Miracle-dz/UniFAR-FTUs huggingface dataset:
The G-Box Transcriptional Regulatory Code in Arabidopsis1[OPEN]

DNA-binding and gene expression data predict which bHLH or bZIP transcription factors are likely regulators of genes near perfect G-box (CACGTG) motifs. Plants have significantly more transcription factor (TF) families than animals and fungi, and plant TF families tend to contain more genes; these expansions are linked to adaptation to environmental stressors. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Finally, we present Ara-BOX-cis (araboxcis.org), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations.
Cognitive ability in early adulthood is associated with later suicide and suicide attempt: the role of risk factors over the life course

Background Cognitive ability/intelligence quotient (IQ) in youth has previously been associated with subsequent completed and attempted suicide, but little is known about the mechanisms underlying the associations. This study aims to assess the roles of various risk factors over the life course in explaining the observed relationships. Method The present investigation is a cohort study based on data on IQ test performance and covariates, recorded on 49 321 Swedish men conscripted in 1969–1970, at ages 18–20 years. Information on suicides and hospital admissions for suicide attempt up to the age of 57 years, childhood and adult socio-economic position, and adult family formation, was obtained from linkage to national registers. Results Lower IQ was associated with increased risks of both suicide and suicide attempt during the 36 years of follow-up. The associations followed a dose–response pattern. They were attenuated by approximately 45% in models controlling for social background, mental ill-health, aspects of personality and behavior, adult socio-economic position and family formation. Based on one-unit decreases in IQ test performance on a nine-point scale, the hazard ratios between ages 35 and 57 years were: for suicide 1.19 [95% confidence interval (CI) 1.13–1.25], fully adjusted 1.10 (95% CI 1.04–1.18); and for suicide attempt 1.25 (95% CI 1.20–1.31), fully adjusted 1.14 (95% CI 1.09–1.20). Conclusions Cognitive ability was found to be associated with subsequent completed and attempted suicide. The associations were attenuated by 45% after controlling for risk factors measured over the life course. Psychiatric diagnosis, maladjustment and aspects of personality in young adulthood, and social circumstances in later adulthood, contributed in attenuating the associations.
Chemically rich seaweeds poison corals when not controlled by herbivores

Coral reefs are in dramatic global decline, with seaweeds commonly replacing corals. It is unclear, however, whether seaweeds harm corals directly or colonize opportunistically following their decline and then suppress coral recruitment. In the Caribbean and tropical Pacific, we show that, when protected from herbivores, ~40 to 70% of common seaweeds cause bleaching and death of coral tissue when in direct contact. For seaweeds that harmed coral tissues, their lipid-soluble extracts also produced rapid bleaching. Coral bleaching and mortality was limited to areas of direct contact with seaweeds or their extracts. These patterns suggest that allelopathic seaweed-coral interactions can be important on reefs lacking herbivore control of seaweeds, and that these interactions involve lipid-soluble metabolites transferred via direct contact. Seaweeds were rapidly consumed when placed on a Pacific reef protected from fishing but were left intact or consumed at slower rates on an adjacent fished reef, indicating that herbivory will suppress seaweeds and lower frequency of allelopathic damage to corals if reefs retain intact food webs. With continued removal of herbivores from coral reefs, seaweeds are becoming more common. This occurrence will lead to increasing frequency of seaweed-coral contacts, increasing allelopathic suppression of remaining corals, and continuing decline of reef corals.
Chlamydia vaccines: recent developments and the role of adjuvants in future formulations

Bacteria of the genus Chlamydia cause a plethora of ocular, genital and respiratory diseases that continue to pose a considerable public health challenge worldwide. The major diseases are conjunctivitis and blinding trachoma, non-gonococcal urethritis, cervicitis, pelvic inflammatory disease, ectopic pregnancy, tubal factor infertility and interstitial pneumonia. The rampart asymptomatic infections prevent timely and effective antibiotic treatments, and quite often clinical presentation of sequelae is the first evidence of an infection. Besides, significant broad coverage in population screening and treatment is economically and logistically impractical, and mass education for public awareness has been ineffective. The current medical opinion is that an efficacious prophylactic vaccine is the best approach to protect humans from chlamydial infections. Unfortunately, a human vaccine has yet to be realized despite successful veterinary vaccines. Fortunately, recent advances in chlamydial immunobiology, cell biology, molecular pathogenesis, genomics, antigen discovery and animal models of infections are hastening progress toward an efficacious vaccine. Thus, it is established that Chlamydia immunity is mediated by T cells and a complementary antibody response, and several potential vaccine candidates have been identified. However, further advances are needed in effective vaccine delivery systems and safe potent adjuvants to boost and sustain immune responses for long-lasting protective immunity. This article focuses on the current status of human chlamydial vaccine research, specifically how application of new delivery systems and human compatible adjuvants could lead to a timely achievement of efficacious Chlamydia vaccines. The ranking of the candidate vaccine antigens for human vaccine development will await the availability of results from studies in which the antigens are tested by comparable experimental standards, such as antigen–adjuvant combination, route of delivery and possible toxicity.
Distinguishing near-falls from daily activities with wearable accelerometers and gyroscopes using Support Vector Machines

Falls are the number one cause of injury in older adults. An individual's risk for falls depends on his or her frequency of imbalance episodes, and ability to recover balance following these events. However, there is little direct evidence on the frequency and circumstances of imbalance episodes (near falls) in older adults. Currently, there is rapid growth in the development of wearable fall monitoring systems based on inertial sensors. The utility of these systems would be enhanced by the ability to detect near-falls. In the current study, we conducted laboratory experiments to determine how the number and location of wearable inertial sensors influences the accuracy of a machine learning algorithm in distinguishing near-falls from activities of daily living (ADLs).
Social eWOM: does it affect the brand attitude and purchase intention of brands?

Purpose The purpose of this paper is to examine how user-generated positive social electronic word-of-mouth (eWOM) via Facebook affects brand attitude and, consequently, influences purchase intention of smartphones. The spending patterns of consumers, particularly decision-makers, have been affected to a substantial degree by the strong presence of brands on the web. eWOM, one among the shape of net product reviews, exercises extensive influence not only on the consumers’ attitude towards the brand but also impacts their buying intentions. Design/methodology/approach A survey-based empirical study was conducted to examine the influence of social eWOM on brand attitude and purchase intention of consumers. Structural equation modeling (SEM) was applied using data collected from 311 respondents comprising users of Facebook. Findings The research established that user-generated positive eWOM on social networking site, Facebook significantly influences brand attitude and purchase intention of consumer electronics. Research limitations/implications The data set used for the study limits generalizing of results, as the data are not representative across industries or across all social media applications. The study provides a useful and interesting insight into the theory and practice of eWOM. It shows how social eWOM, an emerging communication tool, not only helps twenty-first century marketers in reaching customers, but how it also plays a vital role in affecting brand attitude and purchase intention of products. Originality/value This paper provides useful and valuable insights into the relationship between social eWOM, brand attitude and purchase intention of consumer electronics, an area that largely remains unexplored. The study can also be replicated for other products or services for future research.
Pricing via recursive quantization in stochastic volatility models

Abstract We provide the first recursive quantization-based approach for pricing options in the presence of stochastic volatility. This method can be applied to any model for which an Euler scheme is available for the underlying price process and it allows one to price vanillas, as well as exotics, thanks to the knowledge of the transition probabilities for the discretized stock process. We apply the methodology to some celebrated stochastic volatility models, including the Stein and Stein [Rev. Financ. Stud. 1991, (4), 727–752] model and the SABR model introduced in Hagan et al. [Wilmott Mag. , 2002, 84–108]. A numerical exercise shows that the pricing of vanillas turns out to be accurate; in addition, when applied to some exotics like equity-volatility options, the quantization-based method overperforms by far the Monte Carlo simulation.
Pulmonary hypertension in liver transplant

Purpose of reviewPulmonary hypertension patients provide challenging issues to anesthesiology. The condition is more so when it is associated with liver transplant surgery. This situation is especially true when associated with portopulmonary hypertension (POPH), a subdivision of pulmonary hypertension. Understanding the disease process as well as treatment outcome is an important factor for intraoperative management of those patients. Recent findingsThough offering many challenges, mild-to-moderate pulmonary hypertension and POPH patients could be transplanted safely. The most recently published studies describe the mortality of liver transplant patients with severe pulmonary hypertension and POPH to be 100%. The only available option might be a combined liver–lung transplant surgery, an option limited to very few centers. SummaryPublication on intraoperative anesthetic management of patient with pulmonary hypertension and POPH during liver transplant remains sparse. Management requires experience in cardiovascular anesthesia and utilization of knowledge, skills, medications, and tools learned in such cases. Further studies should be conducted on intraoperative use of inhaled and intravenous pulmonary vasodilators for its potential benefits during liver transplant surgery.
High-Precision Position Control of a Linear-Switched Reluctance Motor Using a Self-Tuning Regulator

High-precision position control of linear-switched reluctance motor (LSRM) is important in motion-control industry. The static model-based controller sometimes cannot give satisfactory output performance due to the inherent nonlinearities of LSRM and the uncertainties of the system. In this paper, a self-tuning regulator (STR) based on the pole-placement algorithm is proposed for high-precision position tracking of the LSRM. Following the time-scale characteristics analysis of LSRM position-tracking system and force-characteristic investigation, the position-tracking model is treated as a second-order system. Different from the static model-based control schemes, the dynamic model of the LSRM can be obtained by online estimation. Also, some practical aspects are taken into account. Owing to the unmodeled dynamics and high-frequency measurement noises, there are some oscillations in the practical control signals, and they can be reduced by a properly designed filter. Both the simulation and experimental results demonstrate that, in the control of the proposed STR, the position-tracking system can reproduce the reference signal with the desired performance in harsh ambient. These results confirm that the method is effective and robust in the high-precision position tracking of LSRM.
GaAs solar cells for Indoor Light Harvesting

GaAs solar cells are the highest efficiency single-junction photovoltaic technology. Their wide bandgap lends them to efficient conversion of indoor light. In this paper GaAs solar cells are experimentally compared to Dye Sensitised solar cells, traditionally used for indoor light harvesting. The power density of GaAs solar cells was found to be over 3× greater than DSSC modules under indoor light levels. A credit card sized GaAs cell can provide 0.67 mW or 4 mW to a wireless sensor node in a dimly lit corridor (~200 lux) or well-lit office space (~1000 lux) respectively. A near linear relationship is measured between the open-circuit and maximum power voltages of GaAs solar cells at low light levels allowing their use with power conditioning circuits (MPPT tracking) based on the fractional-voltage method.
Incidence of types of cancer among HIV-infected persons compared with the general population in the United States, 1992-2003.

BACKGROUND Persons who are HIV-infected may be at higher risk for certain types of cancer than the general population. OBJECTIVE To compare cancer incidence among HIV-infected persons with incidence in the general population from 1992 to 2003. DESIGN Prospective observational cohort studies. SETTING United States. PATIENTS 54,780 HIV-infected persons in the Adult and Adolescent Spectrum of HIV Disease Project (47,832 patients) and the HIV Outpatient Study (6948 patients), who contributed 157,819 person-years of follow-up from 1992 to 2003, and 334,802,121 records from the Surveillance, Epidemiology, and End Results program of 13 geographically defined, population-based, central cancer registries. MEASUREMENTS Standardized rate ratios (SRRs) to compare cancer incidence in the HIV-infected population with standardized cancer incidence in the general population. RESULTS The incidence of the following types of non-AIDS-defining cancer was significantly higher in the HIV-infected population than in the general population: anal (SRR, 42.9 [95% CI, 34.1 to 53.3]), vaginal (21.0 [CI, 11.2 to 35.9]), Hodgkin lymphoma (14.7 [CI, 11.6 to 18.2]), liver (7.7 [CI, 5.7 to 10.1]), lung (3.3 [CI, 2.8 to 3.9]), melanoma (2.6 [CI, 1.9 to 3.6]), oropharyngeal (2.6 [CI, 1.9 to 3.4]), leukemia (2.5 [CI, 1.6 to 3.8]), colorectal (2.3 [CI, 1.8 to 2.9]), and renal (1.8 [CI, 1.1 to 2.7]). The incidence of prostate cancer was significantly lower among HIV-infected persons than the general population (SRR, 0.6 [CI, 0.4 to 0.8]). Only the relative incidence of anal cancer increased over time. LIMITATIONS Lower ascertainment of cancer in the HIV cohorts may result in a potential bias to underestimate rate disparities. Tobacco use as a risk factor and the effect of changes in cancer screening practices could not be evaluated. CONCLUSION The incidence of many types of non-AIDS-defining cancer was higher among HIV-infected persons than among the general population from 1992 to 2003.
Estimating Treatment Effects from Counts of Binary Outcomes: A Conditional Likelihood Estimator of Relative Risk

This paper introduces the conditional likelihood estimator of relative risk (CLERR). The CLERR estimates the relative risk of an outcome analogously to the way the conditional logit estimates an odds ratio. Aside from the fact that relative risk is often the preferred measure of association, the CLERR has superior statistical properties, including both unbiasedness and effciency in small and large samples. The CLERR can be thought of as an exact matching approach which allows estimation of treatment effects for binary outcomes, without the need for structural assumptions about the in influence of confounding variables. We apply the CLERR to World Bank's Enterprise Survey data and show that firms with female owners are signifcantly more likely to export than similar firms with only male owners.
Intact fetal cells and cell-free fetal DNA in the maternal circulation

Down syndrome (trisomy 21), which has an incidence of 1 in 800 live births, is considered to be the most frequent etiology of mental retardation and it is the predominant reason for women seeking prenatal diagnosis [Driscoll & Gross, 2009]. Trisomy 21 is used as a benchmark because it is the most common aneuploidy compatible with life and is associated with mental retardation and serious congenital anomalies. Currently used screening tests for aneuploidy are based on the assessment of fetal sonographic markers and/or the evaluation of biochemical markers in the maternal circulation during the first and second trimester. Screening test based on the combination of nuchal translucency assessment and biochemical markers at 11+0-13+6 weeks of gestation may detect 90-94% of pregnancies affected by Down syndrome at a false positive rate of 5% [Kagan et al., 2008]. The current gold standard for diagnosis of trisomy 21 is provided by invasive sampling of fetal genetic material through chorionic villus sampling (CVS) or amniocentesis followed by conventional cytogenetic or DNA analysis; however, both procedures are associated with an increased risk of fetal loss of about 1% and therefore they are recommended for pregnancies considered to be at high risk of fetal trisomy 21 [Alfirevic et al., 2003]. Since 1997, when cell free fetal DNA in maternal circulation was discovered, the research interest has focused on the development of reliable techniques for non-invasive prenatal diagnosis (NIPD) that would allow the direct analysis of fetal genetic material based on the discovery of cell-free fetal (cff) DNA and RNA in the maternal circulation. Current investigation fields of NIPD include fetal Rhesus D genotype determination in RhD negative women, fetal sex determination for sex-linked disorders and the role of cffDNA in pregnancy disorders such as preeclampsia but the holy grail of NIPD remains the detection of fetal aneuploidies [Honda et al., 2002; Bianchi et al., 2005]. The direct analysis of circulating fetal DNA for the NIPD of chromosomal aneuploidies is mainly complicated by the presence of the coexisting background maternal DNA. NIPD will hopefully overcome the limitations of the currently used methods for diagnosing Down syndrome antenatally and make prenatal testing safer for pregnant women and their fetuses. However, irrespective of which strategy is selected for isolating or distinguishing fetal genetic material in maternal plasma, the small quantity of cffDNA and cff mRNA poses severe technical challenges; all these issues should be addressed before the clinical application of these methods as screening test with high sensitivity, specificity and reproducibility.
NDUFAF7 Methylates Arginine 85 in the NDUFS2 Subunit of Human Complex I*

Background: Arginine 85 of NDUFS2, a subunit of mitochondrial complex I, is symmetrically dimethylated. Results: NDUFAF7, a protein methylase in the matrix of mitochondria, modifies arginine 85 of NDUFS2 during assembly of complex I. Conclusion: Methylation of arginine 85 of NDUFS2 is required for assembly of complex I. Significance: The arginine protein methylase, NDUFAF7, is an assembly factor for human complex I. Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 subunits. One arm is embedded in the inner membrane with the other protruding ∼100 Å into the matrix of the organelle. The extrinsic arm contains binding sites for NADH and the primary electron acceptor FMN, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking FMN to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, probably energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Complex I is put together from preassembled subcomplexes. Their compositions have been characterized partially, and at least 12 extrinsic assembly factor proteins are required for the assembly of the complex. One such factor, NDUFAF7, is predicted to belong to the family of S-adenosylmethionine-dependent methyltransferases characterized by the presence in their structures of a seven-β-strand protein fold. In the present study, the presence of NDUFAF7 in the mitochondrial matrix has been confirmed, and it has been demonstrated that it is a protein methylase that symmetrically dimethylates the ω-NG,NG′ atoms of residue Arg-85 in the NDUFS2 subunit of complex I. This methylation step occurs early in the assembly of complex I and probably stabilizes a 400-kDa subcomplex that forms the initial nucleus of the peripheral arm and its juncture with the membrane arm.
Shifting Diets for a Sustainable Food Future

The role of one consumption-based solution: shifting the diets of populations who consume high amounts of calories, protein, and animal-based foods are analysed. Specifically, we consider three interconnected diet shifts: 1. Reduce overconsumption of calories. 2. Reduce overconsumption of protein by reducing consumption of animal-based foods. 3. Reduce consumption of beef specifically.
Do leukoreduction filters passively reduce the transmission risk of human granulocytic anaplasmosis?

Human granulocytic anaplasmosis, caused by Anaplasma phagocytophilum, poses an increasing public health risk in the United States. Since 2000, case reports have increased annually; 2782 cases were reported in 2013. Despite the increasing frequency of clinical cases, only eight cases of transfusion‐transmitted anaplasmosis (TTA) have been reported. We investigated if current leukoreduction practices impact transfusion risk.