bluuebunny/crossref_metadata_2025_split huggingface dataset:
PIM2 Kinase Regulates TIGIT Expression and Function in NK Cells from Multiple Myeloma Patients
Authors: Fu Rong , Liu Zhaoyun , Wang Hao , Li Yiman , Li Nianbin , Peng Fengping , Jiang Fengjuan , Yan Siyang , Meng Nanhao , Liu Hui , Ding Kai 
Published: February 2024

Abstract
PIM2 kinase influences plasma cell generation and bone loss in multiple myeloma (MM), which is highly associated with tumor progression and is a potential therapeutic target. Although PIM2 kinase is essential for natural killer (NK) cell homeostasis and development, its role in NK cells function remains unclear.Here,the expression of PIM2 kinase was reanalyzed in NK cells from MM patients and healthy donors using single-cell RNA sequencing (RNA-seq). The effect of PIM2 kinase on NK cell immune checkpoints and function were analyzed in NK cell and MM cell co-culture system. Mechanistically, The regulation of PIM2 kinase on TIGIT expression on NK cell was explored through NCBI, UCSC, JASPAR, GEPIA databases and ETS-1 knockdown in NK-92 cells.For further clinical application,PIM2 kinase inhibitors were screened in 160 natural flavonoids through kinase functional assays (ADP-Glo).Our findings reveal that PIM2 kinase was highly expressed in NK cells from MM patients and PIM2 kinase inhibitor increased NK cell function and downregulated TIGIT expression. Mechanistically, the PIM2 kinase inhibitor down-regulated TIGIT expression by reducing transcription factor ETS-1, which binds directly to the TIGIT promoter. For pre-clinical translational application, we screened two natural flavonoids kaempferol and quercetin dihydrate, which show higher efficacy in inhibiting PIM2 kinase. Subsequent co-culture system results demonstrated that kaempferol and quercetin dihydrate can decrease TIGIT expression and improved the anti-myeloma function in NK cells.All the above results confirm PIM2 kinase regulates TIGIT expression and function in NK cells from MM patients.PIM2 kinase inhibitor play a vital role in MM therapy.
The Pulsatile Brain, Pulse Pressure, Cognition, and Antihypertensive Treatments in Older Adults: A Functional NIRS Study
Authors: Mohammadi Hanieh , Besnier Florent , Vincent Thomas , Fraser Sarah , Nigam Anil , Lesage Frédéric , Bherer Louis 
Published: February 2024

Abstract

Age-related arterial stiffness increases pulsatility that reaches the cerebral microcirculation, compromises cerebrovascular health and lead to cognitive decline. The presence of cardiovascular risk factors (CVRFs) such as high blood pressure can exacerbate this effect. Despite extensive research on the impact of antihypertensive treatments on reducing arterial stiffness, little is known about the impact of antihypertensive treatments on pulsatility in cerebral microcirculation. This study investigated the impact of antihypertensive treatments on cerebral pulsatility and cognition in older adults with CVRFs. Participants were 42 older adults with diverse CVRFs in two groups of untreated (\(n=\) 21, mean 67.2 \(\pm\) 5.9 years old, 57.1\(\text{\%}\) female) and treated with antihypertensive medications (\(n=\) 21, mean 67.2 \(\pm\) 5.5 years old, 61.1\(\text{\%}\) female). Cognitive scores of processing speed and executive functions were evaluated behaviorally using the four subsets of the Stroop test. A near-infrared spectroscopy (NIRS) device recorded hemodynamics data from the frontal and motor cortex subregions. The data were then used to extract an optical index of cerebral pulsatility. Results indicated that after controlling for CVRFs, the antihypertensive treatment is associated with lower cerebral pulsatility (untreated 33.99 \(\pm\) 6.68 vs. treated 28.88 \(\pm\) 5.39 beats/min, \(p\) \(=\) 0.009). In both groups cerebral pulsatility was associated with pulse pressure (\(p\) \(<\)0.05). Also, treated group had significantly higher cognitive scores in executive functions compared with the untreated group (\(p\) \(<\)0.05). These results suggest that beyond its known effect on blood pressure, antihypertensive treatments might also favor cerebrovascular health by reducing pulsatility in the cerebral microcirculation.
Clinically applicable optimized periprosthetic joint infection diagnosis via AI-based pathology
Authors: Ni Ming , Tao Ye , Hu Hanwen , Li Jie , Luo Yazhi , Wang Shuhao , Zheng Qingyuan , Zhang Tianwei , Zhang Guoqiang 
Published: February 2024

Abstract

Periprosthetic joint infection (PJI) is a severe complication following joint replacement surgery, often requiring complex multi-stage joint revisions or fusion, and imposing significant burdens on individuals and society as a whole. Accurate diagnosis is crucial for effective treatment. This study aimed to enhance the pathological diagnostic accuracy of PJI by standardizing an intelligent pathological diagnostic process, improving its applicability and practicality in clinical settings, and providing guidance for intelligent diagnosis of infectious diseases. We developed supervised learning models, weakly supervised learning models, and unsupervised learning PJI intelligent classification models and conducted image-level, patient-level testing, and visual verification for the first two models. The weakly supervised learning model performed nearly as well as the supervised learning model in image-level tests, achieving comparable levels of accuracy, recall rates, and ROC curves. However, in patient-level testing, the weakly supervised learning model outperformed its supervised learning counterpart. By adjusting the area threshold for the recognition regions, we significantly improved the sensitivity of PJI pathological diagnosis without compromising specificity (AUC curve area of 0.9460 for the supervised model and 0.9078 for the weakly supervised model). Based on our criteria, the existing diagnostic standard for five high-power fields in a single slide was reduced to only 3. The visualization results also revealed structural changes and loosening in the surrounding tissues, apart from localized neutrophil aggregation. Moreover, the distribution patterns of neutrophil morphology might provide clues for the diagnosis and treatment of PJI. Using an intelligent quantification and statistical approach, we successfully elevated the sensitivity of PJI pathological diagnosis to 88.42% and specificity to 92.31%. Moreover, we established unsupervised rapid auxiliary annotation models, supervised classification models, and unsupervised approximate segmentation models, thereby achieving an intelligent PJI diagnosis. Our study lays the foundation for further intelligent optimization of pathological diagnosis of other infectious diseases.
MRI subtypes in Parkinson’s disease:
Unraveling differences across diverse populations and clustering approaches
Authors: Inguanzo Anna , Mohanty Rosaleena , Poulakis Konstantinos , Ferreira Daniel , Segura Bàrbara , Albrecht Franziska , Muehlboeck J-Sebastian , Granberg Tobias , Sjostrom Henrik , Svenningsson Per , Franzen Erika , Junque Carme , Westman Eric 
Published: February 2024

Abstract

Parkinson’s disease (PD) is clinically heterogeneous, which suggests the existence of subtypes; however, there has been no consensus regarding their characteristics. This study included 633 PD individuals across distinct cohorts: unmedicated de novo PD, medicated PD, mild-moderate PD and a cohort based on diagnostic work-up in clinical practice. Additionally, 233 controls were included. Clustering based on cortical and subcortical grey matter measures was conducted with and without adjusting for global atrophy in the entire sample and validated within each cohort. Subtypes were characterized using baseline and longitudinal demographic and clinical data. Unadjusted results identified three clusters showing a gradient of neurodegeneration and symptom severity across both the entire sample and individual cohorts. When adjusting for global atrophy eight clusters were identified, lacking consistency across cohorts in validation. This study identified atrophy-based subtypes in PD, emphasizing the significant impact of global atrophy on subtype number, patterns, and interpretation in cross-sectional analyses.
Triazoles nanoencapsulation in polylactic acid to reduce phytotoxicity in roots
Authors: Beltrán Jahsive Sujey Quintero , Viveros Gabriela Sánchez , Contreras Roberto Gregorio Chiquito , Saito Greta Hanako Rosas , Castro Randy Ortíz , Landa Israel Bonilla , Romero José Luis Olivares , Méndez Felipe Barrera 
Published: February 2024

Abstract
The use of effective fungicides, such as propiconazole, a high-efficacy and broad-spectrum systemic fungicide, has been a common commercial strategy to combat fungal diseases. However, their indiscriminate and uncontrolled use provokes phytotoxicity in plant roots. Therefore, the objective of this study is to reduce the root phytotoxicity of triazole fungicides through their nanoencapsulation in biodegradable polylactic acid polymer matrices. Using the emulsion and solvent evaporation encapsulation method, the obtained nanoparticles had a hydrodynamic diameter of approximately 200 to 400 nm, an encapsulation efficiency of around 40%, a smooth surface, and a zeta potential close to -40 mV, having great colloidal stability. Experiments with Arabidopsis thaliana demonstrated that the nanoencapsulation of a fungicide derived from propiconazole reduced its phytotoxicity, increasing the length of the roots over 70% more than when the molecule was applied directly, losing only about 15% of its antifungal activity, as shown by the test performed on Fusarium solani. This suggests that nanoencapsulation with biodegradable polymer matrices acts as a protective mechanism for plant roots, which may have practical applications in crop protection and the promotion of sustainable agriculture. However, further research is needed to evaluate its efficacy under field conditions and its long-term environmental impact.
Use of passive samplers as sewage surveillance tool to monitor a hepatitis A outbreak at a school in Amsterdam, the Netherlands, Oct 2022 – March 2023
Authors: de Jong Maarten , Loeff Maarten F. Schim van der , Schilperoort Rémy , Vennema Harry , Weijden Charlie van der , Langeveld Jeroen , Welkers Matthijs , Prins Maria , Husman Ana Maria Roda , Fanoy Ewout , Medema Gertjan 
Published: February 2024

Abstract

Background
Enteric hepatitis A virus (HAV) infections during childhood are often asymptomatic but may cause severe illness in adults. To improve public health surveillance we assessed the applicability of sewage monitoring during an HAV outbreak at a primary school.
Methods
Between October 19 and December 27, 2022, five symptomatic HAV cases were notified to the Public Health Service Amsterdam; all attended the same primary school. Passive samplers, small absorbent tools, were deployed in sewage near the school from November 14, 2022, to March 22, 2023. The absorbents were subjected to RNA extraction, HAV PCR testing, and, if positive, sequencing. PCR and sequencing were also performed on plasma and feces samples of HAV cases.
Results
In 22 out of 88 (25%) of sewage samples, HAV RNA was detected. All HAV-RNA-positive sewage samples until 8 February 2023 were subgenotype IB, matching the strain detected in all cases. Another strain of HAV (subgenotype IA) was detected in sewage from 15 February 2023 onwards, without associated cases.
Conclusions
Passive sampler-based sewage monitoring is an effective method to rapidly detect HAV shedding linked to diagnosed cases. It detects unnoticed viral infections and allows monitoring of outbreaks. This suggests that passive sampler-based monitoring is a promising tool supporting the public health response during HAV and other outbreaks.
Sucrose-preferring gut microbes prevent host obesity by producing exopolysaccharides
Authors: Kimura Ikuo , Shimizu Hidenori , Miyamoto Junki , Hisa Keiko , Ohue-Kitano Ryuji , Takada Hiromi , Yamano Mayu , Nishida Akari , Sasahara Daiki , Masujima Yuki , Watanabe Keita , Nishikawa Syota , Takahashi Sakura , Ikeda Takako , Nakajima Yuya , Yoshida Naofumi , Matsuzaki Chiaki , Kageyama Takuya , Hayashi Ibuki , Matsuki Akari , Akashi Ryo , Kitahama Seiichi , Ueyama Masako , Murakami Takumi , Inuki Shinsuke , Irie Junichiro , Satoh-Asahara Noriko , Toju Hirokazu , Mori Hiroshi , Nakaoka Shinji , Yamashita Tomoya , Toyoda Atsushi , Yamamoto Kenji , Ohno Hiroaki , Katayama Takane , Itoh Hiroshi 
Published: February 2024

Abstract

Commensal bacteria affect host health by producing various metabolites from dietary carbohydrates via bacterial glycometabolism; however, the underlying mechanism of action remains unclear. Here, we identified Streptococcus salivarius as a unique anti-obesity commensal bacterium. We found that S. salivarius may prevent host obesity caused by excess sucrose intake via the exopolysaccharide (EPS)-short-chain fatty acid (SCFA)-carbohydrate metabolic axis. Healthy human donor-derived S. salivarius produced high EPS levels from sucrose but not from other sugars. S. salivarius abundance was significantly decreased in human donors with obesity, and the EPS-SCFA bacterial carbohydrate metabolic process was attenuated. Our findings reveal an important mechanism by which host–commensal interactions in glycometabolism affect energy regulation, suggesting an approach for preventing lifestyle-related diseases via prebiotics and probiotics by targeting bacteria and EPS metabolites.
Fine-Tuning GBS Data with Comparison of Reference and Mock Genome Approaches for Advancing Genomic Selection in Less Studied Farmed Species
Authors: Fischer Daniel , Tapio Miika , Bitz Oliver , Iso-Touru Terhi , Kause Antti , Tapio Ilma 
Published: February 2024

Abstract

Background
Diversifying animal cultivation demands efficient genotyping for enabling genomic selection, but non-model species lack efficient genotyping solutions. The aim of this study was to optimize a genotyping-by-sequencing (GBS) double-digest RAD-sequencing (ddRAD) pipeline. Bovine data was used to automate the bioinformatic analysis. The application of the optimization was demonstrated on non-model European whitefish data.
Results
DdRAD data generation was designed for a reliable estimation of relatedness and is scalable to up to 384 samples. The GBS sequencing yielded approximately one million reads for each of the around 100 assessed samples. Optimizing various strategies to create a de-novo reference genome for variant calling (mock reference) showed that using three samples outperformed other building strategies with single or very large number of samples. Adjustments to most pipeline tuning parameters had limited impact on high-quality data, except for the identity criterion for merging mock reference genome clusters. For each species, over 15k GBS variants based on the mock reference were obtained and showed comparable results with the ones called using an existing reference genome. Repeatability analysis showed high concordance over replicates, particularly in bovine while in European whitefish data repeatability did not exceed earlier observations.
Conclusions
The proposed cost-effective ddRAD strategy, coupled with an efficient bioinformatics workflow, enables broad adoption of ddRAD GBS across diverse farmed species. While beneficial, a reference genome is not obligatory. The integration of Snakemake streamlines the pipeline usage on computer clusters and supports customization. This user-friendly solution facilitates genotyping for both model and non-model species.
High density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat
Authors: Wang Xiaoting , Xiang Mingjie , Li Huaizhou , Li Xiaoxiao , Mu Keqing , Huang Shuo , Zhang Yibo , Cheng Xiangrui , Yang Shuqing , Yun Xunying , Singh Ravi P. , Bhavani Sridhar , Zeng Qingdong , Wu Jianhui , Kang Zhensheng , Liu Shengjie , Han Dejun 
Published: February 2024

Abstract

Stripe rust is a global fungal disease that is a serious threat to wheat. Durable resistance is the most effective method of control. Yr30, an adult plant resistance (APR) gene with broad-spectrum effectiveness, was located in the putatively pleiotropic locus or QTL that harbors genes Sr2, Lr27, Pm70, Sb3 and Pbc1. Although the locus has been widely deployed worldwide to achieve durable resistance for over a centenary little is known about the genetic relationship and causal genes because of the effects are small and inconstant in different genetic backgrounds and environments. In this study, we identified a residual heterozygous line (RHL), YM91, derived from Yaco"S"/Mingxian169 F5:6 RIL population, where Yr30 was present alone, resistance was identified as dominant and clearly distinguishable. Through selection of heterozygous plants in YM91, a large mapping population was developed. Yr30 was fine-mapped to a 0.52-cM interval between KASP markers AX-109525141 and YM3B-7 corresponding to a physical distance of 610 kb on chromosome 3BS. A candidate gene TraesCS3B03G0028100 encoding tetratricopeptide repeat protein was identified for Yr30 from 30 high-confidence genes within the interval based on the expression level and sequence variation in whole genome RNA-seq data of cultivars with or without Yr30. Six haplotypes (Hap1-6) were identified among 1,215 wheat accessions based on the 660K array and Yr30-haplotype Hap6 conferred equal or higher resistance than the other five haplotypes. These results will accelerate map-based cloning and molecular-assisted selection of Yr30, a likely source of durable resistance.
Recycling food waste to agriculture through hydrothermal carbonization sustains food-energy-water nexus
Authors: Xu Guohua , hao xu , Chen Tong , Shan Yide , Chen Kang , Ling Ning , Ren Lixuan , Qu Hongye , Berge Nicole , Flora Joseph , Goel Ramesh , Liu Lubo , Liu Zhipeng 
Published: February 2024

Abstract

Recycling underutilized resources from food waste (FW) to agriculture through hydrothermal carbonization (HTC) has been proposed to promote a circular economy in food, energy and water nexus. However, most HTC studies on FW have been conducted at laboratory scale, and little is known on efficacy of field application of HTC products from FW, i.e. aqueous product (AP) and solid hydrocharr(HC), to support agriculture production. To address these gaps, an integrated pilot-scale HTC system in this study is established to evaluate the reaction conditions and procedures for the HTC processing of FW. A peak temperature of 180 ℃ at a residence time of 60 minutes with 3 times recirculation of AP are recommended as the condition to achieve effective recovery of nutrients and water resources, and desirable AP and HC properties. Dilution of the raw AP and composting of the fresh HC eliminate potential phytotoxicity. Applying properly diluted AP and the composted HC can significantly improve plant growth and soil nutrient availability with comparable level to commercial fertilizer and soil amendment, respectively, in both greenhouse and field. The HTC treatment yields the most net negative carbon emission among common processing methods of FW and the direct potential profit. The current integrated pilot-scale study demonstrates that the HTC of FW and the agricultural application of its products have promising environmental advantages and economic feasibility.
Crop yield estimation using biophysical variables: A case study of Sabarkantha district, Gujarat, India
Authors: Roy Atrayee , Saxena Rajat , Kumbhar Vidya , Singh T. P. , Deshpande Gauri 
Published: February 2024

Abstract

A precise estimation of the yield is crucial to maintain well-functioning food security at every tier. It also ensures the income of the producers dependent on the recurrent economic practice of crop insurance. The yield estimation methods used earlier were cost-ineffective and ominous. To overcome it, a semi-physical approach was applied with the help of satellite data to estimate the yield of major crops grown in the Sabarkantha district of Gujarat. Data from Sentinel 2B has been stacked throughout the Rabi season at equal intervals and classified using supervised training sets for the study area. MOD11A2 Version 6, an eight-day composite image of Rabi season, was compiled to analyze the mean night and daytime land surface temperature that depicts the status of temperature stress. The net Primary Product (NPP) of the crops was evaluated with the assistance of a semi-physical model. The accuracy of the result was assessed with the help of the ground truth points. Grain yield results were compared with the average yield statistics that showed Root Mean Square Error (RMSE) deviation of 0.38 for wheat, 0.15 for maize, and 0.19 for both gram and mustard. In conclusion, the semi-physical approach of crop yield estimation meets the accuracy requirements, is feasible, and can be used for various crops. In addition, it is convenient and inexpensive.
Klinefelter syndrome with 48, XXYY karyotype accompanied by diabetic keto-acidosis: a case report and literatures review
Authors: Sun# Ruqiong , Zhou# Xiaoying , Hu Tingting , Zhu Fangying , Xu Fenjuan 
Published: February 2024

Abstract

Klinefelter syndroms(48,XXYY) syndromes are rare sex chromosome aneuploidy disorders characterized by the presence of more extra X and Y chromosomes in males. However, 48,XXYY are less studied, possibly due to its rarity. The incidence of 48,XXYY is estimated at 1:18,000–40,000 male births. While this sex chromosome aneuploidy is associated with multifarious of complex metabolic derangements, physical, psychological and psychosocial features, the clinical description of Klinefelter syndrome 48,XXYY over time has evolved to develop a greater understanding of this complex disorder. This paper reports a case of Klinefelter syndrome with chromosome karyotype 48, XXYY and abnormal glucose metabolism, which was admitted to hospital due to acute complications of diabetic ketoacidosis. Meanwhile, Our aim was to review known evidence about 48,XXYY. And what is known about the prevalence of diabetes in men with klinefelter syndroms, potential mechanisms underlying the observed metabolic phenotype.