bluuebunny/crossref_metadata_2025_split huggingface dataset:
A β-Ketoacyl-CoA Synthase encoded by DDP1 controls rice anther dehiscence and pollen fertility by maintaining lipid homeostasis in the tapetum
Authors: Xu Yibo , Zhou Shixu , Tian Jingfei , Zhao Wenfeng , Wei Jianxin , He Juan , Tan Wenye , Shang Lianguang , He Xinhua , Li Rongbai , Qin Baoxiang 
Published: August 2024

Abstract

Anther dehiscence and pollen fertility are crucial for male fertility in rice. Here, we studied the function of Defective in Dehiscence and Pollen1 (DDP1), a novel member of the KCS family in rice, in regulating anther dehiscence and pollen fertility. DDP1 encodes an endoplasmic reticulum (ER)-localized protein and is ubiquitously expressed in various organs, predominately in the microspores and tapetum. The ddp1 mutant exhibited partial male sterility attributed to defective anther dehiscence and pollen fertility, which was notably distinct from those observed in Arabidopsis thaliana and rice mutants associated with lipid metabolism. Mutations of DDP1 altered the content and composition of wax on anther epidermis and pollen wall, causing abnormalities in their morphology. Moreover, genes implicated in lipid metabolism, pollen development and anther dehiscence exhibited significantly altered expression levels in the ddp1 mutant. These findings indicate that DDP1 controls anther dehiscence and pollen fertility to ensure normal male development by modulating lipid homeostasis in the tapetum, thereby enhancing our understanding of the mechanisms underlying rice anther dehiscence and pollen fertility.
First Report of Fusarium redolens Causing Fusarium Wilt on Vetch (Vicia sativa)
Authors: Labed Imene , Moustafa BANI , Barboucha Ghozlen , Belkouicem Djouhaina , Boushaba Khaoula , Boumegoura Ali , Zarouri Belkacem 
Published: August 2024

Abstract

Common vetch, or Vicia sativa, is an essential forage legume crop used for livestock production and as a green manure crop. In 2022, fusarium wilt symptoms were observed in vetch fields in Constantine province (Northeastern Algeria). The affected plants showed wilting, yellowing of leaves, vascular discoloration of roots and stems and plant death. Morphological and molecular analysis of two recovered isolates confirmed their identity as Fusarium redolens, these isolates were found to be pathogenic on vetch plants. This study represents the first report of F. redolens as a pathogen on Vicia sativa causing fusarium wilt.
Preclinical Safety Assessment of the Oral Administration of Lactobacillus plantarum GUANKE in Animal Models
Authors: Yang Yuewen , Zhang Yanlin , Sun Ruixiang , Du Wenjuan , Liu Yangyang , Zheng Lijun , Ren Zhihong , Li Ming ding , Xu Jianguo 
Published: August 2024

Abstract

Probiotics have a long history as fermented food or food supplements. The health benefits and safety profiles of probiotics are strain-specific and should be evaluated individually. The aim of this study was to assess the safety of the Lactobacillus plantarum GUANKE (GUANKE) strain by conducting pharmacological studies, oral toxicity assessments, and investigating the colonization and translocation of GUANKE in experimental animal models. Three pharmacological studies were conducted to examine the effects of oral administration of GUANKE on gastric emptying, bile secretion, and gastric juice secretion. In an acute toxicity study, rats were orally administrated with different doses of GUANKE and monitored for 14 days. In the subacute toxicity study, both rats and beagles were administrated with varying doses of GUANKE for 28 consecutive days to evaluate hematologic, biochemical, and histological effects. The results showed that GUANKE administration did not result in any adverse effect on hematological parameters, biochemical parameters, urinary parameters, and organ indices. Importantly, no translocation of GUANKE to extra-intestinal organs or blood was observed following administration of the CSFE-labeled strain. In summary, this study demonstrated the safety of GUANKE intake, which encourages its potential application as a probiotic in clinical trials.
Spatiotemporal variability and change of snowfall in Hokkaido: Effects of air and sea surface temperatures rises, ocean currents, and sea ice
Authors: HIGASHINO MAKOTO 
Published: August 2024

Abstract

The impacts of climate change on snowfall have received great interest in cold regions for water resources and flood risk managements. This study investigates the effects of rises in air and the sea surface temperatures, ocean currents, and sea ice on snowfall in Hokkaido, northern Japan over the period from 1961 to 2020 (60 years). Climate data observed at the 22 weather stations operated by the Japan Meteorological Agency (JMA) were analyzed. Obtained warming trends at these stations were all positive and statistically significant. Annual snowfall has increased at the 7 stations, whereas, decreased at the 2 stations. Otherwise, snowfall has neither increased nor decreased. It was found that the snowfall period has shortened mainly in the south coast. This is attributed to the fact that these sites are on the leeward side of the Eurasian monsoon and that air temperatures in the coast and the surface temperature of the Sea off Kushiro have risen sufficiently. The results suggest that the flood risk can increase in response to acceleration of the rise in a level of a river due to early melting snow in spring (March and April). Although the weather stations in the east coast are also on the leeward side, the snowfall period has not shortened. The warming trends in April are very weak in the east coast. The East Sakhalin Current come from the northern Sea of Okhotsk and melting sea ice in spring play an important role in keeping the winter period from shortening.
Machine learning models predict the immunotherapy response in tumor based on DNA methylation
Authors: Gu Zheng , Deng Erle , Ai Jing , Wu Fei , Su Qiang , Yu Junxian 
Published: August 2024

Abstract

Background
The epigenetic control of immune responses plays a crucial role in the development and progression of cancer. The need to identify biomarkers and create new predictive models is crucial in order to reliably estimate response rates in tumour immunotherapy, which are currently low.
Methods
We conducted a screening to identify loci that had variable methylation patterns in response to immunotherapy. We next focused on pathways that are relevant to this response and increased their representation.We investigated the expression of methylation loci associated with immunotherapy in tissues.We have also provided a concise overview of the Qtl features associated with several CpG loci.We examined the relationship between the levels of TMB, NeoAg, and PD-L1 and the effectiveness of immunotherapy.Identification of base preferences in DNA sequences by motif analysis allows for the demonstration of unique sequence patterns linked with DNA methylation.We created a total of seven machine learning models, namely Lasso regression, Xgboost, SVM, random forest, KNN, Naive Bayes, and Decision Tree. We then compared their respective functions and choose the best model..
Result
The five CpG loci that exhibited the most significant response to tumour immunotherapy were cg00045061, cg00107488, cg00056433, cg00090974, and cg00072957.We identified the immunotherapy-associated pathway, the ubiquitination-proteasome system, by screening differentially methylated sites.Upon analysis, we observed that the majority of the CpG loci that exhibited differential methylation were situated on the N Shore region of the CpG island.The GO enrichment analysis identified the top two pathways as modulation of microvillus length and CXCR4 chemokine receptor binding.On the whole the Random Forest model is considered the optimal choice for machine learning((Precision: 0.859,F1score: 0.907.Recalling: 0.941,ROC: 0.654).
Conclusion
Tumour methylation sites have the potential to be used as biomarkers for predicting the effectiveness of tumour immunotherapy and for future clinical applications.The Random Forest model is the most optimal choice among many machine learning algorithms for predicting methylation sites in immunotherapy.
Whole genome resequencing reveals Y-chromosome variants in yak: key insights into genetic diversity and population structure
Authors: Mahar Karan , Goli Rangasai Chandra , Gurao Ankita , Kumar Amod , Gowane Gopal Ramdasji , Chitkara Meenakshi , Ahlawat Sonika , Niranjan Saket Kumar , Jagadeesan K , Pundir Rakesh Kumar , Arora Reena , Kataria Ranjit Singh , Dige Mahesh Shivanand 
Published: August 2024

Abstract

Yak, an economically important bovine species considered as the lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. The Y chromosome is widely recognized for its role in male traits, characterized by paternal inheritance, high mutation rate, and minimal recombination rate or reverse mutation. So, we investigated the Y-chromosome-specific variants in four yak populations namely, Arunachali, Himachali, Ladakhi, and Jinchuan through whole genome resequencing, we identified nearly 274828, 243143, 283774, and 194 228 SNPs, respectively. The intergenic regions held the highest proportion of SNPs, with Jinchuan yaks showing fewer SNPs due to intense selective breeding for reproductive performance and product quality. The Ts/Tv ratios were 1.57, 1.67, 1.55, and 1.99 for Arunachali, Himachali, Ladakhi, and Jinchuan yaks, respectively. SnpEff annotation indicated that most SNPs were intergenic, followed by intronic regions. Key genes identified included ASMT, ASMTL, and SRY, with significant roles in melatonin biosynthesis and male sex determination. Interestingly, we performed Linkage disequilibrium (LD) pruning, which retained only about 20% of SNPs, underscored the complexity of genetic analyses and highlighted the importance of careful LD criteria selection to avoid losing loci under selection. This pioneering mapping of Y-chromosome SNPs in yaks provides essential insights into their genetic landscape and underscores the critical need for precise LD pruning parameters to accurately assess genetic diversity and population differentiation.
Psychological morbidity among coal miners compared to other occupations in Appalachia
Authors: Blanc Paul D. , Trupin Laura , Yelin Edward H. , Katz Patricia P. 
Published: August 2024

Abstract

Objectives
Depressive symptoms, anxiety, and post-traumatic stress disorder (PTSD) are common morbidities among coal miners, but the risk of these morbidities has not been analyzed relative to other occupations taking into account relevant covariates.
Methods
Using random digit dialing, we surveyed men aged 50 or over with a history of employment who resided in counties in Appalachia with high coal workers’ pneumoconiosis (CWP) mortality rates. We used the Primary Care Post-Traumatic Stress (PTSD) Screen and the Brief Trauma Questionnaire to query specific traumatic experiences. We used the Patient Health Questionnaire scale to assess depression symptoms and the Generalized Anxiety Disorder questionnaire to measure anxiety. Multivariable logistic regression analyzed associations between coal mining and depression, anxiety, and PTSD, adjusting for trauma, smoking and demographics.
Results
Of 1,428 participants, 233 (16.3%) reported coal mining employment. Coal mining was associated with increased odds of depression (OR 1.6; 95% CI 1.1 to 2.4) and anxiety (OR 1.7; 95% CI 1.1 to 2.7). Among those with any trauma (n = 711), coal mining was not associated with increased risk of PTSD (OR 0.80; 95% CI 0.5 to 1.3]. Non-coal trauma was associated with three-fold increased odds of anxiety (OR 3.2; 95% CI 2.0 to 5.1); for coal trauma, anxiety was associated with six-fold increased odds (OR 6.0; 95% CI 2.9 to 12.4).
Conclusions
Appalachian region coal miners carry an increased burden of depression and anxiety. This should be recognized by clinicians and at a population level, as worthy of individual and public health intervention.
Temperature dependent survivorship and development of Helicoverpa armigera (Hubner) (Lepidoptera-Noctuidae) on chickpea
Authors: Ahmad Salman 
Published: August 2024

Abstract

Effect of constant temperatures (14°, 16°, 18°, 20°, 22°, 25°, 27°, 30°, 32°, 35° and 36°C) on demography and development ofHelicoverpa armigerawas evaluated under laboratory conditions (with 65% RH and 14L:10D h) on chickpea. Potential fecundity (pf) was significantly reduced to 86 females/female/generation at 35ºC compared to 532 at 27ºC. Intrinsic rate of increase (rm) was minimum (0.0191 females/female/day) at 14ºC and maximum (0.0489) at 30ºC. Estimate of linear regression model showed that lower temperature threshold (Tmin) of egg stage was 7.71ºC. Values of Tminfor 1st, 2nd, 3rd, 4th, 5th and 6th instar were estimated as 4.97º, 10.52º, 4.67º, 4.44º, 5.74º and 4.19ºC, respectively. Total heat requirement for embryonic development was 74.07ºC-day. Degree day (DD) estimated by Arnold method showed that 542.75 DD was required by immature stage ofH. armigerato complete its life cycle at 36ºC. Estimates of cubic polynomial model showed that lower temperature threshold (Tmin) required for embryonic development was 8.47ºC and upper temperature threshold (Tmax) was 38.83ºC. Tminrequired for development of 1st, 2nd, 3rd, 4th, 5th and 6th instar was 9.68º, 8.93º, 10.11º, 12.05º, 9.12º and 10.47ºC, respectively and Tmaxwas 40.84º, 36.53º, 37.38º, 41.59º, 39.53º and 40.26ºC, respectively. It is concluded that pf was maximum at 27ºC while rmat 30ºC. Development ofH. armigeraincreased with increase in temperature and optimum development occurred at the range of 27º to 30ºC. Moreover, demographic parameters ofH. armigeraalong with the thermal effect can be used to develop the models of population growth and prediction.
Extraction of Halite from El-Bardawil Lake, North Sinai, Egypt: Sedimentological attributes and environmental impacts
Authors: Waheed Ahmed , Ghar Mohamed S. Abu El , Hussein Ahmed W. 
Published: August 2024

Abstract

The main goal of the present study is to consider the technology of preparing multi-ecosystem ponds in order to extract pure halite and discuss the sedimentology of this valuable mineral in the shallow modern artificial brine ponds. The lake water passes by three main stages to be prepared and to be ready for extraction of halite from suitable brine solution. The first stage is the concentration stage ponds, where the lake water flows through a series of ponds to increase brine salinity and deposit less soluble salts first (calcium carbonate and calcium sulphate). The other more soluble salts (sodium chloride and magnesium chloride) remain in solution. The second stage is the crystallization stage ponds, where the brine is pumped to solar ponds and left to increase brine density again until most of the halite mineral has crystallized and deposited. The pure halite crystals are crystallized in different sedimentological (e.g., rafts, mounds, cumulates and bottom crusts) and petrographic (e.g., euhedral cubic to subhedral, distorted platy and chevron crystals) forms. Finally, the third stage is the storage ponds, where the residual bittern solution that is left over after recovery of sodium chloride is pumped to storage ponds to precipitate the residual high soluble minerals and salts (magnesium sulphate and magnesium chloride). Saltworks from El-Bardawil Lake don't have economic impact only, but also have environmental impacts through decreasing the salinity of the lake and accordingly kept its ecological systems.
Assessment of information in biological tissues proper to ligands or receptors: A quantitative evaluation in the transgenic animal era
Authors: Watabe Yoshitoku , Takahashi Satoru , Yoshihara Masaharu 
Published: August 2024

Abstract

Objective Transgenic technology has enabled the visualization of signal transduction via ligand—receptor interactions. By using ubiquitous or intrinsic promoters, the impacts of ligand availability and receptor expression on signal transduction can be measured. However, methods for evaluating reporter expression gaps by using these promoters are poorly documented. Here, we applied entropy analysis in an in silico imaginary cell field for future transgenic animal experiments. Results Ligand availability is the bottleneck in signal transduction when intrinsic promoter-driven reporter expression is almost equivalent to ubiquitous promoter-driven reporter expression. Indeed, the mutual information of ubiquitous promoter-driven and intrinsic promoter-driven reporter expression increased as the latter increased. Conversely, receptor expression is the bottleneck when there is a large gap between ubiquitous promoter-driven or intrinsic promoter-driven reporter expression. Importantly, the value of mutual information is dependent on the proportion of ubiquitous promoter-driven reporter expression in the total cells, suggesting that it is necessary to consider ubiquitous promoter-driven reporter expression before evaluating the intrinsic promoter-driven reporter expression and the mutual information. Therefore, the generation of ubiquitous promoter-driven reporter transgenic animals may be useful in the future. In summary, a quantitative method for analyzing the contribution of ligands and receptors in signal transduction that is potentially useful in future transgenic animal experiments is proposed.
Increasing Sensitivity of Winter Wheat Yield to Snow Drought
Authors: Wang Shuo , Chen Huijiao , Zhu Peng , AghaKouchak Amir 
Published: August 2024

Abstract

The global crop ecosystem is critically dependent on snow availability, which has diminished in numerous snow-dependent regions due to increasing snow droughts associated with warmer winters. However, our understanding of crop yield sensitivity to snow droughts and how this sensitivity evolves remains limited. In this study, we find that from 1960 to 2020, approximately 51% of winter wheat croplands have experienced a significant increase (5.3−6.7% per year) in the frequency of snow droughts. To assess the sensitivity of winter wheat yield to snow droughts, we utilized explainable machine learning, gridded yield datasets, and the standardized snow water equivalent index (SWEI) from 1982 to 2016. Our findings reveal a positive association between yield anomalies and SWEI under snow drought conditions and a significant increase in the sensitivity of yield to SWEI over 24% of Northern Hemisphere winter wheat croplands. Additionally, enhanced accumulation of growing degree days, increased vapor pressure deficit (VPD), a slight decrease in total precipitation, and increased heavy rainfall are identified as dominant factors amplifying yield sensitivity to snow droughts. These findings highlight an increasing vulnerability of crop systems to snow droughts over the past three decades, which is crucial for informing risk management and adaptation of agriculture to a warming future with less snow.
Stable Peri-hexacene: A Long-Waited Open-Shell Graphene Fragment
Authors: Zeng Wangdong , Zhang JinJi , Fang Xiaojing , Niu Weiwei , Yu Yiming , Hu Yanlin , Sun Jiawen , Xu Ying , Zhou Zhihua , Zheng Baishu , Jiang Qing , Li Guangwu 
Published: August 2024

Abstract

[n]Peri-acenes ([n]PA) have attracted great interest as promising candidates for nanoelectronics and spintronics. However, the synthesis of large [n]PA (n > 4) is extremely challenging due to their intrinsic open-shell radical character and high reactivity. Herein, we report the successful synthesis and isolation of a derivative (1) of peri-hexacene in crystalline form. The structure of 1 was unequivocally confirmed by X-ray crystallographic analysis. Its ground state, aromaticity and photophysical properties were systematically studied by both experimental methods and theoretical calculations. Although the parent peri-hexacene is calculated to have a very large diradical character (y0 = 94.5%), 1 shows reasonable stability (t1/2 = 24 h under ambient conditions) due to the kinetic blocking. 1 exhibited an open-shell singlet ground state with a small singlet-triplet energy gap (-1.33 kcal/mol from SQUID measurements). 1 has also a narrow HOMO-LUMO energy gap (1.05 eV) and displays amphoteric redox behavior. This work opens new avenues for the design and synthesis of stable zigzag-edged graphene-like molecules with significant diradical character.
Chatbot for the Return of Positive Genetic Screening Results for Hereditary Cancer Syndromes: a Prompt Engineering Study
Authors: Coen Emma , Fiol Guilherme Del , Kaphingst Kimberly A. , Borsato Emerson , Shannon Jackie , Smith Hadley Stevens , Masino Aaron , Allen Caitlin G. 
Published: August 2024

Abstract

Background
The growing demand for genomic testing and limited access to experts necessitate innovative service models. While chatbots have shown promise in supporting genomic services like pre-test counseling, their use in returning positive genetic results, especially using the more recent large language models (LLMs) remains unexplored.
Objective
This study reports the prompt engineering process and intrinsic evaluation of the LLM component of a chatbot designed to support returning positive population-wide genomic screening results.
Methods
We used a three-step prompt engineering process, including Retrieval-Augmented Generation (RAG) and few-shot techniques to develop an open-response chatbot. This was then evaluated using two hypothetical scenarios, with experts rating its performance using a 5-point Likert scale across eight criteria: tone, clarity, program accuracy, domain accuracy, robustness, efficiency, boundaries, and usability.
Results
The chatbot achieved an overall score of 3.88 out of 5 across all criteria and scenarios. The highest ratings were in Tone (4.25), Usability (4.25), and Boundary management (4.0), followed by Efficiency (3.88), Clarity and Robustness (3.81), and Domain Accuracy (3.63). The lowest-rated criterion was Program Accuracy, which scored 3.25.
Discussion
The LLM handled open-ended queries and maintained boundaries, while the lower Program Accuracy rating indicates areas for improvement. Future work will focus on refining prompts, expanding evaluations, and exploring optimal hybrid chatbot designs that integrate LLM components with rule-based chatbot components to enhance genomic service delivery.
POLIFARMÁCIA: UMA REALIDADE NA CRIAÇÃO DE EQUÍDEOS DE ALTO DESEMPENHO
Authors: Maria Larissa Bitencourt Vidal  , De Souza Marcos Vinícius , Trivellato Lanna Neta Alda , Prata Marco Aurélio , De Souza Mendes Carlos Leandro , De Freitas Espeschit Braga Isis , Lopes Azevedo Pedro , Heitor Emery Gomes  
Published: August 2024

A ocorrência de eventos adversos relacionados à administração de fármacos e/ou suplementos é frequente nos equídeos, o que eleva a gravidade de acordo com a complexidade do regime terapêutico. Diariamente, os equídeos de alto desempenho com quadro clínico de diversas afecções simultâneas fazem uso de muitos fármacos e/ou suplementos, o que os torna mais suscetíveis a potenciais interações. Juntamente com a participação quase que semanal desses animais em eventos equestres, surgem inúmeras patologias, o que faz deste grupo os maiores usuários de fármacos e/ou suplementos. Esta alta exigência aumenta o contingente de portadores de doenças crônicas não transmissíveis, que demandam intervenções contínuas e na qual os fármacos e suplementos têm um papel importante. De fato, os riscos pertinentes à utilização inadequada de compostos químicos são maiores nesta categoria animal. Constantemente, nestes animais, observa-se a falta de qualidade da terapia farmacológica, presença de polifarmácia, uso de compostos químicos inadequados e duplicidade terapêutica, o que contribui para um maior risco de reações adversas e interações medicamentosas. Neste contexto, o Médico Veterinário, deve dar atenção especial à polifarmácia e à prescrição de fármacos e/ou suplementos potencialmente inapropriados, para que se alcance, de maneira concreta, um bem-estar ideal.