors: Matsuda Ikki , Ihobe Hiroshi , Tashiro Yasuko , Yumoto Takakazu , Baranga Deborah , Hashimoto Chie 
Published: November 2019

AbstractOne of the goals for primate feeding ecology is to understand the factors that affect inter- and intra-specific variations. Therefore, a detailed description of basic feeding ecology in as many populations and sites as possible is necessary and warrants further understanding. The black-and-white colobus (Colobus guereza) or guereza is widely distributed in Africa and is one of the well-studied colobines in terms of their feeding; they demonstrate considerable variation in their diets in response to local conditions. We studied the diet of a group of guerezas in the Kalinzu Forest, Uganda, for over 30 consecutive months using behavioural observation (4,308 h total), phenology, and vegetation surveys. A total of 31 plant species were consumed by the study group. This study group was predominantly folivorous; the majority of their feeding time was involved in feeding on young leaves (87%). However, during certain times of the year, fruits and seeds accounted for 45% of monthly feeding time. Young leaves of Celtis durandii were by far the most important food, which constituted 58% of the total feeding records. There was a significant increase in the consumption of fruits and flowers once young leaf availability was low, but their consumption of fruits did not significantly increase even when fruit availability was high. Their monthly dietary diversity increased as the number of available plants with young leaves declined, suggesting that much of the dietary diversity in the study group may be attributable to the young leaf portion of their diet. Our findings may help contribute to a better understanding of the dietary adaptations and feeding ecology of guerezas in response to local environmental conditions.
Cavefish brain atlases reveal functional and anatomical convergence across independently evolved populations
Authors: Jaggard James , Lloyd Evan , Yuiska Anders , Patch Adam , Fily Yaouen , Kowalko Johanna E. , Appelbaum Lior , Duboue Erik R. , Keene Alex C. 
Published: November 2019

AbstractEnvironmental perturbation can drive the evolution of behavior and associated changes in brain structure and function. The generation of computationally-derived whole-brain atlases have provided insight into neural connectivity associated with behavior in many model systems. However, these approaches have not been used to study the evolution of brain structure in vertebrates. The Mexican tetra,A. mexicanus, comprises river-dwelling surface fish and multiple independently evolved populations of blind cavefish, providing a unique opportunity to identify neuroanatomical and functional differences associated with behavioral evolution. We employed intact brain imaging and image registration on 684 larval fish to generate neuroanatomical atlases of surface fish and three different cave populations. Analyses of brain regions and neural circuits associated with behavioral regulation identified convergence on hypothalamic expansion, as well as changes in transmitter systems including elevated numbers of catecholamine and hypocretin neurons in cavefish populations. To define evolutionarily-derived changes in brain function, we performed whole brain activity mapping associated with feeding and sleep. Feeding evoked neural activity in different sensory processing centers in surface and cavefish. We also identified multiple brain regions with sleep-associated activity across all four populations, including the rostral zone of the hypothalamus and tegmentum. Together, these atlases represent the first comparative brain-wide study of intraspecies variation in a vertebrate model, and provide a resource for studying the neural basis underlying behavioral evolution.
Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes
Authors: Panda Kaushik , McCue Andrea D. , Slotkin R. Keith 
Published: November 2019

AbstractThe plant-specific RNA Polymerase IV (Pol IV) transcribes heterochromatic regions, including many transposable elements, with the well-described role of generating 24 nucleotide (nt) small interfering RNAs (siRNAs). These siRNAs target DNA methylation back to transposable elements to reinforce the boundary between heterochromatin and euchromatin. In the male gametophytic phase of the plant life cycle, pollen, Pol IV switches to generating primarily 21-22 nt siRNAs, but the biogenesis and function of these siRNAs has been enigmatic. In contrast to being pollen-specific, we identified that Pol IV generates these 21-22 nt siRNAs in sporophytic tissues, likely from the same transcripts that are processed into the more abundant 24 nt siRNAs. The 21-22 nt forms are specifically generated by the combined activities of DICER proteins DCL2/DCL4 and can participate in RNA-directed DNA methylation. These 21-22 nt siRNAs are also loaded into ARGONAUTE1, which is known to function in post-transcriptional regulation. Like other plant siRNAs and microRNAs incorporated into AGO1, we find a signature of genic mRNA cleavage at the predicted target site of these siRNAs, suggesting that Pol IV-generated 21-22 nt siRNAs may function to regulate gene transcript abundance. Our data provides support for the existing model that in pollen Pol IV functions in gene regulation.
Computational Approach for Screening the Whole Proteome of Hantavirus and Designing a Multi-Epitope Subunit Vaccine
Authors: Abdulla Faruq , Nain Zulkar , Hossain Md. Moyazzem , Sayed Sifat Bin , Khan Md. Shakil Ahmed , Adhikari Utpal Kumar 
Published: November 2019

AbstractHantaviruses are a newly zoonotic emerging group of rodent-borne viruses that have a significant impact on global public health by increasing amplitude and magnitude of outbreaks. As no permanent cure yet, it is now growing and challenging interest to develop a vaccine against Hantavirus. This study endeavored to design a robust subunit vaccine using a novel immunoinformatics approach. After meticulous evaluation, top ones from predicted CTL, HTL, and B-cell epitopes were considered as potential vaccine candidates. Among generated four vaccine models with different adjuvant, the model with TLR-4 agonist adjuvant was selected for its high antigenicity, non-allergenicity, and structural quality. The conformational B-cell epitope prediction assured its humoral response inducing ability. Thereafter, the molecular docking and dynamics simulation confirmed a good binding affinity with immune receptor TLR-4 and stability of the vaccine-receptor complex. In immune simulation, significantly high levels of IgM and IgG1 immunoglobulins, TCand TH-cell populations, and various cytokines (i.e. IFN-γ, IL-2 etc.) are coherence with actual immune response and also showed faster antigen clearance for repeated exposures. Finally, disulfide engineering enhanced vaccine stability andin silicocloning confirmed the better expression inE. coliK12. Nonetheless, experimental validation can proof the proposed vaccine’s safety and ability to control Hantavirus infection.
Predictive whisker kinematics reveal context-dependent sensorimotor strategies
Authors: Wallach Avner , Deutsch David , Oram Tess , Ahissar Ehud 
Published: November 2019

AbstractAnimals actively move their sensory organs in order to acquire sensory information. Some rodents, such as mice and rats, employ cyclic scanning motions of their facial whiskers to explore their proximal surrounding, a behavior known as whisking. Here we investigated the contingency of whisking kinematics on the animal’s behavioral context that arises from both internal processes (attention and expectations) and external constraints (available sensory and motor degrees of freedom). We recorded rat whisking at high temporal resolution in two experimental contexts - freely moving or head-fixed – and two spatial sensory configurations – a single row or three caudal whiskers on each side of the snout. We found that rapid sensorimotor twitches, called pumps, occurring during free-air whisking carry information about the rat’s upcoming exploratory direction, as demonstrated by the ability of these pumps to predict consequent head and body locomotion. Specifically, pump behavior during both voluntary motionlessness and imposed head-fixation exposed a backward redistribution of sensorimotor exploratory resources. Further, head-fixed rats employed a wide range of whisking profiles to compensate for the loss of head- and body-motor degrees of freedom. Finally, changing the number of intact vibrissae available to a rat resulted in an alteration of whisking strategy consistent with the rat actively reallocating its remaining resources. In sum, this work shows that rats adapt their active exploratory behavior in a “homeostatic” attempt to preserve sensorimotor coverage under changing environmental conditions and changing sensory capacities, including those imposed by various laboratory conditions.
CRISPR-based screens uncover determinants of immunotherapy response in Multiple Myeloma
Authors: Ramkumar Poornima , Abarientos Anthony B. , Tian Ruilin , Seyler Meghan , Leong Jaime T. , Chen Merissa , Choudhry Priya , Hechler Torsten , Shah Nina , Wong Sandy W. , Martin Thomas G. , Wolf Jeffrey L. , Roybal Kole T. , Pahl Andreas , Taunton Jack , Wiita Arun P. , Kampmann Martin 
Published: November 2019

AbstractCancer cells commonly develop resistance to immunotherapy by loss of antigen expression. Combinatorial treatments that increase levels of the target antigen on the surface of cancer cells have the potential to restore efficacy to immunotherapy. Here, we use our CRISPR interference and CRISPR activation-based functional genomics platform to systematically identify pathways controlling cell-surface expression of the multiple myeloma immunotherapy antigen - B cell maturation antigen, BCMA. We discovered that pharmacological inhibition of HDAC7 and the Sec61 complex increased cell-surface BCMA, including in primary patient cells. Importantly, pharmacological Sec61 inhibition enhanced the anti-myeloma efficacy of a BCMA-targeted antibody-drug conjugate. A CRISPR interference CAR-T coculture screen enabled us to identify both antigen-dependent and -independent mechanisms controlling response of myeloma cells to BCMA-targeted CAR-T cells. Thus, our study demonstrates the potential of CRISPR screens to uncover mechanisms controlling response of cancer cells to immunotherapy and to suggest potential combination therapies.Key PointsUsing CRISPR screens, we systematically identify mechanisms increasing expression of the immunotherapy target BCMA and ADC efficacy.We also identify antigen-independent mechanisms regulating response of cancer cells to BCMA-CAR-T cells.
Transneuronal Dpr12/DIP-δ interactions facilitate compartmentalized dopaminergic innervation ofDrosophilamushroom body axons
Authors: Bornstein Bavat , Alyagor Idan , Berkun Victoria , Meltzer Hagar , Reh Fabienne , Keren-Shaul Hadas , David Eyal , Riemensperger Thomas , Schuldiner Oren 
Published: November 2019

SummaryThe mechanisms controlling wiring of neuronal networks are largely unknown. The stereotypic architecture of theDrosophilamushroom-body (MB) offers a unique system to study circuit assembly. The adult medial MB γ-lobe is comprised of a long bundle of axons that wires with specific modulatory and output neurons in a tiled manner defining five distinct zones. We found that the immunoglobulin superfamily protein Dpr12 is cell-autonomously required in γ-neurons for their developmental regrowth into the distal γ4/5 zones, where both Dpr12 and its interacting protein, DIP-δ, are enriched. DIP-δ functions in a subset of dopaminergic neurons that wire with γ-neurons within the γ4/5 zone. During metamorphosis, these dopaminergic projections arrive to the γ4/5 zone prior to γ-axons, suggesting that γ-axons extend through a prepatterned region. Thus, Dpr12/DIP-δ transneuronal interaction is required for γ4/5 zone formation. Our study sheds light onto molecular and cellular mechanisms underlying circuit formation within subcellular resolution.
Compliant assembly deviation analysis of large-scale thin-walled structures in different clamping schemes via ANCF
Authors: Xu Xun , Yu Haidong , Li Yunyong , Lai Xinmin 
Published: November 2019

Purpose
The structure stiffness is greatly affected by the fixture constraints during assembly due to the flexibility of large-scale thin-walled structures. The compliant deformation of structures is usually not consistent for the non-uniform stiffness in various clamping schemes. The purpose of this paper is to investigate the correlation between the assembly quality and the clamping schemes of structures with various initial deviations and geometrical parameters, which is based on the proposed irregular quadrilateral plate element via absolute nodal coordinate formulation (ANCF).

Design/methodology/approach
Two typical clamping schemes are specified for the large-scale thin-walled structures. Two typical deviation modes are defined in both free and clamping states in the corresponding clamping schemes. The new irregular quadrilateral plate element via ANCF is validated to analyze the compliant deformation of assembled structures. The quasi-static force equilibrium equations are extended considering the factors of clamping constraints and geometric deviations.

Findings
The initial deviations and geometrical parameters strongly affect the assembly deviations of structures in two clamping schemes. The variation tendencies of assembly deviations are demonstrated in details with the circumferential clamping position and axial clamping position in two clamping schemes, providing guidance to optimize the fixture configuration. The assembly quality of structures with deviations can be improved by configuration synthesis of the clamping schemes.

Originality/value
Typical over-constraint clamping schemes and deviation modes in clamping states are defined for large-scale thin-walled structures. The plate element via ANCF is extended to analyze the assembly deviations of thin-walled structures in various clamping schemes. Based on the proposed theoretical model, the effects of clamping schemes and initial deviations on the deformation and assembly deviation propagation of structures are investigated.
Design of e-learning and online tutoring as learning support for academic writing
Authors: Iwasaki Chiaki , Tada Yasuhiro , Furukawa Tomoki , Sasaki Kaede , Yamada Yoshinori , Nakazawa Tsutomu , Ikezawa Tomoya 
Published: November 2019

Purpose
The purpose of this paper is to discuss the development and assessment of learning support environments for academic writing that utilize ICT, such as e-learning and online tutoring, in Japanese higher education. First, the authors introduce the design of an e-learning writing program for the Japanese language and assess whether the program is an effective learning support tool for undergraduates. Second, the authors analyze and assess online tutoring support for academic writing and clarify the merits and disadvantages of online and offline tutoring at writing centers, then suggest instructional strategies by analyzing the writing tutoring process.

Design/methodology/approach
The authors adopted e-learning goals to assess its effectiveness. The authors asked the participants questions they could answer from five-point scales, conducted a paired t-test, and included a free description-type questionnaire. Then, to assess online tutoring, the 12 students took pre- and post-test questionnaires, after which the authors conducted a Wilcoxon signed rank test. In addition, the authors carried out a Kruskal–Wallis rank sum test in order to confirm differences in satisfaction level and the effectiveness of face-to-face tutoring and online tutoring.

Findings
By analyzing the pre- and post-test results, the t-test confirmed that the students found the e-learning system to be effective for nurturing academic literacy. This means the system is appropriate as a support tool for nurturing academic writing, especially writing knowledge and rules, and university must provide a comprehensive learning support environment including e-learning. Next, the authors found no statistically significant difference between face-to-face and online tutoring, although some problems with the writing process remained. So online tutoring has opportunity to promote autonomous learning. The research results make it clear that because of writing centers’ potential and their effectiveness in utilizing ICT tools.

Originality/value
Research findings about academic writing are to improve the tutoring process and writing strategies, such as the use of ICT for academic writing support like e-learning, online tutoring, do not exist. To provide learning opportunity to learners and promote autonomous learning, e-learning and online tutoring are important. For the reasons noted above, it is necessary to provide an alternative writing support environment to students in Japan. Therefore, the authors report on and assess the development of learning support environments for e-learning programs and online tutoring for academic writing at the undergraduate level in Japan.
Micro-enterprise development training and entrepreneurial competencies among low-income households in Malaysia
Authors: Al Mamun Abdullah , Muniady Rajennd , Fazal Syed Ali , Malarvizhi C.A. 
Published: November 2019

Purpose
Low-income households form a significant portion of the Malaysian population. To improve the socio-economic condition of low-income households, development organizations in Malaysia offer a wide range of development trainings, discussions and group or center meetings. This study aims to examine the impact of enterprise development training programs on entrepreneurial competencies among Peninsular Malaysia microentrepreneurs.

Design/methodology/approach
Adopting a cross-sectional design, the authors collected data from 300 randomly selected microentrepreneurs from the list of microentrepreneurs provided by eKasih (the National Poverty Data Bank), across four states of Peninsular Malaysia. Quantitative data were collected through structured interviews with the respondents from October to November 2017.

Findings
The findings revealed that enterprise development training programs significantly affected three of six entrepreneurial competencies (i.e. opportunity recognition competency, organizing competency and relationship competency). These findings highlight the importance of enterprise development training programs towards microentrepreneurs in increasing their competencies.

Originality/value
Through its insights, the study enriches the understanding of low-income communities in emerging economies, while offering significant practical implications. Based on findings, it is recommended that development organizations should therefore continue the current microenterprise development training programs. With improved entrepreneurial competencies, microentrepreneurs can thrive amidst competition yet sustaining business performance.
It tastes better when Bach meets red: the role of music and plate color on food evaluation
Authors: Cho Chloe Hyojin , Mattila Anna , Bordi Peter , Kwon Eunjin 
Published: November 2019

Purpose
The purpose of this paper is to examine the impact of arousal fit between music (auditory cues) and plate color (visual cues) on food evaluations.

Design/methodology/approach
A 2 (background music: high vs low arousal) ×2 (plate color: high vs low arousal) between-subjects experimental design was employed to test the hypotheses. Participants were recruited for a taste test in a food sensory lab located in a university in the northeastern USA. The dependent variable, food evaluation, was analyzed using analysis of covariance (ANCOVA).

Findings
The findings of this study indicate that when the two stimuli had congruent arousal qualities, participants rated the liking and perceived quality of a food item higher than those in the incongruent arousal conditions. More specifically, when the background music was high in arousal quality, participants gave higher evaluations for a food item served on a red (vs blue) plate. Conversely, when a low arousal music piece was played, a blue (vs red) plate resulted in higher food evaluations.

Research limitations/implications
This study contributes to the growing literature on cross-modal correspondence on consumers’ product evaluations. Extending previous research on the congruity effect to the food sensory literature, this study demonstrates the joint effects of background music and plate color on taste perceptions. The results suggest that restaurant operators should be strategic in their choice of physical stimuli.

Originality/value
The present study measured participants taste perceptions while they were exposed to visual and auditory cues. To the best of the authors’ knowledge, this is the first study that empirically demonstrates the impact of multiple environmental factors on taste evaluation.