Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

Transcription factor binding sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (<inline-formula> <tex-math notation="LaTeX">$k = 8\sim$</tex-math><alternatives> <inline-graphic xlink:type="simple" xlink:href="wong-ieq1-2443782.gif"/></alternatives></inline-formula>10). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build TFBS (also known as DNA motif) models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement if choosing di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.
Negative chronotropic effects of fentanyl attenuate beneficial effects of dobutamine on oxygen metabolism: hemodynamic and pharmacokinetic interactions.

Opioids are well known to cause cardiovascular depression. The aim of the present investigation was to determine whether an interaction of opioid derivatives with catecholamines might be involved in these hemodynamic alterations. Six comatose patients were enrolled into a prospective, nonrandomized pilot trial. All patients first received a continuous i.v. infusion of dobutamine (10 microgram. kg-1. min-1) paralleled by continuous administration of midazolam (0.4 mg. kg-1. h-1); thereafter, fentanyl was added i.v. (4 microgram. kg-1. h-1). Hemodynamic parameters as well as dobutamine and endogenous catecholamines plasma levels were determined. The mean arterial blood pressure did not change significantly during the whole study period. The continuous administration of dobutamine (steady-state plasma concentrations: 217 +/- 118 ng. ml-1) increased the beta1-adrenergic receptor-mediated hemodynamic parameters such as heart rate, stroke volume index, cardiac index, and oxygen delivery index (p <.05). The concomitant administration of fentanyl decreased the heart rate-dependent hemodynamic parameters (p <.05), suggesting that fentanyl antagonizes the chronotropic effects of dobutamine. In parallel, dobutamine plasma levels increased significantly (275 +/- 165 ng. ml-1; p <.05). Noteworthy, after administration of fentanyl, oxygen delivery and consumption index returned to baseline values. Radioligand binding experiments on rat cardiac ventricular microsomes ruled out a direct interaction of fentanyl with beta-adrenergic receptors and, more importantly, a fentanyl-induced inhibition of beta-adrenergic receptor G protein coupling. Our observations suggest that fentanyl inhibits the frequency-related hemodynamic changes induced by dobutamine. The underlying mechanism is independent of beta-adrenergic receptors, but is powerful enough to abolish the salutary effect of dobutamine on oxygen delivery and consumption.
Hyponatremia in cirrhosis: Results of a patient population survey

Low serum sodium concentration is an independent predictor of mortality in patients with cirrhosis, but its prevalence and clinical significance is unclear. To evaluate prospectively the prevalence of low serum sodium concentration and the association between serum sodium levels and severity of ascites and complications of cirrhosis, prospective data were collected on 997 consecutive patients from 28 centers in Europe, North and South America, and Asia for a period of 28 days. The prevalence of low serum sodium concentration as defined by a serum sodium concentration ≤135 mmol/L, ≤130 mmol/L, ≤125 mmol/L, and ≤120 mmol/L was 49.4%, 21.6%, 5.7%, and 1.2%, respectively. The prevalence of low serum sodium levels (<135 mmol/L) was high in both inpatients and outpatients (57% and 40%, respectively). The existence of serum sodium <135 mmol/L was associated with severe ascites, as indicated by high prevalence of refractory ascites, large fluid accumulation rate, frequent use of large‐volume paracentesis, and impaired renal function, compared with normal serum sodium levels. Moreover, low serum sodium levels were also associated with greater frequency of hepatic encephalopathy, spontaneous bacterial peritonitis, and hepatorenal syndrome, but not gastrointestinal bleeding. Patients with serum sodium <130 mmol/L had the greatest frequency of these complications, but the frequency was also increased in patients with mild reduction in serum sodium levels (131‐135 mmol/L). In conclusion, low serum sodium levels in cirrhosis are associated with severe ascites and high frequency of hepatic encephalopathy, spontaneous bacterial peritonitis, and hepatorenal syndrome. (HEPATOLOGY 2006;44:1535–1542.)
An African American Student Networking Group in an Urban High School: Experiences and Outcomes

Educational disparities are deeply entrenched in U.S. society. Our research focused on a move toward equity and investment in one Midwestern charter school via the implementation of the African American Student Network. Participants were 15 male and 15 female students in Grades 9 to 12 who participated in the network for one semester. Qualitative analysis of focus group interviews revealed that students in the network experienced safety, support, empowerment, affirmation, and connectedness. Quantitative analysis revealed that pre- and post-test grade point averages (GPAs), disciplinary referrals, and attendance trended in promising directions although there were no statistically significant differences.
Polymorphisms of Genes in Neurotransmitter Systems Were Associated with Alcohol Use Disorders in a Tibetan Population

Studies of linkage and association in various ethnic populations have revealed many predisposing genes of multiple neurotransmitter systems for alcohol use disorders (AUD). However, evidence often is contradictory regarding the contribution of most candidate genes to the susceptibility of AUD. We, therefore, performed a case-control study to investigate the possible associations of genes selected from multiple neurotransmitter systems with AUD in a homogeneous Tibetan community population in China. AUD cases (N = 281) with an alcohol use disorder identification test (AUDIT) score ≥10, as well as healthy controls (N = 277) with an AUDIT score ≤5, were recruited. All participants were genotyped for 366 single nucleotide polymorphisms (SNPs) of 34 genes selected from those involved in neurotransmitter systems. Association analyses were performed using PLINK version 1.07 software. Allelic analyses before adjustment for multiple tests showed that 15 polymorphisms within seven genes were associated with AUD (p<0.05). After adjustment for the number of SNPs genotyped within each gene, only the association of a single marker (rs10044881) in HTR4 remained statistically significant. Haplotype analysis for two SNPs in HTR4 (rs17777298 and rs10044881) showed that the haplotype AG was significantly associated with the protective effect for AUD. In conclusion, the present study discovered that the HTR4 gene may play a marked role in the pathogenesis of AUD. In addition, this Tibetan population sample marginally replicated previous evidence regarding the associations of six genes in AUD.
Online Optimization of Smoothed Piecewise Constant Functions

We study online optimization of smoothed piecewise constant functions over the domain [0, 1). This is motivated by the problem of adaptively picking parameters of learning algorithms as in the recently introduced framework by Gupta and Roughgarden (2016). Majority of the machine learning literature has focused on Lipschitz-continuous functions or functions with bounded gradients. 1 This is with good reason---any learning algorithm suffers linear regret even against piecewise constant functions that are chosen adversarially, arguably the simplest of non-Lipschitz continuous functions. The smoothed setting we consider is inspired by the seminal work of Spielman and Teng (2004) and the recent work of Gupta and Roughgarden---in this setting, the sequence of functions may be chosen by an adversary, however, with some uncertainty in the location of discontinuities. We give algorithms that achieve sublinear regret in the full information and bandit settings.
Embedded Deep Neural Network Processing: Algorithmic and Processor Techniques Bring Deep Learning to IoT and Edge Devices

Deep learning has recently become im-mensely popular for image recognition, as well as for other recognition and pattern matching tasks in, e.g., speech processing, natural language processing, and so forth. The online evaluation of deep neural networks, however, comes with significant computational complexity, making it, until recently, feasible only on power-hungry server platforms in the cloud. In recent years, we see an emerging trend toward embedded processing of deep learning networks in edge devices: mobiles, wearables, and Internet of Things (IoT) nodes. This would enable us to analyze data locally in real time, which is not only favorable in terms of latency but also mitigates privacy issues. Yet evaluating the powerful but large deep neural networks with power budgets in the milliwatt or even microwatt range requires a significant improvement in processing energy efficiency.
Predictors of Injudicious Antibiotic Seeking Behavior

Injudicious use of antibiotics has been defined as use in a manner not consistent with Center for Disease Con- trol and Prevention (CDC) guidelines including using an antibiotic for a viral infection and not finishing the prescribed round of antibiotics. Injudicious use has become a global problem contributing to resistant strains of bacteria that have been linked to serious illnesses in children and adults, increased mortality rates, increased costs outlaid by parents and healthcare providers and longer treatment protocols The purpose of this study was to discover what parental factors are associated with injudicious use of antibiotics. Parents with children age 14 and under completed a questionnaire regarding injudicious antibiotic use with participants recruited over a two-month period. Ethnicity, income, and education were sig- nificant predictors of injudicious antibiotic use. ANOVA revealed less injudicious use with females, Caucasians, and par- ents with higher incomes. Our study identified ethnic minorities, low parental income, less than a high school education and being male as risk factors for injudicious antibiotic seeking behavior by parents. Educational outreach is needed for parents regarding the proper use of antibiotics.
Underwater glider design based on dynamic model analysis and prototype development

Underwater gliders are efficient mobile sensor platforms that can be deployed for months at a time, traveling thousands of kilometers. Here, we describe our development of a coastal 200 m deep underwater glider, which can serve as an ocean observatory platform operating in the East China Sea. Our glider is developed based on dynamic model analysis: steady flight equilibrium analysis gives the varied range of moving mass location for pitch control and the varied vehicle volume for buoyancy control; a stability analysis is made to discuss the relationship between the stability of glider motion and the location of glider wings and rudder by root locus investigation of glider longitudinal- and lateral-directional dynamics, respectively. There is a tradeoff between glider motion stability and control authority according to the specific glider mission requirements. The theoretical analysis provides guidelines for vehicle design, based on which we present the development progress of the Zhejiang University (ZJU) glider. The mechanical, electrical, and software design of the glider is discussed in detail. The performances of glider key functional modules are validated by pressure tests individually; preliminary pool trials of the ZJU glider are also introduced, indicating that our glider functions well in water and can serve as a sensor platform for ocean sampling.
Are Boards Designed to Fail? The Implausibility of Effective Board Monitoring

Abstract In this review, we challenge the idea that directors are well positioned to be effective monitors of management. Moving beyond the logic of incentives and ability, we conceptualize a model based on the premise of boards as groups of individuals obtaining, processing and sharing information and explain how variation in information-processing demands at the director, board and firm level may challenge effective monitoring. We draw on multiple theoretical perspectives to identify these barriers to effective board monitoring. Our goal in reviewing these barriers is to help us take stock of existing research in corporate governance and to better explain board behavior beyond traditional agency and resource dependency accounts. We also aim to uncover gaps in the conceptual and empirical research and suggest areas of fruitful future research.
Do Changes In Affective Responses During Physical Activity Predict Future Physical Activity Behavior In Older Adults

Background: Improving our understanding of modifiable factors related to older adults' moderate-to-vigorous physical activity (MVPA) behaviour may help to inform behaviour change interventions. How older adults experience MVPA, and whether this influences the source of their motivation, may be viable targets. Purpose: To examine if changes in affect during a bout of MVPA were directly and indirectly (via self-determined motivation) associated with future MVPA behaviour older adults. Methods: Data were collected from 82 older adults (Mage=68.43 years) five minutes before, immediately before, during, and five minutes after walking on a treadmill at moderate-to-vigorous intensity for 30 minutes. One month later, participants' MVPA behaviour was assessed during a phone call. Changes in affect were computed by subtracting mean scores before the bout from mean scores during the bout. Data were analyzed via SPSS mediation macro with bootstrap estimation procedures. Results: Adjusting for baseline MVPA, sex, and body mass index, changes in revitalization, positive engagement, and tranquility were directly and positively associated with MVPA (ps<.05). Self-determined motivation was directly and positively related to MVPA (p<.05). Changes in tranquility were indirectly associated with MVPA via self-determined motivation (p<.05). Conclusions: Although the literature supports that MVPA improves affect, this study adds to the evidence that affective responses during MVPA can also influence future MVPA participation. Further, the findings offer a possible explanation for how affective responses may come to influence MVPA. Older adults' affective responses to MVPA should be considered in motivationally-tailored strategies to foster MVPA adherence.
Origin of Polar Order in Dense Suspensions of Phototactic Micro-Swimmers

A main question for the study of collective motion in living organisms is the origin of orientational polar order, i.e., how organisms align and what are the benefits of such collective behaviour. In the case of micro-organisms swimming at a low Reynolds number, steric repulsion and long-range hydrodynamic interactions are not sufficient to explain a homogeneous polar order state in which the direction of motion is aligned. An external symmetry-breaking guiding field such as a mechanism of taxis appears necessary to understand this phonemonon. We have investigated the onset of polar order in the velocity field induced by phototaxis in a suspension of a motile micro-organism, the algae Chlamydomonas reinhardtii, for density values above the limit provided by the hydrodynamic approximation of a force dipole model. We show that polar order originates from a combination of both the external guiding field intensity and the population density. In particular, we show evidence for a linear dependence of a phototactic guiding field on cell density to determine the polar order for dense suspensions and demonstrate the existence of a density threshold for the origin of polar order. This threshold represents the density value below which cells undergoing phototaxis are not able to maintain a homogeneous polar order state and marks the transition to ordered collective motion. Such a transition is driven by a noise dominated phototactic reorientation where the noise is modelled as a normal distribution with a variance that is inversely proportional to the guiding field strength. Finally, we discuss the role of density in dense suspensions of phototactic micro-swimmers.
Non-Hodgkin lymphoma among Brazilian agricultural workers: A death certificate case-control study

ABSTRACT To estimate the non-Hodgkin lymphoma (NHL) mortality risk among agricultural workers in Brazil's southern states, we used death certificates to identify cases of NHL between the ages of 20 and 69 years from residents of nonurban municipalities between 1996 and 2005 (n = 1,317). Controls were randomly selected from those whose underlying cause of death did not include neoplasm or hematological diseases and paired with cases by sex, age, year of death, and state of residence (n = 2,634). Odds of being an agricultural worker among cases and controls were estimated by conditional logistic regression, stratified and adjusted by sex, state, education, and race. An increased risk of death by NHL was observed among agricultural workers 20–39 years old (ORadj = 2.06; 95% CI 95%, 1.20–3.14). Our results suggest that the young agricultural workers from southern Brazil were more likely to die of NHL compared to nonagricultural workers.
Adolescent Personality

The purpose of this study was to investigate convergent and discriminant validity of the five-factor model of adolescent personality in a school setting using three different raters (methods): self-ratings, peer ratings, and teacher ratings. The authors investigated validity through a multitrait-multimethod matrix and a confirmatory factor analysis correlated trait, uncorrelated method model. With the exception of Emotional Stability, each analysis demonstrated similar patterns and together provided support for the convergent and discriminant validity of the five-factor model structure of adolescent personality. However, among the three raters, self-ratings of personality provided a comparatively weaker method for assessing adolescent personality. The influences of agreement between self and other raters are discussed in relation to contrast, perceiver, and target effects; expert observer effects; the degree of acquaintanceship; and the effect of the social context.
School Reform in New York and Chicago

School reform efforts in New York City in 1967 and in Chicago in 1989 provide a laboratory for the comparative study of regime politics in education. Using Long's local game theory, this analysis reveals significant differences in the two city cultures. Differences in the outcomes of the reform efforts can be explained as a product of the ability of city stakeholders to coalesce and advance their interests at the state level.
Adaptation to potassium starvation of wild-type and K+-transport mutant (trk1,2) of Saccharomyces cerevisiae: 2-dimensional gel electrophoresis-based proteomic approach

Saccharomyces cerevisiae wild‐type (BY4741) and the corresponding mutant lacking the plasma membrane main potassium uptake systems (trk1,trk2) were used to analyze the consequences of K+ starvation following a proteomic approach. In order to trigger high‐affinity mode of potassium transport, cells were transferred to potassium‐free medium. Protein profile was followed by two‐dimensional (2‐D) gels in samples taken at 0, 30, 60, 120, 180, and 300 min during starvation. We observed a general decrease of protein content during starvation that was especially drastic in the mutant strain as it was the case of an important number of proteins involved in glycolysis. On the contrary, we identified proteins related to stress response and alternative energetic metabolism that remained clearly present. Neural network‐based analysis indicated that wild type was able to adapt much faster than the mutant to the stress process. We conclude that complete potassium starvation is a stressful process for yeast cells, especially for potassium transport mutants, and we propose that less stressing conditions should be used in order to study potassium homeostasis in yeast.
Risk factors associated with intraocular pressure increase in patients with uveitis treated with the fluocinolone acetonide implant.

IMPORTANCE Elevated intraocular pressure (IOP) is a well-known adverse event associated with the fluocinolone acetonide implant (FAI), but no data are available regarding factors associated with increased risk of IOP elevation in patients treated with the FAI. OBJECTIVE To report risk factors that may predispose patients to elevated IOP after treatment with the FAI. DESIGN, SETTING, AND PARTICIPANTS Data from 3 multicenter, 3-year, prospective, randomized, phase 2b/3 clinical trials evaluating the safety and efficacy of the FAI were pooled and analyzed. Patients had no underlying glaucoma and at least one eye with a history of recurrent noninfectious uveitis affecting the posterior segment. Patients were treated with 1 or more of the following: systemic therapy (corticosteroids or other immunosuppressive drugs) for at least 3 months before enrollment, 2 or more sub-Tenon capsule corticosteroid injections for uveitis management during the 6 months before enrollment, or systemic corticosteroid or sub-Tenon capsule corticosteroid injection therapy required for at least 2 separate recurrences within 6 months before enrollment. MAIN OUTCOMES AND MEASURES Factors evaluated as risk factors for IOP elevation included age, sex, lens status, uveitis severity at enrollment, and location of uveitis. RESULTS Data analyses were based on 641 eyes. A total of 351 eyes did not receive the FAI, whereas 290 eyes had the 0.59-mg FAI placed. An increase in IOP of 10 mm Hg or elevation to 30 mm Hg was seen in 60 untreated eyes (17.1%) and 188 treated eyes (65.1%) (hazard ratio, 5.80; 95% CI, 4.28-7.70; P < .001). A total of 8 untreated eyes (2.3%) required surgical intervention for elevated IOP compared with 93 treated eyes (32.1%) (hazard ratio, 16.48; 95% CI, 8.24-32.96; P < .001). In patients with the FAI, younger age, male sex, and phakic lens status were associated with higher risk of IOP elevation and the need for glaucoma surgery (P = .003, P < .001, and P < .001, respectively). CONCLUSIONS AND RELEVANCE Patients receiving the FAI are at higher risk of developing an IOP increase of 10 mm Hg or an absolute IOP of 30 mm Hg when compared with patients without the FAI. Patients who are male, younger, and phakic are at an even higher risk for elevated IOP and possibly glaucoma surgery.