bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing microbial diversity in soil samples along the Potomac River: implications for environmental health
Authors: Taraboletti Alexandra , King Alexus , Dixon Yasheka , Orr Oshane , Parnell Chevell , Watson Yasheika , Nash Bruce , Esimai Chimdimnma , Ude George 
Published: October 2023

ABSTRACT

In this study, we investigated the microbial diversity and community composition of soil samples collected from various sites along the Potomac River within an urbanized region. The study integrates microbial analysis into an undergraduate chemistry curriculum, bridging theoretical education with practical, real-world applications. Our findings revealed the presence of both typical marine soil bacteria and bacterial taxa indicative of urbanization and waste runoff. Notably, the identified taxa shared among all samples demonstrated a strong presence of
Burkholderiaceae
,
Nitrosomonadaceae
, and
Pedosphaeraceae
, which are associated with agricultural pollution, organochlorine pesticide contamination, and bromochloromethane pollution. We observed significant variations in microbial community diversity across different sampling sites, emphasizing the influence of environmental factors on microbial abundance and diversity. These insights carry significant implications for understanding the consequences of urbanization on soil microbial communities along the Potomac River and can inform strategies for managing and preserving these ecosystems. Further research is warranted to elucidate the effects of soil health and microbial diversity in this region.

IMPORTANCE
This study integrates microbial analysis into an undergraduate chemistry class, offering students a hands-on approach to environmental research. We examined the soil along the urbanized Potomac River, discovering a mix of common marine microbes and others that are indicators of urban waste and pollution. Our findings provide valuable insights into the environmental impacts of urbanization on soil health and reveal the effectiveness of using modern genetic tools to teach students about real-world issues. This innovative educational approach not only deepens students’ understanding of chemistry and ecology but also prepares them to be thoughtful, informed participants in addressing contemporary environmental challenges while shedding light on the state of the soil microbiome near and around the DC metro area.
Olympic Games during nationwide lockdown: sports injuries and illnesses, including COVID-19, at the Beijing 2022 Winter Olympics
Authors: Soligard Torbjørn , Palmer Debbie , Steffen Kathrin , Lopes Alexandre Dias , Grek Natalia , He Xuan , Wang Yan , Grant Marie-Elaine , Toresdahl Brett G , Gilgien Matthias , Budgett Richard , Engebretsen Lars 
Published: October 2023

ObjectiveThe objective of this study is to describe the incidence of injuries and illnesses sustained during the Beijing Winter Olympic Games from 4 February 2022 to 20 February 2022.MethodsWe recorded the daily number of athlete injuries and illnesses (1) through the reporting of all National Olympic Committee (NOC) medical teams and (2) in the polyclinic and medical venues by the Beijing 2022 medical staff.ResultsIn total, 2848 athletes (1276 women, 45%; 1572 men, 55%) from 91 NOCs were followed prospectively for the occurrence of injury and illness. NOC and Beijing 2022 medical staff reported 289 injuries and 109 illnesses, equalling 10.1 injuries and 3.8 illnesses per 100 athletes over the 17-day period. The injury incidence was highest in ski halfpipe (30%), ski big air (28%), snowboard slopestyle (23%) and ski slopestyle (22%), and lowest (1%–2%) in curling, alpine mixed team parallel slalom, Nordic combined and alpine super-G. The illness incidence was highest in ski aerials (10%), skeleton (8%), cross-country skiing (8%) and Nordic combined (7%). In the study period, COVID-19 affected 32 athletes, accounting for 29% of all illnesses affecting 1.1% of all athletes.ConclusionOverall, 10% of the athletes incurred an injury and 4% an illness during the Beijing Winter Olympic Games. The incidence of illnesses overall, which was the lowest yet recorded in the Winter Olympic Games, and COVID-19 was mitigated through comprehensive countermeasures.
Innervation of thumb carpometacarpal joint: implications for diagnostic block and denervation procedures
Authors: Tran John , Peng Philip , Ho Loretta , von Schroeder Herbert , Agur Anne 
Published: October 2023

Introduction
Osteoarthritis (OA) of the thumb carpometacarpal (CMC) joint is a common disorder that negatively impacts hand function. Denervation of the thumb CMC joint has emerged as a viable treatment option. However, the innervation pattern of the thumb CMC joint is controversial. Therefore, the objective of this study was to identify the articular branches supplying the thumb CMC joint and to document their relationship to anatomical landmarks to provide the foundation for image-guided diagnostic block and denervation procedures.

Methods
In 10 formalin-embalmed upper limb specimens articular branches supplying the thumb CMC joint were dissected from their origin to termination. A frequency map documenting the number of articular branches was generated. The frequency map enabled visualization and comparison of the relative area of innervation of the thumb CMC joint by each articular branch.

Results
The thumb CMC joint received innervation from six nerves. These were the deep branch of ulnar nerve (DBUN), dorsal articular nerve (DAN) of the first interosseus space, thenar branch of median nerve (TBMN), palmar cutaneous branch of median nerve (PCBMN), lateral antebrachial cutaneous nerve (LACN) and superficial branch of the radial nerve (SBRN) and/or their branches. Each nerve was found to innervate different aspects of the joint. The DBUN and DAN were found to innervate the posteromedial aspect of the thumb CMC joint, the TBMN and PCBMN anterior/anteromedial aspects, LACN posterolateral/lateral/anterior aspects and SBRN posterolateral/anterolateral aspects.

Conclusions
The thumb CMC joint was innervated by articular branches originating from the SBRN, DAN, LACN, PCBMN, TBMN and DBUN. The documented anatomical relationships provide the foundation to inform selective diagnostic block and denervation of the thumb CMC joint. Further investigations are needed to assess the clinical implications of the current study.
Tumor-Infiltrating CD103+ Tissue-Resident Memory T Cells and CD103−CD8+ T Cells in HNSCC Are Linked to Outcome in Primary but not Metastatic Disease
Authors: von Witzleben Adrian , Ellis Matthew , Thomas Gareth J. , Hoffmann Thomas K. , Jackson Richard , Laban Simon , Ottensmeier Christian H. 
Published: October 2023

Abstract

Purpose:
High numbers of tumor-infiltrating lymphocytes (TIL) are linked to better survival in patients with cancer. Tissue-resident memory T cells (TRM; CD8+CD103+) are recognized as a key player of anticancer immune response. To assess TRM cells in primary, metastatic, and recurrent head and neck squamous cell carcinoma (HNSCC), we developed a tissue microarray (TMA) and used multiplex IHC (MxIHC).

Experimental Design:
Samples from primary tumors of 379 HNSCC cases treated at Southampton Hospitals between 2000 and 2016 were collected and analyzed. Of these, 105 cases had lymph node metastases and 82 recurrences. A TMA was generated with triplicate cores for each sample. MxIHC with a stain-and-strip approach was performed using CD8, CD103, and TIM3. Scanned slides were analyzed (digital image analysis) and quality checked (QC).

Results:
After QC, 194 primary tumors, 76 lymph node metastases, and 65 recurrences were evaluable. Alcohol consumption was statistically significantly correlated with a reduction of TRM cells in primary tumors (nondrinker vs. heavy drinker: P = 0.0036). The known survival benefit of TRM cell infiltration in primary tumors was not found for lymph node metastasis. In recurrences, a high TRM cell number led to a favorable outcome after 12 months. The checkpoint molecule TIM3, was expressed significantly higher on TRM and non-TRM cells in the lymph node compared with primary tumors (P &lt; 0.0001), which was also seen in recurrences (P = 0.0134 and P = 0.0007, respectively).

Conclusions:
We confirm the prognostic impact of TIL in primary tumors and in recurrences. TRM cell density in lymph node metastases was not linked to outcome. The role of TIM3, as a therapeutic target remains to be defined.
Management of Renal Cell Carcinoma: Promising Biomarkers and the Challenges to Reach the Clinic
Authors: Lyskjær Iben , Iisager Laura , Axelsen Christian Tang , Nielsen Tommy Kjærgaard , Dyrskjøt Lars , Fristrup Niels 
Published: October 2023

Abstract
The incidence of renal cell carcinoma (RCC) is increasing worldwide, yet research within this field is lagging behind other cancers. Despite increased detection of early disease as a consequence of the widespread use of diagnostic CT scans, 25% of patients have disseminated disease at diagnosis. Similarly, around 25% progress to metastatic disease following curatively intended surgery. Surgery is the cornerstone in the treatment of RCC; however, when the disease is disseminated, immunotherapy or immunotherapy in combination with a tyrosine kinase inhibitor is the patient's best option. Immunotherapy is a potent treatment, with durable treatment responses and potential to cure the patient, but only half of the patients benefit from the administered treatment, and there are currently no methods that can identify which patients will respond to immunotherapy. Moreover, there is a need to identify the patients in greatest risk of relapsing after surgery for localized disease and direct adjuvant treatment there. Even though several molecular biomarkers have been published to date, we are still lacking routinely used biomarkers to guide optimal clinical management. The purpose of this review is to highlight some of the most promising biomarkers, discuss the efforts made within this field to date, and describe the barriers needed to be overcome to have reliable and robust predictive and prognostic biomarkers in the clinic for renal cancer.
Clinical decision-making and treatment of myelodysplastic syndromes
Authors: Hellström-Lindberg Eva S. , Kröger Nicolaus 
Published: October 2023

Abstract
The myelodysplastic syndromes (MDSs) constitute a profoundly heterogeneous myeloid malignancy with a common origin in the hemopoietic stem cell compartment. Consequently, patient management and treatment are as heterogeneous. Decision-making includes identifying risk, symptoms, and options for an individual and conducting a risk-benefit analysis. The only potential cure is allogeneic stem cell transplantation, and albeit the fraction of patients with MDS who undergo transplant increase over time because of better management and increased donor availability, a majority are not eligible for this intervention. Current challenges encompass to decrease the relapse risk, the main cause of hematopoietic stem cell transplantation failure. Hypomethylating agents (HMAs) constitute firstline treatment for higher-risk MDSs. Combinations with other drugs as firstline treatment has, to date, not proven more efficacious than monotherapy, although combinations approved for acute myeloid leukemia, including venetoclax, are under evaluation and often used as rescue treatment. The treatment goal for lower-risk MDS is to improve cytopenia, mainly anemia, quality of life, and, possibly, overall survival. Erythropoiesis-stimulating agents (ESAs) constitute firstline treatment for anemia and have better and more durable responses if initiated before the onset of a permanent transfusion need. Treatment in case of ESA failure or ineligibility should be tailored to the main disease mechanism: immunosuppression for hypoplastic MDS without high-risk genetics, lenalidomide for low-risk del(5q) MDS, and luspatercept for MDS with ring sideroblasts. Approved therapeutic options are still scarcer for MDS than for most other hematologic malignancies. Better tools to match disease biology with treatment, that is, applied precision medicines are needed to improve patient outcome.
Inhibition of SQSTM1 S403 phosphorylation facilitates the aggresome formation of ubiquitinated proteins during proteasome dysfunction
Authors: Zhang Chenliang , Duan YiChun , Huang Chen , Li Liping 
Published: October 2023

Abstract
Background
Ubiquitin–proteasome-system-mediated clearance of misfolded proteins is essential for cells to maintain proteostasis and reduce the proteotoxicity caused by these aberrant proteins. When proteasome activity is inadequate, ubiquitinated proteins are sorted into perinuclear aggresomes, which is a significant defense mechanism employed by cells to combat insufficient proteasome activity, hence mitigating the proteotoxic crisis. It has been demonstrated that phosphorylation of SQSTM1 is crucial in regulating misfolded protein aggregation and autophagic degradation. Although SQSTM1 S403 phosphorylation is essential for the autophagic degradation of ubiquitinated proteins, its significance in proteasome inhibition-induced aggresome formation is yet unknown. Herein, we investigated the influence of SQSTM1 S403 phosphorylation on the aggresome production of ubiquitinated proteins during proteasome suppression.

Methods
We examined the phosphorylation levels of SQSTM1 S403 or T269/S272 in cells after treated with proteasome inhibitors or/and autophagy inhibitors, by western blot and immunofluorescence. We detected the accumulation and aggresome formation of ubiquitinated misfolded proteins in cells treated with proteasome inhibition by western blot and immunofluorescence. Furthermore, we used SQSTM1 phosphorylation-associated kinase inhibitors and mutant constructs to confirm the regulation of different SQSTM1 phosphorylation in aggresome formation. We examined the cell viability using CCK-8 assay.

Results
Herein, we ascertained that phosphorylation of SQSTM1 S403 did not enhance the autophagic degradation of ubiquitinated proteins during proteasome inhibition. Proteasome inhibition suppresses the phosphorylation of SQSTM1 S403, which facilitated the aggresome production of polyubiquitinated proteins. Interestingly, we found proteasome inhibition-induced SQSTM1 T269/S272 phosphorylation inhibits the S403 phosphorylation. Suppressing S403 phosphorylation rescues the defective aggresome formation and protects cells from cell death caused by unphosphorylated SQSTM1 (T269/S272).

Conclusions
This study shows that inhibition of SQSTM1 S403 phosphorylation facilitates the aggresome formation of ubiquitinated proteins during proteasome dysfunction. SQSTM1 T269/S272 phosphorylation inhibits the S403 phosphorylation, boosting the aggresome formation of ubiquitinated protein and shielding cells from proteotoxic crisis.
Validation of ANG-1 and P-SEL as biomarkers of post-COVID-19 conditions using data from the Biobanque québécoise de la COVID-19 (BQC-19)
Authors: Yamga Eric , Soulé Antoine , Piché Alain , Emad Amin , Durand Madeleine , Rousseau Simon 
Published: October 2023

AbstractThe quest for understanding and managing the long-term effects of COVID-19, often referred to as Long COVID or post-COVID-19 condition (PCC), remains an active research area. Recent findings highlighted angiopoietin-1 (ANG-1) and p-selectin (P-SEL) as potential diagnostic markers, but validation is essential, given the inconsistency in COVID-19 biomarker studies. Leveraging the biobanque québécoise de la COVID-19 (BQC19) biobank, we analyzed the data of 249 participants. Both ANG-1 and P-SEL levels were significantly higher in patients with PCC participants compared with control subjects at 3 months using the Mann-Whitney U test. We managed to reproduce and validate the findings, emphasizing the importance of collaborative biobanking efforts in enhancing the reproducibility and credibility of Long COVID research outcomes.
Untangling an insect’s virome from its endogenous viral elements
Authors: Rozo-Lopez Paula , Brewer William , Käfer Simon , Martin McKayla M. , Parker Benjamin J. 
Published: October 2023

Abstract
Background
Insects are an important reservoir of viral biodiversity, but the vast majority of viruses associated with insects have not been discovered. Recent studies have employed high-throughput RNA sequencing, which has led to rapid advances in our understanding of insect viral diversity. However, insect genomes frequently contain transcribed endogenous viral elements (EVEs) with significant homology to exogenous viruses, complicating the use of RNAseq for viral discovery.

Methods
In this study, we used a multi-pronged sequencing approach to study the virome of an important agricultural pest and prolific vector of plant pathogens, the potato aphid Macrosiphum euphorbiae. We first used rRNA-depleted RNAseq to characterize the microbes found in individual insects. We then used PCR screening to measure the frequency of two heritable viruses in a local aphid population. Lastly, we generated a quality draft genome assembly for M. euphorbiae using Illumina-corrected Nanopore sequencing to identify transcriptionally active EVEs in the host genome.

Results
We found reads from two insect-specific viruses (a Flavivirus and an Ambidensovirus) in our RNAseq data, as well as a parasitoid virus (Bracovirus), a plant pathogenic virus (Tombusvirus), and two phages (Acinetobacter and APSE). However, our genome assembly showed that part of the ‘virome’ of this insect can be attributed to EVEs in the host genome.

Conclusion
Our work shows that EVEs have led to the misidentification of aphid viruses from RNAseq data, and we argue that this is a widespread challenge for the study of viral diversity in insects.
Investigation of milk microbiota of healthy and mastitic Sahiwal cattle
Authors: Salman Mian Muhammad , Nawaz Muhammad , Yaqub Tahir , Mushtaq Muhammad Hassan 
Published: October 2023

Abstract
Background
Sahiwal cattle is an indigenous cattle breed of Pakistan and mastitis is one of the major problems faced by Sahiwal cattle which hinders its production potential. The study was designed to investigate the milk microbiota of healthy and mastitic Sahiwal cattle as part of a multistep project to develop probiotics for the mitigation and control of mastitis. Milk samples of Sahiwal cattle (healthy clinical mastitis and subclinical mastitis) reared under similar husbandry and management practices were processed for 16S rRNA gene base metagenomics analysis.

Results
Results revealed that Proteobacteria were dominant in the healthy group and subclinical mastitis group (56.48% and 48.77%, respectively) as compared to the clinical mastitis group (2.68%). In contrast, Firmicutes were abundant in the clinical mastitis group (64%) as compared to the healthy and subclinical mastitis groups (15.87% and 38.98%, respectively). Dominant species assigned in the healthy group were Ignavibacterium album, Novosphingobium capsulatum, Akkermansia muciniphila and Lactobacillus fermentum.The clinical mastitis group was dominated by Streptococcus dysgalactiae and Corynebacterium bovis, while subclinical mastitis group included Lactobacillus fermentum and uncultured acidobacteriales and Akkermansia muciniphila as dominant species. Alpha diversity indices showed higher microbial diversity in the healthy group compared to the clinical and sub-clinical mastitis groups.

Conclusion
It is concluded that the milk microbiota of healthy sahiwal cattle has higher diversity and dominant taxa in the different groups may be used as signature microbes for mastitis susceptibility. Akkermansia muciniphila is one of candidate specie that was identified and may be used for development of probiotics.
Sex- and reproductive status-specific relationships between body composition and non-alcoholic fatty liver disease
Authors: Cao Yu-tian , Zhang Wen-hui , Lou Yan , Yan Qian-hua , Zhang Yu-juan , Qi Fang , Xiang Liu-lan , Lv Tian-su , Fang Zhu-yuan , Yu Jiang-yi , Zhou Xi-qiao 
Published: October 2023

AbstractBackgroundSex and reproductive status differences exist in both non-alcoholic fatty liver disease (NAFLD) and body composition. Our purpose was to investigate the relationship between body composition and the severity of liver steatosis and fibrosis in NAFLD in different sex and reproductive status populations.MethodsThis cross-sectional study included 880 patients (355 men, 417 pre-menopausal women, 108 post-menopausal women). Liver steatosis and fibrosis and body composition data were measured using FibroScan and a bioelectrical impedance body composition analyzer (BIA), respectively, and the following parameters were obtained: liver stiffness measurement (LSM), controlled attenuation parameter (CAP), waist circumference (WC), body mass index (BMI), percent body fat (PBF), visceral fat area (VFA), appendicular skeletal muscle mass (ASM), appendicular skeletal muscle mass index (ASMI), fat mass (FM), fat free mass (FFM), and FFM to FM ratio (FFM/FM). Multiple ordinal logistic regression (MOLR) was used to analyze the independent correlation between body composition indicators and liver steatosis grade and fibrosis stage in different sex and menopausal status populations.ResultsMen had higher WC, ASM, ASMI, FFM, and FFM/FM than pre- or post-menopausal women, while pre-menopausal women had higher PBF, VFA, and FM than the other two groups (p < 0.001). Besides, men had greater CAP and LSM values (p < 0.001). For MOLR, after adjusting for confounding factors, WC (OR, 1.07; 95% CI, 1.02–1.12; P = 0.011) and FFM/FM (OR, 0.52; 95% CI, 0.31–0.89; P = 0.017) in men and visceral obesity (OR, 4.16; 95% CI, 1.09–15.90; P = 0.037) in post-menopausal women were independently associated with liver steatosis grade. WC and visceral obesity were independently associated with liver fibrosis stage in men (OR, 1.05; 95% CI, 1.01–1.09, P = 0.013; OR, 3.92; 95% CI, 1.97–7.81; P < 0.001, respectively).ConclusionsIncreased WC and low FFM/FM in men and visceral obesity in post-menopausal women were independent correlates of more severe liver steatosis. In addition, increased WC and visceral obesity were independent correlates of worse liver fibrosis in men. These data support the sex- and reproductive status-specific management of NAFLD.