bluuebunny/crossref_metadata_2025_split huggingface dataset:
The name-bearing type of Oligodon quadrilineatus (Jan &amp; Sordelli, 1865) (Squamata: Colubridae)
Authors: DAVID PATRICK , VOGEL GERNOT , VAN ROOIJEN JOHAN , PIERRE LAURE 
Published: March 2024

David et al. (2008) revised the nomenclature and systematics of the Asian colubrid snakes recognized in the literature as the “Oligodon taeniatus-group”. In order to fix the status of Simotes quadrilineatus Jan & Sordelli, 1865, David et al. (2008) designated a neotype. Although Jan & Sordelli (1865: Plate IV: Fig. 3) depicted only one specimen, David et al. (2008) pointed out that four specimens were considered syntypes of S. quadrilineatus in the catalogues of the Muséum national d’Histoire naturelle, Paris (MNHN), all collected by F. Bocourt in Siam between December 1861 and July 1862 (Milne-Edwards 1866; Bocourt 1866). Thanks to the precision of Jan & Sordelli’s drawing of the ventral pattern, in which ventral blotches are clearly visible, it appeared that none of these four specimens was the holotype depicted on Plate 4 of Jan & Sordelli (1865). As a consequence, David et al. (2008) designated as neotype MNHN 1991.1819, an adult female from “Bangkok”, Thailand, belonging to the series collected by F. Bocourt.
Navigating monolingual language ideologies: Educators’ “Yes, BUT” objections to linguistically sustaining pedagogies in the classroom
Authors: Anderson Kate T. , Chang-Bacon Chris , Guzmán Antelo Maria 
Published: March 2024

Aims: We examine how educators articulate tensions between linguistic pluralism and linguistic normativity in written Linguistic Autobiographies through their metacommentary about student language and their role as educators. We specifically focus on “Yes, BUT” objections articulated by 17 participants that frame monolingualism and adherence to idealized forms of English as necessary, despite rhetorical nods to embracing linguistic diversity. Research questions: (1) How do participating educators construct “Yes, BUT” objections to linguistic pluralism in their written Linguistic Autobiographies? (2) What language ideologies inform these objections? (3) What ideological positions for educators are implicated? Design/methodology/approach: Collaborative emergent qualitative coding and inductive discourse analysis. Data and analysis: We analyzed Linguistic Autobiographies written by 50 educators taking an online master’s class in Sociolinguistics for Bilingual Educators and examined features of “Yes, BUT” objections and their ideological justification using collaborative, emergent coding and inductive discourse analysis. Findings/conclusions: We document how educators’ “Yes, BUT” objections illuminate discursive moves that justify the seeming embrace, yet ultimate rejection of, linguistic diversity. Originality: This study disentangles monolingual language ideologies to address objections inherent to educators’ “Yes, BUT” constructions that arise as common barriers in teacher education. We reframe these objections as emergent degrees of linguistic pluralism, which serve as evidence of the contextual difficulties educators often encounter in schools. We thus acknowledge rather than dismiss the tensions educators face in fostering linguistic pluralism. Significance/implications: This study illuminates how language ideologies shape (and possibly offer insights for undoing) complacency in what is often discussed as a long-standing tension between the seemingly mutually exclusive positions of linguistic pluralism and linguistic normativity. We argue that analyzing and addressing these “Yes, BUT” objections in educators’ narratives is key to the disruption of monolingual language ideologies in educational settings and beyond.
Enriched Environments in Stroke Units: Defining Characteristics and Limitations
Authors: Anåker Anna , Kevdzija Maja , Elf Marie 
Published: March 2024

Background: Individuals with stroke rehabilitated in an enriched environment (EE) compared to a non-EE are more likely to participate in cognitive and social activities, promoting their rehabilitation and well-being. There is a need for a more comprehensive understanding of methods to implement EEs within complex health systems, particularly in stroke units. Objective: The aim of this systematic review was to compile the concept of an EE in stroke units. Methods: The literature was sourced from CINAHL, Embase, and Medline databases. A detailed screening and sifting process was used to identify relevant literature. Multiple reviewers independently appraised the identified literature using a Mixed-methods Appraisal Tool. After screening 336 studies, 11 were included. Results: This review reveals an EE is challenging to define and almost exclusively about activities based on access to individual and communal equipment. Generally, there are no common descriptions or conceptual agreements. Conclusions: To the best of our knowledge, this is the first study to systematically review the concept of an EE in stroke units and shows that more studies on EEs are needed. The weak definitions and unclear theoretical backgrounds of an EE in the included studies could challenge operationalization. Future research should be based on more precise definitions of an EE and broader interventions that include changes to built and natural environments.
The TLK-ASF1 histone chaperone pathway plays a critical role in IL-1β–mediated AML progression
Authors: Lin Hsin-Yun , Mohammadhosseini Mona , McClatchy John , Villamor-Payà Marina , Jeng Sophia , Bottomly Daniel , Tsai Chia-Feng , Posso Camilo , Jacobson Jeremy , Adey Andrew , Gosline Sara , Liu Tao , McWeeney Shannon , Stracker Travis H. , Agarwal Anupriya 
Published: March 2024

Abstract
Identifying and targeting microenvironment-driven pathways that are active across acute myeloid leukemia (AML) genetic subtypes should allow the development of more broadly effective therapies. The proinflammatory cytokine interleukin-1β (IL-1β) is abundant in the AML microenvironment and promotes leukemic growth. Through RNA-sequencing analysis, we identify that IL-1β–upregulated ASF1B (antisilencing function-1B), a histone chaperone, in AML progenitors compared with healthy progenitors. ASF1B, along with its paralogous protein ASF1A, recruits H3-H4 histones onto the replication fork during S-phase, a process regulated by Tousled-like kinase 1 and 2 (TLKs). Although ASF1s and TLKs are known to be overexpressed in multiple solid tumors and associated with poor prognosis, their functional roles in hematopoiesis and inflammation-driven leukemia remain unexplored. In this study, we identify that ASF1s and TLKs are overexpressed in multiple genetic subtypes of AML. We demonstrate that depletion of ASF1s significantly reduces leukemic cell growth in both in vitro and in vivo models using human cells. Using a murine model, we show that overexpression of ASF1B accelerates leukemia progression. Moreover, Asf1b or Tlk2 deletion delayed leukemia progression, whereas these proteins are dispensable for normal hematopoiesis. Through proteomics and phosphoproteomics analyses, we uncover that the TLK-ASF1 pathway promotes leukemogenesis by affecting the cell cycle and DNA damage pathways. Collectively, our findings identify the TLK1-ASF1 pathway as a novel mediator of inflammatory signaling and a promising therapeutic target for AML treatment across diverse genetic subtypes. Selective inhibition of this pathway offers potential opportunities to intervene effectively, address intratumoral heterogeneity, and ultimately improve clinical outcomes in AML.
Frontline management of mantle cell lymphoma
Authors: Ryan Christine E. , Armand Philippe , LaCasce Ann S. 
Published: March 2024

Abstract
Despite many recent therapeutic advances, mantle cell lymphoma (MCL) remains a largely incurable disease. Treatments for patients with relapsed/refractory (R/R) disease are limited in number and in response durability. Therefore, improving the efficacy of frontline (1L) treatment, and specifically maximizing the duration of first remission, remains of critical importance to obtain favorable long-term outcomes. As 1L treatments become more effective, improving tolerability is also becoming an increasingly realistic goal. Targeted agents, which are now mainstays of treatment in R/R MCL, are establishing new, paradigm-changing roles in frontline treatment. Here, we review data supporting current standard-of-care approaches and explore 6 main areas of possible focus for advancement of 1L management: optimizing the chemoimmunotherapy (CIT) backbone, adding targeted agents to CIT, redefining the role of autologous stem cell transplantation, improving maintenance therapy, using targeted agent combinations with omission of CIT, and using measurable residual disease–guided therapy. We highlight several ongoing phase 3 trials that may soon impact frontline MCL management, and outline some areas of necessary investigation as the field continues to strive toward a cure for this disease.
Thrombosis risk in single- and double-heterozygous carriers of factor V Leiden and prothrombin G20210A in FinnGen and the UK Biobank
Authors: Ryu Justine , Rämö Joel T. , Jurgens Sean J. , Niiranen Teemu , Sanna-Cherchi Simone , Bauer Kenneth A. , Haj Amelia , Choi Seung Hoan , Palotie Aarno , Daly Mark , Ellinor Patrick T. , Bendapudi Pavan K. 
Published: March 2024

Abstract
The factor V Leiden (FVL; rs6025) and prothrombin G20210A (PTGM; rs1799963) polymorphisms are 2 of the most well-studied genetic risk factors for venous thromboembolism (VTE). However, double heterozygosity (DH) for FVL and PTGM remains poorly understood, with previous studies showing marked disagreement regarding thrombosis risk conferred by the DH genotype. Using multidimensional data from the UK Biobank (UKB) and FinnGen biorepositories, we evaluated the clinical impact of DH carrier status across 937 939 individuals. We found that 662 participants (0.07%) were DH carriers. After adjustment for age, sex, and ancestry, DH individuals experienced a markedly elevated risk of VTE compared with wild-type individuals (odds ratio [OR] = 5.24; 95% confidence interval [CI], 4.01-6.84; P = 4.8 × 10−34), which approximated the risk conferred by FVL homozygosity. A secondary analysis restricted to UKB participants (N = 445 144) found that effect size estimates for the DH genotype remained largely unchanged (OR = 4.53; 95% CI, 3.42-5.90; P &lt; 1 × 10−16) after adjustment for commonly cited VTE risk factors, such as body mass index, blood type, and markers of inflammation. In contrast, the DH genotype was not associated with a significantly higher risk of any arterial thrombosis phenotype, including stroke, myocardial infarction, and peripheral artery disease. In summary, we leveraged population-scale genomic data sets to conduct, to our knowledge, the largest study to date on the DH genotype and were able to establish far more precise effect size estimates than previously possible. Our findings indicate that the DH genotype may occur as frequently as FVL homozygosity and may confer a similarly increased risk of VTE.
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values
Authors: Ahn Seungjun , Datta Somnath 
Published: March 2024

AbstractBackgroundA recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing the network properties between two or more graphs under different biological conditions. However, the existing methods to the DN analysis for microbiome data do not adjust for other clinical differences between subjects.ResultsWe propose a Statistical Approach via Pseudo-value Information and Estimation for Differential Network Analysis (SOHPIE-DNA) that incorporates additional covariates such as continuous age and categorical BMI. SOHPIE-DNA is a regression technique adopting jackknife pseudo-values that can be implemented readily for the analysis. We demonstrate through simulations that SOHPIE-DNA consistently reaches higher recall and F1-score, while maintaining similar precision and accuracy to existing methods (NetCoMi and MDiNE). Lastly, we apply SOHPIE-DNA on two real datasets from the American Gut Project and the Diet Exchange Study to showcase the utility. The analysis of the Diet Exchange Study is to showcase that SOHPIE-DNA can also be used to incorporate the temporal change of connectivity of taxa with the inclusion of additional covariates. As a result, our method has found taxa that are related to the prevention of intestinal inflammation and severity of fatigue in advanced metastatic cancer patients.ConclusionSOHPIE-DNA is the first attempt of introducing the regression framework for the DN analysis in microbiome data. This enables the prediction of characteristics of a connectivity of a network with the presence of additional covariate information in the regression. The package with a vignette of our methodology is available through the CRAN repository (https://CRAN.R-project.org/package=SOHPIE), named SOHPIE (pronounced asSofie). The source code and user manual can be found athttps://github.com/sjahnn/SOHPIE-DNA.
Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere
Authors: ZOUAGUI Rahma , ZOUAGUI Houda , AURAG Jamal , IBRAHIMI Azeddine , SBABOU Laila 
Published: March 2024

Abstract
Background
Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

Results
Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

Conclusions
The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.
Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens
Authors: Kebede Fasil Getachew , Derks Martijn F.L. , Dessie Tadelle , Hanotte Olivier , Barros Carolina Pita , Crooijmans Richard P.M.A. , Komen Hans , Bastiaansen John W.M. 
Published: March 2024

AbstractClimate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6–7 populations per gradient). We performed signatures of selection analyses ($$ {F}_{ST}$$ and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by$$ { F}_{ST }$$and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by $$ {F}_{ST}$$ are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.
Availability and threshold of the vasoactive-inotropic score for predicting early extubation in adults after rheumatic heart valve surgery: a single-center retrospective cohort study
Authors: Zhao Yang , Zhao Hanlei , Huang Jiao , Mei Bo , Xiang Jun , Wang Yizheng , Lin Jingyan , Huang San 
Published: March 2024

Abstract
Background
Early extubation (EEx) is defined as the removal of the endotracheal tube within 8 h postoperatively. The present study involved determining the availability and threshold of the vasoactive-inotropic score (VIS) for predicting EEx in adults after elective rheumatic heart valve surgery.

Methods
The present study was designed as a single-center retrospective cohort study which was conducted with adults who underwent elective rheumatic heart valve surgery with CPB. The highest VIS in the immediate postoperative period was used in the present study. The primary outcome, the availability of VIS for EEx prediction and the optimal threshold value were determined using ROC curve analysis. The gray zone analysis of the VIS was performed by setting the false negative or positive rate R = 0.05, and the perioperative risk factors for prolonged EEx were identified by multivariate logistic analysis. The postoperative complications and outcomes were compared between different VIS groups.

Results
Among the 409 patients initially screened, 379 patients were ultimately included in the study. The incidence of EEx was determined to be 112/379 (29.6%). The VIS had a good predictive value for EEx (AUC = 0.864, 95% CI: [0.828, 0.900], P < 0.001). The optimal VIS threshold for EEx prediction was 16.5, with a sensitivity of 71.54% (65.85–76.61%) and a specificity of 88.39% (81.15–93.09%). The upper and lower limits of the gray zone for the VIS were determined as (12, 17.2). The multivariate logistic analysis identified age (OR, 1.060; 95% CI: 1.017–1.106; P = 0.006), EF% (OR, 0.798; 95% CI: 0.742–0.859; P < 0.001), GFR (OR, 0.933; 95% CI: 0.906–0.961; P < 0.001), multiple valves surgery (OR, 4.587; 95% CI: 1.398–15.056; P = 0.012), and VIS > 16.5 (OR, 12.331; 95% CI: 5.015–30.318; P < 0.001) as the independent risk factors for the prolongation of EEx. The VIS ≤ 16.5 group presented a greater success rate for EEx, a shorter invasive ventilation support duration, and a lower incidence of complications than did the VIS > 16.5 group, while the incidence of reintubation was similar between the two groups.

Conclusion
In adults, after elective rheumatic heart valve surgery, the highest VIS in the immediate postoperative period was a good predictive value for EEx, with a threshold of 16.5.
Time to recovery and its predictors following traumatic injuries among injured victims in Dessie Comprehensive Specialized Hospital, North East of Ethiopia, 2022: a retrospective follow-up study
Authors: Tilahun Lehulu , Zeleke Mulusew , Desu Birhanu , Dagnew Kirubel , Nega Aytenew , Birrie Endalk , Estifanos Nathan , Tegegne Akele , Feleke Asresu 
Published: March 2024

Abstract
Background
Injuries are an extremely important public health problem worldwide. Despite being largely preventable and despite government efforts, injuries continue to be a major public health issue. Thus, the study tends to evaluate the time to recovery and its predictors for traumatic injuries.

Methods
A hospital-based retrospective follow-up study was used. A total of 329 medical charts were actually reviewed. Traumatic injury victims from January 1, 2018–December 31, 2022 were included, and a simple random sampling technique was utilized. The data was gathered by reviewing medical charts. Data was coded and entered into Epi-Data Manager version 4.6.0.4 statistical software and further analyzed using STATA version 17. Descriptive statistics were performed to see the frequency distribution of variables. A Kaplan-Meier survival estimate and log rank test were performed to plot the overall survival curve and compare the difference in recovery among predictor categories, respectively. A model fitness test was done by using the Cox-Snell residual test and Harrell’s C concordance statistic. Finally, a Cox proportional hazard model was fitted to determine the effect of predictors on recovery time from traumatic injuries.

Results
The median time to recovery of traumatic injuries was 5 days (IQR: 3–10 days), with an overall incidence density of 8.77 per 100 person-days of observation. In the multivariable cox proportional regression model, variables such as being male (AHR: 0.384, 95%CI: 0.190–0.776, P-value: 0.008), the Glasgow coma scale of 13–15 (AHR: 2.563, 95%CI: 1.070–6.139, P-value: 0.035), intentional injury (AHR: 1.934, 95%CI: 1.03–3.632, P-value: 0.040), mild traumatic brain injury (AHR: 2.708, 95%CI: 1.095–6.698, P-value: 0.031), and moderate traumatic brain injury (AHR: 2.253, 95%CI: (1.033–4.911, P-value: 0.041) were statistically significant variables.

Conclusions
The median recovery time for traumatically injured respondents was 5 days. Independent predictors such as the Glasgow coma scale, time taken for surgical management, intent of injury, and traumatic brain injury were statistically significant with time to recovery from trauma.