bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary history of sickle-cell mutation: implications for global genetic medicine
Authors: Esoh Kevin , Wonkam Ambroise 
Published: January 2021

Abstract
Resistance afforded by the sickle-cell trait against severe malaria has led to high frequencies of the sickle-cell mutation [HBB; c.20T&gt;A, p.Glu6Val; OMIM: 141900 (HBB-βS)] in most parts of Africa. High-coverage sequencing and genotype data have now confirmed the single African origin of the sickle-cell gene variant [HBB; c.20T&gt;A, p.Glu6Val; OMIM: 141900 (HBB-βS)]. Nevertheless, the classical HBB-like genes cluster haplotypes remain a rich source of HBB-βS evolutionary information. The overlapping distribution of HBB-βS and other disease-associated variants means that their evolutionary genetics must be investigated concurrently. In this review: (1) we explore the evolutionary history of HBB-βS and its implications in understanding human migration within and out of Africa: e.g. HBB haplotypes and recent migration paths of the Bantu expansion, occurrence of ~7% of the Senegal haplotype in Angola reflecting changes in population/SCD dynamics, and existence of all five classical HBB haplotype in Cameroon and Egypt suggesting a much longer presence of HBB-βS in these regions; (2) we discuss the time estimates of the emergence of HBB-βS in Africa and finally, (3) we discuss implications for genetic medicine in understanding complex epistatic interactions between HBB-βS and other gene variants selected under environmental pressure in Africa e.g. variants in HBB, HBA, G6PD, APOL1, APOE, OSBPL10 and RXRA.
Experimental comparison analysis of two heat transfer enhancement methods on a thermochemical reactor
Authors: Han Xiaojing , Liu Shuli , Zeng Cheng , Shen Yongliang , Yang Liu 
Published: January 2021

Abstract
This paper experimentally investigates the performance of a thermochemical reactor for space heating using two heat enhancement methods, copper fins and copper plates. It is evaluated under laboratory conditions with the varying inlet air relative humidity and inlet air flow rate. The evaluated parameters are the reactor air pressure drop, outlet air temperature and outlet water temperature. While improving the reactor performance, the study presents comparative reactor performance of the two methods. The study shows that the copper plate reactor achieves a better desorption performance than the copper fin reactor. In charging, the copper plate reactor can reach the maximum outlet air temperature lifts at 95.1°C in 0.35 h, which is 12.3°C higher than copper fin reactor under the same conditions. In discharging, the peak reactor outlet air temperatures for the two reactors are found under different inlet air flow rate for the different internal air flow characteristics resulted from the copper fins and plates. Also, the copper fin reactor presents higher pressure drop than the copper plate reactor. Additionally, the copper fin reactor presents a slightly higher outlet water temperature in discharging than the plate reactor for the relatively larger thermal contact area between the copper fins and water pipe. Further research should be conducted in improving the reactor performance including reducing the heat loss, reactor optimisation and identifying suitable operating conditions.
Antagonistic Effects of Delia antiqua (Diptera: Anthomyiidae)-Associated Bacteria Against Four Phytopathogens
Authors: Liu Mei , Zhao Xiaoyan , Li Xianxian , Wu Xiaoqing , Zhou Hongzi , Gao Yunxiao , Zhang Xinjian , Zhou Fangyuan 
Published: January 2021

Abstract
Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These functions improve insect host fitness, and provide a novel source of discovering beneficial microbes for industrial and agricultural production. Previously published research found that in the symbiosis formed by the dipteran pest Delia antiqua (Meigen) (Diptera: Anthomyiidae) and its associated bacteria, the bacteria showed effective inhibition of one fungal entomopathogen, Beauveria bassiana. The antifungal activity of those associated bacteria indicates their potential to be used as biocontrol agents for fungal phytopathogens. In this study, we first isolated and identified bacteria associated with D. antiqua using a culture-dependent method. Second, we tested the antifungal activity of these bacteria against four phytopathogens including Fusarium moniliforme, Botryosphaeria dothidea, and two Fusarium oxysporum strains using the dual-culture method. In total, 74 species belonging to 30 genera, 23 families, eight classes, and four phyla were isolated and identified. Among those bacteria, Ochrobactrum anthropi, Morganella morganii, Arthrobacter sp. 3, and Acinetobacter guillouiae showed significant volatile inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum, respectively. Moreover, bacteria including Rhodococcus equi, Leucobacter aridicollis, Paenibacillus sp. 3, and Lampropedia sp. showed significant contact inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum. Our work provides a new source for discovering biocontrol agents against phytopathogens.
Life History and Damage by Systena frontalis F. (Coleoptera: Chrysomelidae) on Vaccinium macrocarpon Ait.
Authors: Jaffe Benjamin D , Rink Stephanie , Guédot Christelle 
Published: January 2021

Abstract
Pest management of emerging pests can be challenging because very little fundamental knowledge is available to inform management strategies. One such pest, the red-headed flea beetle Systena frontalis (Fabricius) (Coleoptera: Chrysomelidae), is increasingly being identified as a pest of concern in cranberries Vaccinium macrocarpon Aiton (Ericales: Ericaceae). To improve our understanding of this pest and to develop more targeted management programs, we conducted field and laboratory studies to characterize the development, seasonal emergence patterns, and density-dependent plant injury. We found that significantly more flea beetle eggs hatched when exposed to sustained cold treatment between 0 and 5°C for 15 wk than at warmer temperatures, and for shorter and longer cold-period durations. The adults emerged sporadically over the summer, were patchily distributed, fed on both fruit and foliage, and preferentially fed on new plant growth. Using soil cores, we found eggs and larvae located relatively deep (&gt;30 cm) in the soil. These patterns indicate that S. frontalis likely overwinters as eggs, and that targeting the larval stage may be the most effective management approach. Despite the cryptic nature of the larvae, continuing to improve our understanding of this life stage will be critical to optimizing control strategies.
A method for characterizing Cas9 variants via a one-million target sequence library of self-targeting sgRNAs
Authors: Tálas András , Huszár Krisztina , Kulcsár Péter István , Varga Julia K , Varga Éva , Tóth Eszter , Welker Zsombor , Erdős Gergely , Pach Péter Ferenc , Welker Ágnes , Györgypál Zoltán , Tusnády Gábor E , Welker Ervin 
Published: January 2021

AbstractDetailed target-selectivity information and experiment-based efficacy prediction tools are primarily available for Streptococcus pyogenes Cas9 (SpCas9). One obstacle to develop such tools is the rarity of accurate data. Here, we report a method termed ‘Self-targeting sgRNA Library Screen’ (SLS) for assaying the activity of Cas9 nucleases in bacteria using random target/sgRNA libraries of self-targeting sgRNAs. Exploiting more than a million different sequences, we demonstrate the use of the method with the SpCas9-HF1 variant to analyse its activity and reveal motifs that influence its target-selectivity. We have also developed an algorithm for predicting the activity of SpCas9-HF1 with an accuracy matching those of existing tools. SLS is a facile alternative to the much more expensive and laborious approaches used currently and has the capability of delivering sufficient amount of data for most of the orthologs and variants of SpCas9.
Are declines in insects and insectivorous birds related?
Authors: Tallamy Douglas W , Shriver W Gregory 
Published: January 2021

Abstract
A flurry of recently published studies indicates that both insects and birds have experienced wide-scale population declines in the last several decades. Curiously, whether insect and bird declines are causally linked has received little empirical attention. Here, we hypothesize that insect declines are an important factor contributing to the decline of insectivorous birds. We further suggest that insect populations essential to insectivorous birds decline whenever non-native lumber, ornamental, or invasive plant species replace native plant communities. We support our hypothesis by reviewing studies that show (1) due to host plant specialization, insect herbivores typically do poorly on non-native plants; (2) birds are often food limited; (3) populations of insectivorous bird species fluctuate with the supply of essential insect prey; (4) not all arthropod prey support bird reproduction equally well; and (5) terrestrial birds for which insects are an essential source of food have declined by 2.9 billion individuals over the last 50 years, while terrestrial birds that do not depend on insects during their life history have gained by 26.2 million individuals, a 111-fold difference. Understanding the consequences of insect declines, particularly as they affect charismatic animals like birds, may motivate land managers, homeowners, and restoration ecologists to take actions that reverse these declines by favoring the native plant species that support insect herbivores most productively.
Sucrose promotes stem branching through cytokinin
Authors: Salam Bolaji Babajide , Barbier Francois , Danieli Raz , Teper-Bamnolker Paula , Ziv Carmit , Spíchal Lukáš , Aruchamy Kalaivani , Shnaider Yula , Leibman Diana , Shaya Felix , Carmeli-Weissberg Mira , Gal-On Amit , Jiang Jiming , Ori Naomi , Beveridge Christine , Eshel Dani 
Published: January 2021

AbstractShoot branching is an important aspect of plant architecture because it substantially affects plant biology and agricultural performance. Sugars play an important role in the induction of shoot branching in several species, including potato (Solanum tuberosum L.). However, the mechanism by which sugars affect shoot branching remains mostly unknown. In the present study, we addressed this question using sugar-mediated induction of bud outgrowth in potato stems under etiolated conditions. Our results indicate that sucrose feeding to detached stems promotes the accumulation of cytokinin (CK), as well as the expression of vacuolar invertase (VInv), an enzyme that contributes to sugar sink strength. These effects of sucrose were suppressed by CK synthesis and perception inhibitors, while CK supplied to detached stems induced bud outgrowth and VInv activity in the absence of sucrose. CK-induced bud outgrowth was suppressed in vinv mutants, which we generated by genome editing. Altogether, our results identify a branching-promoting module, and suggest that sugar-induced lateral bud outgrowth is in part promoted by the induction of CK-mediated VInv activity.
Psychometric Assessment of the Connor-Davidson Resilience Scale for People With Lower-Limb Amputation
Authors: Miller Matthew J , Mealer Meredith L , Cook Paul F , Kittelson Andrew J , Christiansen Cory L 
Published: January 2021

Abstract

Objective
The purpose of this study was to (1) determine the psychometric properties of the 25- and 10-item Connor-Davidson Resilience Scales (CD-RISC25, CD-RISC10) for people with lower-limb amputation (LLA) in middle age or later, and (2) describe relationships of the CD-RISC with biopsychosocial, sociodemographic, and health variables.

Methods
Participants were included if their most recent LLA was 1 or more years prior, if they were independently walking with a prosthesis, and if they were between 45 and 88 years of age (N = 122; mean = 62.5 years of age [SD = 8]; 59.5 [mean = 58] months since LLA; 88.5% male; 82.0% with dysvascular etiology; 68.0% with unilateral transtibial LLA). Psychometric analyses included assessment of skewness, floor and ceiling effects, internal consistency, and agreement between versions. Correlation analyses were used to determine associations between the CD-RISC with disability, perceived functional capacity, falls efficacy, life-space, anxiety, depression, self-efficacy, social support, sociodemographic, and health variables. Additionally, quartiles of participants were identified using CD-RISC25 and CD-RISC10 scores and compared using ANOVA and post-hoc comparisons for disability, perceived functional capacity, falls efficacy, and life-space.

Results
Skewness, floor, and ceiling effects of both CD-RISC versions were acceptable. Both versions of the CD-RISC were internally consistent (CD-RISC25: α = .92; CD-RISC10: α = .89). The CD-RISC25 and CD-RISC10 were highly correlated with disability, perceived functional capacity, falls efficacy, anxiety, depression, and self-efficacy (r = 0.52–0.67). CD-RISC25 and CD-RISC10 quartile differences, especially the lowest quartile, were identified for disability, perceived functional capacity, falls efficacy, and life-space.

Conclusion
The CD-RISC25 and CD-RISC10 have acceptable psychometric properties for use with people who have LLA. CD-RISC scores are associated with clinically relevant biopsychosocial measures targeted by physical therapist intervention following LLA.

Impact
The CD-RISC may be an appropriate tool to measure resilience following LLA.
Management of Central Venous Access in Children With Intestinal Failure
Authors: Wendel Danielle , Mezoff Ethan A. , Raghu Vikram K. , Kinberg Sivan , Soden Jason , Avitzur Yaron , Rudolph Jeffrey A. , Gniadek Michelle , Cohran Valeria C. , Venick Robert S. , Cole Conrad R. 
Published: January 2021

ABSTRACTIntestinal failure requires the placement and maintenance of a long‐term central venous catheter for the provision of fluids and/or nutrients. Complications associated with this access contribute to significant morbidity and mortality, while the loss of access is an increasingly common reason for intestinal transplant referral. As more emphasis has been placed on the prevention of central line‐associated bloodstream infections and new technologies have developed, care for central lines has improved; however, because care has evolved independently in local centers, care of central venous access varies significantly in this vulnerable population. The present position paper from the Intestinal Failure Special Interest Group of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) reviews current evidence and provides recommendations for central line management in children with intestinal failure.
Early prediction of renal graft function: Analysis of a multi-centre, multi-level data set
Authors: Blazquez-Navarro Arturo , Bauer Chris , Wittenbrink Nicole , Wolk Kerstin , Sabat Robert , Dang-Heine Chantip , Neumann Sindy , Roch Toralf , Wehler Patrizia , Blazquez-Navarro Rodrigo , Olek Sven , Thomusch Oliver , Seitz Harald , Reinke Petra , Hugo Christian , Sawitzki Birgit , Babel Nina , Or-Guil Michal 
Published: January 2021

ABSTRACTIntroductionLong-term graft survival rates after renal transplantation are still moderate. We aimed to build an early predictor of an established long-term outcomes marker, the glomerular filtration rate (eGFR) one year post-transplant (eGFR-1y).Materials and MethodsA large cohort of 376 patients was characterized for a multi-level bio-marker panel including gene expression, cytokines, metabolomics and antibody reactivity profiles. Almost one thousand samples from the pre-transplant and early post-transplant period were analysed. Machine learning-based predictors were built employing stacked generalization.ResultsPre-transplant data led to a prediction achieving a Pearson’s correlation coefficient of r=0.39 between measured and predicted eGFR-1y. Two weeks post-transplant, the correlation was improved to r=0.63, and at the third month, to r=0.76. eGFR values were remarkably stable throughout the first year post-transplant and were the best estimators of eGFR-1y already two weeks post-transplant. Several markers were associated with eGFR: The cytokine stem cell factor demonstrated a strong negative correlation; and a subset of 19 NMR bins of the urine metabolome data was shown to have potential applications in non-invasive eGFR monitoring. Importantly, we identified the expression of the genes TMEM176B and HMMR as potential prognostic markers for changes in the eGFR.DiscussionOur multi-centre, multi-level data set represents a milestone in the efforts to predict transplant outcome. While an acceptable predictive capacity was achieved, we are still very far from predicting changes in the eGFR precisely. Further studies employing further marker panels are needed in order to establish predictors of eGFR-1y for clinical application; herein, gene expression markers seem to hold the most promise.
swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution
Authors: Chen Lulu , Wu Chiung-Ting , Lin Chia-Hsiang , Dai Rujia , Liu Chunyu , Clarke Robert , Yu Guoqiang , Van Eyk Jennifer E. , Herrington David M. , Wang Yue 
Published: January 2021

AbstractMotivationComplex biological tissues are often a heterogeneous mixture of several molecularly distinct cell or tissue subtypes. Both subtype compositions and expressions in individual samples can vary across different biological states or conditions. Computational deconvolution aims to dissect patterns of bulk gene expression data into subtype compositions and subtype-specific expressions. Typically, existing deconvolution methods can only estimate averaged subtype-specific expressions in a population, while detecting differential expressions or co-expression networks in particular subtypes requires unique subtype expression estimates in individual samples. Different from population-level deconvolution, however, individual-level deconvolution is mathematically an underdetermined problem because there are more variables than observations.ResultsWe report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and subtype-specific expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm andℓ2,1-norm regularized matrix factorization problem. We determine hyperparameter values using a cross-validation scheme with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. The swCAM is implemented in open-source R scripts. Experimental results on realistic simulation data show that swCAM can accurately estimate subtype-specific expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk expression data. Application of swCAM to bulk-tissue data of 320 samples from bipolar disorder patients and controls identified changes in cell proportions, expression and coexpression modules in patient neurons. Mitochondria related genes showed significant changes suggesting an important role of energy dysregulation in bipolar disorder.Availability and implementationThe R Scripts of swCAM is freely available athttps://github.com/Lululuella/swCAM. A user’s guide and a vignette are provided.Contactyuewang@vt.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Molecular Mechanism of the N501Y Mutation for Enhanced Binding between SARS-CoV-2’s Spike Protein and Human ACE2 Receptor
Authors: Luan Binquan , Wang Haoran , Huynh Tien 
Published: January 2021

AbstractCoronavirus disease 2019 (COVID-19) has been an ongoing global pandemic for over a year. Recently, an emergent SARS-CoV-2 variant (B.1.1.7) with an unusually large number of mutations had become highly contagious and wide-spreading in United Kingdom. From genome analysis, the N501Y mutation within the receptor binding domain (RBD) of the SARS-CoV-2’s spike protein might have enhanced the viral protein’s binding with the human angiotensin converting enzyme 2 (hACE2). The latter is the prelude for the virus’ entry into host cells. So far, the molecular mechanism of this enhanced binding is still elusive, which prevents us from assessing its effects on existing therapeutic antibodies. Using all atom molecular dynamics simulations, we demonstrated that Y501 in mutated RBD can be well coordinated by Y41 and K353 in hACE2 through hydrophobic interactions, increasing the overall binding affinity between RBD and hACE2 by about 0.81 kcal/mol. We further explored how the N501Y mutation might affect the binding between a neutralizing antibody (CB6) and RBD. We expect that our work can help researchers design proper measures responding to this urgent virus mutation, such as adding a modified/new neutralizing antibody specifically targeting at this variant in the therapeutic antibody cocktail.Abstract Figure
Differential taphonomic effects of petroleum seeps and karstic sinkholes on ancient dire wolf teeth: Hydrocarbon impregnation preserves fossils for chemical and histological analysis
Authors: Sholts Sabrina B. , Hlusko Leslea J. , Carlson Joshua P. , Wärmländer Sebastian K. T. S. 
Published: January 2021

ABSTRACTHistological analysis of teeth can yield information on an organism’s growth and development, facilitating investigations of diet, health, environment, and long-term responses to selective pressures. In the Americas, an extraordinary abundance of Late Pleistocene fossils including teeth has been preserved in petroleum seeps, constituting a major source of information about biotic changes and adaptations at the end of the last glacial period. However, the usefulness of these fossils for histological studies is unclear, due to the unknown taphonomic effects of long-term deposition in petroleum. Here, we compare histological and chemical analyses on dire wolf (Canis dirus) teeth obtained from two different environments, i.e. a petroleum seep (Rancho La Brea tar pits, California) and a carstic sinkhole (Cutler Hammock sinkhole, Florida). Optical and scanning electron microscopy (SEM) together with X-ray diffraction (XRD) analysis revealed excellent preservation of dental microstructure in the seep sample, and the petroleum-induced discoloration was found not to interfere with the histological and chemical examination. By comparison, teeth from the sinkhole sample showed severe degradation and contamination of the dentine by exogenous substances. These results indicate that petroleum seep assemblages are useful, or even ideal, environments for preserving the integrity of fossil material for chemical and histological analysis.