Miracle-dz/UniFAR-FTUs huggingface dataset:
Rampant C¡U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a data set of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean of 5.5 to 9.5 nucleotide differences from each other, consistent with a midrange coronavirus substitution rate of 3 10 4 substitutions/site/ year. Almost one-half of sequence changes were C¡U transitions, with an 8-fold base frequency normalized directional asymmetry between C¡U and U¡C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARSCoV, Middle East respiratory syndrome [MERS]-CoV), and decreasing ratios were observed in other human coronaviruses (HCoV-NL63, -OC43, -229E, and -HKU1) proportionate to their increasing divergence. C¡U transitions underpinned almost one-half of the amino acid differences between SARS-CoV-2 variants and occurred preferentially in both 5= U/A and 3= U/A flanking sequence contexts comparable to favored motifs of human APOBEC3 proteins. Marked base asymmetries observed in nonpandemic human coronaviruses (U A G C) and low G C contents may represent long-term effects of prolonged C¡U hypermutation in their hosts. The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their shortand long-term evolution. Repeated cycles of mutation and reversion in favored mutational hot spots and the widespread occurrence of amino acid changes with no adaptive value for the virus represent a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks and are not incorporated by standard models used in molecular epidemiology inves-
Interactive comment on “Description and evaluation of aerosol in UKESM1 and HadGEM3-GC3.1 CMIP6 historical simulations” by

Aerosol modeling is a major challenge, in particular aerosol-cloud interactions. This work evaluates the performance of the GLOMAP-mode modal aerosol scheme when implemented in the GCM HadGEM3-GC3.1, and the larger ESM UKESM1 which is built on top of that GCM. The authors provide a comprehensive description of relevant differences between the two models. Using an ensemble of results from each model, they describe relevant differences in the aerosol simulations by each model when using GLOMAP, performing extensive comparison to observations. They also evaluate the effect of implementing a parameterization for marine primary organic aerosol emissions into UKESM1.
Short-Term Contemplative Practices with Vocalization Alter Psychological States in an Unexperienced Student Sample

Traditional contemplative practices including yoga and meditation have been shown to cause plastic changes to the neurophysiological, psychological, and somatic functions in adult humans. Would desirable changes in psychological states occur when unexperienced participants engage in short-term contemplative practices? The present study examined changes in affective and relevant psychological states when university undergraduate students with no daily training of yoga or meditation participated in a session of contemplative practices that involve vocalization. Ten university undergraduate students were assigned to a practice group, and participated in a session of contemplative practices lasting for approximately 75 minutes. Specific content of the practice included mantra meditation with vocalization, prostration with mantra chanting, and “overtone chanting,” i.e., a traditional contemplative practice originated in the Nyingma school of Tibetan Buddhism in which participants continuously vocalize vowels in a group. The practice session was guided by a professional yoga instructor. In addition, another 18 undergraduates who were also naïve to meditation were assigned to the control group, and engaged in a 75-min free description regarding the content of the lecture course in which these students participated. Both prior to and immediately after the session, participants from these two groups completed an identical battery of questionnaires concerning positive/negative affect (PANAS), state anxiety (STAI-S), and degree of relaxation. For the practice group, scores of anxiety significantly decreased and those of relaxation significantly increased after the practice session. By contrast, statistically significant changes in the scores failed to be observed for the control group. These results support the notion that short-term contemplative practices that involve continuous vocalization can cause desirable changes to the psychological states such as reducing anxiety and enhancing relaxation, regardless of prior experience with the contemplative training. Future studies may focus on the effect of each specific form of practice, long-term effects of repeated practice sessions, as well as potential changes at the neurophysiological level including autonomic nervous system activities and cerebral hemodynamics.
Association Between Serum Uric Acid Levels and Progression of Coronary Artery Calcification in Asian Population

Background: Coronary artery calcium (CAC) is associated coronary heart disease risk. In addition, CAC progression is associated with worsening coronary atherosclerosis and predicts future cardiac events. We aimed to investigate risk factors for the progression of CAC in an asymptomatic Japanese population using low dose computed tomography (CT) lung cancer screening performed during routine health checkup.Methods: The risk factors for CAC progression were analyzed in 771 asymptomatic subjects who underwent repeated CAC measurement. Results: Of the 771 subjects, 632 (82.0%) were males with a mean age of 56 years old, 208 (27.0%) had a history of hypertension, 299 (38.8%) had dyslipidemia, 81 (10.5%) had diabetes mellitus, and 180 (23.3%) had hyperuricemia. During observation, 103 (13.4%) subjects had CAC progression, while 515 subjects (66.8%) showed no calcification. On multivariate analysis, increasing uric acid level was significantly associated with the progression of CAC (odds ratio 1.203, 95% confidence interval 1.045-1.387, P = 0.010). Conclusions: The results of this study show that hyperuricemia is associated with CAC progression in asymptomatic Japanese subjects.
Computational Modeling Indicates A Decreased Affinity of SARS-CoV-2 to ACE2 by Steroids

The novel coronavirus disease (COVID-19) presently poses significant concerns around the world. Latest reports show that the degree of disease and mortality of COVID-19 infected patients may vary from gender to gender with a very high risk of death for seniors. It was hypothesized that sex steroid hormones estradiol (E2), progesterone (P4), testosterone (T), and dexamethasone (DEX) may change the interaction of coronavirus spike protein (CSP) with angiotensin converting enzyme-2 (ACE2). Data showed that E2 was more strongly to interact with the main protease of the coronavirus, while T had the lowest affinity for CSP. The binding energy of the CSP to ACE2 was increased in the presence of steroids; the greatest increase was observed by DEX and E2. The binding free energy of the CSP to ACE2 was the highest in the presence of E2 and DEX. Together, the interaction between CSP and ACE2 can be disrupted by E2 and to a greater extent by DEX, in part explaining the lower incidence of COVID-19 infection in women than men. The potential use of E2 and DEX to reduce coronavirus attachment to ACE2 in the early phase of the coronavirus invasion needs to be clinically investigated.
Activity recognition and animation of activities of daily living

Activities of Daily Living (ADL) can give us information about an individual’s health, both physical and mental. They are captured using sensors and then processed and recognized into different activities. Activity recognition is the process of understanding a person’s movement and actions. In this work, we develop a language in a simple grammar that describes the activity and uses it to recognize the activity. We call this language as Activities of Daily Living Description Language, or A(DL) 2 in short. Even after an activity has been recognized, the data it represents is still digital data and it would take some expertise and time to understand it. To overcome this problem, a system that can visualize and animate individuals’ activity in real time without violating any privacy issues, can be built. This will not only help in understanding the current state of individual but will also help those who are in charge of monitoring them remotely like nurses, doctors, family members, thereby rendering better care and support especially to the elderly people who are aging. We propose a real time activity recognition and animation system that recognizes and animates the individual’s activity. We experimented with one of the basic ADLs, walking, and found the result satisfactory. Individuals location is tracked using sensors and is sent to the recognition system which then decides the type of activity in real time by using the language to describe it, and then the data is sent to a visualization system which animates that activity. When fully developed, this system intends to serve the purpose of providing better health care and immediate support to the people in need.
Cationic polyesters bearing pendent amino groups prepared by thiol–ene chemistry

A straightforward approach based on thiol–ene click chemistry was used to prepare novel functional polyesters containing amino groups. First, a series of well-defined alkene-functional poly(e-caprolactone)s were prepared by ring-opening polymerization of α-allyl-e-caprolactone with e-caprolactone in toluene and in bulk using tin 2-ethylhexanoate as catalyst. These functional polyesters were fully characterized by 1H NMR, GPC, and MALDI-TOF MS. The resulting random copolyesters were obtained with a wide range of molar masses from 3000 to 50 000 g mol−1 and a good incorporation of the α-allyl-e-caprolactone monomer unit. Then, thiol–ene reaction of alkene-functional PCL with the 2-(Boc-amino)ethanethiol was used to prepare efficiently polyesters bearing protected amino groups without chain degradation. Finally, cationic and water-soluble polyesters bearing free amino groups were recovered by cleavage of the Boc protecting group. These aminated polyesters were characterized by 1H NMR in deuterated water.
Role of Acacia seyal on Selected Soil Properties and Sorghum Growth and Yield: A Case Study of Guba Lafto District, North Wollo, Ethiopia

Acacia seyal is one of the multipurpose parkland agroforestry tree species in eastern and southern Africa. It is a common on-farm tree in the Rift Valley of Ethiopia, but information is limited on its effect on soil properties and sorghum growth and yield. The study was conducted to evaluate its effect on selected soil properties and sorghum growth and yield in Guba Lafto district of northern Ethiopia. Six isolated and closely comparable Acacia seyal trees growing on sorghum farms were purposely selected, and plots were marked under the canopy of trees with three radial distances (0–2 m, 2–4 m, and 4–6 m) and one outside of the tree canopy (10 m away from any tree). Soil samples from each distance zone were taken between 0–20 cm and 20–40 cm soil depths for soil property analysis. Four quadrates with 1 m2 at each distance zone in four directions were laid for sorghum growth and yield attribute valuation. The results showed that only total nitrogen (TN) was significantly higher ( ) at the subsoil layer under the canopy compared to an open area, while other selected soil parameters were not affected by the tree species. Sorghum biomass yield ( ) and grain yield ( ) were significantly lower under the canopy of the trees than in the open area. Generally, Acacia seyal had little effect in improving soil properties and showed a negative effect on sorghum yield and growth. Further research on its effect under wide area coverage of parkland system should be performed to bring a radical shift on the intercropping farming system.
In vitro synthesis of berberine, a pharmacologically important isoquinoline alkaloid in callus cultures of Tinospora cordifolia

Callus cultures were raised from young green leaf segments of the medicinal climber Tinospora cordifolia in Murashige and Skoog’s media containing different growth regulator regime. The in vitro callus cultures were analysed for the accumulation of active principle through high-performance liquid chromatography. Quantitative analysis of berberine was achieved by thin-layer chromatography and UV-absorbance method. Callus cultures accumulated an appreciable amount of berberine. A maximum of 355 μg/g dry wt accumulation of berberine was noted when the callus was grown in the presence of 2 mg/l 2, 4-D and 0.1 mg/l BA. However, maximum callus growth was achieved in the presence of 0.5 mg/l BA and 2 mg/l 2,4-D. Maximum tissue growth didn't favour an increased accumulation of the berberine. Enhanced accumulation of berberine was found when callus growth was less and therefore may be associated with the stress faced by in vitro tissues. The experimental results indicate that it is desirable to adopt two different growth regulator regime - one for accelerated callus growth and another for enhanced in vitro synthesis of berberine. The in vitro cultures of T. cordfiolia also offers an ideal system for understanding the studies on elucidating alternate routes of berberine biosynthetic pathway as well as possible elite cells for scaling up of berberine.
BATCH VERSUS COLUMN METHOD FOR DETERMINING DISTRIBUTION OF ORGANICS BETWEEN SOIL AND WATER PHASES

The batch equilibrium and a continuous flow (column) procedures were compared to determine if similar pesticide distribution coefficients could be obtained for the two methods. Using a low infiltration rate of 2.7 cm day−1, essentially identical values were obtained by the two methods for the distribution of napropamide and lindane between the sorbed and solution phases in a Pachappa sandy loam. Values for Koc of 421 and 1300 L kg−1 were measured for napropamide and lindane, respectively, at 20°C. Distribution coefficients decreased with increasing temperature. In the column experiments, similar values for the distribution coefficients were obtained regardless of whether the amounts of pesticide sorbed were determined by direct extraction of the soil or by the difference between quantities added to the columns and the quantities of solute in the effluent. Both linear and Freundlich isotherm models were used to calculate distribution coefficients. The soil column breakthrough curves were reproducible in duplicate runs for both napropamide and lindane. When distribution coefficients were estimated using a chemical retardation factor from the column experiments, the coefficients were consistently larger than those determined by the batch equilibrium method.
Changes in hematological, biochemical, and blood gases parameters in response to progressive inclusion of nitrate in the diet of Holstein calves

Background and Aim: Nitrate (NO3-) reduces enteric methane emissions and could be a source of non-protein nitrogen in ruminant feeds. Nonetheless, it has a potential toxic effect that could compromise animal health and production. The purpose of this study was to determine the effects of progressive inclusion of NO3- in the diet on the hematological, biochemical, and blood gases parameters, in turn, the effects on feed intake and live weight gain (LWG) in Holstein calves. Materials and Methods: Eighteen Holstein heifers and steers (nine animals/treatment) were maintained in individual pens for 45 days. Animals were randomly allocated to either a control or nitrate diet (ND) (containing 15 g of NO3-/kg of dry matter [DM]). The biochemical parameters and blood gases were analyzed only in the NO3- group on days: -1, 1, 7, 13, 19, and 25 corresponding to 0, 20, 40, 60, 80, and 100% of the total inclusion of NO3- in the diet, respectively. In addition, DM intake (DMI) and LWG were evaluated among dietary treatments. Results: Feeding the ND did not influence DMI or LWG (p>0.05). Methemoglobin (MetHb) and deoxyhemoglobin increased according to the NO3- concentrations in the diet (p<0.05), while an opposite effect was observed for oxyhemoglobin and carboxyhemoglobin (p<0.05). Hematocrit levels decreased (p<0.05), while albumin, alanine aminotransferase, and gamma-glutamyl transpeptidase concentrations were not modified (p>0.05). However, glucose, urea, aspartate aminotransferase (AST), and retinol concentrations increased (p<0.05) according to the NO3- concentrations in the diet. Conclusion: This study confirmed that the progressive inclusion of 123 g of NO3-/animal/day in the diet could be safe without affecting DMI and LWG of Holstein calves. In turn, a dose-response effect of the MetHb, glucose, urea, AST, and retinol was observed, but these values did not exceed reference values. These results highlighted the importance of using a scheme of progressive inclusion of NO3- in the diet of calves to reduce the risks of NO3- toxicity.
Solid-Pseudopapillary Neoplasm of the Pancreas: A 63-Case Analysis of Clinicopathologic and Immunohistochemical Features and Risk Factors of Malignancy

Purpose Solid-pseudopapillary neoplasm (SPN) of the pancreas, a rare tumor, has low malignant potential. However, some patients develop metastasis and recurrence after resection, with aggressive biological behaviors. This study aimed to explore the features and risk factors associated with the aggressive biological behaviors of SPNs. Patients and Methods We retrospectively analyzed the clinicopathological and long-term follow-up data of 63 patients diagnosed with SPN at the First Affiliated Hospital of Bengbu Medical College between January 2007 and February 2019. Results Sixty-three patients presented atypical clinical symptoms. The median tumor size was 7.0 cm (range, 2.4–17 cm), and imaging features were solid and cystic or solid tumors with uneven density. Frequent and diffuse nuclear LEF1 protein expression (94.2%) was observed with LEF1 having a higher sensitivity and specificity. Overall survival significantly correlated with tumor size, Ki-67 index, and lymph node metastasis (P < 0.05). Conclusion SPN is a rare low-grade malignancy with a specific pseudopapillary structure. LEF1 is an effective biomarker of SPNs. Although SPNs generally display indolent biological behavior, a large tumor size, high proliferation index, and lymph node metastasis may be risk factors for the aggressive behavior and poor prognosis of SPN.
Preregistered Replication of “Feeling Superior Is a Bipartisan Issue: Extremity (Not Direction) of Political Views Predicts Perceived Belief Superiority”

There is currently a debate in political psychology about whether dogmatism and belief superiority are symmetric or asymmetric across the ideological spectrum. Toner, Leary, Asher, and Jongman-Sereno (2013) found that dogmatism was higher among conservatives than liberals, but both conservatives and liberals with extreme attitudes reported higher perceived superiority of beliefs. In the current study, we conducted a preregistered direct and conceptual replication of this previous research using a large nationally representative sample. Consistent with Toner et al.’s findings, our results showed that conservatives had higher dogmatism scores than liberals, whereas both conservative and liberal extreme attitudes were associated with higher belief superiority compared with more moderate attitudes. As in their study, we also found that whether conservative or liberal attitudes were associated with higher belief superiority was topic dependent. Contrasting Toner et al.’s findings, our results also showed that ideologically extreme individuals had higher dogmatism. We discuss implications of these results for theoretical debates in political psychology.
Fiber orientation effect on fracture toughness of silk fiber-reinforced zeolite/HDPE composites

The aim of this work is to investigate the fracture toughness and deformation of silk fiber (SF)-reinforced zeolite (Z)/high density polyathylene (HDPE) composites. The chopped SFs are arranged in the thickness middle of the dry mixture of Z/HDPE powder that has been prepared in a mold. Composites were produced by the compression molding to produce double-edge notch tensile (DENT). The fracture toughness characterization was carried out based on essential work of fracture method. The results show that the presence of SF increased the essential fracture work even though the non-essential fracture work for Z/HDPE was higher than S-Z/HDPE. The evolution of plastic zone growth coincides with the growth of the fracture process zone (FPZ) whose height has no effect on energy consumption.
Automating Metamorphic Testing in Large Scale Systems

Software testing is a crucial part of software development. It enables assurance, of correctness, completeness, and reliability of software systems. Most state-of-the-art software testing techniques employ approaches that require the tester to have some kind of an oracle in order to evaluate the outcomes of the tests within the suite. Metamorphic testing[1] is specifically designed to test software without such an oracle. The idea is to identify and refine a set of metamorphic relations between the software inputs and outputs. Just to give an abstract example, for a square root function sqrt(x) the relation x = sqrt(x)· sqrt(x) should hold under reasonable floating point accuracies.
LHF Connect: a DIY telepresence robot against COVID-19

This contribution describes a case study of a “do-it-yourself” (DIY) opensource service and related product to help combating the COVID-19 emergency. It illustrates the birth of LHF Connect, a project designed to facilitate communication between patients isolated in COVID-19 hospitals’ ward and their relatives. LHF Connect is a teleoperated robot that can move in autonomy around the hospital. A User Centered Design approach, methods and specific tools helped in managing crucial steps of the design process such as i) the collection of needs coming from the context, stakeholders and end-users; ii) defining the service blueprint; iii) imagining finishing concepts; and iv) managing the communication activities. The initiative has been promoted by a multidisciplinary team of researchers (mainly roboticists with the help of specific competences coming from Design discipline).
Development of a multipurpose alpha detection procedure for enriched uranium in urine

Abstract An anion exchange-liquid scintillation procedure for detecting enriched uranium alpha emissions in urine is described. Uranium is removed from extraneous elements by anion exchange. The uranium is eluted from the column and extracted into a liquid scintillator before being counted in a photon-electron rejecting alpha liquid scintillation spectrometer. The average recovery was 92 percent at the 0.9 dpm level.