bluuebunny/crossref_metadata_2025_split huggingface dataset:
RAD18 opposes transcription-associated genome instability through FANCD2 recruitment
Authors: Wells James P. , Chang Emily Yun-chia , Dinatto Leticia , White Justin , Ryall Stephanie , Stirling Peter C. 
Published: June 2022

AbstractDNA replication is a vulnerable time for genome stability maintenance. Intrinsic stressors, as well as oncogenic stress, can challenge replication by fostering conflicts with transcription and stabilizing DNA:RNA hybrids. RAD18 is an E3 ubiquitin ligase for PCNA that is involved in coordinating DNA damage tolerance pathways to preserve genome stability during replication. In this study, we show that RAD18 deficient cells have higher levels of transcription-replication conflicts and accumulate DNA:RNA hybrids that induce DNA double strand breaks and replication stress. We find that these effects are driven in part by failure to recruit the Fanconi Anemia protein FANCD2 at difficult to replicate and R-loop prone genomic sites. While RAD18 is important for FANCD2 localization after splicing inhibition or aphidicolin treatment, it is comparatively less important during interstrand crosslink repair. Thus, we highlight a RAD18 dependent pathway promoting FANCD2-mediated suppression of R-loops and transcription-replication conflicts.AUTHOR SUMMARYGenome instability, a state in which cells acquire mutations more quickly, drives cancer initiation and progression. DNA is normally protected from such mutations by a host of specialized factors that recognize and repair potentially damaging circumstances. Here we describe under-appreciated links between a protein called RAD18, which recognizes potentially damaging stress, and a phenomenon called a transcription-replication conflict. If not repaired such conflicts can lead to DNA breaks. We find that RAD18 plays an important role in recruiting another repair protein called FANCD2 to sites of transcription-replication conflicts. By doing so, RAD18 protects the human genome from damage when it is faced with stresses such as those seen in cancer cells. This work provides new insight to how the FANCD2 protein is brought to potentially damaging sites in our genomes.
Structural inventory of cotranslational protein folding by the eukaryotic RAC complex
Authors: Kišonaitė Miglė , Wild Klemens , Lapouge Karine , Gesé Genís Valentín , Kellner Nikola , Hurt Ed , Sinning Irmgard 
Published: June 2022

AbstractFolding of nascent chains emerging from the ribosome is a challenge in cellular protein homeostasis, which in eukaryotes is met by an Hsp70 chaperone triad directly binding at the ribosomal tunnel exit. The conserved ribosome-associated complex (RAC) consists of the non-canonical Hsp70 Ssz1 and the J-domain protein Zuotin (Zuo1), which in fungi acts together with the canonical Hsp70 protein Ssb. Here, we determined high-resolution cryo-electron microscopy structures of RAC bound to the 80S ribosome. RAC adopts two distinct conformations accommodating continuous ribosomal rotation by a flexible lever arm. The heterodimer is held together by a tight interaction between the Ssz1 substrate-binding domain (SBD) and the N-terminus of Zuo1, with additional contacts between the Ssz1 nucleotide-binding domain (NBD) and the Zuo1 J- and ZHD domains that form a rigid unit. The Zuo1 HPD-motif conserved in J-proteins is masked by the Ssz1 NBD, different from the canonical Hsp70 J-protein contact, however, allowing to position Ssb for activation by Zuo1. Our data provide the basis for understanding how RAC cooperates with Ssb at the ribosome in dynamic nascent chain interaction and protein folding.
The ontogeny of asymmetry in echolocating whales
Authors: Lanzetti Agnese , Coombs Ellen J. , Miguez Roberto Portela , Fernandez Vincent , Goswami Anjali 
Published: June 2022

AbstractExtreme asymmetry of the skull is one of the most distinctive traits that characterizes toothed whales (Odontoceti, Cetacea). The origin and function of cranial asymmetry are connected to the evolution of echolocation, the ability to use high frequency sounds to navigate the surrounding environment. Although this novel phenotype must arise through changes in cranial development, the ontogeny of cetacean asymmetry has never been investigated. Here we use three-dimensional geometric morphometric to quantify the changes in degree of asymmetry and skull shape during prenatal and postnatal ontogeny for five genera spanning odontocete diversity (oceanic dolphins, porpoises, and beluga). Asymmetry in early ontogeny starts low and tracks phylogenetic relatedness of taxa. Distantly-related taxa that share aspects of their ecology overwrite these initial differences via heterochronic shifts, ultimately converging on comparable high levels of skull asymmetry. Porpoises maintain low levels of asymmetry into maturity and present a decelerated rate of growth, likely retained from the ancestral condition. Ancestral state reconstruction of allometric trajectories demonstrates that both paedomorphism and peramorphism contribute to cranial shape diversity across odontocetes. This study provides a striking example of how divergent developmental pathways can produce convergent ecological adaptations, even for some of the most unusual phenotypes exhibited among vertebrates.
The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years
Authors: De Carvalho Mickael , Jia Guo-Song , Srinivasa Ananya Nidamangala , Billmyre R. Blake , Xu Yan-Hui , Lange Jeffrey J. , Sabbarini Ibrahim M. , Du Li-Lin , Zanders Sarah E. 
Published: June 2022

AbstractMeiotic drivers are selfish elements that bias their own transmission into more than half of the viable progeny produced by a driver+/driver− heterozygote. Meiotic drivers are thought to exist for relatively short evolutionary timespans because a driver gene or gene family is often found in a single species or in a group of very closely related species. Additionally, drivers are generally considered doomed to extinction when they spread to fixation or when suppressors arise. In this study, we examine the evolutionary history of the wtf meiotic drivers first discovered in the fission yeast Schizosaccharomyces pombe. We identify homologous genes in three other fission yeast species S. octosporus, S. osmophilus, and S. cryophilus, which are estimated to have diverged over 100 million years ago from the S. pombe lineage. Synteny evidence supports that wtf genes were present in the common ancestor of these four species. Moreover, the ancestral genes were likely drivers as wtf genes in S. octosporus cause meiotic drive. Our findings indicate that active meiotic drive systems can be maintained for long evolutionary timespans.
Multiple resistance of Colletotrichum truncatum from soybean to QoI and MBC fungicides in Brazil
Authors: Rogério Flávia , Linhares de Castro Renata Rebellato , Massola Júnior Nelson Sidnei , Boufleur Thaís Regina , dos Santos Ricardo Feliciano 
Published: June 2022

AbstractColletotrichum truncatum, the most relevant fungal species associated with soybean anthracnose, is responsible for major losses in the crop. Chemical control via fungicide application is still the most effective strategy for the control of soybean foliar diseases. However, the increase in anthracnose incidence in some regions of Brazil indicates that current chemical control has not been effective against anthracnose. In this study, we assessed the fungicide sensitivity of C. truncatum lineages using isolates representing two important regions of soybean production in Brazil to the fungicides azoxystrobin, thiophanate-methyl, difenoconazole, and fludioxonil. We characterized the molecular resistance to quinone-outside inhibitors (QoI), methyl benzimidazole carbamates (MBC) and demethylation inhibitors (DMI) fungicide groups based on amino acid sequences of the cytochrome b (cytb), β-tubulin gene (β-tub), and P450 sterol 14a-demethylases (CYP51) genes. Multiple resistance of C. truncatum isolates to QoI and MBC was observed associated with mutation points in the β-tub (E198A and F200Y) and cytb (G143A). Alternatively, low EC50 values were found for fludioxonil and difenoconazole indicating high efficacy. Analysis of C. truncatum genomes revealed two potential DMI targets, CYP51A and CYP51B, and higher genetic variability in the CYP51A gene. A slight correlation between genetic differentiation of C. truncatum populations and fungicide sensibility was found (Student’s t-test <0.001). To our knowledge, this is the first report of multiple resistance to QoI and MBC fungicides in C. truncatum in Brazil.Highlights-Multiple resistance of C. truncatum to azoxystrobin and thiophanate-methyl-C. truncatum isolates are sensitive to difenoconazole and fludioxonil-Presence of E198A and F200Y β-tubulin mutations and G143A cytochrome b mutation-Presence of CYP51A and CYP51B paralogues and higher genetic variability in the CYP51A
Comparative genomic insights into bacterial induction of larval settlement and metamorphosis in the upside-down jellyfish Cassiopea
Authors: Ohdera Aki , Attarwala Khushboo , Wu Victoria , Henry Rubain , Laird Henry , Hofmann Dietrich K. , Fitt William K. , Medina Mónica 
Published: June 2022

AbstractBacterial biofilm is crucial in inducing the larval transition from pelagic to benthic environments for marine organisms. Bacteria can therefore dictate species distribution and success of the individual. Despite the importance of marine bacteria to animal ecology, the identity of inductive microbes for many invertebrates are unknown. We isolated bacteria belonging to multiple phyla are capable of inducing settlement and metamorphosis in the upside-down jellyfish Cassiopea xamachana. The most inductive isolates belonged to the genus Pseudoalteromonas, a marine bacterium known to induce the pelago-benthic transition in other marine invertebrates. In sequencing the genome of the isolated Pseudoalteromonas and an inductive Vibrio, we found biosynthetic pathways previously implicated in larval settlement were absent in these Cassiopea inducing taxa. Comparative analysis of the Pseudoalteromonas and Vibrio revealed shared genes that could underlie the inductive capacity of these two bacteria. Thus, C. xamachana are capable of responding to multiple bacterial species, but they may be responding to a common cue produced by multiple taxa. These findings could provide hints to the ecological success of C. xamachana compared to sympatric congeneric species within mangrove environments and provide avenues to investigate the evolution of animal-microbe interactions.
Allopatric montane wren-babblers exhibit similar song notes but divergent vocal sequences
Authors: Jagan M. Abhinava , Bhat Ananda Shikhara , Krishnan Anand 
Published: June 2022

AbstractThe songs of passerine birds consist of notes temporally arranged into vocal sequences following syntactic structures, and function both in courtship and territorial defense. Geographic barriers are important drivers of avian speciation, and also influence the divergence of song. However, there is relatively little quantitative study of the relationship between geographic barriers and the syntactic structure of vocal sequences. Here, we investigate interspecific divergence in song notes and syntax within a genus of allopatric montane Asian wren-babblers (Spelaeornis). Employing a robust quantitative analytical framework and song recordings from publicly accessible databases, we find thatSpelaeornisappear to have undergone diversification in song syntax without divergence in note parameters. Broadly, we find three different syntactic structures across the eight species in the genus, each occurring in a different geographic region in Asia, with two species apparently exhibiting intermediate syntax. Species within the genus appear to possess similar song notes, but subgroups confined to different geographic regions (eg: hills south of the Brahmaputra river) arrange these notes according to different syntactic rules to construct songs. Our computational framework to examine signal structure and diversification across multiple scales of signal organization has potential implications for our understanding of speciation, signal evolution and more broadly in fields such as linguistic diversification.
Natural variation in C. elegans short tandem repeats
Authors: Zhang Gaotian , Wang Ye , Andersen Erik C. 
Published: June 2022

AbstractShort tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1-6 bp in the reference genome of C. elegans. Of these STRs, 27,636 harbored polymorphisms across 540 wild strains and only 9,691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared to the reference genome, the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed the lowest STR diversity and constrained STR mutations. STR diversity also showed similar genetic divergence and selection signatures among wild strains as in previous studies using single-nucleotide variants. We further identified STR variation in two mutation accumulation line panels that were derived from two wild strains and found background-dependent and fitness-dependent STR mutations. Overall, our results delineate the first large-scale characterization of STR variation in wild C. elegans strains and highlight the effects of selection on STR mutations.
Independence and effectiveness of Shariah department officers to ensure Shariah compliance: evidence from Islamic banks in Bangladesh
Authors: Alam Md. Kausar , Tabash Mosab I. , Thakur Oli Ahad , Rahman Md. Mizanur , Siddiquii M. Naim , Hasan Safiqul 
Published: June 2022

PurposeThe study aims to examine the independence and effectiveness of the Shariah department officers of the Islamic banks in Bangladesh as the Shariah supervisory board (SSB) provides the annual Shariah report and Shariah resolutions based on the reports of the Shariah department officers.Design/methodology/approachThe study applied a qualitative case study to achieve the research objectives. Data were collected through face-to-face interviews with the regulators, Shariah supervisory boards, Shariah department executives, and experts from the central bank and Islamic banks of Bangladesh.FindingsThe study illustrates that Shariah department officers/Shariah officers in Bangladesh seem to lack independence and decision-making authority in accomplishing ex-post Shariah governance functions (i.e. Shariah audit, Shariah compliance and Shariah review) as well as ensuring Shariah compliance. The Shariah officers cannot work spontaneously on practical issues without any interference. The Shariah officers also have to answer to the management regarding their Shariah functions and are not allowed to come up with any opinions without the authority’s authorization.Research limitations/implicationsThe study has significant contributions to the central bank and Islamic banks in Bangladesh. This research suggests that regulators, SSB, and Islamic banks should focus on ensuring Shariah compliance and protecting the independence of Shariah department officers as they are mainly related to practical monitoring of Shariah issues. It also suggests that Shariah department officers should directly report to SSB rather than the management regarding Shariah’s compliance and audit issues.Originality/valueThis study is unique in the context of Bangladesh and the global context as a whole for Shariah department officers.
Behind a cup of coffee: international market structure and competitiveness
Authors: Gois Tafarel Carvalho , Thomé Karim Marini , Balogh Jeremiás Máté 
Published: June 2022

Purpose
This study aims to analyse the structure and the competitiveness of the international coffee market.

Design/methodology/approach
To describe the international market structure, this study uses Herfindahl–Hirschman index, net export index (NEI), and to measure export competitiveness revealed symmetric comparative advantage (RSCA). Finally, survival function analyses were developed using the Kaplan–Meier product-limit estimator to characterize the stability and duration of the competitiveness in the international coffee market.

Findings
The results reveal that the imports and exports market structure are unconcentrated. NEI shows that several countries are stable in their commercial characteristics (imports, exports and re-exports), nevertheless, NEI also revealed countries transitioning through the commercial characteristics, that the international coffee market structure presents dynamic commercial characteristics. The result for (RSCA shows that Uganda, Ethiopia, Honduras, Brazil, Colombia, Guatemala and Indonesia had the highest values and also resulted in better survival rates along with Italy, India, Mexico and Switzerland. The stability of RSCA indices is investigated by regression analysis, showing a tendency to increase expertise in coffee exports from 2015.

Originality/value
This study provides a comprehensive and recent analysis of the international coffee market structure and competitiveness, contributing to the analysis of the international market of the product.
Global scientific literature on human resource development: a bibliometric analysis using Scopus database
Authors: Pham-Duc Binh , Tran Trung , Huu Hoang Dung , Bao Do Chau 
Published: June 2022

Purpose
This paper aims to analyze the development of global human resource development (HRD) articles published in journals indexed in the Scopus database since 1960s until present time.

Design/methodology/approach
A publication collection of 1,905 articles collected from the Scopus database was downloaded and analyzed by using bibliometric techniques available in the VOSviewer and Biblioshiny software.

Findings
Three different development stages of HRD research have been identified: a seeding stage between 1962 and 1989, a growth stage between 1990 and 2007 and a development stage from 2008 onward. The USA and the UK were the biggest contributors who participated to 30.02% and 12.55% of articles in the collection and received 43.82% and 19.54% of the total number of citations, respectively. Scholars with the most publications and citations are mostly from the USA and the UK, and nine over ten most cited articles having first author’s affiliation located there. Emerald Group is the most popular publishing house, as five over ten most popular journals belong to this publishing house.

Originality/value
After six decades of development, it is necessary to examine the evolution of HRD research, its characteristics and its intellectual framework as this type of analysis is not yet available in the literature. This study helps scholars better understand this research field, as well as better prepare for future work in HRD.
Trainees’ aversions of employee training programs
Authors: Andoh Raphael Papa Kweku , Annan-Prah Elizabeth Cornelia , Owusu Emmanuel Afreh , Agyei Paul Mensah 
Published: June 2022

Purpose
Training evaluation is an important part of training programs and evaluating the reactions of trainees is of immense value, but there are few studies on this level of evaluation, as it is a neglected area of research. More so, when trainee reactions to training are poor, human resource managers together with learning and development professionals are able to improve on training programs. Nonetheless, no study has focussed on the aversions of trainees to training, and so this study aims to investigate the aversions of trainees regarding employee training.

Design/methodology/approach
This study uses the exploratory research design and obtains data from trainees in an online survey using an open-ended question. Thematic text analyses of the statements of 118 respondents are performed using a two-level coding process.

Findings
A total of 15 first-level codes are identified from the texts and categorized into five second-level codes. Further analyses culminate in the identification of two broad themes; trainers’ presentation aversions and organization of training aversions.

Practical implications
Attention must be given to the aversions of trainees in the training evaluation literature. This is because of the considerable amount of information that can be generated and based on that, identify the weaknesses inherent in employee training programs and ultimately improve this critical human resource function within organizations. In attending to the trainee aversions, the least and most reported should be resolved holistically for training objectives to be achieved.

Originality/value
Trainee reaction studies are scarce in the training literature. In addition, most of the existing trainee reaction studies focus on satisfaction while using closed-ended questionnaires. To the best of the authors’ knowledge, this is the first study that focuses on the aversions of trainees and which uses an open-ended question.
The relative importance of click-through rates (CTR) versus watch time for YouTube views
Authors: Wilson Linus T. 
Published: June 2022

Purpose
This study aims to analyze whether average video watch time or click-through rates (CTR) on YouTube videos are more closely associated with high numbers of views per subscriber using linear regressions.

Design/methodology/approach
In 2018, YouTube began releasing CTR data to its video creators. Since 2012, YouTube has emphasized how it favors watch time over clicks in its recommendations to viewers. To the best of the author’s knowledge, this is the first academic study looking at that CTR data to test what matters more for views on YouTube. Is watch time or CTR more important to getting views on YouTube?

Findings
The author analyzed new video releases on YouTube. This paper finds almost no or limited evidence that higher percent audience retention or total average watch time per view, respectively, are associated with more views on YouTube. Instead, videos with higher CTR got significantly more views.

Originality/value
The author knows no other study that tests the relative importance of CTR or watch time per view in predicting views for new videos on YouTube.
Assessing the utilisation of industrial waste as aggregate and manufactured sand: microstructural and durability characteristics on high-performance concrete
Authors: Reddy Kamasani Chandrasekhar , Siddamreddy Sateesh Reddy 
Published: June 2022

PurposeUtilising industrial waste, such as fly ash (FA) and bagasse ash (BA), reduces waste management and increases mechanical strength. Concrete is modified with FA and BA in the cool bonded method of concrete preparation.Design/methodology/approachThe study used to partially replace cement with BA powder at proportions 0, 5, 10, 15, 20 and 25% and coarse aggregates are replaced with FA aggregates made with FA and cement using a cold-bonded technique at proportions 0–25%. FA aggregates were made at 10:90, 15:85, 20:80 and 25:75 proportions of cement and FA. The FA aggregates at the best proportion 15:85 was selected as a coarse aggregate by conducting tests like specific gravity, crushing value, impact value and water absorption tests.FindingsThe addition of 30% content decreases porosity by 21% and increases strength significantly at 28 days. Microstructure evolution is carried out to identify material behaviour.Originality/valueMechanical and durable properties such as flexural strength, tensile strength, water absorption test, acid and alkaline tests are conducted on M50 grade concrete after 3–28 days of curing.