Miracle-dz/UniFAR-FTUs huggingface dataset:
A Review on Herbal Secondary Metabolites Against COVID-19 Focusing on the Genetic Variants of SARS-CoV-2

Context: An outbreak of the new coronavirus disease 2019 (COVID-19) was reported in Wuhan, China, in December 2019, subsequently affecting countries worldwide and causing a pandemic. Although several vaccines, such as mRNA vaccines, inactivated vaccines, and adenovirus vaccines, have been licensed in several countries, the danger of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants persists. To date, Alpha (B.1.1.7), Beta (B.1.351, B.1.351.2, B.1.351.3), Delta (B.1.617.2, AY.1, AY.2, AY. 3), Gamma (P.1, P.1.1, P.1.2), and Iota (B.1 .526) circulating in the United States, Kappa (B.1.617.1) in India, Lambda (C.37) in Peru and Mu (B.1.621) in Colombia are considered the variants of concern and interest. Evidence Acquisition: Data were collected through the end of August 2021 by searching PubMed, Scopus, and Google Scholar databases. There were findings from in silico, in vitro cell-based, and non-cell-based investigations. Results: The potential and safety profile of herbal medicines need clarification to scientifically support future recommendations regarding the benefits and risks of their use. Conclusions: Current research results on natural products against SARS-CoV-2 and variants are discussed, and their specific molecular targets and possible mechanisms of action are summarized.
Compound Homozygous Rare Mutations in PLCE1 and HPS1 Genes Associated with Autosomal Recessive Retinitis Pigmentosa in Pakistani Families

Background: Retinitis pigmentosa (RP) belongs to pigmentary retinopathies, a generic name for all retinal dystrophies with a major phenotypical and genotypical variation, characterized by progressive reduction of photo-receptor functionality of the rod and cone. Global prevalence of RP is ~ 1/4000 and it can be inherited as autosomal dominant (adRP), autosomal recessive (arRP) or X- linked (xlRP). We designed this study to identify causative mutations in Pakistani families affected with arRP. Methods: In 2019, we recruited two unrelated Pakistani consanguineous families affected with progressive vision loss and night blindness from Punjab region. Clinical diagnosis confirmed the; bone spicule pigmentation of the retina, and an altered electroretinogram (EGR) response. Proband and healthy individual from each family were subjected for whole-exome sequencing (WES). Various computational tools were used to analyze the Next Generation Sequencing (NGS) data and to predict the pathogenicity of the identified mutations. Results: WES data analysis highlighted two missense homozygous variants at position c.T1405A (p.S469T) in PLCE1 and c.T11C (p.V4A) in HPS1 genes in proband of both families. Healthy individuals of two families were tested negative for p.S469T and p.V4A mutations. The variant analysis study including molecular dynamic simulations predicted mutations as disease causing. Conclusion: Compound effect of mutations in rarely linked PLCE1 and HPS1 genes could also cause RP. This study highlights the potential application of WES for a rapid and precise molecular diagnosis for heterogeneous genetic diseases such as RP.
MND1 functions as a potential prognostic biomarker associated with cell cycle and immune infiltration in kidney renal clear cell carcinoma

Kidney renal clear cell carcinoma (KIRC) is a common and invasive subtype of renal tumors, which has poor prognosis and high mortality. MND1 is a meiosis specific protein that participates in the progress of diverse cancers. Nonetheless, its function in KIRC was unclear. Here, TIMER, TCGA, GEO databases and IHC found MND1 expression is upregulated in KIRC, leading to poor overall survival, and MND1 can serve as an independent prognostic factor. Moreover, enrichment analysis revealed the functional relationship between MND1 and cell cycle, immune infiltration. EdU and transwell assays confirmed that MND1 knockdown surely prohibited the proliferation, migration, and invasion of KIRC cells. Additionally, immune analysis showed that MND1 displayed a strong correlation with various immune cells. Interference with MND1 significantly reduces the expression of chemokines. TCGA and GEO databases indicated that MND1 expression is significantly related to two m6A modification related gene (METTL14, IGF2BP3). Finally, the drug sensitivity analysis revealed 7 potentially sensitive drugs for KIRC patients with high MND1 expression. In conclusion, MND1 can be used as a prognostic biomarker for KIRC and provides clues regarding cell cycle, immune infiltrates and m6A. Sensitive drugs may be an effective treatment strategy for KIRC patients with high expression of MND1.
Outliers and Robustness for Ordinal Data

This chapter tackles the topics of robustness and multivariate outlier detection for ordinal data. We initially review outlier detection methods in regression for continuous data and give an example which shows that graphical tools of data analysis or traditional diagnostic measures based on all the observations are not sufficient to detect multivariate atypical observations. Then we focus on ordinal data and illustrate how to detect atypical measurements in customer satisfaction surveys. Next, we review the generalized linear model of ordinal regression and apply it to the ABC survey. The chapter concludes with an analysis of a set of diagnostics to check the goodness of the suggested model and the presence of anomalous observations.
SPECTROPHOTOMETRIC INDICES AND METAL CONTENT OF GALACTIC GLOBULAR CLUSTERS

Spectrophotometric indices for $18$ Galactic globular clusters, obtained from CCD observations and careful reductions, were used to determine reliable calibrations on metallicity $[Fe/H]$. The indices were measured in the bandpasses adopted by Burnstein et al. (\cite{BFGK84}). Adding other observations of Burnstein et al. (\cite{BFGK84}) we obtained our results from an homogeneous sample of indices for $26$ globular clusters. Relations with indices defined by other Authors and with metallicity photometric indices or parameters were also computed. In each case the relations are quite satisfactory. Observational data were compared with synthetic indices derived from Buzzoni's (\cite{B89}) models and detailed discussions were performed for $Mg_2$, $Fe_{52}$, and $H_\beta$. The observational points seem to be systematically shifted with respect to the fiducial lines traced by the models. The scenario confirms that a certain degree of oxygen enhancement would be necessary to obtain a better agreement between observed data and theoretical predictions. This enhancement, however, removes some of the disagreement, but not all of it. The dependence of the observed $Fe_{52}$ and $H_\beta$ indices on the metal content for different HB morphologies was considered. Finally, some results were also discussed from a statistical point of view. A principal component analysis was applied to the index sample to study the number of independent parameters necessary to reproduce the observations. The whole index set is completely consistent with a one-parameter family.
Optimization of the W7-X pumping system

Analysis of neutral particle transport is of importance for the successful steady-state divertor operation proposed for the stellarator W7-X. In addition to the range of magnetic configurations and the incident energy flux, the divertor design for W7-X is also being optimized for an additional control over the plasma using the particle sources in the divertor region [1]. The present work aims at characterizing the plasma and neutral particle transport processes in the plasma edge region using the 3D Monte Carlo code EMC3-EIRENE [2, 3]. The self-consistent analysis of plasma and neutral transport is done in order to optimize the divertor operation by effectively controlling the exposure of neutral particles in subdivertor volume to the edge plasma. The study involves simulation of the plasma transport to determine the density, temperature and flow velocity profiles
Max vs Min: Independent Component Analysis with nearly Linear Sample Complexity

We present an efficient algorithm for standard ICA that needs only a nearly linear number of samples and has polynomial time complexity. The algorithm is a recursive version of the Fourier PCA method of Goyal et al. Its analysis is based on properties of random polynomials, namely the spacings of an ensemble of polynomials.
COMPARISON BETWEEN WEIBULL AND COX PROPORTIONAL HAZARDS MODELS

The time for an event to take place in an individual is called a survival time. Examples include the time that an individual survives after being diagnosed with a terminal illness or the time that an electronic component functions before failing. A popular parametric model for this type of data is the Weibull model, which is a flexible model that allows for the inclusion of covariates of the survival times. If distributional assumptions are not met or cannot be verified, researchers may turn to the semi-parametric Cox proportional hazards model. This model also allows for the inclusion of covariates of survival times but with less restrictive assumptions. This report compares estimates of the slope of the covariate in the proportional hazards model using the parametric Weibull model and the semi-parametric Cox proportional hazards model to estimate the slope. Properties of these models are discussed in Chapter 1. Numerical examples and a comparison of the mean square errors of the estimates of the slope of the covariate for various sample sizes and for uncensored and censored data are discussed in Chapter 2. When the shape parameter is known, the Weibull model far out performs the Cox proportional hazards model, but when the shape parameter is unknown, the Cox proportional hazards model and the Weibull model give comparable results.
Aerobic Exercise Training Rejuvenates the Human Skeletal Muscle Methylome Ten Years after Breast Cancer Treatment and Survival

Cancer survivors suffer impairments in skeletal muscle (SkM) in terms of reduced mass and function. Interestingly, human SkM possesses an epigenetic memory of earlier stimuli, such as exercise. Long-term retention of epigenetic changes in SkM following cancer survival and/or exercise training have not yet been studied. We therefore investigated genome-wide DNA methylation (methylome) in SkM following a 5-month, 3/week aerobic training intervention in breast cancer survivors 10-14 years after diagnosis and treatment. These results were compared to breast cancer survivors who remained untrained and to age-matched controls with no history of cancer, who undertook the same training intervention. SkM biopsies were obtained before(pre) and after(post) the 5-month training period and InfiniumEPIC 850K DNA methylation arrays performed. The breast cancer survivors displayed a significant retention of increased DNA methylation (i.e., hypermethylation) at a larger number of differentially methylated positions (DMPs) compared with healthy age-matched controls pre-training. Training in cancer survivors led to an exaggerated number of DMPs with a hypermethylated signature occurring at random non-regulatory regions across the DNA compared with training in healthy age-matched controls. However, the opposite occurred in important gene regulatory regions, where training in cancer survivors elicited a considerable reduction in methylation (i.e., hypomethylation) in 99% of the DMPs located in CpG islands within promoter regions. Importantly, training was able to reverse the hypermethylation identified in cancer survivors back towards a hypomethylated signature that was observed pre-training in healthy age-matched controls at 300 (out of 881) of these island/promoter associated CpGs. Pathway enrichment analysis identified training in cancer survivors evoked this predominantly hypomethylated signature in pathways associated with: Cell cycle, DNA replication/repair, transcription, translation, mTOR signalling and the proteosome. Differentially methylated region (DMR) analysis also identified genes: BAG1, BTG2, CHP1, KIFC1, MKL2, MTR, PEX11B, POLD2, S100A6, SNORD104 and SPG7 as hypermethylated in breast cancer survivors, with training reversing these CpG island/promoter associated DMRs towards a hypomethylated signature. Training also elicited a largely different epigenetic response in healthy individuals than that observed in cancer survivors, with very few overlapping changes. Only one gene, SIRT2, was identified as having altered methylation in cancer survivors at baseline as well as after training in both the cancer survivors and healthy controls. In conclusion, human SkM muscle retains a hypermethylated signature as long as 10-14 years after breast cancer treatment and survival. Five months of aerobic training rejuvenated the SkM methylome towards signatures identified in healthy age-matched individuals in gene regulatory regions.
Object and activity detection from aerial video

Aerial video surveillance has advanced significantly in recent years, as inexpensive high-quality video cameras and airborne platforms are becoming more readily available. Video has become an indispensable part of military operations and is now becoming increasingly valuable in the civil and paramilitary sectors. Such surveillance capabilities are useful for battlefield intelligence and reconnaissance as well as monitoring major events, border control and critical infrastructure. However, monitoring this growing flood of video data requires significant effort from increasingly large numbers of video analysts. We have developed a suite of aerial video exploitation tools that can alleviate mundane monitoring from the analysts, by detecting and alerting objects and activities that require analysts’ attention. These tools can be used for both tactical applications and post-mission analytics so that the video data can be exploited more efficiently and timely. A feature-based approach and a pixel-based approach have been developed for Video Moving Target Indicator (VMTI) to detect moving objects at real-time in aerial video. Such moving objects can then be classified by a person detector algorithm which was trained with representative aerial data. We have also developed an activity detection tool that can detect activities of interests in aerial video, such as person-vehicle interaction. We have implemented a flexible framework so that new processing modules can be added easily. The Graphical User Interface (GUI) allows the user to configure the processing pipeline at run-time to evaluate different algorithms and parameters. Promising experimental results have been obtained using these tools and an evaluation has been carried out to characterize their performance.
Modeling of indoor thermal comfort in the intelligent building

Thermal comfort is generally determined with the Fanger model, which originates from the 60’s. Its accuracy can be considered disputable and it is often challenged, however it is the basis for the international standards up to this day - namely ISO 7730 and ASHRAE-55 (US standard). The present work aims to develop a modified correlation based on experimental measurements made with questionnaires and the Testo 400 microclimate meter. The original model is modified in such a way that the concentration of carbon dioxide is taken into account (the original model does not take it into account at all). The experimental results have proven to be in good agreement with the modified correlation in the wide range of CO2 levels. The modification that included CO2 provided more accurate results than the original model, proving that the concept is justified.
d-Branes in the Stream

Evolution of extended data is considered in various flow problems, using Nambu brackets as a tool applicable to all cases. Extra dimensions, N-brackets, and extended structures are first employed to linearize the Euler equations. N-bracket induced evolutions of strings, membranes, and other d-branes are then discussed in detail.
Using ADMM for Hybrid System MPC

Model Predictive control (MPC) has been studied extensively because of its ability to handle constraints and its great properties in terms of stability and performance [Mayne et al., 2000]. We have in this thesis focused on MPC of Hybrid Systems, i.e. systems with both continuous and discrete dynamics. More specifically, we look at problems that can be cast as Mixed Integer Quadratic Programming (MIQP) problems which we are solving using a Branch and Bound technique. The problem is in this way reduced to solving a large number of constrained quadratic problems. However, the use in real time systems puts a requirement on the speed and efficiency of the optimization methods used. Because of its low computational cost, there have recently been a rising interest in the Alternating Direction Method of Multiplies (ADMM) for solving constrained optimization problems. We are in this thesis looking at how the different properties of ADMM can be used and improved for these problems, as well as how the Branch and Bound solver can be tailored to accompany ADMM. We have two main contributions to ADMM that mitigate some of the downsides with the often ill-conditioned problems that arise from Hybrid Systems. Firstly, a technique for greatly improving the conditioning of the problems, and secondly, a method to perform fast line search within the solver. We show that these methods are very efficient and can be used to solve problems that are otherwise hard or impossible to precondition properly.
Evaluation of Differences in Response of DOD Portable Instruments and Solid-State Detectors used by MEXT for Measurement of External Radiations with Attention to the Cosmic Radiation Component

Abstract : This report discusses cosmic radiation and summarizes its contributions to radiation dose from external sources and the implications on measurement of external dose-rate using either pressurized ion chambers (PICs) or thallium-activated sodium iodide [NaI(Tl)]. The report finds that some NaI(Tl) systems under respond to cosmic radiation above 3 MeV deposited energy. These differences are offered as one of several contributors to the lower values of external dose rates measured by Japan s Ministry of Education, Culture, Sports, Science, and Technology (MEXT) using NaI(Tl) compared to DOD/DOE measurements using PICs. The report concludes that such limitations must be accounted for in performing assessments of dose from external sources.
Predictors of All-Cause Mortality Among People With Human Immunodeficiency Virus (HIV) in a Prospective Cohort Study in East Africa and Nigeria

Abstract Background Introduction of antiretroviral therapy (ART) has been associated with a decline in human immunodeficiency virus (HIV)-related mortality, although HIV remains a leading cause of death in sub-Saharan Africa. We describe all-cause mortality and its predictors in people living with HIV (PLWH) in the African Cohort Study (AFRICOS). Methods AFRICOS enrolls participants with or without HIV at 12 sites in Kenya, Uganda, Tanzania, and Nigeria. Evaluations every 6 months include sociobehavioral questionnaires, medical history, physical examination, and laboratory tests. Mortality data are collected from medical records and survivor interviews. Multivariable Cox proportional hazards models were used to calculate adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for factors associated with mortality. Results From 2013 through 2020, 2724 PLWH completed at least 1 follow-up visit or experienced death. Of these 58.4% were females, 25.8% were aged ≥ 50 years, and 98.3% were ART-experienced. We observed 11.42 deaths per 1000 person-years (95% CI: 9.53–13.68) with causes ascertained in 54% of participants. Deaths were caused by malignancy (28.1%), infections (29.7%), and other non-HIV related conditions. Predictors of mortality included CD4 ≤ 350 cells/µL (aHR 2.01 [95% CI: 1.31–3.08]), a log10copies/mL increase of viral load (aHR 1.36 [95% CI: 1.22–1.51]), recent fever (aHR 1.85[95% CI: 1.22–2.81]), body mass index < 18.5 kg/m2 (aHR 2.20 [95% CI: 1.44–3.38]), clinical depression (aHR 2.42 [95% CI: 1.40–4.18]), World Health Organization (WHO) stage III (aHR 2.18 [95% CI: 1.31–3.61]), a g/dL increase in hemoglobin (aHR 0.79 [95% CI: .72–.85]), and every year on ART (aHR 0.67 [95% CI: .56–.81]). Conclusions The mortality rate was low in this cohort of mostly virally suppressed PLWH. Patterns of deaths and identified predictors suggest multiple targets for interventions to reduce mortality.
Observation of 1D Fermi arc states in Weyl semimetal TaAs

Abstract Fermi arcs on Weyl semimetals exhibit many exotic quantum phenomena. Usually found on atomically flat surfaces with approximate translation symmetry, Fermi arcs are rooted in the peculiar topology of bulk Bloch bands of 3D crystals. The fundamental question of whether a 1D Fermi arc can be probed remains unanswered. Such an answer could significantly broaden potential applications of Weyl semimetals. Here, we report a direct observation of robust edge states on atomic-scale ledges in TaAs using low-temperature scanning tunneling microscopy/spectroscopy. Spectroscopic signatures and theoretical calculations reveal that the 1D Fermi arcs arise from the chiral Weyl points of bulk crystals. The crossover from 2D Fermi arcs to eventual complete localization on 1D edges was arrested experimentally on a sequence of surfaces. Our results demonstrate extreme robustness of the bulk-boundary correspondence, which offers topological protection for Fermi arcs, even in cases in which the boundaries are at the atomic-scale. The persistent 1D Fermi arcs can be profitably exploited in miniaturized quantum devices.
The outcome measure of proximal humerus fracture treated by open reduction and internal fixation with proximal humerus internal locking system based on oxford shoulder score

Objective: Proximal humerus fractures became one of the most prevalent upper extremity fractures during recent decades. The use of scoring systems has been taken under consideration to estimate the surveillance, prognosis, and post-operative outcomes. During this study, we investigated the outcome measure of proximal humerus fracture treated by open reduction and internal fixation (ORIF) with plate based on oxford shoulder score (OSS). Furthermore, we tried to propose a new classification system for OSS that could be of prognostic value. Methods: Patients with proximal humerus fracture treated by open reduction enrolled in the study. Persian version of the OSS was completed by the patients. Data were analyzed using SPSS-22. Results: Forty-four patients including 24 women and 20 men were assessed. The mean age was 54.61 (SD ± 19.371) years. The use of a spoon and fork at the same time had the best score and hanging the clothes up in a wardrobe with the operated hand had the worst score in the questionnaire. Comparison of OSS and number of physiotherapy session showed that patients with best outcome had least number of physiotherapy’s session, but it was not statistically significant. Conclusion: OSS is useful to evaluate the function of the traumatized shoulder. We suggest classifying the OSS score into three range groups, good (total score 12–28), moderate (total score 29–44), and bad (total scores 45–60).