bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolving impact of the COVID-19 pandemic in chronic dialysis recipients over the course of pandemic waves and COVID-19 vaccination rollout: a French national study
Authors: Leye Elhadji , El Karoui Khalil , Delory Tristan , Espagnacq Maude , Khlat Myriam , Le Coeur Sophie , Lapidus Nathanaël , Hejblum Gilles
Published: April 2024

Background

This observational study aims to assess the impact of the pandemic on the evolving of kidney transplantations, survival, and vaccination in chronic dialysis recipients (CDR) over the COVID-19 pandemic subperiods.

Methods

Using the French national health claims database, incident persons with end stage kidney disease in years 2015 to 2021 treated with dialysis were followed-up until December 31, 2022. Kidney transplantion and survival over pandemic subperiods versus the prepandemic period were investigated using longitudinal models with time-dependent covariates. Moreover, the impact of cumulative doses of COVID-19 vaccine on hospitalization and survival were compared between CDR and matched-control individuals.

Findings

Follow-up of the 71,583 CDR and 143,166 controls totalized 639,341 person-years (CDR: 184,909; controls: 454,432). The likelihood of receiving a kidney transplant decreased during all pandemic subperiods except one. Mortality in CDR increased during the 3 wave subperiods (hazard ratio (HR [95% confidence interval]): 1.19 [1.13–1.27], 1.19 [1.15–1.23], and 1.12 [1.07–1.17], respectively). While vaccine coverage declined with each booster dose, receiving such doses was associated with lower risks of COVID-19-related hospitalization (0.66 [0.56–0.77], 0.83 [0.72–0.94] for 1stbooster versus 2nddose and 2ndbooster versus 1stbooster, respectively) and death (corresponding HR: 0.55 [0.51–0.59], 0.88 [0.83–0.95]). Evolving patterns in mortality and vaccination outcomes were similar in CDR and controls.

Interpretation

The impact of the pandemic in CDR was not specific of the kidney diseaseper se. Study results also suggest future research aimed at increasing adherence to vaccine booster doses.

Funding

Initiative Économie de la Santé de Sorbonne Université (Idex Sorbonne Université, programmes Investissements d’Avenir) ; Ministère de la Solidarité et de la Santé (PREPS 20-0163).
Impact of the 2013 WHO guidelines for screening and treatment of cervical precancerous lesions on women’s screening rates, by HIV-status, in East and Southern Africa: A regression discontinuity design analysis
Authors: Chipanta David , Osborne Connie , Bohlius Julia , Shakarishvilia Ani , Amo-Agyei Silas , Nyondo-Mipando Alinane Linda , Estill Janne Anton Markus , Keiser Olivia
Published: April 2024

Introduction

In 2013, the World Health Organization (WHO) issued guidelines for cervical pre-cancer screening. It recommended screening women aged 30–49, and younger women once they tested HIV-positive. Subsequent WHO guidelines recommended screening women living with HIV (WLHIV) starting at age 25. However, the impact of 2013 guidelines and age to start screening on screening has not been studied.

Methods

We used a regression discontinuity design (RDD) analysis of population-based data to assess the impact of the 2013 WHO guidelines on the screening rates for women according to HIV status and age group in Ethiopia, Malawi, Rwanda, Tanzania, Zambia, and Zimbabwe. The outcome was self-reported ever having been screened for cervical pre-cancer between 2008 and 2018. We compared the screening rates according to HIV status and age group, before and after age 25 years. And before and after 2014, the year countries adopted the 2013 guidelines. We then used a data-driven optimal bandwidth selection procedure to estimate the guidelines’ average treatment effect (ATE), with a local polynomial regression discontinuity and robust bias-corrected confidence intervals. We validated the RDD methodology overall and for women with a significant ATE at the country-level analysis.

Results

We included 73179 women: 6680 (9.1%) living with HIV, 4328 (5.9%) with unknown HIV status, and 62171 (85.0) with a negative HIV status. 5726 (7.9%) reported having ever been screened; 4022 (6.5%) with unknown HIV status, 525 (12.1%) with a negative HIV status and 1179 (17.7%) living with HIV. Adolescent girls and young women living with HIV (AGYWLHIV) aged 15–24 reported screening less often (917 (13.7%)) than their peers with unknown (1677 (38.8%)) or positive HIV status (27278 (43.9%)) (P<0.001), or older women. The ATE of screening was 0 for women with unknown or positive HIV status, for whom the RDD was valid.

Conclusion

We found no evidence the 2013 WHO guidelines increased or reduced women’s cervical pre- cancer screening. However, AGYWLHIV reported screening less often. Policy makers should lower the age to start screening WLHIV from 25 to 15 to screen more AGYWLHIV. Studies are required to examine the impact of the guidelines on cervical pre-cancer screening in more countries.
Blood pressure, cardiometabolic traits and cardiovascular events in women with uterine fibroids: a genetic correlation and Mendelian randomization study
Authors: Henry Joséphine , Berrandou Takiy , Brewster Lizzy M. , Bouatia-Naji Nabila
Published: April 2024

Background

Uterine fibroids (UFs) are under-studied uterus neoplasms, affecting women of reproductive age and often leading to hysterectomy. Clinical series suggest impaired cardiometabolic features including hypertension in UFs. We investigated potential genetic links between blood pressure (BP), several cardiometabolic traits and events and UFs.

Methods

We used summary statistics of genome-wide association studies (GWAS) for UFs and 18 traits related to BP and cardio-metabolism. We applied linkage disequilibrium score regression to estimate genetic correlations and GCTA-mtCOJO for adjusted correlations. Univariate and bi-directional Mendelian randomization (MR) were used to test causal associations with UFs. We computed inverse variance-weighted. Weighted median estimation and MR-Egger regression were computed for sensitivity analyses. Multiple testing was addressed by Bonferroni correction.

Results

UFs significantly correlated with systolic (rg=0.08,P=8.7×10−5) and diastolic (rg=0.12,P=8.2×10−8) BP, including after adjustment on body mass index (BMI). UFs positively corelated with BMI (rg=0.11,P=4.1×10−4), waist-to-hip ratio (WHR) (rg=0.09,P=7.3×10−3), diabetes (rg=0.15,P=1.9×10−5) and triglycerides (TG) (rg=0.17,P=7.6×10−7). We identified a negative correlation with sex hormone-binding globulin (SHBG) (rg=-0.16,P=3×10−4), a marker of bio-availability of sex-steroids. We found no evidence for shared genetics with vascular diseases, except migraine (rg=0.08,P=5.8×10−7). MR analyses supported BMI, WHR, TG and SHBG, to causally associate with increased risk for UFs.

Conclusions

Our study shows that UFs share substantial genetic basis with traits related to BP, obesity, diabetes, in addition to migraine, a predominantly female vascular condition. We provide MR-based evidence for central obesity, visceral fat traits and sex-steroids bio-availability as relevant genetic risk factors for UFs.
The Current State & Sentiment of Artificial Intelligence in North American Anesthesiology Residency Programs
Authors: Elliott Tyler V , Goldstein Joseph C , Goldstein Heidi V
Published: April 2024

Purpose

This study aims to investigate the current state and sentiment of artificial intelligence (AI) training in North American anesthesiology residency programs, assessing existing AI education landscapes, identifying barriers to implementation, and understanding program directors’ expectations for AI’s impact on the field.

Methods

A cross-sectional survey targeted anesthesiology program directors across North America. The survey, conducted anonymously via Qualtrics, gauged their AI training offerings, sentiments towards AI’s influence, and familiarity with AI educational policies. Information on questionnaire development, administration, and data analysis was included.

Results

Of the 163 programs surveyed, 32 responded, yielding a response rate of 19.6%. A substantial 81% of responding program directors reported no current AI training. Despite this, 67% anticipate AI’s transformative impact. Only 19% currently offer AI/ML training. Standardized presentation of results with accompanying numerators and denominators were employed.

Conclusion

The findings reveal a significant gap between the recognition of AI’s importance and the current offering of training in anesthesiology residency programs. Barriers to implementation include resource constraints and time limitations, exacerbated by the pandemic. Overcoming these barriers and aligning positive sentiments with educational offerings is crucial for preparing future physicians for the AI-driven healthcare landscape.

Implication Statement

This study exposes a substantial gap between the positive anticipation of AI’s impact on anesthesiology and the current lack of training in North American residency programs. Recognizing this disparity is crucial for swiftly implementing comprehensive AI education, ensuring future anesthesiologists navigate healthcare’s evolving landscape adeptly.

Disclosures

The authors have no competing interests or financial interests to disclose. There was no funding associated with the completion of this study.
Mutant phenotypes and comprehensive expression analyses reveal roles for CLAVATA in moss vegetative and reproductive development and fertility
Authors: Venza Zoe Nemec , Greiff George R. L. , Harrison C. Jill
Published: April 2024

The CLAVATA pathway regulates meristem size in angiosperms, but bryophytes have distinct meristematic activities to vascular plants, and gametophytic CLAVATA functions are divergent between species. Here we analysed the promoter activities of all CLAVATA peptide and receptor-encoding genes in the mossPhyscomitrium patens, and using mutants, identified requirements for PpCLV1 and PpRPK2 receptors in male and female reproductive development and fertility. In gametophytes, all 12CLAVATAgenes were expressed in foraging filaments (caulonemata) and leaves (phyllids), but most tissues showed highly specific patterns of promoter activity.PpCLE3expression specifically marked gametophyte shoot (gametophore) apical cells andPpCLV1bandPpRPK2expression marked overlapping apical domains. Expression in male (antheridia) and female (archegonia and eggs) reproductive tissues led us to use mutants to identify roles forPpCLV1a, PpCLV1bandPpRPK2in fertility and reproductive development. In sporophytes, the foot was a common site ofPpCLEexpression, and all genes were expressed in stomata. NoPpCLEactivity specifically marked the embryonic apical cells, and embryonicPpCLV1bandPpRPK2expression marked distinct apical and basal domains. Thus,P. patensstem cell activity is likely regulated by different genes in gametophytes and sporophytes, and promoter evolution was a likely driver of diversification of CLAVATA function.

Plain language summary

Whilst gene gain and duplication contributed to the origin of land plants and diversification of seed plants, significant gene loss is associated with morphological adaptation in bryophytes. In the moss,Physcomitrium patens,CLAVATAgenes expanded from low ancestral numbers, showing exquisite cell type specificity in expression. Our results suggest co-option of CLAVATA into many different developmental processes during moss evolution.
AlbuMAX supplemented media induces the formation of transmission-competentP. falciparumgametocytes
Authors: Graumans Wouter , van der Starre Alex , Stoter Rianne , van Gemert Geert-Jan , Andolina Chiara , Ramjith Jordache , Kooij Taco , Bousema Teun , Proellochs Nicholas
Published: April 2024

Asexual blood stage culture ofPlasmodium falciparumis routinely performed but reproducibly inducing commitment to and maturation of viable gametocytes remains difficult. Culture media can be supplemented with human serum substitutes to induce commitment but these generally only allow for long-term culture of asexual parasites and not transmission-competent gametocytes due to their different lipid composition. Recent insights demonstrated the important roles lipids play in sexual commitment; elaborating on this we exposed ring stage parasites (20-24 hours hpi) for one day to AlbuMAX supplemented media to trigger induction to gametocytogenesis. We observed a significant increase in gametocytes after AlbuMAX induction compared to serum. We also tested the transmission potential of AlbuMAX inducted gametocytes and found a significant higher oocyst intensity compared to serum. We conclude that AlbuMAX supplemented media induces commitment, allows a more stable and predictable production of transmittable gametocytes than serum alone.

Highlights

Gametocytes are formed when asexual parasites commit to sexual differentiation.

Sexual commitment can be promoted by environmental stressors in media formulations.

Short exposure of young asexual parasites to the serum substitute AlbuMAX achieves high proportion of committed gametocytes that are transmission-competent.
Global organization of phenylpropanoid and anthocyanin pathways revealed by proximity labeling of trans-cinnamic acid 4-hydroxylase (CYP73A412) inPetunia inflatapetal protoplasts
Authors: Aravena-Calvo Javiera , Busck-Mellor Silas , Laursen Tomas
Published: April 2024

The phenylpropanoid pathway is one of the main carbon sinks in plants, channeling phenylalanine towards thousands of products including monolignols, stilbenes, flavonoids and volatile compounds. The enzymatic steps involved in many of these pathways are well characterized, however the physical organization of these enzymes within the plant cell remains unknown Proximity-dependent labeling allows untargeted determination of protein interactionsin vivo, and therefore stands as an attractive alternative to targeted binary assays for determining global protein-protein interaction networks. In this study, we show a TurboID-based proximity labeling system developed to study protein interaction networks of the core phenylpropanoid pathway in petunia. Here, the endoplasmic reticulum (ER) membrane anchored cytochrome P450 cinnamic acid 4-hydroxylase (C4H, CYP73A412) fromPetunia inflatawas coupled to TurboID and expressed in protoplasts derived from anthocyanin-rich petunia petals. Potential interactors were isolated using streptavidin beads, digested and quantified by mass spectrometry. Among the enriched proteins, we identified multiple soluble enzymes from the late anthocyanin pathway, other CYP73 isoforms, as well as additional ER membrane anchored CYPs includingp-coumaric acid 3-hydroxylase (C3’H, CYP98A2). Our results suggest that CYP73A412 co-localizes with enzymes from the phenylpropanoid- and downstream anthocyanin pathways, supporting the idea that CYP73s may serve as ER anchoring points for these metabolic pathways. Moreover, this study demonstrates the feasibility of using protoplasts to perform global mapping of protein network for enzymes in their native cellular environment.
Merkel cell polyomavirus protein ALTO modulates TBK1 activity to support persistent infection
Authors: Wang Ranran , Senay Taylor E. , Luo Tiana T. , Regan James M. , Salisbury Nick , Galloway Denise , You Jianxin
Published: April 2024

While Merkel cell polyomavirus (MCPyV or MCV) is an abundant virus frequently shed from healthy skin, it is one of the most lethal tumor viruses in immunocompromised individuals, highlighting the crucial role of host immunity in controlling MCPyV oncogenic potential. Despite its prevalence, very little is known about how MCPyV interfaces with the host immune response to maintain asymptomatic persistent infection and how inadequate control of MCPyV infection triggers MCC tumorigenesis. In this study, we discovered that the MCPyV protein, known as the Alternative Large Tumor Open Reading Frame (ALTO), effectively primes and activates the STING signaling pathway. It recruits Src kinase into the complex of STING downstream kinase TBK1 to trigger its autophosphorylation, which ultimately activates the subsequent antiviral immune response. Combining single-cell analysis with both loss- and gain-of-function studies of MCPyV infection, we demonstrated that the activity of ALTO leads to a decrease in MCPyV replication. Thus, we have identified ALTO as a crucial viral factor that modulates the STING-TBK1 pathway, creating a negative-feedback loop that limits viral infection and maintains a delicate balance with the host immune system. Our study reveals a novel mechanism by which a tumorigenic virus-encoded protein can link Src function in cell proliferation to the activation of innate immune signaling, thereby controlling viral spread and sustaining persistent infection. Our previous findings suggest that STING also functions as a tumor suppressor in MCPyV-driven oncogenesis. This research provides a foundation for investigating how disruptions in the finely tuned virus-host balance, maintained by STING, could alter the fate of MCPyV infection, potentially encouraging malignancy.

Author summary

Merkel cell polyomavirus (MCPyV) is a small DNA virus responsible for the majority cases of Merkel Cell Carcinoma (MCC), a rare yet highly aggressive form of cancer. While MCPyV latently infects a vast majority of individuals, the mechanisms governing its control, persistence, and oncogenic triggers remain obscure. Our research reveals that the MCPyV-derived Alternative Large Tumor Open Reading Frame (ALTO) protein primes and activates the cGAS-STING- TBK1 innate immune pathway within cells. Such activation elicits an antiviral response, effectively curbing MCPyV replication. This phenomenon illustrates the virus’s cunning strategy to exploit cellular mechanisms, ensuring low viral presence while facilitating long-term infection. Consequently, our study sheds light on a novel tactic utilized by MCPyV to maintain a persistent infection in its host.
Fragility of ER homeostatic regulation underlies haploid instability in human somatic cells
Authors: Ishida-Ishihara Sumire , Yaguchi Kan , Sato Kimino , Yoshizawa Koya , Miura Sena , Yang Guang , Veszelyi Krisztina , Banhegyi Gabor , Margittai Eva , Uehara Ryota
Published: April 2024

Mammalian somatic cells are generally unstable in the haploid state, resulting in haploid-to-diploid conversion within a short time frame. However, cellular and molecular principles that limit the sustainability of somatic haploidy remain unknown. In this study, we found the haploidy-linked vulnerability to ER stress as a critical cause of haploid intolerance in human somatic cells. Pharmacological induction of ER stress selectively induced apoptosis in haploid cells, facilitating the replacement of haploids by co-existing diploidized cells in a caspase-dependent manner. Biochemical analyses revealed that unfolded protein response (UPR) was activated with similar dynamics between haploids and diploids upon ER stress induction. However, haploids were less efficient in solving proteotoxic status, resulting in a bias toward a proapoptotic mode of UPR signaling. Artificial replenishment of chaperone function or inhibition of a UPR signal transducer ATF6 substantially alleviated the haploidy-linked upregulation of proapoptotic signaling and improved haploid cell retention under ER stress. These data demonstrate that the ER stress-driven haploid instability stems from inefficient proteostatic control that alters the functionality of UPR to cause apoptosis selectively in haploids. Interestingly, haploids suffered a higher level of protein aggregation even in unperturbed conditions, and the long-term stability of the haploid state was significantly improved by alleviating their natural proteotoxicity. Based on these results, we propose that the haploidy-specific vulnerability to ER stress creates a fundamental cause of haploid intolerance in mammalian somatic cells. Our findings provide new insight into the principle that places a stringent restriction on the evolution of animal life cycles.
In vitrohost transcriptomics duringCryptococcus neoformans,Cryptococcus gattii, andCandida albicansinfection of South African volunteers
Authors: Doyle Ronan , Kannambath Shichina , Pittman Alan , Goliath Rene , Kumar Vinod , Meintjes Graeme , Milburn James , Netea Mihai G. , Harrison Thomas S , Jarvis Joseph N , Bicanic Tihana
Published: April 2024

Cryptococcus neoformans,Cryptococcus gattiiandCandida albicansare opportunistic fungal pathogens associated with infections in immunocompromised hosts. Cryptococcal meningitis (CM) is the leading fungal cause of HIV-related deaths globally, with the majority occurring in Africa. The human immune response toC. albicansinfection has been studied extensively in large genomics studies whereas cryptococcal infections, despite their severity, are comparatively understudied. Here we investigated the transcriptional response of immune cells afterin vitrostimulation within vitro C. neoformans,C. gattiiandC. albicansinfection of peripheral blood mononuclear cells (PBMCs) collected from healthy South African volunteers. We found a lower transcriptional response to cryptococcal stimuli compared toC. albicansand unique expression signatures from all three fungal stimuli. This work provides a starting point for further studies comparing the transcriptional signature of CM in immunocompromised patients, with the goal of identifying biomarkers of disease severity and possible novel treatment targets.
Cross Potential Selection: A Proposal for Optimizing Crossing Combinations in Recurrent Selection Based on the Ability of Future Inbred Lines
Authors: Sakurai Kengo , Hamazaki Kosuke , Inamori Minoru , Kaga Akito , Iwata Hiroyoshi
Published: April 2024

In plant breeding programs, rapid production of novel varieties is highly desirable. Genomic selection allows the selection of superior individuals based on genomic estimated breeding values. However, it is worth noting that superior individuals may not always be superior parents. The choice of the crossing pair significantly influences the genotypic value of the resulting progeny. This study introduced a new strategy for selecting crossing pairs, termed Cross Potential Selection (CPS), designed to expedite the production of novel varieties. The CPS assesses the potential of each crossing pair to generate a novel variety. It considers the segregation of each crossing pair and computes the expected genotypic values of the topperforming individuals, assuming that the progeny distribution of genotypic values follows a normal distribution. We simulated a 10-year breeding program to compare CPS with three other selection strategies. CPS consistently demonstrated the highest genetic improvements among the four strategies in early cycles. In particular, during the middle cycles of the breeding program, CPS exhibited the highest genetic improvement of 73% of the 300 independent breeding simulations. In a long-term breeding scheme, some progeny distributions of genotypic values may deviate from normal distribution, affecting the efficiency of CPS. Nevertheless, compared with the other three strategies, CPS achieved significant short-term genetic improvements. In conclusion, CPS holds substantial promise for enhancing the efficiency of plant breeding programs.

Article Summary

This study introduces a novel plant breeding strategy termed Cross Potential Selection (CPS), which was designed to expedite the production of novel varieties. The CPS evaluates the potential of each crossing pair for the target generation. Through comparative breeding simulations, CPS demonstrated superior performance over the three alternative breeding strategies, particularly in the early cycles. These findings suggest that CPS holds significant promise for enhancing plant breeding efficiency.
Construction of whole cell bacterial biosensors as an alternative environmental monitoring technology to detect naphthenic acids in oil sands process-affected water
Authors: Bookout Tyson , Shideler Steve , Cooper Evan , Goff Kira , Headley John V , Gieg Lisa M , Lewenza Shawn
Published: April 2024

After extraction of bitumen from oil sands deposits, the oil sand process-affected water (OSPW) is stored in tailings ponds. Naphthenic acids in tailings ponds have been identified as the primary contributor to toxicity to aquatic life. As an alternative to other analytical methods, here we identify bacterial genes induced after growth in naphthenic acids and use synthetic biology approaches to construct a panel of candidate biosensors for NA detection in water. The main promoters of interest were theatuARpromoters from a naphthenic acid degradation operon and upstream TetR regulator, themarRoperon which includes a MarR regulator and downstream naphthenic acid resistance genes, and a hypothetical gene with a possible role in fatty acid biology. Promoters were printed and cloned as transcriptionalluxreporter plasmids that were introduced into a tailings pond-derivedPseudomonasspecies. All candidate biosensor strains were tested for transcriptional responses to naphthenic acid mixtures and individual compounds. The three priority promoters respond in a dose-dependent manner, which allows semi-quantitative measurements, to simple, acyclic and complex NA mixtures, and each promoter has unique NA specificities. The limits of NA detection from the various NA mixtures ranged between 1.5 - 15 mg/L. TheatuAandmarRpromoters also detected NA in small volumes of OSPW samples and were induced by extracts of the panel of OSPW samples. While biosensors have been constructed for other hydrocarbons, here we describe a biosensor approach that could be employed in environmental monitoring of naphthenic acids in oil sands mining wastewater.
Identification of transposable element families from pangenome polymorphisms
Authors: Sierra Pío , Durbin Richard
Published: April 2024

Background

Transposable Elements (TEs) are fragments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.

Results

We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool,pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies.

Conclusions

Our results show thatpanterais sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.
AVibrio choleraeType IV restriction system targets glucosylated 5-hydroxyl methyl cytosine to protect against phage infection
Authors: Gomez Jasper B. , Waters Christopher M.
Published: April 2024

A major challenge faced byVibrio choleraeis constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation,V. choleraehas evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized more were encoded inV. choleraegiven the relative paucity of phage that have been isolated which infect this species. Using aV. choleraegenomic library, we identified a Type IV restriction system consisting of two genes within a 16kB region of theVibriopathogenicity island-2 that we name TgvA and TgvB (Type I-embeddedgmrSD-like system ofVPI-2). We show that both TgvA and TgvB are required for defense against T2, T4, and T6 by targeting glucosylated 5-hydroxymethylcytosine (5hmC). T2 or T4 phages that lose the glucose modification are resistant to TgvAB defense but exhibit a significant evolutionary tradeoff becoming susceptible to other Type IV restriction systems that target unglucosylated 5hmC. We show that additional phage defense genes are encoded in VPI-2 that protect against other phage like T3, secΦ18, secΦ27 and λ. Our study uncovers a novel Type IV restriction system inV. cholerae, increasing our understanding of the evolution and ecology ofV. choleraewhile highlighting the evolutionary interplay between restriction systems and phage genome modification.

Abstract Importance

Bacteria are constantly being predated by bacteriophage (phage). To counteract this predation, bacteria have evolved a myriad of defense systems. Some of these systems specifically digest infecting phage by recognizing unique base modifications present on the phage DNA. Here, we discover a Type IV restriction system encoded inV. choleraethat we name TgvAB and demonstrate it recognizes and restricts phage that have 5-hydroxymethylcytosine glucosylated DNA. Moreover, the evolution of resistance to TgvAB render phage susceptible to other Type IV restriction systems, demonstrating a significant evolutionary tradeoff. These results enhance our understanding of the evolution ofV. choleraeand more broadly how bacteria evade phage predation.
SwinCell: a transformer-based framework for dense 3D cellular segmentation
Authors: Zhang Xiao , Lin Zihan , Wang Liguo , Chu Yong S. , Yang Yang , Xiao Xianghui , Lin Yuewei , Liu Qun
Published: April 2024

Segmentation of three-dimensional (3D) cellular images is fundamental for studying and understanding cell structure and function. However, 3D cellular segmentation is challenging, particularly for dense cells and tissues. This challenge arises mainly from the complex contextual information within 3D images, anisotropic properties, and the sensitivity to internal cellular structures, which often lead to miss-segmentation. In this work, we introduce SwinCell, a 3D transformer-based framework that leverages Swin-transformer for flow prediction and effectively distinguishes individual cell instances in 3D. We demonstrate the broad utility of the SwinCell in the segmentation of nuclei, colon tissue cells, and dense cultured cells. SwinCell strikes a balance between maintaining detailed local feature recognition and understanding broader contextual information. Tested extensively with both public and in-house 3D cell imaging datasets, SwinCell shows superior performance in segmenting dense cells in 3D, making it a powerful 3D segmentation tool for cellular analysis that could expedite research in cell biology and tissue engineering.
Wax ester synthase overexpression affects stomatal development, water consumption and growth of poplars
Authors: Amirkhosravi Ashkan , Strijkstra Gerrit-Jan , Keyl Alisa , Häffner Felix , Lipka Ulrike , Herrfurth Cornelia , Feussner Ivo , Polle Andrea
Published: April 2024

Poplars are important fast-growing biomass crops. Their water-spending lifestyle renders them susceptible to drought and threatens plantations under global climate change with extended periods of water deprivation. The cuticle and stomatal regulation are major traits to protect plants from uncontrolled water loss. Here, we targeted the wax biosynthesis pathway ofPopulusxcanescensby overexpressing jojoba (Simmondsia chinensis) wax ester synthase (ScWS) to improve cuticular properties. ScWSexpression caused accumulation of lipid droplets inside the cells, decreased transcript levels of endogenous wax biosynthetic genes, and moderate shifts in surface wax composition but did not affect non-stomatal water loss. During short- and long-term drought scenarios under greenhouse and outdoor conditions, ScWSlines showed decreased stomatal conductance and increased water-use-efficiencies leading to a water-saving phenotype and delayed leaf shedding. This phenotype was caused by a high fraction (80%) of wax-occluded or semi-occluded stomata, and was accompanied by suppression ofOCCLUDED STOMATAL PORE1(OSP1), known to cause abberant wax accumulation at the stomatal ledges as found here. Occluded stomata limited poplar photosynthesis under high but not under low light intensities. Leaf damage and insect scores did not reveal differences compared with wild-type plants. Biomass production of ScWSlines was unaffected in short-term experiments but dropped below that of wild-type poplars at the end of two field seasons, indicating a growth trade-off. In conclusion, our study pinpoints a tight connection between wax biosynthesis and stomatal features and opens a new avenue to improve poplar water consumption by optimizing stomatal ledges with refined biotechnological approaches.
Prediction of effective equivalent linear temperature gradients in bonded concrete overlays of asphalt pavements
Authors: Donnelly Charles A. , Sen Sushobhan , DeSantis John W. , Vandenbossche Julie M.
Published: April 2024

Purpose

The time-varying equivalent linear temperature gradient (ELTG) significantly affects the development of faulting and must therefore be accounted for in pavement design. The same is true for faulting of bonded concrete overlays of asphalt (BCOA) with slabs larger than 3 x 3 m. However, the evaluation of ELTG in Mechanistic-Empirical (ME) BCOA design is highly time-consuming. The use of an effective ELTG (EELTG) is an efficient alternative to calculating ELTG. In this study, a model to quickly evaluate EELTG was developed for faulting in BCOA for panels 3 m or longer in size, whose faulting is sensitive to ELTG.

Design/methodology/approach

A database of EELTG responses was generated for 144 BCOAs at 169 locations throughout the continental United States, which was used to develop a series of prediction models. Three methods were evaluated: multiple linear regression (MLR), artificial neural networks (ANNs), and multi-gene genetic programming (MGGP). The performance of each method was compared, considering both accuracy and model complexity.

Findings

It was shown that ANNs display the highest accuracy, with an R2 of 0.90 on the validation dataset. MLR and MGGP models achieved R2 of 0.73 and 0.71, respectively. However, these models consisted of far fewer free parameters as compared to the ANNs. The model comparison performed in this study highlights the need for researchers to consider the complexity of models so that their direct implementation is feasible.

Originality/value

This research produced a rapid EELTG prediction model for BCOAs that can be incorporated into the existing faulting model framework.
Information searching in cultural heritage archives: a user study
Authors: Borlund Pia , Pharo Nils , Liu Ying-Hsang
Published: April 2024

Purpose

The PICCH research project contributes to opening a dialogue between cultural heritage archives and users. Hence, the users are identified and their information needs, the search strategies they apply and the search challenges they experience are uncovered.

Design/methodology/approach

A combination of questionnaires and interviews is used for collection of data. Questionnaire data were collected from users of three different audiovisual archives. Semi-structured interviews were conducted with two user groups: (1) scholars searching information for research projects and (2) archivists who perform their own scholarly work and search information on behalf of others.

Findings

The questionnaire results show that the archive users mainly have an academic background. Hence, scholars and archivists constitute the target group for in-depth interviews. The interviews reveal that their information needs are multi-faceted and match the information need typology by Ingwersen. The scholars mainly apply collection-specific search strategies but have in common primarily doing keyword searching, which they typically plan in advance. The archivists do less planning owing to their knowledge of the collections. All interviewees demonstrate domain knowledge, archival intelligence and artefactual literacy in their use and mastering of the archives. The search challenges they experience can be characterised as search system complexity challenges, material challenges and metadata challenges.

Originality/value

The paper provides a rare insight into the complexity of the search situation of cultural heritage archives, and the users’ multi-facetted information needs and hence contributes to the dialogue between the archives and the users.
An approach-inhibition model of shared leadership: the effect of vertical leader’s multi-source power
Authors: Song Zhigang , Gu Qinxuan
Published: April 2024

Purpose

Drawing on power approach-inhibition theory, this study develops a conditional indirect effect model to explore how team vertical leader position and expert power indirectly impact members’ shared leadership through vertical leader’s empowering behaviors.

Design/methodology/approach

Multi-source data was collected using a field survey research design. The final sample includes 944 employees in 164 teams from 14 companies in China.

Findings

This study found that the interaction of team vertical leader position power and expert power was positively related to their empowering behaviors, which in turn were positively associated with shared leadership. Moreover, our post hoc-analysis revealed the moderating effect of team power distance orientation on the relationship between vertical leader empowering behaviors and shared leadership.

Originality/value

This study sheds light on shared leadership literature by examining vertical leader position and expert power as antecedents. We also offer new directions for exploring how power functions by discussing leadership through the lens of power approach-inhibition theory.
A systematic literature review on sustainable HRM and its relations with employees' attitudes: state of art and future research agenda
Authors: Gomes Gabriela Pedro , Coelho Arnaldo , Ribeiro Neuza
Published: April 2024

Purpose

The interest in sustainable human resource management has grown in the last decades. However, comprehensive, and systematic research concentrating on the evolution of this field, is still needed. The purpose of this study is to provide an overview and synthesis of the existing body of knowledge on human resource management (HRM) related to sustainability through a bibliometric study of articles published until 2022, identifying the most relevant research in this field. In the literature review, special attention is given to articles that link sustainable HRM to employees’ attitudes, identifying gaps and future research opportunities.

Design/methodology/approach

A bibliometric analysis and literature review was conducted over 105 documents obtained from the WoS database, using VOSviewer software program, from which 27 were selected for full-text reading. The applied database filters were: document type (article and early access); index (SSCI and SCI-expanded) and year (2019–2022).

Findings

The results show that: sustainable HRM literature is growing, especially after 2019; “Sustainability” is the journal with more publications; and England is the leading country. The network of co-occurrence of keywords analysis unveiled that performance, job satisfaction and behaviors are the most frequently studied topics in HRM.

Practical implications

For successful adoption of sustainable HRM practices, organizations should engage all staff comprehensively, focusing not only on consistent implementation but also on fostering a supportive organizational climate. This is vital for establishing a sustainable workplace where employees who strongly identify with the organization are less willing to leave it.

Originality/value

Through the Systematic Literature Review carried out on the articles published from 2019 to 2022, it was possible to identify opportunities for future research. These topics include employees' perceptions of the implementation of sustainable HRM practices in companies, as well as the impact of these practices on their attitudes and behaviors, taking into account the various HRM practices.
How has blended learning impacted tourism and hospitality graduates in employability? Feedback from graduates and tourism industry employers
Authors: Guden Nafiya , Safaeimanesh Farzad
Published: April 2024

Purpose

The aim of this empirical research is to define blended learning (BL) in the context of tourism education and discuss its effectiveness in learning and, upon completion, the employability of graduates in due cause.

Design/methodology/approach

The qualitative research consists of 22 in-depth interviews with experts from the tourism industry and graduates. The sampling method was purposive (judgmental), and open-ended questions were asked in order to encourage the interviewee to be expressive and to share their views and opinions on what the impact of the BL program has been.

Findings

The study found that the most significant obstacles were a lack of funding, a lack of cooperation from the local and various levels of government and a lack of knowledge about sustainable tourism product development among local residents.

Originality/value

During the COVID-19 pandemic, the majority of the tourism schools and university departments have developed a combination of mixed learning to include online, classroom and sector experience, which can be summarized as BL. This research suggests that BL has provided for a blend of skills and, as a result, employable graduates.
The Position of Khatak in Pashto Dialectology
Authors: Khatak Munazza Saeed
Published: April 2024

Pashto is a major language of the Iranian family with multiple dialects spoken in Pakistan and Afghanistan. In this paper, I examine the phonological inventory of the previously little known Khatak Pashto by a comparison with the well‐known Yusufzai, of the Northeast dialect of the language. I use primary data collected from Karak and Mardan districts of northwest Pakistan. In my analysis, I identify the similarities between these two varieties and the differences, based on at least eleven phonological isoglosses including the feature of vowel nasality, which split the two. I conclude by supporting the case for a distinct Central dialect area to represent the position of Khatak Pashto.
Phenological patterns in ecology: Problems using circular statistics and solutions based on simulations
Authors: Willig Michael R. , Rojas‐Sandoval Julissa , Presley Steven J.
Published: April 2024

Quantification of phenological patterns (e.g. migration, hibernation or reproduction) should involve statistical assessments of non‐uniform temporal patterns. Circular statistics (e.g. Rayleigh test or Hermans‐Rasson test) provide useful approaches for doing so based on the number of individuals that exhibit particular activities during a number of time intervals.

This study used monthly reproductive activity as an example to illustrate problems in applying circular statistics to data when marginal totals characterize experimental designs (e.g. the number of reproductively active individuals per time interval depends on sampling effort or sampling success). We illustrate the nature of this problem by crafting four exemplar data sets and developing a bootstrapping simulation procedure to overcome complications that arise from the existence of marginal totals. In addition, we apply circular statistics and our bootstrapping simulation to empirical data on the reproductive phenology of six species of Neotropical bats from the Amazon.

Because sampling effort or success can differ among time intervals, circular statistics can produce misleading results of two types: those suggesting uniform phenologies when empirical patterns are markedly modal, and those suggesting non‐uniform phenologies when empirical patterns are uniform. The bootstrapping simulation overcomes these limitations: the exemplar phenology in which the percentage of reproductively active individuals is modal is appropriately identified as non‐uniform based on the bootstrapping approach, and the exemplar phenology in which the percentage of reproductively active individuals is invariant is appropriately identified as uniform based on the bootstrapping approach. The reproductive phenology of each of the six empirical examples is non‐uniform based on the bootstrapping approach, and this is true for bats species with unimodal peaks or bimodal peaks.

In addition to problems with marginal totals, a review of analyses of phenological patterns in ecology identified two other frequent issues in the application of circular statistics: sampling bias and pseudoreplication. Each of these issues and potential solutions are also discussed. By providing source code for the execution of the Rayleigh test and Hermans‐Rasson test, along with the code for the bootstrapping simulation, we offer a useful tool for assessing non‐random phenologies when marginal totals characterize experimental designs.
Perioperative urinary ketosis and metabolic acidosis in patients fasted for undergoing gynecologic surgery
Authors: Lim Leerang , Park Sang Joon , Kang Christine , Oh Seung‐Young , Ryu Ho Geol , Lee Hannah
Published: April 2024

Background

Our bodies have adaptive mechanisms to fasting, in which glycogen stored in the liver and muscle protein are broken down, but also lipid mobilisation is triggered. As a result, glycerol and fatty acids are released into the bloodstream, increasing the production of ketone bodies in liver. However, there are limited studies on the incidence of perioperative urinary ketosis, the intraoperative blood glucose changes and metabolic acidosis after fasting for surgery in non‐diabetic adult patients.

Methods

We conducted a retrospective cohort study involving 1831 patients undergoing gynecologic surgery under general anesthesia from January to December 2022. Ketosis was assessed using a postoperative urine test, while blood glucose levels and acid–base status were collected from intraoperative arterial blood gas analyses.

Results

Of 1535 patients who underwent postoperative urinalysis, 912 (59.4%) patients had ketonuria. Patients with ketonuria were younger, had lower body mass index, and had fewer comorbidities than those without ketonuria. After adjustments, younger age, higher body mass index and surgery starting late afternoon were significant risk factors for postoperative ketonuria. Of the 929 patients assessed with intraoperative arterial blood gas analyses, 29.0% showed metabolic acidosis. Multivariable logistic regression revealed that perioperative ketonuria and prolonged surgery significantly increased the risk for moderate‐to‐severe metabolic acidosis.

Conclusion

Perioperative urinary ketosis and intraoperative metabolic acidosis are common in patients undergoing gynecologic surgery, even with short‐term preoperative fasting. The risks are notably higher in younger patients with lower body mass index. Optimization of preoperative fasting strategies including implementation of oral carbohydrate loading should be considered for reducing perioperative metabolic derangement due to ketosis.