Miracle-dz/UniFAR-FTUs huggingface dataset:
Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1

We have fortuitously identified a nucleotide sequence that decreases expression of a reporter gene in the yeast Saccharomyces cerevisiae 20-fold when inserted into an intron. The primary effect of the insertion is a decrease in pre-mRNA abundance accompanied by the appearance of 3'-truncated transcripts, consistent with premature transcriptional termination and/or pre-mRNA degradation. Point mutations in the cis element relieve the negative effect, demonstrating its sequence specificity. A novel yeast protein, named Nrd1, and a previously identified putative helicase, Sen1, help mediate the negative effect of the cis element. Sen1 is an essential nuclear protein that has been implicated in a variety of nuclear functions. Nrd1 has hallmarks of a heterogeneous nuclear ribonucleoprotein, including an RNA recognition motif, a region rich in RE and RS dipeptides, and a proline- and glutamine-rich domain. An N-terminal domain of Nrd1 may facilitate direct interaction with RNA polymerase II. Disruption of the NRD1 gene is lethal, yet C-terminal truncations that delete the RNA recognition motif and abrogate the negative effect of the cis element nevertheless support cell growth. Thus, expression of a gene containing the cis element could be regulated through modulation of the activity of Nrd1. The recent identification of Nrd1-related proteins in mammalian cells suggests that this potential regulatory pathway is widespread among eukaryotes.
Are leukotrienes involved in human uterine contractility?

Summary. The effects of leukotrienes (LT) on the contractility of human and rat myometrial strips in vitro were compared with the effects of prostaglandins (PGs) and oxytocin. Preparations of human myometrial membranes were investigated for the presence and characteristics of LTC4 receptors. Neither the peptido‐leukotrienes (LTC4, LTD4, LTE4) nor LTB4 had any consistent effect, stimulatory or inhibitory, on human pregnant or non‐pregnant myometrium, at doses up to 1·25 μM; nor did they have any effect in rat non‐pregnant myometrium. As expected, PGE2, PGF2α (0·3 μM) and oxytocin (5 nM) stimulated human pregnant myometrium. PGF2α stimulated and PGE2 inhibited human non‐pregnant myometrium but oxytocin had no effect; all three compounds stimulated rat non‐pregnant myometrium. The binding of 3H‐LTC4 to human myometrium was specific (LTC4> LTD4 >>> LTE4, LTB4, PGE2, PGF2α, arachidonic acid) but of low affinity compared with the binding of 3H‐PGE2 to the same membrane preparations. These data support the view that leukotrienes have little direct influence on myometrial contractility.
Serotypes of Chlamydia trachomatis and risk for development of cervical squamous cell carcinoma.

CONTEXT Human papillomavirus (HPV) infection has been established as a cause of cervical cancer. Epidemiologic studies suggest that Chlamydia trachomatis infection also confers increased risk for cervical squamous cell carcinoma (SCC). Whether this risk is serotype-specific is unknown. OBJECTIVE To study the association between exposure to different C trachomatis serotypes and subsequent development of cervical SCC. DESIGN AND SETTING Longitudinal, nested case-control study within a cohort of 530 000 women who provided samples to serum banks in Finland, Norway, and Sweden. The data files were linked to respective national cancer registries. SUBJECTS One hundred twenty-eight women who had developed invasive cervical SCC at least 12 months following serum donation. Each case had 3 matched controls. MAIN OUTCOME MEASURE Risk for the development of cervical SCC by IgG antibodies to 10 different C trachomatis serotypes, adjusted for antibodies to HPV types 16, 18, and 33 and for serum cotinine levels. RESULTS Of specific C trachomatis serotypes, serotype G was most strongly associated with SCC (adjusted odds ratio [OR], 6.6; 95% confidence interval [CI], 1. 6-27.0). Other serotypes associated with SCC were I (OR, 3.8; 95% CI, 1.3-11.0) and D (OR, 2.7; 95% CI, 1.3-5.6). Presence of serum IgG antibodies to more than 1 serotype increased the adjusted ORs for SCC (P<.001 for trend). CONCLUSIONS Chlamydia trachomatis serotype G is most strongly associated with subsequent development of cervical SCC. Increasing numbers of exposures to different C trachomatis serotypes also increases risk. Our results strengthen the evidence that there is a link between past C trachomatis infection and cervical SCC.
Estimating the Entropy of Binary Time Series: Methodology, Some Theory and a Simulation Study

Abstract: Partly motivated by entropy-estimation problems in neuroscience, we present adetailed and extensive comparison between some of the most popular and effective entropyestimation methods used in practice: The plug-in method, four different estimators basedon the Lempel-Ziv (LZ) family of data compression algorithms, an estimator based on theContext-Tree Weighting (CTW) method, and the renewal entropy estimator.M ETHODOLOGY : Three new entropy estimators are introduced; two new LZ-basedestimators, and the “renewal entropy estimator,” which is tailored to data generated by abinary renewal process. For two of the four LZ-based estimators, a bootstrap procedure isdescribed for evaluating their standard error, and a practical rule of thumb is heuristicallyderived for selecting the values of their parameters in practice. T HEORY : We prove that,unlike their earlier versions, the two new LZ-based estimators are universally consistent,that is, they converge to the entropy rate for every ﬁnite-valued, stationary and ergodicprocess. An effective method is derived for the accurate approximation of the entropy rateof a ﬁnite-state hidden Markov model (HMM) with known distribution. Heuristiccalculations are presented and approximate formulas are derived for evaluating the bias andthe standard error of each estimator. S
Electron Beam Induced Etching

27 Introduction. 27 Experimental Results . 28 Process Modeling . 31 Precursor EBIE Model . 31 Electron Flux Limited Regime . 32 Mass Transport Limited Regime (Type I) . 33 Precursor EBIE Model with Surface Diffusion . 36 Precursor-Product EBIE Model . 38 Mass Transport Limited (Type II) . 40 Electron Beam Induced Product Dissociation . 41 Additional Experimental . 47 Summary . 50 Chapter 3: Time Dependent Behavior . 54 Overview . 54 Analytical Solutions . 54 Small Product Residence Time, Electron Flux Limited Regime . 58 Small Product Residence Time, Mass Transport Limited Regime . 64 Large Product Residence Time, Electron Flux Limited Regime. 74 Large Product Residence Time, Mass Transport Limited Regime . 78 Zero Electron Flux, Refresh Region . 89
Combined Competitive Flow Control and Routing in Multi-User Communication Networks with Hard Side-Constraints

We consider in this paper the problem of combined flow control and routing in a noncooperative setting, where each user is faced with a multicriterion optimization problem, formulated as the minimization of one criterion subject to constraints on others. We address here the basic questions of existence and uniqueness of equilibrium. We show that an equilibrium indeed exists, but it may not be unique due to the multi-criteria nature of the problem. We are able, however, to obtain uniqueness in some weaker sense under appropriate conditions; we show in particular that the link utilizations are uniquely determined at equilibrium and the normalized Nash equilibrium is unique.
Effect of Sleep Apnea and Continuous Positive Airway Pressure on Cardiac Structure and Recurrence of Atrial Fibrillation

Background Sleep apnea (SA) is associated with an increased risk of atrial fibrillation (AF). We sought to determine the effect of SA on cardiac structure in patients with AF, whether therapy for SA was associated with beneficial cardiac structural remodelling, and whether beneficial cardiac structural remodelling translated into a reduced risk of recurrence of AF after pulmonary venous isolation (PVI). Methods and Results A consecutive group of 720 patients underwent a cardiac magnetic resonance study before PVI. Patients with SA (n=142, 20%) were more likely to be male, diabetic, and hypertensive and have an increased pulmonary artery pressure, right ventricular volume, atrial dimensions, and left ventricular mass. Treated SA was defined as duration of continuous positive airway pressure therapy of >4 hours per night. Treated SA patients (n=71, 50%) were more likely to have paroxysmal AF, a lower blood pressure, lower ventricular mass, and smaller left atrium. During a follow‐up of 42 months, AF recurred in 245 patients. The cumulative incidence of AF recurrence was 51% in patients with SA, 30% in patients without SA, 68% in patients with untreated SA, and 35% in patients with treated SA. In a multivariable model, the presence of SA (hazard ratio 2.79, CI 1.97 to 3.94, P<0.0001) and untreated SA (hazard ratio 1.61, CI 1.35 to 1.92, P<0.0001) were highly associated with AF recurrence. Conclusions Patients with SA have an increased blood pressure, pulmonary artery pressure, right ventricular volume, left atrial size, and left ventricular mass. Therapy with continuous positive airway pressure is associated with lower blood pressure, atrial size, and ventricular mass, and a lower risk of AF recurrence after PVI.
Clustered Blind Beamforming From Ad-Hoc Microphone Arrays

Microphone arrays have been used in various applications to capture conversations, such as in meetings and teleconferences. In many cases, the microphone and likely source locations are known a priori, and calculating beamforming filters is therefore straightforward. In ad-hoc situations, however, when the microphones have not been systematically positioned, this information is not available and beamforming must be achieved blindly. In achieving this, a commonly neglected issue is whether it is optimal to use all of the available microphones, or only an advantageous subset of these. This paper commences by reviewing different approaches to blind beamforming, characterizing them by the way they estimate the signal propagation vector and the spatial coherence of noise in the absence of prior knowledge of microphone and speaker locations. Following this, a novel clustered approach to blind beamforming is motivated and developed. Without using any prior geometrical information, microphones are first grouped into localized clusters, which are then ranked according to their relative distance from a speaker. Beamforming is then performed using either the closest microphone cluster, or a weighted combination of clusters. The clustered algorithms are compared to the full set of microphones in experiments on a database recorded on different ad-hoc array geometries. These experiments evaluate the methods in terms of signal enhancement as well as performance on a large vocabulary speech recognition task.
Soft Syntactic Constraints for Word Alignment through Discriminative Training

Word alignment methods can gain valuable guidance by ensuring that their alignments maintain cohesion with respect to the phrases specified by a monolingual dependency tree. However, this hard constraint can also rule out correct alignments, and its utility decreases as alignment models become more complex. We use a publicly available structured output SVM to create a max-margin syntactic aligner with a soft cohesion constraint. The resulting aligner is the first, to our knowledge, to use a discriminative learning method to train an ITG bitext parser.
Random Walks and Evolving Sets: Faster Convergences and Limitations

Analyzing the mixing time of random walks is a well-studied problem with applications in random sampling and more recently in graph partitioning. In this work, we present new analysis of random walks and evolving sets using more combinatorial graph structures, and show some implications in approximating small-set expansion. On the other hand, we provide examples showing the limitations of using random walks and evolving sets in disproving the small-set expansion hypothesis. - We define a combinatorial analog of the spectral gap, and use it to prove the convergence of non-lazy random walks. A corollary is a tight lower bound on the small-set expansion of graph powers for any graph. - We prove that random walks converge faster when the robust vertex expansion of the graph is larger. This provides an improved analysis of the local graph partitioning algorithm using the evolving set process. - We give an example showing that the evolving set process fails to disprove the small-set expansion hypothesis. This refutes a conjecture of Oveis Gharan and shows the limitations of local graph partitioning algorithms in approximating small-set expansion.
A Development of Polarization Experimental Processes and Analysis Mechanical Behavior for COC and PVDF Films

The paper is investigated the polarization properties and mechanical behavior of new piezoelectric polymer material plates by experimental procedures and finite element analysis. In this study, the PVDF materials is used to produce the piezoelectric polymer layer and the coating film, we have provided a nice procedures for manufacturing piezoelectric polymer plates (PVDF). In order to find the proper proportion of the PVDF to achieve the best material properties, the mechanical behavior of displacements and stresses for the electrets is investigated by experimental measurement and finite element analysis (with ANSYS). It is investigated whether the thicknesses of specimens are affected the polarization. The paper is presented modal analysis techniques for piezoelectric thin plates.
Capsaicin: From Plants to a Cancer-Suppressing Agent

Capsaicinoids are plant secondary metabolites, capsaicin being the principal responsible for the pungency of chili peppers. It is biosynthesized through two pathways involved in phenylpropanoid and fatty acid metabolism. Plant capsaicin concentration is mainly affected by genetic, environmental and crop management factors. However, its synthesis can be enhanced by the use of elicitors. Capsaicin is employed as food additive and in pharmaceutical applications. Additionally, it has been found that capsaicin can act as a cancer preventive agent and shows wide applications against various types of cancer. This review is an approach in contextualizing the use of controlled stress on the plant to increase the content of capsaicin, highlighting its synthesis and its potential use as anticancer agent.
The Endocrine Disruptor 4-Nonylphenol Promotes Adipocyte Differentiation and Induces Obesity in Mice

Background/Aim: The environmental obesogen hypothesis proposes that exposure to endocrine disruptors during developmental “window” contributes to adipogenesis and the development of obesity. Implication of environmental endocrine disruptor such as 4Nonylphenol (4-NP) on adipose tissue development has been poorly investigated. Methods: 3T3-L1 preadipocytes were incubated with different doses of 4-NP. Six-week-old C57BL/6J male mice received an intraperitoneal injection of vehicle, troglitazone or 4-NP (0.5 mg/kg). Gene expression of adipogenic regulators was analyzed. Pregnant mice were dosed by gavage with vehicle or 4-NP (0.05, 0.25 or 0.5 mg/kg) from day 12 of gestation until day 7 of lactation. The body weight, liver weight, fat mass, and serum lipids and glucose levels were measured in offspring at postnatal day 60. Results: Low concentration of 4-NP induced adipocyte differentiation, glycerol-3-phosphate dehydrogenase activity, and expression of peroxisome proliferator-acivated receptor γ as well as its target genes required for adipogenesis. 4-NP perturbed key regulators of adipogenesis and lipogenic pathway in vivo. Perinatal exposure to 4-NP increased body weight, fat mass, and serum total cholesterol and glucose levels in offspring. Conclusions: 4-NP may be expected to increase the incidence of obesity and can act as a potential chemical stressor for obesity and obesity-related disorders.
Tracking Malware using Internet Activity Data

Forensic Investigation into security incidents often includes the examination of huge lists of internet activity gathered from a suspect computer. In today’s age of increased internet usage, the internet activity log on any given system could produce a huge list of websites. This, couples with the fact that a huge percentage of malware is now distributed via the internet, often through compromised websites, means that valuable clues regarding the source and identity of malware infections are often hidden within the internet activity logs on a computer. While a multitude of tools exist to extract internet activity data from a host computer, most do not filter this activity data. As a result, an investigator could be faced with thousands of website URL’s to sift through for clues regarding malware infection. In this paper, we discuss some of the ways that computers are infected, and why internet activity data is an important resource that must be analyzed in a forensic investigation. We then present a tool that utilizes the Google Safe Browsing Lookup API, which is an extension of the broader Google Safe Browsing API, to do quick lookups on long lists of URL’s and significantly narrow the list to enable the investigator to conduct a more efficient investigation. KeywordsMalware Investigation, Internet Activity Data, Google
Efficacy of Kinesiology Taping for Recovery from Occupational Wrist Disorders Experienced by a Physical Therapist

[Purpose] The aim of this paper was to report the efficacy of kinesiology taping for recovery from wrist pain and limited range of motion (ROM) in a physical therapist with repetitive strain injuries. [Subjects] A 32 year-old male physical therapist developed recurring severe pain in the dominant wrist and limited active ROM with extremely painful supination. [Methods] The kinesiology tape was applied to the lumbricals, musculi interossei dorsales, palmares, the wrist extensor and flexor muscles, and the wrist joint for 3 weeks for an average of 10 h/day. [Results] After application of the kinesiology tape, the Numeric Pain Rating Scale and Patient-rated Wrist Evaluation scores decreased, and the Patient-Specific Functional Scale score increased in comparison with the initial score. [Conclusion] Repeated kinesiology taping of the wrist muscles and joint could be an effective method for recovery from occupational wrist disorders experienced by physical therapists.
High Glucose Increases Acetylcholine-Induced Ca2+ Entry and Protein Expression of STIM1

Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disea se and a major risk factor for endothelial dysfunction. In the cur rent study, we have explored glucose-induced abnormal intracellular cal cium (Cai) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low gl ucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca i, however, there was a significant increase of acetylcholine-induced Ca 2+ entry. Western blots illustrated that exposure to HG also increased STIM 1 (Stromal Interaction Molecule 1), but not Orai1 (the pore fo rming subunit), protein expression levels. Although the link betwee n HG-induced changes in STIM1 expression, enhanced Ca 2+ entry and endothelial dysfunction requires further study, the current dat a re suggestive that targeting these pathways may reduce the impact of HG on endothelial function. Keywords—store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction
PI3K-AKT-mTOR Pathway is Dominant over Androgen Receptor Signaling in Prostate Cancer Cells

Background: Androgen receptor (AR) and the phosphatidylinositol-3 kinase (PI3K) signaling are two of the most important pathways implicated in prostate cancer. Previous work has shown that there is crosstalk between these two pathways; however, there are conflicting findings and the molecular mechanisms are not clear. Here we studied the AR–PI3K pathway crosstalk in prostate cancer cells in vitro as well as in vivo. Methods: Quantitative PCR, Western analysis, reporter assays, and proliferation analyses in vitro and in vivo were used to evaluate the effect of PI3K pathway inhibition on AR signaling and cell growth. Results: Transcriptional activity of AR was increased when the PI3K pathway was inhibited at different levels. In the androgen responsive prostate cancer cell line LNCaP, androgen and the mTOR inhibitor rapamycin synergistically activated androgen target genes. Despite increased androgen signaling, rapamycin treatment reduced LNCaP cell growth; the AR antagonist bicalutamide potentiated this effect. Furthermore, the rapamycin derivative CCI-779 reduced the growth of CWR22 prostate cancer xenografts while increasing AR target gene expression. Conclusions: These findings suggest that inhibition of the PI3K pathway activates AR signaling. Despite the increase in AR signaling which has proliferative effects, the result of PI3K pathway inhibition is antiproliferative. These findings suggest that the PI3K pathway is dominant over AR signaling in prostate cancer cells which should be considered in developing novel therapeutic strategies for prostate cancer.
Distribution-Specific Agnostic Boosting

We consider the problem of boosting the accuracy of weak learning algorithms in the agnostic learning framework of Haussler (1992) and Kearns et al. (1992). Known algorithms for this problem (Ben-David et al., 2001; Gavinsky, 2002; Kalai et al., 2008) follow the same strategy as boosting algorithms in the PAC model: the weak learner is executed on the same target function but over different distributions on the domain. We demonstrate boosting algorithms for the agnostic learning framework that only modify the distribution on the labels of the points (or, equivalently, modify the target function). This allows boosting a distribution-specific weak agnostic learner to a strong agnostic learner with respect to the same distribution. When applied to the weak agnostic parity learning algorithm of Goldreich and Levin (1989) our algorithm yields a simple PAC learning algorithm for DNF and an agnostic learning algorithm for decision trees over the uniform distribution using membership queries. These results substantially simplify Jackson's famous DNF learning algorithm (1994) and the recent result of Gopalan et al. (2008). We also strengthen the connection to hard-core set constructions discovered by Klivans and Servedio (1999) by demonstrating that hard-core set constructions that achieve the optimal hard-core set size (given by Holenstein (2005) and Barak et al. (2009)) imply distribution-specific agnostic boosting algorithms. Conversely, our boosting algorithm gives a simple hard-core set construction with an (almost) optimal hard-core set size.