bluuebunny/crossref_metadata_2025_split huggingface dataset:
Existing actin filaments orient new filament growth to provide structural memory of filament alignment during cytokinesis
Authors: Li Younan , Munro Edwin 
Published: April 2020

AbstractDuring cytokinesis, animal cells rapidly remodel the equatorial cortex to build an aligned array of actin filaments called the contractile ring. Local reorientation of filaments by equatorial contraction is thought to underlie the emergence of filament alignment during ring assembly. Here, combining single molecule analysis and modeling in one-cellC. elegansembryos, we show that filaments turnover is far too fast for reorientation of single filaments by equatorial contraction/cortex compression to explain the observed alignment, even if favorably oriented filaments are selectively stabilized. Instead, by tracking single Formin/CYK-1::GFP speckles to monitor local filament assembly, we identify a mechanism that we call filament-guided filament assembly (FGFA), in which existing filaments serve as templates to guide/orient the growth of new filaments. We show that FGFA sharply increases the effective lifetime of filament orientation, providing structural memory that allows slow equatorial contraction to build and maintain highly aligned filament arrays, despite rapid turnover of individual filaments.
Origin, Conservation, and Loss of Alternative Splicing Events that Diversify the Proteome in Saccharomycotina Budding Yeasts
Authors: Hurtig Jennifer E. , Kim Minseon , Orlando-Coronel Luisa J. , Ewan Jellisa , Foreman Michelle , Notice Lee-Ann , Steiger Michelle A. , van Hoof Ambro 
Published: April 2020

AbstractMany eukaryotes use alternative splicing to express multiple proteins from the same gene. However, while the majority of mammalian genes are alternatively spliced, other eukaryotes use this process less frequently. The budding yeastSaccharomyces cerevisiaehas been successfully used to study the mechanism of splicing and the splicing machinery, but alternative splicing in yeast is relatively rare and has not been extensively studied. We have recently shown that the alternative splicing ofSKI7/HBS1is widely conserved, but that yeast and a few other eukaryotes have replaced this one alternatively spliced gene with a pair of duplicated unspliced genes as part of a whole genome doubling (WGD). Here we show that other examples of alternative splicing that were previously found to have functional consequences are widely conserved within the Saccharomycotina. We also show that the most common mechanism by which alternative splicing has disappeared is by the replacement of an alternatively spliced gene with duplicate genes. Saccharomycetaceae that diverged before WGD use alternative splicing more frequently thanS. cerevisiae. This suggests that the WGD is a major reason for the low frequency of alternative splicing in yeast. We anticipate that whole genome doublings in other lineages may have had the same effect.
Caspases from Scleractinian Coral Show Unique Regulatory Features
Authors: Shrestha Suman , Tung Jessica , Grinshpon Robert D. , Swartz Paul , Hamilton Paul T. , Dimos Bradford , Mydlarz Laura , Clark A. Clay 
Published: April 2020

AbstractDiseases affecting coral have led to massive decline and altered the community structure of reefs. In response to immune challenges, cnidaria activate apoptotic or autophagic pathways, and the particular pathway correlates with disease sensitivity (apoptosis) or resistance (autophagy). Although cnidaria contain complex apoptotic signaling pathways, similar to those in vertebrates, the mechanisms leading to cell death are largely unexplored. We identified and characterized two caspases each fromOrbicella faveolata, a disease-sensitive stony coral, andPorites astreoides, a disease-resistant stony coral. The four caspases are predicted homologs of human caspases-3 and −7, but OfCasp3a and PaCasp7a contain an amino-terminal caspase activation and recruitment domain (CARD) similar to human initiator/inflammatory caspases. In contrast, OfCasp3b and PaCasp3 have short pro-domains, like human effector caspases. We show that OfCasp3a and PaCasp7a are DxxDases, like human caspases-3 and −7, while OfCasp3b and PaCasp3 are more similar to human caspase-6, with VxxDase activity. Our biochemical analyses suggest a mechanism in coral in which the CARD-containing DxxDase is activated on death platforms, but the protease does not directly activate the VxxDase. We also report the first X-ray crystal structure of a coral caspase, that of PaCasp7a determined at 1.57Å resolution. The structure reveals overall conservation of the caspase-hemoglobinase fold in coral as well as an N-terminal peptide bound near the active site that may serve as a regulatory exosite. The binding pocket has been observed in initiator caspases of other species, suggesting mechanisms for the evolution of substrate selection while maintaining common activation mechanisms of CARD-mediated dimerization.
Flow over seal whiskers: importance of geometric features for force and frequency response
Authors: Lyons Kathleen , Murphy Christin T. , Franck Jennifer A. 
Published: April 2020

AbstractThe complex undulated geometry of seal whiskers has been shown to substantially modify the turbulent structures directly downstream, resulting in a reduction of hydrodynamic forces as well as modified vortex-induced-vibration response when compared with smooth whiskers. Although the unique hydrodynamic response has been well documented, an understanding of the fluid flow effects from each geometric feature remains incomplete. In this computational investigation, nondimensional geometric parameters of the seal whisker morphology are defined in terms of their hydrodynamic relevance, such that wavelength, aspect ratio, undulation amplitudes, symmetry and undulation off-set can be varied independently of one another. A two-factor fractional factorial design of experiments procedure is used to create 16 unique geometries, each of which dramatically amplifies or attenuates the geometric parameters compared with the baseline model. The flow over each unique topography is computed with a large-eddy simulation at a Reynolds number of 500 with respect to the mean whisker thickness and the effects on force and frequency are recorded. The results determine the specific fluid flow impact of each geometric feature which will inform both biologists and engineers who seek to understand the impact of whisker morphology or lay out a framework for biomimetic design of undulated structures.
A new pathway for forming acetate and synthesizing ATP during fermentation in bacteria
Authors: Zhang Bo , Bowman Courtney , Hackmann Timothy J. 
Published: April 2020

ABSTRACTMany bacteria and other organisms form acetate during fermentation. Forming acetate from high energy-precursors (acetyl-CoA or acetyl phosphate) is one of the few ways that fermentative bacteria generate ATP. Here we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in bacteria. We found the bacteriumCutibacterium granulosumformed acetate during fermentation of glucose. With enzymatic assays, we showed it formed acetate using a pathway involving two enzymes. The first enzyme, succinyl-CoA:acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. This pathway is common in eukaryotes, but it has not been found in bacteria or other organisms. We found two related bacteria (C.acnesandAcidipropionibacterium acidipropionici) also used this pathway. None used the most common pathway for forming acetate in bacteria (involving acetate kinase and phosphotransacetylase). The SCACT/SCS pathway may be used by many bacteria, not justC.granulosumand relatives. When we searched genomes for bacteria known to form acetate, we found over 1/6 encoded this pathway. These bacteria belong to 104 different species and subspecies in 12 different phyla. With this discovery, all five pathways known to form acetate and ATP during fermentation can be found in bacteria. This discovery is important to manipulating fermentation and to the evolution of biochemical pathways.
Divergence in photoperiod responses of a classical biological control agentNeogalerucella calmariensis(Coleoptera: Chrysomelidae) across a climatic and latitudinal gradient
Authors: Wepprich Tyson , Grevstad Fritzi S. 
Published: April 2020

AbstractA key knowledge gap in classical biological control is to what extent insect agents evolve to novel environments. The introduction of biological control agents to new photoperiod regimes and climates may disrupt the coordination of diapause timing that evolved to the growing season length in the native range. We tested whether populations ofNeogalerucella calmariensis(L.) have evolved in response to the potential mismatch of their diapause timing since their intentional introduction to the United States from Germany in the 1990s. Populations collected from 39.4° to 48.8° latitude in the western USA were reared in growth chambers to isolate the effects of photoperiod on diapause induction and development time. For all populations, shorter day lengths increased the proportion of beetles that entered diapause instead of reproducing. The critical photoperiods, or the day length at which half of a population diapauses, differed significantly among the sampled populations, generally decreasing at lower latitudes. The latitudinal trend reflects changes in growing season length, which determines the number of generations possible, and in local day lengths at the time beetles are sensitive to this cue. Development times were similar across populations, with one exception, and did not vary with photoperiod. These results show that there was sufficient genetic variation from the two German source populations to evolve different photoperiod responses across a range of environmental conditions. This study adds to the examples of rapid evolution of seasonal adaptations in introduced insects.
Tocotrienol decreases β-amyloid mediated toxicity inCaenorhabditis elegansmodel of Alzheimer’s disease
Authors: Yuen Chee Wah , Halim Mardani Abdul , Murugaiyah Vikneswaran , Najimudin Nazalan , Azzam Ghows 
Published: April 2020

AbstractAlzheimer’s disease (AD) is a neurological disease caused by the accumulation of extracellular senile plaques consisting of β-amyloid peptide (Aβ) in the brain. A transgenicCaenorhabditis eleganswhich demonstrated paralysis due to the expression of human beta amyloid Aβ42gene was used to study the anti-paralysis effect of mixed tocotrienols. The content of the mixed tocotrienols were 12.1% α-, 2.7% β-, 18.6% γ-, and 8.1% δ-tocotrienols. Mixed tocotrienols significantly delayed the Aβ-induced paralysis in the transgenic nematode and exhibited anti-oxidant properties towards Aβ-generated oxidative stress. The mixture also presented potent inhibitory activities against Aβ aggregation with an IC50value of 600 ng/ml. It is concluded that mixed tocotrienols could potentially serve as a new therapeutic candidate for AD.
Selective Peptidomimetic Inhibitors of NTMT1/2: Rational design, synthesis, characterization, and crystallographic studies
Authors: Mackie Brianna D. , Chen Dongxing , Dong Guangping , Dong Cheng , Parker Haley , Tooley Christine E. Schaner , Noinaj Nicholas , Min Jinrong , Huang Rong 
Published: April 2020

ABSTRACTProtein N-terminal methyltransferases (NTMTs) methylate the α-N-terminal amines of proteins starting with the canonical X-P-K/R motif. Genetic studies imply that NTMT1 regulates cell mitosis and DNA damage repair. Herein, we report the rational design and development of the first potent peptidomimetic inhibitors for NTMT1. Biochemical and co-crystallization studies manifest thatBM30(IC50of 0.89 ± 0.10 µM) is a competitive inhibitor to the peptide substrate and noncompetitive to the cofactor S-adenosylmethionine.BM30exhibits over 100-fold selectivity to NTMT1/2 among a panel of 41 methyltransferases, indicating the potential to achieve high selectivity when targeting the peptide substrate binding site of NTMT1/2. Its cell-permeable analog DC432 (IC50of 54 ± 4 nM) decreases the N-terminal methylation level of SET protein in HCT116 cells. This proof-of principle study provides valuable probes for NTMT1/2 and highlights the opportunity to develop more cell-potent inhibitors to elucidate the function of NTMTs in future.
The IDR-containing protein PID-2 affects Z granules and is required for piRNA-induced silencing in the embryo
Authors: Placentino Maria , de Jesus Domingues António Miguel , Schreier Jan , Dietz Sabrina , Hellmann Svenja , de Albuquerque Bruno F. M. , Butter Falk , Ketting René F. 
Published: April 2020

AbstractInCaenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent, and heritable over many generations. This state is named RNAe. It is unknown how and when RNAe is established, and how it is maintained. We show that maternally provided 21U RNAs can be sufficient to trigger RNAe in embryos. Additionally, we identify the IDR-containing protein PID-2, as a factor required to establish and maintain RNAe. PID-2 interacts with two novel, partially redundant, eTudor domain proteins, PID-4 and PID-5. Additionally, PID-5 has a domain related to the X-prolyl aminopeptidase protein APP-1, and binds APP-1, implicating N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in theC. eleganssmall RNA silencing network.
Analysis of ISCB honorees and keynotes reveals disparities
Authors: Le Trang T. , Himmelstein Daniel S. , Hippen Anderson Ariel A. , Gazzara Matthew R. , Greene Casey S. 
Published: April 2020

AbstractDelivering a keynote talk at a conference organized by a scientific society, or being named as a fellow by such a society, indicates that a scientist is held in high regard by their colleagues. To explore if the distribution of such indicators of esteem in the field of bioinformatics reflects the composition of this field, we compared the gender, name-origin, country of affiliation and race/ethnicity of 412 researchers who had been recognized by theInternational Society for Computational Biology(75 fellows and 337 keynote speakers) with over 170,000 researchers who had been the last authors on computational biology papers between 1993 and 2019. The proportion of female fellows and keynote speakers was similar to that of the field overall. However, names of East Asian origin have been persistently underrepresented among fellows and keynote speakers. Moreover, fellows and keynote speakers with an affiliation in the United States were overrepresented by a factor of 2.1; almost two thirds of this excess was accounted for by a deficit of 101 fellows and keynote authors from China, India, France and Italy. Within the US, we found an excess of white fellows and keynote speakers and a depletion of Asian fellows and keynote speakers.
Methods to improve UAV performance using hybrid-electric architectures
Authors: Yezeguelian Axel , Isikveren Askin T. 
Published: April 2020

Purpose
When comparing and contrasting different types of fixed-wing military aircraft on the basis of an energetic efficiency figure-of-merit, unmanned aerial vehicles (UAVs) dedicated to tactical medium-altitude long-endurance (MALE) operations appear to have significant potential when hybrid-electric propulsion and power systems (HEPPS) are implemented. Beginning with a baseline Eulair drone, this paper aims to examine the feasibility of retro-fitting with an Autarkic-Parallel-HEPPS architecture to enhance performance of the original single diesel engine.

Design/methodology/approach
In view of the low gravimetric specific energy performance attributes of batteries in the foreseeable future, the best approach was found to be one in which the Parallel-HEPPS architecture has the thermal engine augmented by an organic rankine cycle (ORC). For this study, with the outer mould lines fixed, the goal was to increase endurance without increasing the Eulair drone maximum take-off weight beyond an upper limit of +10%. The intent was to also retain take-off distance and climb performance or, where possible, improve upon these aspects. Therefore, as the focus of the work was on power scheduling, two primary control variables were identified as degree-of-hybridisation for useful power and cut-off altitude during the en route climb phase. Quasi-static methods were used for technical sub-space modelling, and these modules were linked into a constrained optimisation algorithm.

Findings
Results showed that an Autarkic-Parallel-HEPPS architecture comprising an ORC thermal energy recovery apparatus and high-end year-2020 battery, the endurance of the considered aircraft could be increased by 11%, i.e. a total of around 28 h, including de-icing system, in-flight recharge and emergency aircraft recovery capabilities. The same aircraft with the de-icing functionality removed resulted in a 20% increase in maximum endurance to 30 h.

Practical implications
Although the adoption of Series/Parallel-HEPPS only solutions do tend to generate questionable improvements in UAV operational performance, combinations of HEPPS with energy recovery machines that use, for example, an ORC, were found to have merit. Furthermore, such architectural solutions could also offer opportunity to facilitate additional functions like de-icing and emergency aircraft recovery during engine failure, which is either not available for UAVs today or prove to be prohibitive in terms of operational performance attributes when implemented using a conventional PPS approach.

Originality/value
This technical paper highlights a new degree of freedom in terms of power scheduling during climbing transversal flight operations. A control parameter of cut-off altitude for all types of HEPPS-based aircraft should be introduced into the technical decision-making/optimisation/analysis scheme and is seen to be a fundamental aspect when conducting trade-studies with respect to degree-of-hybridisation for useful power.
Pilot-aircraft haptic feedback tests
Authors: Zikmund Pavel , Horpatzká Michaela , Dubnický Lukáš , Macík Miroslav , Jebáček Ivo 
Published: April 2020

Purpose
The purpose of this study is to lead to an improvement in pilot-aircraft interaction. The goal of the performed tests is an assessment of haptic feedback, which mediates flight parameters to the pilot. Pedals indicate side-slip angle by vibrations, whereas a sliding element inside the control stick is able to continuously indicate both angles of attack and side-slip.

Design/methodology/approach
Haptic feedback applied on rudder pedals and control stick were tested on a flight simulator and flight tests in a couple of tasks. Pilot workload, readability of feedback and side-slip were then evaluated when the flight was turning.

Findings
As a useful instrument for aircraft control, haptic feedback was assessed. The feedback settings were then individually perceived, and haptic feedback slightly improved side-slip while turning in a flight test; however, the results are not statistically significant.

Practical implications
The tests provided promising results for human pilot performance. The training phase and personal settings of haptic feedback is an approach for improving the performance of human pilots.

Originality/value
The designed and tested device is a unique tool for improving pilot-aircraft interaction. This study brings valuable experiences from its flight simulator and in-flight tests.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/AEAT-12-2019-0265/
Are jacks-of-all-trades successful entrepreneurs? Revisiting Lazear's theory of entrepreneurship
Authors: Kurczewska Agnieszka , Mackiewicz Michał 
Published: April 2020

PurposeThe purpose of this paper is to identify human capital factors that pertain both to setting up and successfully running a business. To achieve this objective, the authors apply and extend the theory of career choice offered by Lazear (2005) that explains individual selection into entrepreneurship.Design/methodology/approachThe authors hypothesise that individuals with broader educational and professional backgrounds are more likely to start a business and are more likely to run a business in the long term. The authors tested the hypotheses using unique data from 800 current entrepreneurs, 800 employees who were previously entrepreneurs and 842 employees with no entrepreneurial experience, by means of a logit regression with robust standard errors and extensive robustness checks.FindingsThe authors empirically show that individuals with more diverse educational and professional backgrounds tend to have both greater chances of starting a company, as well as a higher probability of entrepreneurial success. Surprisingly, having managerial experience proved to exert a negative influence on the likelihood of starting a business while having an insignificant impact on the odds of entrepreneurial success.Research limitations/implicationsThe findings are informative for those planning or pursuing an entrepreneurial career, but they are also relevant for the purpose of entrepreneurship education.Originality/valueThe author's extend the body of research supporting Lazear's (2005) theory by showing that broad education and professional experience not only contribute to a higher propensity to start a company but they are also success factors in business per se.
Predicting abandonment of brand social media accounts
Authors: Sanders W. Scott , Freberg Karen 
Published: April 2020

PurposeThe purpose of this study is to describe online factors that predict abandonment of social media accounts.Design/methodology/approachThis study conducts an analysis of 3,380 Twitter corporate brand accounts belonging to Interbrand's top 100 global brands to determine if brand posting behavior and network position predicts the length of time accounts survive.FindingsResults found that both posting volume and consistency as well as network position were significant predictors of account survival time yet surprisingly, the number of account followers was not. Brand social media accounts were often not formally closed or protected but allowed to fall inactive.Originality/valueDespite the existence of a healthy body of research on why individuals quit social media, there is little research on how brands' abandon their social media accounts or the factors that predict abandonment. This study identifies indicators for at-risk accounts and provides guidance regarding best practices when abandoning accounts.