Miracle-dz/UniFAR-FTUs huggingface dataset:
Open sharing of genomic data: Who does it and why?

We explored the characteristics and motivations of people who, having obtained their genetic or genomic data from Direct-To-Consumer genetic testing (DTC-GT) companies, voluntarily decide to share them on the publicly accessible web platform openSNP. The study is the first attempt to describe open data sharing activities undertaken by individuals without institutional oversight. In the paper we provide a detailed overview of the distribution of the demographic characteristics and motivations of people engaged in genetic or genomic open data sharing. The geographical distribution of the respondents showed the USA as dominant. There was no significant gender divide, the age distribution was broad, educational background varied and respondents with and without children were equally represented. Health, even though prominent, was not the respondents’ primary or only motivation to be tested. As to their motivations to openly share their data, 86.05% indicated wanting to learn about themselves as relevant, followed by contributing to the advancement of medical research (80.30%), improving the predictability of genetic testing (76.02%) and considering it fun to explore genotype and phenotype data (75.51%). Whereas most respondents were well aware of the privacy risks of their involvement in open genetic data sharing and considered the possibility of direct, personal repercussions troubling, they estimated the risk of this happening to be negligible. Our findings highlight the diversity of DTC-GT consumers who decide to openly share their data. Instead of focusing exclusively on health-related aspects of genetic testing and data sharing, our study emphasizes the importance of taking into account benefits and risks that stretch beyond the health spectrum. Our results thus lend further support to the call for a broader and multi-faceted conceptualization of genomic utility.
Nitrogen-Dependent Posttranscriptional Regulation of the Ammonium Transporter AtAMT1;11[W][OA]

Ammonium transporter (AMT) proteins of the AMT family mediate the transport of ammonium across plasma membranes. To investigate whether AMTs are regulated at the posttranscriptional level, a gene construct consisting of the cauliflower mosaic virus 35S promoter driving the Arabidopsis (Arabidopsis thaliana) AMT1;1 gene was introduced into tobacco (Nicotiana tabacum). Ectopic expression of AtAMT1;1 in transgenic tobacco lines led to high transcript levels and protein levels at the plasma membrane and translated into an approximately 30% increase in root uptake capacity for 15N-labeled ammonium in hydroponically grown transgenic plants. When ammonium was supplied as the major nitrogen (N) form but at limiting amounts to soil-grown plants, transgenic lines overexpressing AtAMT1;1 did not show enhanced growth or N acquisition relative to wild-type plants. Surprisingly, steady-state transcript levels of AtAMT1;1 accumulated to higher levels in N-deficient roots and shoots of transgenic tobacco plants in spite of expression being controlled by the constitutive 35S promoter. Moreover, steady-state transcript levels were decreased after addition of ammonium or nitrate in N-deficient roots, suggesting a role for N availability in regulating AtAMT1;1 transcript abundance. Nitrogen deficiency-dependent accumulation of AtAMT1;1 mRNA was also observed in 35S:AtAMT1;1-transformed Arabidopsis shoots but not in roots. Evidence for a regulatory role of the 3′-untranslated region of AtAMT1;1 alone in N-dependent transcript accumulation was not found. However, transcript levels of AtAMT1;3 did not accumulate in a N-dependent manner, even though the same T-DNA insertion line atamt1;1-1 was used for 35S:AtAMT1;3 expression. These results show that the accumulation of AtAMT1;1 transcripts is regulated in a N- and organ-dependent manner and suggest mRNA turnover as an additional mechanism for the regulation of AtAMT1;1 in response to the N nutritional status of plants.
Paleogene tropical Pacific : Clues to circulation, productivity, and plate motion

[1] Stratigraphic data from 63 Deep Sea Drilling Project and Ocean Drilling Program (ODP) sites that sample the lower Neogene and Paleogene sediments of the tropical Pacific have been compiled and put on the biostratigraphic and paleomagnetic timescale refined by ODP Leg 199 scientists. Sediment accumulation rates have been calculated for ten intervals ranging in age from 10 to 56 Ma and have been plotted for the midpoint of each interval at the associated paleoposition for each site used. A fixed hot spot model was used for reconstruction of the Pacific lithospheric plate. All such reconstructed intervals show the development of a tongue of high accumulation rates associated with the oceanographic divergence at the geographic equator. The development of this equatorial band is weakest between 46 and 56 Ma, the time of the peak warmth in Paleogene climate. Possible motion of the Hawaiian hot spot or true polar wander between 46 and 56 Ma appears to have had little effect on the plate rotation estimate of the position of the equator. In addition to temporal changes in the calcite compensation depth and in productivity, the biggest change in the patterns of sediment accumulation rates in the eastern tropical Pacific was the development of a relatively strong divergence between 6° and 10°N, near the region of divergence between the modern North Equatorial Current and the North Equatorial Counter Current. Changes in the equatorial circulation appear to be associated in time with the opening and closing of oceanic gateways, particularly the complex closing of the Caribbean-Pacific gateway.
Structuring multilevel discrete-event systems with dependency structure matrices

In this paper, we present a systematic approach to transform a set of plant models and requirement models into a tree-structured multilevel discrete-event system to which multilevel supervisory controller synthesis can be applied. By analyzing the dependencies between the plants and the requirements using dependency structure matrix techniques, a multilevel clustering can be calculated. Since one of the major drawbacks of synthesizing supervisory controllers is state space explosion, multiple attempts exist to overcome this computational difficulty, such as modular, hierarchical, decentralized, and, recently developed, multilevel supervisory control synthesis. Unfortunately, the modeler needs to provide additional information as input for most of these non-monolithic synthesis procedures. For those supervisory control synthesis procedures that require additional information, no systematic approach exists in literature to transform any set of plant models and requirement models to the appropriate input needed for a particular synthesis procedure. The presented approach is applied to a model of a lock and a model of an MRI scanner patient support table.
Breed Influence on Feeder Calf Prices Circular

1 Respectively, Assistant Professor, Assistant Professor, and Specialist, Department of Agricultural Economics and Agricultural Business, New Mexico State University, Las Cruces. ABStrACt Cow-calf producers select for genetic traits that create profitability in their output—feeder calves—but are constrained by environmental factors; this is readily apparent in the southwestern United States. The use of exotic-origin or Bos indicus cattle in this region allows producers to utilize otherwise unproductive rangeland, as many Bos taurus cattle cannot thrive in semiarid conditions. This paper examines price differentials between feeder calves of exotic origin and those of European origin. Specifically, a hedonic price model is used to analyze sales data from feeder calf teleauctions in the Southwest over a six-year period.
Insulin Sensitivity and Secretion Changes After Gastric Bypass in Normotolerant and Diabetic Obese Subjects

Objective: To elucidate the mechanisms of improvement/reversal of type 2 diabetes after Roux-en-Y gastric bypass (RYGB). Methods: Fourteen morbidly obese subjects, 7 with normal glucose tolerance and 7 with type 2 diabetes, were studied before and 1 month after RYGB by euglycemic hyperinsulinemic clamp (EHC), by intravenous glucose tolerance test (IVGTT) and by oral glucose tolerance test (OGTT) in 3 different sessions. Intravenous glucose tolerance test IVGTT and OGTT insulin secretion rate (ISR) and sensitivity were obtained by the minimal model. Glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) were measured. Six healthy volunteers were used as controls. Results: Total ISR largely increased in diabetic subjects only when glucose was administered orally (37.8 ± 14.9 vs 68.3 ± 22.8 nmol; P < 0.05, preoperatively vs postoperatively). The first-phase insulin secretion was restored in type 2 diabetic after the IVGTT (&PHgr;1 × 10−9: 104 ± 54 vs 228 ± 88; P < 0.05, preoperatively vs postoperatively; 242 ± 99 in controls). Insulin sensitivity by EHC (M × 102) was slightly but significantly improved in both normotolerant and diabetic subjects (1.46 ± 0.22 vs 1.37 ± 0.55 mmol·min−1·kg−1; P < 0.05 and 1.53 ± 0.23 vs 1.28 ± 0.62 mmol·min−1·kg−1; P < 0.05, respectively). Quantitative insulin sensitivity check index was improved in all normotolerant (0.32 ± 0.02 vs 0.30 ± 0.02; P < 0.05) and diabetic subjects (0.33 ± 0.03 vs 0.31 ± 0.02; P < 0.05). GIP and GLP-1 levels increased both at fast and after OGTT mainly in type 2 diabetic subjects. Conclusions: The large increase of ISR response to the OGTT together with the restoration of the first-phase insulin secretion in diabetic subjects might explain the reversal of type 2 diabetes after RYGB. The large incretin secretion after the oral glucose load might contribute to the increased ISR.
A prospective trial of dynamic contrast-enhanced MRI perfusion and fluorine-18 FDG PET-CT in differentiating brain tumor progression from radiation injury after cranial irradiation.

BACKGROUND The aim of this study was to assess the effectiveness of fluorine-18 fluorodeoxyglucose (FDG) PET-CT and dynamic contrast-enhanced (DCE) MRI in differentiating tumor progression and radiation injury in patients with indeterminate enhancing lesions after radiation therapy (RT) for brain malignancies. METHODS Patients with indeterminate enhancing brain lesions on conventional MRI after RT underwent brain DCE-MRI and PET-CT in a prospective trial. Informed consent was obtained. Lesion outcomes were determined by histopathology and/or clinical and imaging follow-up. Metrics obtained included plasma volume (Vp) and volume transfer coefficient (K(trans)) from DCE-MRI, and maximum standardized uptake value (SUVmax) from PET-CT; lesion-to-normal brain ratios of all metrics were calculated. The Wilcoxon rank sum test and receiver operating characteristic analysis were performed. RESULTS The study included 53 patients (29 treated for 29 gliomas and 24 treated for 26 brain metastases). Progression was determined in 38/55 (69%) indeterminate lesions and radiation injury in 17 (31%). Vpratio (VP lesion/VP normal brain, P < .001), K(trans) ratio (P = .002), and SUVratio (P = .002) correlated significantly with diagnosis of progression versus radiation injury. Progressing lesions exhibited higher values of all 3 metrics compared with radiation injury. Vpratio had the highest accuracy in determining progression (area under the curve = 0.87), with 92% sensitivity and 77% specificity using the optimal, retrospectively determined threshold of 2.1. When Vpratio was combined with K(trans) ratio (optimal threshold 3.6), accuracy increased to 94%. CONCLUSIONS Vpratio was the most effective metric for distinguishing progression from radiation injury. Adding K(trans) ratio to Vpratio further improved accuracy. DCE-MRI is an effective imaging technique for evaluating nonspecific enhancing intracranial lesions after RT.
Estimation and Inference of Quantile Regression for Survival Data Under Biased Sampling

ABSTRACT Biased sampling occurs frequently in economics, epidemiology, and medical studies either by design or due to data collecting mechanism. Failing to take into account the sampling bias usually leads to incorrect inference. We propose a unified estimation procedure and a computationally fast resampling method to make statistical inference for quantile regression with survival data under general biased sampling schemes, including but not limited to the length-biased sampling, the case-cohort design, and variants thereof. We establish the uniform consistency and weak convergence of the proposed estimator as a process of the quantile level. We also investigate more efficient estimation using the generalized method of moments and derive the asymptotic normality. We further propose a new resampling method for inference, which differs from alternative procedures in that it does not require to repeatedly solve estimating equations. It is proved that the resampling method consistently estimates the asymptotic covariance matrix. The unified framework proposed in this article provides researchers and practitioners a convenient tool for analyzing data collected from various designs. Simulation studies and applications to real datasets are presented for illustration. Supplementary materials for this article are available online.
Ethos and the Construction of a Believable Character for Information Systems

Within information science, work on information credibility often focuses on generalized models of user assessment behavior and associated properties that mark credible information across document types, user groups, and communicative purposes. As conceptualized within the field of rhetoric, however, ethos, or a form of persuasive appeal that centers around a speaker’s believability, is situational. A speaker generates ethos within a particular text by constructing a character that aligns with the values of a selected audience for a specific rhetorical event. In this paper, I define ethos and contrast it with ideas of credibility from information science. I then illustrate how information systems generate ethos by analyzing two schemes for organizing information, the Women’s Thesaurus and the DrugSense newsbot concept dictionary, showing how these two schemes use different strategies to build ethos with different audiences. I conclude by discussing how rhetorical concepts such as ethos can help illuminate the ways in which information systems function as communicative devices, and how this understanding might facilitate system design. As social software continues to proliferate, and the division blurs between user and designer, between content consumer and content provider, research on the expressive potential of information systems seems particularly apt.
Andreana Panayi : THE PREVALENCE OF BODY DYSMORPHIC DISORDER IN PATIENTS UNDERGOING COSMETIC SURGERY : A SYSTEMATIC REVIEW Psychiatria Danubina

Body dysmorphic disorder (BDD) is a somatoform disorder characterised by a distressing obsession with an imagined or slight appearance defect, which can significantly impair normal day-to-day functioning. Patients with BDD often first present, and are hence diagnosed, in cosmetic surgery settings. Several studies have investigated the prevalence rate of BDD in the general population or have done so for patients referring to cosmetic medical centers. To date, however, no review has been undertaken to compare the prevalence in the general community versus in a cosmetic surgery setting. Despite the lack of such a review it is a commonly held belief that BDD is more common in patients seeking cosmetic surgery. The current study aims to review the available literature in order to investigate whether BDD is indeed more prevalent in patients requesting cosmetic surgery, and if that is the case, to provide possible reasons for the difference in prevalence. In addition this review provides evidence on the effectiveness of cosmetic surgery as a treatment of BDD.
A Comparison of Bt Transgene, Hybrid Background, Water Stress, and Insect Stress Effects on Corn Leaf and Ear Injury and Subsequent Yield

ABSTRACT Experimentally manipulated water and insect stresses were applied to field-grown corn with different Bacillus thuringiensis (Bt) transgenes and no Bt transgenes, and different non transgenic hybrid backgrounds (2011 and 2012, Corpus Christi, TX). Differences in leaf injury, ear injury, and yield were detected among experimental factors and their interactions. Under high and low water stress, injury from noctuid larvae (Lepidoptera: Noctuidae) on leaves during vegetative growth (primarily from fall armyworm, Spodoptera frugiperda J.E. Smith) and on developing ears (primarily from corn earworm, Helicoverpa zea [Boddie]) was lowest on more recent releases of Bt hybrids (newer Bt hybrids) expressing Cry1A. 105+Cry2Ab2 and Cry 3Bbl, compared with earlier Bt hybrids (older Bt hybrids) expressing CrylAb and Cry3Bbl and non-Bt hybrids. High water stress led to increased leaf injury under substantial fall armyworm feeding pressure in 2011 (as high as 8.7 on a 1–9 scale of increasing injury). In contrast, ear injury by corn earworm (as high as 20 cm2 of surface area of injury) was greater in low water stress conditions. Six hybrid backgrounds did not influence leaf injury, while ear injury differences across hybrid backgrounds were detected for non-Bt and older Bt hybrid versions. While newer Bt hybrids expressing Cry1A.105+Cry2Ab2 and Cry 3Bbl had consistent low leaf injury and high yield and low but less consistent ear injury across six hybrid backgrounds, water stress was a key factor that influenced yield. Bt transgenes played a more variable and lesser role when interacting with water stress to affect yield. These results exemplify the interplay of water and insect stress with plant injury and yield, their interactions with Bt transgenes, and the importance of these interactions in considering strategies for Bt transgene use where water stress is common.
Inactivation of faecal bacteria in wastewater by methylene blue and visible light

The high inactivation of faecal indicators [faecal coliforms (FC), E. coli and faecal streptococci (FS)] using a combination of methylene blue (MB) with natural sunlight or artificial visible light determined on a small scale, was dependent mainly on the MB concentration, its application process and pH. In order to avoid primarily leaching of the compound into the environment and to further understand the MB photosensitization mechanisms, MB should be properly immobilized within resin. The FC and FS were found to be susceptible to the photodynamic action of MB fixed to the support. The mechanism of faecal bacteria inactivation by MB also seems to be a combination of Type I and Type II processes, and the relative efficiency of each of them depends notably on the experimental conditions. In parallel, the MB stability under light “photobleaching” has been studied by optical absorption spectroscopy. It has been shown that it was dependent essentially on pH, nature of the medium (distilled water and secondary .
Study with reflected ultrasound of patients with mitral valve repair.

As part of a follow-up investigation in mitral annuloplasty by reflected ultrasound, 39 studies have been carried out in I5 patients who underwent mitral valve reconstructive operations. The rate of diastolic toward closure movemeiit from point E (EF speed) and total amplitude did not correlate with the final valve orifice dimension obtained at operation. Mitral stenosis and incompetence were shown within the first 6 months after repair. Such a noninvasive technique is therefore regarded as an additional method of study of the structural andfunctional state of the mitral valve after annuloplasty and the subsequent changes in time. The contribution of mitral ring movement to the familiar mitral echogram pattern is discussed passim.
Increased Susceptibility to Low Doses of a Carcinogen of Epidermal Cells in Stimulated DNA

The increased susceptibility of epidermal cells to a carcinogen following a single prior treatment with croton oil and its correla tion with increaced DNA synthesis following croton oil was con firmed. The effect of croton oil on DNA synthesis was local rather than systemic, just as Pound found its effect on increased susceptibility to a carcinogento belocalratherthan systemic. The effect of prior treatment with croton oil was diminished and finally obliterated by increasing dosages of the carcinogen.
ANTIOXIDANT ACTIVITY OF ETHANOLIC EXTRACT OF Maranta arundinacea .L TUBEROUS RHIZOMES

Free radicals contribute to more than one hundred disorders in humans. The ethanolic extract of M.arundinacea . L (Marantacea) was screened for antioxidant activity using 1,1-diphenyl-2-picryl hydroxyl (DPPH) quenching assay, 2,2’-azinobis-3-ethylbenzothiozoline-6-sulfonic acid (ABTS) cation decolorization test, Reducing power, scavenging capacity towards hydrogen peroxide (H2O2) radical, nitric oxide (NO) radical inhibition activity using established assay procedures and Ferric Reducing Antioxidant Power (FRAP) Assay. The extract exhibited high antiradical activity against DPPH, ABTS, hydrogen peroxide and nitric oxide radicals with IC50 value of 293.4, 297.4, 336.1, and 258.7 µg/ml respectively. The Reducing power and Ferric Reducing Antioxidant Power (FRAP) increased with increasing concentration of the sample. The antioxidant activity of the sample was comparable with that of the standard butylated hydroxyl toluene (BHT).
Gastro-oesophageal reflux treatment for asthma in adults and children.

BACKGROUND Asthma and gastro-oesophageal reflux are both common medical conditions and often co-exist. Studies have shown conflicting results concerning the effects of lower oesophageal acidification as a trigger of asthma. Furthermore, asthma might precipitate gastro-oesophageal reflux. Thus a temporal association between the two does not establish that gastro-oesophageal reflux triggers asthma. Randomised trials of a number of treatments for gastro-oesophageal reflux in asthma have been conducted to determine whether treatment of reflux improves asthma. OBJECTIVES The objective of this review was to evaluate the effectiveness of treatments for gastro-oesophageal reflux in terms of their benefit on asthma. SEARCH STRATEGY The Cochrane Airways Group trials register, review articles and reference lists of articles were searched. SELECTION CRITERIA Randomised controlled trials of treatment for oesophageal reflux in adults and children with a diagnosis of both asthma and gastro-oesophageal reflux. DATA COLLECTION AND ANALYSIS Trial quality and data extraction were carried out by two independent reviewers. Authors were contacted for confirmation or more data. MAIN RESULTS Twelve trials met the inclusion criteria. Interventions included proton pump inhibitors (n=6), histamine antagonists (n=5), surgery (n=1) and conservative management (n=1). Treatment duration ranged from 1 week to 6 months. A temporal association between asthma and gastro-oesophageal reflux was investigated in 4 trials and found to be present in a proportion of participants in these trials. Anti-reflux treatment did not consistently improve lung function, asthma symptoms, nocturnal asthma or the use of asthma medications. REVIEWER'S CONCLUSIONS In asthmatic subjects with gastro-oesophageal reflux, (but who were not recruited specifically on the basis of reflux-associated respiratory symptoms), there was no overall improvement in asthma following treatment for gastro-oesophageal reflux. Subgroups of patients may gain benefit, but it appears difficult to predict responders.