Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of influenza vaccination in patients with asthma

BACKGROUND: Although annual influenza vaccination is recommended for persons with asthma, its effectiveness in this patient population is not well described. We evaluated the effect of influenza vaccination in the current and previous seasons in preventing influenza among people with asthma. METHODS: Using population health data from the Navarre region of Spain for the 2015/16 to 2019/20 influenza seasons, we conducted a test-negative case–control study to assess the effect of influenza vaccination in the current and 5 previous seasons. From patients presenting to hospitals and primary health care centres with influenza-like illness who underwent testing for influenza, we estimated the effects of influenza vaccination among patients with asthma overall and between those presenting as inpatients or outpatients, as well as between patients with and without asthma. RESULTS: Of 1032 patients who had asthma and were tested, we confirmed that 421 had influenza and the remaining 611 were test-negative controls. We found that the average effect of influenza vaccination was 43% (adjusted odds ratio [OR] 0.57, 95% confidence interval [CI] 0.40 to 0.80) for current-season vaccination regardless of previous doses, and 38% (adjusted OR 0.62, 95% CI 0.39 to 0.96) for vaccination in previous seasons only. Effects were similar for outpatients and inpatients. Among patients with asthma and confirmed influenza, current-season vaccination did not reduce the odds of hospital admission (adjusted OR 1.05, 95% CI 0.51 to 2.18). Influenza vaccination effects were similar for patients with and without asthma. INTERPRETATION: We estimated that, on average, current or previous influenza vaccination of people with asthma prevented almost half of influenza cases. These results support recommendations that people with asthma receive influenza vaccination.
Long covid—mechanisms, risk factors, and management

Abstract Since its emergence in Wuhan, China, covid-19 has spread and had a profound effect on the lives and health of people around the globe. As of 4 July 2021, more than 183 million confirmed cases of covid-19 had been recorded worldwide, and 3.97 million deaths. Recent evidence has shown that a range of persistent symptoms can remain long after the acute SARS-CoV-2 infection, and this condition is now coined long covid by recognized research institutes. Studies have shown that long covid can affect the whole spectrum of people with covid-19, from those with very mild acute disease to the most severe forms. Like acute covid-19, long covid can involve multiple organs and can affect many systems including, but not limited to, the respiratory, cardiovascular, neurological, gastrointestinal, and musculoskeletal systems. The symptoms of long covid include fatigue, dyspnea, cardiac abnormalities, cognitive impairment, sleep disturbances, symptoms of post-traumatic stress disorder, muscle pain, concentration problems, and headache. This review summarizes studies of the long term effects of covid-19 in hospitalized and non-hospitalized patients and describes the persistent symptoms they endure. Risk factors for acute covid-19 and long covid and possible therapeutic options are also discussed.
Integrating Phylogenetic Biomarker Data and Qualitative Approaches: An Example of HIV Transmission Clusters as a Sampling Frame for Semistructured Interviews and Implications for the COVID-19 Era

Mixed methods studies of human disease that combine surveillance, biomarker, and qualitative data can help elucidate what drives epidemiological trends. Viral genetic data are rarely coupled with other types of data due to legal and ethical concerns about patient privacy. We developed a novel approach to integrate phylogenetic and qualitative methods in order to better target HIV prevention efforts. The overall aim of our mixed methods study was to characterize HIV transmission clusters. We combined surveillance data with HIV genomic data to identify cases whose viruses share enough similarities to suggest a recent common source of infection or participation in linked transmission chains. Cases were recruited through a multi-phase process to obtain consent for recruitment to semi-structured interviews. Through linkage of viral genetic sequences with epidemiological data, we identified individuals in large transmission clusters, which then served as a sampling frame for the interviews. In this article, we describe the multi-phase process and the limitations and challenges encountered. Our approach contributes to the mixed methods research field by demonstrating that phylogenetic analysis and surveillance data can be harnessed to generate a sampling frame for subsequent qualitative data collection, using an explanatory sequential design. The process we developed also respected protections of patient confidentiality. The novel method we devised may offer an opportunity to implement a sampling frame that allows for the recruitment and interview of individuals in high-transmission clusters to better understand what contributes to spread of other infectious diseases, including COVID-19.
A framework for achieving sustainability by overcoming the challenges of the construction supply chain during the design process

Abstract This paper aims to develop a framework to achieve sustainability by overcoming the challenges of the construction supply chain (CCSC) during the design process. To achieve this, two approaches, namely theoretical and practical, were used to accomplish four objectives. For the theoretical approach, based on literature review and case studies, the objective used was to identify, classify and validate the challenges that the construction supply chain (CSC) encounter. For the practical approach, a survey questionnaire was employed to quantify the CCSC and investigate the perception of architectural design firms (ADFs) in Egypt towards achieving sustainability by overcoming the CCSC during the design process. Based on the results, the research developed a framework to overcome the CCSC as an approach towards achieving sustainability in construction projects during the design process. The research identified and validated 20 challenges that the CSC encounter towards achieving sustainability during the design process. These challenges were classified under four categories, namely (1) design and technical process; (2) coordination, information flow and accuracy; (3) material specification, technology, supplier rework and whole life cycle cost; and (4) skills gap of the qualified architects and design managers and non-compliance to building codes, regulations, laws and standards. In addition, a survey questionnaire was employed to rank these challenges according to their importance on 1–5 Likert scale using the measure of central tendency and dispersion and relative importance index (RII).
Suicide among Ugandan university students: evidence from media reports for 2010–2020

University students are in transition to adulthood and face multiple challenges that may lead to suicide. They are reported to have a higher risk of suicide by the World Health Organization. As there is no national suicide database in Uganda, we analysed student suicide using the press/media reports of suicides published between 2010 and 2020. A total of deaths by 23 suicide were identified: 19 were males, relationship problems were the main suicide reason (n = 6) and hanging was the most frequently used suicide method (n = 7). A strategic intervention to tackle suicide risk among university students is warranted.
Testing the accuracy of 3D automatic landmarking via genome-wide association studies

Background Various advances in 3D automatic phenotyping and particularly in landmark-based geometric morphometric methods have been made, but only a few studies have tested the reliability of such automatic procedures in morphometric analyses. It is generally accepted that automatic landmarking compromises the capture of the actual biological variation, and this not only affects its performance to effectively detect differences among sample means but also the structure of covariance matrices. However, no studies have directly tested the actual impact of such landmarking approaches in analyses requiring a large number of specimens and for which the precision of phenotyping is crucial to capture an actual biological signal adequately. Results Here, we use a recently developed 3D atlas-based automatic landmarking method to test its accuracy in detecting QTLs associated with craniofacial development of the house mouse skull and lower jaws for a large number of specimens (circa 700) that were previously phenotyped via a semiautomatic landmarking method complemented with manual adjustment. We compare both landmarking methods with univariate and multivariate mapping of the skull and the lower jaws. In the univariate mapping, the automatic approach failed to recover the same SNPs and found only 1 out of 17 previously identified QTLs for the skull, but found one new QTL. Similarly, for the lower jaws, the automatic approach failed to recover the same SNPs but found 2 neighbouring SNPs for 1 out of 8 previously identified QTLs. For centroid size, the same general results were recovered by the automatic method for both the skull and lower jaws, with the same peak SNP being found for the lower jaws. In the multivariate mapping, the automatic approach did not detect the same markers nor QTLs having their regions overlapping with the ones identified with the semi-automatic procedure for the skull, while the same marker, which is also the peak SNP and sole QTL, was recovered by the automatic pipeline for lower jaws. Conclusion Our results confirm the notion that information is lost in the automated landmarking procedure but somewhat dependent on the analyzed structure. The automatic method seems to capture certain types of structures slightly better, such as lower jaws whose shape is almost entirely summarized by its outline and could be assimilated as a 2D flat object. By contrast, the more apparent 3D features exhibited by a structure such as the skull are not adequately captured by the automatic method. We conclude that using 3D atlas-based automatic landmarking methods requires careful consideration of the experimental question and the cautious interpretation of their results.
GM1 mediates the formation and maintenance of cytotoxic Aβ oligomers

The aggregation of amyloid beta (Aβ) peptide is associated with Alzheimer’s disease (AD) pathogenesis. Cell membrane composition, especially monosialotetrahexosylganglioside (GM1), is known to promote the formation of Aβ fibrils, yet little is known about the roles of GM1 in the early steps of Aβ oligomer formation. Here, by using GM1-contained liposomes as a mimic of neuronal cell membrane, we demonstrate that GM1 is a critical trigger of Aβ oligomerization and aggregation. We find that GM1 not only promotes the formation of Aβ fibrils, but also facilitates the maintenance of Aβ oligomers on liposome membranes. We structurally characterize the Aβ oligomers formed on the membrane and find that GM1 captures Aβ by binding to its arginine-5 residue. To interrogate the mechanism of Aβ oligomer toxicity, we design a new liposome-based Ca2+-encapsulation assay and provide new evidence for the Aβ ion channel hypothesis. Finally, we conduct cell viability assay to determine the toxicity of Aβ oligomers formed on membranes. Overall, by uncovering the roles of GM1 in mediating early Aβ oligomer formation and maintenance, our work provides a novel direction for pharmaceutical research for AD.
Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer

Although cancer immunotherapy with PD-(L)1 blockade is now routine treatment for patients with lung cancer, remarkably little is known about acquired resistance. We examined 1,201 patients with NSCLC treated with PD-(L)1 blockade to clinically characterize acquired resistance, finding it to be common (occurring in more than 60% of initial responders), with persistent but diminishing risk over time, and with distinct metastatic and survival patterns compared to primary resistance. To examine the molecular phenotype and potential mechanisms of acquired resistance, we performed whole transcriptome and exome tumor profiling in a subset of NSCLC patients (n=29) with acquired resistance. Systematic immunogenomic analysis revealed that tumors with acquired resistance generally had enriched signals of inflammation (including IFNγ signaling and inferred CD8+ T cells) and could be separated into IFNγ upregulated and stable subsets. IFNγ upregulated tumors had putative routes of resistance with signatures of dysfunctional interferon signaling and mutations in antigen presentation genes. Transcriptomic profiling of cancer cells from a murine model of acquired resistance to PD-(L)1 blockade also showed evidence of dysfunctional interferon signaling and acquired insensitivity to in vitro interferon gamma treatment. In summary, we characterized clinical and molecular features of acquired resistance to PD-(L)1 blockade in NSCLC and found evidence of ongoing but dysfunctional IFN response. The persistently inflamed, rather than excluded or deserted, tumor microenvironment of acquired resistance informs therapeutic strategies to effectively reprogram and reverse acquired resistance.
Structure insights, thermodynamic profiles, dsDNA melting activity, and liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid N-terminal domain binding to DNA

The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD), either with or without the SR-rich motif (SR), upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on specificity for N-NTD/N-NTD-SR interaction with TRS, including an unfavorable energetic contribution to binding along with hydrogen bonds between the triple-thymidine (TTT) motif in the dsTRS and β-sheet II due to the defined position and orientation of the DNA duplex, a well-defined pattern (ΔH > 0 and ΔS > 0 for ssTRS, and ΔH < 0 and ΔS < 0 for dsTRS) for the thermodynamic profile of binding, and a preference for TRS in the formation of liquid condensates when compared to a non-specific sequence. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity.
Gammaherpesvirus infection licenses age-associated B cells for pathogenicity in MS and EAE

While age-associated B cells (ABCs) are known to expand and persist following viral infection and during autoimmunity, their interactions are yet to be studied together in these contexts. Epstein-Barr virus (EBV) infection has long been implicated in multiple sclerosis (MS), and it is not known whether ABCs could play a role in mediating viral contribution to autoimmunity. Here, we show that the circulating ABC population is expanded in people with MS and that EBV infection and MS status differentially impact the circulating ABC phenotype. We then directly compared ABCs during viral infection and autoimmunity using mouse models of EBV, gammaherpesvirus 68 (γHV68), and MS, experimental autoimmune encephalomyelitis (EAE). We observed that splenic ABCs are expanded in a sex-biased manner during both latent virus infection and EAE, and each event drives the ABC population to opposing phenotypes. We have previously shown that latent γHV68 infection exacerbates EAE and here we show that mice lacking ABCs fail to display γHV68-enhanced disease. Collectively, these findings indicate that latent viral infection and central nervous system autoimmunity differentially impact the ABC population and suggests that viral infections such as EBV prime ABCs to contribute pathogenically in MS.
Research Update: Strain and composition effects on ferromagnetism of Mn0.05Ge0.95 quantum dots

Mn0.05Ge0. 95 quantum dots (QDs) samples were grown by molecular beam epitaxy on Si substrates and 15-nm-thick fully strained Si0.8Ge0. 2 virtual substrates, respectively. The QDs samples grown on the Si0.8Ge0. 2 virtual substrates show a significant ferromagnetism with a Curie temperature of 227 K, while the QDs samples grown on the Si substrates are non-ferromagnetic. Microstructures of the QDs samples were characterized by high resolution transmission electron microscopy and synchrotron radiation X-ray diffraction. Interdependence between microstructure and ferromagnetism of Mn-doped Ge QDs was investigated. For the QDs sample grown on the strained Si0.8Ge0. 2 virtual substrate, although the ferromagnetic phase Mn5Ge3 clusters were found to be formed in small dome-shaped dots, the significant ferromagnetism observed in that sample is attributed to ferromagnetic phase Mn-doped large dome-shaped Ge QDs, rather than to the ferromagnetic phase Mn5Ge3 clusters. The fully strained Si0.8Ge0. 2 virtual substrates w.
MERTK on mononuclear phagocytes regulates T cell antigen recognition at autoimmune and tumor sites

Understanding mechanisms of immune regulation is key to developing immunotherapies for autoimmunity and cancer. We examined the role of mononuclear phagocytes during peripheral T cell regulation in type 1 diabetes and melanoma. MERTK expression and activity in mononuclear phagocytes in the pancreatic islets, promoted islet T cell regulation, resulting in reduced sensitivity of T cell scanning for cognate antigen in pre-diabetic islets. MERTK-dependent regulation led to reduced T cell activation and effector function at the disease site in the islets and prevented rapid progression of type 1 diabetes. In human islets, MERTK-expressing cells were increased in remaining insulin-containing islets of type 1 diabetic patients, suggesting that MERTK protects the islets from autoimmune destruction. MERTK also regulated T cell arrest in melanoma tumors. These data indicate that MERTK signaling in mononuclear phagocytes drives T cell regulation at inflammatory disease sites in peripheral tissues through a mechanism that reduces the sensitivity of scanning for antigen leading to reduced responsiveness to antigen.
Efficacy and Safety of Remimazolam in Endoscopic Sedation—A Systematic Review and Meta-Analysis

Background: The aim of this systematic review and meta-analysis was to investigate the efficacy and safety of remimazolam in clinical endoscopic procedure sedation. Methods: The authors searched the databases of PubMed, Embase, and Cochrane Library for studies published until January 2, 2021, that reported remimazolam sedation for endoscopic procedures. The sedative efficiency and the incidence of adverse events were assessed as outcomes. Cochrane Review Manager Software 5.3 was used to perform the statistical analyses. Results: Seven relevant studies involving a total of 1,996 patients were identified. We conducted a meta-analysis of the different controls used in the studies, that is, the placebo, midazolam, and propofol. The results demonstrated that remimazolam had a strong sedative effect, and its sedative efficiency was significantly higher than that of placebo [OR = 0.01, 95% CI: (0.00, 0.10), I2 = 30%, p <0.00001]. The sedative efficiency of remimazolam was significantly higher than that of midazolam [OR = 0.12, 95% CI: (0.08, 0.21), I2 = 0%, p < 0.00001] but lesser than that of propofol [OR = 12.22, 95% CI: (1.58, 94.47), I2 = 0%, p = 0.02]. Regarding the adverse events, remimazolam is associated with a lower incidence of hypotension than placebo and midazolam. Similarly, remimazolam was associated with a lower incidence of hypotension and hypoxemia than propofol. Conclusions: Remimazolam is a safe and effective sedative for patients undergoing endoscopic procedures. The sedative efficiency of remimazolam was significantly higher than that of midazolam but slightly lower than that of propofol. However, the respiration and circulation inhibitory effects of remimazolam were weaker than those of midazolam and propofol.
BCR Affinity Influences T-B Interactions and B Cell Development in Secondary Lymphoid Organs

B cells produce high-affinity immunoglobulins (Igs), or antibodies, to eliminate foreign pathogens. Mature, naïve B cells expressing an antigen-specific cell surface Ig, or B cell receptor (BCR), are directed toward either an extrafollicular (EF) or germinal center (GC) response upon antigen binding. B cell interactions with CD4+ pre-T follicular helper (pre-Tfh) cells at the T-B border and effector Tfh cells in the B cell follicle and GC control B cell development in response to antigen. Here, we review recent studies demonstrating the role of B cell receptor (BCR) affinity in modulating T-B interactions and the subsequent differentiation of B cells in the EF and GC response. Overall, these studies demonstrate that B cells expressing high affinity BCRs preferentially differentiate into antibody secreting cells (ASCs) while those expressing low affinity BCRs undergo further affinity maturation or differentiate into memory B cells (MBCs).
Soil Characteristics and Hydromorphological Patterns Control Denitrification at the Floodplain Scale

Nitrate pollution in aquatic ecosystems is still a major problem in Germany. There is a great potential to permanently remove nitrate from aquatic systems through denitrification as a relevant ecosystem function. However, the controlling factors and the dimension of the denitrification potential are still not fully understood due to the high complexity of the process. This study presents the combined assessment of potential soil denitrification rates, physical and chemical soil parameters, and hydrological parameters from six floodplains of four large German rivers, namely the Rhine, the Elbe, the Weser, and the Main. Based on multivariate statistics, results show that the denitrification potential of soil was almost solely controlled by soil pH. The lab assays showed mean soil denitrification potentials of 6.4–11.4 mg N m−2 h−1 (pH < 7) and 23.0–30.5 mg N m−2 h−1 (pH > 7). We contend that when upscaling these estimates to annual rates of potential denitrification, the duration of average inundation should be incorporated, as this accounts for water saturation and nutrient supply − the major controlling variables for denitrification. Results provide evidence that the denitrification potential can only be fully exploited in frequently inundated floodplains. Thus, despite favorable soil conditions for denitrification, floodplains that have suffered from anthropogenic impacts, lose their importance in nitrate removal for the river system. We conclude that pH and lateral hydrological connectivity are likely to be key factors that should be considered when estimating denitrification as an ecosystem function.