Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating the error variance in a high-dimensional linear model

The lasso has been studied extensively as a tool for estimating the coefficient vector in the high-dimensional linear model; however, considerably less is known about estimating the error variance in this context. In this paper, we propose the natural lasso estimator for the error variance, which maximizes a penalized likelihood objective. A key aspect of the natural lasso is that the likelihood is expressed in terms of the natural parameterization of the multi-parameter exponential family of a Gaussian with unknown mean and variance. The result is a remarkably simple estimator of the error variance with provably good performance in terms of mean squared error. These theoretical results do not require placing any assumptions on the design matrix or the true regression coefficients. We also propose a companion estimator, called the organic lasso, which theoretically does not require tuning of the regularization parameter. Both estimators do well empirically compared to pre-existing methods, especially in settings where successful recovery of the true support of the coefficient vector is hard. Finally, we show that existing methods can do well under fewer assumptions than previously known, thus providing a fuller story about the problem of estimating the error variance in high-dimensional linear models.
Time Series Analysis of the Southern Oscillation Index using Bayesian Additive Regression Trees

Bayesian additive regression trees (BART) is a regression technique developed by Chipman et al. (2008). Its usefulness in standard regression settings has been clearly demonstrated, but it has not been applied to time series analysis as yet. We discuss the difficulties in applying this technique to time series analysis and demonstrate its superior predictive capabilities in the case of a well know time series: the Southern Oscillation Index.
Reduced bias for respondent‐driven sampling: accounting for non‐uniform edge sampling probabilities in people who inject drugs in Mauritius

People who inject drugs are an important population to study to reduce transmission of blood‐borne illnesses including human immunodeficiency virus and hepatitis. We estimate the human immunodeficiency virus and hepatitis C prevalence among people who inject drugs in Mauritius. Respondent‐driven sampling (RDS), which is a widely adopted link tracing sampling design used to collect samples from hard‐to‐reach human populations, was used to collect this sample. The random‐walk approximation underlying many common RDS estimators assumes that each social relationship (edge) in the underlying social network has an equal probability of being traced in the collection of the sample. This assumption does not hold in practice. We show that certain RDS estimators are sensitive to the violation of this assumption. To address this limitation in current methodology, and the effect that it may have on prevalence estimates, we present a new method for improving RDS prevalence estimators using estimated edge inclusion probabilities, and we apply this to data from Mauritius.
Comparison of Dynamic Treatment Regimes with An Ordinal Outcome

Sequential multiple assignment randomized trials (SMART) are used to develop optimal treatment strategies for patients based on their medical histories in different branches of medical and behavioral sciences where a sequence of treatments are given to the patients; such sequential treatment strategies are often called dynamic treatment regimes. In the existing literature, the majority of the analysis methodologies for SMART studies assume a continuous primary outcome. However, ordinal outcomes are also quite common in medical practice; for example, the quality of life (poor, moderate, good) is an ordinal variable. In this work, first, we develop the notion of dynamic generalized odds-ratio ($dGOR$) to compare two dynamic treatment regimes embedded in a 2-stage SMART with an ordinal outcome. We propose a likelihood-based approach to estimate $dGOR$ from SMART data. Next, we discuss some results related to $dGOR$ and derive the asymptotic properties of it's estimate. We derive the required sample size formula. Then, we extend the proposed methodology to a $K$-stage SMART. Finally, we discuss some alternative ways to estimate $dGOR$ using concordant-discordant pairs and multi-sample $U$-statistic. A simulation study shows the performance of the estimated $dGOR$ in terms of the estimated power corresponding to the derived sample size. We analyze data from STAR*D, a multistage randomized clinical trial for treating major depression, to illustrate the proposed methodology. A freely available online tool using R statistical software is provided to make the proposed method accessible to other researchers and practitioners.
On characterizations of the covariance matrix

The covariance matrix is well-known for its following properties: affine equivariance, additivity, independence property and full affine equivariance. Generalizing the first one leads into the study of scatter functionals, commonly used as plug-in estimators to replace the covariance matrix in robust statistics. However, if the application requires also some of the other properties of the covariance matrix listed earlier, the success of the plug-in depends on whether the candidate scatter functional possesses these. In this short note we show that under natural regularity conditions the covariance matrix is the only scatter functional that is additive and the only scatter functional that is full affine equivariant.
On the lengths of t-based confidence intervals

Confidence interval is a basic type of interval estimation in statistics. When dealing with samples from a normal population with the unknown mean and the variance, the traditional method to construct t-based confidence intervals for the mean parameter is to treat the n sampled units as n groups and build the intervals. Here we propose a generalized method. We first divide them into several equal-sized groups and then calculate the confidence intervals with the mean values of these groups. If we define “better” in terms of the expected length of the confidence interval, then the first method is better because the expected length of the confidence interval obtained from the first method is shorter. We prove this intuition theoretically. We also specify when the elements in each group are correlated, the first method is invalid, while the second can give us correct results in terms of the coverage probability. We illustrate this with analytical expressions. In practice, when the data set is extremely large and distributed in several data centers, the second method is a good tool to get confidence intervals, in both independent and correlated cases. Some simulations and real data analyses are presented to verify our theoretical results.
Distance-Distributed Design for Gaussian Process Surrogates

Abstract A common challenge in computer experiments and related fields is to efficiently explore the input space using a small number of samples, that is, the experimental design problem. Much of the recent focus in the computer experiment literature, where modeling is often via Gaussian process (GP) surrogates, has been on space-filling designs, via maximin distance, Latin hypercube, etc. However, it is easy to demonstrate empirically that such designs disappoint when the model hyperparameterization is unknown, and must be estimated from data observed at the chosen design sites. This is true even when the performance metric is prediction-based, or when the target of interest is inherently or eventually sequential in nature, such as in blackbox (Bayesian) optimization. Here we expose such inefficiencies, showing that in many cases a purely random design is superior to higher-powered alternatives. We then propose a family of new schemes by reverse engineering the qualities of the random designs which give the best estimates of GP length scales. Specifically, we study the distribution of pairwise distances between design elements, and develop a numerical scheme to optimize those distances for a given sample size and dimension. We illustrate how our distance-based designs, and their hybrids with more conventional space-filling schemes, outperform in both static (one-shot design) and sequential settings.
Multiscale inference and long‐run variance estimation in non‐parametric regression with time series errors

We develop new multiscale methods to test qualitative hypotheses about the function m in the non‐parametric regression model Yt,T=m(t/T)+ɛt with time series errors ɛt. In time series applications, m represents a non‐parametric time trend. Practitioners are often interested in whether the trend m has certain shape properties. For example, they would like to know whether m is constant or whether it is increasing or decreasing in certain time intervals. Our multiscale methods enable us to test for such shape properties of the trend m. To perform the methods, we require an estimator of the long‐run error variance σ2=Σl=−∞∞cov(ε0,εl) . We propose a new difference‐based estimator of σ2 for the case that {ɛt} belongs to the class of auto‐regressive AR(∞) processes. In the technical part of the paper, we derive asymptotic theory for the proposed multiscale test and the estimator of the long‐run error variance. The theory is complemented by a simulation study and an empirical application to climate data.
Construction and Production of Concatameric Human TNF Receptor-Immunoglobulin Fusion Proteins

Tumor necrosis factor-a (TNF-a) and lymphotoxin-a (LT-α, TNF-β) can initiate and perpetuate human diseases such as multiple sclerosis (MS), rheumatoid arthritis (RA), and insulin-dependent diabetes mellitus (IDDM). TNFs can be blocked by the use of soluble TNF receptors. However, since monomeric soluble receptors generally exhibit low affinity or function as agonists, the use of monomeric soluble receptors has been limited in the case of cytokines such as TNF-a, TNF-β, interleukin (IL)-1, IL-4, IL-6, and IL-13, which have adapted to a multicomponent receptor system. For these reasons, very high-affinity inhibitors were created for the purpose of a TNFs antagonist to bind the TNFR and trigger cellular signal by using the multistep polymerase chain reaction method. First, recombinant simple TNFR-Ig fusion proteins were constructed from the cDNA sequences encoding the extracellular domain of the human p55 TNFR (CD120a) and the human p75 TNFR (CD120b), which were linked to hinge and constant regions of human IgG 1 heavy chain, respectively using complementary primers (CP) encoding the complementary sequences. Then, concatameric TNFR-Ig fusion proteins were constructed using recombinant PCR and a complementary primer base of recombinant simple TNFR-Ig fusion proteins. For high level expression of recombinant fusion proteins, Chinese hamster ovary (CHO) cells were used with a retroviral expression system. The transfected cells produced the simple concatameric TNFR-Ig fusion proteins capable of binding TNF and inactivating it. These soluble versions of simple concantameric TNFR-Ig fusion proteins gave rise to multiple forms such as simple dimers and concatameric homodimers. Simple TNFR-Ig fusion proteins were shown to have much more reduced TNF inhibitory activity than concatameric TNFR-Ig fusion proteins. Concatameric TNFR-Ig fusion proteins showed higher affinity than simple TNFR-Ig fusion proteins in a receptor inhibitor binding assay (RIBA). Additionally, concatameric TNFR-Ig fusion proteins were shown to have a progressive effect as a TNF inhibitor compared to the simple TNFR-Ig fusion proteins and conventional TNFR-Fc in cytotoxicity assays, and showed the same results for collagen induced arthritis (CIA) in mice in vivo.
Effects of Curcumin, the Active Ingredient of Turmeric(Curcuma longa), on Regulation of Glutamate-induced Toxicity and Activation of the Mitogen-activated Protein Kinase Phosphatase-1 (MKP-1) in HT22 Neuronal Cell

Glutamate causes neurotoxicity through formation of reactive oxygen species and activation of mitogen-activated protein kinase (MAPK) pathways. MAPK phosphatase-1 (MKP-1) is one of the phosphatases responsible for dephosphorylation/deactivation of three MAPK families: the extracellular signal-regulated kinase-1/2 (ERK-1/2), the c-Jun N-terminal kinase-1/2 (JNK-1/2), and the p38 MAPK. In this report, the potential involvement of MKP-1 in neuroprotective effects of curcumin, the active ingredient of turmeric (Curcuma longa), was examined using HT22 cells. Glutamate caused cell death and activation of ERK-1/2 but not p38 MAPK or JNK-1/2. Blockage of ERK-1/2 by its inhibitor protected HT22 cells against glutamate-induced toxicity. Curcumin attenuated glutamate-induced cell death and ERK-1/2 activation. Interestingly, curcumin induced MKP-1 activation. In HT22 cells transiently transfected with small interfering RNA against MKP-1, curcumin failed to inhibit glutamate-induced ERK-1/2 activation and to protect HT22 cells from glutamate-induced toxicity. These results suggest that curcumin can attenuate glutamate-induced neurotoxicity by activating MKP-1 which acts as the negative regulator of ERK-1/2. This novel pathway may contribute to and explain at least one of the neuroprotective actions of curcumin.
Characterization of Grain Mold Resistance in Sorghum [Sorghum Bicolor (L.) Moench]

Characterization of Grain Mold Resistance in Sorghum [ Sorghum b ic o lo r (L.) Moench]. (December 1986) Gregory Allan Forbes, B.A., Murray State University, Murray Ky. ; M.S., Texas A&M University, College Station. Chairman of Advisory Committee: Dr. R. A. Frederiksen Sorghum grain lots with various levels of resistance to sorghum grain mold (SGM) were evaluated for several loss parameters: kernel weight, kernel density, electrolyte leachate level, percentage germination, vigor, and visual quality appraisal; and two indirect measures of disease intensity, ergosterol level and colony­ forming units (CFU) of Fusarium m o n i/ i fo r m e . Ergosterol level was significantly correlated with CFU (r= +0.94), visual rating (r= +0.92), leachate level (r= +0.90), and percentage germination (r= -0.86). Leachate level was highly correlated with germination (r= -0.98). In all cases, correlation coefficients for the standard deviation of kernel weight were higher than for the mean. Fitting variables to a theoretical linear model resulted in a highly significant cultivar x treatment (treatment = inoculated vs. noninoculated) interaction for kernel weight. Two greenhouse inoculation procedures, vacuum infiltration and panicle spraying differented among resistant and susceptible cultivars and caused symptoms similar to those resulting from
Effects of alfalfa (fresh, silage, hay) on the fatty acid and conjugated linoleic acid amounts in lamb muscles and fats

Le but de cette etude etait d'evaluer les effets de la luzerne fraiche, en ensilage ou sechee sur la qualite de la viande chez l'agenau. Pour cela, 40 agneaux Akkaraman de 4 mois ont ete repartis en 4 groupes egaux en fonction de la ration recue: les controles ont ete nourris avec de la paille de ble alors que les autres animaux ont recu de la luzerne fraiche, en ensilage ou en foin (respectivement groupes AF, AS et AD) pendant 98 jours puis la composition en acides gras de la ration, des muscles (semi-membraneux, long dorsal, deltoide et gluteobiceps) et des graisses (sous-cutanee et de la queue) ont ete determinees par chromatographie en phase gazeuse. La luzerne a presente une teneur plus faible en acides gras satures et une teneur plus elevee en acides gras poly-insatures que la paille de ble. En parallele, les concentrations en acides gras satures dans le muscle et la graisse ont ete significativement plus elevees chez les controles alors que les concentrations significativement les plus elevees en poly-insatures ont ete observees chez les agneaux nourris avec de la luzerne, surtout sous forme fraiche. Les proportions en ω3 et en ω6 tels que respectivement, l'acide linolenique et l'acide linoleique ainsi que celles en CLA ont ete notablement et significativement augmentees dans les graisses et les muscles (a l'exception du gluteobiceps en ce qui concerne les ω3) des agneaux recevant de la luzerne quelque soit sa forme de distribution. Ces resultats demontrent que l'utilisation de luzerne comme fourrage dans la ration des agneaux ameliore nettement la composition en graisse de la viande.
Ação antiproliferativado flavonoide morina e do extrato da folha de oliveira (Oleaeuropaea L.) contra a linhagem de célula H460

This study investigates possible apoptosis induction mechanism by the flavonoid morin and the olive leaf extract (Olea europaea L.) in non-small lung cancer cells (H460). The treatment with morin and olive leaves extract resulted in growth inhibition and induction of apoptosis in H460 cells lines measured by the MTT assay methods and confirmed by fluorescence microscopy, flow cytometry analysis. The data indicated that themurin and the extract of olive decreased the cell viability percentage rates of 7.22 ± 1,54% and 62.37 ± 2,85% in the concentrations of 800 µM and µg/mL, respectively. The highest percentage rates of cell death by apoptosis were 100% for themorin in a concentration of 800 µM and 70.49 ± 5.91% for the olive extract in a concentration of 800 µg/mL. These findings were associated with altered mitochondrial membrane potential, whose value is 54.91% for the murin concentration of 400 µM and 42.2% for the olive extract in a concentration of 800 mg / mL, suggesting involvement of the intrinsic pathway of cell death by apoptosis. Therefore, the morin and the olive extract affect the cell viability of H460 cell lines inducing cell death by apoptosis.
Diffuse brain invasion of glioma cells requires β1 integrins

Diffuse invasion of brain tissue by single tumor cells is a characteristic feature of gliomas and a major reason why these tumors cannot be completely resected. The molecular basis of brain invasion is poorly understood. We regulated the expression of beta 1 integrins, the major group of extracellular matrix receptors, in astrocytic tumor cells by using a tetracycline-dependent transcription control system. Rat C6 glioma cells were stably transfected with (a) the tetracycline-controlled transactivator (tTA) gene, (b) antisense beta 1 cDNA under the control of a tTA/tetracycline-responsive promoter, and (c) the beta-galactosidase (lacZ) gene for histochemical identification. In one clone, C6TL beta, beta 1 protein levels were unaffected in the presence of tetracycline, but they were reduced by 60% in the absence of tetracycline because of production of antisense mRNA. C6TL beta cells were transplanted into the striatum of nude mice. After 14 days in the presence of tetracycline in the drinking water, tumors showed diffuse brain invasion, mainly along vascular basement membranes. In the absence of tetracycline, however, tumor cells were compact and generally well delineated from the surrounding brain tissue. These data, ie, blocking of brain invasion by antisense beta 1 mRNA, either because of disturbed interaction of beta 1 with brain extracellular matrix components or interference with beta 1-dependent signaling pathways, strongly suggest that beta 1 integrins are required for diffuse brain invasion of gliomas.
Characterization of Culturable Thermophilic Actinobacteria from Livingston Island, Antarctica

Thermophilic microorganisms in Antarctica are poorly investigated. This paper reports partial characterization and biosynthetic abilities of 26 thermophilic actinobacteria isolated from soil and penguin excrements samples from Livingston Island, Antarctica. About 15% of the tested Antarctic actinobacteria were able to tolerate up to 4% NaCl in the growth medium. We found that all strains are sensitive to eight, and 77% to ten of the 12 tested antibiotics suggesting relatively low anthropogenic impact in this Antarctic region. The Antarctic actinobacteria were tested for hydrolytic enzymes activity, antibiotic and hemolytic activity. It was found that all strains were able to hydrolyze starch, 81% - tributirin, and 65% casein. All Antarctic actinobacteria demonstrated hemolytic activity, and about 27% - antimicrobial activity against some common bacterial pathogens. The results obtained revealed promising strains producers of industrially important thermostable enzymes and antibiotic compounds.
MSFA-Frequency-Aware Transformer for Hyperspectral Images Demosaicing

Hyperspectral imaging systems that use multispectral filter arrays (MSFA) capture only one spectral component in each pixel. Hyperspectral demosaicing is used to recover the non-measured components. While deep learning methods have shown promise in this area, they still suffer from several challenges, including limited modeling of non-local dependencies, lack of consideration of the periodic MSFA pattern that could be linked to periodic artifacts, and difficulty in recovering high-frequency details. To address these challenges, this paper proposes a novel de-mosaicing framework, the MSFA-frequency-aware Transformer network (FDM-Net). FDM-Net integrates a novel MSFA-frequency-aware multi-head self-attention mechanism (MaFormer) and a filter-based Fourier zero-padding method to reconstruct high pass components with greater difficulty and low pass components with relative ease, separately. The advantage of Maformer is that it can leverage the MSFA information and non-local dependencies present in the data. Additionally, we introduce a joint spatial and frequency loss to transfer MSFA information and enhance training on frequency components that are hard to recover. Our experimental results demonstrate that FDM-Net outperforms state-of-the-art methods with 6dB PSNR, and reconstructs high-fidelity details successfully.
Possible biological functions for the expression of endogenous retroviral gene products in human placental tissues.

: In human placental tissues the expression of the endogenous retroviral gene plays a particular role seeming responsible in the limitation of the diffusion of the exogenous retroviral particles. There is a peculiar significance of the role of proviral sequences, insertions and transcripts as well as of the hormones. Nevertheless the precise biological function remains at the greatest part ignored.
Antimicrobial susceptibility testing of Staphylococcus aureus isolated from apparently healthy humans and animals in Maiduguri, Nigeria

Staphylococcus aureus was isolated from apparently healthy humans, sheep , goats and cattle. A total of 250 samples were collected, 130 was from humans, 40 each from sheep, goats and cattle respectively. The pr evalence of Staphylococcus aureus from humans was 52.3%, sheep 42.5%, goats 30.0% and cattle 37.5%. The overall isolation rate was 44.8%. Human were found to harbour more S. aureus than the animals. The isolates were tested against 13 antimicrobial agents. Of these, Ciproxin, Norfloxacin, Rifampicin, Strept omycin, and Erythromycin showed the highest activity against S. aureus while Cefotaxime, Ceftazimide and Ampiclox showed least activity. It was concluded that Ciproxin, Norf loxacin, Rifampicin, Streptomycin, and Erythromycin may be the drug of choice in the treatment of infections caused by S. aureus .