Miracle-dz/UniFAR-FTUs huggingface dataset:
The Gene Ontology Task at BioCreative IV

Gene Ontology (GO) annotation is a common task among model organism database (MOD) groups. It is a very time-consuming and labor-intensive task, thus often considered as one of the bottlenecks in literature curation. There is a growing need for semior fully-automated GO curation techniques that will help database curators rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The lack of relevant training data and opportunities for interaction between text mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two sub-tasks: a) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and b) to automatically identify relevant GO terms for the genes in a given article (a concept recognition task). With the support from five MODs, we provided teams with nearly 4,000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available due to the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we find an overall improvement in performance for recognizing GO terms when comparing to similar task results in the past. Future work should focus on improving performance of GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation. Introduction Manual Gene Ontology (GO) annotation is the task of human curators assigning gene functional information using GO terms through reading the biomedical literature. This is a common task among Model Organism Database (MOD) groups (1) and can be time-consuming and laborintensive. Thus, manual GO annotation is often considered one of the bottlenecks in literature-
The lack of effect of benzalkonium chloride on the cilia of the nasal mucosa in patients with perennial allergic rhinitis: a combined functional, light, scanning and transmission electron microscopy study

Background Controversy still exists about the effect of 0.02% benzalkonium chloride (BKC). a preservative in many nasal sprays, on human nasal epithelium in vivo. Objective To determine the safety of BKC by assessing its effect on the function and morphology of cilia of human nasal epithelium.
Health applications and grid technologies

Biology and genomics in the near future will play a major role in day to day activities related with health. Today biologists and doctors work together in order to decode and analyze large amount of data extracted from the DNA analysis of proteins. Advanced health applications will be needed in order to store, retrieve, process the large amount of data – being produced today by genomics and bioinformatics analysis – in order to extract useful results in a reasonable time frame. In this paper we present the results from our research regarding the use of grid technologies with health applications. We present the current status of standardization activities and working groups, which are currently involved with the specification of health applications and the standardization of needed components such us security, functionality, etc., which are being introduced by the use of grid technologies. Keywords—grid technologies, health applications, health grid, genomic medicine, grid enable pharmaceutical, open grid services, distributed systems.
Prevalence of exercise-induced bronchospasm in a cohort of varsity college athletes.

INTRODUCTION Exercise-induced bronchospasm (EIB) occurs more commonly in elite athletes than in the general population. There have been relatively few prevalence studies examining EIB in college athletes despite studies which have shown significant morbidity from asthma attacks related to exercise occurring in athletes in this age group. None of the previous studies utilized eucapnic voluntary hyperpnea (EVH) testing, which is the currently recommended test to document EIB in Olympians. METHODS Varsity athletes at The Ohio State University underwent EVH testing to assess for EIB. RESULTS One hundred seven athletes from 22 sports participated. Forty-two of 107 athletes (39%) were EIB positive according to EVH results. Thirty-six of 42 EIB-positive athletes (86%) had no prior history of EIB or asthma. There were no significant differences in the prevalence of EIB according to sex of the athlete (P=0.65) or ventilation demands of the sport (P=0.64). Symptoms were not predictive of EIB (P=0.44). The prevalence of EIB was 36% in athletes with negative symptoms and 35% for those with positive symptoms. Athletes in high-ventilation sports were significantly more symptomatic (48%) than athletes in low-ventilation sports (25%) (P=0.02); however, there was no difference in the prevalence of EIB between the two groups (P=0.64). CONCLUSIONS Varsity athletes show a high incidence of EIB when objectively diagnosed by a variety of pulmonary function criteria. Sex of the athlete or ventilation demands of the sport does not affect the prevalence of EIB. The use of symptoms to diagnose EIB is not predictive of whether athletes have objectively documented EIB. Empiric diagnosis and treatment of EIB on the basis of subjective symptoms alone may lead to an increased number of inaccurate diagnoses and increased morbidity.
Usher syndrome clinical types I and II: could ocular symptoms and signs differentiate between the two types?

PURPOSE Usher syndrome types I and II are clinical syndromes with substantial genetic and clinical heterogeneity. We undertook the current study in order to identify ocular symptoms and signs that could differentiate between the two types. METHODS Sixty-seven patients with Usher syndrome were evaluated. Based on audiologic and vestibular findings, patients were classified as either Usher type I or II. The severity of the ocular signs and symptoms present in each type were compared. RESULTS Visual acuity, visual field area, electroretinographic amplitude, incidence of cataract and macular lesions were not significantly different between Usher types I and II. However, the ages when night blindness was perceived and retinitis pigmentosa was diagnosed differed significantly between the two types. CONCLUSIONS There seems to be some overlap between types I and II of Usher syndrome in regard to the ophthalmologic findings. However, night blindness appears earlier in Usher type I (although the difference in age of appearance appears to be less dramatic than previously assumed). Molecular elucidation of Usher syndrome may serve as a key to understanding these differences and, perhaps, provide a better tool for use in clinical diagnosis, prognosis and genetic counseling.
Frost flowers growing in the Arctic ocean‐atmosphere–sea ice–snow interface: 2. Mercury exchange between the atmosphere, snow, and frost flowers

[1] Frost flowers are ice crystals that grow on refreezing sea ice leads in Polar Regions by wicking brine from the sea ice surface and accumulating vapor phase condensate. These crystals contain high concentrations of mercury (Hg) and are believed to be a source of reactive halogens, but their role in Hg cycling and impact on the fate of Hg deposited during atmospheric mercury depletion events (AMDEs) are not well understood. We collected frost flowers growing on refreezing sea ice near Barrow, Alaska (U.S.A.) during an AMDE in March 2009 and measured Hg concentrations and Hg stable isotope ratios in these samples to determine the origin of Hg associated with the crystals. We observed decreasing Δ199Hg values in the crystals as they grew from new wet frost flowers (mean Δ199Hg = 0.77 ± 0.13‰, 1 s.d.) to older dry frost flowers (mean Δ199Hg = 0.10 ± 0.05‰, 1 s.d.). Over the same time period, mean Hg concentrations in these samples increased from 131 ± 6 ng/L (1 s.d.) to 180 ± 28 ng/L (1 s.d.). Coupled with a previous study of Hg isotopic fractionation during AMDEs, these results suggest that Hg initially deposited to the local snowpack was subsequently reemitted during photochemical reduction reactions and ultimately accumulated on the frost flowers. As a result of this process, frost flowers may lead to enhanced local retention of Hg deposited during AMDEs and may increase Hg loading to the Arctic Ocean.
ATP-binding cassette transporter A1 (ABCA1) affects total body sterol metabolism.

BACKGROUND AND AIMS Members of the family of ABC transporters are involved in different processes of sterol metabolism, and ABCA1 was recently identified as a key regulator of high-density lipoprotein (HDL) metabolism. Our aim was to further analyze the role of ABCA1 in cholesterol metabolism. METHODS ABCA1-deficient mice (ABCA1-/-) and wild-type mice were compared for different aspects of sterol metabolism. Intestinal cholesterol absorption was determined by a dual stable isotope technique, and analysis of fecal, plasma, and tissue sterols was performed by gas chromatography/mass spectrometry. Key regulators of sterol metabolism were investigated by Northern and Western blot analyses or enzyme activity assays. RESULTS ABCA1-disrupted sv129/C57BL/6 hybrid mice showed a significant reduction in intestinal cholesterol absorption. The decrease in cholesterol absorption was followed by an enhanced fecal loss of neutral sterols, whereas fecal bile acid excretion was not affected. Total body cholesterol synthesis was significantly increased, with enhanced 3-hydroxy-3-methyglutaryl-coenzyme A (HMG-CoA) reductase observed in adrenals and spleen. In addition, ABCA1-/- mice showed markedly increased concentrations of cholesterol precursors in the plasma, lung, intestine, and feces. Reduced HMG-CoA reductase messenger RNA and enzyme activity in the liver suggest that enhanced cholesterol synthesis in ABCA1-/- mice occurs in peripheral tissues rather than the liver. CONCLUSIONS The metabolism of cholesterol and cholesterol precursors is markedly affected by a lack of ABCA1 function.
Implantation and embryonic development in the ovariectomized-adrenalectomized hamster.

Ten groups, five to ten animals per group were used in demonstrating that progesterone plus cortisol acetate can induce implantation and maintain embryonic growth in hamsters subjected to ovariectomy and adrenalectomy on Day 1 or on Day 4 of pregnancy, Fetal weights on Day 14 were, however, significantly lower than in sham-operated control animals, although they were not different from those in animals only ovariectomized and given progesterone. It is concluded, therefore, that it is unnecessary to invoke secretion of estrogen either from the ovaries or from the adrenals for induction of implantation in hamsters.
The parallel rational Arnoldi algorithm

Since version 2.4 of the RKToolbox, the rat krylov function can simulate the parallel construction of a rational Krylov basis. This is done by imposing various nonzero patterns in a so-called continuation matrix T . Simply speaking, the j-th column of this matrix contains the coefficients of the linear combination of j rational Krylov basis vectors which have been used to compute the next (j + 1)-th basis vector. Therefore T is an upper triangular matrix.
Revised Algorithm for Estimating Light Extinction from IMPROVE Particle Speciation Data

Abstract The Interagency Monitoring of Protected Visual Environments (IMPROVE) particle monitoring network consists of approximately 160 sites at which fine particulate matter (PM2.5) mass and major species concentrations and course particulate matter (PM10) mass concentrations are determined by analysis of 24-hr duration sampling conducted on a 1-day-in-3 schedule. A simple algorithm to estimate light extinction from the measured species concentrations was incorporated in the 1999 Regional Haze Rule as the basis for the haze metric used to track haze trends. A revised algorithm was developed that is more consistent with the recent atmospheric aerosol literature and reduces bias for high and low light extinction extremes. The revised algorithm differs from the original algorithm in having a term for estimating sea salt light scattering from Cl - ion data, using 1.8 instead of 1.4 for the mean ratio of organic mass to measured organic carbon, using site-specific Rayleigh scattering based on site elevation and mean temperature, employing a split component extinction efficiency associated with large and small size mode sulfate, nitrate and organic mass species, and adding a term for nitrogen dioxide (NO2) absorption for sites with NO2 concentration information. Light scattering estimates using the original and the revised algorithms are compared with nephelometer measurements at 21 IMPROVE monitoring sites. The revised algorithm reduces the underprediction of high haze periods and the overprediction of low haze periods compared with the performance of the original algorithm. This is most apparent at the hazier monitoring sites in the eastern United States. For each site, the PM10 composition for days selected as the best 20% and the worst 20% haze condition days are nearly identical regardless of whether the basis of selection was light scattering from the original or revised algorithms, or from nephelometer-measured light scattering.
Late diagnosis of oxalosis in an adult patient: findings on bone radiography.

P nmary hyperoxaluria type 1 (PH! ) is a hereditary metabolic disease caused by a deficiency of the hepatic-specific peroxisomal enzyme, alanine-glyoxalate aminotransferase, and is characterized by an overproduction of oxalate. Renal deposition of insoluble calcium oxalate leads to urolithiasis or nephrocalcinosis and finally to chronic renal failure. At this stage of chronic renal failure, oxalate starts to accumulate in other tissues such as bone, constituting SyStemiC oxalosis [1]. Clinically, PH! is an cxtremely heterogeneous disease. Most commonly, symptoms and renal failure occur in childhood and early adulthood. Infrequently, the patient remains asymptomatic until late in adult life [1, 2]. Radiographic bone lesions of oxalosis in children and young patients have been extensively described [3, 4]. In older patients, radiographic bone lesions are less specific and can mimic those of renal osteodystrophy. The diagnosis is then difficult to make, and the symptoms can be attributed to secondary hyperparathyroidism, which may also complicate the course of the disease after long-term hemodialysis, superimposing radiographic abnormalities. Furthermore, it is important to distinguish patients with PH! and no associated secondary hyperparathyroidism from those with associated hyperparathyroidism, to avoid useless and harmful parathyroidectomy. In the present case, we report some radiographic features suggesting the diagnosis of oxalate osteopathy late in adult life.
Multiple IGBTs open circuit faults diagnosis in voltage source inverter fed induction motor using modified slope method

This paper deals with multiple insulated gate bipolar transistor (IGBTs) open circuit faults detection and localization in a pulse width modulation (PWM) voltage source inverter (VSI) fed induction motor based on a modified slope method. Firstly, a detection algorithm was used to calculate the slope of the current-vector trajectory in complex plan αβ. This algorithm detects the faulty bridge. Second, the Schmitt-trigger is used for the phase's currents monitoring. This circuit determines the phase's currents polarity and detect whether the current in the faulty arm is positive or negative. The analysis of two combined information makes it possible to diagnose the two simultaneous IGBTs open circuit fault within inverter. The proposed technique is developed and implemented to vector control induction motor drives. An experimental setup in the laboratory is used to compare the simulation results and the experimental results and to evaluate the performances of the proposed method.
Age-related differences of blood pressure profile in essential hypertension.

The purpose was to assess age-related circadian changes of blood pressure profile (BPP) employing a truncated Fourier series with four harmonics (tFs) in patients with essential hypertension. The study was performed on 32 patients with essential hypertension divided in two groups: (A) 15 patients younger than 55 years and (B) 17 patients older than 60 years. Systolic blood pressure (SBP) and diastolic blood pressure (DBP) were monitored every 20 minutes for 24 h with a noninvasive portable device (SpaceLabs 90202). To evaluate the existence of SBP and DBP circadian rhythms a one-sample runs-test was performed and the mesor, amplitude, and acrophase from the overall curve of each patient were obtained by tFs. In both groups, SBP and DBP profiles showed a first peak in the late morning and a second peak in the early evening around the same hours. The two peaks in the SBP profile were higher and the two peaks in the DBP profile were lower in older patients than in younger ones (p < .01, p < .05, p < .3, p < .05). The truncated Fourier series with four harmonics evidences different age-related BP profiles characterized by two peaks with higher SBP and lower DBP in elderly patients. These changes of BPP are in accordance with the reported higher risk of cardiovascular events observed around the same hours.
Immunomodulators, sFas and Fas‐L as potential noninvasive predictors of IFN treatment in patients with HCV genotype‐4

Summary. Recent studies have indicated that cytokines can be used as markers for disease progression in hepatitis C virus (HCV)‐infected patients, therefore this study was conducted to determine the influence of pegylated IFN vs standard IFN on interleukin‐2 receptor (IL‐2R), IL‐6R, IL‐8, TNFR‐I, TNFR‐II, sFas, and sFas‐L in Egyptian patients with chronic hepatitis C genotype 4, as no previous studies have been performed on this genotype. We also aim at establishing a possible relationship between these cytokines and the response to INF to determine whether they can be used as noninvasive markers for the response to INF therapy and as monitors for the outcome of treatment. Thirty‐eight patients with chronic HCV hepatitis were investigated for the serum levels of the previously mentioned cytokines in a randomized opened controlled trial (22 patients treated with pegylated IFN and 16 patients treated with standard IFN). Cytokine levels were measured by ELISA at 0, 1 and 12 months of IFN therapy. There was marked increase in the serum levels of IL‐2R and IL‐6R in nonresponders to pegylated interferon, IL‐8, TNFR‐I and II were significantly higher in nonresponders to standard interferon but were also high in responders of pegylated interferon. sFas and sFas‐L showed high levels among responders to pegylated interferon but the standard interferon was again less effective in this regard. Serum levels of TNFR‐II, sFas and sFas‐L have the potential to be used as serological markers for response to pegylated IFN therapy, and IL‐8 is a predictor for nonresponse. Moreover, TNFR‐I and II have the potential to be used as markers of response to standard IFN treatment. The persistent correlation between sFas and TNFR‐II may elaborate the possible role of pegylated IFN in the induction of apoptosis as a possible new mechanism of viral clearance during treatment with pegylated interferon treatment.
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Abstract EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.
An epidemiological profile of elderly suicides in Hong Kong

Suicide rates in Hong Kong increased with age, and the highest suicide rate occurred among the oldest age groups. Hong Kong has one of the highest elderly suicide rates in the world. The elderly suicide rate was four to five times above the average. Furthermore, gender differences were observed among different marital status groups. For example, single males had a much higher rate than single females and married males had a higher rate than their widowed counterparts. The suicide rate for an economically inactive person was six times higher than for an active one. Jumping has become increasingly common and seems to substitute for other methods of suicide. Winter months and the Chinese New Year period had the lowest suicide occurrence. Some explanations are given. © 1998 John Wiley & Sons, Ltd.
Renal activation of extracellular signal-regulated kinase in rats with autosomal-dominant polycystic kidney disease.

BACKGROUND Abnormal proliferation of renal tubule epithelial cells is a central factor in the biogenesis and sustained expansion of cysts in autosomal-dominant polycystic kidney disease (ADPKD). Recent evidence from in vitro studies of human cyst wall epithelial cells has implicated a role for the mitogen-activated protein (MAP) kinase pathway in this aberrant proliferation. To determine the extent to which this signaling pathway is involved in cyst pathogenesis in vivo, we measured the expression of select components of the MAP kinase cascade in Han:SPRD rats with ADPKD at an early stage of the disease. METHODS Kidneys of 8-week-old normal Han:SPRD rats (+/+) or rats heterozygous (Cy/+) for ADPKD were examined by Western blot analysis and immunohistochemistry to determine the expression of extracellular-regulated kinase (ERK), phosphorylated ERK (P-ERK), Raf-1 (MAPKKK), phosphorylated Raf-1 (P-Raf-1), B-Raf, Rap-1 and phosphorylated protein kinase A (P-PKA). RESULTS P-ERK was expressed to a greater extent in Cy/+ kidneys (3.74 +/- 1.07 fold) than in normal kidneys, whereas ERK abundance was not different. P-Raf-1 levels were higher in Cy/+ than in +/+ kidneys (1.53 +/- 0.08 fold) consistent with upstream stimulation of receptor tyrosine kinase. B-Raf and Raf-1 abundances were greater in Cy/+ than in +/+ (1.74 +/- 0.25 and 1.27 +/- 0.08 fold, respectively). In Cy/+, immunohistochemistry showed increased P-ERK and B-Raf expression in the abnormal mural epithelial cells within cysts. These findings, together with the detection of P-PKA and the small G protein, Rap-1, in cyst epithelial cells, implicate a potential role for cyclic adenosine monophosphate (AMP) in the activation of ERK in ADPKD cells. CONCLUSIONS We conclude that the MAP kinase pathway is activated to the level of ERK in the abnormal mural epithelial cells lining cysts in animals with a dominantly inherited type of polycystic kidney disease. We suggest that cAMP, acting through PKA, Rap-1 and B-Raf, may contribute to the activation of ERK in a way that complements receptor tyrosine kinase-mediated agonists in the promotion of cyst enlargement.