bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single microRNA-Hox gene module controls complex movement in morphologically-distinct developmental forms ofDrosophila
Authors: Issa AR. , Picao-Osorio J. , Rito N. , Chiappe M.E. , Alonso C.R. 
Published: January 2019

ABSTRACTMovement is the main output of the nervous system. It emerges during development to become a highly coordinated physiological process essential to the survival and adaptation of the organism to the environment. Similar movements can be observed in morphologically-distinct developmental stages of an organism, but it is currently unclear whether these movements have a common or diverse molecular basis. Here we explore this problem inDrosophilafocusing on the roles played by the microRNA (miRNA) locusmiR-iab4/8which was previously shown to be essential for the fruit fly larva to correct its orientation if turned upside down (self-righting) (Picao-Osorio et al., 2015). Our study shows thatmiR-iab4is required for normal self-righting across all threeDrosophilalarval stages. Unexpectedly, we also discover that this miRNA is essential for normal self-righting behaviour in theDrosophilaadult, an organism with radically different morphological and neural constitution. Through the combination of gene-expression, optical imaging and quantitative behavioural approaches we provide evidence thatmiR-iab4exerts its effects on adult self-righting behaviour through repression of theHoxgeneUltrabithorax (Ubx)(Morgan, 1923; Sánchez-Herrero et al., 1985) in a specific set of motor neurons that innervate the adultDrosophilaleg. Our results show that thismiRNA-Hoxmodule affects the function, rather than the morphology of motor neurons and indicate that post-developmental changes inHoxgene expression can modulate behavioural outputs in the adult. Altogether our work reveals that a commonmiRNA-Hoxgenetic module can control complex movement in morphologically-distinct organisms and describes a novel post-developmental role of theHoxgenes in adult neural function.
Genetic control of pod dehiscence in domesticated common bean: Associations with range expansion and local aridity conditions
Authors: Parker Travis A. , Mier y Teran Jorge C. Berny , Palkovic Antonia , Jernstedt Judy , Gepts Paul 
Published: January 2019

SignificancePlant domestication has radically modified crop morphology and development. Nevertheless, many crops continue to display some atavistic characteristics that were advantageous to their wild ancestors, such as pod dehiscence (PD). Domesticated common bean (Phaseolus vulgaris), a nutritional staple for millions of people globally, shows considerable variation in PD. Here, we identified multiple genetic regions controlling PD in common bean grown throughout geographically distributed lineages. For example, on chromosome Pv03,PvPdh1shows a single base-pair substitution that is strongly associated with decreased PD and expansion of the crop into northern Mexico, where the arid conditions promote PD. The environmental dependency and genetic redundancy explain the maintenance of atavistic traits under domestication. Knowledge of PD genetics will assist in developing aridity-adapted varieties.AbstractA reduction in pod dehiscence (PD) is an important part of the domestication syndrome in legumes, including common bean. Despite this, many modern dry bean varieties continue to suffer yield reductions due to dehiscence, an atavistic trait, which is particularly problematic in hot, dry environments. To date, the genetic control of this important trait has been only partially resolved. Using QTL mapping and GWAS, we identified major PD QTLs in dry beans on chromosomes Pv03, Pv05, Pv08, and Pv09, three of which had not been described previously. We further determined that the QTL on chromosome Pv03, which is strongly associated with PD in Middle American beans, includes a dirigent-like candidate gene orthologous toPod dehiscence 1 (Pdh1)of soybean. In this gene, we identified a substitution in a highly conserved amino acid that is unique to PD-resistant varieties. This allele is associated with the expansion of Middle American domesticated common beans into the arid environments of northern Mexico, resulting in a high allelic frequency in the domesticated ecogeographic race Durango. The polygenic redundancy and environmental dependency of PD resistance may explain the maintenance of this atavistic characteristic after domestication. Use of these alleles in breeding will reduce yield losses in arid growing conditions, which are predicted to become more widespread in coming decades.
HSA+immature cardiomyocytes persist in the adult heart and expand after ischemic injury
Authors: Valente Mariana , Resende Tatiana Pinho , Nascimento Diana Santos , Burlen-Defranoux Odile , Dupont Benoit , Cumano Ana , Pinto-do-Ó Perpétua 
Published: January 2019

AbstractThe assessment of the regenerative capacity of the heart has been compromised by the lack of surface signatures to characterize cardiomyocytes. Here, combined multiparametric surface marker analysis with single cell transcriptional profiling and in vivo transplantation, identify the main fetal cardiac populations and their progenitors. We found that cardiomyocytes at different stages of differentiation co-exist during development. We identified a population of immature HSA/CD24+cardiomyocytes that persists throughout life and that, unlike other cardiomyocyte subsets, actively proliferates up to one week of age and engraft cardiac tissue upon transplantation. In adult heart HSA/CD24+cardiomyocytes appear as mononucleated cells that cycle and increase in frequency after infarction. Our work identified cell surface signatures that allow the prospective isolation of cardiomyocytes at any developmental stage and the detection of adult cardiomyocytes poised for activation in response to ischemic stimuli. This work opens new perspectives in the understanding and treatment of heart pathologies.
Transcriptional landscape of DNA repair genes underpins a pan-cancer prognostic signature associated with cell cycle dysregulation and tumor hypoxia
Authors: Chang Wai Hoong , Lai Alvina G. 
Published: January 2019

AbstractOveractive DNA repair contributes to therapeutic resistance in cancer. However, pan-cancer comparative studies investigating the contribution of all DNA repair genes in cancer progression employing an integrated approach have remained limited. We performed a multicohort retrospective analysis to determine the prognostic significance of 138 DNA repair genes in 16 cancer types (n=16,225). Cox proportional hazards analyses revealed a significant variation in the number of prognostic genes between cancers; 81 genes were prognostic in clear cell renal cell carcinoma while only two genes were prognostic in glioblastoma. We reasoned that genes that were commonly prognostic in highly correlated cancers revealed by Spearman’s correlation analysis could be harnessed as a molecular signature for risk assessment. A 10-gene signature, uniting prognostic genes that were common in highly correlated cancers, was significantly associated with overall survival in patients with clear cell renal cell (P<0.0001), papillary renal cell (P=0.0007), liver (P=0.002), lung (P=0.028), pancreas (P=0.00013) or endometrial (P=0.00063) cancers. Receiver operating characteristic analyses revealed that a combined model of the 10-gene signature and tumor staging outperformed either classifiers when considered alone. Multivariate Cox regression models incorporating additional clinicopathological features revealed that the signature was an independent predictor of overall survival. Tumor hypoxia is associated with adverse outcomes. Consistent across all six cancers, patients with high 10-gene and high hypoxia scores had significantly higher mortality rates compared to those with low 10-gene and low hypoxia scores. Functional enrichment analyses revealed that high mortality rates in patients with high 10-gene scores were attributable to an overproliferation phenotype. Death risk in these patients was further exacerbated by concurrent mutations of a cell cycle checkpoint protein, TP53. The 10-gene signature identified tumors with heightened DNA repair ability. This information has the potential to radically change prognosis through the use of adjuvant DNA repair inhibitors with chemotherapeutic drugs.
A Data-Driven Transcriptional Taxonomy of Adipogenic Chemicals to Identify White and Brite Adipogens
Authors: Kim Stephanie , Reed Eric , Monti Stefano , Schlezinger Jennifer 
Published: January 2019

AbstractBackgroundChemicals in disparate structural classes activate specific subsets of PPARγ’s transcriptional programs to generate adipocytes with distinct phenotypes.ObjectivesOur objectives were to 1) establish a novel classification method to predict PPARγ ligands and modifying chemicals, and 2) create a taxonomy to group chemicals based on their effects on PPARγ’s transcriptome and downstream metabolic functions. We tested the hypothesis that environmental adipogens highly ranked by the taxonomy, but segregated from therapeutic PPARγ ligands, would induce white but not brite adipogenesis.Methods3T3-L1 cells were differentiated in the presence of 76 chemicals (negative controls, nuclear receptor ligands known to influence adipocyte biology, potential environmental PPARγ ligands). Differentiation was assessed by measuring lipid accumulation. mRNA expression was determined by RNA-Seq and validated by RT-qPCR. A novel classification model was developed using an amended random forest procedure. A subset of environmental contaminants identified as strong PPARγ agonists were analyzed by their effects on lipid handling, mitochondrial biogenesis and cellular respiration in 3T3-L1 cells and human preadipocytes.ResultsWe used lipid accumulation and RNA sequencing data to develop a classification system that 1) identified PPARγ agonists, and 2) sorted chemicals into likely white or brite adipogens. Expression of Cidec was the most efficacious indicator of strong PPARγ activation. Two known environmental PPARγ ligands, tetrabromobisphenol A and triphenyl phosphate, which sorted distinctly from therapeutic ligands, induced white adipocyte genes but failed to induce Pgc1a and Ucp1, and induced fatty acid uptake but not mitochondrial biogenesis in 3T3-L1 cells. Moreover, two chemicals identified as highly ranked PPARγ agonists, tonalide and quinoxyfen, induced white adipogenesis without the concomitant health-promoting characteristics of brite adipocytes in mouse and human preadipocytes.DiscussionA novel classification procedure accurately identified environmental chemicals as PPARγ ligands distinct from known PPARγ-activating therapeutics. The computational and experimental framework has general applicability to the classification of as-yet uncharacterized chemicals.
Fast and accurate reference-guided scaffolding of draft genomes
Authors: Alonge Michael , Soyk Sebastian , Ramakrishnan Srividya , Wang Xingang , Goodwin Sara , Sedlazeck Fritz J. , Lippman Zachary B , Schatz Michael C. 
Published: January 2019

AbstractBackgroundAs the number of new genome assemblies continues to grow, there is increasing demand for methods to coalesce contigs from draft assemblies into pseudomolecules. Most current methods use genetic maps, optical maps, chromatin conformation (Hi-C), or other long-range linking data, however these data are expensive and analysis methods often fail to accurately order and orient a high percentage of assembly contigs. Other approaches utilize alignments to a reference genome for ordering and orienting, however these tools rely on slow aligners and are not robust to repetitive contigs.ResultsWe present RaGOO, an open-source reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in just minutes. With the pseudomolecules constructed, RaGOO identifies structural variants, including those spanning sequencing gaps that are not reported by alternative methods. We show that RaGOO accurately orders and orients contigs into nearly complete chromosomes based on de novo assemblies of Oxford Nanopore long-read sequencing from three wild and domesticated tomato genotypes, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open-source with an MIT license at https://github.com/malonge/RaGOO.ConclusionsWe demonstrate that with a highly contiguous assembly and a structurally accurate reference genome, reference-guided scaffolding with RaGOO outperforms error-prone reference-free methods and enable rapid pan-genome analysis.
Novel mutations within PRSS1 Gene that could potentially cause hereditary pancreatitis: Using Comprehensive in silico Approach
Authors: Mustafa Mujahed I. , Abdelmoneim Abdelrahman H. , Elfadol Nafisa M. , osman Soada A. , Abdelhameed Tebyan A. , Hassan Mohamed A. 
Published: January 2019

AbstractBackgroundHereditary pancreatitis (HP) is an autosomal dominant disorder with incomplete penetrance characterized by recurring episodes of severe abdominal pain often presenting in childhood. The comprehensive in silico analysis of coding SNPs, and their functional impacts on protein level, still remains unknown. In this study, we aimed to identify the pathogenic SNPs in PRSS1 gene by computational analysis approach.Materials and MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict Single-nucleotide polymorphisms influence on protein structure and function.ResultTwo novel mutations out of 339 nsSNPs that are found be deleterious effect on the PRSS1 structure and function.ConclusionThis is the first in silico analysis in PRSS1 gene, which will be a valuable resource for future targeted mechanistic and population-based studies.
Increase in stable isotope ratios driven by metabolic alterations in amphipods exposed to the beta-blocker propranolol
Authors: Ek Caroline , Yu Zhenyang , Garbaras Andrius , Oskarsson Hanna , Wiklund Ann-Kristin Eriksson , Kumblad Linda , Gorokhova Elena 
Published: January 2019

AbstractAnthropogenic pressures, such as contaminant exposure, may affect stable isotope ratios in biota. These changes are driven by alterations in the nutrient allocation and metabolic pathways induced by specific stressors. In a controlled microcosm study with the amphipod Gammarus spp., we studied effects of the β-blocker propranolol on stable isotope signatures (δ15N and δ13C), elemental composition (%C and %N), and growth (protein content and body size) as well as biomarkers of oxidative status (antioxidant capacity, ORAC; lipid peroxidation, TBARS) and neurological activity (acetylcholinesterase, AChE). Based on the known effects of propranolol exposure on cellular functions, i.e., its mode of action (MOA), we expected to observe a lower scope for growth, accompanied by a decrease in protein deposition, oxidative processes and AChE inhibition, with a resulting increase in the isotopic signatures. The observed responses supported most of these predictions. In particular, %N was positively affected by propranolol, whereas both protein allocation and body size declined. Moreover, both ORAC and TBARS levels decreased with increasing propranolol concentration, with the decrease being more pronounced for TBARS, which indicates the prevalence of the antioxidative processes. These changes resulted in a significant increase of the δ15N and δ13C values in the propranolol-exposed animals compared to the control. These findings suggest that MOA of β-blockers may be used to predict sublethal effects in nontarget species, including inhibited AChE activity, improved oxidative balance, and elevated stable isotope ratios. The latter also indicates that metabolism-driven responses to environmental contaminants can alter stable isotope signatures, which should be taken into account when interpreting trophic interactions in the food webs.
Preliminary design of 3D printed fittings for UAV
Authors: Mieloszyk Jacek , Tarnowski Andrzej , Kowalik Michal , Perz Rafal , Rzadkowski Witold 
Published: January 2019

Purpose
Additive manufacturing technology, also commonly called as 3D printing technology, is entering rapidly into the aerospace world and seems to be its future. Many manufacturing processes are replaced by this technology because the ease of use, low costs and new possibilities to make complicated parts. However, there are only few solutions which present manufacturing of structurally critical parts.

Design/methodology/approach
Complete process of deriving loads, design of fitting geometry, numerical validation, manufacturing and strength testing was presented. The emphasis was made to show specific features of 3D technology in printed fittings for UAV.

Findings
The research confirms that the technology can be used for the application of fittings manufacturing. Attention needs to be paid, during the design process, to account for specific features of the 3D printing technology, which is described in details.

Practical implications
Without a doubt, additive manufacturing is useful for manufacturing complicated parts within limited time and with reduction cost. It was also shown that the manufactured parts can be used for highly loaded structures.

Originality/value
The paper shows how additive manufacturing technology can be used to produce significantly loaded parts of airplanes’ structure. Only few such examples were presented till now.
Determining effective mentor characteristics in inter-organizational mentoring for managers: an approach based on academics’ and practitioners’ perspectives
Authors: Gisbert-Trejo Nuria , Landeta Jon , Albizu Eneka , Fernández-Ferrín Pilar 
Published: January 2019

PurposeThe purpose of this paper is to explore the essential mentor characteristics for effective inter-organizational mentoring. This kind of HR development technique, where mentor and mentee belong to different organizations, is becoming increasingly popular and so far has been scarcely studied.Design/methodology/approachFirst, a rigorous literature analysis to identify primary mentor characteristics for managers and professionals has been performed; second, a Delphi analysis has determined their relevance according to the opinion of 125 experienced mentors, mentees and program coordinators that have carried out inter-organizational mentoring processes in Spain; and third, an exploratory factor analysis has reclassified the mentor characteristics into a smaller number of factors.FindingsIn total, 29 relevant mentor characteristics have been identified and valued. The foregoing characteristics are related to seven underlying dimensions or factors that serve to characterize an effective mentor for inter-organizational mentoring programs.Originality/valueThe research extends the existing literature regarding mentor characteristics of those mentors who are engaged in inter-organizational mentoring. In addition, this work offers a valuable contribution to inter-organizational mentoring research based in a Delphi method that includes both academic and practitioner perspectives in a cultural context that may have not received previous attention. The findings can be valuable for both academics who investigate this topic of growing interest, and for practitioners who must face the selection and training of mentors.
What makes hotel online reviews credible?
Authors: Lo Ada S. , Yao Sharon Siyu 
Published: January 2019

Purpose
This study aims to adopt a cognitive heuristic approach to investigate the interaction effect of a message source characteristic (reviewer expertise [RE]) and two message structure characteristics (review rating consistency [RC] and review valence [RV]) on the perceived credibility of hotel online reviews.

Design/methodology/approach
Data were collected from 242 university students and were analyzed by three-way analysis of variance through a 2 × 2 factorial experiments using a simulated hotel review page on TripAdvisor.

Findings
Results show a three-way interaction effect of RE, RC and RV on the perceived credibility of hotel online reviews. The main effects of the three factors are also determined. Higher perceived credibility scores are found for negative reviews, reviews written by experts and reviews with a consistent rating.

Research limitations/implications
This study adopts an experimental approach and is the first to investigate the three-way interactions of message source and message structure characteristics of online hotel reviews. Data were collected from students in a university in Hong Kong. Results may not be generalizable to other markets.

Practical implications
Results suggest that reviews written by experts have higher perceived credibility. Hotels should pay attention to the content of online reviews and the expertise level of reviewers. Efforts should be exerted to create positive experiences for hotel guests that motivate expert reviewers to write positive reviews. Note that negative reviews have higher perceived credibility than positive ones. Hotels should promptly address negative reviews and provide professional responses to reviewers. Platform operators of user-generated content (UGC) should create well-defined reviewer profiles that can serve as cues that communicate the different expertise of reviewers.

Originality/value
This study is the first to test the three-way interaction effect of RE, RC and RV on the perceived credibility of hotel online reviews. Results provide recommendations to hotels and UGC operators and enable them to benefit from emerging UGC usage.
Pedagogy and public-funded research: an exploratory study of skills in digital humanities projects
Authors: Garwood Deborah A. , Poole Alex H. 
Published: January 2019

PurposePublic-funded research in digital humanities (DH) enhances institutional and individual research missions and contributes open data to a growing base of globally networked knowledge. The Digging into Data 3 challenge (DID3) (2014–2016) is an international, interdisciplinary and collaborative grant initiative, and the purpose of this paper is to explore skills that faculty and students brought to projects and others they acquired and shared on collaborative teams.Design/methodology/approachRooted in the naturalistic paradigm, this qualitative case study centers on semi-structured interviews with 53 participants on 11 of the 14 DID3 projects. Documentary evidence complements empirical evidence; analysis is constructivist and grounded.FindingsHailing from diverse academic research institutions, centers and repositories, participants brought 20 types of discipline-based or interdisciplinary expertise to DID3 projects. But they reported acquiring or refining 27 other skills during their project work. While most are data-related, complementary programming, management and analytical skills push disciplinary expertise toward new frontiers. Project-based learning and pedagogy function symbiotically; participants therefore advocate for aligning problem-solving skills with pedagogical objectives at home institutions to prepare for public-funded DH projects. A modified content analysis juxtaposes DID3 skills with those advanced in 23 recent DH syllabi to identify commonalities and gaps.Originality/valuePedagogy has an important yet under-researched and underdeveloped role in public-funded DH research.