Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing the Sensitivity of Conjunctival Swabs from Confirmed COVID-19 Patients

Objective To investigate the incidence of COVID-19 viral RNA in the conjunctiva of patients priorly confirmed to have COVID-19, using a conjunctival swab and to determine swab sensitivity. Methods This cross-sectional study enrolled patients who tested positive for COVID-19 with PCR via nasopharyngeal swabs. Conjunctival swabs were collected for each patient and subjected to RT-PCR assay. Demographic data and clinical history of patients were investigated and analysed. Results In this study, 4.9% of the patients tested positive with conjunctival swabs for COVID-19; 29.9%, 28.7%, 20.1%, and 12.2% of the patients had fever, shortness of breath, cough, and red eye, respectively. Among all patients, 18.9% and 73.2% had a history of traveling and contact with positive COVID-19 cases, respectively. There were significant correlations between the conjunctival results and diabetes (P=0.049) and hypertension (P=0.002). Traveling was a risk factor for positive conjunctival swab testing (P=0.016). The sensitivity of the conjunctival swab was 4.8%. Conclusion Among all positive cases of COVID-19, a small percentage had positive results when tested using a conjunctival swab. Conjunctival swabs have very low sensitivity for the detection of COVID-19. However, tears could still be a mode of disease transmission, especially from patients to eye care specialists.
Outcomes of Antibiotics in Adults with “Difficult to Treat” Asthma or the Overlap Syndrome

Purpose Macrolides are a recommended treatment option for severe asthma, but data for “difficult-to-treat” asthma, the asthma-COPD “overlap” syndrome, and treatment duration beyond one year are lacking. We present long-term data from community practice experience providing insights for practice and research. Methods We report data from (1) baseline (pre-treatment) chart review of antibiotic-treated asthma patients and (2) follow-up telephone interviews documenting severe exacerbations (NIH criteria), Asthma Control Test (ACT) scores, and asthma controller use at baseline and follow-up, analyzed using a “before-after” model. Results A total of 101 patients (mean age 55.6 years (Sd 16.8), 66 females) were included. None had ever taken high dose inhaled corticosteroids and 79 (78.2%) were severely uncontrolled (ACT score ≤15) before treatment. Coexisting COPD was present in 62 (61.4%) patients. Azithromycin or azithromycin plus doxycycline was primarily prescribed with a median treatment duration of 12 months and median follow-up duration of 22 months. Severe exacerbations in the month before treatment occurred in 50.5% vs 17.8% at follow-up (P<0.0001). Mean ACT score increased from 12.2 to 20.6 (P<0.0001). The number of patients taking controller medications decreased (P<0.0001 for inhaled corticosteroids; P<0.001 for long-acting beta agonist/long-acting muscarinic antagonist; P<0.05 for leukotriene receptor antagonists). Of the 79 severely uncontrolled patients, 51 (64.6%) became controlled at follow-up, and of these 51, 27 (52.9%) continued to take antibiotics while 24 (47.1%) had discontinued antibiotics earlier yet remained controlled. Conclusion Antibiotic treatment may be beneficial in a significant proportion of “difficult to treat” asthma patients beyond one year, including some patients with the overlap syndrome and/or who fail to meet criteria for refractoriness.
COVID-19-associated diarrhea

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged as a highly virulent respiratory pathogen that is known as the causative agent of coronavirus disease 2019 (COVID-19). Diarrhea is a common early symptom in a significant proportion of patients with SARS-CoV-2 infection. SARS-CoV-2 can infect and replicate in esophageal cells and enterocytes, leading to direct damage to the intestinal epithelium. The infection decreases the level of angiotensin-converting enzyme 2 receptors, thereby altering the composition of the gut microbiota. SARS-CoV-2 elicits a cytokine storm, which contributes to gastrointestinal inflammation. The direct cytopathic effects of SARS-CoV-2, gut dysbiosis, and aberrant immune response result in increased intestinal permeability, which may exacerbate existing symptoms and worsen the prognosis. By exploring the elements of pathogenesis, several therapeutic options have emerged for the treatment of COVID-19 patients, such as biologics and biotherapeutic agents. However, the presence of SARS-CoV-2 in the feces may facilitate the spread of COVID-19 through fecal-oral transmission and contaminate the environment. Thus gastrointestinal SARS-CoV-2 infection has important epidemiological significance. The development of new therapeutic and preventive options is necessary to treat and restrict the spread of this severe and widespread infection more effectively. Therefore, we summarize the key elements involved in the pathogenesis and the epidemiology of COVID-19-associated diarrhea.
Correlation of NUCB2/Nesfatin-1 with Cytokine Levels in Primary Open-Angle Glaucoma

Purpose Nesfatin-1 is produced in various tissues of the body including the hypothalamus. Neuroprotective properties of the neuropeptide hormone Nesfatin-1 were recently described. The aim of the study was to analyze the molecule Nesfatin-1 as a possible biomarker in POAG with neuroprotective properties pointing out the retinal-hypothalamic axis as target site in POAG and to obtain a molecular signature of cytokines in POAG as neuroinflammatory processes are a key factor of glaucoma development. Methods In this study, n=35 patients with moderate and advanced POAG (mean age 65.0y, IOP 13.9±3.0mmHg) and n=35 healthy controls (mean age 51.6y, IOP 14.3±2.7mmHg) were included. Clinical parameters including IOP, cup to disc ratio (CDR), glaucoma medication and retinal nerve fiber layer thickness (RNFL) were recorded. Plasma was collected for NUCB2/nesfatin-1 measurement using a Nesfatin-1 ELISA and for detection of 13 inflammatory cytokines using a multiplex bead-based immunoassay (MagPix). Multiple linear regression analysis was performed to adjust for confounding factors. Results Sex-independent or sex-dependent variables showed no significant differences in the Nesfatin-1 level (p>0.05). As a trend, an increase in NUCB2/nesfatin-1 in male glaucoma patients was found. Increased concentrations of 11 cytokines (GM-CSF, Interferon-γ, Interleukin-1β, IL-2, 4, 5, 6, 7, 10, 12 and TNF-α) were detected in POAG. The female glaucoma patients demonstrated elevated cytokine concentrations compared to male patients. NUCB2/nesfatin-1 showed a significant correlation to IL-2 and IL-13 levels in POAG. Stepwise multiple regression analysis showed no difference in NUCB2/nesfatin-1 level between POAG and healthy controls after adjusting for sex and age (all p>0.05). Conclusion As a trend, male POAG patients showed increased plasma NUCB2/nesfatin-1 levels. We further found inflammation as contributing factor to the pathogenesis of glaucoma, with a greater inflammatory response in women.
Intention to Care for COVID-19 Patients Among Nurses Working at Health Care Institutions of Debre Tabor Town, North Central Ethiopia

Background Coronavirus disease 2019 (COVID-19) has caused many challenges for health care providers. Nurses meet patients with coronavirus disease and offer care for newly communicable diseases. Despite global and national efforts to prevent the spread, the outbreak is still on a rise, and studies on the health care behaviors of nurses were scarce in the study setting. Therefore, this study was intended in addressing nurses’ intention to care for coronavirus disease 19 patients and its determinants among nurses working at Debre Tabor town Health Care Institutions, 2020. Methodology An institutional-based cross-sectional study was conducted among 163 nurses working at health care institutions of Debre Tabor Town, from June 01 to 15/2020. The data were collected using tools with a self-administration questionnaire adapted from the theory of planned behavior and different kinds of literatures. All nurses working at Debre Tabor health care institutions were included. Data were entered using Epi-data 4.2. 0.0 statistical software, and analysis was done by Stata version 14 statistical software. Binary logistic regression model was used for analysis. Strength of association was measured using the odds ratio with 95% CI, and the level of significance was estimated at P-value ≤0.05. Results Nurses’ intention to care for COVID-19 patient was 59.5% (95% CI; 58.7:60.3). Having better working experience (adjusted odds ratio (AOR) =2.3:95% CI; 1.120, 4.910), caring experience for infectious disease (AOR=2.5; 95% CI: 1.10, 5.50), good perceived behavioral control (AOR=2.33; 95% CI: 1.13, 4.8), and subjective norms (AOR= 2.14; 95% CI: 1.05, 4.36) were significantly associated with intention of caring behavior. Conclusion Nurses’ intention to care for COVID-19 patients was low. Working experience, the experience of caring for infectious disease, self-efficacy, and subjective norm were independently related with nurses’ caring intention. The government should work on improving nurse’s confidence in disaster management, design disaster management nursing education, and frequent support of nurses.
Fecal microbiota transplantation for irritable bowel syndrome: An intervention for the 21st century

Irritable bowel syndrome (IBS) affects about 12% of the global population. Although IBS does not develop into a serious disease or increase mortality, it results in a considerable reduction in the quality of life. The etiology of IBS is not known, but the intestinal microbiota appears to play a pivotal role in its pathophysiology. There is no effective treatment for IBS, and so the applied treatments clinically focus on symptom relief. Fecal microbiota transplantation (FMT), an old Chinese treatment, has been applied to IBS patients in seven randomized controlled trials (RCTs). Positive effects on IBS symptoms in various degrees were obtained in four of these RCTs, while there was no effect in the remaining three. Across the seven RCTs there were marked differences in the selection processes for the donor and treated patients, the transplant dose, the route of administration, and the methods used to measure how the patients responded to FMT. The present frontier discusses these differences and proposes: (1) criteria for selecting an effective donor (superdonor); (2) selection criteria for patients that are suitable for FMT; (3) the optimal FMT dose; and (4) the route of transplant administration. FMT appears to be safe, with only mild, self-limiting side effects of abdominal pain, cramping, tenderness, diarrhea, and constipation. Although it is early to speculate about the mechanisms underlying the effects of FMT, the available data suggest that changes in the intestinal bacteria accompanied by changes in fermentation patterns and fermentation products (specifically short-chain fatty acids) play an important role in improving the IBS symptoms seen after FMT. FMT appears to be a promising treatment for IBS, but further studies are needed before it can be applied in everyday clinical practice.
Computational systems-biology approaches for modeling gene networks driving epithelial–mesenchymal transitions

Epithelial–mesenchymal transition (EMT) is an important biological process through which epithelial cells undergo phenotypic transitions to mesenchymal cells by losing cell–cell adhesion and gaining migratory properties that cells use in embryogenesis, wound healing, and cancer metastasis. An important research topic is to identify the underlying gene regulatory networks (GRNs) governing the decision making of EMT and develop predictive models based on the GRNs. The advent of recent genomic technology, such as single-cell RNA sequencing, has opened new opportunities to improve our understanding about the dynamical controls of EMT. In this article, we review three major types of computational and mathematical approaches and methods for inferring and modeling GRNs driving EMT. We emphasize (1) the bottom-up approaches, where GRNs are constructed through literature search; (2) the top-down approaches, where GRNs are derived from genome-wide sequencing data; (3) the combined top-down and bottom-up approaches, where EMT GRNs are constructed and simulated by integrating bioinformatics and mathematical modeling. We discuss the methodologies and applications of each approach and the available resources for these studies.
Predicting Survival for Patients with Malignant Pleural Effusion: Development of the CONCH Prognostic Model

Background Malignant pleural effusion (MPE) is a frequent complication of advanced malignancies that leads to a poor quality of life and limits treatment options. Objective The objective of this study was to identify biomarkers of survival in patients with MPE, which will greatly facilitate the clinical management of this complication. Methods This retrospective study recruited patients who had been pathologically diagnosed with MPE, regardless of the type of primary cancer, at Beijing Chao-Yang Hospital over 158 months. Demographic, clinical, hematological, and pleural fluid data were collected and analyzed as potential predictors of survival, and a new predictive model was developed based on Cox and logistic regression analyses. Results In our alternative prognostic model (n = 281), four routinely detected variables, namely, carcinoembryonic antigen (CEA) level, monocyte count, N-terminal pro B-type natriuretic peptide (NT-pro-BNP) level, and pleural effusion chloride level on admission, were identified as predictors (the CONCH prognostic score). Patients were divided into three prognosis subgroups based on risk stratification, with median survival periods of 17, 11, and 5 months, respectively. In comparison with the low-risk group, patients in the medium- and high-risk groups showed significantly poorer survival (medium-risk group: hazard ratio [HR], 1.586; 95% confidence interval [CI], 1.047–2.402; P = 0.029; high-risk group: HR, 4.389; 95% CI, 2.432–7.921; P < 0.001). Conclusion Four routinely detected variables were used to develop the CONCH scoring system, which was confirmed to be an accurate prognostic score for patients with MPE. This system can guide the selection of interventions and management for MPE.
Hepatocellular carcinoma in viral and autoimmune liver diseases: Role of CD4+ CD25+ Foxp3+ regulatory T cells in the immune microenvironment

More than 90% of cases of hepatocellular carcinoma (HCC) occurs in patients with cirrhosis, of which hepatitis B virus and hepatitis C virus are the leading causes, while the tumor less frequently arises in autoimmune liver diseases. Advances in understanding tumor immunity have led to a major shift in the treatment of HCC, with the emergence of immunotherapy where therapeutic agents are used to target immune cells rather than cancer cells. Regulatory T cells (Tregs) are the most abundant suppressive cells in the tumor microenvironment and their presence has been correlated with tumor progression, invasiveness, as well as metastasis. Tregs are characterized by the expression of the transcription factor Foxp3 and various mechanisms ranging from cell-to-cell contact to secretion of inhibitory molecules have been implicated in their function. Notably, Tregs amply express checkpoint molecules such as cytotoxic T lymphocyte-associated antigen 4 and programmed cell-death 1 receptor and therefore represent a direct target of immune checkpoint inhibitor (ICI) immunotherapy. Taking into consideration the critical role of Tregs in maintenance of immune homeostasis as well as avoidance of autoimmunity, it is plausible that targeting of Tregs by ICI immunotherapy results in the development of immune-related adverse events (irAEs). Since the use of ICI becomes common in oncology, with an increasing number of new ICI currently under clinical trials for cancer treatment, the occurrence of irAEs is expected to dramatically rise. Herein, we review the current literature focusing on the role of Tregs in HCC evolution taking into account their opposite etiological function in viral and autoimmune chronic liver disease, and we discuss their involvement in irAEs due to the new immunotherapies.
Influence of Low Total Triiodothyronine Levels on Bone Turnover Markers in Type 2 Diabetes Mellitus

Purpose The aim of this study was to investigate whether low total triiodothyronine (TT3) could affect bone turnover in patients with type 2 diabetes mellitus (T2DM). Materials and Methods This is a cross-sectional study that recruited 577 patients with T2DM, 141 patients formed the low TT3 group (TT3<1.30nmol/L) and 436 patients formed the control group (TT3≥1.30nmol/L), and the low TT3 group was further subdivided into four groups based on the TT3 level. To investigate whether TT3 level is associated with poor glycemic control, all participants were divided into high glycosylated hemoglobin (HbA1c) group and low HbA1c group using HbA1c 10.5% as the boundary. Results The levels of OC and PINP were significantly lower in the low TT3 group compared with the control group (P < 0.05). TT3 positively correlated with OC and PINP (r = 0.219, P = 0.009; r = 0.208, P = 0.019) in the low TT3 group, and this positive correlation still existed after adjusting for other factors in multilinear regression analysis. Next, we want to find a cut-off point to prevent osteoporosis, we divided the patients in the low TT3 group into four groups based on the TT3 level, the levels of OC and PINP were significantly lower in the TT3 < 1.00 nmol/L group than in the TT3 ≥ 1.00 nmol/L groups. Conclusion In patients with T2DM, low TT3 levels are associated with impaired bone formation. What’s more, bone formation was significantly impaired when TT3 was <1.00 nmol/L.
Burnout in health care providers working in the intensive care units of a tertiary care hospital, South India—a questionnaire-based survey

Background The intensive care unit (ICU) is a special section of the hospital where intense monitoring and patient care are required. Health care providers (HCPs) who work in the ICU are exposed to a stressful environment and, in the long run, this may lead to exhaustion and burnout. It is observed that the burnout in HCPs in the ICU may have an impact on patient care and the psychological wellbeing of the caregiver. Thus, we aimed to assess the burnout in HCPs working in the ICUs of a tertiary care hospital in South India. Methods A single-center, questionnaire-based survey was carried out by HCPs who work in the ICUs of a tertiary care hospital in South India. A Google form link was created after obtaining approval from the Institutional Ethics Committee. The link was then circulated to the HCPs who work in the ICU and the responses were collected. The Google form fetched data related to demographics, profession, area of work, duration of work per day, total days of work in the ICU during the work period, and details of night duty. The Oldenburg burnout inventory questionnaire was used to measure burnout in the HCPs. Results A total of 60 HCPs with a mean age of 23.37±2.93 years, consented and filled out the online questionnaire. Of the 60 HCPs, 41 (68.33%) were females and 19 (31.67%) were males. Most of the participants were working in adult medical ICUs. The overall burnout level in all the participants was 2.39± 0.31, with the exhaustion level being 2.45±0.43 and the disengagement level being 2.32± 0.31. Between 70% and 80% of HCPs experienced high levels of burnout while working in the ICUs. Work area, work duration, sleep duration, and clinical experience had an impact on burnout levels of the HCPs. Conclusion Most of the HCPs who work in the ICU experience high levels of burnout. Lack of clinical experience in the ICU and long work hours with lack of sleep can increase burnout in the HCPs.
Crystal structure determination of organic thin-films: the example of 2,2′ :6′,2″-ternaphthalene

Abstract This work presents a method for solving the crystal structure of an organic thin-film prepared on an isotropic surface. Combining specular X-ray diffraction and grazing incidence X-ray diffraction, a full structure solution is exemplarily derived for crystals of the molecule ternaphthalene (NNN). The data are analysed following a classic approach, first, by indexing the Bragg peak pattern and, second, by solving the structure using the experimentally observed intensities. Direct space methods with a rigid-body refinement are applied. The result shows that the NNN crystallizes in a layered herringbone structure. The calculated peak intensities based on this structure are in excellent agreement with the experimentally observed intensities. Overall, following this approach, the crystal structure of the molecule NNN grown in a preferred orientation within thin-films could be unambigously solved providing a general pathway for future thin-film structure solutions.
O ct 2 01 6 Disentangling random thermal motion of particles and collective expansion of source from transverse momentum spectra in high energy collisions

In the framework of a multisource thermal model, we describe experimental results of the transverse momentum spectra of final-state light flavour particles produced in gold-gold (Au-Au), copper-copper (Cu-Cu), lead-lead (Pb-Pb), proton-lead (p-Pb), and proton-proton (p-p) collisions at various energies, measured by the PHENIX, STAR, ALICE, and CMS Collaborations, by using the Tsallisstandard (Tsallis form of Fermi-Dirac or Bose-Einstein), Tsallis, and twoor three-component standard distributions which can be in fact regarded as different types of “thermometers” or “thermometric scales” and “speedometers”. A central parameter in the three distributions is the effective temperature which contains information on the kinetic freeze-out temperature of the emitting source and reflects the effects of random thermal motion of particles as well as collective expansion of the source. To disentangle both effects, we extract the kinetic freeze-out temperature from the intercept of the effective temperature (T ) curve as a function of particle’s rest mass (m0) when plotting T versus m0, and the mean transverse flow velocity from the slope of the mean transverse momentum (〈pT 〉) curve as a function of mean moving mass (m) when plotting 〈pT 〉 versus m.
The importance of social zeitgeber in paediatric type 1 narcolepsy: What we can learn from the COVID‐19 restrictions adopted in Italy?

The lockdown due to the new coronavirus pandemic (COVID‐19) has led to unparalleled changes in several aspects of human behaviour. During the lockdown, the general population delayed sleep timing and spent more time in bed; however, little is known on the effects of COVID‐19 restriction on children and adolescents suffering type 1 narcolepsy. In the last months of 2019, we performed follow‐up actigraphy in 18 type 1 narcolepsy children and adolescents under stable pharmacological treatment with sodium oxybate. We contacted these patients for a follow‐up actigraphy during the first Italian lockdown. Actigraphs and the Epworth Sleepiness Scale for children and adolescents (ESS‐CHAD) have been sent to participants’ homes. Differences in motor activity were analysed through functional linear modelling. During lockdown, type 1 narcolepsy children and adolescents went to bed and woke up later, slept more during the daytime and napped more frequently. No difference emerged in time in bed, estimated total sleep time and nocturnal sleep quality. Similarly, no difference emerged in ESS‐CHAD and body mass index. The time‐series analysis of motor activity documented reduced activity during the early morning and in the evening during the lockdown period compared with pre‐lockdown. Our study objectively showed that type 1 narcolepsy children and adolescents delayed the sleep phase and slept more during the daytime during the lockdown. The analysis of type 1 narcolepsy children and adolescents’ behaviour during the lockdown has provided new information that could pave the way to a personalized school programme.