Miracle-dz/UniFAR-FTUs huggingface dataset:
Prenatal Exposure to TCDD Triggers Significant Modulation of microRNA Expression Profile in the Thymus That Affects Consequent Gene Expression

Background MicroRNAs (miRs) are a class of small RNAs that regulate gene expression. There are over 700 miRs encoded in the mouse genome and modulate most of the cellular pathways and functions by controlling gene expression. However, there is not much known about the pathophysiological role of miRs. TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin), an environmental contaminant is well known to induce severe toxicity (acute and chronic) with long-term effects. Also, in utero exposure of fetus to TCDD has been shown to cause thymic atrophy and alterations in T cell differentiation. It is also relevant to understand “the fetal basis of adult disease” hypothesis, which proposes that prenatal exposure to certain forms of nutritional and environmental stress can cause increased susceptibility to clinical disorders later in life. In the current study, therefore, we investigated the effects of prenatal exposure to TCDD on miR profile in fetal thymocytes and searched for their possible role in causing thymic atrophy and alterations in the expression of apoptotic genes. Methodology/Principal Findings miR arrays of fetal thymocytes post exposure to TCDD and vehicle were performed. Of the 608 mouse miRs screened, 78 miRs were altered more than 1.5 fold and 28 miRs were changed more than 2 fold in fetal thymocytes post-TCDD exposure when compared to vehicle controls. We validated the expression of several of the miRs using RT-PCR. Furthermore, several of the miRs that were downregulated contained highly complementary sequence to the 3′-UTR region of AhR, CYP1A1, Fas and FasL. Also, the Ingenuity Pathway Analysis software and database was used to analyze the 78 miRs that exhibited significant expression changes and revealed that as many as 15 pathways may be affected. Conclusions/Significance These studies revealed that TCDD-mediated alterations in miR expression may be involved in the regulation of its toxicity including cancer, hepatic injury, apoptosis, and cellular development.
A different kind of contextual effect: geographical clustering of cocaine incidence in the USA

Study objective: Outline the use of the pairwise odds ratio (PWOR) to quantify the extent to which a binary outcome clusters geographically. Quantify the extent to which first experience with cocaine is spatially correlated within US neighbourhoods and cities. Quantify geographical clustering of first experience with cocaine by neighbourhood context. Design: Estimate the PWOR of incident cocaine experience at two levels (neighbourhood, city) and compare across years. Within years, estimate the PWOR by neighbourhood disadvantage and test for trend. Setting: US National Household Survey on Drug Abuse. Participants: Civilian, non-institutionalised household residents of the United States age 12 years and older interviewed in person during 1979, 1988, 1990, 1991, 1992, 1993. Main results: First experience with cocaine clusters within US neighbourhoods and cities. There is some evidence that the spatial correlation of first experience with cocaine increases with percentage of neighbourhood households living in poverty. Conclusions: The gradient in spatial correlation of incident cocaine experience by neighbourhood poverty level is consistent with current theories of concentrated disadvantage. The possibility that the direction of the poverty gradient might change over the course of a drug epidemic is discussed.
Genotype and maternal environment affect belowground interactions between Arabidopsis thaliana and its competitors

Ecological interactions between different species are not fixed, but they may depend, at least to some extent, on the particular genotypes involved as well as on the environmental conditions experienced by previous generations. We used a set of natural genotypes of Arabidopsis thaliana, that previously experienced contrasting nutrient and herbivory conditions, to test for the influences of genetic variation and maternal effects on competitive interactions between Arabidopsis and the weedy annuals Anagallis arvensis and Senecio vulgaris. We used activated carbon to discriminate between resource competition and allelopathy components of plant-plant interactions. There was a clear competitive hierarchy: Senecio > Arabidopsis > Anagallis. Although we found no evidence for allelopathic potential of Arabidopsis, our results indicate that both Anagallis and Senecio exerted negative (direct or indirect) allelopathic effects on Arabidopsis. There were significant differences among Arabidopsis genotypes in their competitive effects on both neighbor species, as well as in their response to competition. Maternal environments significantly influenced not only the growth and fitness of Arabidopsis itself, but also its competitive effect on Anagallis. We found, however, no evidence that maternal environments affected the competitive effect on Senecio or overall competitive response of Arabidopsis. Generally, resource competition played a greater role than allelopathy, and genotype effects were more important than maternal effects. Our study demonstrates that ecological interactions, such as plant competition, are complex and multi-layered, and that, in particular, the influence of genetic variation on interactions with other species should not be overlooked.
Genetic Diversity of Sturmiopsis parasitica Curran (Diptera: Tachinidae)

Abstract Sturmiopsis parasitica Curran (Diptera: Tachinidae) is a widely spread parasitoid of various lepidopteran stem borers including Eldana saccharina Walker (Lepidoptera: Pyralidae), Busseola fusca (Fuller) and Sesamia calamistis Hampson (Lepidoptera: Noctuidae) in western, eastern and southern Aenica. As the Aenican sugarcane stalk borer, E. saccharina, is currently the most economically important insect pest in South Aenican sugarcane there is an urgent need to develop a control strategy for the management of this pest. S. parasitica has been tested as a biological control agent against E. saccharina with limited success. In seeking possible reasons for this limited success we tested whether there is genetic differentiation among populations of S. parasitica and whether there are hostassociated lineages of S. parasitica enom B. fusca and E. saccharina. To assess these hypotheses, DNA sequences of cytochrome oxidase I (COI), a mitochondrial proteincoding gene, were obtained enom fifteen specimens collected in western, eastern and southern Aenica. Phylogenetic analysis of these sequences using maximum parsimony grouped the specimens into two main clades, one of which is further subdivided. Examination of pairwise sequence divergence levels supports the hypothesis of two cryptic lineages. However, further supportive evidence is necessary before revising the taxonomy of the species.
IL-17 and IL-22 in Cerebrospinal Fluid and Plasma Are Elevated in Guillain-Barré Syndrome

Guillain-Barré syndrome (GBS) is an acute autoimmune-mediated inflammatory demyelinating disease that causes rapidly progressing paralysis and occasionally respiratory failure. We hypothesized that interleukin (IL)-17 and IL-22 are elevated in GBS and participate in the autoimmune inflammatory response of GBS. We used sandwich enzyme-linked immunosorbent assay (ELISA) to measure the IL-17 and IL-22 levels in the CSF, and plasma from 22 GBS patients at the acute phase and 18 healthy controls (HC). The results show that CSF and plasma levels of IL-17 and IL-22 are elevated in GBS patients compared with HC. IL-17 and IL-22 levels in CSF, respectively, are correlated with GBS disability scale scores (GDSs). Meanwhile, IL-17 and IL-22 levels in CSF, IL-22 in CSF, and plasma of GBS patients have positive correlation, respectively. The increased levels of IL-17 and IL-22 in CSF may be explained by the disruption of blood-brain barrier (BBB) and peripheral nervous system (PNS) local inflammation in GBS. Meanwhile, the elevated levels of these two cytokines in plasma suggest the activation of Th17 and Th22 cells in the systemic immune response of GBS. Our data provide preliminary evidence that GBS is associated with high levels of IL-17 and IL-22 in CSF and plasma. These cytokines display pathogenic potential and may serve as useful biomarkers for GBS.
Compressed Sensing over ℓp-balls: Minimax mean square error

We consider the compressed sensing problem where the object x<inf>0</inf> ∈ ℝ<sup>N</sup> is to be recovered from incomplete measurements y = Ax<inf>0</inf>+z. Here the sensing matrix A is an n×N random matrix with Gaussian entries and n &#60; N. A popular method of sparsity-promoting reconstruction is ℓ<sup>1</sup>-penalized least-squares reconstruction (aka LASSO, Basis Pursuit).
A State Space Approach to the Inverse of LPTV Filters

In this paper, a state space approach for computing the inverse of a general single-input single-output linear periodically time-varying filter is proposed. The inverse of the filter is derived by first constructing the inverse of an LPTV filter. The result is then extended to obtain the inverse of the IIR filter. Compared with existing approaches using other techniques, the proposed approach is quite straightforward, hence, can reduce the computational complexity
Compiling for EDGE architectures

Explicit data graph execution (EDGE) architectures offer the possibility of high instruction-level parallelism with energy efficiency. In EDGE architectures, the compiler breaks a program into a sequence of structured blocks that the hardware executes atomically. The instructions within each block communicate directly, instead of communicating through shared registers. The TRIPS EDGE architecture imposes restrictions on its blocks to simplify the microarchitecture: each TRIPS block has at most 128 instructions, issues at most 32 loads and/or stores, and executes at most 32 register bank reads and 32 writes. To detect block completion, each TRIPS block must produce a constant number of outputs (stores and register writes) and a branch decision. The goal of the TRIPS compiler is to produce TRIPS blocks full of useful instructions while enforcing these constraints. This paper describes a set of compiler algorithms that meet these sometimes conflicting goals, including an algorithm that assigns load and store identifiers to maximize the number of loads and stores within a block. We demonstrate the correctness of these algorithms in simulation on SPEC2000, EEMBC, and microbenchmarks extracted from SPEC2000 and others. We measure speedup in cycles over an Alpha 21264 on microbenchmarks.
Cumulative genetic risk and prefrontal activity in patients with schizophrenia.

The lack of consistency of genetic associations in highly heritable mental illnesses, such as schizophrenia, remains a challenge in molecular psychiatry. Because clinical phenotypes for psychiatric disorders are often ill defined, considerable effort has been made to relate genetic polymorphisms to underlying physiological aspects of schizophrenia (so called intermediate phenotypes), that may be more reliable. Given the polygenic etiology of schizophrenia, the aim of this work was to form a measure of cumulative genetic risk and study its effect on neural activity during working memory (WM) using functional magnetic resonance imaging. Neural activity during the Sternberg Item Recognition Paradigm was measured in 79 schizophrenia patients and 99 healthy controls. Participants were genotyped, and a genetic risk score (GRS), which combined the additive effects of 41 single-nucleotide polymorphisms (SNPs) from 34 risk genes for schizophrenia, was calculated. These risk SNPs were chosen according to the continuously updated meta-analysis of genetic studies on schizophrenia available at www.schizophreniaresearchforum. org. We found a positive relationship between GRS and left dorsolateral prefrontal cortex inefficiency during WM processing. GRS was not correlated with age, performance, intelligence, or medication effects and did not differ between acquisition sites, gender, or diagnostic groups. Our study suggests that cumulative genetic risk, combining the impact of many genes with small effects, is associated with a known brain-based intermediate phenotype for schizophrenia. The GRS approach could provide an advantage over studying single genes in studies focusing on the genetic basis of polygenic conditions such as neuropsychiatric disorders.
A Chandra X-ray detection of the L dwarf binary Kelu-1 - Simultaneous Chandra and Very Large Array observations

Context. Magnetic activity in ultracool dwarfs, as measured in X-rays and Hα, shows a steep decline after spectral type M7-M8. So far, no L dwarf has been detected in X-rays. In contrast, L dwarfs may have higher radio activity than M dwarfs. Aims. We observe L and T dwarfs simultaneously in X-rays and radio to determine their level of magnetic activity in the context of the general decline of magnetic activity with cooler effective temperatures. Methods. The field L dwarf binary Kelu-1 was observed simultaneously with Chandra and the Very Large Array. Results. Kelu-1AB was detected in X-rays with LX = 2.9 +1.8 −1.3 × 10 25 erg s −1 , while it remained undetected in the radio down to a 3σ limit of LR ≤ 1.4 × 10 13 erg s −1 Hz −1 . We argue that, whereas the X-ray and Hα emissions decline in ultracool dwarfs with decreasing effective temperature, the radio luminosity stays (more or less) constant across M and early-L dwarfs. The radio surface flux or the luminosity may better trace magnetic activity in ultracool dwarfs than the ratio of the luminosity to the bolometric luminosity. Conclusions. Deeper radio observations (and at short frequencies) are required to determine if and when the cut-off in radio activity occurs in L and T dwarfs, and what kind of emission mechanism takes place in ultracool dwarfs.
Household Energy Conservation Investment and the Uninformed Consumer Hypothesis (with Alexander M. Brill and Kevin A. Hassett)

AbstractIncreasing consumption of energy in the consumer market along with “low” levels ofinvestment in energy conservation technology has raised considerable concern among publicpolicy analysts. Many believe that the high reported consumer discount rates along with lowaudit participation rates by many segments of the population reflect consumer ignorance ratherthan true structural parameters, which has led to substantial expenditures on policies designed toeducate consumers. In this paper, we explore the “uninformed consumer hypothesis” by relatingthe decision to invest in energy saving insulation to one’s level of education, presuming thisshould be correlated with an individual’s probability of being well informed, along with anumber of variables that help proxy for the economic returns to home improvement, and thediscount rates that individuals apply to them. Although a cursory examination of our dataconfirms previous results, tests performed on a more formalized model show that the economicvariables are found to be important determinants of home improvement behavior, but theeducation variables are not.
A Consistent Information Criterion for Support Vector Machines in Diverging Model Spaces

Information criteria have been popularly used in model selection and proved to possess nice theoretical properties. For classification, Claeskens et al. (2008) proposed support vector machine information criterion for feature selection and provided encouraging numerical evidence. Yet no theoretical justification was given there. This work aims to fill the gap and to provide some theoretical justifications for support vector machine information criterion in both fixed and diverging model spaces. We first derive a uniform convergence rate for the support vector machine solution and then show that a modification of the support vector machine information criterion achieves model selection consistency even when the number of features diverges at an exponential rate of the sample size. This consistency result can be further applied to selecting the optimal tuning parameter for various penalized support vector machine methods. Finite-sample performance of the proposed information criterion is investigated using Monte Carlo studies and one real-world gene selection problem.
Implementing ranking strategies using text signatures

Signature files provide an efficient access method for text in documents, but retrieval is usually limited to finding documents that contain a specified Boolean pattern of words. Effective retrieval requires that documents with similar meanings be found through a process of plausible inference. The simplest way of implementing this retrieval process is to rank documents in order of their probability of relevance. In this paper techniques are described for implementing probabilistic ranking strategies with sequential and bit-sliced signature tiles and the limitations of these implementations with regard to their effectiveness are pointed out. A detailed comparison is made between signature-based ranking techniques and ranking using term-based document representatives and inverted files. The comparison shows that term-based representations are at least competitive (in terms of efficiency) with signature files and, in some situations, superior.
Factors Affecting Continued Usage of Internet Banking Among Egyptian Customers

This research aims to understand and explain customers continued intention to use internet banking in Egypt. The research starts with reviewing well-known theories of behavioural intentions such as the theory of reasoned action, the theory of planned behaviour, the theory of decomposed planned behaviour, the technology acceptance model ,and the diffusion of innovations theory as well as the use of these theories in self service technologies such as internet banking . By using a sample of users of internet banking services, perceived ease-of-use was found to be the strongest predictor of intentions to continued usage of internet banking services. Demographic variables had no significant effect on continued usage of internet banking services. Finally, perceived risk had no relationship with customer continued intention to use the service. The research concludes with study limitations and suggestions for future research.
Feedback regulation of angiotensin converting enzyme activity and mRNA levels by angiotensin II.

Although renin and angiotensinogen are known to be subject to feedback regulation, the effects of angiotensin II (Ang II) on the regulation of angiotensin converting enzyme (ACE) gene expression and enzymatic activity have not yet been studied. Therefore, the effects of exogenous Ang II infusion and ACE inhibition on ACE mRNA expression were examined. Ang II was infused intravenously in male Sprague-Dawley rats for 3 days at 100 (low dose), 300 (medium dose), or 1,000 (high dose) ng/kg per minute (n = 8 for each group). Compared with control (vehicle infusion, n = 8), Ang II infusion increased plasma Ang II concentration (62, 101, 126 [p < 0.05], and 187 [p < 0.05] fmol/ml) and mean arterial blood pressure (106, 119 [p < 0.05], 134 [p < 0.05], and 125 mm Hg for control, low, medium, and high doses, respectively). Ang II infusion decreased ACE mRNA levels in the lung (57%, 52%, and 51%; p < 0.05 for each) and testis (49%, 63%, and 53% of control for low, medium, and high doses, respectively; p < 0.05 for each), two major sites of ACE synthesis. There was, albeit less pronounced, a parallel decrease in pulmonary ACE activity (4.38, 3.92, 3.07 [p < 0.05], and 3.48 [p < 0.05] nM/mg per minute for control, medium, and high doses, respectively). In contrast, serum (54, 50, 48, and 38 [p < 0.05] nM/ml per minute) and testicular (2.63, 2.08 [p < 0.05], 2.24, and 2.18 nM/mg per minute for control, low, medium, and high doses, respectively) ACE activities displayed only minimal change in animals infused with Ang II. (ABSTRACT TRUNCATED AT 250 WORDS)
Ritual well-being: toward a social signaling model of religion and mental health

ABSTRACT Religion is positively correlated with subjective well-being across a variety of contexts, but convincing causal models are lacking. Some researchers have suggested that religion may boost self-control, and thus well-being, by requiring effortful rituals. This article proposes that costly signaling theory provides a vital explanatory tool for understanding these relationships. Signaling theories posit that religious adherents signal their commitment to religious collectives through difficult or anhedonic activities and rituals, creating a cost barrier for entry which protects religious communities against free riders. Because costly signaling behaviors require the inhibition of prepotent responses and intentional exposure to aversive stimuli, committed adherents build self-control over time. Subjective well-being is thus modeled as a longitudinal product of subjective investment in a religious social collective and the self-regulation abilities that emerge from signaling that investment. This emphasis on a feedback cycle driven by social signaling represents a novel contribution to investigations of religion and well-being. New longitudinal research in social investment theory and self-control lends the model conceptual credibility.
Optimization by Simulated Annealing: An Experimental Evaluation; Part I, Graph Partitioning

In this and two companion papers, we report on an extended empirical study of the simulated annealing approach to combinatorial optimization proposed by S. Kirkpatrick et al. That study investigated how best to adapt simulated annealing to particular problems and compared its performance to that of more traditional algorithms. This paper (Part I) discusses annealing and our parameterized generic implementation of it, describes how we adapted this generic algorithm to the graph partitioning problem, and reports how well it compared to standard algorithms like the Kernighan-Lin algorithm. (For sparse random graphs, it tended to outperform Kernighan-Lin as the number of vertices become large, even when its much greater running time was taken into account. It did not perform nearly so well, however, on graphs generated with a built-in geometric structure.) We also discuss how we went about optimizing our implementation, and describe the effects of changing the various annealing parameters or varying the basic annealing algorithm itself.
Characterization of Mycobacterium smegmatis Expressing the Mycobacterium tuberculosis Fatty Acid Synthase I (fas1) Gene

ABSTRACT Unlike most other bacteria, mycobacteria make fatty acids with the multidomain enzyme eukaryote-like fatty acid synthase I (FASI). Previous studies have demonstrated that the tuberculosis drug pyrazinamide and 5-chloro-pyrazinamide target FASI activity. Biochemical studies have revealed that in addition to C16:0, Mycobacterium tuberculosis FASI synthesizes C26:0 fatty acid, while the Mycobacterium smegmatis enzyme makes C24:0 fatty acid. In order to express M. tuberculosis FASI in a rapidly growing Mycobacterium and to characterize the M. tuberculosis FASI in vivo, we constructed an M. smegmatis Δfas1 strain which contained the M. tuberculosis fas1 homologue. The M. smegmatis Δfas1 (attB::M. tuberculosis fas1) strain grew more slowly than the parental M. smegmatis strain and was more susceptible to 5-chloro-pyrazinamide. Surprisingly, while the M. smegmatis Δfas1 (attB::M. tuberculosis fas1) strain produced C26:0, it predominantly produced C24:0. These results suggest that the fatty acid elongation that produces C24:0 or C26:0 in vivo is due to a complex interaction among FASI, FabH, and FASII and possibly other systems and is not solely due to FASI elongation, as previously suggested by in vitro studies.