bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harnessing CRISPR/Cas12a Technology to Combat Wheat Dwarf Virus Without Genetic Modification
Authors: Baran Buse , Teymur Tarık , Morca Ali Ferhan , Konuk Muhsin , Taştan Cihan 
Published: July 2024

ABSTRACTWheat (Triticum aestivumL.) is a staple crop globally, but its yield and quality are significantly affected by viral diseases, particularly the Wheat Dwarf Virus (WDV). Developing antiviral strategies is crucial for enhancing wheat productivity. This study aims to investigate the use of CRISPR/Cas12a as an antiviral agent against WDV without the need for genetic modification of the host plants. WDV genomic DNAs were isolated from wheat and barley samples collected from various regions in Turkey and other countries. Guide RNAs (gRNAs) targeting conserved regions in the coat protein (CP) gene of WDV were designed and synthesized. The CRISPR/Cas12a ribonucleoprotein (RNP) complex was tested for its ability to induce DNA cleavage in WDV genomes through in vitro assays, and results were analysed using agarose gel electrophoresis. The designed gRNAs effectively induced DNA cleavage in WDV genomes, with gRNA1 showing consistent performance across all tested isolates. gRNA2 exhibited variability, successfully targeting seven out of ten isolates. No off-target effects were observed in control assays, confirming the specificity of the gRNAs. The CRISPR/Cas12a system, guided by specifically designed gRNAs, can effectively target and cleave WDV genomes, providing a potent, non-GMO antiviral strategy. This approach has potential applications for managing WDV infections in wheat and barley, highlighting its versatility and effectiveness.
Large-scale genome analyses provide insights into Hymenoptera evolution
Authors: He Chun , Yang Yi , Zhao Xianxin , Li Junjie , Cai Yuting , Peng Lijia , Liu Yuanyuan , Xiong Shijiao , Mei Yang , Yan Zhichao , Wang Jiale , Xiao Shan , Teng Ziwen , Gao Xueke , Xue Hui , Fang Qi , Ye Gongyin , Ye Xinhai 
Published: July 2024

AbstractThe order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, sting, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.
Regulation of the poly(A) Polymerase Star-PAP by a Nuclear Phosphoinositide Signalosome
Authors: Wen Tianmu , Chen Mo , Cryns Vincent L. , Anderson Richard A. 
Published: July 2024

AbstractStar-PAP is a noncanonical poly(A) polymerase that controls gene expression. Star-PAP was previously reported to bind the phosphatidylinositol 4-phosphate 5-kinase PIPKI⍺ and its product phosphatidylinositol 4,5-bisphosphate, which regulate Star-PAP poly(A) polymerase activity and expression of specific genes. Recent studies have revealed a nuclear PI signaling pathway in which the PI transfer proteins PITP⍺/β, PI kinases and phosphatases bind p53 to sequentially modify protein-linked phosphatidylinositol phosphates and regulate its function. Here we demonstrate that multiple phosphoinositides, including phosphatidylinositol 4-monophosphate and phosphatidylinositol 3,4,5-trisphosphate are also coupled to Star-PAP in response to stress. This is initiated by PITP⍺/β binding to Star-PAP, while the Star-PAP-linked phosphoinositides are modified by PI4KII⍺, PIPKI⍺, IPMK, and PTEN recruited to Star- PAP. The phosphoinositide coupling enhances the association of the small heat shock proteins HSP27/⍺B-crystallin with Star-PAP. Knockdown of the PITPs, kinases, or HSP27 reduce the expression of Star-PAP targets. Our results demonstrate that the PITPs generate Star-PAP-PIPn complexes that are then modified by PI kinases/phosphatases and small heat shock proteins that regulate the linked phosphoinositide phosphorylation and Star-PAP activity in response to stress.
Dynamics of X chromosome hyper-expression and inactivation in male tissues during stick insect development
Authors: Djordjevic Jelisaveta , Tran Van Patrick , Toubiana William , Labédan Marjorie , Dumas Zoé , Aury Jean-Marc , Cruaud Corinne , Istace Benjamin , Labadie Karine , Noel Benjamin , Parker Darren J , Schwander Tanja 
Published: July 2024

AbstractDifferentiated sex chromosomes are frequently associated with major transcriptional changes: the evolution of dosage compensation (DC) to equalize gene expression between the sexes and the establishment of meiotic sex chromosome inactivation (MSCI). Our study investigates the mechanisms and developmental dynamics of dosage compensation and meiotic sex chromosome inactivation in the stick insect speciesT. poppense. Stick insects are characterized by XX/XO sex determination and an X chromosome which likely evolved prior to the diversification of insects over 450 Mya. We generated a chromosome-level genome assembly and analyzed gene expression from various tissues (brain, gut, antennae, leg, and reproductive tract) across developmental stages in both sexes. Our results show that complete dosage compensation is maintained in male somatic tissues throughout development, mediated by upregulation of the single X chromosome. Contrarily, in male reproductive tissues, dosage compensation is present only in the early nymphal stages. As males reach the 4th nymphal stage and adulthood, X-linked gene expression diminishes, coinciding with the onset of MSCI. This reduction is associated with histone modifications indicative of transcriptional silencing, aligning with meiotic progression. These findings reveal the dynamic regulation of X-linked gene expression inT. poppense, and suggest that reduced X-expression in insect testes is generally driven by MSCI rather than an absence of dosage compensation mechanisms. Our work provides critical insights into sex chromosome evolution and the complex interplay of dosage compensation and MSCI across tissues and developmental stages.
The genetics of fruit skin separation in date palm
Authors: Younuskunju Shameem , Mohamoud Yasmin A. , Mathew Lisa Sara , Mayer Klaus F. X. , Suhre Karsten , Malek Joel A. 
Published: July 2024

AbstractThe physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. In this study, we show that there is both an environmental and genetic contribution to the fruit skin separation phenotype. We show that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. A genome-wide association study was conducted using genome data of 199 samples collected from 14 countries that identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.
Towards edge processing of images from insect camera traps
Authors: Bjerge Kim , Karstoft Henrik , Høye Toke T. 
Published: July 2024

AbstractInsects represent nearly half of all known multicellular species but knowledge about them lacks behind most vertebrate species. In part for this reason, they are often neglected in biodiversity conservation policies and practice. Computer vision tools, such as insect camera traps, for automated monitoring have the potential to revolutionize insect study and conservation. To further advance insect camera trapping and the analysis of their image data, effective image processing pipelines are needed. In this paper, we present a flexible and fast processing pipeline designed to analyse these recordings by detecting, tracking and classifying nocturnal insects in a broad taxonomy of 15 insect classes and resolution of individual moth species. A classifier with anomaly detection is proposed to filter dark, blurred, or partially visible insects that will be uncertain to classify correctly. A simple track-by-detection algorithm is proposed to track classified insects by incorporating feature embeddings, distance and area cost. We evaluated the computational speed and power performance of different edge computing devices (Raspberry Pi’s and NVIDIA Jetson Nano) and compared various time-lapse strategies with tracking. The minimum difference was found for 2-minute time-lapse intervals compared to tracking with 0.5 frames per second, however, for insects with fewer than one detection per night, the Pearson correlation decreases. Shifting from tracking to time-lapse monitoring would reduce the amount of recorded images and be able to perform edge processing of images in real-time on a camera trap with Raspberry Pi. The Jetson Nano is the most energy-efficient solution, capable of real-time tracking at nearly 0.5 fps. Our processing pipeline was applied to more than 5.7 million images recorded at 0.5 frames per second from 12 light camera traps during two full seasons located in diverse habitats, including bogs, heaths and forests.
Enhancing reproducibility and decentralization in single cell research with biocytometry
Authors: Fikar Pavel , Alvarez Laura , Berne Laura , Cienciala Martin , Kan Christopher , Kasl Hynek , Luo Mona , Novackova Zuzana , Ordonez Sheyla , Sramkova Zuzana , Holubova Monika , Lysak Daniel , Avery Lyndsay , Caro Andres A. , Crowder Roslyn N. , Diaz-Martinez Laura A. , Donley David W. , Giorno Rebecca R. , Guttilla Reed Irene K. , Hensley Lori L. , Johnson Kristen C. , Kim Paul , Kim Audrey Y. , LaGier Adriana J. , Newman Jamie J. , Padilla-Crespo Elizabeth , Reyna Nathan S. , Tsotakos Nikolaos , Al-Saadi Noha N. , Appleton Tayler , Arosemena-Pickett Ana , Bell Braden A. , Bing Grace , Bishop Bre , Forde Christa , Foster Michael J. , Gray Kassidy , Hasley Bennett L. , Johnson Kennedy , Jones Destiny Jen’a , LaShall Allison C. , McGuire Kennedy , McNaughton Naomi , Morgan Angelina M. , Norris Lucas , Ossman Landon A. , Rivera-Torres Paollette A. , Robison Madeline E. , Thibodaux Kathryn , Valmond Lescia , Georgiev Daniel 
Published: July 2024

AbstractBiomedicine today is experiencing a shift towards decentralized data collection, which promises enhanced reproducibility and collaboration across diverse laboratory environments. This inter-laboratory study evaluates the performance of biocytometry, a method utilizing engineered bioparticles for enumerating cells based on their surface antigen patterns. In a decentralized framework, spanning 78 assays conducted by 30 users across 12 distinct laboratories, biocytometry consistently demonstrated significant statistical power in discriminating numbers of target cells at varying concentrations as low as 1 cell per 100,000 background cells. User skill levels varied from expert to beginner capturing a range of proficiencies. Measurement was performed in a decentralized environment without any instrument cross-calibration or advanced user training outside of a basic instruction manual. The results affirm biocytometry to be a viable solution for immunophenotyping applications demanding sensitivity as well as scalability and reproducibility and paves the way for decentralized analysis of rare cells in heterogeneous samples.
Oviductin sets the species-specificity of the mammalian zona pellucida
Authors: de la Fuente Daniel , Maroto Maria , Cajas Yulia N , Cañón-Beltrán Karina , Fernandez-Gonzalez Raul , Munoz-Maceda Ana , Sanchez-Puig Juana M , Blasco Rafael , Cots Paula , Aviles Manuel , Rizos Dimitrios , Gutiérrez-Adán Alfonso 
Published: July 2024

AbstractThe zona pellucida (ZP) is vital for species-specific fertilization as this barrier mediates sperm-oocyte binding. Here, we determined whether sperm from distant mammalian orders (Carnivora, Primates, and Rodentia) could penetrate bovine oocytes by examining the role of bovine oviductal fluid and species-specific oviductal glycoprotein (OVGP1 or oviductin) from bovine, murine, or human sources in modulating the species-specificity of bovine and murine oocytes. Sperm from all the species were found to penetrate intact bovine ovarian oocytes to form hybrid embryos. However, contact with oviductal fluid or bovine, murine, or human OVGP1, conferred the ZP species-specificity, allowing only the penetration of the corresponding sperm regardless of the ZP’s origin. Glycolytic and microstructural analyses revealed that OVGP1 covers the pores present in the ZP and that OVGP1 glycosylation determines sperm specificity. This suggests specific fertilization capacity is acquired in the oviduct through the ZP’s incorporation of specific oviductin.TeaserThe oocyte zona pellucida needs to interact with an oviduct protein called OVGP1 to ensure that only sperm from the same species can fertilize the egg.
A two-component signature determines which rust fungi secreted proteins are translocated into the cells of the host plant
Authors: Lawrence Gregory J 
Published: July 2024

AbstractRust diseases of plants are caused by parasitic fungi that feed off living plant cells by means of haustoria that form within plant cells. These haustoria also secrete a large number of proteins, some of which remain in the matrix surrounding the haustoria while others are translocated through a membrane into the cytoplasm of the plant cell. These latter proteins would be expected to possess a signature marking them out for translocation but, to date, no such signature has been identified. An examination of a set of wheat rust proteins known to be translocated to the cytoplasm of the wheat cell, together with an analysis of 1208 wheat stem rust (Puccinia graminisf. sp.tritici) secretome proteins, provides evidence that the translocation signature contains two components. The first component consists of a positively-charged amino acid at position 1, 2 or 3 (and possibly 4 or greater) upstream of the hydrophobic region in the signal peptide. The second component consists of a positively-charged amino acid at position 21 downstream of the signal peptide. A similar analysis of flax rust (Melampsora lini) secretome proteins indicates that the first component is the same as that of the wheat stem rust secretome proteins but that the second component consists of a positively-charged amino acid at position (16)17-20 downstream of the signal peptide. The flax rust signature may also be employed by wheat stem rust in its pycnial stage when growing on its alternate dicot host, barberry. Being able to identify which rust haustorial secreted proteins go to the plant cytoplasm and which to the extrahaustorial matrix should facilitate work aimed at identifying the function of each of the secreted proteins and, also, work aimed at elucidating the translocation mechanism, an understanding of which could open up new approaches to rust control.
Selective Outcome Reporting in Cancer Studies: A Scoping Review
Authors: Hinkel Jennifer , Heneghan Carl , Bankhead Clare 
Published: July 2024

AbstractBackgroundUnbiased reporting of clinical study results is essential for evidence-based medicine. However, Selective Outcome Reporting (SOR) leads to Outcome Reporting Bias (ORB) and is prevalent across disease areas, including oncology. This scoping review aims to: (a) describe the current state of research on SOR in cancer studies, (b) assess the prevalence of SOR, (c) understand methods and definitions used in SOR assessment, (d) map available evidence and identify research gaps, and (e) discuss research and policy implications.MethodsA systematic literature search was conducted using keywords related to endpoint discrepancies and oncology. Studies were screened, deduplicated, and evaluated. The JBI Critical Appraisal Checklist for Systematic Reviews and Research Synthesis was used for quality assessment.ResultsSix systematic reviews, each including 24 to 217 cancer clinical trials, were analysed. SOR prevalence varied from 4% to 79%, with a median rate of 12%. Definitions of endpoint discrepancies varied, complicating direct comparisons. SOR was identified as over-reporting, under-reporting, or misreporting outcomes.ConclusionSOR is a significant issue in oncology clinical trials, with implications for evidence synthesis, clinical practice, and policy. The lack of consistent definitions and detailed protocol reporting contributes to the challenge. Enhancing transparency and standardisation in outcome reporting could mitigate ORB and improve the reliability of clinical evidence. Implications: Future research should focus on consistent SOR definitions and improved protocol transparency. Policymakers and regulators should promote standards to reduce SOR and ensure transparent and trustworthy clinical trial outcomes.
Genomic insight into theComamonas kerstersiiisolated from diarrheal patients in Bangladesh
Authors: Rib Noshin Ibnat , Shams Fariza , Hossain Sakib Abrar , Sadique Abdus , Alam Jahidul , Debnath Pronoy , Hossain Arman , Rahman Aura , Tabassum Syeda Naushin , Huq Tahrima Saiha , Hossain Maqsud 
Published: July 2024

AbstractThis study marks the first identification and genomic characterization ofComamonas kerstersiiisolates from diarrheal patients in Bangladesh. C. kerstersiiis a gram-negative opportunistic bacterium which has also been reported in several clinical samples, including urine, blood, stool, peritoneal liquid, sputum. We carried out the whole genome sequencing of threeC. kerstersiiisolates for the first time in Bangladesh with an aim to analyze genomic features in 3 different strains isolated from Bangladesh. Seven AMR genes, aph(6)-Id, aph(3’’)-Ib, mph(E), mph(F), msr(E), sul2, and tet(A), have been observed in all the strains. We identified several virulence factors including copper homeostasis genes, type IV pili and type VI secretion system. phage regions and IncQ1 plasmid were also detected.
Enhancing Automated Medical Coding: Evaluating Embedding Models for ICD-10-CM Code Mapping
Authors: Klotzman Vanessa 
Published: July 2024

AbstractPurposeThe goal of this study is to enhance automated medical coding (AMC) by evaluating the effectiveness of modern embedding models in capturing semantic similarity and improving the retrieval process for ICD-10-CM code mapping. Achieving consistent and accurate medical coding practices is crucial for effective healthcare management.MethodsWe compared the performance of embedding models, including text-embedding-3-large, text-embedding-004, voyage-large-2-instruct, and mistralembed, against ClinicalBERT. These models were assessed for their ability to capture semantic similarity between long and short ICD-10-CM descriptions and to improve the retrieval process for mapping diagnosis strings from the eICU database to the correct ICD-10-CM codes.ResultsThe text-embedding-3-large and text-embedding-004 models outperformed ClinicalBERT in capturing semantic similarity, with text-embedding-3-large achieving the highest accuracy. For ICD-10 code retrieval, the voyage-large-2-instruct model demonstrated the best performance. Using the 15 nearest neighbors provided the best results. Increasing the number beyond this did not improve accuracy due to a lack of meaningful information.ConclusionModern embedding models significantly outperform specialized models like ClinicalBERT in AMC tasks. These findings underscore the potential of these models to enhance medical coding practices, in spite of the challenges with ambiguous diagnosis descriptions.
The Efficacy and Safety of Pembrolizumab, Ipilimumab, and Nivolumab Monoteraphy and Combination for Colorectal Cancer: A Systematic Review and Meta-Analysis
Authors: Adrianto Albertus Ari , Riwanto Ignatius , Sadhana Udadi , Paramita Dewi Kartikawati , Setyawan Henry , Tjandra Kevin Christian , Respati Danendra Rakha Putra , Rampengan Derren David Christian Homenta , Ramadhan Roy Novri , Jangkang Gastin Gabriel , Mahati Endang 
Published: July 2024

AbstractBackgroundColorectal cancer (CRC) ranks third globally in cancer-related mortality, with rising incidence, particularly in Asia, projecting a 60% surge by 2030. Metastatic CRC (mCRC) presents a significant challenge with a grim 5-year survival rate of 14%. Emerging evidence suggests that tumors with DNA mismatch repair deficiency (dMMR) and high microsatellite instability (MSI-H) respond well to immune checkpoint inhibitors (ICIs), marking a paradigm shift in therapeutic approaches. This systematic review and meta-analysis aim to comprehensively assess Pembrolizumab, Nivolumab, and the combination of Nivolumab and Ipilimumab in advanced CRC, considering their significant antitumor efficacy in MSI-H/dMMR mCRC.MethodsFollowing PRISMA guidelines and Cochrane Handbook standards, this study covers 2014 to 2024, involving advanced CRC patients treated with ICIs. A comprehensive literature search employed 12 independent authors across eight databases. Parameters such as overall survival, progression-free survival, and objective response rate were extracted.The Cochrane Collaboration’s Risk of Bias version 2 tool assessed risk. Statistical analysis utilized mean difference and risk ratios with random-effect models due to anticipated heterogeneity. Robustness was ensured through publication bias analysis and sensitivity meta-analysis. Linear regression explored associations in subgroup analysis.ResultsThe meta-analysis evaluated ORR and OS across different immunotherapy interventions. Nivolumab, Nivolumab+Ipilimumab, and Pembrolizumab exhibited varying ORR and OS effect sizes with corresponding heterogeneity levels. Progression-free survival (PFS) analysis also showed diverse effect sizes and heterogeneity levels across the three interventions. The study provides a comprehensive overview of response rates and survival outcomes for these immunotherapies in advanced CRC.ConclusionsThe study concludes that combination immunotherapy, particularly Nivolumab and Ipilimumab, presents a promising avenue for advanced CRC treatment, showing superior efficacy. Pembrolizumab monotherapy also exhibited promise. While the study offers valuable insights, the identified heterogeneity emphasizes the need for additional research. Adverse effects were generally low, supporting the viability of the studied immunotherapies. The study acknowledges limitations and calls for ongoing investigation to refine and validate these findings, marking a pioneering effort in systematically comparing short-term and long-term effects of anti-CTLA-4 and anti-PD-1 therapies in CRC.