bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction in vertical transmission rate of bean common mosaic virus in bee-pollinated common bean plants
Authors: Mhlanga Netsai M. , Pate Adrienne E. , Arinaitwe Warren , Carr John P. , Murphy Alex M. 
Published: July 2024

AbstractVertical transmission, the transfer of pathogens across generations, is a critical mechanism for the persistence of plant viruses. The transmission mechanisms are diverse, involving direct invasion through the suspensor and virus entry into developing gametes before achieving symplastic isolation. Despite the progress in understanding vertical virus transmission, the environmental factors influencing this process remain largely unexplored. We investigated the complex interplay between vertical transmission of plant viruses and pollination dynamics, focusing on common bean (Phaseolus vulgaris). The intricate relationship between plants and pollinators, especially bees, is essential for global ecosystems and crop productivity. We explored the impact of virus infection on seed transmission rates, with a particular emphasis on bean common mosaic virus (BCMV), bean common mosaic necrosis virus (BCMNV), and cucumber mosaic virus (CMV). Under controlled growth conditions, BCMNV exhibited the highest seed transmission rate, followed by BCMV and CMV. Notably, in the field, bee-pollinated BCMV-infected plants showed a reduced transmission rate compared to self-pollinated plants. This highlights the influence of pollinators on virus transmission dynamics. The findings demonstrate the virus-specific nature of seed transmission and underscore the importance of considering environmental factors, such as pollination, in understanding and managing plant virus spread.
Neuroanatomical correlates of musicianship in left-handers
Authors: Villar-Rodríguez Esteban , Marin-Marin Lidón , Avila César , Parcet Maria Antònia 
Published: July 2024

Abstract
Background
Left-handedness is a condition that reverses the typical left cerebral dominance of motor control to an atypical right dominance. The impact of this distinct control — and its associated neuroanatomical peculiarities — on other cognitive functions such as music processing or playing a musical instrument remains unexplored. Previous studies in right-handed population have linked musicianship to a larger volume in the (right) auditory cortex and a larger volume in the (right) arcuate fasciculus.

Results
In our study, we reveal that left-handed musicians (n = 55), in comparison to left-handed non-musicians (n = 75), exhibit a larger gray matter volume in both the left and right Heschl’s gyrus, critical for auditory processing. They also present a higher number of streamlines across the anterior segment of the right arcuate fasciculus. Importantly, atypical hemispheric lateralization of speech (notably prevalent among left-handers) was associated to a rightward asymmetry of the AF, in contrast to the leftward asymmetry exhibited by the typically lateralized.

Conclusions
These findings suggest that left-handed musicians share similar neuroanatomical characteristics with their right-handed counterparts. However, atypical lateralization of speech might potentiate the right audiomotor pathway, which has been associated with musicianship and better musical skills. This may help explain why musicians are more prevalent among left-handers and shed light on their cognitive advantages.
Human milk composition and infant anthropometrics: overview of a systematic review with clinical and research implications
Authors: Azad Meghan B. , Brockway Meredith M. , Reyes Sarah M. 
Published: July 2024

Abstract
Background
Despite global public health organizations endorsing breastfeeding or human milk (HM) as the optimal source of nutrition for infants, detailed knowledge of how HM composition influences infant growth is lacking. In this commentary we summarize and interpret the key findings of a large systematic review on HM components and child growth (N = 141 articles included). We highlight the most consistent associations, discuss study quality issues, explore socio-economic and time trends in this body of research, and identify gaps and future research directions.

Key Findings of Systematic Review
We grouped HM components into three categories: micronutrients (28 articles), macronutrients (57 articles), and bioactives (75 articles). Overall, we struggled to find consistent associations between HM components and infant growth. The majority of studies (85%) were of moderate or low-quality, with inconsistent HM collection and analysis strategies being identified as the most substantial quality concerns. Additional quality issues included failing to account for potential confounding by factors such as breastfeeding exclusivity and maternal body mass index.

Considerations for Future Human Milk Research
Many opportunities exist for the future of HM research. Using untargeted metabolomics will expand our understanding of HM components beyond previously defined and well-understood components. Machine learning will allow researchers to investigate HM as an integrated system, rather than a collection of individual components. Future research on HM composition should incorporate evidence-based HM sampling strategies to encompass circadian variation as well as infant consumption. Additionally, researchers need to focus on developing high quality growth data using consistent growth metrics and definitions. Building multidisciplinary research teams will help to ensure that outcomes are meaningful and clinically relevant.

Conclusion
Despite a large body of literature, there is limited quality evidence on the relationship between HM composition and infant growth. Future research should engage in more accurate collection of breastfeeding data, use standardized HM collection strategies and employ assays that are validated for HM. By systematically evaluating the existing literature and identifying gaps in existing research methods and practice, we hope to inspire standardized methods and reporting guidelines to support robust strategies for examining relationships between HM composition and child growth.
TaqTth-hpRNA: a novel compact RNA-targeting tool for specific silencing of pathogenic mRNA
Authors: Xu Chong , Cao Jiyanuo , Qiang Huanran , Liu Yu , Wu Jialin , Luo Qiudan , Wan Meng , Wang Yujie , Wang Peiliang , Cheng Qian , Zhou Guohua , Sima Jian , Guo Yongjian , Xu Shu 
Published: July 2024

AbstractPathogenic allele silencing is a promising treatment for genetic hereditary diseases. Here, we develop an RNA-cleaving tool, TaqTth-hpRNA, consisting of a small, chimeric TaqTth, and a hairpin RNA guiding probe. With a minimal flanking sequence-motif requirement, in vitro and in vivo studies show TaqTth-hpRNA cleaves RNA efficiently and specifically. In an Alzheimer’s disease model, we demonstrate silencing of mutant APPswe mRNA without altering the wild-type APP mRNA. Notably, due to the compact size of TaqTth, we are able to combine with APOE2 overexpression in a single AAV vector, which results in stronger inhibition of pathologies.
Equol: a metabolite of gut microbiota with potential antitumor effects
Authors: Lv Jing , Jin Shengkai , Zhang Yuwei , Zhou Yuhua , Li Menglu , Feng Ninghan 
Published: July 2024

AbstractAn increasing number of studies have shown that the consumption of soybeans and soybeans products is beneficial to human health, and the biological activity of soy products may be attributed to the presence of Soy Isoflavones (SI) in soybeans. In the intestinal tracts of humans and animals, certain specific bacteria can metabolize soy isoflavones into equol. Equol has a similar chemical structure to endogenous estradiol in the human body, which can bind with estrogen receptors and exert weak estrogen effects. Therefore, equol plays an important role in the occurrence and development of a variety of hormone-dependent malignancies such as breast cancer and prostate cancer. Despite the numerous health benefits of equol for humans, only 30-50% of the population can metabolize soy isoflavones into equol, with individual variation in gut microbiota being the main reason. This article provides an overview of the relevant gut microbiota involved in the synthesis of equol and its anti-tumor effects in various types of cancer. It also summarizes the molecular mechanisms underlying its anti-tumor properties, aiming to provide a more reliable theoretical basis for the rational utilization of equol in the field of cancer treatment.
The C-terminal proline-rich repeats of Enteropathogenic E. coli effector EspF are sufficient for the depletion of tight junction membrane proteins and interactions with early and recycling endosomes
Authors: Ansari Imran , Mandal Anupam , Kansal Kritika , Walling Pangertoshi , Khan Sumbul , Aijaz Saima 
Published: July 2024

Abstract
Background
Enteropathogenic E. coli (EPEC) causes acute infantile diarrhea accounting for significant morbidity and mortality in developing countries. EPEC uses a type three secretion system to translocate more than twenty effectors into the host intestinal cells. At least four of these effectors, namely EspF, Map, EspG1/G2 and NleA, are reported to disrupt the intestinal tight junction barrier. We have reported earlier that the expression of EspF and Map in MDCK cells causes the depletion of the TJ membrane proteins and compromises the integrity of the intestinal barrier. In the present study, we have examined the role of the proline-rich repeats (PRRs) within the C-terminus of EspF in the depletion of the tight junction membrane proteins and identified key endocytosis markers that interact with EspF via these repeats.

Results
We generated mutant EspF proteins which lacked one or more proline-rich repeats (PRRs) from the N-terminus of EspF and examined the effect of their expression on the cellular localization of tight junction membrane proteins. In lysates derived from cells expressing the mutant EspF proteins, we found that the C-terminal PRRs of EspF are sufficient to cause the depletion of TJ membrane proteins. Pull-down assays revealed that the PRRs mediate interactions with the TJ adaptor proteins ZO-1 and ZO-2 as well as with the proteins involved in endocytosis such as caveolin-1, Rab5A and Rab11.

Conclusions
Our study demonstrates the direct role of the proline-rich repeats of EspF in the depletion of the TJ membrane proteins and a possible involvement of the PRRs in the endocytosis of host proteins. New therapeutic strategies can target these PRR domains to prevent intestinal barrier dysfunction in EPEC infections.
Power-law scaling in intratumoral microbiota of colorectal cancer
Authors: Dovrolis Nikolas , Gazouli Maria , Rigal François , Whittaker Robert J. , Matthews Thomas J. , Georgiou Konstantinos , Theodoropoulos George , Triantis Kostas A. 
Published: July 2024

AbstractIt has recently been proposed that the study of microbial dynamics in humans may gain insights from island biogeographical theory. Here, we test whether the diversity of the intratumoral microbiota of colorectal cancer tumors (CRC) follows a power law with tumor size akin to the island species-area relationship. We confirm a direct correlation between the quantity of Amplicon Sequence Variants (ASVs) within CRC tumors and tumor sizes, following a (log)power model, explaining 47% of the variation. Understanding the processes involved, potentially through the analogy of tumors and islands, may ultimately contribute to future clinical and therapeutic strategies.
MRI radiomics enhances radiologists’ ability for characterizing intestinal fibrosis in patients with Crohn’s disease
Authors: Zhang Mengchen , Zeng Yinghou , Fang Zhuang-nian , Wang Yang-di , Zhang Ruo-nan , Ye Ziyin , Cao Qing-hua , Mao Ren , Sun Canhui , Chen Zhi-hui , Huang Bingsheng , Li Xue-hua 
Published: July 2024

Abstract
Objectives
We aimed to develop MRI-based radiomic models (RMs) to improve the diagnostic accuracy of radiologists in characterizing intestinal fibrosis in patients with Crohn’s disease (CD).

Methods
This retrospective study included patients with refractory CD who underwent MR before surgery from November 2013 to September 2021. Resected bowel segments were histologically classified as none-mild or moderate-severe fibrosis. RMs based on different MR sequence combinations (RM1: T2WI and enhanced-T1WI; RM2: T2WI, enhanced-T1WI, diffusion-weighted imaging [DWI], and apparent diffusion coefficient [ADC]); RM3: T2WI, enhanced-T1WI, DWI, ADC, and magnetization transfer MRI [MTI]), were developed and validated in an independent test cohort. The RMs’ diagnostic performance was compared to that of visual interpretation using identical sequences and a clinical model.

Results
The final population included 123 patients (81 men, 42 women; mean age: 30.26 ± 7.98 years; training cohort, n = 93; test cohort, n = 30). The area under the receiver operating characteristic curve (AUC) of RM1, RM2, and RM3 was 0.86 (p = 0.001), 0.88 (p = 0.001), and 0.93 (p = 0.02), respectively. The decision curve analysis confirmed a progressive improvement in the diagnostic performance of three RMs with the addition of more specific sequences. All RMs performance surpassed the visual interpretation based on the same MR sequences (visual model 1, AUC = 0.65, p = 0.56; visual model 2, AUC = 0.63, p = 0.04; visual model 3, AUC = 0.77, p = 0.002), as well as the clinical model composed of C-reactive protein and erythrocyte sedimentation rate (AUC = 0.60, p = 0.13).

Conclusions
The RMs, utilizing various combinations of conventional, DWI and MTI sequences, significantly enhance radiologists’ ability to accurately characterize intestinal fibrosis in patients with CD.

Critical relevance statement
The utilization of MRI-based RMs significantly enhances the diagnostic accuracy of radiologists in characterizing intestinal fibrosis.

Key Points

MRI-based RMs can characterize CD intestinal fibrosis using conventional, diffusion, and MTI sequences.

The RMs achieved AUCs of 0.86–0.93 for assessing fibrosis grade.

MRI-radiomics outperformed visual interpretation for grading CD intestinal fibrosis.

Graphical Abstract
An unexpected case of an adnexal hydatid cyst in a pregnant woman: a case report
Authors: Brezeanu Ana-Maria , Brezeanu Dragoș , Tica Vlad-Iustin 
Published: July 2024

Abstract
Background
Cystic echinococcosis, also known as hydatid disease, is a chronic and endemic illness caused by infection with a parasite called Echinococcus granulosus. In Romania, this disease has an incidence rate of 5.6 per 100,000 individuals, which is the highest in the Dobrogea region. The liver is the most affected site, accounting for 68.8% of cases, followed by the lungs at 17.2%. While cases of hydatid disease in the genital organs are rare, occurring at an incidence rate of only 0.5%, it is worth noting that cases of this disease in pregnancy worldwide are also rare, occurring at an incidence rate of 1 in 20,000 to 1 in 30,000 pregnancies.

Case report
A 15-year-old Eastern-European woman who was 12 weeks pregnant presented to the emergency room with acute pelvic pain, dysuria, and frequent urination. Her laboratory tests showed that she had a urinary tract infection, and pelvic ultrasound revealed that she had a mass on her right adnexa. Despite receiving treatment, her symptoms did not improve, and she had to undergo surgery to remove the mass, which turned out to be a hydatic cyst. She also had to undergo a cesarean section to deliver her baby owing to fetal distress during labor.

Conclusions
This medical case report provides a detailed description of a pelvic hydatid cyst that was discovered during pregnancy. What makes this case particularly noteworthy is the cyst’s unusual location—it was found at the level of the right broad ligament of the uterus. Despite the complexity of the situation, the patient was able to receive effective treatment and the cyst was successfully managed with great outcomes for both the patient and the newborn. We hope that this report serves as a valuable example of how medical professionals can navigate challenging cases and provide optimal care for their patients.
CPSign: conformal prediction for cheminformatics modeling
Authors: Arvidsson McShane Staffan , Norinder Ulf , Alvarsson Jonathan , Ahlberg Ernst , Carlsson Lars , Spjuth Ola 
Published: July 2024

AbstractConformal prediction has seen many applications in pharmaceutical science, being able to calibrate outputs of machine learning models and producing valid prediction intervals. We here present the open source software CPSign that is a complete implementation of conformal prediction for cheminformatics modeling. CPSign implements inductive and transductive conformal prediction for classification and regression, and probabilistic prediction with the Venn-ABERS methodology. The main chemical representation is signatures but other types of descriptors are also supported. The main modeling methodology is support vector machines (SVMs), but additional modeling methods are supported via an extension mechanism, e.g. DeepLearning4J models. We also describe features for visualizing results from conformal models including calibration and efficiency plots, as well as features to publish predictive models as REST services. We compare CPSign against other common cheminformatics modeling approaches including random forest, and a directed message-passing neural network. The results show that CPSign produces robust predictive performance with comparative predictive efficiency, with superior runtime and lower hardware requirements compared to neural network based models. CPSign has been used in several studies and is in production-use in multiple organizations. The ability to work directly with chemical input files, perform descriptor calculation and modeling with SVM in the conformal prediction framework, with a single software package having a low footprint and fast execution time makes CPSign a convenient and yet flexible package for training, deploying, and predicting on chemical data. CPSign can be downloaded from GitHub at https://github.com/arosbio/cpsign.Scientific contribution CPSign provides a single software that allows users to perform data preprocessing, modeling and make predictions directly on chemical structures, using conformal and probabilistic prediction. Building and evaluating new models can be achieved at a high abstraction level, without sacrificing flexibility and predictive performance—showcased with a method evaluation against contemporary modeling approaches, where CPSign performs on par with a state-of-the-art deep learning based model.
LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification
Authors: Zhou Ruifeng , Fan Jing , Li Sishu , Zeng Wenjie , Chen Yilun , Zheng Xiaoshan , Chen Hongyang , Liao Jun 
Published: July 2024

Abstract
Background
Previous deep learning methods for predicting protein binding pockets mainly employed 3D convolution, yet an abundance of convolution operations may lead the model to excessively prioritize local information, thus overlooking global information. Moreover, it is essential for us to account for the influence of diverse protein folding structural classes. Because proteins classified differently structurally exhibit varying biological functions, whereas those within the same structural class share similar functional attributes.

Results
We proposed LVPocket, a novel method that synergistically captures both local and global information of protein structure through the integration of Transformer encoders, which help the model achieve better performance in binding pockets prediction. And then we tailored prediction models for data of four distinct structural classes of proteins using the transfer learning. The four fine-tuned models were trained on the baseline LVPocket model which was trained on the sc-PDB dataset. LVPocket exhibits superior performance on three independent datasets compared to current state-of-the-art methods. Additionally, the fine-tuned model outperforms the baseline model in terms of performance.

Scientific contribution
We present a novel model structure for predicting protein binding pockets that provides a solution for relying on extensive convolutional computation while neglecting global information about protein structures. Furthermore, we tackle the impact of different protein folding structures on binding pocket prediction tasks through the application of transfer learning methods.

Graphical Abstract
Duck STING mediates antiviral autophagy directing the interferon signaling pathway to inhibit duck plague virus infection
Authors: Tian Bin , Tian Yanming , Wang Xuetong , Cai Dongjie , Wu Liping , Wang Mingshu , Jia Renyong , Chen Shun , Zhu Dekang , Liu Mafeng , Yang Qiao , Wu Ying , Zhao Xinxin , Zhang Shaqiu , Sun Di , Huang Juan , Ou Xumin , Wu Zhen , Cheng Anchun 
Published: July 2024

AbstractMigratory birds are important vectors for virus transmission, how migratory birds recognize viruses and viruses are sustained in birds is still enigmatic. As an animal model for waterfowl among migratory birds, studying and dissecting the antiviral immunity and viral evasion in duck cells may pave a path to deciphering these puzzles. Here, we studied the mechanism of antiviral autophagy mediated by duck STING in DEF cells. The results collaborated that duck STING could significantly enhance LC3B-II/I turnover, LC3B-EGFP puncta formation, and mCherry/EGFP ratio, indicating that duck STING could induce autophagy. The autophagy induced by duck STING is not affected by shRNA knockdown of ATG5 expression, deletion of the C-terminal tail of STING, or TBK1 inhibitor BX795 treatment, indicating that duck STING activated non-classical selective autophagy is independent of interaction with TBK1, TBK1 phosphorylation, and interferon (IFN) signaling. The STING R235A mutant and Sar1A/B kinase mutant abolished duck STING induced autophagy, suggesting binding with cGAMP and COPII complex mediated transport are the critical prerequisite. Duck STING interacted with LC3B through LIR motifs to induce autophagy, the LIR 4/7 motif mutants of duck STING abolished the interaction with LC3B, and neither activated autophagy nor IFN expression, indicating that duck STING associates with LC3B directed autophagy and dictated innate immunity activation. Finally, we found that duck STING mediated autophagy significantly inhibited duck plague virus (DPV) infection via ubiquitously degraded viral proteins. Our study may shed light on one scenario about the control and evasion of diseases transmitted by migratory birds.