bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving the source of branch length variation in the Y chromosome phylogeny
Authors: Swiel Yaniv , Kelso Janet , Peyrégne Stéphane 
Published: July 2024

AbstractGenetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length variation of Y chromosome lineages has been observed, notably amongst those that are highly diverged from the human reference Y chromosome. Understanding the origin of this variation, which has previously been attributed to changes in generation time, mutation rate, or efficacy of selection, is important for accurately reconstructing human evolutionary and demographic history.Here, we analyze Y chromosomes from present-day and ancient modern humans, as well as Neandertals, and show that branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment. We show that masking fast-evolving, highly divergent regions of the human Y chromosome mitigates the effect of this bias and enables more accurate determination of branch lengths in the Y chromosome phylogeny. Finally, we show that this approach allows us to estimate the age of ancient samples from Y chromosome sequence data and provide updated TMRCA estimates using the portion of the Y chromosome where the effect of reference bias is minimised.
The Enemy Within: how pathogen-free are your commercial specific pathogen-free mice?
Authors: Mark David , Trolan Mia , Douce Gillian , Roe Andrew J , McHugh Rebecca E 
Published: July 2024

AbstractHere, we report the incidental isolation and genome sequencing of anE. coliO157:H7 strain isolated from the faeces of commercial, specific-pathogen free mice (BALB/c). The isolate, subsequently named EC_MP01 was found to carry both Shiga toxin 2a and the Locus of Enterocyte Effacement (LEE) pathogenicity island, major virulence factors associated with severe disease in humans. This report draws attention to the limitations of existing screening systems and highlights how strain carriage influence the outputs from such studies.
Cytoplasmic mRNA capping enzyme is regulated by hypoxia inducible factor HIF1α and controls stability of the target lncRNAs during hypoxia
Authors: Islam Safirul , Mukherjee Chandrama 
Published: July 2024

AbstractHypoxia-inducible factors (HIFs) regulate the expression of several hypoxia-responsive RNAs (HRR) to sustain cellular homeostasis. Cytoplasmic pool of mRNA capping enzyme (cCE) has been shown to recap its substrate uncapped mRNAs or long noncoding RNAs (lncRNAs) present in the cytoplasm, preventing their degradation, even during arsenite-induced oxidative stress. Here, we examined the effect of hypoxia on cCE and its function in regulating the substrate lncRNAs. Hypoxia induces expression of cCE in HIF1α dependent manner as evidenced by Chromatin immunoprecipitation and HIF1α inhibitor experiments. Furthermore, we found cCE post-transcriptionally controls the stability of its target lncRNAs amidst hypoxia. These results suggest that cCE may act as a posttranscriptional modulator that could alter the cellular response to hypoxia by stabilizing cCE-targeted lncRNAs.
Toxic Small Alarmone Synthetase FaRel2 inhibits translation by pyrophosphorylating tRNAGlyand tRNAThr
Authors: Kurata Tatsuaki , Takegawa Masaki , Ohira Takayuki , Syroegin Egor A. , Atkinson Gemma C. , Johansson Marcus J.O. , Polikanov Yury S. , Garcia-Pino Abel , Suzuki Tsutomu , Hauryliuk Vasili 
Published: July 2024

AbstractTranslation-targeting toxic Small Alarmone Synthetases (toxSAS) are effectors of bacterial Toxin-Antitoxin systems that pyrophosphorylate the 3’-CCA end of tRNA to prevent aminoacylation. toxSAS are implicated in antiphage immunity: phage detection triggers the toxSAS activity to shut down viral production. We show that the toxSAS FaRel2 inspects the tRNA acceptor stem to specifically select tRNAGlyand tRNAThr. The 1st, 2nd, 4thand 5thbase pairs the stem act as the specificity determinants. We show that the toxSASs PhRel2 and CapRelSJ46differ in tRNA specificity from FaRel2, and rationalise this through structural modelling: while the universal 3’-CCA end slots into a highly conserved CCA recognition groove, the acceptor stem recognition region is variable across toxSAS diversity. As phages use tRNA isoacceptors to overcome tRNA-targeting defences, we hypothesise that highly evolvable modular tRNA recognition allows for the escape of viral countermeasures through tRNA substrate specificity switching.
Subconcussive head impacts sustained during American football alter gut microbiome diversity and composition
Authors: Pelland Zack , Zafar Aziz , Ay Ahmet , Belanger Ken 
Published: July 2024

ABSTRACTSubconcussive head impacts (SHIs) are a public health concern amongst at-risk populations. SHIs are hits to the head that do not typically generate symptoms and are unlikely to meet diagnostic criteria for mild traumatic brain injury (mTBI). Changes in the gut microbiome have been associated with mTBIs and implicated in both acute recovery from and neurodegenerative pathologies associated with repeated mTBI. This study monitored the gut microbiomes and head impact exposure of collegiate American football players across a competition season to determine if SHIs lead to acute and longer-term changes to the gut microbiome. SHI exposure correlates with changes in microbial diversity and composition three days post-exposure, the athletes’ gut microbiomes change significantly across the season, and mixed effects modeling provides evidence for cumulative effects of SHIs. These data provide the first evidence for a link between SHIs and changes in the diversity and composition of the gut microbiome.
Evaluating the effects of archaic protein-altering variants in living human adults
Authors: Molz Barbara , Lana Alberro Mikel , Eising Else , Schijven Dick , Alagöz Gökberk , Francks Clyde , Fisher Simon E. 
Published: July 2024

AbstractAdvances in paleo-genetics allowed the identification of protein-coding changes arising on the lineage leading toHomo sapiens, by comparing genomes of present-day and archaic hominins. Experimental validation of the potential impact of such changes has so far been restricted to functional assays and model organisms. Large-scale biobanking now makes it possible to identify present-day carriers of archaic alleles and to directly assess phenotypic consequences in living adults. We queried exomes of half a million people in the UK Biobank at 37 genomic positions with supposedly fixed human-specific protein-coding changes. This yielded 103 carriers at 17 positions, with variable allele counts across ancestries. Contrasting carriers and non-carriers of an exemplary archaic allele inSSH2, we observed no deviation from the norm in a range of health, psychological, and cognitive traits. We also identified 62 archaic-allele carriers for aTKTL1missense change, previously shown to have large effects on cortical neurogenesis in brain organoids and animal models. Carriers did not show differences in relevant anatomical brain measures, and a substantial proportion had college/university degrees. This work offers an empirical demonstration of how large-scale biobank investigations of living adults can transform our understanding of human evolution. The findings challenge the notion of fixed human-specific genomic changes, highlight that individual interrogation of relevant sites is unlikely to yield major insights into the emergence of complex human traits, and emphasise the importance of including diverse ancestries when investigating origins of our species.
Natural variation in starvation sensitivity maps to a point mutation in phospholipase IPLA2-VIA inDrosophila melanogaster
Authors: Williams Shawn B. , Franklin Brian , Lemieux Faye A. , Rand David M 
Published: July 2024

AbstractResistance to starvation is a classic complex trait, where genetic and environmental variables can greatly modify an animal’s ability to survive without nutrients. In this study, we investigate the genetic basis of starvation resistance using complementary quantitative and classical genetic mapping inDrosophila melanogaster. Using the Drosophila Genetics Reference Panel (DGRP) as a starting point, we queried the genetic basis of starvation sensitivity in one of the most sensitive DGRP lines. We localize a major effect locus modifying starvation resistance to the phospholipase iPLA2-VIA. This finding is consistent with the work of others which demonstrate the importance of lipid regulation in starvation stress. Furthermore, we demonstrate that iPLA2-VIA plays a role in the maintenance of sugar reserves post-starvation, which highlights a key dynamic between lipid remodeling, sugar metabolism and resistance to starvation stress.
Mapping the human hematopoietic stem and progenitor cell hierarchy through integrated single-cell proteomics and transcriptomics
Authors: Furtwängler Benjamin , Üresin Nil , Richter Sabrina , Schuster Mikkel Bruhn , Barmpouri Despoina , Holze Henrietta , Wenzel Anne , Grønbæk Kirsten , Theilgaard-Mönch Kim , Theis Fabian J. , Schoof Erwin M. , Porse Bo T 
Published: July 2024

SummarySingle-cell transcriptomics (scRNA-seq) has enabled the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, since proteins are the main functional entities in cells, the exclusive use of mRNA measurements comes at the risk of missing important biological information. Here we leverage recent technological advances in single-cell proteomics by Mass Spectrometry (scp-MS) to generate the first scp-MS dataset of anin vivodifferentiation hierarchy encompassing over 2,500 human CD34+ hematopoietic stem and progenitor cells. Through integration with scRNA-seq, we identify proteins that are important for stem cell quiescence, which were not indicated by their mRNA transcripts, and demonstrate functional expression covariance during differentiation that is only detectable on protein level. Finally, we show that modeling translation dynamics can infer cell progression during differentiation and explain 45% more protein variation from mRNA than linear correlation. Our work serves as a framework for future single-cell multi-omics studies across biological systems.
Autophagy inhibition in intestinal stem cells favors enteroendocrine cell differentiation through Stat92E activity
Authors: Lacarrière-Keïta Camille , Nassari Sonya , Jean Steve 
Published: July 2024

ABSTRACTBecause the intestinal epithelium faces many stresses, dysregulation of essential mechanisms governing gut homeostasis, such as autophagy, has been associated with inflammatory bowel pathologies. InDrosophila melanogaster, the inhibition of autophagy, specifically in adult intestinal stem cells (ISCs), affects their number differently through aging. Appropriate intestinal renewal requires a balance between ISC proliferation and differentiation. Herein, we show that in adult ISCs, the loss of core autophagy genes and regulators of autophagosome-lysosome fusion increased the enteroendocrine cell population and transcriptional activity of Stat92E. Functional experiments with cell fate regulators involved in enteroendocrine or enterocyte differentiation or proliferation suggested that dysfunctional autophagy in adult ISCs enhanced Stat92E activity downstream of Hop/JAK kinase. Finally, lineage-tracing analyses confirmed that autophagy inhibition autonomously promotes enteroendocrine cell differentiation without affecting enterocyte differentiation. Thus, our data demonstrates that, under homeostatic conditions, basal autophagy limits enteroendocrine cell differentiation by controlling Stat92E activity.
Storage stability, nutritional and qualitative attributes of biscuits enriched with terebinth, flaxseed and sesame seeds
Authors: Karakoç Fatma Burcu , Ertaş Nilgün , Aslan Mine 
Published: July 2024

PurposeThe utilization of oilseeds in food formulations is prevalent due to their health benefits and nutritional value. These protein-rich oilseeds serve as an affordable and essential source of nutrients and bioactive compounds, fulfilling human protein requirements. As such, this study sought to investigate the impact of partially replacing wheat flour with oilseeds in different proportions on the nutritional and quality characteristics of biscuits.Design/methodology/approachOilseeds, including terebinth, sesame and flaxseed, were partially substituted with wheat flour in amounts of 0, 5, 10, 15, 20 and 25%. The effects of this substitution on the storage stability, nutritional content and physical properties of the resulting biscuits were examined.FindingsThe L* (from 69.75 to 54.06) and b* (from 28.59 to 21.60) color values of biscuits decreased with the supplement of oilseeds. The oilseeds addition increased the protein, fat, energy, and ash values of biscuits. At the highest level of added terebinth, sesame and flaxseed, respectively, the amounts measured were 5984.62 mgGAE/kg, 1553.85 mgGAE/kg and 2169.23 mgGAE/kg, which were higher than the control biscuits (715.39 mgGAE/kg). The incorporation of oilseeds resulted in a substantial decrease in pH and peroxide values, while the moisture content was increased throughout the 6-month storage period. The use of terebinth in biscuits led to better oxidative stability than sesame and flaxseed-containing samples. The biscuit samples with terebinth had a longer induction time. The lowest induction time of biscuits with 25% flaxseed was chosen, approximately 3.5 h.Research limitations/implicationsOilseed flours, which are rich in lipids, have been shown to enhance the quality of biscuits. However, further studies could aim to reduce the amount of shortening used to improve their quality even further. Reducing the shortening could keep the lipid content at an acceptable amount, especially considering consumers' current expectations for low-fat foods.Practical implicationsPlant-based bioactive are generally known as secondary metabolites and have promising therapeutic attributes, especially antioxidative properties.Social implicationsThanks to this composition, some of these seeds have proven effective in controlling and preventing metabolic diseases (hypertension, hypercholesterolemia, diabetes, coronary heart disease and several types of cancer) as well as providing interesting properties to foods.Originality/valueAs result, oilseeds can be successfully used as functional and sustainable food ingredients to improve the functional, nutritional and storage stability of biscuits.
Appraisal of policy measures at the beginning of a pandemic: Empirical evidence from the first four months and 12 months of the COVID-19 pandemic
Authors: du Plessis Emile 
Published: July 2024

PurposeThe rapid spread of the COVID-19 pandemic upended societies across the world, with billions forced into lockdowns. As countries contemplated instating and rolling back lockdown measures, and considered the impact of pandemic fatigue on policy measures, and furthermore to prepare for the improved management of future pandemics, this study examines the effectiveness of policy measures in limiting the spread of infections and fatalities.Design/methodology/approachThe methodological approach in the study centres on a fixed effects panel regression analysis and employs the COVID-19 Government Response Stringency Index, which comprises eight containment measures and three health campaigns, with progressive degrees of stringency, in order to investigate the efficacy of government policies.FindingsFindings suggest that some government policies were effective at reducing implicit mortality rates, infection cases and fatalities during the first four months of the COVID-19 pandemic. Solid stringency measures to reduce mortality rates include public gathering restrictions on more than 100 attendees, and international travel limits for developed countries and islands. Fatalities can further be reduced through the closing of public transport, whereas infection cases also experience benefits from public information campaigns. Comparable results are observed in a robustness test across 12 months.Originality/valueSome non-pharmaceutical policies are shown to be more effective than others at reducing the spread of infections, fatalities and mortality rates, and support policymakers to manage future pandemics more effectively.
Product-as-a-service from B2C retailers' perspective: a framework of challenges and mitigations
Authors: Koers Lisanne , Steffens Solveigh , Tamerus Saskia , Forslund Helena 
Published: July 2024

PurposeProduct-as-a-Service (PaaS) has the potential to enable closed-loop supply chains (CLSC) and decrease environmental impact, but it is only applied on a small scale. The purpose of this paper is to explore and develop a framework of challenges and corresponding mitigations encountered by Business-to-Consumer (B2C) retailers when transitioning to PaaS.Design/methodology/approachData collection drew on a qualitative interview study with two industry experts and four PaaS B2C retailers from different Dutch industries.FindingsA framework was developed linking 26 challenges in eight clusters—financial, product-related, supply chain-related, consumer-related, human resources, research and development/technology, regulatory and industry-related—to 24 mitigations. The mitigations were elaborated, and theoretical insights for matching challenges with mitigations were provided.Research limitations/implicationsThis study expands PaaS literature to the generally under-researched retail context. It contributes to CLSC literature by applying it to a less-studied context, thereby revealing many supply chain-related challenges and mitigations encountered by B2C retailers.Practical implicationsThe framework offers practical guidance to retail managers for overcoming or preventing challenges in PaaS, in their endeavours toward adopting environmentally sustainable practices.Social implicationsThe study creates awareness about environmental sustainability and the potential to reduce societal impact, in which a PaaS-enabled CLSC is one step.Originality/valueStudying PaaS and CLSC in a retail context is timely and novel.
Mobile money, food security and coping strategies in a post-conflict and fragile context: evidence from Burundi
Authors: Atta-Aidoo Jonathan , Bizoza Saidi , Matthew Ester Cosmas , Saleh Abdulkarim Onah 
Published: July 2024

PurposeAttaining the Sustainable Development Goal 2 (SDG2) of zero hunger continues to be a challenge in most parts of Sub-Saharan Africa. However, financial inclusion is seen as a potential pathway for reducing food insecurity among poor households. Mobile money is a financial inclusion instrument that is easily accessible to poor households and has the potential to increase the level of financial inclusion. This paper contributes to the literature by examining the determinants of mobile money adoption, its effects on household food security and the choice of coping strategies in Burundi, a post-conflict and fragile country.Design/methodology/approachUsing survey data that involved 860 households in Burundi, we adopted the Household Hunger Scale (HHS) developed under the Food and Nutrition Technical Assistance Project to measure household food security. We further employ the endogenous switching regression treatment effects model for ordered outcomes and the multivariate probit model to achieve our aims.FindingsThe results of our study reveal that the adoption of mobile money is influenced by factors such as gender, marital status, age, formal education, membership in a social network, area of residence and access to a tarred road network. Additionally, the food security status of a household was determined by marital status, formal education, social network membership, access to tarred roads, off-farm income, access to credit and land tenure security. We confirm that mobile money adoption has a significantly positive effect on the food security status of households with heterogeneity in gender and area of residence. We also find that mobile money adoption reduces the likelihood of households adopting consumption-related coping strategies.Practical implicationsThe promotion of mobile money should, therefore, be included in Burundi’s national food security policies.Originality/valueThis study contributes to the literature by providing empirical evidence on the effect of mobile money adoption on household food security and the choice of coping strategies in a post-conflict context.
Asymmetric thresholds of macroeconomic volatility's impact on stock volatility in developing economies: a study in Vietnam
Authors: Nguyen Lien Thi , Nguyen Minh Thi , Nguyen The Manh 
Published: July 2024

PurposeThis paper examines the impact of macroeconomic volatility on stock volatility, both under normal conditions and during the COVID-19 pandemic in Vietnam.Design/methodology/approachWe extend the existing Exponential Generalized Autoregressive Conditional Heteroskedasticity model by adding a new component: the thresholds – the levels of macroeconomic volatility at which the market may respond differently. These thresholds are estimated for both positive and negative volatility.FindingsThe impact of macroeconomic volatility on stock volatility is asymmetric: there are thresholds of macroeconomic volatility at which its pattern changes. These thresholds are higher in the case of positive volatility compared with negative volatility. The thresholds were also higher during the COVID-19 pandemic. Macroeconomic variables influence stock volatility differently depending on market conditions. While GDP is more significant in normal periods, interest rates affect it in both normal and unstable phases.Research limitations/implicationsOur models consider only two variables representing macroeconomic variables: interest rate and GDP. Furthermore, only one lag period of the variables is included in the analysis. In the future, more macrovariables and longer lags could be included when computational techniques advance.Practical implicationsPolicymakers should consider the impact of macroeconomic volatility on the stock market when designing policies, especially at thresholds. Similarly, investors should pay more attention to macroeconomic volatility when constructing and managing their portfolios, particularly when such volatility is close to thresholds.Originality/valueThe inclusion of thresholds as parameters to be estimated into the model provides more insights into the impact of macroeconomic variables on stock volatility.