Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep convolutional neural network recovers pure absorbance spectra from highly scatter‐distorted spectra of cells

Infrared spectroscopy of cells and tissues is prone to Mie scattering distortions, which grossly obscure the relevant chemical signals. The state‐of‐the‐art Mie extinction extended multiplicative signal correction (ME‐EMSC) algorithm is a powerful tool for the recovery of pure absorbance spectra from highly scatter‐distorted spectra. However, the algorithm is computationally expensive and the correction of large infrared imaging datasets requires weeks of computations. In this paper, we present a deep convolutional descattering autoencoder (DSAE) which was trained on a set of ME‐EMSC corrected infrared spectra and which can massively reduce the computation time for scatter correction. Since the raw spectra showed large variability in chemical features, different reference spectra matching the chemical signals of the spectra were used to initialize the ME‐EMSC algorithm, which is beneficial for the quality of the correction and the speed of the algorithm. One DSAE was trained on the spectra, which were corrected with different reference spectra and validated on independent test data. The DSAE outperformed the ME‐EMSC correction in terms of speed, robustness, and noise levels. We confirm that the same chemical information is contained in the DSAE corrected spectra as in the spectra corrected with ME‐EMSC.
Impact of smoking on coronavirus disease 19 severity

not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jmv.26456. This article is protected by copyright. All rights reserved. A cc ep te d A rt ic le Rohin Reddy ORCID iD: 0000-0002-4726-157X Impact of smoking on COVID-19 severity. Rohin K. Reddy, Walton N. Charles, Alexandros Sklavounos, Paul T. Seed and Ankur Khajuria Department of Surgery and Cancer, Imperial College London, United Kingdom Department of Women and Children’s Health, King’s College London, United Kingdom
Criteria Used for the Diagnosis of Myofascial Trigger Points in Clinical Trials on Physical Therapy

Supplemental Digital Content is available in the text. Objective: The objective of this study was to conduct an updated systematic review of diagnostic criteria for myofascial trigger points (MTrPs) used in clinical trials of physical therapy interventions from 2007 to 2019. Methods: MEDLINE and Physiotherapy Evidence Database (PEDro) were searched using the following MeSH keywords: “trigger points,” “trigger point,” “myofascial trigger point,” “myofascial trigger points,” “myofascial pain,” and “myofascial pain syndrome. ” The MeSH keywords were combined by using Boolean operators “OR”/“AND. ” All physiotherapy clinical trials including patients with musculoskeletal conditions characterized by at least 1 active MTrP or latent MTrP in any body area were selected. We pooled data from an individual criterion and criteria combinations used to diagnose MTrPs. The protocol was developed in accordance with the PRISMA-P guidelines. Results: Of 478 possibly relevant publications, 198 met the inclusion criteria. Of these 198 studies, 129 studies (65.1%) stated specifically the diagnostic criteria used for MTrPs in the main text, 56 studies (28.3%) failed to report any method whereby MTrP was diagnosed, and 13 studies (6.6%) adopted expert-based definitions for MTrPs without specification. Of 129 studies, the 6 criteria applied most commonly were: “spot tenderness” (n=125, 96.9%), “referred pain” (95, 73.6%), “local twitch response” (63, 48.8%), pain recognition (59, 45.7%), limited range of motion” (29, 22.5%), and “jump sign” (10, 7.8%). Twenty-three combinations of diagnostic criteria were identified. The most frequently used combination was “spot tenderness,” “referred pain,” and “local twitch response” (n=28 studies, 22%). Conclusions: A number of the included studies failed in properly reporting the MTrP diagnostic criteria. Moreover, high variability in the use of MTrP diagnostic was also observed. Spot tenderness, referred pain, and local twitch response were the 3 most popular criteria (and the most frequently used combination). A lack of transparency in the reporting of MTrP diagnostic criteria is present in the literature. Registry: This systematic review was registered under the Centre for Reviews and Dissemination, PROSPERO number: CRD42018087420.
Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-Flavor Baijiu Fermentation

The metabolism and accumulation of flavor compounds in Chinese Baijiu are driven by microbiota succession and their inter-related metabolic processes. Changes in the microbiome composition during Baijiu production have been examined previously; however, the respective metabolic functions remain unclear. Using shotgun metagenomic sequencing and metabolomics, we examined the microbial and metabolic characteristics during light-flavor Baijiu fermentation to assess the correlations between microorganisms and their potential functions. During fermentation, the bacterial abundance increased from 58.2% to 97.65%, and fermentation resulted in the accumulation of various metabolites, among which alcohols and esters were the most abundant. Correlation analyses revealed that the levels of major metabolites were positively correlated with bacterial abundance but negatively with that of fungi. Gene annotation showed that the Lactobacillus species contained key enzyme genes for carbohydrate metabolism and contributed to the entire fermentation process. Lichtheimia ramosa, Saccharomycopsis fibuligera, Bacillus licheniformis, Saccharomyces cerevisiae, and Pichia kudriavzevii play major roles in starch degradation and ethanol production. A link was established between the composition and metabolic functions of the microbiota involved in Baijiu fermentation, which helps elucidate microbial and metabolic patterns of fermentation and provides insights into the potential optimization of Baijiu production.
Impact of Viral Lysis on the Composition of Bacterial Communities and Dissolved Organic Matter in Deep-Sea Sediments

Viral lysis is a main mortality factor for bacteria in deep-sea sediments, leading to changing microbial community structures and the release of cellular components to the environment. Nature and fate of these compounds and the role of viruses for microbial diversity is largely unknown. We investigated the effect of viruses on the composition of bacterial communities and the pool of dissolved organic matter (DOM) by setting up virus-induction experiments using mitomycin C with sediments from the seafloor of the Bering Sea. At the sediment surface, no substantial prophage induction was detected, while incubations from 20 cm below seafloor showed a doubling of the virus-to-cell ratio. Ultra-high resolution mass spectrometry revealed an imprint of cell lysis on the molecular composition of DOM, showing an increase of molecular formulas typical for common biomolecules. More than 50% of these compounds were removed or transformed during incubation. The remaining material potentially contributed to the pool of refractory DOM. Next generation sequencing of the bacterial communities from the induction experiment showed a stable composition over time. In contrast, in the non-treated controls the abundance of dominant taxa (e.g., Gammaproteobacteria) increased at the expense of less abundant phyla. Thus, we conclude that viral lysis was an important driver in sustaining bacterial diversity, consistent with the “killing the winner” model.
Influences of Semaphorin 3A Expression on Clinicopathological Features, Human Papillomavirus Status, and Prognosis in Oropharyngeal Carcinoma

Human papillomavirus (HPV) infection is now identified as a major etiologic factor for oropharyngeal cancer (OPC), and HPV positivity is well established better prognostic marker in OPC. Now, predictable markers for the prognosis of the patients who are stratified by HPV has been investigated in. Semaphorin 3A (SEMA3A) is a well-known axon guidance molecule in the nervous system. It is also known as a tumor suppressor in various cancers. In the present study, we examined the relationships between SEMA3A and clinicopathologic features, especially HPV status, and neoangiogenesis, and its prognostic significance for OPC patients. Thirty-two OPC patients and 17 normal patients were analyzed for SEMA3A expression by immunohistochemical analysis. We also analyzed 22 OPC specimens for CD34 expression as a marker of neoangiogenesis. SEMA3A was significantly downregulated in OPC compared with chronic tonsillitis tissues (p = 0.005). SEMA3A expression was negatively correlated with CD34 expression (r = −0.466, p = 0.033). Moreover, the higher SEMA3A expression cohort showed better survival than the lower SEMA3A expression cohort regardless of HPV status (p = 0.035). These results suggest that SEMA3A expression is a prognostic marker for survival regardless of HPV status and is associated with anti-angiogenesis in OPC.
Hypertensive Disorders of Pregnancy and Risk of Cardiovascular Disease-Related Morbidity and Mortality: A Systematic Review and Meta-Analysis

Introduction: Several studies have demonstrated that there is a higher risk of cardiovascular disease (CVD) in women with a history of hypertensive disorders of pregnancy (HDP). However, effect sizes varied greatly between these studies, and a complete overview of the existing data in the literature is lacking. We aimed to evaluate the association between HDP and the risk of CVD-related morbidity and mortality. Methods: Systematic literature searches were conducted in several electronic databases from inception to July 2019. Exposure of interest was any type of HDP. Outcomes of interest included any CVD, CVD-related mortality, and hypertension. Results: Sixty-six cohort and 7 case-control studies involving >13 million women were included. The overall combined relative risks (RRs) for women with a history of HDP compared with the reference group were 1.80 (95% confidence interval [CI] 1.67–1.94) for any CVD, 1.66 (1.49–1.84) for coronary artery heart disease, 2.87 (2.14–3.85) for heart failure, 1.60 (1.29–2.00) for peripheral vascular disease, 1.72 (1.50–1.97) for stroke, 1.78 (1.58–2.00) for CVD-related mortality, and 3.16 (2.74–3.64) for hypertension. Significant heterogeneity was partially explained by all or part of the variables including type of exposure, follow-up time, geographic region, and sample source. Conclusions: Women with a history of HDP are at an increased risk of future CVD-related morbidity and mortality. Our study highlights the importance of life-long monitoring of cardiovascular risk factors in women with a history of HDP.
Distinct oligomeric structures of the YoeB–YefM complex provide insights into the conditional cooperativity of type II toxin–antitoxin system

Abstract YoeB–YefM, the widespread type II toxin–antitoxin (TA) module, binds to its own promoter to autoregulate its transcription: repress or induce transcription under normal or stress conditions, respectively. It remains unclear how YoeB–YefM regulates its transcription depending on the YoeB to YefM TA ratio. We find that YoeB–YefM complex from S.aureus exists as two distinct oligomeric assemblies: heterotetramer (YoeB–YefM2–YoeB) and heterohexamer (YoeB–YefM2–YefM2–YoeB) with low and high DNA-binding affinities, respectively. Structures of the heterotetramer alone and heterohexamer bound to promoter DNA reveals that YefM C-terminal domain undergoes disorder to order transition upon YoeB binding, which allosterically affects the conformation of N-terminal DNA-binding domain. At TA ratio of 1:2, unsaturated binding of YoeB to the C-terminal regions of YefM dimer forms an optimal heterohexamer for DNA binding, and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifically recognize the 5′-TTGTACAN6AGTACAA-3′ palindromic sequence, resulting in transcriptional repression. In contrast, at TA ratio of 1:1, binding of two additional YoeB molecules onto the heterohexamer induces the completely ordered conformation of YefM and disassembles the heterohexamer into two heterotetramers, which are unable to bind the promoter DNA optimally due to steric clashes, hence derepresses TA operon transcription.
Ethics Trade-Off Between Hazards Prevention and the Safeguard of Death Dignity During COVID-19

Urgent measures established to contain the transmission of COVID-19 and prevent biological hazards included very restrictive interventions on public Holy Masses and funerals. Italy banned any burial procedure and the decision particularly affected both catholic and islamic communities. The dignity of death and the religious competence as cultural competence during COVID-19 epidemic represent important aspects of the epidemic preparedness. This article provides relevant considerations about the topic from an ethical perspective.
European Society of Cardiology methodology for the development of quality indicators for the quantification of cardiovascular care and outcomes.

AIMS It is increasingly recognised that tools are required for assessing and benchmarking quality of care in order to improve it. The European Society of Cardiology (ESC) is developing a suite of quality indicators (QIs) to evaluate cardiovascular care and support the delivery of evidence-based care. This paper describes the methodology used for their development. METHODS AND RESULTS We propose a four-step process for the development of the ESC QIs. For a specific clinical area with a gap in care delivery, the QI development process includes: 1) the identification of key domains of care by constructing a conceptual framework of care; 2) the construction of candidate QIs by conducting a systematic review of the literature; 3) the selection of a final set of QIs by obtaining expert opinions using the modified Delphi method; and 4) the undertaking of a feasibility assessment by evaluating different ways of defining the QI specifications for the proposed data collection source. For each of the four steps, key methodological areas need to be addressed to inform the implementation process and avoid misinterpretation of the measurement results. CONCLUSION Detailing the methodology for the ESC QIs construction enables healthcare providers to develop valid and feasible metrics to measure and improve the quality of cardiovascular care. As such, high-quality evidence may be translated into clinical practice and the 'evidence-practice' gap closed.
The functions of kinesin and kinesin-related proteins in eukaryotes

ABSTRACT Kinesins constitute a superfamily of ATP-driven microtubule motor enzymes that convert the chemical energy of ATP hydrolysis into mechanical work along microtubule tracks. Kinesins are found in all eukaryotic organisms and are essential to all eukaryotic cells, involved in diverse cellular functions such as microtubule dynamics and morphogenesis, chromosome segregation, spindle formation and elongation and transport of organelles. In this review, we explore recently reported functions of kinesins in eukaryotes and compare their specific cargoes in both plant and animal kingdoms to understand the possible roles of uncharacterized motors in a kingdom based on their reported functions in other kingdoms.
Design and rationale of DUTCH-AF: a prospective nationwide registry programme and observational study on long-term oral antithrombotic treatment in patients with atrial fibrillation

Introduction Anticoagulation therapy is pivotal in the management of stroke prevention in atrial fibrillation (AF). Prospective registries, containing longitudinal data are lacking with detailed information on anticoagulant therapy, treatment adherence and AF-related adverse events in practice-based patient cohorts, in particular for non-vitamin K oral anticoagulants (NOAC). With the creation of DUTCH-AF, a nationwide longitudinal AF registry, we aim to provide clinical data and answer questions on the (anticoagulant) management over time and of the clinical course of patients with newly diagnosed AF in routine clinical care. Within DUTCH-AF, our current aim is to assess the effect of non-adherence and non-persistence of anticoagulation therapy on clinical adverse events (eg, bleeding and stroke), to determine predictors for such inadequate anticoagulant treatment, and to validate and refine bleeding prediction models. With DUTCH-AF, we provide the basis for a continuing nationwide AF registry, which will facilitate subsequent research, including future registry-based clinical trials. Methods and analysis The DUTCH-AF registry is a nationwide, prospective registry of patients with newly diagnosed ‘non-valvular’ AF. Patients will be enrolled from primary, secondary and tertiary care practices across the Netherlands. A target of 6000 patients for this initial cohort will be followed for at least 2 years. Data on thromboembolic and bleeding events, changes in antithrombotic therapy and hospital admissions will be registered. Pharmacy-dispensing data will be obtained to calculate parameters of adherence and persistence to anticoagulant treatment, which will be linked to AF-related outcomes such as ischaemic stroke and major bleeding. In a subset of patients, anticoagulation adherence and beliefs about drugs will be assessed by questionnaire. Ethics and dissemination This study protocol was approved as exempt for formal review according to Dutch law by the Medical Ethics Committee of the Leiden University Medical Centre, Leiden, the Netherlands. Results will be disseminated by publications in peer-reviewed journals and presentations at scientific congresses. Trial registration number Trial NL7467, NTR7706 (https://www.trialregister.nl/trial/7464).
MDA-MB-231 Breast Cancer Cells Resistant to Pleurocidin-Family Lytic Peptides Are Chemosensitive and Exhibit Reduced Tumor-Forming Capacity

Direct-acting anticancer (DAA) peptides are cytolytic peptides that show promise as novel anticancer agents. DAA peptides bind to anionic molecules that are abundant on cancer cells relative to normal healthy cells, which results in preferential killing of cancer cells. Due to the mechanism by which DAA peptides kill cancer cells, it was thought that resistance would be difficult to achieve. Here, we describe the generation and characterization of two MDA-MB-231 breast cancer cell-line variants with reduced susceptibility to pleurocidin-family and mastoparan DAA peptides. Peptide resistance correlated with deficiencies in peptide binding to cell-surface structures, suggesting that resistance was due to altered composition of the cell membrane. Peptide-resistant MDA-MB-231 cells were phenotypically distinct yet remained susceptible to chemotherapy. Surprisingly, neither of the peptide-resistant breast cancer cell lines was able to establish tumors in immune-deficient mice. Histological analysis and RNA sequencing suggested that tumorigenicity was impacted by alternations in angiogenesis and extracellular matrix composition in the peptide-resistant MDA-MB-231 variants. Collectively, these data further support the therapeutic potential of DAA peptides as adjunctive treatments for cancer.
Methods for detection of Aspergillus fumigatus

Aspergillus fumigatus is a ubiquitous and pathogenic fungus.A. fumigatus and its toxin contaminate food supplies and feedstuff,and cause great harm to human and animal,which brought about great economical losses.Rapid and accurate detection for Aspergillus fumigatus was of great significance on food safety and fast diagnosis of disease.Based on researches reported in recent years,the developments of detection methods for Aspergillus fumigatus,included microbiological differentiate,immunology,and molecular biology techniques were introduced in this review.
Global variability in seawater Mg:Ca and Sr:Ca ratios in the modern ocean

Significance Seawater elemental composition, namely Mg:Ca and Sr:Ca ratios are widely used in marine sciences. Our new single-laboratory global dataset, combined with past data of seawater Mg:Ca and Sr:Ca ratios, suggests that modern ocean variability is significant across different environments, being similar to the changes during the Neogene Period (20 Ma). Because there is large variability in seawater ratios, we cannot assume that secular changes derived from fossilized taxa with varied ecological niches and from diverse ecosystems provide an unbiased representation of past global seawater chemistry. We suggest that the problem of inconsistencies in previous studies of, for example, paleo conditions from different fossil taxa may be reduced by accounting for taxonomic differences, ecosystems, and abiotic processes to overcome the regional environmental effect. Seawater Mg:Ca and Sr:Ca ratios are biogeochemical parameters reflecting the Earth–ocean–atmosphere dynamic exchange of elements. The ratios’ dependence on the environment and organisms' biology facilitates their application in marine sciences. Here, we present a measured single-laboratory dataset, combined with previous data, to test the assumption of limited seawater Mg:Ca and Sr:Ca variability across marine environments globally. High variability was found in open-ocean upwelling and polar regions, shelves/neritic and river-influenced areas, where seawater Mg:Ca and Sr:Ca ratios range from ∼4.40 to 6.40 mmol:mol and ∼6.95 to 9.80 mmol:mol, respectively. Open-ocean seawater Mg:Ca is semiconservative (∼4.90 to 5.30 mol:mol), while Sr:Ca is more variable and nonconservative (∼7.70 to 8.80 mmol:mol); both ratios are nonconservative in coastal seas. Further, the Ca, Mg, and Sr elemental fluxes are connected to large total alkalinity deviations from International Association for the Physical Sciences of the Oceans (IAPSO) standard values. Because there is significant modern seawater Mg:Ca and Sr:Ca ratios variability across marine environments we cannot absolutely assume that fossil archives using taxa-specific proxies reflect true global seawater chemistry but rather taxa- and process-specific ecosystem variations, reflecting regional conditions. This variability could reconcile secular seawater Mg:Ca and Sr:Ca ratio reconstructions using different taxa and techniques by assuming an error of 1 to 1.50 mol:mol, and 1 to 1.90 mmol:mol, respectively. The modern ratios’ variability is similar to the reconstructed rise over 20 Ma (Neogene Period), nurturing the question of seminonconservative behavior of Ca, Mg, and Sr over modern Earth geological history with an overlooked environmental effect.