bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-course RNA-seq analysis of upland cotton (Gossypium hirsutum L.) responses to Southern root-knot nematode (Meloidogyne incognita) during compatible and incompatible interactions
Authors: Khanal Sameer , Kumar Pawan , da Silva Mychele B. , Singh Rippy , Suassuna Nelson , Jones Don C. , Davis Richard F. , Chee Peng W. 
Published: February 2025

Abstract

Background
The Southern root-knot nematode (Meloidogyne incognita) poses a substantial threat to cotton (Gossypium hirsutum L.) by causing significant agricultural losses. Host plant resistance is the most plausible approach for minimizing these losses. QTL mapping and early transcriptomic studies have identified candidate genes within the QTL regions on chromosome 11 (qMi-C11) and chromosome 14 (qMi-C14). Although these QTL regions have been fine-mapped and candidate genes identified, expression profiling of Meloidogyne-Gossypium interactions across different stages of infection could further refine the list of candidate genes. This study advances our understanding of the molecular mechanisms underlying the resistance conferred by qMi-C11 and qMi-C14 against Southern root-knot nematode.

Results
Using time-course RNA-seq analyses across nematode developmental phases, we uncovered transcriptomic events—both genome-wide and within QTL intervals—underlying defense responses during compatible interactions (with Cocker 201, a susceptible line) and incompatible interactions (with M-120 RNR, a resistant line). Basal defense responses were observed in both compatible and incompatible interactions, with stronger expression in the incompatible interaction. Nematode-responsive genes associated with defense pathways showed distinct dynamics, characterized by repression during compatible interactions and early induction, greater diversity, and heightened upregulation during incompatible interactions. This study uncovers a broad repertoire of disease resistance and putative resistance genes, as well as pathogenesis-related genes, ligands, and receptors, that are differentially expressed in response to nematode parasitism. Mapping of these genes across the cotton genome identified promising candidates, including Gh_A11G3090 (PUB21) and Gh_A11G2836 (RPPL1) within the chromosome 11 QTL region, andGh_D02G0257 (RLP12) and Gh_D02G0259 (RLP12) within the chromosome 14 QTL region.

Conclusions
The findings of this study deepen our understanding of host-nematode interactions, identify candidate genes for downstream applications, and contribute to advancements in resistance breeding and sustainable nematode management strategies.
Socio-economic position, area-level deprivation and gradients in cancer incidence: England and Wales, 1971–2016
Authors: Hiatt Robert A. , Xun Wei , Santiago-Rodríguez Eduardo J. , Pikhartova Jitka , Shelton Nicola 
Published: February 2025

Abstract

Background
Social gradients for cancer mortality and survival have been reported but are less clear for cancer incidence where social factors external to health care systems are likely to be of more etiologic importance.

Methods
We examined social gradients in cancer incidence using data from the Office for National Statistics Longitudinal Study (ONS-LS), which selects an approximately 1.1% representative sample of the population of England and Wales. Data were analyzed for each successive ten-year census period from 1971–2011 with outcome data to 2016, the latest date available. Socioeconomic position of individuals was assessed using the National Statistics Socio-economic classification (NS-SEC). Areal level deprivation was measured using deciles of the Townsend Index. Cancer outcomes from the National Cancer Intelligence Network linked to the ONS-LS were examined for all cancers, and more common individual cancer sites. We used logistic regression to generate odds ratios to estimate the risk of a first incident cancer within each follow-up period.

Results
The 1971 ONS-LS census sample population initially comprised 257,803 individuals updated each census; and by 2016 137,755 incident cancer cases. Social gradients in cancer incidence were present for individual cancer sites of lung, stomach, and cervix for both individual and areal measures of socioeconomic standing with the least advantaged having higher incidence rates. Reverse gradients were present for prostate and breast cancers. The relationship of SES to increased cancer incidence for these common cancers is consistent with prior literature, but the striking gradients in these relationships reveal the strong association of SES factors with increasing social disadvantage for these cancers.

Conclusion
The findings demonstrate the importance of socioeconomic position in the incidence of some common cancers prior to diagnosis and treatment and reinforces the need for further research to address the contribution of upstream social determinants in the etiology of cancer.
Transforming liver transplant allocation with artificial intelligence and machine learning: a systematic review
Authors: Pruinelli Lisiane , Balakrishnan Kiruthika , Ma Sisi , Li Zhigang , Wall Anji , Lai Jennifer C. , Schold Jesse D. , Pruett Timothy , Simon Gyorgy 
Published: February 2025

Abstract

Background
The principles of urgency, utility, and benefit are fundamental concepts guiding the ethical and practical decision-making process for organ allocation; however, LT allocation still follows an urgency model.

Aim
To identify and analyze data elements used in Machine Learning (ML) and Artificial Intelligence (AI) methods, data sources, and their focus on urgency, utility, or benefit in LT.

Methods
A comprehensive search across Ovid Medline and Scopus was conducted for studies published from 2002 to June 2023. Inclusion criteria targeted quantitative studies using ML/AI for candidates, donors, or recipients. Two reviewers assessed eligibility and extracted data, following PRISMA guidelines.

Results
A total of 20 papers were included, synthesizing results into five major categories. Eight studies were led by a Spanish team, focusing on donor-recipient matching and proposing machine learning models to predict post- LT survival. Other international studies addressed organ supply-demand issues and developed predictive models to optimize LT outcomes. The studies highlight the potential of ML/AI to enhance LT allocation and outcomes. Despite advancements, limitations included the lack of robust transplant-related benefit models and improvements in urgency models compared to MELD.

Discussion
This review highlighted the potential of AI and ML to enhance liver transplant allocation and outcomes. Significant advancements were noted, but limitations such as the need for better urgency models and the absence of a transplant-related benefit model remain. Most studies emphasized utility, focusing on survival outcomes. Future research should address the interpretability and generalizability of these models to improve organ allocation and post-LT survival predictions.
Searching for potential Culicoides vectors of four orbiviruses in Yunnan Province, China
Authors: Li Zhan Hong , Wang Yi Nan , Deng Jia Ming , Li Le , Yang Lian Jiang , Chen Xinq Qiang , Wang Wen Hua , Lu Fu You , Tang Zhong Jie , Wang Dong Mei , Duan Ying Liang 
Published: February 2025

Abstract

Background
Some species of Culicoides (Diptera, Ceratopogonidae) are major vectors for arboviruses, and Yunnan Province is a key area for arbovirus prevalence in China. Therefore, this study attempts to search for potential Culicoides vectors for the common orbiviruses bluetongue virus (BTV), epizootic hemorrhagic disease virus (EHDV), Palyam virus (PALV) and Tibet orbivirus (TIBOV) in Yunnan Province, China.

Methods

Culicoides specimens were collected from 16 counties in Yunnan Province, China, using UV traps and tested for BTV, EHDV, PALV and TIBOV through one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 543 conspecific pools of Culicoides containing 9895 specimens were tested.

Results
A total of 46 species belonging to 8 subgenera and 2 groups were recognized. A total of 19 species and a Culicoides subgenus Trithecoides complex were tested using RT-qPCR. One pool of Culicoides shortti Smith & Swaminath and one pool of Culicoides orientalis Macfie tested positive for BTV, one pool of Culicoides oxystoma Kieffer tested positive for PALV, and four pools of Culicoides jacobsoni Macfie tested positive for TIBOV. All the tested samples were negative for EHDV, and all the tested C. subgenus Trithecoides midges were negative for any virus.

Conclusions

Culicoides shortti was identified as a potential BTV vector for the first time. Culicoides jacobsoni was confirmed as a potential TIBOV vector and C. orientalis as a potential BTV vector. Culicoides oxystoma was also shown to be a natural carrier of PALV using the RT-qPCR method.

Graphical Abstract
Knowledge and practice among caregivers having children with autism in Bangladesh: findings from a cross-sectional study
Authors: Al Imran Md. , Islam Md. Saiful , Hossain Md. Sharif , Pardhan Shahina , Bari Nakiba , Zeba Zebunnesa 
Published: February 2025

Abstract

Background
Autism spectrum disorder (ASD) is a term used to describe a group of conditions characterized by difficulties with social skills, speech, repetitive behaviors, and nonverbal communication. There is no cure for autism, however, early diagnosis and intervention can increase the chance of treatment success. If parents or caregivers do not have sound knowledge about autism, problems can become more complicated. The study aimed to assess the knowledge and practice among caregivers having children with ASD in Bangladesh.

Methods
A cross-sectional survey was conducted among 68 caregivers of children with ASD in the selected area of Mymensingh city, Bangladesh. The data were collected from May to June 2021 through face-to-face interviews by a semi-structured questionnaire including informed consent, socio-demographics, as well as questions regarding knowledge (12-item) and practice (6-item) towards children with ASD using a purposive sampling technique. The data were analyzed using the SPSS software (version 25.0).

Results
The mean score of knowledge among caregivers having children with ASD was 7.16 (SD = 2.09) out of 12 (59.67%). The mean score of practice among caregivers having children with ASD was 3.16 (SD = 1.10) out of 6 (52.67%). There were no significant mean differences in the mean knowledge and practice scores among participants’ different socio-demographic categories. 95.6% of caregivers have not received any formal training to care for children with ASD, and more than half (57.4%) believed that mixing with good friends would make the necessary change in children with ASD. 97.1% of the children with ASD did not have any health insurance with 72.1% receiving government allowance for ASD.

Conclusions
The findings indicated inadequate knowledge and practice among caregivers of children with ASD. The study suggests an immediate health education program is needed, as well as appropriate practice for children with ASD in Bangladesh.
Unveiling antimicrobial stewardship competence among Italian nurses: results from a nationwide survey
Authors: Danielis Matteo , Buttiron Webber Tania , Barchielli Chiara , Mongardi Maria , Regano Domenico 
Published: February 2025

Abstract

Background
The development of nursing competencies in antimicrobial stewardship (AMS) is influenced by a two-dimensional model, encompassing both internal and environmental factors. In the context of Italian clinical nursing, this study aims to assess and measure these aspects.

Methods
Employing a cross-sectional online survey design, nurses from various clinical specialties in Italy were involved. The questionnaire assessed individual variables, knowledge, attitudes, practices, as well as structural and process-related variables influencing AMS. Statistical analyses were performed, encompassing descriptive statistics, Pearson correlation, and multiple linear regression.

Results
A total of 1,651 nurses aswered the survey, with a participation rate of 50.8%. The participant demographic revealed that 77% were female, and they had an average of 15 years of experience. Workplace and regional factors were found to significantly impact both AMS practices and attitudes. Surgical nurses reported higher practices scores (β = 0.467, P <.01), while critical care nurses scored lower (β= -0.398, P <.01). Regarding perceptions of structure, workplace characteristics significantly influenced nurses’ scores, indicating lower perceptions among surgical nurses compared to their medical counterparts (β= -0.315, P <.01).

Conclusions
The study reveals the intricate interplay between internal and external factors that impact nurses’ AMS competence. This underscores the urgent need for targeted interventions and education initiatives to enhance nurses’ AMS competencies. Specifically, addressing variations in settings and nurses’ behaviours becomes imperative for achieving improved patient outcomes.
Evaluating the predictive power of metacognitive reading strategies across diverse educational contexts
Authors: Ghimire Nirmal , Mokhtari Kouider 
Published: February 2025

Abstract

Background
Metacognitive reading strategies, such as monitoring and regulating one’s reading processes, are critical for enhancing reading comprehension and achievement. However, their effectiveness can vary across different educational contexts and student populations, necessitating flexible instructional approaches. This study examines the predictive utility of metacognitive reading strategies on metacognitive reading skills and reading achievement scores using data from the PISA 2018 assessment. Specifically, it compares the effectiveness of these strategies across four distinct educational contexts: the United States, OECD countries, non-OECD countries that participated in the assessment (Partner Countries), and the census data (Full Sample).

Methods
A multi-stage analytical approach was used, combining Random Forest models for feature importance analysis with survey-weighted linear regression to assess the relationships of reading strategies on metacognitive skills and reading achievement. The analysis utilized data from the PISA 2018 Student Questionnaire, which included responses from 612,004 students across 79 countries. The study focused on three key metacognitive reading skills: Understanding and Remembering, Summarizing, and Assessing Credibility, as well as reading achievement scores based on ten plausible values.

Results
The Random Forest analysis identified several metacognitive reading strategies as consistent predictors of metacognitive reading skills, with some variations in relative importance by educational setting. Notable metacognitive reading strategies included underlining important parts of the text, carefully checking the representation of important facts in summaries, and verifying information on websites. These strategies showed a positive correlation with higher metacognitive skills and overall reaching achievement. The direction of the relationships between metacognitive reading strategies, metacognitive skills, and reading achievement scores was consistent across contexts, indicating a modest yet significant association between strategy use and both outcomes.

Conclusions
This study enhances our understanding of how metacognitive reading strategies influence reading skills and achievement in diverse educational settings. The findings highlight the potential benefits of reinforcing specific strategies to support students' reading comprehension. Given the consistent positive relationships between strategy use, metacognitive skills, and reading achievement, targeted interventions to promote these strategies could effectively improve reading comprehension across diverse educational contexts.
Utility and usability of a dengue NS1 rapid diagnostic as a self-test
Authors: Zulkifli Nurfatihah , Che-Kamaruddin Naim , Hazan Atiqah , Kim-Kee Tan , Rajagopal Sivalingam , AbuBakar Sazaly 
Published: February 2025

Abstract

Background
Early detection of dengue fever is pivotal to help differentiate against other febrile illnesses, especially in the dengue-endemic regions. Currently, febrile patients would have to go to the healthcare facility to get tested for dengue. A diagnostic approach that empowers febrile persons to perform their own tests is needed. Here, we evaluated the utility and the usability of the dengue NS1 rapid diagnostic test and whether it could be accepted as a home self-test. A lateral flow immunochromatography test (ICT) using DENV NS1 was converted to a possible self-test kit by providing the kit with a test device, an alcohol swab, a lancet, a disposable dropper, an assay buffer, and a test manual.

Methods
Twenty volunteers were recruited for this study. The participants performed the self-test under the observation of trained observers who recorded if any procedural error was committed. The results of each test were interpreted by the participants using a given interpretation table.

Results
Ninety-five percent (95%) of the study participants found the instruction manual was easy to follow and 70% felt the test kit was easy to use. Additionally, 80% of the participants successfully obtained the expected results. A majority (80%) would consider using the test kit if needed and would recommend it to family members and friends. Seventy percent (70%) of the participants, most of whom with monthly income of less than USD417, were willing to pay less than USD2 for the test kit.

Conclusion
Findings from the study suggested that a self-test diagnostic for dengue fever is highly acceptable and, hence, could be a viable approach for the early detection of the infection.

Trial registration MRECID.NO: 2022628-11345.
TC10 on endosomes regulates the local balance between microtubule stability and dynamics through the PAK2-JNK pathway and promotes axon outgrowth
Authors: Koinuma Shingo , Miyaji Misa , Akiyama Suzuka , Ito Yasuyuki , Takemura Hiroshi , Wada Naoyuki , Igarashi Michihiro , Nakamura Takeshi 
Published: February 2025

ABSTRACT
The neuronal cytoskeleton comprises microtubules, actin filaments and neurofilaments, and plays a crucial role in axon outgrowth and transport. Microtubules and actin filaments have attracted considerable attention in axon regeneration studies. We have previously shown that TC10 (also known as RhoQ), a Rho family GTPase that promotes axon outgrowth through membrane addition, is required for efficient axon regeneration. This study demonstrates that TC10 on recycling endosomes, but not on the plasma membrane, balances microtubule stability and dynamics in the axons, thereby counteracting axon retraction. TC10 ablation reduced the phosphorylation of SCG10 (also known as STMN2) and MAP1B, which are neuronal microtubule-binding proteins and JNK substrates. Consistent with this, JNK phosphorylation was decreased in TC10-knockout neurons compared to in wild-type neurons. Furthermore, TC10 deletion significantly reduced PAK2 autophosphorylation. PAK2 was found on Rab11-positive endosomes in cell bodies and axons, and its localization to endosomes was reduced by TC10 loss. PAK inhibition reduced tubulin acetylation and JNK phosphorylation in axons. Furthermore, MKK4 and MKK7 (also known as MAP2K4 and MAP2K7, respectively) were found to mediate signaling from TC10-activated PAK to JNK on JIP1-positive endosomes. Overall, TC10 transmits a microtubule-regulatory signal from PAK2 to SCG10 and MAP1B via JNK on axonal endosomes.
Training researchers to engage in policy in the United States: mapping the growth and diversity of programme models
Authors: Akerlof K.L. , Schenk Todd , Bankston Adriana , Mitchell Kelsey , Syl Aniyah , Eddy Lisa , Hall Sarah L. , Lad Nikita , Lake Samuel J. , Ostrom Robert B.J. , Rosenberg Jessica L. , Schwartz Mark R. , Sisti Abigail R. , Smith Christopher T. , Solomon Lee , Velez Anne-Lise K. 
Published: February 2025

Background:
Programmes that provide scientists and engineers with support to engage in public policy have proliferated in the United States, with many opportunities available for training, networking and placements within government and government-facing organisations. This trend suggests that an evolution may be occurring at the science–policy interface. However, there is little extant data on the structure, aims and impacts of these programmes.
Aims and objectives:
This study maps the current landscape of US programmes seeking to train researchers at all career stages to engage in policy. We focus on Virginia, a state with a substantial number and diversity of programmes, to assess: (1) how they conceptualise their audiences, activities and impacts; and (2) which roles in policy and types of evidence use they address.
Methods:
We developed a database of US policy programmes (n=174) and conducted a case study of those in Virginia through surveys and interviews with their leaders (n=12).
Findings:
The majority (57%) of science policy programmes are state-based. These programmes include student organisations, government placements and fellowships, and academic certificates, degrees, and other trainings. While these reflect diverse models for how to engage researchers in policy, Virginia programme leaders across these categories similarly conceived long-term impacts, audiences and activities, researcher roles in policy, and types of decision-maker evidence use. And they perceived limited ability to implement evidence-based approaches within their programmes.
Discussion and conclusion:
Building additional programmatic capacity – through shared learning and partnerships – could lend support to this emerging trend in science policy with implications for US research and governance.
Blessed Acts of Oblivion
Authors: Heywood Paolo 
Published: February 2025

This essay explores the ethics of forgetting as a technology of the self. Forgetfulness is a feature of a range of contexts of political conflict and “difficult” heritage. Such forgetfulness is often imagined as an imposition (as when states deny the freedom to remember) or a weakness (as when people are thought to repress uncomfortable or difficult memories). Here, by contrast, I examine a context of difficult heritage and political conflict in which people forget some things by remembering others, and I highlight the ways in which it is often hard to disentangle the primary process. Rather than ask whether the point is what you remember or what you forget, alternative and more interesting questions are revealed, I suggest, by asking what kind of subject constitutes the ideal end result.

Riassunto
Questo articolo esplora l’etica dell’oblio come tecnologia del sé. L’oblio è una caratteristica di una serie di contesti di conflitto politico e di “eredità difficili”. Tale oblio è spesso immaginato come un’imposizione (come quando uno stato nega la libertà di ricordare) o come una debolezza (come quando si pensa che una persona reprima ricordi scomodi o difficili). Qui, al contrario, esamino un contesto di eredità difficile e di conflitto politico in cui le persone dimenticano alcune cose ricordandone altre, e sottolineo come spesso sia difficile districare quale processo sia primario. Piuttosto che chiedersi se il punto sia ciò che si ricorda o ciò che si dimentica, suggerisco che domande alternative e più interessanti si rivelano chiedendo quale tipo di soggetto sia il risultato ideale.