bluuebunny/crossref_metadata_2025_split huggingface dataset:
A deep learning method for predicting knee osteoarthritis radiographic progression from MRI
Authors: Schiratti Jean-Baptiste , Dubois Rémy , Herent Paul , Cahané David , Dachary Jocelyn , Clozel Thomas , Wainrib Gilles , Keime-Guibert Florence , Lalande Agnes , Pueyo Maria , Guillier Romain , Gabarroca Christine , Moingeon Philippe 
Published: October 2021

Abstract
Background
The identification of patients with knee osteoarthritis (OA) likely to progress rapidly in terms of structure is critical to facilitate the development of disease-modifying drugs.

Methods
Using 9280 knee magnetic resonance (MR) images (3268 patients) from the Osteoarthritis Initiative (OAI) database , we implemented a deep learning method to predict, from MR images and clinical variables including body mass index (BMI), further cartilage degradation measured by joint space narrowing at 12 months.

Results
Using COR IW TSE images, our classification model achieved a ROC AUC score of 65%. On a similar task, trained radiologists obtained a ROC AUC score of 58.7% highlighting the difficulty of the classification task. Additional analyses conducted in parallel to predict pain grade evaluated by the WOMAC pain index achieved a ROC AUC score of 72%. Attention maps provided evidence for distinct specific areas as being relevant in those two predictive models, including the medial joint space for JSN progression and the intra-articular space for pain prediction.

Conclusions
This feasibility study demonstrates the interest of deep learning applied to OA, with a potential to support even trained radiologists in the challenging task of identifying patients with a high-risk of disease progression.
Improving hospital-based point-of-care ultrasound cleaning practices using targeted interventions: a pre–post study
Authors: Van Kalsbeek Daniel , Enroth Karl , Lyden Elizabeth , Rupp Mark E. , Smith Christopher J. 
Published: October 2021

Abstract
Background
Point-of-care ultrasound (POCUS) devices are becoming more widely used in healthcare and have the potential to act as fomites. The objective of this project was to study the thoroughness of cleaning of POCUS machines before and after a quality improvement initiative. We designed a mixed-methods, pre/post study which took place over the course of one year at a university-affiliated health center. Cleaning rates of four ultrasound machines used by hospital medicine and critical care medicine services were evaluated using fluorescent marking. Interventions targeted physicians’ knowledge of best practices and improved access to cleaning supplies. Pre- and post-intervention cleaning rates were compared using a generalized linear model. The impact of the corona virus disease of 2019 (COVID-19) pandemic on baseline cleaning rates was also evaluated. Physicians’ attitudes and knowledge of cleaning practices were evaluated via unpaired pre/post surveys.

Results
There was significant improvement in thoroughness of cleaning following intervention (pre 0.62, SE 0.05; post 0.89, SE 0.07), p < 0.0001). There was no difference in baseline cleaning rates before (0.63, SE 0.09) and after (0.61, SE 0.1) the onset of the COVID-19 pandemic (p = 0.78). Post-intervention surveying found improved understanding of guideline-based cleaning practice, better performance on knowledge-based questions, and fewer reported barriers to machine cleaning.

Conclusion
Thoroughness of cleaning of POCUS machines can be improved with practical interventions that target knowledge and access to cleaning supplies.
Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA
Authors: Kerachian Mohammad Amin , Azghandi Marjan , Mozaffari-Jovin Sina , Thierry Alain R. 
Published: October 2021

AbstractMethylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
Atypical presentation of autoimmune hepatitis–primary sclerosing cholangitis overlap syndrome associated with hypereosinophilia: a case report and review of the literature
Authors: Hatami Behzad , Rahmani Seraji Hamide , fallahi Mohaddese 
Published: October 2021

AbstractBackgroundAutoimmune hepatitis–primary sclerosing cholangitis overlap syndrome is a form of autoimmune hepatitis with cholestatic features and is characterized by negative anti-mitochondrial antibody and cholangiographic changes on magnetic resonance cholangiopancreatography or endoscopic retrograde cholangiopancreatography. Peripheral blood hypereosinophilia in conjunction with autoimmune hepatitis–primary sclerosing cholangitis overlap syndrome has not been reported yet. Here we present a case of autoimmune hepatitis–primary sclerosing cholangitis overlap syndrome with hypereosinophilia.Case presentationA 33-year-old Iranian man with the fatigue, jaundice, elevated liver enzymes and alkaline phosphatase, and hypereosinophilia was referred to our hospital. Viral and autoimmune hepatitis were excluded, and secondary workups for hypereosinophilia were all negative. Magnetic resonance cholangiopancreatography showed beaded appearance of intra- and extrahepatic biliary tree, and liver biopsy revealed interface hepatitis. Therefore, the diagnosis of autoimmune hepatitis–primary sclerosing cholangitis overlap syndrome was made, and prednisolone, azathioprine, and ursodeoxycholic acid was initiated. His jaundice and peripheral blood eosinophilia resolved after 2 weeks, and he became completely asymptomatic.ConclusionEosinophils might contribute to the clinical presentation and disease complications.
Expression of cytokines in dairy cattle mammary gland parenchyma during chronic staphylococcal infection
Authors: Kawecka-Grochocka Ewelina , Zalewska Magdalena , Rzewuska Magdalena , Kościuczuk Ewa , Ząbek Tomasz , Sakowski Tomasz , Marczak Sylwester , Bagnicka Emilia 
Published: October 2021

AbstractThe study aim was to determine the expression of genes potentially related to chronic mastitis at the mRNA and protein levels, viz. chemokine C–C motif receptor 1 (CCR1), C–C motif chemokine ligand 2 (CCL2), C–C motif chemokine ligand 5 (CXCL5), tumor necrosis factor α (TNFα), interleukin 1β (IL-1β), interleukin 6 (IL-6), interleukin 8 (IL-8), interleukin 18 (IL-18), in bovine mammary gland parenchyma. The study examines the differences in expression of selected genes between cows with chronic mastitis caused by coagulase-positive (CoPS) or coagulase-negative staphylococci (CoNS) and those with healthy udders (H). Samples were collected from the udder quarters from 40 Polish Holstein–Friesian cows; 54 of these samples were chosen for analysis based on microbiological analysis of milk taken two days before slaughter. They were categorized into three groups: CoPS (N = 27), CoNS (N = 14) and H (N = 13). The RNA expression was analyzed by RT-qPCR and protein concentration by ELISA. No differences in the mRNA levels of seven genes (TNFα, IL-18, CCR1, IL-1β, CCL2, IL-8, IL-6) and four proteins (TNFα, IL-18, CCR1, IL-1β) were identified between the CoPS and H groups. Higher transcript levels of CXCL5 (p ≤ 0.05) gene were noted in CoPS than in H. Compared to H, higher concentrations of IL-8 and CXCL5 (p ≤ 0.05) were observed in CoPS (0.05 < p < 0.1) and CCL2 (0.05 < p < 0.1) in CoNS, while lower levels of Il-6 were found in CoPS. This may suggest that during chronic mastitis the organism stops producing pro-inflammatory cytokines, probably to protect the host tissues against their damage during prolonged infection.
Neuromedin B promotes chondrocyte differentiation of mesenchymal stromal cells via calcineurin and calcium signaling
Authors: Maumus Marie , Fonteneau Guillaume , Ruiz Maxime , Assou Said , Boukhaddaoui Hassan , Pastoureau Philippe , De Ceuninck Frédéric , Jorgensen Christian , Noel Danièle 
Published: October 2021

Abstract
Background
Articular cartilage is a complex tissue with poor healing capacities. Current approaches for cartilage repair based on mesenchymal stromal cells (MSCs) are often disappointing because of the lack of relevant differentiation factors that could drive MSC differentiation towards a stable mature chondrocyte phenotype.

Results
We used a large-scale transcriptomic approach to identify genes that are modulated at early stages of chondrogenic differentiation using the reference cartilage micropellet model. We identified several modulated genes and selected neuromedin B (NMB) as one of the early and transiently modulated genes. We found that the timely regulated increase of NMB was specific for chondrogenesis and not observed during osteogenesis or adipogenesis. Furthermore, NMB expression levels correlated with the differentiation capacity of MSCs and its inhibition resulted in impaired chondrogenic differentiation indicating that NMB is required for chondrogenesis. We further showed that NMB activated the calcineurin activity through a Ca2+-dependent signaling pathway.

Conclusion
NMB is a newly described chondroinductive bioactive factor that upregulates the key chondrogenic transcription factor Sox9 through the modulation of Ca2+ signaling pathway and calcineurin activity.

Graphical abstract
On discrete weighted Hardy type inequalities and properties of weighted discrete Muckenhoupt classes
Authors: Saker S. H. , Rabie S. S. , Agarwal R. P. 
Published: October 2021

AbstractIn this paper, first we prove some new refinements of discrete weighted inequalities with negative powers on finite intervals. Next, by employing these inequalities, we prove that the self-improving property (backward propagation property) of the weighted discrete Muckenhoupt classes holds. The main results give exact values of the limit exponents as well as the new constants of the new classes. As an application, we establish the self-improving property (forward propagation property) of the discrete Gehring class.
New version of fractional Simpson type inequalities for twice differentiable functions
Authors: Hezenci Fatih , Budak Hüseyin , Kara Hasan 
Published: October 2021

AbstractSimpson inequalities for differentiable convex functions and their fractional versions have been studied extensively. Simpson type inequalities for twice differentiable functions are also investigated. More precisely, Budak et al. established the first result on fractional Simpson inequality for twice differentiable functions. In the present article, we prove a new identity for twice differentiable functions. In addition to this, we establish several fractional Simpson type inequalities for functions whose second derivatives in absolute value are convex. This paper is a new version of fractional Simpson type inequalities for twice differentiable functions.
TREM2 modulates differential deposition of modified and non-modified Aβ species in extracellular plaques and intraneuronal deposits
Authors: Joshi Pranav , Riffel Florian , Kumar Sathish , Villacampa Nàdia , Theil Sandra , Parhizkar Samira , Haass Christian , Colonna Marco , Heneka Michael T. , Arzberger Thomas , Herms Jochen , Walter Jochen 
Published: October 2021

AbstractProgressive accumulation of Amyloid-β (Aβ) deposits in the brain is a characteristic neuropathological hallmark of Alzheimer’s disease (AD). During disease progression, extracellular Aβ plaques undergo specific changes in their composition by the sequential deposition of different modified Aβ species. Microglia are implicated in the restriction of amyloid deposits and play a major role in internalization and degradation of Aβ. Recent studies showed that rare variants of the Triggering Receptor Expressed on Myeloid cells 2 (TREM2) are associated with an increased risk for AD. Post-translational modifications of Aβ could modulate the interaction with TREM2, and the uptake by microglia. Here, we demonstrate that genetic deletion of TREM2 or expression of a disease associated TREM2 variant in mice lead to differential accumulation of modified and non-modified Aβ species in extracellular plaques and intraneuronal deposits. Human brains with rare TREM2 AD risk variants also showed altered deposition of modified Aβ species in the different brain lesions as compared to cases with the common variant of TREM2. These findings indicate that TREM2 plays a critical role in the development and the composition of Aβ deposits, not only in extracellular plaques, but also intraneuronally, that both could contribute to the pathogenesis of AD.
Clinical significance of lactate clearance in patients with cardiogenic shock: results from the RESCUE registry
Authors: Park Ik Hyun , Yang Jeong Hoon , Jang Woo Jin , Chun Woo Jung , Oh Ju Hyeon , Park Yong Hwan , Ko Young-Guk , Yu Cheol Woong , Kim Bum Sung , Kim Hyun-Joong , Lee Hyun Jong , Jeong Jin-Ok , Gwon Hyeon-Cheol 
Published: October 2021

AbstractBackgroundLimited data are available on the clinical significance of lactate clearance (LC) in patients with cardiogenic shock (CS). This study investigated the prognostic role of LC in CS patients.MethodsWe analyzed data from 628 patients in the RESCUE registry, a multicenter, observational cohort enrolled between January 2014 and December 2018. Univariable logistic regression analysis was performed to determine the prognostic implications of 24 h LC, and then patients were divided into two groups according to the cut-off value of 24 h LC (high lactate clearance [HLC] group vs. low lactate clearance [LLC] group). The primary outcome was in-hospital mortality. We also assessed all-cause mortality at 12 month follow-up and compared the prognostic performance of 24 h LC according to initial serum lactate level.ResultsIn the univariable logistic regression analysis, 24 h LC was associated with in-hospital mortality (odds ratio 0.989, 95% confidence interval [CI] 0.985–0.993,p < 0.001), and the cut-off value for the LC of the study population was 64%. The HLC group (initial 24 h LC ≥ 64%, n = 333) had a significantly lower incidence of in-hospital death than the LLC group (n = 295) (25.5% in the HLC group vs. 42.7% in the LLC group,p < 0.001). During 12 months of follow-up, the cumulative incidence of all-cause death was significantly lower in the HLC group than in the LLC group (33.0% vs. 48.8%; hazard ratio 0.55; 95% CI 0.42–0.70;p < 0.001). In subgroup analysis, 24 h LC predicted in-hospital mortality better in patients with initial serum lactate > 5 mmol/L than in those with serum lactate ≤ 5 mmol/L (c-statistics of initial serum lactate > 5 mmol/L = 0.782 vs. c-statistics of initial serum lactate ≤ 5 mmol/L = 0.660,p = 0.011).ConclusionsHigher LC during the early phase of CS was associated with reduced risk of in-hospital and 12 month all-cause mortalities. Patients with LC ≥ 64% during the 24 h after CS onset could expect a favorable prognosis, especially those with an initial serum lactate > 5 mmol/L.Trial registration:RESCUE (REtrospective and prospective observational Study to investigate Clinical oUtcomes and Efficacy of left ventricular assist device for Korean patients with cardiogenic shock), NCT02985008, Registered December 5, 2016—retrospectively and prospectively registered,https://clinicaltrials.gov/ct2/show/record/NCT02985008
Effects of dexamethasone on immune dysfunction and ventilator-associated pneumonia in COVID-19 acute respiratory distress syndrome: an observational study
Authors: Cour Martin , Simon Marie , Argaud Laurent , Monneret Guillaume , Venet Fabienne 
Published: October 2021

AbstractDexamethasone improves survival of patients with COVID-19 acute respiratory distress syndrome, but might shorten the delay between the start of invasive mechanical ventilation and the occurrence of ventilator-associated pneumonia, suggesting possible worsening of COVID-19-induced immune dysfunction with this treatment. In a prospective observational study, we found that mechanically ventilated patients with COVID-19 treated with dexamethasone presented earlier ventilator-associated pneumonia, had significantly lower monocyte Human Leukocyte Antigen-DR expression and number of circulating CD4 + cells after ICU admission, than those not treated with corticoids.
The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers
Authors: Wang Wen , Gao Xiaolong , Zheng Sisi , Lancuo Zhuoma , Li Ying , Zhu Lilin , Hou Jianping , Hai Jiayi , Long Xin , Chen Hanxi , Druzyaka Alexey , Sharshov Kirill 
Published: October 2021

Abstract
Background
Himalayan Griffons (Gyps himalayensis), large scavenging raptors widely distributed in Qinghai-Tibetan Plateau, have evolved a remarkable ability to feed on carcasses without suffering any adverse effects. The gut microbiome plays an important role in animal physiological and pathological processes, and has also been found to play a health protective role in the vulture adaptation to scavenging. However, the microbial taxonomic diversity (including nonculturable and culturable microbes), functions, and metabolites related to Himalayan Griffons have not been fully explored.

Methods
In the present study, the 28 fecal samples of the Himalayan Griffons and 8 carrion samples were collected and sequenced using high-throughput 16S rRNA gene sequencing methods to analyze the composition and functional structures of the microbiomes. Twelve fecal samples of the Himalayan Griffons were analyzed using untargeted Liquid Chromatography Mass Spectroscopy (LC–MS) to identify metabolites. We used different culture conditions to grow Himalayan Griffons gut microbes. Inhibitory effects of gut beneficial bacteria on 5 common pathogenic bacteria were also tested using the Oxford cup method.

Results
According to the results of the culture-independent method, a high abundance of four major phyla in Himalayan Griffons were identified, including Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria. The most abundant genera were Fusobacterium, followed by Clostridium_sensu_stricto_1, Cetobacterium, Epulopiscium, and Bacteroides. The predicted primary functional categories of the Himalayan Griffons’ gut microbiome were associated with carbohydrate and amino acid metabolism, replication and repair, and membrane transport. LC–MS metabolomic analysis showed a total of 154 metabolites in all the fecal samples. Cultivation yielded 184 bacterial isolates with Escherichia coli, Enterococcus faecium, Enterococcus hirae, and Paeniclostridium sordellii as most common isolates. Moreover, 7 potential beneficial gut bacteria isolated showed certain inhibition to 5 common pathogenic bacteria.

Conclusions
Our findings broaden and deepen the understanding of Himalayan Griffons’ gut microbiome, and highlighted the importance of gut microbiome-mediated adaptation to scavenging habits. In particular, our results highlighted the protective role of gut beneficial bacteria in the Himalayan Griffons against pathogenic bacteria that appear in rotten food resources.
Evaluation of bioactivity and phytochemical screening of endophytic fungi isolated from Ceriops decandra (Griff.) W. Theob, a mangrove plant in Bangladesh
Authors: Munshi Mita , Sohrab Md. Hossain , Begum Mst. Nadira , Rony Sattyajit Roy , Karim Md. Adnan , Afroz Farhana , Hasan Md. Nazmul 
Published: October 2021

Abstract
Background
Due to increasing number of individuals within the world having health issues caused by varied cancers, drug-resistant microorganism, parasitic protozoans, and fungi could be a cause for alarm. Endophyte’s are a unique source of medicinal compounds which requires an intensive seek for newer and simpler agents to handle these sickness issues is currently advancing. This study explores the description of endophytic fungi of Ceriops decandra (Griff.) W. Theob., a mangrove plant growing in mangrove forest, Sundarban, Bangladesh.

Methods
The endophytic fungi of experimental plants were identified by DNA amplification and sequencing of the internal transcribed spacer (ITS) region Moreover, cytotoxicity, antioxidant and antimicrobial tests were assessed. In addition, the screening of extracts was performed by visual detection using UV light.

Results
Three fungi namely CEDBE-1, CEDLE-6 and CEDLE-10 (internal strain no) were isolated as endophytic fungi and identified as Fusarium oxysporum, Clonostachys spp. and Fusarium solani respectively on the basis of morphological characteristics and DNA sequencing. The isolates were cultured at 280 C±2 for 21 days in Potato Dextrose Agar (PDA) media. The extracts of fungal isolates were examined at 100 µg/disc concentration for the screening of antibacterial activity and exhibited no activity against tested human pathogenic bacteria. The strain CEDBE-1 showed highest antioxidant activity of IC50 value of 31.07 µg/mL comparing with the positive control ascorbic acid (0.74) and BHA (7.79) µg/mL. All isolates exhibited strong cytotoxic activity using brine shrimp lethality bioassay compared with the positive control tamoxifen. Preliminary chemical screening of the fungal extracts by thin layer chromatography technique revealed the presence of various compounds.

Conclusions
The findings indicate that endophytic fungal isolates explored from C. decandra has diversified biological activities which may be potential source of leads for new drug development.
Depression among health workers caring for patients with COVID-19 in Egypt
Authors: Elgohary Hayam Mohamed , Sehlo Mohammad Gamal , Bassiony Medhat Mohamed , Youssef Usama Mahmoud , Elrafey Dina Sameh , Amin Shimaa Ibrahim 
Published: October 2021

Abstract
Background
Health care workers caring for patients with COVID-19 pandemic are prone to extraordinary stressors and psychological problems. The aim of this study was to estimate the prevalence and risk factors of major depressive disorder among health care providers who are caring for patients with COVID-19.

Methods
Two hundred-seventy of health care workers were screened for depressive symptoms by DASS-21 Questionnaire. Only 152 of the participants accepted to be interviewed using SCID-I for diagnosis of major depressive disorder.

Results
According to DASS-21, 28.1% of HCWs had mild-to-moderate depressive symptoms, and 64.8% with severe symptoms. Of 152 who were interviewed using SCID-I, 74.3% were diagnosed with major depression disorder.
Young age, decreased sleep hours, female sex, past history of a psychiatric disease, fear of COVID-19 infection for themselves or their relatives, and fear of death with COVID-19 for themselves or their relatives were significant predictors for major depressive disorder and its severity.

Conclusion
Major depressive disorder is common among HCWs during COVID-19 pandemic. Screening for depression, particularly for young females, and early treatment are recommended.