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EnrichDO: a global weighted model for Disease Ontology enrichment analysis
Biomedical ontologies organize biomedical findings into hierarchical structures and controlled vocabularies, which are human-readable and machine-computable. Biomedical ontologies have been widely studied and applied in biomedical research and clinical practice [1]. Gene Ontology (GO) is arguably the most successful example of a biomedical ontology.
Prevention of glucocorticoid-induced impairment of bone metabolism - a randomized, placebo-controlled, single Centre proof-of-concept clinical trial
Oral glucocorticoid (GC) therapy rapidly and deleteriously affects bone metabolism and blood glucose regulation. The gut microbiota regulates bone metabolism and a prior study found that Limosilactobacillus reuteri ATCC PTA6475 (L.reuteri) reduced bone loss over 12 months in older women. Mice treated either with broad-spectrum antibiotics or with L.reuteri did not experience GC-induced trabecular bone loss.
COBREXA 2: tidy and scalable construction of complex metabolic models
Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed models that utilize multiple kinds of constraint systems poses a significant coding overhead, complicating implementation of new types of analyses.
An integrated approach for the accurate detection of HERV-K HML-2 transcription and protein synthesis
Human endogenous retroviruses (HERVs) occupy a large portion (8%) of the host genome. They comprise thousands of elements, divided into 10 supergroups and 39 clades (1). Due to terminal recombination of the two nearly identical LTRs originally situated at the elements’ ends (2), the vast majority of HERVs have been reduced to solo LTRs, while only ca. 10% maintain full-length or near full-length status.
Epidemiology and pathogen characteristics of infections following solid organ transplantation
Solid organ transplantation (SOT) recipients have a heightened risk for infection due to prolonged immunosuppressive drug use following transplant procedures. The occurrence of post-transplant infections is influenced not only by the transplanted organ type but also by varied factors. The kidney is the most common organ in SOT, followed by the liver, heart, and lung.
Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network
Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce.
CELEBRIMBOR: Core and accessory genes from metagenomes
Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches.
Air monitoring by nanopore sequencing
The air microbiome encompasses a broad spectrum of bioaerosols, including bacteria, archaea, fungi, viruses, bacterial endotoxins, mycotoxins, and pollen [1].
Gut microbial signatures of patients with diarrhea-predominant irritable bowel syndrome and their healthy relatives
Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder, encompassing diarrhea-predominant irritable bowel syndrome (IBS-D). Here, we utilized 16S rDNA gene sequencing to identify potential microbial drivers of IBS-D. Thirty healthy relatives and 27 patients with IBS-D were recruited. Clinical data and fecal samples were collected from patients and controls. 16S rDNA gene sequencing was performed to obtain fecal bacterial data.
Metabolomics reveals the implication of acetoacetate and ketogenic diet therapy in radioiodine-refractory differentiated thyroid carcinoma
Thyroid carcinoma is the most common malignancy of the endocrine system and the ninth most common cancer.1 Differentiated thyroid carcinoma (DTC), including papillary thyroid carcinoma (PTC) and follicular thyroid carcinoma (FTC), are identified based on histopathological criteria and account for approximately 90% of thyroid malignancies.2 Patients with DTC have a favorable prognosis after surgery, postoperative radioiodine therapy, and thyroid stimulating hormone (TSH) inhibition therapy.3...
Automated Quantitative CD8+ Tumor-Infiltrating Lymphocytes and Tumor Mutation Burden as Independent Biomarkers in Melanoma Patients Receiving Front-Line Anti-PD-1 Immunotherapy
Programmed death 1 (PD-1) is a receptor expressed by activated T and B cells which binds to PD-L1 (B7-H1)1,2 and PD-L2 (B7-DC).3,4 PD-1 negatively regulates T-cell functions through the engagement of PD-L1, which is expressed by a wide variety of tissues.1-4 In tumors, tumor-antigen (TA)-specific CD8+ T cells exhibit a diminished capability to produce cytokines, proliferate and eliminate tumor cells in a progressive and hierarchical fashion.5-7 TA-specific T cells express PD-1 and other...
17-month longitudinal surface sampling study carried out on public transport vehicles operating in England during the COVID-19 pandemic identified low levels of SARS-CoV-2 RNA contamination | Journal of Applied Microbiology | Oxford Academic
To monitor severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA contamination in vehicles operating in England during the pandemic, to better understand transmission risk of SARS-CoV-2 on public transport. We collected 1 314 surface samples between December 2020 and April 2022 on trains and buses managed by five different transport operators. The presence of SARS-CoV-2 RNA was investigated through reverse transcription polymerase chain reaction (RT-PCR).
Storage, Disposal, and Use of Opioids Among Cancer Patients in Central China: A Multi-Center Cross-Sectional Study
Pain is a prevalent and excruciating symptom experienced by patients with cancer that significantly affects their overall quality of life. It is widely acknowledged that opioids play a crucial role in cancer pain management,1 and many cancer patients require long-term home use of opioid medications for pain relief. All opioids inherently carry varying degrees of risk of abuse and are strictly regulated by countries worldwide.
Five-Year Follow-Up of POLARIS-01 Phase II Trial: Toripalimab as Salvage Monotherapy in Chinese Patients With Advanced Melanoma
Anti-PD-1 immunotherapy, pembrolizumab, and toripalimab have been sequentially approved for patients with advanced melanoma refractory to standard therapy in China in 2018.
Two Hematological Markers Predicting the Efficacy and Prognosis of Neoadjuvant Chemotherapy Using Lobaplatin Against Triple-Negative Breast Cancer
Triple-negative breast cancer (TNBC) accounts for 10%-20% of all breast cancers.1 It has high recurrence and metastasis rates and has the worst prognosis among the known breast cancer subtypes.2 There are no clear treatment targets for this cancer, and the treatment options are limited. Currently, neoadjuvant therapy is the standard treatment for patients with early-stage TNBC who have lymph node-positive tumors or tumors that are >2 cm in size.
Treatment and Prognosis of Male Breast Cancer: A Multicentric, Retrospective Study Over 11 Years in the Czech Republic
Breast cancer (BC) is a frequent cancer type in females (female breast cancer, FBC), but male breast cancer (MBC) is very rare. However, the incidence of MBC has been increasing in recent years.1-3 The incidence of MBC in the Czech Republic is consistent with worldwide statistics. The number of new MBC cases was 1.33 per 100 000 in the period 2016-2020, an increase by 6.4% from the period 2011-2015, and has doubled over the past 30 years (0.7 per 100 000 in 1991-1995; Supplementary Table S1).
Discovery and timing of pulsar J2016+3711 in supernova remnant CTB 87 with FAST
Pulsar wind nebulae (PWNe), one of the most important components of supernova remnants (SNRs), are produced by the relativistic winds of rotation-powered neutron stars as they interact with the surroundings. None the less, only about 1 percent of the known pulsars are found to be directly associated with PWNe and SNRs (e.g. Lyne & Graham-Smith 2012).
Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier
Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya.
The prevalence of killer yeasts and double-stranded RNAs in the budding yeast Saccharomyces cerevisiae
Killer toxins are antifungal proteins produced by many species of “killer” yeasts, including the brewer's and baker's yeast Saccharomyces cerevisiae. Screening 1 270 strains of S. cerevisiae for killer toxin production found that 50% are killer yeasts, with a higher prevalence of yeasts isolated from human clinical samples and winemaking processes. Since many killer toxins are encoded by satellite dsRNAs associated with mycoviruses, S.
A Novel HRD Signature Is Predictive of FOLFIRINOX Benefit in Metastatic Pancreatic Cancer
Pancreatic cancer (PC) is the 4th leading cause of cancer-related death with a 5-year survival of only 11%.1 For patients with locally advanced or metastatic cancer, systemic chemotherapy is standard of care with FOLFIRINOX (leucovorin and fluorouracil plus irinotecan and oxaliplatin) and GP (gemcitabine and paclitaxel) both listed as preferred regimens in the NCCN guidelines for pancreatic adenocarcinoma.2 Clinical data suggests that patients treated with FOLFIRINOX may have modestly better...
Exploring the presence of markers of decidualisation in the fallopian tubes: a systematic review
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Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia
Abstract Human multipotent mesenchymal stromal/stem cells (MSCs) have been utilized in cell therapy for various diseases and their clinical applications are expected to increase in the future. However, the variation in MSC-based product quality due to the MSC heterogeneity has resulted in significant constraints in the clinical utility of MSCs. Therefore, we hypothesized that it might be important to identify and ensure/enrich suitable cell subpopulations for therapies using MSC-based products.
Hyperglycaemia in CF adversely affects BK channel function critical for mucus clearance
Charles D. Bengtson, Michael D. Kim, Abeer Anabtawi, Jianghua He, John S. Dennis, Sara Miller, Makoto Yoshida, Nathalie Baumlin, Matthias Salathe European Respiratory Journal 2020; DOI: 10.1183/13993003.00509-2020 Abstract Large-conductance, Ca2+-activated, voltage-dependent K+ (BK) channel function is critical for adequate airway hydration and mucociliary function. In airway epithelia, BK function is regulated by its γ subunit leucine-rich repeat-containing protein 26 (LRRC26).
Placebos in chronic pain: evidence, theory, ethics, and use in clinical practice
Education Placebos in chronic...
Novel airway smooth muscle-mast cell interactions and a role for the TRPV4-ATP axis in non-atopic asthma
Sara J. Bonvini, Mark A. Birrell, Eric Dubuis, John J. Adcock, Michael A. Wortley, Pauline Flajolet, Peter Bradding, Maria G. Belvisi European Respiratory Journal 2020 56: 1901458; DOI: 10.1183/13993003.01458-2019 Abstract Mast cell–airway smooth muscle (ASM) interactions play a major role in the immunoglobulin (Ig)E- dependent bronchoconstriction seen in asthma but less is known about IgE-independent mechanisms of mast cell activation.
Novel coronavirus infection in newborn babies aged <28 days in China
Zhi-Jiang Zhang, Xue-Jie Yu, Tao Fu, Yu Liu, Yan Jiang, Bing Xiang Yang, Yongyi Bi European Respiratory Journal 2020 55: 2000697; DOI: 10.1183/13993003.00697-2020 Abstract Neonates are susceptible to SARS-CoV-2 infection. The symptoms in neonates were milder and outcomes were less severe compared to adults. Intrauterine vertical transmission is not impossible but direct evidence is still lacking.
Successful Pseudomonas aeruginosa eradication improves outcomes after lung transplantation: a retrospective cohort analysis
Benedicte De Muynck, Anke Van Herck, Annelore Sacreas, Tobias Heigl, Janne Kaes, Arno Vanstapel, Stijn E. Verleden, Arne P. Neyrinck, Laurens J. Ceulemans, Dirk E. Van Raemdonck, Katrien Lagrou, Bart M. Vanaudenaerde, Geert M. Verleden, Robin Vos the Leuven Lung Transplant Group European Respiratory Journal 2020; DOI: 10.1183/13993003.01720-2020 Abstract Background Long-term survival after lung transplantation (LTx) is hampered by development of chronic lung allograft dysfunction (CLAD).
Association Between Ages and Clinical Characteristics and Outcomes of Coronavirus Disease 2019
Yang Liu, Bei Mao, Shuo Liang, Jia-wei Yang, Hai-wen Lu, Yan-hua Chai, Lan Wang, Li Zhang, Qiu-hong Li, Lan Zhao, Yan He, Xiao-long Gu, Xiao-bin Ji, Li Li, Zhi-jun Jie, Qiang Li, Xiang-yang Li, Hong-zhou Lu, Wen-hong Zhang, Yuan-lin Song, Jie-ming Qu, Jin-fu Xu on behalf of the Shanghai Clinical Treatment Experts Group for COVID-19 European Respiratory Journal 2020; DOI: 10.1183/13993003.01112-2020 Abstract Age significantly determined the clinical features and prognosis of the disease.
Novel Coronavirus Infection in Newborn Babies Under 28 Days in China
Zhi-Jiang Zhang, Xue-Jie Yu, Tao Fu, Yu Liu, Yan Jiang, Bing Xiang Yang, Yongyi Bi European Respiratory Journal 2020; DOI: 10.1183/13993003.00697-2020 Abstract Previous studies described the clinical features of Covid-19 in adults and infants under 1 year of age. Little is known about features, outcomes and intrauterine transmission potential in newborn babies aged 28 days or less. Through systematical searching, we identified 4 infections in newborn babies in China as of March 13.
Diagnostic sensitivity of SILVAMP TB-LAM (FujiLAM) point-of-care urine assay for extra-pulmonary tuberculosis in people living with HIV
Andrew D. Kerkhoff, Bianca Sossen, Charlotte Schutz, Elena Ivanova Reipold, Andre Trollip, Emmanuel Moreau, Samuel G. Schumacher, Rosie Burton, Amy Ward, Mark P. Nicol, Graeme Meintjes, Claudia M.
Effects of suboptimal adherence of CPAP-therapy on symptoms of obstructive sleep apnea: a randomised, double-blind, controlled trial
Thomas Gaisl, Protazy Rejmer, Sira Thiel, Sarah R. Haile, Martin Osswald, Malgorzata Roos, Konrad E. Bloch, John R. Stradling, Malcolm Kohler European Respiratory Journal 2019; DOI: 10.1183/13993003.01526-2019 Abstract Introduction Continuous positive airway pressure (CPAP) is currently the treatment of choice for sleepiness in patients with obstructive sleep apnea (OSA), however, adherence is often thought to be suboptimal.
Distinct effects of ruxolitinib and interferon-alpha on murine JAK2V617F myeloproliferative neoplasm hematopoietic stem cell populations
Abstract JAK2V617F is the most common mutation in patients with BCR-ABL negative myeloproliferative neoplasms (MPNs). The eradication of JAK2V617F hematopoietic stem cells (HSCs) is critical for achieving molecular remissions and cure. We investigate the distinct effects of two therapies, ruxolitinib (JAK1/2 inhibitor) and interferon-alpha (IFN-α), on the disease-initiating HSC population.
Diagnostic sensitivity of SILVAMP TB-LAM (FujiLAM) point-of-care urine assay for extra-pulmonary tuberculosis in people living with HIV
Andrew D. Kerkhoff, Bianca Sossen, Charlotte Schutz, Elena Ivanova Reipold, Andre Trollip, Emmanuel Moreau, Samuel G. Schumacher, Rosie Burton, Amy Ward, Mark P. Nicol, Graeme Meintjes, Claudia M. Denkinger, Tobias Broger European Respiratory Journal 2019; DOI: 10.1183/13993003.01259-2019 Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team.
Targeting TMEM16A to reverse vasoconstriction and remodelling in idiopathic pulmonary arterial hypertension
Rita Papp, Chandran Nagaraj, Diana Zabini, Bence M. Nagy, Miklós Lengyel, Davor Skofic Maurer, Neha Sharma, Bakytbek Egemnazarov, Gabor Kovacs, Grazyna Kwapiszewska, Leigh M. Marsh, Andelko Hrzenjak, Gerald Höfler, Miroslava Didiasova, Malgorzata Wygrecka, Laura K.
Targeting TMEM16A to reverse vasoconstriction and remodelling in idiopathic PAH
Rita Papp, Chandran Nagaraj, Diana Zabini, Bence M. Nagy, Miklós Lengyel, Davor Skofic Maurer, Neha Sharma, Bakytbek Egemnazarov, Gabor Kovacs, Grazyna Kwapiszewska, Leigh M.
Contribution of specific diseases and injuries to changes in health adjusted life expectancy in 187 countries from 1990 to 2013: retrospective observational study
Research Contribution of...
Familial colorectal cancer risk in half siblings and siblings: nationwide cohort study
Research Familial colorectal...
Pulmonary rehabilitation is effective in patients with tuberculosis pulmonary sequelae
Dina Visca, Elisabetta Zampogna, Giovanni Sotgiu, Rosella Centis, Laura Saderi, Lia D'Ambrosio, Valentina Pegoraro, Patrizia Pignatti, Marcela Muňoz-Torrico, Giovanni Battista Migliori, Antonio Spanevello European Respiratory Journal 2019 53: 1802184; DOI: 10.1183/13993003.02184-2018 Abstract The majority of patients completing anti-tuberculosis treatment have sequelae and benefit from pulmonary rehabilitation http://ow.ly/WyOH30nFQLV Acknowledgements This article belongs to the scientific...
Effects of short-term continuous positive airway pressure withdrawal on cerebral vascular reactivity measured by blood oxygen level-dependent magnetic resonance imaging in obstructive sleep apnoea: a randomised controlled trial
Sira Thiel, Franziska Lettau, Protazy Rejmer, Cristina Rossi, Sarah R. Haile, Esther I. Schwarz, Anna S. Stöberl, Noriane A. Sievi, Andreas Boss, Anton S. Becker, Sebastian Winklhofer, John R. Stradling, Malcolm Kohler European Respiratory Journal 2019 53: 1801854; DOI: 10.1183/13993003.01854-2018 Abstract Impaired cerebral vascular reactivity (CVR) increases long-term stroke risk. Obstructive sleep apnoea (OSA) is associated with peripheral vascular dysfunction and vascular events.
A guide to systematic review and meta-analysis of prognostic factor studies
Research A guide to systematic...
Effects of short-term CPAP withdrawal on cerebral vascular reactivity measured by BOLD MRI in OSA: a randomised controlled trial
Abstract Introduction: Impaired cerebral vascular reactivity (CVR) increases long-term stroke risk. Obstructive sleep apnoea (OSA) is associated with peripheral vascular dysfunction and vascular events. The aim of this trial was to evaluate the effect of continuous positive airway pressure (CPAP) withdrawal on CVR. Methods: 41 OSA patients (88% male, mean age 57±10 yrs.) were randomised to subtherapeutic, or continuation of therapeutic, CPAP.
ERS/ECDC Statement: European Union standards for tuberculosis care, 2017 update
AbstractThe International Standards for Tuberculosis Care define the essential level of care for managing patients who have or are presumed to have tuberculosis, or are at increased risk of developing the disease. The resources and capacity in the European Union (EU) and the European Economic Area permit higher standards of care to secure quality and timely TB diagnosis, prevention and treatment.
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