bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glutamine metabolism prognostic index predicts tumour microenvironment characteristics and therapeutic efficacy in ovarian cancer
Authors: Gao Lingling , Wei Zheng , Ying Feiquan , Huang Lin , Zhang Jingni , Sun Si , Wang Zehua , Cai Jing , Zhang Yuan 
Published: March 2024

AbstractMounting evidence has highlighted the multifunctional characteristics of glutamine metabolism (GM) in cancer initiation, progression and therapeutic regimens. However, the overall role of GM in the tumour microenvironment (TME), clinical stratification and therapeutic efficacy in patients with ovarian cancer (OC) has not been fully elucidated. Here, three distinct GM clusters were identified and exhibited different prognostic values, biological functions and immune infiltration in TME. Subsequently, glutamine metabolism prognostic index (GMPI) was constructed as a new scoring model to quantify the GM subtypes and was verified as an independent predictor of OC. Patients with low‐GMPI exhibited favourable survival outcomes, lower enrichment of several oncogenic pathways, less immunosuppressive cell infiltration and better immunotherapy responses. Single‐cell sequencing analysis revealed a unique evolutionary trajectory of OC cells from high‐GMPI to low‐GMPI, and OC cells with different GMPI might communicate with distinct cell populations through ligand‐receptor interactions. Critically, the therapeutic efficacy of several drug candidates was validated based on patient‐derived organoids (PDOs). The proposed GMPI could serve as a reliable signature for predicting patient prognosis and contribute to optimising therapeutic strategies for OC.
A deep learning method to identify and localize large‐vessel occlusions from cerebral digital subtraction angiography
Authors: Warman Roshan , Warman Pranav I. , Warman Anmol , Bueso Tulio , Ota Riichi , Windisch Thomas , Neves Gabriel 
Published: March 2024

AbstractBackground and purposeAn essential step during endovascular thrombectomy is identifying the occluded arterial vessel on a cerebral digital subtraction angiogram (DSA). We developed an algorithm that can detect and localize the position of occlusions in cerebral DSA.MethodsWe retrospectively collected cerebral DSAs from a single institution between 2018 and 2020 from 188 patients, 86 of whom suffered occlusions of the M1 and proximal M2 segments. We trained an ensemble of deep‐learning models on fewer than 60 large‐vessel occlusion (LVO)‐positive patients. We evaluated the model on an independent test set and evaluated the truth of its predicted localizations using Intersection over Union and expert review.ResultsOn an independent test set of 166 cerebral DSA frames with an LVO prevalence of 0.19, the model achieved a specificity of 0.95 (95% confidence interval [CI]: 0.90, 0.99), a precision of 0.7450 (95% CI: 0.64, 0.88), and a sensitivity of 0.76 (95% CI: 0.66, 0.91). The model correctly localized the LVO in at least one frame in 13 of the 14 LVO‐positive patients in the test set. The model achieved a precision of 0.67 (95% CI: 0.52, 0.79), recall of 0.69 (95% CI: 0.46, 0.81), and a mean average precision of 0.75 (95% CI: 0.56, 0.91).ConclusionThis work demonstrates that a deep learning strategy using a limited dataset can generate effective representations used to identify LVOs. Generating an expanded and more complete dataset of LVOs with obstructed LVOs is likely the best way to improve the model's ability to localize LVOs.
Using social media to infer the diffusion of an urban contact dialect: A case study of Multicultural London English
Authors: Ilbury Christian , Grieve Jack , Hall David 
Published: March 2024

AbstractSociolinguistic research has demonstrated that ‘urban contact dialects’ tend to diffuse beyond the speech communities in which they first emerge. However, no research has attempted to explore the distribution of these varieties across an entire nation nor isolate the social mechanisms that propel their spread. In this paper, we use a corpus of 1.8 billion geo‐tagged tweets to explore the spread of Multicultural London English (MLE) lexis across the United Kingdom. We find evidence for the diffusion of MLE lexis from East and North London into other ethnically and culturally diverse urban centres across England, particularly those in the South (e.g. Luton), but find lower frequencies of MLE lexis in the North of England (e.g. Manchester), and in Scotland and Wales. Concluding, we emphasise the role of demographic similarity in the diffusion of linguistic innovations by demonstrating that this variety originated in London and diffused into other urban areas in England through the social networks of Black and Asian users.
Predictive validity of a pressure injury risk assessment tool at different time‐points in patients admitted to the intensive care unit
Authors: Cobos‐Vargas Angel , Acosta‐Romero Maria , Camado‐Sojo Luis , Alba‐Fernández Carmen , Rodriguez‐Delgado Esther , Colmenero Manuel 
Published: March 2024

AbstractBackgroundMultiple risk assessment scales are available for predicting the development of pressure injuries (PIs) in patients in the intensive care unit (ICU). Most PI risk assessment tools have been validated at the time of admission; however, another time point during treatment could better reflect clinical changes and therefore, the risk of PIs.AimThe study aimed to examine the predictive validity of PI risk assessment scale designed for ICU patients, the conscious level, mobility, haemodynamic, oxygenation and nutrition (COMHON) index, at several time points or intervals during ICU stay.Study DesignThis was an observational prospective study undertaken over a period of 1 year (July 2021–June 2022). Patients admitted to ICU for >3 days were included. The number, location and degree of the PIs were recorded. The level of risk for developing PIs during the stay was determined by calculating the COMHON scores at admission, and 72 h, as well as the highest and mean score. Predictive validity was studied using accuracy parameters and areas under the receiver operating characteristic curve (AUC). The best cutoff point was also determined and used to compare risk between categories.ResultsOf the 286 patients included in the study, 160 (59%) were male. The level of severity evaluated using the APACHE II scale was 18.4 ± 5.8 points. Invasive mechanical ventilation was used in 32.1% (n = 92) of the patients and 20.6% (n = 59) received high flow oxygen therapy. The incidence of PI was 15.4% (n = 44), with sacral location in 47.7% (n = 21) and grade II in 75% (n = 33) of the patients. The AUC was 0.907 (0.872–0.942); 0.881 (0.842–0.920); 0.877 (0.835–0.920) and 0.749 (0.667–0.831) at the mean, the highest, 72 h and ICU admission scores, respectively. The best cutoff point was 13 in all patients. The risk of developing a PI was 6.4 times higher in the high‐risk group (>13 points).ConclusionsThe best predictive capacity for the COMHON index risk assessment was the mean and highest scores. The predictive accuracy was higher on the third day of the patient's stay than on admission, and this was attributed to the clinical changes observed in some patients over the course of their critical illness.Relevance for Clinical PracticePatients in ICU are at high risk of developing PIs, therefore, preventive measures should be maximized. Risk assessment should be carried out sequentially owing to the changes that patients present throughout their ICU stay and preventive measures should be used according to the risk level.
The activation of Arabidopsis axillary buds involves a switch from slow to rapid committed outgrowth regulated by auxin and strigolactone
Authors: Nahas Zoe , Ticchiarelli Fabrizio , van Rongen Martin , Dillon Jean , Leyser Ottoline 
Published: March 2024

Summary

Arabidopsis thaliana (Arabidopsis) shoot architecture is largely determined by the pattern of axillary buds that grow into lateral branches, the regulation of which requires integrating both local and systemic signals.

Nodal explants – stem explants each bearing one leaf and its associated axillary bud – are a simplified system to understand the regulation of bud activation. To explore signal integration in bud activation, we characterised the growth dynamics of buds in nodal explants in key mutants and under different treatments.

We observed that isolated axillary buds activate in two genetically and physiologically separable phases: a slow‐growing lag phase, followed by a switch to rapid outgrowth. Modifying BRANCHED1 expression or the properties of the auxin transport network, including via strigolactone application, changed the length of the lag phase. While most interventions affected only the length of the lag phase, strigolactone treatment and a second bud also affected the rapid growth phase.

Our results are consistent with the hypothesis that the slow‐growing lag phase corresponds to the time during which buds establish canalised auxin transport out of the bud, after which they enter a rapid growth phase. Our work also hints at a role for auxin transport in influencing the maximum growth rate of branches.
Identifying quantitative trait locus and candidate genes for maize (Zea mays L.) plant architecture traits based on segregating populations constructed by high‐generation sister lines
Authors: Sun Ruidong , Zhou Xiaohang , Li Yimeng , Liu Ying , Liu Xihang , Ding Mingyang , Lv Xiangling , Li Fenghai 
Published: March 2024

AbstractLeaf length, width and angle are important traits in the architecture of maize plants. Delving into the genetic mechanisms of these traits is of utmost significance for promoting population yield. In this study, we employed the high‐generation sister lines PCU and PCM, which have significant differences in leaf morphological traits, as parental entities for the creation of F2 and F2:3 populations. Through quantitative trait locus (QTL) mapping of the traits in the three ear leaves by ICIM, 55 QTL were obtained, with six stable QTL selected across divergent populations. These QTL had physical spans ranging from 0.34 to 44.8 Mbp. Through gene annotation and qRT‐PCR, Zm00001d007382, Zm00001d035965, Zm00001d042777 and Zm00001d020641 were predicted as potential candidates for regulating maize plant architecture. The results of this study lay a foundation for analysing the genetic mechanisms of maize plant architecture traits and cloning‐related genes.
Inside the ivory tower, the view from a “space invader”: An exploratory study into the ways racialized PhD students experience white ignorance in elite universities in the UK
Authors: Lootens Elif , Fúnez‐Flores Jairo I. 
Published: March 2024

AbstractThis paper examines the experiences of racialized PhD students in British elite universities. It is framed by Mills' (2007) conception of white ignorance and reflects on the power of whiteness that shapes everyday experiences in such places of privilege. For Mills, the production of racism relies on epistemological processes that produce ignorance, and which promote various ways of ignoring the histories and legacies of European colonialism. Research has shown that professors find it difficult to talk about racism and coloniality within higher education. Professors responses are important as they may affect the outcomes of conducting research for PhD students, yet there is less understanding of how racialized PhD students experience or address white ignorance. Using in‐depth interviews with 14 racialized PhD students, this paper critically examines the intertwined relationship between the coloniality of knowledge and white ignorance within elite universities in the United Kingdom. While universities have been regarded as “neutral” knowledge‐producing institutions, this study challenges the assumptions, interactions, and practices of higher education disciplines in the social sciences, namely anthropology and sociology. Based on the findings of this work, we argue that white ignorance is an epistemic strategy that justifies racial domination within and beyond the halls of academia.
miR156‐PvSPL2 controls culm development by transcriptional repression of switchgrass CYTOKININ OXIDASE/DEHYDROGENASE4
Authors: Yang Ruijuan , Wu Zhenying , Sun Ying , Liu Yuchen , Hang Yuqing , Liu Min , Liu Yajun , Wang Xiaoshan , Liu Wenwen , Fu Chunxiang 
Published: March 2024

SUMMARYCulm development in grasses can be controlled by both miR156 and cytokinin. However, the crosstalk between the miR156‐SPL module and the cytokinin metabolic pathway remains largely unknown. Here, we found CYTOKININ OXIDASE/DEHYDROGENASE4 (PvCKX4) plays a negative regulatory role in culm development of the bioenergy grass Panicum virgatum (switchgrass). Overexpression of PvCKX4 in switchgrass reduced the internode diameter and length without affecting tiller number. Interestingly, we also found that PvCKX4 was always upregulated in miR156 overexpressing (miR156OE) transgenic switchgrass lines. Additionally, upregulation of either miR156 or PvCKX4 in switchgrass reduced the content of isopentenyl adenine (iP) without affecting trans‐zeatin (tZ) accumulation. It is consistent with the evidence that the recombinant PvCKX4 protein exhibited much higher catalytic activity against iP than tZ in vitro. Furthermore, our results showed that miR156‐targeted SPL2 bound directly to the promoter of PvCKX4 to repress its expression. Thus, alleviating the SPL2‐mediated transcriptional repression of PvCKX4 through miR156 overexpression resulted in a significant increase in cytokinin degradation and impaired culm development in switchgrass. On the contrary, suppressing PvCKX4 in miR156OE transgenic plants restored iP content, internode diameter, and length to wild‐type levels. Most strikingly, the double transgenic lines retained the same increased tiller numbers as the miR156OE transgenic line, which yielded more biomass than the wild type. These findings indicate that the miR156‐SPL module can control culm development through transcriptional repression of PvCKX4 in switchgrass, which provides a promising target for precise design of shoot architecture to yield more biomass from grasses.
Post‐transfusion biotin‐labeled red blood cell survival studies in pediatric sickle cell disease with antibodies of uncertain significance
Authors: Yee Marianne E. M. , Zerra Patricia E. , McCoy James W. , Covington Mischa L. , Stowell Sean R. , Joiner Clinton H. , Lough Christopher M. , Delvadia Bhaveshkumar B. , Josephson Cassandra D. , Roback John D. , Fasano Ross M. 
Published: March 2024

AbstractBackgroundRed blood cell (RBC) antibodies are common in multiply transfused patients with sickle cell disease (SCD). Unlike RBC alloantibodies, the potential of autoantibodies to cause post‐transfusion hemolysis may be uncertain. Biotin‐labeling provides a direct measurement of red cell survival (RCS) over time, thus can be used to assess the clinical significance of RBC antibodies. Antibodies to biotinylated RBC (B‐RBC) occasionally are detected after exposure, which may impact B‐RBC survival in subsequent RCS studies.Study Design and MethodsPediatric patients with SCD receiving monthly chronic transfusions underwent RCS studies, receiving aliquots of allogeneic RBC labeled at distinct densities of biotin (2–18 μg/mL). B‐RBC survival was followed for 4 months post‐transfusion, and B‐RBC antibody screening for 6 months. Patients with warm autoantibodies (WAA) or B‐RBC antibodies are reported here.ResultsRBC antibodies were detected during RCS in four patients: one with WAA, one with WAA followed by B‐RBC‐specific antibodies, and two with transient B‐RBC antibodies within the first 5 weeks of exposure. B‐RBC half‐lives (T50) ranged 37.6–61.7 days (mean 47.8 days). There was no evidence of increased hemolysis or accelerated B‐RBC clearance in the presence of WAA or B‐RBC antibodies.DiscussionBiotinylation of allogenic RBC can be used to assess the possible effects of RBC antibodies on transfusion survival in individual cases, particularly when it is uncertain if the detected antibodies may result in hemolysis. In the cases presented here, neither WAA nor B‐RBC antibodies were associated with significant shortening of B‐RBC survival in individuals with SCD.
Irredundant bases for the symmetric group
Authors: Roney‐Dougal Colva M. , Wu Peiran 
Published: March 2024

AbstractAn irredundant base of a group acting faithfully on a finite set is a sequence of points in that produces a strictly descending chain of pointwise stabiliser subgroups in , terminating at the trivial subgroup. Suppose that is or acting primitively on , and that the point stabiliser is primitive in its natural action on points. We prove that the maximum size of an irredundant base of is , and in most cases . We also show that these bounds are best possible.
The modern alchemy of clinical pathology: turning the output of microbiology laboratory operations into gold
Authors: Kanjilal Sanjat 
Published: March 2024

ABSTRACT

The clinical microbiology laboratory generates a huge amount of high-quality data that play a vital role in clinical care. With proper extraction, cleaning, analysis, and validation pipelines, these data can serve multiple other purposes that include supporting laboratory operations, understanding local epidemiology, informing hospital-specific policies, and public health surveillance. In this review, I use one of the core activities of the microbiology laboratory, antimicrobial susceptibility testing (AST), to illustrate several potential applications of next-generation data analytics. The first involves continuous monitoring of commercial AST systems using comparisons of minimum inhibitory concentration (MIC) distributions over time to trigger re-verification when statistically significant differences are detected. An extension of this is temporal analysis of joint MIC distributions to understand performance for multidrug-resistant organisms. More sophisticated analyses involve linking microbiologic data to clinical metadata to gain insight into the clinical validity of AST data and to inform treatment policies. The elements of a robust, validated analysis engine using routine data streams already exist, but numerous challenges must be overcome to make it a reality. Most importantly, it will require the sustained collaboration and advocacy of hospital leadership, microbiologists, clinicians, antimicrobial stewardship, data scientists, and regulatory agencies. Though no small feat, achieving this vision would provide an important resource for microbiology laboratories facing a rapidly evolving practice landscape and further cement its role as an integral part of a learning health system.
Complete genome sequence of plant growth-promoting
Bacillus stratosphericus
AIMST-CREST02 isolated from bulk soil of a paddy field
Authors: Sivaprakasam Sumitra , Mohd Azim Khan Nur Arisa , Yee Fan Tan , Kumarasan Yukgehnaish , Sicheritz-Pontén Thomas , Petersen Bent , Mohd Hata Erneeza , Vadamalai Ganesan , Parimannan Sivachandran , Rajandas Heera 
Published: March 2024

ABSTRACT

Here, we present the complete genome of a plant growth-promoting strain,
Bacillus stratosphericus
AIMST-CREST02 isolated from the bulk soil of a high-yielding paddy plot. The genome is 3,840,451 bp in size with a GC content of 41.25%. Annotation predicted the presence of 3,907 coding sequences, including genes involved in auxin biosynthesis regulation and gamma-aminobutyric acid (GABA) metabolism.
Building citizen science intelligence for outbreak preparedness and response: a mixed-method study in nine countries to assess knowledge, readiness and feasibility
Authors: Tan Yi-Roe , Nguyen Manh Duc , Mubaira Caroline Antonia , Kajungu Dan , Kumar Dinesh , Canlas Felipe C , Sunaryoko Firli Yogiteten , Maharjan Gyanu Raja , Khosa Harjyot , Hauter Ingo , Thiga Joan , Anowar Md. Mazharul , Okwen Patrick , Kutadza Tariro , Chikanya Walter , Choisy Marc , Yap Peiling 
Published: March 2024

IntroductionCitizen science (CS) is an emerging approach in public health to harness the collective intelligence of individuals to augment traditional scientific efforts. However, citizens’ viewpoint, especially the hard-to-reach population, is lacking in current outbreak-related literature. We aim to understand the awareness, readiness and feasibility of outbreak-related CS, including digitally enabled CS, in low-income and middle-income countries.MethodsThis mixed-method study was conducted in nine countries between October 2022 and June 2023. Recruitment through civil society targeted the general population, marginalised/indigenous groups, youth and community health workers. Participants (aged ≥18 years) completed a quantitative survey, and a subset participated in focus group discussions (FGDs).Results2912 participants completed the survey and 4 FGDs were conducted in each country. Incorporating participants’ perspectives, CS is defined as the practice of active public participation, collaboration and communication in all aspects of scientific research to increase public knowledge, create awareness, build trust and facilitate information flow between citizens, governments and scientists. In Bangladesh, Indonesia, the Philippines, Cameroon and Kenya, majority were unaware of outbreak-related CS. In India and Uganda, majority were aware but unengaged, while in Nepal and Zimbabwe, majority participated in CS before. Engagement approaches should consider different social and cultural contexts, while addressing incentivisation, attitudes and practicality factors. Overall, 76.0% expressed interest in digital CS but needed training to build skills and confidence. Digital CS was perceived as convenient, safer for outbreak-related activities and producing better quality and quantity of data. However, there were concerns over non-inclusion of certain groups, data security and unclear communication.ConclusionCS interventions need to be relatable and address context-specific factors influencing CS participation. Digital CS has the potential to facilitate collaboration, but capacity and access issues must be considered to ensure inclusive and sustainable engagement.