bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Characteristics of Pediatric Parainfluenza Virus Infections: A Comparative Analysis of Parainfluenza Virus Serotypes 1–4 From April 2021 to October 2023 in Hokkaido, Japan
Authors: Sanada Atsushi , Kondo Kenji , Takahashi Funa , Higashide Yukiko , Kunizaki Jun , Hoshino Emiko , Sakurai Nodoka , Mori Toshihiko 
Published: June 2024

Background:
Parainfluenza virus (PIV) is widely known as a causative virus of acute respiratory tract infections in children, and 4 serotypes (PIV-1–PIV-4) have been identified. The purpose of the present study was to clarify the clinical characteristics of the PIV serotypes in pediatric PIV infections in Japan.

Methods:
Between April 2021 and October 2023, 8821 children aged <16 years who presented with respiratory symptoms underwent multiplex polymerase chain reaction analyses at the Department of Pediatrics, NTT Medical Center Sapporo. All 1490 cases in which PIV was detected were analyzed for their clinical characteristics by PIV serotypes.

Results:
Of the 1490 cases, 608 were positive for a single PIV serotype: 91 (13.5%) for PIV-1, 54 (4.8%) for PIV-2, 361 (62.1%) for PIV-3 and 102 (19.6%) for PIV-4. The median ages were 3.5 years for PIV-1, 5.4 years for PIV-2, 1.9 years for PIV-3 and 2.2 years for PIV-4, with a significantly older age for PIV-2. Compared with the other serotypes, croup was significantly more common in PIV-1 and lower respiratory tract infection was significantly more common in PIV-4. Of the 608 cases with a single PIV serotype, 114 were hospitalized. The proportion of hospitalized patients was higher for PIV-4 than for the other PIV serotypes, but the difference was not significant.

Conclusions:
Lower respiratory tract infection was more frequent in PIV-4 than in the other PIV serotypes, and PIV-4 infection may increase the risk of hospitalization.
Association Between Menopausal Symptoms and Work-Related Factors Among Female Workers in Japan
Authors: Sawamoto Naoya , Okawara Makoto , Ishimaru Tomohiro , Tateishi Seiichiro , Horie Shigeo , Yasui Toshiyuki , Fujino Yoshihisa 
Published: June 2024

Objective
Although menopausal symptoms are an important issue for female workers, their association with work-related factors is not well studied. Here, we explored the association between work-related factors and menopausal symptoms in Japan.

Methods
A cross-sectional study was conducted in 2023 among all 1465 female employees of a large Japanese company. Associations between occupational factors and moderate or severe menopausal symptoms, as measured by the Menopause Rating Scale (MRS), were examined using logistic regression analysis.

Results
Several workplace-related factors were significantly associated with moderate or severe menopausal symptoms, including company support and the number of night shifts. A marginally significant association was also seen for commuting time.

Conclusions
Workplace menopause interventions for the factors identified in this study may satisfy unmet needs.
Schistosomal colitis mimicking inflammatory bowel disease: a case report from Sudan
Authors: Alajab Mohamed B. , Rafei Ahmed , Abdo Abdelmoneim E. 
Published: June 2024

Introduction:
Schistosomiasis, caused by parasitic Schistosoma species, is a common neglected tropical disease prevalent in sub-Saharan Africa, including Sudan. While urinary tract infections are more frequent, intestinal schistosomiasis is rare. The disease presents with nonspecific symptoms, often leading to misdiagnosis as inflammatory bowel disease (IBD).

Case presentation:
A 23-year-old male farmer from Gezira, Sudan, presenting with intermittent bloody diarrhea and mild left lower abdominal pain for 6 months. Despite multiple diagnoses and treatments for dysentery and IBD, his symptoms persisted. Colonoscopy revealed edematous mucosa with scattered whitish spots in the rectum, sigmoid, descending, and transverse colon, with normal findings in the ascending colon and cecum. Biopsies confirmed eosinophilic colitis with schistosomal egg shells. The patient was treated with praziquantel, leading to the resolution of symptoms within 2 weeks.

Clinical discussion:
Schistosomiasis, caused by Schistosoma mansoni, commonly manifests with myalgia, fever, and rash, alongside abdominal symptoms. Diarrhea, abdominal pain, constipation, and weight loss are common. Stool examination and serological tests aid in diagnosis, but colonoscopy can reveal characteristic findings, such as edematous mucosa and schistosomal nodules. Early diagnosis and treatment with praziquantel are essential to prevent complications and improve patient outcomes.

Conclusion:
This case emphasizes the importance of considering schistosomiasis in endemic areas when evaluating patients with colitis symptoms. Healthcare providers should maintain a high index of suspicion for this condition, especially in patients with nonspecific gastrointestinal symptoms and a history of travel to endemic areas. Early diagnosis and treatment are crucial to prevent complications and improve outcomes.
IDENTIFICATION OF A NOVEL SEPSIS PROGNOSIS MODEL: BASED ON TRANSCRIPTOME AND PROTEOME ANALYSIS
Authors: Chen Haoran , Xue Haoyue , Tang Xinyi , Wang Chen , Li Xiaomin , Xie Yongpeng 
Published: June 2024

ABSTRACT
Sepsis is a highly prevalent and deadly disease. Currently, there is a lack of ideal biomarker prognostis models for sepsis. We attempt to construct a model capable of predicting the prognosis of sepsis patients by integrating transcriptomic and proteomic data. Through analysis of proteomic and transcriptomic data, we identified 25 differentially expressed genes (DEGs). Single-factor Cox-Lasso regression analysis identified 16 DEGs (overall survival-DEGs) associated with patient prognosis. Through multifactor Cox-Lasso regression analysis, a prognostic model based on these 16 genes was constructed. Kaplan-Meier survival analysis and receiver operating characteristic curve analysis were used to further validate the high stability and good predictive ability of this prognostic model with internal and external data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of overall survival-DEGs and differentially expressed genes between high and low-risk groups based on the prognostic model revealed significant enrichment in immune-related pathways, particularly those associated with viral regulation.
Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing inEscherichia coli
Authors: Farrar Alison , Turner Piers , El Sayyed Hafez , Feehily Conor , Chatzimichail Stelios , Crook Derrick , Andersson Monique , Oakley Sarah , Barrett Lucinda , Nellåker Christoffer , Stoesser Nicole , Kapanidis Achillefs 
Published: June 2024

AbstractRapid antibiotic susceptibility tests (ASTs) are an increasingly important part of clinical care as antimicrobial resistance (AMR) becomes more common in bacterial infections. Here, we use the spatial distribution of fluorescently labelled ribosomes to detect intracellular changes associated with antibiotic susceptibility in singleE. colicells using a convolutional neural network (CNN). By using ribosome-targeting probes, a single fluorescence cell image provides data for cell segmentation and susceptibility phenotyping. Using 50,722 images of cells from an antibiotic-susceptible laboratory strain ofE. coli, we showed that antibiotics with different mechanisms of action result in distinct ribosome phenotypes, which can be identified by a CNN with high accuracy (99%, 96%, and 91% for ciprofloxacin, gentamicin, and chloramphenicol). With 6E. colistrains isolated from bloodstream infections, we used 34,205 images of ribosome phenotypes to train a CNN that could classify susceptible cells with 92% accuracy and resistant cells with 99% accuracy. Such accuracies correspond to the ability to differentiate susceptible and resistant samples with 99% confidence with just 2 cells, meaning that this method could eliminate lengthy sample culturing steps and could determine in vitro susceptibility with 30 minutes of antibiotic treatment. Our ribosome phenotype method should also be able to identify phenotypes in other strains and species.
Imaging single particle profiler to study nanoscale bioparticles using conventional confocal microscopy
Authors: Sych Taras , Görgens André , Steiner Loïc , Gucluer Gozde , Huge Ylva , Alamdari Farhood , Johansson Markus , Aljabery Firas , Sherif Amir , Gabrielsson Susanne , EL Andaloussi Samir , Sezgin Erdinc 
Published: June 2024

AbstractSingle particle profiler is a unique methodology to study nanoscale bioparticles such as liposomes, lipid nanoparticles, extracellular vesicles and lipoproteins in single particle and high throughput manner. The original version requires the single photon counting modules for data acquisition. Here, we present imaging-based SPP (iSPP) which can be performed by imaging a spot over time in common imaging mode with photomultiplier tubes. We also provide a user-friendly software with graphical user interface to facilitate the application of this technique. We demonstrate that iSPP can be used to decipher lipid-protein interactions, membrane modifications by drugs and the heterogeneity of extracellular vesicles isolated from cells lines and urine of human donors.
Loss of chromosome cytoband 13q14.2 orchestrates breast cancer pathogenesis and drug response
Authors: Shahrouzi Parastoo , Azimzade Youness , Brankiewicz Wioletta , Bhatia Sugandha , Kunke David , Richard Derek , Tekpli Xavier , Kristensen Vessela N. , Duijf Pascal H.G. 
Published: June 2024

Breast cancer (BCa) is a major global health challenge, characterized by chromosomal instability (CIN) and subsequent acquisition of extensive somatic copy number alterations (CNAs). CNAs including amplifications and deletions, significantly influence intra-tumor heterogeneity and the tumor microenvironment (TME). Among these, the loss of chromosome 13q14.2 emerges as a considerable factor in BCa pathogenesis and treatment responses. We provide evidence that this genomic alteration is under positive selective pressure, correlating with poorer patient survival. Furthermore, through multi-omic andin vitroanalyses, we uncover a dual role of 13q14.2 loss: it confers a survival advantage to tumor cells and modulate the cell cycle and pro-apoptotic pathways in cancer cells, affecting macrophages population in the TME, while paradoxically increasing tumor susceptibility toBCL2inhibitors. These findings suggest that targeting 13q14.2 as a biomarker in BCa could enhance the efficacy of existing treatments and offer a new avenue for improving clinical outcomes in BCa.Abstract FigureFigure 1.Graphical abstract
Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)
Authors: Walavalkar Kaivalya , Gupta Shivani , Kresoja-Rakic Jelena , Raingeval Mathieu , Mungo Chiara , Santoro Raffaella 
Published: June 2024

AbstractGene position in the nuclear space plays an important role in gene regulation. This is exemplified by repressive chromatin domains frequently contacting nuclear lamina or nucleoli. The nucleolus undergoes structural changes in response to various cellular states, potentially impacting genome organization. However, how the 3D-genome organization responds to nucleolar states has remained underinvestigated due to the lack of methods able to identify nucleolar associated domains (NADs) in single cells and under nucleolar stress. To address this, we developed NoLMseq, a method combining laser-capture microdissection and DNA sequencing to map NADs in single cells. NoLMseq identified many unexplored features of chromosome organization around single nucleoli such as NAD heterogeneity among ESCs, culminating in two major populations with distinct chromatin states. NADs prevalently contact nucleoli in a monoallelic manner and allelic nucleolar contact frequency mirrors gene expression and chromatin states. NoLMseq also revealed how chromosomes reorganise around nucleoli under nucleolar stress conditions, highlighting the importance of nucleolus integrity in genome organization and 3D-genome response to nucleolar stress. The results demonstrated that NoLMseq accurately measures chromosome contacts around single healthy and stressed nucleoli and it will be a critical tool to study NADs within biological populations and determine how the 3D-genome responds to nucleolar stress in healthy and disease states.
Multiomic insights into sucrose accumulation in sugarcane
Authors: Aono Alexandre Hild , Pimenta Ricardo José Gonzaga , Diniz Jéssica Faversani , Carrasco Marishani Marin , Hosaka Guilherme Kenichi , Correr Fernando Henrique , Garcia Ana Letycia Basso , Costa Estela Araujo , Coutinho Alisson Esdras , Pinto Luciana Rossini , Landell Marcos Guimarães de Andrade , Xavier Mauro Alexandre , Perecin Dilermando , Carneiro Monalisa Sampaio , Balsalobre Thiago Willian , Kuroshu Reginaldo Massanobu , Margarido Gabriel Rodrigues , de Souza Anete Pereira 
Published: June 2024

AbstractSugarcane (Saccharumspp.) holds significant economic importance in sugar and biofuel production. Despite extensive research, understanding highly quantitative traits, such as sucrose content, remains challenging due to the complex genomic landscape of the crop. In this study, we conducted a multiomic investigation to elucidate the genetic architecture and molecular mechanisms governing sucrose accumulation in sugarcane. Using a biparental cross (IACSP95-3018 × IACSP93-3046) and a genetically diverse collection of sugarcane genotypes, we evaluated the soluble solids (Brix) and sucrose content (POL) across various years and environments. Both populations were genotyped using a genotyping-by-sequencing (GBS) approach, with single nucleotide polymorphisms (SNPs) identified via bioinformatics pipelines. Genotype‒phenotype associations were established using a combination of traditional linear mixed-effect models and machine learning algorithms. Furthermore, we conducted an RNA sequencing (RNA-Seq) experiment on genotypes exhibiting distinct Brix and POL profiles across different developmental stages. Differentially expressed genes (DEGs) potentially associated with variations in sucrose accumulation were identified. All findings were integrated through a comprehensive gene coexpression network analysis. Strong correlations among the evaluated characteristics were observed, with estimates of modest to high heritabilities. By leveraging a broad set of SNPs identified for both populations, we identified several SNPs potentially linked to phenotypic variance. Our examination of genes close to these markers facilitated the association of such SNPs with DEGs in genotypes with contrasting sucrose levels. Through the integration of these results with a gene coexpression network, we delineated a set of genes potentially involved in the regulatory mechanisms of sucrose accumulation in sugarcane, collectively contributing to the definition of this critical phenotype. Our findings constitute a significant resource for biotechnology and plant breeding initiatives. Furthermore, our genotype‒phenotype association models hold promise for application in genomic selection, offering valuable insights into the molecular underpinnings governing sucrose accumulation in sugarcane.
Dachsous and Fat coordinately repress the Dachs-Dlish-Approximated complex to control growth
Authors: Matakatsu Hitoshi , Fehon Richard G. 
Published: June 2024

AbstractTwo protocadherins, Dachsous (Ds) and Fat (Ft), regulate organ growthin Drosophilavia the Hippo pathway. Ds and Ft bind heterotypically to regulate the abundance and subcellular localization of a ‘core complex’ consisting of Dachs, Dlish and Approximated. This complex localizes to the junctional cortex where it promotes growth by repressing the pathway kinase Warts. Ds is believed to promote growth by recruiting and stabilizing the core complex at the junctional cortex, while Ft represses growth by promoting degradation of core complex components.Here, we examine the functions of intracellular domains of Ds and Ft and their relationship to the core complex. While Ds promotes accumulation of the core complex proteins in cortical puncta, it is not required for core complex assembly. Indeed, the core complex assembles maximally in the absence of both Ds and Ft. Furthermore, while Ds promotes growth in the presence of Ft, it represses growth in the absence of Ft by removing the core complex from the junctional cortex. Ft similarly recruits core complex components, however it normally promotes their degradation. Our findings reveal that Ds and Ft constrain tissue growth by repressing the default ’on’ state of the core complex.
Phage-plasmid hybrids are found throughout diverse environments and encode niche-specific functional traits
Authors: Mullet J. , Zhang L. , Pruden A. , Brown C.L. 
Published: June 2024

ABSTRACTPhage-plasmids are unique mobile genetic elements that function as plasmids and temperate phages. While it has been observed that such elements often encode antibiotic resistance genes and defense system genes, little else is known about other functional traits they encode. Further, no study to date has documented their environmental distribution and prevalence. Here, we performed genome sequence mining of public databases of phages and plasmids utilizing a random forest classifier to identify phage-plasmids. We recovered 5,742 unique phage-plasmid genomes from a remarkable array of disparate environments, including human, animal, plant, fungi, soil, sediment, freshwater, wastewater, and saltwater environments. The resulting genomes were used in a comparative sequence analysis, revealing functional traits/accessory genes associated with specific environments. Host-associated elements contained the most defense systems (including CRISPR and anti-CRISPR systems) as well as antibiotic resistance genes, while other environments, such as freshwater and saltwater systems, tended to encode components of various biosynthetic pathways. Interestingly, we identified genes encoding for certain functional traits, including anti-CRISPR systems and specific antibiotic resistance genes, that were enriched in phage-plasmids relative to both plasmids and phages. Our results highlight that phage-plasmids are found across a wide-array of environments and likely play a role in shaping microbial ecology in a multitude of niches.IMPORTANCEPhage-plasmids are a novel, hybrid class of mobile genetic element which retain aspects of both phages and plasmids. However, whether phage-plasmids represent merely a rarity or are instead important players in horizontal gene transfer and other important ecological processes has remained a mystery. Here, we document that these hybrids are encountered across a broad range of distinct environments and encode niche-specific functional traits, including the carriage of antibiotic biosynthesis genes and both CRISPR and anti-CRISPR defense systems. These findings highlight phage-plasmids as an important class of mobile genetic element with diverse roles in multiple distinct ecological niches.
PSMF1variants cause a phenotypic spectrum from early-onset Parkinson’s disease to perinatal lethality by disrupting mitochondrial pathways
Authors: Magrinelli Francesca , Tesson Christelle , Angelova Plamena R. , Salazar-Villacorta Ainara , Rodriguez Jose A. , Scardamaglia Annarita , Chung Brian Hon-Yin , Jaconelli Matthew , Vona Barbara , Esteras Noemi , Kwong Anna Ka-Yee , Courtin Thomas , Maroofian Reza , Alavi Shahryar , Nirujogi Raja , Severino Mariasavina , Lewis Patrick A. , Efthymiou Stephanie , O’Callaghan Benjamin , Buchert Rebecca , Sofan Linda , Lis Pawel , Pinon Chloé , Breedveld Guido J. , Chui Martin Man-Chun , Murphy David , Pitz Vanessa , Makarious Mary B. , Cassar Marlene , Hassan Bassem A. , Iftikhar Sana , Rocca Clarissa , Bauer Peter , Tinazzi Michele , Svetel Marina , Samanci Bedia , Hanağası Haşmet A. , Bilgiç Basar , Obeso José A. , Kurtis Monica M. , Cogan Guillaume , Başak Ayşe Nazlı , Kiziltan Güneş , Gül Tuğçe , Yalçın Gül , Elibol Bülent , Barišić Nina , Ng Earny Wei-Sen , Fan Sze-Shing , Hershkovitz Tova , Weiss Karin , Raza Alvi Javeria , Sultan Tipu , Azmi Alkhawaja Issam , Froukh Tawfiq , E Alrukban Hadeel Abdollah , Fauth Christine , Schatz Ulrich A. , Zöggeler Thomas , Zech Michael , Stals Karen , Varghese Vinod , Gandhi Sonia , Blauwendraat Cornelis , Hardy John A. , Lesage Suzanne , Bonifati Vincenzo , Haack Tobias B. , Bertoli-Avella Aida M. , Steinfeld Robert , Alessi Dario R. , Steller Hermann , Brice Alexis , Abramov Andrey Y. , Bhatia Kailash P. , Houlden Henry 
Published: June 2024

AbstractDissecting biological pathways highlighted by Mendelian gene discovery has provided critical insights into the pathogenesis of Parkinson’s disease (PD) and neurodegeneration. This approach ultimately catalyzes the identification of potential biomarkers and therapeutic targets. Here, we identifyPSMF1as a new gene implicated in PD and childhood neurodegeneration. We find that biallelicPSMF1missense and loss-of-function variants co-segregate with phenotypes from early-onset PD and parkinsonism to perinatal lethality with neurological manifestations across 15 unrelated pedigrees with 22 affected subjects, showing clear genotype-phenotype correlation.PSMF1encodes the proteasome regulator PSMF1/PI31, a highly conserved, ubiquitously expressed partner of the 20S proteasome and neurodegeneration-associated F-box-O 7 and valosin-containing proteins. We demonstrate thatPSMF1variants impair mitochondrial membrane potential, dynamics and mitophagy in patient-derived fibroblasts. Additionally, we develop models ofpsmf1knockdownDrosophilaandPsmf1conditional knockout mouse exhibiting age-dependent motor impairment, with diffuse gliosis in mice. These findings unequivocally link defective PSMF1 to early-onset PD and neurodegeneration and suggest mitochondrial dysfunction as a mechanistic contributor.
Comparison between 70% ethyl alcohol and 10% formalin as fixative mediums in surgical cooperation campaigns: a pilot study
Authors: Montero Javier Arredondo , Vega Elena Carracedo , Fortes Paula Ortolá , Anaut Mónica Bronte , de Azúa-Ciria Yerani Ruiz , Fernández-Ariza Adriana , Ibérico Alejandra Moreno , Rodríguez Jessica Paulina , Pascual Carlos Bardají , Troyas Rosa Guarch 
Published: June 2024

AbstractBackgroundThe lack of adequate resources in international cooperation limits the study of anatomopathological specimens. The literature on potentially inexpensive and available fixation media is scarce.Material and methodsOur surgical team prospectively collected specimens during cooperation campaigns developed in Senegal. Lesions were fixed in parallel in 10% formalin (FF) and 70% ethyl alcohol (AF). Hematoxylin and eosin sections (HE) and immunohistochemistry (IHC) techniques were performed. Images were anonymized and assessed by two senior and two junior pathologists, who evaluated the quality of staining and diagnostic feasibility using an anonymized questionnaire.ResultsThree surgical specimens were included: 1 lymph node (3 HE, 4 IHC), one seborrheic keratosis (2 HE, 5 IHC), and one branchial remnant (2 HE, 2 IHC). Fixation times were similar in all the specimens (10-13 days). All FF HE were diagnostic. AF H&E was 100% diagnostic in the 5/7 sections and 75% in the remaining sections. In most cases, pathologists preferred FF. CK7, P40, EMA, CKAE1/AE3, and TTF1 were 100% diagnostic in both groups. CD20, CD45, and EMA were 100% diagnostic (FF) and 75% diagnostic (AF). CD10 was 75% diagnostic (FF) and 25% diagnostic (AF). BCL6 was 75% diagnostic (FF) and 100% diagnostic (AF). IHC preferences were inconsistent.Conclusions70% ethyl alcohol has a worse fixation profile than 10% formalin but allows diagnosis in most cases. The immunoreactivity observed is variable depending on the tissue and the stain used. Based on these findings, it can be considered an inexpensive, readily available, and potentially helpful fixation medium for diagnosis in developing countries where surgical cooperation campaigns are conducted. Nevertheless, future studies of larger sample sizes and characterizing other histologic subtypes are needed to confirm these findings.