bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repeated translocation of a supergene underlying rapid sex chromosome turnover inTakifugufish
Authors: Kabir Ahammad , Ieda Risa , Hosoya Sho , Fujikawa Daigaku , Atsumi Kazufumi , Tajima Shota , Nozawa Aoi , Hirase Shotaro , Koyama Takashi , Nakamura Osamu , Kadota Mitsutaka , Nishimura Osamu , Kuraku Shigehiro , Nakamura Yasukazu , Kobayashi Hisato , Toyota Atsushi , Tasumi Satoshi , Kikuchi Kiyoshi 
Published: November 2021

AbstractRecent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genusTakifugu, in which one strong candidate sex-determining gene,Amhr2, has been identified. To trace the processes involved in transitions in the sex determination system in this genus, we studied 12 species and found that while theAmhr2locus likely determines sex in the majority ofTakifuguspecies, three species have acquired sex-determining loci at different chromosomal locations. Nevertheless, the generation of genome assemblies for the three species revealed that they share a portion of the male-specific supergene that contains a candidate sex-determining gene,GsdfY, along with genes that potentially play a role in male fitness. The shared supergene span approximately 100 kb and are flanked by two duplicated regions characterized by CACTA transposable elements. These results suggest that the shared supergene has taken over the role of sex-determining locus fromAmhr2in lineages leading to the three species, and repeated translocations of the supergene underlie the turnover of sex chromosomes in these lineages. These findings highlight the underestimated role of a mobile supergene in the turnover of sex chromosomes in vertebrates.SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.
A3D Database: Structure-based Protein Aggregation Predictions for the Human Proteome
Authors: Badaczewska-Dawid Aleksandra E. , Garcia-Pardo Javier , Kuriata Aleksander , Pujols Jordi , Ventura Salvador , Kmiecik Sebastian 
Published: November 2021

AbstractMotivationProtein aggregation is associated with highly debilitating human disorders and constitutes a major bottleneck for producing therapeutic proteins. Our knowledge of the human protein structures repertoire has dramatically increased with the recent development of the AlphaFold (AF) deep-learning method. This structural information can be used to understand better protein aggregation properties and the rational design of protein solubility. This article uses the Aggrescan3D (A3D) tool to compute the structure-based aggregation predictions for the human proteome and make the predictions available in a database form.ResultsHere, we present the A3D Database, in which we analyze the AF-predicted human protein structures (for over 17 thousand non-membrane proteins) in terms of their aggregation properties using the A3D tool. Each entry of the A3D Database provides a detailed analysis of the structure-based aggregation propensity computed with A3D. The A3D Database implements simple but useful graphical tools for visualizing and interpreting protein structure datasets. We discuss case studies illustrating how the database could be used to analyze physiologically relevant proteins. Furthermore, the database enables testing the influence of user-selected mutations on protein solubility and stability, all integrated into a user-friendly interface.Availability and implementationA3D Database is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/hproteome
Revisiting the effect of pharmaceuticals on transmission stage formation in the malaria parasite Plasmodium falciparum
Authors: Thommen Basil T. , Passecker Armin , Buser Tamara , Hitz Eva , Voss Till S. , Brancucci Nicolas M. B. 
Published: November 2021

AbstractMalaria parasites rely on specialized stages, called gametocytes, to ensure human-to-human transmission. The formation of these sexual precursor cells is initiated by commitment of blood stage parasites to the sexual differentiation pathway. Plasmodium falciparum, the most virulent of six parasite species infecting humans, employs nutrient sensing to control the rate at which sexual commitment is initiated, and the presence of stress-inducing factors, including antimalarial drugs, has been linked to increased gametocyte production in vitro and in vivo. These observations suggest that therapeutic interventions may promote gametocytogenesis and malaria transmission. Here, we engineered a P. falciparum reporter line to quantify sexual commitment rates after exposure to antimalarials and other pharmaceuticals commonly prescribed in malaria-endemic regions. Our data reveal that some of the tested drugs indeed have the capacity to elevate sexual commitment rates in vitro. Importantly, however, these effects are only observed at drug concentrations that inhibit parasite survival and only rarely result in a net increase of gametocyte production. Using a drug-resistant parasite reporter line, we further show that the gametocytogenesis-promoting effect of drugs is linked to general stress responses rather than to compound-specific activities. Altogether, we provide conclusive evidence for the absence of mechanistic links between the regulation of sexual commitment and the activity of commonly used pharmaceuticals in vitro. Our data hence contradict scenarios in which therapeutic interventions would promote the spread of drug-resistant parasites or malaria transmission in general.
A general framework for straightforward model construction of multi-component thermodynamic equilibrium systems
Authors: Geertjens Nick H. J. , de Vink Pim J. , Wezeman Tim , Markvoort Albert J. , Brunsveld Luc 
Published: November 2021

AbstractMathematical modelling of molecular systems helps elucidating complex phenomena in (bio)chemistry. However, equilibrium conditions in systems consisting of more than two components can typically not be analytically determined without assumptions and resulting (semi-)numerical models are not trivial to derive by the non-expert. Here we present a framework for equilibrium models that utilizes a general derivation method capable of generating custom models for complex molecular systems, based on the simple, reversible reactions describing these systems. Several molecular systems are revisited via the framework and demonstrate the simplicity, the generality and validity of the approach. The ease of use of the framework and the ability to both analyze systems and gain additional insights in the underlying parameters strongly aids the analysis and understanding of molecular equilibrium systems. This conceptual framework severely reduces the time and expertise requirements which currently impede the broad integration of these highly valuable models into chemical research.
AMPK promotes Arf6 activation in a kinase-independent manner upon energy deprivation
Authors: Chen Kuan-Jung , Hsu Jia-Wei , Lee Fang-Jen S. 
Published: November 2021

AbstractAMP-activated protein kinase (AMPK) is a crucial cellular nutrient and energy sensor that maintains energy homeostasis. AMPK also governs cancer cell invasion and migration by regulating gene expression and activating multiple cellular signaling pathways. ADP-ribosylation factor 6 (Arf6) can be activated via nucleotide exchange by guanine nucleotide exchange factors (GEFs), and its activation also regulates tumor invasion and migration. By studying GEF-mediated Arf6 activation, we elucidated that AMPK functions as a noncanonical GEF for Arf6 in a kinase-independent manner. Moreover, by examining the physiological role of the AMPK-Arf6 axis, we determined that AMPK activates Arf6 upon glucose starvation and 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR) treatment. We further identified the binding motif in the C-terminal regulatory domain of AMPK that is responsible for promoting Arf6 activation and thus inducing cell migration and invasion. These findings reveal a noncanonical role of AMPK in which its C-terminal regulatory domain serves as a GEF for Arf6 during energy deprivation.
Use of commercially available natural language processing software to identify bleeding from the medical record
Authors: Walker Andrew L. , Watson Cheri , Butcher Ryan , Abedin Zameer , Yandell Mark , Shah Rashmee U. 
Published: November 2021

AbstractBackgroundReal-world evidence derived from the electronic medical record (EMR) is increasingly prevalent. How best to ascertain cardiovascular outcomes from EMRs is unknown. We sought to validate a commercially available natural language processing (NLP) software to extract bleeding events.MethodsWe included patients with atrial fibrillation and cancer seen at our cancer center from 1/1/2016 to 12/31/2019. A query set based on SNOMED CT expressions was created to represent bleeding from 11 different organ systems. We ran the query against the clinical notes and randomly selected a sample of notes for physician validation. The primary outcome was the positive predictive value (PPV) of the software to identify bleeding events stratified by organ system.ResultsWe included 1370 patients with mean age 72 years old (SD 1.5) and 35% female. We processed 66,130 notes; the NLP software identified 6522 notes including 654 unique patients with possible bleeding events. Among 1269 randomly selected notes, the PPV of the software ranged from 0.921 for neurologic bleeds to 0.571 for OB/GYN bleeds. Patterns related to false positive bleeding events identified by the software included historic bleeds, hypothetical bleeds, missed negatives, and word errors.ConclusionsNLP may provide an alternative for population-level screening for bleeding outcomes in cardiovascular studies. Human validation is still needed, but an NLP-driven screening approach may improve efficiency.
Diagnosing the service quality of perishable-food logistics: temperature-sensitive milk delivery
Authors: Wu Pei-Ju , Lin Liang-Tay , Huang Chi-Chang 
Published: November 2021

PurposeHigh-quality cold-chain logistics are key to effectively managing the quality of temperature-sensitive foods. Hence, this study investigates the service quality of such logistics, using a real-life case of temperature-sensitive milk delivery.Design/methodology/approachThis study focuses on developing business analytics for quality control in cold-chain perishable-food logistics, grounded in normal accident theory and stakeholder theory, and tests them using real-world data.FindingsThe empirical business-analytics results indicate that cargo locations, logistics status and delivery times are the essential factors that influence the quality of temperature-sensitive milk.Research limitations/implicationsThis study confirms that a combination of normal accident theory and stakeholder theory can be usefully applied to the development of strategies for managing perishable-food logistics. As such, its proposed business analytics provide a fresh foundation for research on logistics quality management.Practical implicationsThe balance between efficiency and service quality in a logistics system should be assessed carefully, and logistics companies should collaborate with their stakeholders and can help to mitigate potential cold-chain risks.Originality/valueThis pioneering analytical study explores the essential quality issues that confront cold chains and demonstrates how to extract vital insights from temperature-sensitive food logistics monitoring data. As such, it represents a noteworthy contribution to the field of logistics quality management.
Learning from interorganizational projects
Authors: Iftikhar Rehab , Ahola Tuomas , Butt Aurangzeab 
Published: November 2021

PurposeThe purpose of this study is to consolidate the existing research on interorganizational projects and to explore how organizations learn by closely examining multilevel learning, that is, organizational and interorganizational learning.Design/methodology/approachThis article adopts a single case study approach, examining the Islamabad–Rawalpindi Metro project in Pakistan, with data consisting of interview results and archival data. An inductive approach is used for data analysis.FindingsAn empirically grounded learning model was developed based on an interorganizational project following eight lessons: capacity building, personality traits of leadership, working procedures, impeccable planning and implementation, involvement of stakeholders, design compatibility, investigation of underground services, conditions and maintenance of databases, and conceive rational timelines. These lessons learned were classified into three categories: (1) organizational capacity, (2) organizational embeddedness and (3) collective awareness.Originality/valueThis paper develops a novel learning model that can deepen our understanding of the practices and processes involved in multilevel learning. This study contributes to and extends the literature on organizational and interorganizational learning by studying an interorganizational setting.
Individuals' psychosocial voice barriers in lean problem-solving teams
Authors: Latif Mohammad Abdul , Vang Jan , Sultana Rebeca 
Published: November 2021

PurposeVoice role identification and the psychosocial voice barriers represented by implicit voice theories (IVTs) affect lean team members' prosocial voice behavior and thereby lean team performance. This paper investigates how role definition and IVTs influence individual lean team-members' prosocial voice behavior during lean implementation.Design/methodology/approachThis research was conducted in four case readymade garment (RMG) factories in Bangladesh following a mixed-method research approach dominated by a qualitative research methodology. Under the mixed-method design, this research followed multiple research strategies, including intervention-based action research and case studies.FindingsThe findings suggest that voice role perception affects the voice behavior of the individual lean team members. The findings also demonstrate that voice role definition significantly influences individually held implicit voice beliefs in lean teams.Research limitations/implicationsThis research was conducted in four sewing lines in four RMG factories in Bangladesh. There is a need for a cross-sector and cross-country large-scale study that follows the quantitative research methods in different contexts.Practical implicationsThis research contributes to the operations management literature, especially in lean manufacturing, by presenting the difficulties of mobilizing employee voice in lean problem-solving teams. This work provides new knowledge to managers to address challenges and opportunities to ensure decent work and to improve productivity.Originality/valueThis research raises a key issue of employee voice and its influence on lean performance which addresses two critical areas of employee voice behavior in lean teams: team-members' voice role perception and implicit voice beliefs that influence their voice behavior in the workplace, thereby influencing team performance.
Modeling commercial vehicle drivers’ acceptance of advanced driving assistance system (ADAS)
Authors: Xu Yueru , Ye Zhirui , Wang Chao 
Published: November 2021

PurposeAdvanced driving assistance system (ADAS) has been applied in commercial vehicles. This paper aims to evaluate the influence factors of commercial vehicle drivers’ acceptance on ADAS and explore the characteristics of each key factors. Two most widely used functions, forward collision warning (FCW) and lane departure warning (LDW), were considered in this paper.Design/methodology/approachA random forests algorithm was applied to evaluate the influence factors of commercial drivers’ acceptance. ADAS data of 24 commercial vehicles were recorded from 1 November to 21 December 2018, in Jiangsu province. Respond or not was set as dependent variables, while six influence factors were considered.FindingsThe acceptance rate for FCW and LDW systems was 69.52% and 38.76%, respectively. The accuracy of random forests model for FCW and LDW systems is 0.816 and 0.820, respectively. For FCW system, vehicle speed, duration time and warning hour are three key factors. Drivers prefer to respond in a short duration during daytime and low vehicle speed. While for LDW system, duration time, vehicle speed and driver age are three key factors. Older drivers have higher respond probability under higher vehicle speed, and the respond time is longer than FCW system.Originality/valueFew research studies have focused on the attitudes of commercial vehicle drivers, though commercial vehicle accidents were proved to be more severe than passenger vehicles. The results of this study can help researchers to better understand the behavior of commercial vehicle drivers and make corresponding recommendations for ADAS of commercial vehicles.
From canopy complementarity to asymmetric competition: The negative relationship between structural diversity and productivity during succession
Authors: Yi Xiaoxia , Wang Ningning , Ren Haibao , Yu Jianping , Hu Tianyu , Su Yanjun , Mi Xiangcheng , Guo Qinghua , Ma Keping 
Published: November 2021

Abstract

Positive relationships between structural diversity and forest productivity have been documented in controlled experiments and early secondary forests, however, negative relationships have also been observed in late successional forests. The mechanisms causing observed relationships between structural diversity and productivity are not well‐established, but complementarity among crowns and asymmetric competition have been suggested.

We used LiDAR and repeated census data to examine the relationship between canopy structural diversity and productivity in nine 1‐ha subtropical forest plots along a disturbance gradient in southeastern China. We quantified the relative importance of community composition, species diversity, canopy structural diversity, leaf area index (LAI) and disturbance regime on productivity using piecewise structural equation modelling. We also tested how vertical leaf area distribution affected productivity.

Contrary to many prior observations, we found a negative relationship between canopy structural diversity and forest productivity. The negative effect may stem from asymmetric competition between overstorey and understorey leaves, leading to a lower leaf area efficiency (i.e. wood production per leaf area). Asymmetric competition was suggested by a negative relationship between understorey leaf area and total productivity. Changes in community composition over the disturbance gradient, but not species diversity, had a significant effect on productivity.

Synthesis. Our study suggests that leaf area and canopy structural diversity have contrasting effects on productivity in this subtropical forest, and this needs to be considered when estimating rates of carbon sequestration in secondary forests. The negative effect of asymmetric competition on productivity is comparable to that of the shift in species composition over succession, highlighting the role of canopy structural diversity in shaping forest productivity.
Cardioprotective effects of amiodarone in a rat model of epilepsy‐induced cardiac dysfunction
Authors: Harb Inas A. , Ashour Hend , Mostafa Abeer , El Hanbuli Hala M. , Nadwa Eman Hassan 
Published: November 2021

AbstractCardiac dysfunction is one of the leading causes of death in epilepsy. The anti‐arrhythmic drug, amiodarone, is under investigation for its therapeutic effects in epilepsy. We aimed to evaluate the possible effects of amiodarone on cardiac injury during status epilepticus, as it can cause prolongation of the QT interval. Five rat groups were enrolled in the study; three control groups (1) Control, (2) Control‐lithium and (3) Control‐Amio, treated with 150 mg/kg/intraperitoneal amiodarone, (4) Epilepsy model, induced by sequential lithium/pilocarpine administration, and (5) the epilepsy‐Amio group. The model group expressed a typical clinical picture of epileptiform activity confirmed by the augmented electroencephalogram alpha and beta spikes. The anticonvulsive effect of amiodarone was prominent, it diminished (p < 0.001) the severity of seizures and hence, deaths and reduced serum noradrenaline levels. In the model group, the electrocardiogram findings revealed tachycardia, prolongation of the corrected QT (QTc) interval, depressed ST segments and increased myocardial oxidative stress. The in‐vitro myocardial performance (contraction force and – (df/dt)max) was also reduced. Amiodarone decreased (p < 0.001) the heart rate, improved ST segment depression, and myocardial contractility with no significant change in the duration of the QTc interval. Amiodarone preserved the cardiac histological structure and reduced the myocardial injury markers represented by serum Troponin‐I, oxidative stress and IL‐1. Amiodarone pretreatment prevented the anticipated cardiac injury induced during epilepsy. Amiodarone possessed an anticonvulsive potential, protected the cardiac muscle and preserved its histological architecture. Therefore, amiodarone could be recommended as a protective therapy against cardiac dysfunction during epileptic seizures with favourable effect on seizure activity.
Drops join to make a stream: high‐throughput nanoscale cultivation to grasp the lettuce root microbiome
Authors: Persyn Antoine , Mueller André , Goormachtig Sofie 
Published: November 2021

SummaryRoot endospheres house complex and diverse bacterial communities, of which many strains have not been cultivated yet by means of the currently available isolation techniques. The Prospector® (General Automation Lab Technologies, San Carlos, CA, USA), an automated and high‐throughput bacterial cultivation system, was applied to analyse the root endomicrobiome of lettuce (Lactuca sativa L.). By using deep sequencing, we compared the results obtained with the Prospector and the traditional solid medium culturing and extinction methods. We found that the species richness did not differ and that the amount of previously uncultured bacteria did not increase, but that the bacterial diversity isolated by the three methods varied. In addition, the tryptic soy broth and King's B media provided a lower, but different, diversity of bacteria than that of Reasoner's 2A (R2A) medium when used within the Prospector system and the number of unique bacterial strains did not weigh up against those isolated with the R2A medium. Thus, to cultivate as broad a variety of bacteria as possible, divergent isolation techniques should be used in parallel. Thanks to its speed and limited manual requirements, the Prospector is a valuable system to enlarge root microbiome culture collections.