Miracle-dz/UniFAR-FTUs huggingface dataset:
Atomic charges derived from semiempirical methods

It is demonstrated that semiempirical methods give electrostatic potential (ESP) derived atomic point charges that are in reasonable agreement with ab initio ESP charges. Furthermore, we find that MNDO ESP charges are superior to AM1 ESP charges in correlating with ESP charges derived from the 6‐31G* basis set. Thus, it is possible to obtain 6‐31G* quality point charges by simply scaling MNDO ESP charges. The charges are scaled in a linear (y = Mx) manner to conserve charge. In this way researchers desiring to carry out force field simulations or minimizations can obtain charges by using MNDO, which requires much less computer time than the corresponding 6‐31G* calculation.
Burn Center Management of Severe Necrotic Cutaneous Polyarteritis Nodosa in a Patient With a History of Thymoma

Cutaneous polyarteritis nodosa (cPAN) is a rare, necrotizing vasculitis involving the small- and medium-sized vessels of the dermis and subcutaneous tissues. We report a severe case of cPAN in a patient with an atypical presentation of extensive bilateral lower extremity ulcerations with full-thickness necrosis managed at a burn center. A 70-year-old female with a three-month history of necrotizing cPAN to the bilateral lower extremities underwent surgical excision and autografting at an outside hospital. Postoperatively, she had total graft loss and was begun on prednisone. In the outpatient setting, she was tapered off prednisone and subsequently began to experience an acceleration of the disease process. She was then transferred to our regional burn center for bilateral escharotomy and management of her non-healing, tender, necrotic wounds with distinctive black-brown eschar. One year later, the patient’s wounds continue to decrease in size and heal with her daily regimen of 15 mg of prednisone, 50 mg of cyclophosphamide, and topical silver sulfadiazine application. With the increasing volume of non-burn wound admissions to burn centers primarily of dermatologic etiology, it becomes crucial for burn specialists to familiarize themselves with severe presentations of vasculitides, including cPAN. Further research is necessary to understand the atypical manifestations of this disease for more timely diagnosis and treatment.
Current Status of COVID-19 Vaccine Development: Focusing on Antigen Design and Clinical Trials on Later Stages

The global outbreak of coronavirus disease 2019 (COVID-19) is still threatening human health, economy, and social life worldwide. As a counteraction for this devastating disease, a number of vaccines are being developed with unprecedented speed combined with new technologies. As COVID-19 vaccines are being developed in the absence of a licensed human coronavirus vaccine, there remain further questions regarding the long-term efficacy and safety of the vaccines, as well as immunological mechanisms in depth. This review article discusses the current status of COVID-19 vaccine development, mainly focusing on antigen design, clinical trials in later stages, and immunological considerations for further study.
Room temperature surface diffusion mechanisms observed by scanning tunneling microscopy

Using in situ electrochemical scanning tunneling microscopy, we have discovered several processes that mediate room temperature annealing of the gold (111) surface. These process are shown to be governed by motion of step‐edge adatoms and not terrace adatoms. This behavior emphasizes the importance of cooperative effects in low temperature crystal growth. A model of pit motion is proposed based on a random walk of step adatoms. This model predicts that the diffusivity is inversely proportional to the cube of the radius of a pit or island.
Predator community and resource use jointly modulate the inducible defense response in body height of crucian carp

Abstract Phenotypic plasticity can be expressed as changes in body shape in response to environmental variability. Crucian carp (Carassius carassius), a widespread cyprinid, displays remarkable plasticity in body morphology and increases body depth when exposed to cues from predators, suggesting the triggering of an antipredator defense mechanism. However, these morphological changes could also be related to resource use and foraging behavior, as an indirect effect of predator presence. In order to determine whether phenotypic plasticity in crucian carp is driven by a direct or indirect response to predation threat, we compared twelve fish communities inhabiting small lakes in southeast Norway grouped by four categories of predation regimes: no predator fish, or brown trout (Salmo trutta), perch (Perca fluviatilis), or pike (Esox lucius) as main piscivores. We predicted the body shape of crucian carp to be associated with the species composition of predator communities and that the presence of efficient piscivores would result in a deeper body shape. We use stable isotope analyses to test whether this variation in body shape was related to a shift in individual resource use—that is, littoral rather than pelagic resource use would favor the development of a specific body shape—or other environmental characteristics. The results showed that increasingly efficient predator communities induced progressively deeper body shape, larger body size, and lower population densities. Predator maximum gape size and individual trophic position were the best variables explaining crucian carp variation in body depth among predation categories, while littoral resource use did not have a clear effect. The gradient in predation pressure also corresponded to a shift in lake productivity. These results indicate that crucian carp have a fine‐tuned morphological defense mechanism against predation risk, triggered by the combined effect of predator presence and resource availability.
Depression and Obsessive-Compulsive Disorders Amid the COVID-19 Pandemic in Saudi Arabia

Introduction: Coronavirus disease 2019 (COVID-19) is a global pandemic with significant morbidity and mortality. The Saudi government adopted mandatory home quarantine and curfew hours for all residents, excluding essential service workers. During the lockdown, the public's fear of infection can adversely impact mental health, causing psychological distress. The objective of this research is to assess frequency of depression and obsessive-compulsive disorder (OCD) among the general population during COVID-19 pandemic in Saudi Arabia. Methodology: This was a cross-sectional study using the Patient Health Questionnaire (PHQ-9) and Obsessive-Compulsive Inventory-Revised assessment test (OCI-R) in Arabic and English languages distributed via social media platforms. Chi-square test was used with significance determined at p<0.005. Results: We received a total of 2187 responses. Our results showed that being female, single, and unemployed had a higher frequency of suffering from depression whereas higher income levels and higher education was associated with less depression frequency. Increasing age, males, married individuals, higher income groups, higher levels of education and employed individuals were more likely to have OCD during COVID-19 pandemic. Conclusion: The COVID-19 pandemic period is associated with significant mental health risks among the Saudi population. The results can provide further scientific support to better understand the impact of quarantine on psychological distress and mental health during emergency and disaster situations.
Hibernacula microclimate and declines in overwintering bats during an outbreak of white‐nose syndrome near the northern range limit of infection in North America

Abstract We document white‐nose syndrome (WNS), a lethal disease of bats caused by the fungus Pseudogymnoascus destructans (Pd), and hibernacula microclimate in New Brunswick, Canada. Our study area represents a more northern region than is common for hibernacula microclimate investigations, providing insight as to how WNS may impact bats at higher latitudes. To determine the impact of the March 2011 arrival of Pd in New Brunswick and the role of hibernacula microclimate on overwintering bat mortality, we surveyed bat numbers at hibernacula twice a year from 2009 to 2015. We also collected data from iButton temperature loggers deployed at all sites and data from HOBO temperature and humidity loggers at three sites. Bat species found in New Brunswick hibernacula include Myotis lucifugus (Little Brown Bat) and M. septentrionalis (Northern Long‐eared Bat), with small numbers of Perimyotis subflavus (Tricolored Bat). All known hibernacula in the province were Pd‐positive with WNS‐positive bats by winter 2013. A 99% decrease in the overwintering bat population in New Brunswick was observed between 2011 and 2015. We did not observe P. subflavus during surveys 2013–2015 and the species appears to be extirpated from these sites. Bats did not appear to choose hibernacula based on winter temperatures, but dark zone (zone where no light penetrates) winter temperatures did not differ among our study sites. Winter dark zone temperatures were warmer and less variable than entrance or above ground temperatures. We observed visible Pd growth on hibernating bats in New Brunswick during early winter surveys (November), even though hibernacula temperatures were colder than optimum for in vitro Pd growth. This suggests that cold hibernacula temperatures encountered near the apparent northern range limit for Pd do not sufficiently slow fungal growth to prevent the onset of WNS and associated bat mortality over the winter.
Prevalence and clinical correlates of insomnia symptoms and their association with quality of life in Chinese patients with HBV-related liver disease

Objective This study aimed to describe the one-month prevalence of insomnia symptoms (insomnia hereafter) and the demographic and clinical correlates, and its association with quality of life (QOL) in Chinese patients with HBV-related liver disease. Method A total of 689 patients with HBV-related liver disease in Beijing, China formed the study sample. Three forms of insomnia including difficulty initiating sleep (DIS), difficulty maintaining sleep (DMS) and early morning awakening (EMA) were assessed using standardized questions. QOL was measured using the Medical Outcomes Study Short Form 12 (SF-12). Results The one-month prevalence of at least one type of insomnia was 69.5%, while DIS, DMS and EMA were 60.4%, 54.7% and 50.9%, respectively. Only 4.8% of patients suffering from insomnia received treatment. Multiple logistic regression analyses revealed that pre-existing medical conditions were positively associated with DIS and EMA; patients with more severe depressive symptoms were more likely to have DIS, DMS and EMA; local residents were less likely to have DIS; and those who were married and older were more likely to have DMS. Insomnia was not independently associated with QOL. Conclusions Insomnia is common in Chinese patients with HBV-related liver disease with a very low rate of treatment. Greater attention should be given to identify and treat insomnia in this patient population.
Exploring polypharmacy phenomenon in newly diagnosed relapsing–remitting multiple sclerosis: a cohort ambispective single-centre study

Aims: We aimed to examine the frequency of polypharmacy in a large cohort of patients at the time of diagnosis of relapsing–remitting multiple sclerosis (RRMS) and to explore its effects on discontinuation of first disease-modifying treatment (DMT) using survival analysis. Methods: This was a cohort ambispective single-centre study. We enrolled RRMS patients starting their first DMT between 1st January 2013 and 31st December 2015. According to the number of medicines prescribed (except DMTs), we divided the patients into three groups: no-poly RRMS, minor-poly RRMS (from one to three medications), and major-poly RRMS (more than three medications). Results: A total of 392 RRMS patients were enrolled (mean age 41.1). The minor-poly RRMS group included 61 patients (15.6%) and the major-poly RRMS group included 112 (28.6%). Individuals in these groups were older and had higher median body mass index (BMI) than patients in the no-poly RRMS group (p < 0.05). Upon multinomial regression analysis, older age at onset was associated with minor and major polypharmacy (OR 1.050, CI 1.010–1.093, p = 0.015 and OR 1.063, CI 1.026–1.101, p = 0.001, respectively) and higher BMI was associated with major polypharmacy (OR 1.186, CI 1.18–1.29, p = 0.001). The rates of discontinuation of first DMT were similar among the three groups (50.7% for no-Poly RRMS, 50.8% for minor-Poly RRMS, and 53.3% for major-Poly RRMS, p = 0.264). At log-Rank test, there were no differences among the three groups (p = 0.834). Conclusion: Polypharmacy was more common in older RRMS patients with high BMI.
“Established” Respiratory Treatment in Acute Respiratory Distress Syndrome: Scientific Rigor or a Square Peg in a Round Hole?

Dr. Hardin, in his editorial (1), surmises that there is nothing new under the sun, particularly that established ventilatory approaches should also be applied to coronavirus disease (COVID-19) acute respiratory distress syndrome (ARDS) (C-ARDS). We know of only two trials in unselected (“average”) ARDS that provide significant results: one establishing that 6 ml/kg is better than 12 ml/kg and the other establishing that positive end-expiratory pressure (PEEP) higher than 15 cm H2O increases mortality. Further advances in ARDS treatment were only proved or suggested in subgroups: prone position if PaO2/FIO2 ratio is below 150 mm Hg and higher PEEP in hyperinflammatory phenotypes. Therefore, subgroups deviate from the average ARDS behavior and require modification of standard management. Like many, we are not so certain that all patients benefit from 6 ml/kg predicted body weight VT—or tolerate the suggested entries of a PEEP–FIO2 table. Outcomes from intermediate VT may be, on average, equivalent to a lower VT (2). Many clinicians seem to have already figured this out; VT in all groups of the Panwar study (3) was set in the 7–8 ml/kg range, which is similar to those in the quoted article by Hager and colleagues (4). Lung protection is linked to repetitive excessive “strain;” consequently, VT is ideally set individually in relation to gas volume or compliance (i.e., driving pressure) rather than predicted body weight. In patients with relatively preserved lung gas volumes (e.g., many with early-stage COVID-19), very low VTs may lead to dyspnea or asynchronies, adversely affecting the outcome. Conversely, even VT of 6 ml/kg may be excessive for some patients with very severe ARDS. In this context, it does not seem a paradox that in LUNG-SAFE (Large Observational Study to Understand the Global Impact of Severe Acute Respiratory Failure), patients with better compliance had a larger VT, and we do not think it reasonable to presume that these patients would have necessarily benefited from lower VT (1). Just as one VT does not translate into the same strain, a higher PEEP may improve oxygenation and outcome (i.e., if there is extensive recruitable lung tissue), or overstretch compliant airspaces. That some small minority of patients with broadly defined ARDS might be found that resemble some stage of the evolving C-ARDS physiology is hardly surprising. What is different, however, is that unexpectedly high gas volumes and compliance occur routinely despite infiltrates and impressive hypoxemia in the early stages of C-ARDS (5). Therefore, why infer that considering respiratory mechanics and recruitability when choosing VT and PEEP is somehow heretical, advocating a strategy “the same as it ever was”? Patients with C-ARDS are not your “average” ARDS. n Author disclosures are available with the text of this letter at www.atsjournals. org.
Modeling flow-induced crystallization of polymers

A depletion of molecules long enough to form precursors [3] is incorporated in gp. Furthermore, we assume that flow inhibits nucleation. A simple step function, where τpn jumps from infinity to zero as the flow is switched off, suffices for the experiments used here. Growth of pointlike precursors into threadlike precursors is also modeled, but this part has not been validated by experiments yet.
Effect of Lactic Acid Bacteria on Beef Steak Microbial Flora Stored Under Modified Atmosphere and on Listeria Monocytogenes in Broth Cultures

Beef steaks were inoculated with one or other of two protective strains of lactic acid bacteria, the bacteriocinogenic Lactobacillus sakei CTC 372 or the uncharacterised Lactobacillus CTC 711. They were stored under modified atmospheres (20–40% CO2). Inoculation of meat with both strains inhibited the growth of the spoilage bacteria. Neither CO2 in the pack atmosphere, inoculation with protective strains, nor a combination of both, affected formation of metmyoglobin or the development of off-odours. The formation of metmyoglobin in meat pigments and the sensory odour scores were compatible to those of fresh meat which had not undergone either oxidative deterioration or microbial spoilage. Listeria monocytogenes were inhibited in broth by meat surface microbiota containing either of the protective strains. With an initial population of 5.6 log cfu/mL, after 7 days incubation at 3°C, Listeria monocytogenes were recovered at log mean population of 2.8 log cfu/mL when neither protective strain was present. At 8°C, the population of Listeria monocytogenes recovered were reduced by about 2.5 or 1.5 log cfu/mL in the presence of Lactobacillus sakei CTC 372 or Lactobacillus CTC 711, respectively. At 25°C, the population of Listeria monocytogenes recovered from broth containing either protective strain were about 5 log cfu/mL less than the population recovered from broth containing Listeria monocytogenes only.
LC-MS/MS-Based Quantitative Proteomics Analysis of Different Stages of Non-Small-Cell Lung Cancer

Lung cancer has a higher incidence rate and mortality rate than all other cancers. Early diagnosis and treatment of lung cancer remain a major challenge, and the 5-year survival rate of its patients is only 15%. Basic and clinical research, especially the discovery of biomarkers, is crucial for improving the diagnosis and treatment of lung cancer patients. To identify novel biomarkers for lung cancer, we used the iTRAQ8-plex labeling technology combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze the serum and urine of patients with different stages of lung adenocarcinoma and healthy individuals. A total of 441 proteins were identified in the serum, and 1,161 proteins were identified in the urine. The levels of elongation factor 1-alpha 2, proteasome subunit alpha type, and spermatogenesis-associated protein increased significantly in the serum of patients with lung cancer compared with those in healthy controls. The levels of transmembrane protein 143, cadherin 5, fibronectin 1, and collectin-11 decreased significantly in the serum of patients with metastases compared with those of nonmetastatic lung cancer patients. In the urine of stage III and IV lung cancer patients, the prostate-specific antigen and prostatic acid phosphatase decreased significantly, whereas neutrophil defensin 1 increased significantly. The results of LC-MS/MS were confirmed by enzyme-linked immunosorbent assay (ELISA) for transmembrane protein 143, cadherin 5, fibronectin 1, and collectin-11 in the serum. These proteins may be a potential early diagnosis and metastasis biomarkers for lung adenocarcinoma. Furthermore, the relative content of these markers in the serum and urine could be used to determine the progression of lung adenocarcinoma and achieve accurate staging and diagnosis.
Risk Factors of Diarrhoea among Children Under Five Years in Southwest Nigeria

Diarrhoea is the passage of three or more loose or liquid stools per day or more frequent passage than is normal for an individual. Diarrhoea alters the microbiome, thus the immune system, and is a significant cause of morbidity and mortality in young children. This study evaluated the association between the risk factors and diarrhoea prevalence among children under five years in Lagos and Ogun States, located in Southwest Nigeria. Participants included 280 women aged 15–49 years and children aged 0–59 months. The study used quantitative data, which were assessed by a structured questionnaire. Data obtained were analyzed using the Statistical Package for the Social Sciences Software Version 25.0 and Microsoft Excel 2013. The relationships and/or association between variables were evaluated using Pearson's Chi Square and logistic regression tests. One hundred and eighteen (42%) of the children were male, and 162 (58%) were female. The majority of the children belonged to the age group 0–11 months (166). Age (p=0.113) and gender (p=0.366) showed no significant association with diarrhoea among the children. The majority of the mothers belonged to the age group 30–34. Multivariate analysis showed that the mother's level of education (95% CI for OR = 11.45; P=0.0001) and family income (95% CI for OR = 7.61, P=0.0001) were the most significant risk factors for diarrhoea among children. Mother's educational status, mother's employment, and family income were the factors significantly associated with diarrhoea in Southwest Nigeria. The study recommends that female education should be encouraged by the right government policy to enhance the achievement of the sustainable development goal three (SDG 3) for the possible reduction of neonates and infants' deaths in Nigeria.
Immunization Status and Challenges During COVID-19 and Associated Factors Among Children Aged 10–23 Months in South Region, Ethiopia 2020

Background The worldwide COVID-19 pandemic is overstressing health systems and Essential health services and vaccination services are disrupted. Immunization is a confirmed gizmo for governing and even eliminating communicable diseases. Objective This study aims to assess the challenge and status of immunization during COVID-19 and associated factors among children aged 10–23 months south Nation Nationality and People Region Ethiopia. Methods and Materials: community-based mixed quantitative and qualitative cross-sectional study was done in southwest Ethiopia. Data was collected using semi-structured questionnaires and in-depth interviews. After that, the data were edited, coded, and move in into Epi info version 7.2 for data management then transported to SPSS version 25 for analysis. The analyzed data were presented by tables, graphs, figures, and text form. Results According to this study, the prevalence of incomplete immunization was found to be 809 (62.2%) with (95% CI: 59.5, 64.8). In multivariable analysis waiting time at a health facility (AOR=0.04, 95% CI 0.0001,0.004), education (AOR=5.08,95% CI2.31,11.14), place of delivery (AOR=2.34,95% CI 4.96,6.089), fearing of COVID-19 (AOR=3.62,95% CI 1.72,7.64) and do not understand the separation care of COVID-19 and other health services (AOR=2.85,95% CI1.38,5.9) were significantly associated factors. Conclusion The prevalence of incomplete immunization among children aged 10–23 months was very high in this study as compared to the other studies done in a different pocket of Ethiopia. Consecutively, reducing waiting time at a health facility, avoiding unnecessary fear of COVID-19, and promoting immunization in a different area of southwest Ethiopia along with health extension workers are recommended.