bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing underestimation of waterborne disease risks due to fecal indicator bacteria bound in aggregates
Authors: Angelescu Dan E , Abi-Saab David , Ganaye Raphael , Wanless David , Wong Joyce 
Published: November 2024

Abstract

Aims
This study aims to identify and address significant limitations in current culture-based regulatory methods used for monitoring microbiological water quality. Specifically, these methods’ inability to distinguish between planktonic forms and aggregates containing higher bacterial loads and associated pathogens may lead to a severe underestimation of exposure risks, with critical public health implications.

Methods and results
We employed a novel methodology combining size fractionation with ALERT (Automatic Lab-in-a-vial E.coli Remote Tracking), an automated rapid method for comprehensive quantification of culturable fecal indicator bacteria (FIB). Our findings reveal a substantial and widespread presence of aggregate-bound indicator bacteria across various water matrices and geographical locations. Comprehensive bacterial counts consistently exceeded those obtained by traditional methods by significant multiples, such as an average of 3.4× at the Seine River 2024 Olympic venue, and occasionally up to 100× in irrigation canals and wastewater plant effluent. These results, supported by microscopic and molecular analyses, underscore a systematic bias in global water safety regulatory frameworks.

Conclusions
Our research demonstrates the inadequacy of traditional culture-based techniques in assessing microbiological risks posed by aggregate-bound FIB and associated pathogens, particularly in water matrices affected by FIB-rich fecal particles from recent sewer overflows or sediment, which can carry higher infectious risks. Incorporating comprehensive FIB analysis techniques, including molecular methods and rapid culture-based approaches as shown in this study, offers a promising and effective solution to these risk assessment limitations.
Pediococcus pentosaceus RC007 and Saccharomyces boulardii RC009 as antibiotic alternatives for gut health in post-weaning pigs
Authors: Parada Julián , Magnoli Alejandra , Poloni Valeria , Corti Isgro Maite , Rosales Cavaglieri Lorenzo , Luna María Julieta , Carranza Alicia , Cavaglieri Lilia 
Published: November 2024

Abstract

Aims
The aim of the present study was to evaluate a novel probiotic Pediococcus pentosaceus RC007 used alone and convined with Saccharomyces cerevisiae var. boulardii RC009, as in-feed additives to substitute the nontherapeutic use of antibiotics, and evaluate the different structural characteristics of intestinal bacterial populations between groups, correlated with pig production performance.

Methods and results
The in vivo study was conducted on post-weaning pigs, from 21 to 56 days old. Three dietary treatments were included: T1—basal diet (BD—control group); T2—BD with P. pentosaceus RC007; and T3—BD with a mix of P. pentosaceus RC007 and S. boulardii RC009. The weight gain increase of pigs consuming non-therapeutic antibiotics was similar to those that did not consume antibiotics during the study (P = 0.0234), but had better health indicators. The use of a probiotic combination increased carcass weight and significantly reduced the lumbar fat thickness. In terms of taxonomic composition, there was a tendency to modify the abundance of Proteobacteria, Cyanobacteria, Enterobacteriaceae, and Lactobacillaceae in pigs that consumed the additives. The genus Butyricicoccus, Collinsella, and Ruminococcus tended to be more abundant in the microbiota of pigs at T3.

Conclusions
For the first time, the results of the present study indicate that P. pentosaceus RC007 and S. boulardii RC009, a probiotic combination, could be a good substitute for antibiotics in improving pig production performance, while also contributing to a healthier gut microbiota, especially with the reduced abundance of Proteobacteria and Cyanobacteria.
Variation of six local poplar clones in growth and eco-physiological traits in two types of arid valleys
Authors: Mao Liang , Liu Jie , Xiang Xiang , Tian Feifei , Yang Linkai , Wan Xueqin , Yang Hanbo , He Fang , Chen Gang , Chen Lianghua 
Published: November 2024

Abstract
Six clones of native poplars were used in a field trial to investigate variations in survival, growth, and adaptation to arid-warm and arid-hot valleys. In the arid-hot valley, clone Y1-2 exhibited the highest survival rate and growth condition, surpassing other clones, while clones B7-4 and P3-6 demonstrated superior survival and growth performance in the arid-warm valley. Clone B7-4 displayed the highest soluble sugar content in leaves across both habitats. SOD and APX activities, along with MDA content in leaves, were higher in the arid-hot valley for all clones compared to the arid-warm valley. Long-term water use efficiency, as indicated by δ13C in leaves, was significantly higher for all clones in the arid-hot valley, particularly for H1-6, T3-2, and P3-6. Increases in upper epidermis thickness were observed in clones E1, B7-4, and P3-6, while Y1-2 exhibited a higher palisade parenchyma thickness (PT) in the arid-hot valley compared to the arid-warm valley. Vein densities were higher in leaves of clones E-1, B7-4, Y1-2, and P3-6 in both valleys compared to other clones, with B7-4 showing a significant increase in mean vein width in the arid-hot valley. In conclusion, the superior growth performance of clone B7-4 in the arid-warm valley may be attributed to its stronger osmotic adjustment and higher capacity to maintain water transportation through venation. The exceptional performance of clone Y1-2 in the arid-hot valley may be associated with its compact arrangement of PT, as well as its stronger capacity for hydraulic transport and antioxidant resistance in leaves.
Mesenteroaxial gastric volvulus in an elderly patient 5 years after Nissen fundoplication and hiatal hernia repair
Authors: Gill Harpreet , Guan Angel , Nguyen Alexandra , Kim So Un , Bhat Gunjan , Malkoc Aldin , Patel Sunal 
Published: November 2024

Abstract
Gastric volvulus is a rare and potentially life-threatening condition that usually presents acutely and requires immediate intervention via either endoscopic or surgical detorsion. Most often, it presents secondary to a hiatal hernia, with herniation and torsion of the stomach through the hiatus. Only a small subset of patients present with gastric volvulus after Nissen fundoplication for hiatal hernia repair. We report the case of an elderly patient with a previous hiatal hernia repair with Nissen fundoplication who presented with an intra-abdominal gastric volvulus that developed over the course of several months. The combination of her surgical history and volvulus etiology made her disease rare. She was treated with laparoscopic surgery and gastropexy with gastrostomy tube placement, which led to the resolution of the upper gastrointestinal symptoms.
Nuclear transfer leads to aberrant cell cycle regulation and translation, as determined by gene expression, and selection of mitochondrial DNA in porcine blastocysts
Authors: Penn Alexander , Andreas Eryk , Okada Takashi , St John Justin C 
Published: November 2024

Abstract
Nuclear transfer technologies, such as metaphase II spindle transfer (MII-ST), are being developed to overcome poor oocyte quality and prevent children from acquiring severe mitochondrial DNA (mtDNA) disease. However, it is unclear whether these technologies perturb gene expression, and mtDNA carryover can be reduced to minimal levels. Using our pig model, we isolated individual karyoplasts with limited mtDNA carryover (306 ± 49 copies) from mature oocytes. First, we reintroduced the spindle into its original cytoplast (autologous), fertilized and cultured the resultant embryos to the hatching blastocyst stage of development. Following RNA-seq, 64 genes were differentially expressed at false discovery rate &lt; 0.05 and 1327 genes at P&lt; 0.05. Pathways associated with cell cycle and epigenetic regulation and genes associated with nuclear–mitochondrial interactions were upregulated whilst protein translation pathways were downregulated. We then transferred karyoplasts to third-party cytoplasts (heterologous) and undertook mtDNA next-generation sequencing of two-cell to hatching blastocyst stage preimplantation embryos. Nine of twenty embryos possessed two mitochondrial genomes. Our outcomes show that autologous nuclear transfer alone significantly changes hatching blastocyst gene expression; very low levels of mtDNA carryover can be preferentially replicated during early development; and nuclear and mitochondrial synchrony has not been re-established.
A thematic analysis of shared decision-making in consultations with patients with a presumed brain tumor and neurosurgeons
Authors: Bras Iris J M , Joosen Margot C W , Rutten Geert-Jan M , van Vugt Ingrid J M , Sitskoorn Margriet M , Boele Florien W , Hoogendoorn Petra , Gehring Karin 
Published: November 2024

Abstract

Background
Patients with brain tumors, family members, and healthcare professionals face complex healthcare decisions that can significantly impact everyday life. Engaging in shared decision-making (SDM) can help ensure treatment decisions align with patients’ preferences and goals. Little is known about the decision-making process in neurosurgical consultations. This study aims to qualitatively explore and describe the SDM process during neurosurgical consultations for patients with a presumed brain tumor.

Methods
The first consultation between patients with presumed glioma or meningioma and their neurosurgeons was audio-recorded and transcribed. Decision-making models were used as sensitization concepts, with coding carried out inductively. We employed a reflexive thematic analysis to develop themes and subthemes until saturation was beginning to emerge.

Results
Analyzing eleven consultations, we developed three main themes and twelve subthemes. The results depict decision-making guided by neurosurgeons (theme 1), with varying degrees of engagement from patients and family members (theme 2) and personalization of the decision-making process based on the medical situation and everyday life priorities (theme 3). The consultations lacked specific attention to the everyday life priorities of the patients.

Conclusions
The decision-making processes seemed to focus primarily on medically informing patients with a presumed brain tumor, in line with informed decision-making. However, less emphasis was placed on learning more about the patient’s everyday life and preferences to integrate into the decision-making process, which is key to SDM. Incorporating patient goals may lead to greater personalization and decisions that align with both the patient’s medical situation and their goals.
Coping with an awake brain tumor resection in patients and their primary contacts: A qualitative study
Authors: Kranenburg Leonieke W , van Ark Tom , van Haren Mathijs M J , Schouten Joost W , Busschbach Jan J , Klimek Markus 
Published: November 2024

Abstract

Background
The diagnosis and awake removal of a brain tumor is a major life event. A better understanding of the needs of this group of patients and their primary contacts in the perioperative trajectory can further improve care.

Methods
Adult patients who underwent an awake craniotomy (AC) in the Erasmus MC, the Netherlands and their primary contacts were interviewed 1–2 weeks prior to surgery and 2–4 weeks after surgery. Semi-structured interviews on the impact of the diagnosis on their lives and coping mechanisms with the AC procedure were conducted. Interview transcripts were analyzed in accordance with the principles of grounded theory.

Results
Twenty-one patients and 19 primary contacts were interviewed at least once during this period. Analyses and coding of the transcripts resulted in a conceptual model, distinguishing coping with the disease and coping with specific procedures of AC. In general, participants tended to rely on their pre-existing ways of coping. Situation-specific coping mostly refers to perceiving control, and related to that, trust in the medical team.

Conclusions
Patients with a brain tumor and their primary contacts perceive coping with the AC procedure as a part of coping with the disease. Although the procedure may be perceived as stressful, at the same time it offers hope and prospect. In coping with the specifics of the AC procedure, we found that feeling in control and as an extension of that, trust in the AC team were key aspects.
Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri
Authors: Suda Ryo A , Kubota Shosei , Kumar Vinod , Castric Vincent , Krämer Ute , Morinaga Shin-Ichi , Tsuchimatsu Takashi 
Published: November 2024

Abstract
Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (∼50, 000 years ago). The ecological niche modeling predicted the geographic or distribution range shifts from southern coastal regions to northern coastal and mountainous areas, possibly in association with the population size fluctuations. Through genome-wide association analyses of bioclimatic variables and selection scans, we investigated whether climate-associated loci are enriched in the extreme tails of selection scans, and demonstrated the prevailing signatures of selection, particularly toward a warmer climate in southern subpopulations and a drier environment in northern subpopulations, which may have taken place during or after the LGP. Our study highlights the importance of integrating climate associations, selection scans and population demographic analyses for identifying genomic signatures of population-specific adaptation, which would also help us predict the evolutionary responses to future climate changes.
The advancements of organoids push the boundaries of glioblastoma research
Authors: Cui Gang , Xue Song , Wang Xiaoshan , Song Wei 
Published: November 2024

Abstract
Glioblastoma (GBM) is a malignant tumor of the nervous system, which is difficult to treat due to its strong invasiveness, rapid progression, and poor prognosis. To understand the complex biological behavior of glioblasts and the interaction between tumors and hosts, a new in vitro platform based on human cells is required, which can summarize the complex cellular structure and cell diversity of the human brain, as well as the biological behavior of GBM. Organoids are 3D self-organizing tissues, partially similar to source tissues, which can simulate the structure and physiological functions of organs or tissues in vitro. In this review, we underline the widespread application of different types of GBOs models in GBM pathogenesis, including cells derived, tumor tissues derived, and other co-culture models, as well as their application and shortcomings in the treatment of GBM.
Mobile health applications for individuals with psoriatic arthritis
Authors: Awad Rami , Pham Tammy , Stratton Jackie , Leibowitz Evan , Solomon Daniel H 
Published: November 2024

Abstract

Objectives
Mobile health applications (apps) hold promise as tools for symptom tracking and management of chronic rheumatic diseases such as PsA. Apps for PsA have not been systematically evaluated. We conducted a comprehensive review of apps designed for patients with PsA.

Methods
The iOS and Android app stores were searched using the term ‘arthritis’ and individual app descriptions were reviewed for ‘psoriatic arthritis’. Apps were downloaded and rated using the Mobile Application Rating Scale (MARS). Additionally, the apps were evaluated to determine functionality, use of symptom scales and potential for integration within clinical care.

Results
The search was conducted in spring 2024 and 130 apps were found that mentioned ‘arthritis’. Seven had specific mentions of PsA in their description. We found several other relevant apps by following recommendations in the app stores. In total, 10 apps for patients with PsA were identified. MARS scores suggest they were moderate to excellent in quality. The functionality of the 10 apps differed: 7 allowed for symptom tracking, 3 allowed for data export to health records, 2 allowed for medication tracking and 1 contained a patient community platform. The symptom tracking capabilities varied widely and we could find only one published study of any of the apps.

Conclusions
We analysed apps for PsA to identify potential unmet needs and found that there are few publicly available apps, their functionality varies tremendously and testing of these apps is almost non-existent. There appears to be room for improvement of apps for PsA.
Attention Deficit Hyperactivity Disorder Among Youth at Clinical High Risk of Psychosis
Authors: Braun Amy , Liu Lu , Bearden Carrie E , Cadenhead Kristin S , Cornblatt Barbara A , Keshavan Matcheri , Mathalon Daniel H , Perkins Diana O , Stone William S , Tsuang Ming T , Walker Elaine F , Woods Scott W , Cannon Tyrone D , Addington Jean 
Published: November 2024

Abstract

Background
Attention Deficit Hyperactivity Disorder (ADHD) affects a significant proportion of the population and is associated with numerous adverse outcomes including lower educational attainment, occupational challenges, increased substance use, and various mental health issues including psychosis. This study examined the demographic, clinical, cognitive, social cognitive, and functional differences between youth at clinical high-risk (CHR) for psychosis with and without comorbid ADHD.

Method
Data were drawn from the North American Prodrome Longitudinal Studies (NAPLS2 and NAPLS3), which included 764 and 710 CHR individuals, respectively. After applying exclusion criteria, the sample consisted of 271 CHR participants with ADHD and 1118 without ADHD. All data were examined cross-sectionally.

Results
Compared with the non-ADHD group, the ADHD group was younger, had more difficulties with role functioning, premorbid functioning, and social cognition, were more likely to have a comorbid learning disorder, and reported less depression symptoms. There were no significant differences between the groups on positive or negative psychotic symptoms, transition rates, adverse events, or other comorbid disorders including substance use and depression.

Discussion
Comorbid ADHD is likely not a significant predictor of transition to psychosis among CHR youth; however, those CHR with ADHD may experience symptoms at a younger age than those without and present with a distinct clinical profile.
Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/µ test
Authors: Paradis Nicholas J , Wu Chun 
Published: November 2024

Abstract
Accurately identifying mutations under beneficial selection in viral genomes is crucial for understanding their molecular evolution and pathogenicity. Traditional methods like the Ka/Ks test, which assesses non-synonymous (Ka) versus synonymous (Ks) substitution rates, assume that synonymous substitutions at synonymous sites are neutral and thus is equal to the mutation rate (µ). Yet, evidence suggests that synonymous sites in translated regions (TRs) and untranslated regions (UTRs) can be under strong beneficial selection (Ks &gt; µ) and strongly conserved (Ks ≈ 0), leading to false predictions of adaptive mutations from codon-by-codon Ka/Ks analysis. Our previous work used a relative substitution rate test (c/µ, c: substitution rate in UTR/TR, and µ: mutation rate) to identify adaptive mutations in SARS-CoV-2 genome without the neutrality assumption of the synonymous sites. This study refines the c/µ test by optimizing µ value, leading to a smaller set of nucleotide and amino acid sites under beneficial selection in both UTR (11 sites with c/µ &gt; 3) and TR (69 nonsynonymous sites: c/µ &gt; 3 and Ka/Ks &gt; 2.5; 107 synonymous sites: Ks/µ &gt; 3). Encouragingly, the top two mutations in UTR and 70% of the top nonsynonymous mutations in TR had reported or predicted effects in the literature. Molecular modeling of top adaptive mutations for some critical proteins (S, NSP11, and NSP5) was carried out to elucidate the possible molecular mechanism of their adaptivity.
Long-term Clinical and Radiographic Results of Posteromedial Lateral Release for Neuromuscular Clubfoot Deformity
Authors: May Jared M. , DeMaio Emily L. , Larson Jill E. 
Published: November 2024

Background:
Clubfoot occurs in up to 50% of patients with spina bifida (SB) and 90% with arthrogryposis (AR). Many of these patients with neuromuscular clubfoot deformity fail conservative casting and require surgery with posteromedial lateral release (PMLR). Limited data exist for the outcomes of PMLR in patients with SB and AR.

Methods:
Retrospective chart review was performed on PMLR in patients with SB and AR from January 2007 to June 2022, excluding those with follow-up <3 years or incomplete charts. Radiographic measurements were obtained pre-PMLR and post-PMLR when available.

Results:
In total, 51 patients with 79 cases of clubfeet treated with PMLR at a tertiary children’s hospital were identified. Of those, 35 patients with 54 cases of clubfeet treated with PMLR were analyzed, including 22 patients (29 feet) with SB and 13 patients (25 feet) with AR. In the SB cohort, 41% of feet required reoperation at an average of 4.6 years, and 76% of AR feet required reoperation at an average of 4.7 years post-PMLR. In addition, 21% of SB feet and 8% of AR feet required 2 or more reoperations. Talectomy was required post-PMLR in 24% of SB feet and 40% of AR feet at an average of 4.9 and 5.9 years, respectively. Younger age at time of PMLR was associated with significantly increased reoperation rates in AR (P=0.01). Greater change in calcaneus-fifth metatarsal angle after PMLR was associated with a future need for reoperation (P=0.047). Greater talo-first metatarsal angle after PMLR was associated with a future need for reoperations of any kind (P=0.040) in SB.

Conclusions:
Although PMLR remains a safe and successful treatment in the short term, many neuromuscular clubfeet will require additional procedures. Younger age and greater preoperative versus postoperative changes in calcaneus-fifth metatarsal and postoperative talo-first metatarsal angles were associated with increased reoperation rate. These results help orthopaedic surgeons counsel families about the long-term prognosis of clubfoot treatment in SB and AR.

Level of evidence:
Level IV.