Miracle-dz/UniFAR-FTUs huggingface dataset:
The potential genetic network of human brain SARS-CoV-2 infection

The literature reports several symptoms of SARS-CoV-2 in humans such as fever, cough, fatigue, pneumonia, and headache. Furthermore, patients infected with similar strains (SARS-CoV and MERS-CoV) suffered testis, liver, or thyroid damage. Angiotensin-converting enzyme 2 (ACE2) serves as an entry point into cells for some strains of coronavirus (SARS-CoV, MERS-CoV, SARS-CoV-2). Our hypothesis was that as ACE2 is essential to the SARS-CoV-2 virus invasion, then brain regions where ACE2 is the most expressed are more likely to be disturbed by the infection. Thus, the expression of other genes which are also over-expressed in those damaged areas could be affected. We used mRNA expression levels data of genes provided by the Allen Human Brain Atlas (ABA), and computed spatial correlations with the LinkRbrain platform. Genes whose co-expression is spatially correlated to that of ACE2 were then clustered into 16 groups, depending on the organ in which they are the most expressed (as described by the NCBI genes database). The list of organs where genes sharing local over-expression with the ACE2 gene are the most expressed is astonishingly similar to the organs affected by Covid-19.
Optical Aberration Correction via Phase Diversity and Deep Learning

In modern microscopy imaging systems, optical components are carefully designed to obtain diffraction-limited resolution. However, live imaging of large biological samples rarely attains this limit because of sample induced refractive index inhomogeneities that create unknown temporally variant optical aberrations. Importantly, these aberrations are also spatially variant, thus making it challenging to correct over wide fields of view. Here, we present a framework for deep-learning based wide-field optical aberration sensing and correction. Our model consists of two modules which take in a set of three phase-diverse images and (i) estimate the wavefront phase in terms of its constituent Zernike polynomial coefficients and (ii) perform blind-deconvolution to yield an aberration-free image. First, we demonstrate our framework on simulations that incorporate optical aberrations, spatial variance, and realistic modelling of sensor noise. We find that our blind deconvolution achieves a 2-fold improvement in frequency support compared to input images, and our phase-estimation achieves a coefficient of determination (r2) of at least 80% when estimating astigmatism, spherical aberration and coma. Second, we show that our results mostly hold for strongly varying spatially-variant aberrations with a 30% resolution improvement. Third, we demonstrate practical usability for light-sheet microscopy: we show a 46% increase in frequency support even in imaging regions affected by detection and illumination scattering.
Paternal exposure to the pesticide DDT induces intergenerational programming of breast cancer predisposition via sperm miRNA

DNA sequence accounts for the majority of disease heritability, including cancer. However, it is becoming clear that environmentally-induced epigenetic inheritance can also occur. Epidemiological studies have shown that maternal exposure to the pesticide DDT in pregnancy is associated with increased breast cancer risk in women. Yet, the effects of paternal exposure to this and other pesticides on the progeny’s breast cancer development has not been investigated.Male mice (c57bl/6) were exposed to DDT or to a control-vehicle (CO) solution and used for sperm collection or mating with unexposed females to produce the DDT or CO daughters. In another experiment, normal mouse embryos (zygote stage) were injected with miRNA-10b and implanted into surrogate mothers to produce miR-10b offspring. DDT daughters or miRNA-10b females were used to study breast cancer development and metabolic parameters. Paternal sperm was used for RNA-seq analysis and miRNA expression levels.Pre-conception paternal DDT exposure altered the sperm small non-coding RNA load, with an increase in miRNAs and a specific surge in miRNA-10b levels. DDT offspring weighed less at birth and at weaning, but became overweight and showed metabolic dysfunction in adulthood compared to CO. DDT daughters also showed increased mammary tumorigenesis, developing more aggressive tumors that grew faster than in CO. This tumor phenotype was linked to suppression of the AMPK energy sensing pathway and mTOR activation in mammary tissues. Remarkably, embryonic injection of miRNA-10b recapitulated the mammary gland and tumor phenotypes observed in DDT daughters.To our knowledge, this is the first report of an association between paternal DDT exposure and breast cancer in offspring. Paternal DDT-induced programming of breast cancer development in daughters is mechanistically linked to sperm miRNA-10b. The impact of DDT and other endocrine disrupting chemicals on sperm and programming of breast and other cancers in offspring needs to be evaluated in humans.
Metagenomic evidence for a polymicrobial signature of sepsis

Our understanding of the host component of sepsis has made significant progress. However, detailed study of the microorganisms causing sepsis, either as single pathogens or microbial assemblages, has received far less attention. Metagenomic data offer opportunities to characterise the microbial communities found in septic and healthy individuals. In this study we apply gradient-boosted tree classifiers and a novel computational decontamination technique built upon SHapley Additive exPlanations (SHAP) to identify microbial hallmarks which discriminate blood metagenomic samples of septic patients from that of healthy individuals. Classifiers had high performance when using the read assignments to microbial genera (AUROC = 0.995), including after removal of species ‘confirmed’ as the cause of sepsis through clinical testing (AUROC = 0.915). Models trained on single genera were inferior to those employing a polymicrobial model and we identified multiple co-occurring bacterial genera absent from healthy controls. Importance While prevailing diagnostic paradigms seek to identify single pathogens, our results point to the involvement of a polymicrobial community in sepsis. We demonstrate the importance of the microbial component in characterising sepsis, which may offer new biological insights into the aetiology of sepsis and allow the development of clinical diagnostic or even prognostic tools.
Food intake dependent and independent effects of heat stress on lactation and mammary gland development

With a growing population, a reliable food supply is increasingly important. Heat stress reduces livestock meat and milk production. Genetic selection of high producing animals increases endogenous heat production, while climate change increases exogenous heat exposure. Both sources of heat exacerbate the risk of heat-induced depression of production. Rodents are valuable models to understand mechanisms conserved across species. Heat exposure suppresses feed intake across homeothermic species including rodents and production animal species. We assessed the response to early-mid lactation or late gestation heat exposure on milk production and mammary gland development/function, respectively. Using pair-fed controls we experimentally isolated the food intake dependent and independent effects of heat stress on mammary function and mass. Heat exposure (35°C, relative humidity 50%) decreased daily food intake. When heat exposure occurred during lactation, hypophagia accounted for approximately 50% of the heat stress induced hypogalactia. Heat exposure during middle to late gestation suppressed food intake, which was fully responsible for the lowered mammary gland weight of dams at parturition. However, the impaired mammary gland function in heat exposed dams measured by metabolic rate and lactogenesis could not be explained by depressed food consumption. In conclusion, mice recapitulate the depressed milk production and mammary gland development observed in dairy species while providing insight regarding the role of food intake. This opens the potential to apply genetic, experimental and pharmacological models unique to mice to identify the mechanism by which heat is limiting animal production. Summary Statements This study demonstrates that heat stress decreases lactation and mammary development through food intake dependent and independent mechanisms.
PMS

Single-source HTTP adaptive streaming solutions (HAS) have become the de facto solutions to deliver live video over the Internet. By avoiding video stalling events that are mainly caused by the lack of throughput at client or at server side, HAS solutions increase the end users’ quality of experience (QoE). We propose to pragmatically extend HAS with our MS-Stream solution that simultaneously utilizes several servers. MS-Stream aims at offering high QoE for live content delivery by exploiting expanded bandwidth and link diversity in distributed heterogeneous infrastructures. By leveraging end users’ connectivity capacities, we further extend the QoE and scalability capabilities of our proposal by exposing a hybrid P2P/multisource live-streaming solution (P2P/MS-Stream (PMS)), achieving trade-offs between the system’s scale and the end users’ QoE. We propose a distributed quality adaptation algorithm run by every peer, along with a local optimization method of the usage of the server infrastructure made available. Large-scale evaluations conducted with 300 peers located in France permits validating our approach and algorithms over flash crowd events and allow us to conclude that PMS can reach the optimal trade-offs between QoE and system scale.
Different Load Distributions Affect Acute Neuromuscular Responses and Muscle Thickness in Resistance-Trained Men

The aim of the present study was to compare acute neuromuscular responses and muscle thickness of a resistance training session with continuous- vs. grouped-sets. The experimental procedures were performed across three sessions in a crossover and random fashion. During the first session, all subjects were familiarized and the 10RM load was determined for both exercises: biceps curl (BC) and triceps extension (TE). The following two sessions were randomized for continuous- or grouped-sets. For continuous-sets, 8 sets of 10RM for each exercise (BC and TE) were performed sequentially, while for grouped-sets, each exercise was alternated every 4 sets until 8 sets of 10RM for each exercise were completed. Two minutes of rest was used between sets and exercises. Volume load and muscle thickness (biceps brachii, MTBB, and triceps brachii, MTTB) were measured pre- and post-exercise. Peak force and myoelectric activity (iEMG) were measured for each exercise (BC and TE) and each muscle (biceps brachii and triceps brachii) during a maximal voluntary isometric contraction test. Results demonstrated that volume load was significantly greater in grouped-sets for both exercises (P<0.001). MTBB and MTTB increased after both sessions (P<0.001), however, there was a greater effect with continuous-sets when compared to grouped-sets (P=0.001). Peak force decreased for both exercises and sets (P<0.05). iEMG decreased only after continuous-sets for both muscles (P<0.001). In conclusion, continuous- and grouped-sets resulted in specific neuromuscular responses and similar muscle thickness for prime movers. Continuous-sets decreased peak force, volume load, and muscle activity, and increased muscle thickness, while grouped-sets decreased peak force and maintained a high volume load.
A Study on Secondary Bacterial Infections Associated withDermatological Lesions and their Antimicrobial Susceptibility Pattern in a Tertiary Care Hospital

INTRODUCTION: Skin and soft-tissue infection is defined as an inflammatory microbial invasion of the epidermis, dermis and subcutaneous tissues. One common etiology of skin and soft tissue infection is the secondary bacterial infection that complicates the skin lesions. The dose, route and duration of the antimicrobial treatment in these patients are predicated with the knowledge of the potential pathogens with their antimicrobial sensitivity. This study was conducted at the Institute of Microbiology, Madras Medical college, Chennai , to isolate the pathogens from patients with secondarily infected skin lesions (Psoriasis, Atopic dermatitis, Pemphigus lesions and Leprosy with infected ulcer) from various sites and to determine their antimicrobial susceptibility pattern . MATERIALS AND METHODS: 200 patients (≥18 yrs) with signs and symptoms of secondary infection of skin lesions attending the department of Dermatology, Rajiv Gandhi Government General Hospital, Chennai were included in the study. Pus and blood samples were collected from these patients and processed by standard microbiological techniques. RESULT: Out of 200 samples 63, 62, 52 and 23 samples were taken respectively from Atopic Dermatitis/Eczema, Pemphigus, Psoriasis and Leprosy with infected ulcer, including 114 inpatiens and 86 outpatients. 88% of samples were positive for culture. Aerobic gram positive organisms accounts for 59.9% followed by aerobic gram negative 37.27% and anaerobic organisms 2.83%. In Atopic Dermatitis/Eczema 57.7% of isolates were Staphylococcus aureus followed by Streptococcus pyogenes, Enterobacteriacea and anaerobic organisms. Most common isolate in Psoriasis was Staphylococcus aureus (64%) followed by Enteric gram negative bacilli and Staphylococcus epidermidis. Pseudomonas aeroginosa (48%) was the most common organism in leprosy with infected ulcer followed by Proteus vulgaris (22%). Blood culture from17 in patients, [11 from Pemphigus (1.77%) and 6 from Psoriasis (1.15%)] resulted in MRSA isolation from two cases of Pemphigus. ESBL producers were 62.5%. All the ESBL producers were sensitive to Imipenem. 64% Staphylococcus aureus were MSSA and 36% were MRSA. All MRSA were positive for mec A gene . MRSA from OP patients (CA MRSA) showed higher positivity for Pvl gene 90% and 22% of MRSA from IP patients (HA MRSA) were positive for Pvl gene. All the Methicillin resistant Staphylococcus aureus were sensitive to vancomycin. CONCLUSION: MRSA with higher rate of resistance to many routinely used antibiotics and Enterobacteriaceae with higher levels of ESBL production were isolated. Hence bacterial culture and sensitivity of specimens from the secondarily infected skin lesions should be performed to confirm the bacterial etiology and to initiate effective antibiotic treatment so as to decrease the morbidity and mortality of these patients, that also limits the misuse of antimicrobials which would prevent the emergence of resistant bacterial strains in the hospital and the community.
Evaluating Deep Learning for Image Classification in Adversarial Environment

SUMMARY Due to the superior performance, deep learning has been widely applied to various applications, including image classiﬁcation, bioinformatics, and cybersecurity. Nevertheless, the research investigations on deep learning in the adversarial environment are still on their prelimi-nary stage. The emerging adversarial learning methods, e.g., generative adversarial networks, have introduced two vital questions: to what degree the security of deep learning with the presence of adversarial examples is; how to evaluate the performance of deep learning models in adversarial environment, thus, to raise security advice such that the selected application system based on deep learning is resistant to adversarial examples. To see the answers, we leverage image classiﬁcation as an example application scenario to propose a framework of Evaluating Deep Learning for Image Classiﬁca-tion (EDLIC) to conduct comprehensively quantitative analysis. Moreover, we introduce a set of evaluating metrics to measure the performance of different attacking and defensive techniques. After that, we conduct extensive experiments towards the performance of deep learning for image classiﬁcation under di ﬀ erent adversarial environments to validate the scalability of EDLIC. Finally, we give some advice about the selection of deep learning models for image classiﬁcation based on these comparative results.
Nursing management protocol for mothers of children having ventricular peritoneal shunt

Introduction Ventricular peritoneal shunts are considered to be permanent catheters with long-term complications. Management of ventricular peritoneal shunts presents major challenges later in children and their parents’ life, requiring multidisciplinary care from nurses. Aim This study was undertaken to evaluate the effects of nursing management protocols on mothers with children having ventricular peritoneal shunts. Research design A quasi-experimental design was used for the present study. Setting The present study was conducted at the Neurology Outpatient Clinic at Benha University Hospital followed by home visits. Sample A purposive sample of children visiting the Neurology Outpatient Clinic with ventricular peritoneal shunts during a period of 6 months was included. The study included 39 children. Two tools were used for data collection. A structured interview questionnaire was designed and consisted of four parts: part one included sociodemographic characteristics of the mother and child; part two included past and present medical history of the child; part three included mothers’ knowledge regarding ventricular peritoneal shunts, including its meaning, signs of infection, complications, prevention, and treatment; part four included others practices of mothers regarding ventricular peritoneal shunt care such as preventing of infection in the shunt area, preventing other infections, nutrition, treatment, and regular follow-up.
Thermal and Mineral Sensitivity of Oil-in-Water Emulsions Stabilised using Lentil Proteins

Oil-in-water emulsion systems formulated with plant proteins are of increasing interest to food researchers and industry due to benefits associated with cost-effectiveness, sustainability and animal well-being. The aim of this study was to understand how the stability of complex model emulsions formulated using lentil proteins are influenced by calcium fortification (0 to 10 mM CaCl2) and thermal processing (95 or 140 °C). A valve homogeniser, operating at first and second stage pressures of 15 and 3 MPa, was used to prepare emulsions. On heating at 140 °C, the heat coagulation time (pH 6.8) for the emulsions was successively reduced from 4.80 to 0.40 min with increasing CaCl2 concentration from 0 to 10 mM, respectively. Correspondingly, the sample with the highest CaCl2 addition level developed the highest viscosity during heating (95 °C × 30 s), reaching a final value of 163 mPa·s. This was attributed to calcium-mediated interactions of lentil proteins, as confirmed by the increase in the mean particle diameter (D[4,3]) to 36.5 µm for the sample with 6 mM CaCl2, compared to the unheated and heated control with D[4,3] values of 0.75 and 0.68 µm, respectively. This study demonstrated that the combination of calcium and heat promoted the aggregation of lentil proteins in concentrated emulsions.
COVID-19 Autopsies, Oklahoma, USA

Abstract Objectives To report the methods and findings of two complete autopsies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals who died in Oklahoma (United States) in March 2020. Methods Complete postmortem examinations were performed according to standard procedures in a negative-pressure autopsy suite/isolation room using personal protective equipment, including N95 masks, eye protection, and gowns. The diagnosis of coronavirus disease 2019 (COVID-19) was confirmed by real-time reverse transcriptase polymerase chain reaction testing on postmortem swabs. Results A 77-year-old obese man with a history of hypertension, splenectomy, and 6 days of fever and chills died while being transported for medical care. He tested positive for SARS-CoV-2 on postmortem nasopharyngeal and lung parenchymal swabs. Autopsy revealed diffuse alveolar damage and chronic inflammation and edema in the bronchial mucosa. A 42-year-old obese man with a history of myotonic dystrophy developed abdominal pain followed by fever, shortness of breath, and cough. Postmortem nasopharyngeal swab was positive for SARS-CoV-2; lung parenchymal swabs were negative. Autopsy showed acute bronchopneumonia with evidence of aspiration. Neither autopsy revealed viral inclusions, mucus plugging in airways, eosinophils, or myocarditis. Conclusions SARS-CoV-2 testing can be performed at autopsy. Autopsy findings such as diffuse alveolar damage and airway inflammation reflect true virus-related pathology; other findings represent superimposed or unrelated processes.
Monsoon weather and early childhood health in India

Background India is expected to experience an increase in the frequency and intensity of extreme weather events in the coming decades, which poses serious risks to human health and wellbeing in the country. Objective This paper aims to shed light on the possible detrimental effects of monsoon weather shocks on childhood undernutrition in India using the Demographic and Health Survey 2015–16, in combination with geo-referenced climate data. Methods Undernutrition is captured through measures of height-for-age, weight-for-height, stunting and wasting among children aged 0–59 months. The standardised precipitation and evapotranspiration index (SPEI) is used to measure climatic conditions during critical periods of child development. Results The results of a multivariate logistic regression model show that climate anomalies experienced in utero and during infancy are associated with an increased risk of child undernutrition; exposure to excessive monsoon precipitation during these early periods of life elevates the risk of stunting, particularly for children in the tropical wet and humid sub-tropical regions. In contrast, the risk of stunting is reduced for children residing in the mountainous areas who have experienced excessive monsoon precipitation during infancy. The evidence on the short-term effects of climate shocks on wasting is inconclusive. We additionally show that excessive precipitation, particularly during the monsoon season, is associated with an increased risk of contracting diarrhoea among children under five. Diseases transmitted through water, such as diarrhoea, could be one important channel through which excessive rainfall increases the risk of stunting. Conclusions We find a positive association between childhood undernutrition and exposure to excessive monsoon precipitation in India. Pronounced differences across climate zones are found. The findings of the present analysis warn of the urgent need to provide health assistance to children in flood-prone areas.