Miracle-dz/UniFAR-FTUs huggingface dataset:
M-Estimators of Scatter with Eigenvalue Shrinkage

A popular regularized (shrinkage) covariance estimator is the shrinkage sample covariance matrix (SCM) which shares the same set of eigenvectors as the SCM but shrinks its eigenvalues toward its grand mean. In this paper, a more general approach is considered in which the SCM is replaced by an M-estimator of scatter matrix and a fully automatic data adaptive method to compute the optimal shrinkage parameter with minimum mean squared error is proposed. Our approach permits the use of any weight function such as Gaussian, Huber’s, or t weight functions, all of which are commonly used in M-estimation framework. Our simulation examples illustrate that shrinkage M-estimators based on the proposed optimal tuning combined with robust weight function do not loose in performance to shrinkage SCM estimator when the data is Gaussian, but provide significantly improved performance when the data is sampled from a heavy-tailed distribution.
Dynamics on Multiple Potential Energy Surfaces: Quantitative Studies of Elementary Processes Relevant to Hypersonics.

The determination of thermal and vibrational relaxation rates of triatomic systems suitable for application in hypersonic model calculations is discussed. For this, potential energy surfaces for ground and electronically excited state species need to be computed and represented with high accuracy and quasiclassical or quantum nuclear dynamics simulations provide the basis for determining the relevant rates. These include thermal reaction rates, state-to-state cross sections, or vibrational relaxation rates. For exemplary systems - [NNO], [NOO], and [CNO] - all individual steps are described and a literature overview for them is provided. Finally, as some of these quantities involve considerable computational expense, for the example of state-to-state cross sections the construction of an efficient model based on neural networks is discussed. All such data is required and being used in more coarse-grained computational fluid dynamics simulations.
EncDBDB: Searchable Encrypted, Fast, Compressed, In-Memory Database Using Enclaves

Data confidentiality is an important requirement for clients when outsourcing databases to the cloud. Trusted execution environments, such as Intel SGX, offer an efficient solution to this confidentiality problem. However, existing TEE-based solutions are not optimized for column-oriented, in-memory databases and pose impractical memory requirements on the enclave. We present EncDBDB, a novel approach for client-controlled encryption of a column-oriented, in-memory databases allowing range searches using an enclave. EncDBDB offers nine encrypted dictionaries, which provide different security, performance, and storage efficiency tradeoffs for the data. It is especially suited for complex, read-oriented, analytic queries as present, e.g., in data warehouses. The computational overhead compared to plaintext processing is within a millisecond even for databases with millions of entries and the leakage is limited. Compressed encrypted data requires less space than a corresponding plaintext column. Furthermore, EncDBDB’s enclave is very small reducing the potential for security-relevant implementation errors and side-channel leakages.
Phosphoproteomic analysis of mammalian infective Trypanosoma brucei subjected to heat shock suggests atypical mechanisms for thermotolerance

The symptoms of African sleeping sickness, caused by the parasite Trypanosoma brucei, can include periods of fever as high as 41 °C which triggers a heat shock response in the parasite. To capture events involved in sensing and responding to heat shock in the mammalian infective form we have conducted a SILAC-based quantitative proteomic and phosphoproteomic analysis of T. brucei cells treated at 41 °C for 1h. Our analysis identified 193 heat shock responsive phosphorylation sites with an average of 5-fold change in abundance, but only 20 heat shock responsive proteins with average of 1.5-fold change. These data indicate that protein abundance does not rapidly respond (≤1 h) to heat shock, and that the changes observed in phosphorylation site abundance are larger and more widespread. The heat shock responsive phosphorylation sites showed enrichment of RNA binding proteins with putative roles in heat shock response included P-body / stress granules and the eukaryotic translation initiation 4F complex. The ZC3H11-MKT1 complex, which stabilises mRNAs of thermotolerance proteins, appears to represent a key signal integration node in the heat shock response.
Ground deformation analysis on road infrastructure in north buton Indonesia using interferometric synthetic aperture radar (Insar)

We investigate ground deformation that occurred on national road infrastructure in North Buton Regency, South East Sulawesi, Indonesia. This research conducted to obtain spatial information about ground deformation occurred. Road infrastructure plays an important role in economic and transportation particularly in North Buton. Road damage will cause losses both economically and security. The method of the research was Interferometric Synthetic Aperture Radar (InSAR). InSAR uses two SAR Images from two different acquisitions to generate interferogram and then ground deformation parameter. We used Sentinel-1 images acquisition years of 2015 and 2017. We found that the ground deformation occurred between -118 to +20 millimeters during the year of 2015 and 2017 acquisition or about -59 to +10 millimeters per year and its direction from north to south of the road body. The movement of ground deformation is dominated downward movement which it is estimated strength affected by the presence of faults near the location.
Sustained Virologic Response Rates of Sofosbuvir and Velpatasvir in Patients with Hepatitis C Genotype 3: A Meta-Analysis

Context Patients with hepatitis C virus (HCV) genotype 3 are regarded as a difficult-to-cure population in an era of direct-acting antiviral treatment.ObjectivesThis meta-analysis aimed to evaluate sustained virologic response rates resulting from a fixed-dose combination of sofosbuvir (SOF) and velpatasvir (VEL), also known as Epclusa® (Gilead, Forster City, CA) in patients with HCV genotype 3.MethodsIn this study, we searched PubMed/MEDLINE, Embase, and the Cochrane Library for relevant studies from inception until May 3rd, 2019. The primary outcome measure used was the rate of the sustained virological response at week-12 (SVR12) post-treatment. The heterogeneity of results was evaluated, and influence analyses were performed using the R software. In addition, publication bias was assessed using the funnel and Egger tests.ResultsEleven trials (n = 2246 patients) were included in this meta-analysis. The pooled SVR12 rate in patients with HCV-genotype 3 (GT3) was 94.6% with a random effect model by inverse method (95% Cl 92.5% - 96.1%, I2 = 53%, P = 0.02). A subpopulation analysis indicated that the pooled SVR12 rates were 96.3% in GT3 patients with compensated cirrhosis and 94.0% in GT3 patients with prior anti-HCV treatment. Moreover, influence analysis suggested that the most significant source of heterogeneities resulted from one trial, which enrolled most patients with HCV subtype 3b.ConclusionsOur meta-analysis showed a high SVR12 rate of SOF/VEL in GT3 patients regardless of compensated cirrhosis the status and/or a history of previous interferon-based treatments. These results highlight the need for more trials investigating the effectiveness of the SOF/VEL regimen in patients with HCV subtype 3b.
Decision-Making Power of Married Women on Family Planning Use and Associated Factors in Dinsho Woreda, South East Ethiopia

Background Women’s decisions on family planning use have multiple benefits to the family and community at large. In developing countries like Ethiopia, the choice of women to use a contraceptive is challenged by social and environmental factors that mitigate their ability to decide independently and freely. This study therefore determined the level of women's decision-making power on family planning use and associated factors among married women in the study area. Methods A community-based cross-sectional study was conducted in Dinsho woreda from March to April 2017. A simple random sampling technique was used to select 373 married women. A structured and pre-tested questionnaire was used to collect data by trained data collectors under continuous supervision. Multivariable logistic regression was performed to identify factors associated with women's decision-making power on family planning use. Crude and adjusted odds ratios with 95% confidence interval were used and p-value of <0.05 was considered as statistical significance. Results A total of 344 (92.2%) women participated in the study. Of the total respondents, 179 (52%) of women had good decision-making power on modern family planning use. Multivariable analysis showed that younger age (adjusted odds ratio [AOR] =8.59 [1.61, 45.80]), good participation in household decision-making (AOR =2.65 [1.46, 4.79]), positive attitude towards family planning (AOR =2.34 [1.31, 4.19]), and better knowledge towards family planning (AOR =3.04 [1.49, 6.22]) were factors statistically significantly associated with married women's decision-making power on family planning use. Conclusion and Recommendation Women's knowledge and attitudes toward family planning and their participation in household decision-making increased the likelihood of women's decision-making power for modern family planning use. There is a need to adopt a more comprehensive approach to reach men and women on modern family planning, to help women to decide freely without any restriction.
Improving fermented virgin coconut oil quality by using microwave heating

The study aimed to improve the quality of fermented virgin coconut oil (FVCO) under microwave heating. The FVCO was collected from a local farmer in Aceh Besar District. A microwave oven at frequency of 2,450MHz and power of 800Wwas used to heat 40ml FVCO in a ceramic bowl by the variation heating time i.e. 40, 50, and 60s. The parameters observed were temperature, moisture content, free fatty acid (FFA), and peroxide value. Results showed that the quality of FVCO did not meet the quality standards such as Codex Alimentarius, Asian and Pacific Coconut Community (APCC), and the Indonesian National Standard (SNI). However, the study found that the microwave heating time had influenced the FVCO temperature significantly where the final temperature had reached 71-87°C. However, there were no significant influences of microwave heating time to the moisture, FFA, and peroxide value of FVCO. It could be caused by the short time used in this experiment; therefore, it is suggested to extend the heating time for further study.
Cultural Identity-Induced Social Exclusion of an Ethnic Minority Group and Communal Conflicts in North-Central Nigeria

Qualitative research has suggested that minority groups suffer discrimination. Some had focused on the effects of discrimination and prejudicial treatments of groups that are referred to as socially-devalued. This has also provoked greater interest in theorizing on the relationship between explanatory causal factors of discrimination against these groups. This study contributes to this body of research findings by focusing on an ethnic minority group that has been subjected to various discriminatory treatments on the basis of ancestral/historical difference. It examines the relationship between some exclusionary ethno-cultural variables and their effect on conflict occurrence. Conflict is depicted here as the dependent variable while the ethno-cultural variablesexclusion, deprivations, identity formation, and migration are considered as independent variables. This study adopts the quantitative approach using the Chi-Square analysis to investigate the relationship between these variables based on the Mean of the responses from the administered questionnaires, while Regression analysis was used to examine the impact of the independent variables (cultural identity formation, social exclusion, migration history, deprivation, and segregation) on the dependent variable (communal conflict). The findings from the regression analysis show that a significant relationship exists between all the independent variables and the dependent variable, while from the Chi-square analysis, the findings reveal that except for deprivation, all other independent variables have a positive relationship with the dependent variable.
Purple sweet potato color protects against hepatocyte apoptosis through Sirt1 activation in high-fat-diet-treated mice

Background Recent evidence indicates that the inhibition of hepatocyte apoptosis is possible to develop a potential therapeutic strategy for nonalcoholic fatty liver disease (NAFLD). Our previous work suggested that purple sweet potato color (PSPC), a class of naturally occurring anthocyanins, effectively improved many features of high-fat diet (HFD)-induced NAFLD. However, whether PSPC ameliorates HFD-induced hepatocyte apoptosis has never been investigated. Objective Here we investigated the effects of PSPC on HFD-induced hepatic apoptosis and the mechanisms underlying these effects. Design Mice were divided into four groups: Control group, HFD group, HFD + PSPC group and PSPC group. PSPC was administered by daily oral gavage at doses of 700 mg/kg/day for 20 weeks. EX-527 (a SirT1-selective inhibitor) and Sirt1 siRNA were used to demonstrate the Sirt1 dependence of PSPC-mediated effects on apoptotic and survival signaling pathways in vivo and in vitro. Results Our results showed that PSPC reduced body weights, hepatic triglyceride contents, histopathological lesions and serum ALT levels in a mouse model of NAFLD induced by HFD. Furthermore, PSPC attenuated HFD-induced hepatocyte apoptosis ratio from 7.27 ± 0.92% to 1.79 ± 0.27% in mouse livers, which is insignificant compared with that of controls. Moreover, PSPC activated Sirt1 by boosting NAD+ level in HFD-treated mouse livers. Furthermore, PSPC promoted Sirt1-dependent suppression of P53-mediated apoptotic signaling and activation of Akt survival signaling pathway in HFD-treated mouse livers, which was confirmed by EX527 treatment. Moreover, Sirt1 knockdown abolished these ameliorative effects of PSPC on apoptosis and P53 acetylation and protein expression in PA-treated L02 cells. Ultimately, PSPC reduced Caspase-3 activation and Bax level, and elevated the Bcl-2 level in HFD-treated mouse livers. Conclusion PSPC protected against HFD-induced hepatic apoptosis by promoting Sirt1- dependent inhibition of p53-apoptotic pathway and facilitation of Akt survival pathway. This study indicates that PSPC is a candidate for nutritional intervention of NAFLD.
Tumor-Specific T Cell Activation in Malignant Brain Tumors

Due to their delicate locations as well as aggressive and infiltrative behavior, malignant brain tumors remain a therapeutic challenge. Harnessing the efficacy and specificity of the T-cell response to counteract malignant brain tumor progression and recurrence, represents an attractive treatment option. With the tremendous advances in the current era of immunotherapy, ongoing studies aim to determine the best treatment strategies for mounting a tumor-specific immune response against malignant brain tumors. However, immunosuppression in the local tumor environment, molecular and cellular heterogeneity as well as a lack of suitable targets for tumor-specific vaccination impede the successful implementation of immunotherapeutic treatment strategies in neuro-oncology. In this review, we therefore discuss the role of T cell exhaustion, the genetic and antigenic landscape, potential pitfalls and ongoing efforts to overcome the individual challenges in order to elicit a tumor-specific T cell response.
Silicon Confers Soybean Resistance to Salinity Stress Through Regulation of Reactive Oxygen and Reactive Nitrogen Species

Salt stress is one of the major abiotic stressors that causes huge losses to the agricultural industry worldwide. Different strategies have been adopted over time to mitigate the negative impact of salt stress on plants and reclaim salt-affected lands. In the current study, we used silicon (Si) as a tool for salinity alleviation in soybean and investigated the influence of exogenous Si application on the regulation of reactive oxygen and reactive nitrogen species and other salt stress–related parameters of the treated plants. Our results revealed that the canopy temperature was much higher in sole NaCl–treated plants but declined in Si + NaCl–treated plants. Furthermore, the chlorophyll contents decreased with sole NaCl treatment, whereas Si + NaCl–treated plants showed improved chlorophyll contents. In addition, Si application normalized the photosynthetic responses, such as transpiration rate (E) and net photosynthesis rate (PN) in salt-treated plants, and reduced the activity of ascorbate peroxidase and glutathione under salt stress. The expression levels of antioxidant-related genes GmCAT1, GmCAT2, and GmAPX1 started to decline at 12 h after addition of Si to NaCl-treated plants. Similarly, the S-nitrosothiol and nitric oxide (NO)–related genes were upregulated in the salt stress condition but reduced after Si supplementation. Si application downregulated genes associated with reactive oxygen species and reactive nitrogen species and reduced enzymatic and non-enzymatic antioxidants of the treated plants. Results of the current study conclude that Si mitigated the adverse effects of NaCl-induced stress by modulating the crosstalk between antioxidants and NO scavengers. It is suggested that Si may be used in agricultural systems for alleviating salt stress.
In utero Exposure to Maternal Chronic Inflammation Transfers a Pro-Inflammatory Profile to Generation F2 via Sex-Specific Mechanisms

Generational transfer of maladaptations in offspring have been reported to persist for multiple generations in conditions of chronic inflammation, metabolic and psychological stress. Thus, the current study aimed to expand our understanding of the nature, potential sex specificity, and transgenerational plasticity of inflammatory maladaptations resulting from maternal chronic inflammation. Briefly, F1 and F2 generations of offspring from C57/BL/6 dams exposed to a modified maternal periconception systemic inflammation (MSPI) protocol were profiled in terms of leukocyte and splenocyte counts and cytokine responses, as well as glucocorticoid sensitivity. Overall, F1 male and female LPS groups presented with glucocorticoid hypersensitivity (with elevated corticosterone and increased leukocyte glucocorticoid receptor levels) along with a pro-inflammatory phenotype, which carried over to the F2 generation. The transfer of inflammatory and glucocorticoid responsiveness from F1 to F2 is evident, with heritability of this phenotype in F2. The findings suggest that maternal (F0) perinatal chronic inflammation resulted in glucocorticoid dysregulation and a resultant pro-inflammatory phenotype, which is transferred in the maternal lineage but seems to affect male offspring to a greater extent. Of further interest, upregulation of IL-1β cytokine responses is reported in female offspring only. The cumulative maladaptation reported in F2 offspring when both F1 parents were affected by maternal LPS exposure is suggestive of immune senescence. Given the potential impact of current results and the lack of sex-specific investigations, more research in this context is urgently required.
Associations of Serum Cathepsin K and Polymorphisms in CTSK Gene With Bone Mineral Density and Bone Metabolism Markers in Postmenopausal Chinese Women

Cathepsin K plays an important role in bone resorption. The reports of the association of serum cathepsin K with bone mineral density (BMD) and bone turnover markers are conflicting and the role of serum cathepsin K as a bone turnover marker is unclear. The aims of the study were as follows: (1) to investigate the association of serum cathepsin K with BMD and markers of bone turnover and (2) to evaluate the correlations of single-nucleotide polymorphisms (SNPs) within the CTSK gene with serum cathepsin K, BMD, and markers of bone metabolism in postmenopausal Chinese women. A cross-sectional study was conducted with 1752 postmenopausal Chinese women. Four tagging SNPs (rs12085336, rs12746973, rs4379678, and rs10847) of the CTSK gene were genotyped. Serum cathepsin K of 768 and markers of bone metabolism of 1752 including serum intact PTH, 25-hydroxyvitamin D [25(OH)D], procollagen type 1 N-terminal propeptide (P1NP), and β-CrossLaps of type I collagen containing cross- linked C-telopeptide (β-CTX) were measured. The BMD of the lumbar spine and proximal femur were measured by dual-energy X-ray absorptiometry (DXA). No significant relationship was detected between serum cathepsin K and age, BMI, BMD or bone metabolic markers (all P > 0.05) after adjustment for age and BMI. We failed to identify any significant association between the genotypes or haplotypes of CTSK and BMD, bone turnover markers, or serum cathepsin K. Neither serum cathepsin K nor CTSK gene polymorphisms was correlated with BMD or bone turnover markers. Genetic polymorphisms of CTSK may not be a major contributor to variations in the serum cathepsin K or BMD in postmenopausal Chinese women. The results implied that serum cathepsin K may not be viewed as a substitute for bone turnover markers.
Validity of Field Methods to Estimate Fat-Free Mass Changes Throughout the Season in Elite Youth Soccer Players

The aim of this study was to determine the most effective anthropometric equations or bioelectrical impedance analysis (BIA) devices for quantifying the sensitivity to change in fat-free mass (FFM) in elite young soccer players, in comparison with measurements using dual-energy X-ray absorptiometry (DXA), between the pre- and mid-season. A total of 40 elite youth soccer players participated in this study. DXA values provided a criterion measure of FFM. Correlation coefficients, biases, limits of agreement, and differences were used as measures of sensitivity to change. All body density, skinfold, and anthropometric equations and BIA devices used to obtain FFM data showed positive and very large correlations (r from 0.70 to 0.89) with DXA. A significant increase in FFM was shown between time points using DXA, BIA, and all anthropometric equations (p < 0.01). The magnitudes of differences were small for DXA, BIA inbody and all anthropometric equations except those of Faulkner (1966), Durnin and Rahaman (1967), Brook (1971), and Sarría et al. (1998). Six anthropometric equations [Faulkner (1966), Durnin and Womersley (1974), Carter (1982), Slaughter et al. (1988), Reilly et al. (2009), and Munguia-Izquierdo et al. (2018)] and BIA Tanita showed no statistical differences compared to DXA, with a low bias. We concluded that the equations developed by Durnin and Womersley (1974), Carter (1982), Slaughter et al. (1988), Reilly et al. (2009), and Munguia-Izquierdo et al. (2018) showed the best sensitivity in assessing FFM changes between pre- and mid-season in elite youth soccer players.