Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Toll‐like receptors in the pathogenesis of COVID‐19

Coronavirus disease 2019 (COVID‐19), caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has led to a pandemic since March 2020. The exact pathogenesis of SARS‐CoV‐2 and the role of each component of the innate and adaptive immune system is still unknown. However, available data from other coronavirus families, such as SARS‐CoV and the Middle East respiratory syndrome and also new findings could be useful for a better understanding of SARS‐CoV‐2. Toll‐like receptors (TLR) play an important role in recognition of viral particles and activation of the innate immune system. Activation of TLR pathways leads to secretion of pro‐inflammatory cytokines, such as interleukin‐1 (IL‐1), IL‐6, and tumor necrosis factor‐α, as well as type 1 interferon. Different TLRs, like TLR2, TLR3, TLR4, TLR6, TLR7, TLR8, and TLR9 are potentially important in COVID‐19 infection. It is also worth mentioning that we should bear in mind both the beneficial and harmful effects of TLR in confronting COVID‐19 infection. TLRs could be a potential target in controlling the infection in the early stages of disease and production of vaccine against SARS‐CoV‐2.
Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing

Abstract Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s−1 and a processivity of >10.5 kb at 25°C.
Thallus Growth Stage and Geographic Origin Shape Microalgal Diversity in Ramalina farinacea Lichen Holobionts

Lichen symbioses are microecosystems hosting many other living organisms besides the two major lichen symbionts (i.e., lichenized fungi [the mycobiont] and green microalgae or cyanobacteria [the photobiont]). Recent investigations evidenced that other fungi, non‐photosynthetic bacteria, and microalgae co‐inhabit within the lichen thalli, but their diversity and their roles are still underinvestigated. Here we present an ad hoc stratified sampling design and in‐depth Illumina paired‐end metabarcoding approach to explore microalgal diversity in lichen thalli of the model species Ramalina farinacea from different ecologies. Lichen thalli were surveyed according to three different sizes, and different thallus parts were considered for molecular, bioinformatics, and community diversity analyses. The results revealed that microalgal diversity strongly depends on the growth stage of the thalli, the geographic area, and the habitat type. The results also show that microalgal diversity does not vary along the thallus branches (lacinias)—that is, it does not correlate with the apical growth and founder effects—and that there is no balanced co‐presence of two main photobionts as previously established in R. farinacea. The sampling design performed here minimizes bias in the assessment of photobiont diversity in lichens and is proposed to be reliable and applicable to further study microalgal diversity in lichen symbioses.
Effect of alginate-pectin composition on drug release characteristics of microcapsules

Microencapsulation of model drug, acetylsalicylic acid into bio-based polymer, alginate-pectin matrix has been undertaken in this work to characterize the microcapsules based on their composition. Different proportions of the alginate-pectin solutions prepared with drug were homogenized and atomized using nitrogen gas into 1.0 M calcium chloride solution to form sol-gel microcapsules. Drug loaded microcapsules were dried using microwave energy under vacuum at low temperature. Average particle size of the microcapsules was found to be 90 micron. Scanning electron microscopy graphs and Fourier Transform Infrared Spectroscopy analysis on the microcapsules confirm the presence of drug in the polymer matrix. X-ray diffraction pattern showed that the microstructure was more like an amorphous pattern. Drug release of the microcapsules was tested in three different pH levels of 1.2, 7.4 and 8.2. Slow and controlled release of drug was observed at all the pH levels. Increase in pectin increased the drug release and also the release was more in acidic pH (1.2) as 75.6% for alginate: pectin-20 : 80.
Airborne concentrations of chrysotile asbestos during operation of industrial crane controls and maintenance of associated arc chutes

Some industrial crane control panels were historically equipped with chrysotile-containing arc chutes. Because of the paucity of data regarding potential exposure from such equipment, we used a simulation approach to quantify the release of chrysotile from arc chutes in two functional 1970s-era industrial crane control panels during operation and maintenance. Two experienced operators separately simulated operation of crane controls under load; one of these operators then simulated two arc chute maintenance protocols: sanding (protocol 1) and scraping, sanding, and blowing (protocol 2). The original arc chutes contained approximately 36% chrysotile. Personal breathing zone (PBZ) (n = 8) and area samples (n = 8) were collected and analyzed using phase contrast microscopy (PCM) and transmission electron microscopy. PCM-equivalent (PCME) concentrations were derived, from which 8-h time-weighted averages (TWA) were calculated. During operation, chrysotile was identified in one of the four PBZ samples, equivalent to a PCME concentration of 0.012 f/cm3 (8-h TWA: 0.011 f/cm3). During protocols 1 and 2, chrysotile was identified in all PBZ samples (n = 4); PCME concentrations (and corresponding 8-h TWA) were <0.013 and 0.021 f/cm3 (0.001 and 0.004 f/cm3) and 0.013 and 0.017 f/cm3 (0.003 f/cm3), respectively. Many of the airborne chrysotile fibers had matrix attached, supporting the low exposure potential during this work. These data indicate very low, if any, exposures to chrysotile asbestos during the simulated scenarios. In addition, these data could assist with refining assumptions in exposure reconstruction and inform the state-of-the science on low-level chrysotile exposure.
Biomarker Discovery in Patients with Immunotherapy-Treated Melanoma with Imaging Mass Cytometry

Purpose: Imaging mass cytometry (IMC) is among the first tools with the capacity for multiplex analysis of more than 40 targets, which provides a novel approach to biomarker discovery. Here, we used IMC to characterize the tumor microenvironment of patients with metastatic melanoma who received immunotherapy in efforts to find indicative factors of treatment response. In spite of the new power of IMC, the image analysis aspects are still limited by the challenges of cell segmentation. Experimental Design: Here, rather than segment, we performed image analysis using a newly designed version of the AQUA software to measure marker intensity in molecularly defined compartments: tumor cells, stroma, T cells, B cells, and macrophages. IMC data were compared with quantitative immunofluorescence (QIF) and digital spatial profiling. Results: Validation of IMC results for immune markers was confirmed by regression with additional multiplexing methods and outcome assessment. Multivariable analyses by each compartment revealed significant associations of 12 markers for progression-free survival and seven markers for overall survival (OS). The most compelling indicative biomarker, beta2-microglobulin (B2M), was confirmed by correlation with OS by QIF in the discovery cohort and validated in an independent published cohort profiled by mRNA expression. Conclusions: Using digital image analysis based on pixel colocalization to assess IMC data allowed us to quantitively measure 25 markers simultaneously on formalin-fixed, paraffin-embedded tissue microarray samples. In addition to showing high concordance with other multiplexing technologies, we identified a series of potentially indicative biomarkers for immunotherapy in metastatic melanoma, including B2M.
Deoxynivalenol Induces Caspase-8-Mediated Apoptosis through the Mitochondrial Pathway in Hippocampal Nerve Cells of Piglet

Deoxynivalenol (DON) is a common trichothecene mycotoxin found worldwide. DON has broad toxicity towards animals and humans. However, the mechanism of DON-induced neurotoxicity in vitro has not been fully understood. This study investigated the hypothesis that DON toxicity in neurons occurs via the mitochondrial apoptotic pathway. Using piglet hippocampal nerve cells (PHNCs), we evaluated the effects of different concentrations of DON on typical indicators of apoptosis. The obtained results demonstrated that DON treatment inhibited PHNC proliferation and led to morphological, biochemical, and transcriptional changes consistent with apoptosis, including decreased mitochondrial membrane potential, mitochondrial release of cytochrome C (CYCS) and apoptosis inducing factor (AIF), and increased abundance of active cleaved-caspase-9 and cleaved-caspase-3. Increasing concentrations of DON led to decreased B-cell lymphoma-2 (Bcl-2) expression and increased expression of BCL2-associated X (Bax) and B-cell lymphoma-2 homology 3 interacting domain death agonist (Bid), which in turn increased transcriptional activity of the transcription factors AIF and P53 (a tumor suppressor gene, promotes apoptosis). The addition of a caspase-8 inhibitor abrogated these effects. These results reveal that DON induces apoptosis in PHNCs via the mitochondrial apoptosis pathway, and caspase-8 is shown to play an important role during apoptosis regulation.
A descriptive analysis of clinical characteristics of COVID-19 among healthcare workers in a district specialist hospital.

INTRODUCTION COVID-19 is a highly transmissible respiratory virus that has affected millions of people worldwide in the span of months. The burden of disease among healthcare workers (HCW) has not been well studied despite reports of infectivity and transmission around the world. Two HCW in Hospital Teluk Intan (HTI) contracted COVID-19 while attending a social event. They were in close proximity with colleagues upon returning to work, resulting in the spread of infection among other HCW in HTI. OBJECTIVE The objectives of this paper are to gain a better understanding of the key presenting symptoms of COVID-19 in HCWs in a district specialist hospital, to establish the proportion of symptomatic COVID-19 cases among HCWs and its severity and to determine the time taken from onset of symptoms or perceived exposure to diagnostic testing. METHODOLOGY This is a retrospective descriptive analysis of clinical characteristics of subjects infected with COVID-19 among HCW in HTI. Their demography and clinical characteristics were recorded. RESULTS There were 47 HCW in HTI who tested positive for COVID-19. The mean age of the patients was 37.5 years old. 7 patients (15.2%) had at least more than one comorbidity. Average duration of time from perceived close contact to onset of symptom was 4.5 days, while the mean duration of time from symptoms to first positive RT-PCR result was 3.4 days. Six patients (13.0%) were asymptomatic throughout, whereas 40 (87.0%) had at least one symptom prior to hospitalization. The most commonly reported symptoms were fever (65.2%), sore throat (39.1%) and cough (37.0%). In terms of severity of symptoms, the majority of patients experienced mild symptoms (Group 2, 52.2%). Two patients (4.3%) with multiple comorbidities had severe disease requiring ICU admission and mechanical ventilation. There were no mortalities, and the longest staying patient was hospitalized for 18 days. The high rates of infectivity among HCW in HTI can be attributed to working in close proximity while in the asymptomatic incubation phase, while no HCW directly involved in the care of COVID-19 positive patients were tested positive. CONCLUSION We report that HCW share similar clinical characteristics of COVID-19 infection as those of non HCW patients in earlier studies. The infection can spread rapidly within healthcare settings via close contacts among infected HCWs. As such, we advocate distancing when working and usage of personal protective equipment when treating patients with respiratory illness to reduce transmission of COVID-19.
Incidence and severity of pertussis hospitalisations in infants aged less than 1 year in 37 hospitals of six EU/EEA countries, results of PERTINENT sentinel pilot surveillance system, December 2015 to December 2018.

IntroductionPERTINENT is a pilot active surveillance system of infants hospitalised with pertussis in six European Union/European Economic Area countries (37 hospitals, seven sites). AimThis observational study aimed to estimate annual pertussis incidence per site from 2016 to 2018 and respective trends between 2017 and 2018. Pertussis cases were described, including their severity.MethodsWe developed a generic protocol and laboratory guidelines to harmonise practices across sites. Cases were hospitalised infants testing positive for Bordetella pertussis by PCR or culture. Sites collected demographic, clinical, laboratory data, vaccination status, and risk/protective factors. We estimated sites' annual incidences by dividing case numbers by the catchment populations.ResultsFrom December 2015 to December 2018, we identified 469 cases (247 males; 53%). The median age, birthweight and gestational age were 2.5 months (range: 0-11.6; interquartile range (IQR): 2.5), 3,280 g (range: 700-4,925; IQR: 720) and 39 weeks (range: 25-42; IQR: 2), respectively. Thirty cases (6%) had atypical presentation either with cough or cyanosis only or with absence of pertussis-like symptoms. Of 330 cases with information, 83 (25%) were admitted to intensive care units including five deceased infants too young to be vaccinated. Incidence rate ratios between 2018 and 2017 were 1.43 in Czech Republic (p = 0.468), 0.25 in Catalonia (p = 0.002), 0.71 in France (p = 0.034), 0.14 in Ireland (p = 0.002), 0.63 in Italy (p = 0.053), 0.21 in Navarra (p = 0.148) and zero in Norway.ConclusionsIncidence appeared to decrease between 2017 and 2018 in all but one site. Enhanced surveillance of hospitalised pertussis in Europe is essential to monitor pertussis epidemiology and disease burden.
Detection and whole genome sequencing of murine norovirus in animal facility in Italy

Abstract Viruses belonging to the genus Norovirus (NoV) of the family Caliciviridae are the major cause of acute viral gastroenteritis worldwide. NoVs are classified into 10 genogroups (GI-GX), and those belonging to the genogroup GV are able to infect several species of rodents. To evaluate the circulation of MNV among mice housed in an Italian facility, sampling was performed over two separate periods, in 2011, and 3 years later in 2014. During the two samplings, 75 fecal samples were collected from healthy mice housed in the animal facility and subjected to RT-PCR for viral detection. After the analysis, 41/75 animals (54.6%) resulted positive for the presence of MNV in feces. Nucleotide sequencing revealed the presence of two MNV variants co-circulating in both 2011 and 2014. One MNV strain was isolated on RAW264.7 cell line, and subjected to full genome sequencing. Our study showed that the murine noroviruses are widespread in the investigated animal facility, despite guidelines for animal care and maintenance. Full genome sequence analysis of the MNV strain described in this study showed a correlation with other strains circulating in Europe. Understanding the molecular epidemiology of this virus should give insight into its natural history and evolution in mice.
Non-Pharmacological Interventions to Improve Chronic Disease Risk Factors and Sleep in Shift Workers: A Systematic Review and Meta-Analysis

Shift work is associated with adverse chronic health outcomes. Addressing chronic disease risk factors including biomedical risk factors, behavioural risk factors, as well as sleep and perceived health status, affords an opportunity to improve health outcomes in shift workers. The present study aimed to conduct a systematic review, qualitative synthesis, and meta-analysis of non-pharmacological interventions targeting chronic disease risk factors, including sleep, in shift workers. A total of 8465 records were retrieved; 65 publications were eligible for inclusion in qualitative analysis. Random-effects meta-analysis were conducted for eight eligible health outcomes, including a total of thirty-nine studies. Interventions resulted in increased objective sleep duration (Hedges’ g = 0.73; CI: 0.36, 1.10, k = 16), improved objective sleep efficiency (Hedges’ g = 0.48; CI: 0.20, 0.76, k = 10) and a small increase in both subjective sleep duration (Hedges’ g = 0.11; CI: −0.04, 0.27, k = 19) and sleep quality (Hedges’ g = 0.11; CI: −0.11, 0.33, k = 21). Interventions also improved perceived health status (Hedges’ g = 0.20; CI: −0.05, 0.46, k = 8), decreased systolic (Hedges’ g = 0.26; CI: −0.54, 0.02, k = 7) and diastolic (Hedges’ g = 0.06; CI: −0.23, 0.36, k = 7) blood pressure, and reduced body mass index (Hedges’ g = −0.04; CI: −0.37, 0.29, k = 9). The current study suggests interventions may improve chronic disease risk factors and sleep in shift workers; however, this could only be objectively assessed for a limited number of risk factor endpoints. Future interventions could explore the impact of non-pharmacological interventions on a broader range of chronic disease risk factors to better characterise targets for improved health outcomes in shift workers.
SpiNet: A Deep Neural Network for Schatten p-norm Regularized Medical Image Reconstruction.

PURPOSE To propose a generic deep learning based medical image reconstruction model (named as SpiNet) that can enforce any Schatten p-norm regularization with 0 < p ≤ 2, where the p can be learnt (or fixed) based on the problem at hand. METHODS Model based deep learning architecture for solving inverse problems consists of two parts, a deep learning based denoiser and an iterative data consistency solver. The former has either L2 norm or L1 norm enforced on it, which are convex and can be easily minimized. This work proposes a method to enforce any p norm on the noise prior where 0 < p ≤ 2. This is achieved by using Majorization Minimisation algorithm, which upper bounds the cost function with a convex function, thus can be easily minimised. The proposed SpiNet has the capability to work for a fixed p or it can learn p based on the data. The network was tested for solving the inverse problem of reconstructing magnetic resonance (MR) images from undersampled k space data and the results were compared with a popular model based deep learning architecture MoDL which enforces L2 norm along with other compressive sensing based algorithms. This comparison between MoDL and proposed SpiNet was performed for undersampling rates (R) of 2x, 4x, 6x, 8x, 12x, 16x and 20x. Multiple figures of merit such as PSNR, SSIM and NRMSE were utilized in this comparison. A two tailed t-test was performed for all undersampling rates and for all metrices for proving the superior performance of proposed SpiNet compared to MoDL. For training and testing, the same dataset that was utilized in MoDL implementation was deployed. RESULTS The results indicate that for all undersampling rates, the proposed SpiNet shows higher PSNR and SSIM and lower NRMSE than MoDL. However, for low undersampling rates of 2x and 4x, there is no significant difference in performance of proposed SpiNet and MoDL in terms of PSNR and NRMSE. This can be expected as the learnt p value is close to 2 (norm enforced by MoDL). For higher undersampling rates ≥ 6 x, SpiNet significantly outperforms MoDL in all metrices with improvement as high as 4 dB in PSNR and 0.5 points in SSIM. CONCLUSION As deep learning based medical image reconstruction methods are gaining popularity, the proposed SpiNet provides a generic framework to incorporate Schat-ten p-norm regularization with 0 < p ≤ 2 with an added advantage of providing superior performance compared to its counterparts. The proposed SpiNet also has useful addition of Schatten p-norm value in regularization term being automatically chosen based on the available training data.
Preparation and Characterization of Potato Starch Based Low Density Polyethylene/Low Density Polyethylene Grafted Maleic Anhydride Biodegradable Polymer Composite

Polysaccharide-filled plastics have attracted immense interest from research scientists as a means to develop a biodisintegrable polymer. The objective of the present study is to develop a biodisintegrable polymer composite using potato starch, which may be a step toward an alternative user friendly polymer composite. Keeping in mind the compatibility issue between potato starch and polyethylene, we used a base material with a polar group in its low density polyethylene (LDPE) backbone. Polymer composite sheets with a combination of potato starch, LDPE, and LDPE grafted maleic anhydride (LDPE-g-mA) were prepared. The LDPE and LDPE-g-mA were used in equal amounts and as a base material. The starch contents varied between 0 and 30%. The composites so prepared were tested for their thermal and mechanical properties. The results show that the thermal stability and melting temperature of these composites did not change significantly with various combinations of potato starch. The mechanical testing results show that tensile strength of material could be maintained at up to 15% mixing of potato starch in composites, and at up to 5% mixing of potato starch the percentage elongation was intact.
Prevalence of antibiotic self-medication behavior and related factors among children aged 0 to 5 years

ABSTRACT Background: Self-medication behavior has great adverse effects on children. The aims of this study were to assess the prevalence of self-medication with antibiotics (SMA) among children aged 0–5 years and explore the related factors. Methods: A cross-sectional survey was conducted from 1 July 2019 to 31 July 2019 in Wuhan, Hubei Province (Central China). A structured questionnaire was used to collect data from 1188 parents of children aged 0–5 years on sociodemographic characteristics, SMA among children, antibiotic knowledge and health beliefs of SMA. Results: Of the 1188 participants, 14.32% had self-medicated their children with antibiotics in the past 6 months. The higher the degree of perceived threat (OR = 0.94, 95%CI: 0.89–1.00) and self-efficacy (OR = 0.94, 95%CI: 0.89–0.98), the less likely parents were to self-medicate their children. On the contrary, the higher the degree of perceived barriers, the more likely parents were to self-medicate their children with antibiotics (OR = 1.058, 95%CI: 1.01–1.11). Conclusions: Health beliefs of parents were significantly associated with SMA among children. In addition to extensive health education, the Chinese government should also improve the accessibility and quality of health services to reduce the barriers of parental behavior change.