Miracle-dz/UniFAR-FTUs huggingface dataset:
Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis

Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropicalis assembly and annotation lacked the resolution required for ChIA-PET we improve the genome assembly version 4.1 and annotations using data derived from the paired end tag (PET) sequencing technologies and approaches (e.g., DNA-PET [gPET], RNA-PET etc.). The large insert (~10Kb, ~17Kb) paired end DNA-PET with high throughput NGS sequencing not only significantly improved genome assembly quality, but also strongly reduced genome “fragmentation”, reducing total scaffold numbers by ~60%. Next, RNA-PET technology, designed and developed for the detection of full-length transcripts and fusion mRNA in whole transcriptome studies (ENCODE consortia), was applied to capture the 5' and 3' ends of transcripts. These amendments in assembly and annotation were essential prerequisites for the ChIA-PET analysis of TH transcription regulation. Their application revealed complex regulatory configurations of target genes and the structures of the regulatory networks underlying physiological responses. Our work allowed us to improve the quality of Xenopus tropicalis genomic resources, reaching the standard required for ChIA-PET analysis of transcriptional networks. We consider that the workflow proposed offers useful conceptual and methodological guidance and can readily be applied to other non-conventional models that have low-resolution genome data.
Dispersión atmosférica de las emisiones de una chimenea alta en terreno complejo

El objetivo general de esta tesis doctoral es el estudio de la dispersion de las emisiones sulfurosas de una fuente puntual elevada en un entorno topografico complejo de la peninsula iberica. Mediante experimentacion y modelizacion numerica, esta investigacion establece las pautas de caracterizacion tanto de la adveccion (a traves de la reconstruccion del campo de vientos tridimensional), como de la dispersion turbulenta (a partir de la comparacion de las medidas experimentales con los resultados de las simulaciones numericas). Para escenarios dispersivos caracterizados por un campo de turbulencia Quasi-Homogeneo y estacionario (fundamentalmente para situaciones invernales advectivas) y para escalas de tiempo lagrangiano mucho menores que el tiempo de transporte, se ha determinado estadisticamente que las condiciones de estabilidad son dos veces mas inestables que las predichas por las aproximaciones clasicas de Pasquill-Turner Briggs-Guifford. Para escenarios dispersivos convectivos ha sido posible describir numericamente los forzamientos orograficos que afectan a la dispersion atmosferica de las emisiones de la central termica de Andorra (Teruel). La puesta a punto de una adecuada metodologia ha permitido caracterizar numericamente la adveccion del penacho regida por las circulaciones mesoescalares y el patron de impactos en un entorno de 90 Km en torno a la chiminea.
Suicidality in chronic pain: a review of the prevalence, risk factors and psychological links

Background. This paper reviews and integrates the growing literature concerning the prevalence of and risk factors for suicidality in chronic pain. Method. A series of systematic searches in MEDLINE and PsychINFO identified 12 relevant articles examining suicide, suicide attempts, and suicidal ideation in chronic pain. A selection of theoretical and empirical work identifying psychological processes that have been implicated in both the pain and suicide literature and which may be related to increased suicidality was also reviewed. Results. Relative to controls, risk of death by suicide appeared to be at least doubled in chronic pain patients. The lifetime prevalence of suicide attempts was between 5% and 14% in individuals with chronic pain, with the prevalence of suicidal ideation being ~20%. Eight risk factors for suicidality in chronic pain were identified, including the type, intensity and duration of pain and sleep-onset insomnia co-occuring with pain, which appeared to be pain-specific. Helplessness and hopelessness about pain, the desire for escape from pain, pain catastrophizing and avoidance, and problem-solving deficits were highlighted as psychological processes relevant to the understanding of suicidality in chronic pain. Conclusions. Programmatic research is urgently required to investigate the role of both general and pain-specific risk factors for suicidality, to examine how the psychological processes mentioned above mediate or exacerbate suicidality, and to develop enhanced interventions for pain patients at risk.
INVESTIGATING THE FIFTH SEMESTER STUDENTS’ ABILITY OF STMIK PELITA NUSANTARA IN TOEFL

The objectives of this descriptive qualitative study were (1) to find out the student’s ability in TOEFL and (2) to identify the TOEFL sub skills which were required in the improvement. Twenty three students of class MI V Reguler and Executive Class in STMIK Pelita Nusantara Lubuk Pakam were conducted as participants. To examine students’ TOEFL scores, a paper-based TOEFL test was used. The test scores were used to find out the students’ ability at the beginning of the study. Then, the results were analyzed to identify the students’ problem in sub-skills of TOEFL. The data were identified and sub-skill was identified based on Phillips (2003). The findings of the study showed that: (1) the fifth semester students’ ability of STMIK Pelita Nusantara in doing TOEFL test is at Poor level with the most dominant score is below 400, consists of 21 students in that level with 91.30%. Then, there were only a few students, 2 persons with the percentage 8.69%. (2) the fifth semester students’ of STMIK Pelita Nusantara Nusantara is considered as the most difficult for them with the avarage of 5.28 is the listening, while reading section is considered as the easiest one for the fifth semester students of STMIK Pelita Nusantara, with the average of 6.94. Based on the findings, it can be concluded that overall all of the students in this study required further training to improve their TOEFL scores; therefore, it recommended the development of module and training plans according to the outcomes of this analysis study.
Breslow thickness and Clark level in melanoma

Thickness is known to be an important survival prognosticator for cutaneous melanoma, but controversy exists as to whether Clark level of invasion retains prognostic significance once thickness has been accounted for. A recent proposal to eliminate Clark level from the staging system for melanoma of the American Joint Committee on Cancer (AJCC) prompted the authors to investigate whether level adds useful prognostic information to Breslow thickness. They used the data base of the New York University Melanoma Cooperative Group (NYU‐MCG) Registry.
Physiological Profile and Activity Pattern of Minor Gaelic Football Players

Abstract Cullen, BD, Roantree, M, McCarren, A, Kelly, DT, O'Connor, PL, Hughes, SM, Daly, PG, and Moyna1, NM. Physiological profile and activity pattern of minor Gaelic football players. J Strength Cond Res 31(7): 1811–1820, 2017—The purpose of this study was to evaluate the physiological profile and activity pattern in club- and county-level under-18 (U-18) Gaelic football players relative to playing position. Participants (n = 85) were analyzed during 17 official 15-a-side matches using global positioning system technology (SPI Pro X II; GPSports Systems, Canberra, Australia) and heart rate (HR) telemetry. During the second part of this study, 63 participants underwent an incremental treadmill test to assess their maximal oxygen uptake (V[Combining Dot Above]o2max) and peak HR (HRmax). Players covered a mean distance of 5,774 ± 737 m during a full 60-minute match. The mean %HRmax and %V[Combining Dot Above]O2max observed during the match play were 81.6 ± 4.3% and 70.1 ± 7.75%, respectively. The playing level had no effect on the distance covered, player movement patterns, or %HRmax observed during match play. Midfield players covered significantly greater distance than defenders (p = 0.033). Playing position had no effect on %HRmax or the frequency of sprinting or high-intensity running during match play. The frequency of jogging, cruise running, striding (p = 0.000), and walking (p = 0.003) was greater in the midfield position than in the forward position. Time had a significant effect (F (1,39) = 33.512, p-value = 0.000, and = 0.462) on distance covered and %HRmax, both of which showed a reduction between playing periods. Gaelic football is predominantly characterized by low-to-moderate intensity activity interspersed with periods of high-intensity running. The information provided may be used as a framework for coaches in the design and prescription of training strategies. Positional specific training may be warranted given the comparatively greater demands observed in the midfield playing position. Replicating the demands of match play in training may reduce the decline in distance covered and %HRmax observed during the second half of match play.
METAL CHELATES IN THE STORAGE AND TRANSPORT OF NEUROTRANSMITTERS: INTERACTIONS OF METAL IONS WITH BIOGENIC AMINES 1

Abstract— Equilibrium studies on the interaction of biogenic amines with iron (Fe2+ and Fe3+) and magnesium (Mg2+) were undertaken in an attempt to correlate the stabilities of metal‐amine chelates and the reported granule‐binding affinities of the biogenic amines. By means of potentiometric equilibrium measurements at 25°C and an ionic strength of 10 (KNO3) the formation constants of the Fe2+ chelates with norepinephrine (NE) and adenosine‐S‐triphosphate (ATP) were determined. Possible structures were derived for the co‐ordinate binding of Fe2 + with NE. The interactions of Fe2+ and Fe2+‐ATP with NE were investigated and the formation of Fe2+‐NE‐ATP (1:1:1) mixed ligand ternary chelate was proposed on the basis of the equilibrium data. Information obtained from chelation studies of Fe2+ with pyrocatechol and ethanolamine taken together with the data obtained on the Fe2+‐NE system indicated that the binding of Fe2+ by NE was probably via the pyrocatechol moiety. Equilibrium constants for the binding of tyramine (TA) dopamine (DA) and NE with Mg2+ were also determined. The equilibrium data obtained on the Mg2+‐amine systems indicated a correlation between the metal‐amine binding affinities and the structure and amine‐release (and storage) activities of the biogenic amines. A consideration of the stabilities of the Fe2+ and Mg2+ chelates together with the occurrence of these metal ions in synaptosomes suggests their possible involvement in the intra vesicular amine‐binding and storage sites.
The association between suicide ideation and sensory impairment among elderly Koreans

Objectives: The purpose of this cross-sectional study was to examine the relationship between sensory impairment and suicide ideation among elderly Koreans. Methods: Data from the 2010–2012 Korea National Health and Nutrition Examination Survey V was used. Participants included 3636 older adults (≥65 years) who received hearing and vision tests; participants also completed assessments of covariates and suicide ideation. Results: The risk of suicide ideation was 1.43–1.65 times higher among participants with visual impairment than in those without impairment. Moreover, the risk was 1.60–1.76 times higher among those with both auditory and visual impairments than the risk for those without any impairment. Conclusion: This study found an association between sensory impairment and suicide ideation in elderly individuals. Therefore, it seems necessary that interventions that reduce or prevent sensory impaired elders’ suicide ideation are needed, which may be an indicator of mental health problems or poor quality of life.
Cardiac involvement in infantile Sandhoff disease

Abstract: An 18‐month‐old boy with enzyme assay‐confirmed infantile Sandhoff disease (MIM 268800) is reported. Besides the classical neurological features, this patient exhibited severe mitral regurgitation secondary to mitral valve prolapse and mild aortic regurgitation from aortic valve prolapse. He also had asymmetric hypertrophy of the interventricular septum without left ventricular outflow tract obstruction.
Lung Cancer with Localized Ground-Glass Attenuation Represents Early-Stage Adenocarcinoma in Nonsmokers

Background: Studies of lung cancer showing localized ground-glass attenuation (GGA) on thin-section computed tomography (TSCT) have been limited to resected stage IA adenocarcinomas. This study aimed to clarify the features of localized GGA cancer as a distinct clinicoradiological entity through a survey of lung cancers of all types. Methods: From 2000 through 2002, 492 patients with newly diagnosed stage I–IV lung cancer underwent TSCT at a single institution. The tumors were semiquantitatively classified into four groups on the basis of GGA area as a percentage of the whole tumor shadow (GGA ratio) on TSCT images: 100%, 99–50%, 49–1%, and 0%. The relationship between clinicopathological data and the GGA ratio, predictors of the presence of GGA, survival data, and prognostic factors were evaluated retrospectively. Results: All localized GGA cancers were adenocarcinomas (p < 0.05). A GGA component was not found in patients with advanced cancer (p < 0.05). GGA cancer was related to nonsmoking status (Odds ratio 6.17, p < 0.05). A threshold tumor size of 30 mm in GGA cancer (hazard ratio, 2.86; p < 0.01) and the GGA ratio (hazard ratio, 4.17; p < 0.01) were independent prognostic factors. Survival rates were higher in patients with a GGA ratio ≥50% and stage IB lung cancer than in patients with a GGA ratio <50% and stage IA lung cancer. Conclusion: Localized GGA cancer, with presurgical prognostic factors of tumor size and GGA ratio, represents early-stage lung adenocarcinoma in nonsmokers.
Vitamin D and asthma: current perspectives

Purpose of reviewTo review the current evidence on the relationship between vitamin D and asthma. Recent findingsThe rising morbidity and tremendous socioeconomic burden of asthma have prompted efforts to seek modifiable environmental and nutritional factors that contribute to the asthma epidemic. The association between low levels of vitamin D and asthma has been supported by many, but not all observational and epidemiologic studies. Recently, several controlled clinical trials have been undertaken to explore the effect of vitamin D supplementation on asthma control and respiratory tract infections. While some trials support the beneficial role of vitamin D supplementation in reducing asthma severity in children, several trials have found no beneficial role in adults. SummaryGiven the high prevalence of vitamin D insufficiency in children and adults worldwide and recent randomized controlled trials of vitamin D in asthma, supplementation with vitamin D cannot be recommended as adjunctive therapy for asthma.
Changes in Spring Phenology in the Three-Rivers Headwater Region from 1999 to 2013

Abstract: Vegetation phenology is considered a sensitive indicator of terrestrial ecosystem response to global climate change. We used a satellite-derived normalized difference vegetation index to investigate the spatiotemporal changes in the green-up date over the Three-Rivers Headwater Region (TRHR) from 1999 to 2013 and characterized their driving forces using climatic data sets. A significant advancement trend was observed throughout the entire study area from 1999 to 2013 with a linear tendency of 6.3 days/decade ( p < 0.01); the largest advancement trend was over the Yellow River source region (8.6 days/decade, p < 0.01). Spatially, the green-up date increased from the southeast to the northwest, and the green-up date of 87.4% of pixels fell between the 130th and 150th Julian day. Additionally, about 91.5% of the study area experienced advancement in the green-up date, of which 80.2%, mainly distributed in areas of vegetation coverage increase, experienced a significant advance. Moreover, it was found that the green-up date and its trend were significantly correlated with altitude. Statistical analyses showed that a 1-°C increase in spring temperature would induce an advancement in the green-up date of 4.2 days. We suggest that the advancement of the green-up date in the TRHR might be attributable principally to warmer and wetter springs.
^ THE IMPACTS OF INFORMATION TECHNOLOGY AND MANAGERIAL PROACTIVENESS IN BUILDING NET-ENABLED ORGANIZATIONAL RESILIENCE

The ability of an organization to generate variety is important for enhancing its organizational resilience when faced with volatilities from the environment. Using the context of integrated multichannel net-enabled retail organizations, we conceptualized organizational resilience as a higher-order capability comprising of two capabilities in terms ofinnovativeness and agility. Innova-tiveness reflects the scope aspect while agility represents the speed aspect of resilience. Based on a survey of 125 net-enabled retail organizations, we found that high levels of information technology capability and managerial proactiveness both significantly enhance organizational resilience. In addi tion, more resilient organizations perform better under turbulent environ ments. The construction of metrics to measure organizational resilience and the development of a structural model to elucidate the resilience building process and its performance consequences provide useful managerial and research implications.
Prevalence and clinical outcome associated with preexisting malnutrition in acute renal failure: a prospective cohort study.

Malnutrition is a frequent finding in hospitalized patients and is associated with an increased risk of subsequent in-hospital morbidity and mortality. Both prevalence and prognostic relevance of preexisting malnutrition in patients referred to nephrology wards for acute renal failure (ARF) are still unknown. This study tests the hypothesis that malnutrition is frequent in such clinical setting, and is associated with excess in-hospital morbidity and mortality. A prospective cohort of 309 patients admitted to a renal intermediate care unit during a 42-mo period with ARF diagnosis was studied. Patients with malnutrition were identified at admission by the Subjective Global Assessment of nutritional status method (SGA); nutritional status was also evaluated by anthropometric, biochemical, and immunologic parameters. Outcome measures included in-hospital mortality and morbidity, and use of health care resources. In-hospital mortality was 39% (120 of 309); renal replacement therapies (hemodialysis or continuous hemofiltration) were performed in 67% of patients (206 of 309); APACHE II score was 23.1+/-8.2 (range, 10 to 52). Severe malnutrition by SGA was found in 42% of patients with ARF; anthropometric, biochemical, and immunologic nutritional indexes were significantly reduced in this group compared with patients with normal nutritional status. Severely malnourished patients, as compared to patients with normal nutritional status, had significantly increased morbidity for sepsis (odds ratio [OR] 2.88; 95% confidence interval [CI], 1.53 to 5.42, P < 0.001), septic shock (OR 4.05; 95% CI, 1.46 to 11.28, P < 0.01), hemorrhage (OR 2.98; 95% CI, 1.45 to 6.13, P < 0.01), intestinal occlusion (OR 5.57; 95% CI, 1.57 to 19.74, P < 0.01), cardiac dysrhythmia (OR 2.29; 95% CI, 1.36 to 3.85, P < 0.01), cardiogenic shock (OR 4.39; 95% CI, 1.83 to 10.55, P < .001), and acute respiratory failure with mechanical ventilation need (OR 3.35; 95% CI, 3.35 to 8.74, P < 0.05). Hospital length of stay was significantly increased (P < 0.01), and the presence of severe malnutrition was associated with a significant increase of in-hospital mortality (OR 7.21; 95% CI, 4.08 to 12.73, P < 0.001). Preexisting malnutrition was a statistically significant, independent predictor of in-hospital mortality at multivariable logistic regression analysis both with comorbidities (OR 2.02; 95% CI, 1.50 to 2.71, P < 0.001), and with comorbidities and complications (OR 2.12; 95% CI, 1.61 to 2.89, P < 0.001). Malnutrition is highly prevalent among ARF patients and increases the likelihood of in-hospital death, complications, and use of health care resources.
Epstein-Barr virus infection-associated smooth-muscle tumors in patients with AIDS.

BACKGROUND The aim of our study is to describe the unusual clinical manifestations of smooth-muscle tumors (SMTs) in patients with acquired immunodeficiency virus (AIDS) and to demonstrate the association between Epstein-Barr virus (EBV) infection and SMTs. METHODS Nine patients with AIDS and SMTs were characterized at Chulalongkorn Hospital (Bangkok, Thailand) from 2001 through 2003. Tumor tissues suitable for immunohistochemical analysis and in situ hybridization were assayed for SMTs and EBV, respectively. Plasma and serum samples were tested for EBV by real-time quantitative polymerase chain reaction and serologic analysis. RESULTS The study included 8 adults and 1 child (3 males and 6 females). All patients had CD4 cell counts of <200 cells/microL. By the end of the study, 3 patients had died, and 6 patients had survived. The sites of SMTs were the epidura (5 intracranial and 4 intraspinal SMTs), vocal cords (2), adrenal glands (2), abdominal wall (2), iris (1), liver (1), lung (1), orbit (1), and thigh (1). Seven patients had multicentric SMTs involving intracranial sites only (4 SMTs), extra- and intracranial sites (3), or extracranial sites only (2), which occurred either concurrently or sequentially. We found evidence of EBV infection, as determined by in situ hybridization, in all SMTs. Furthermore, EBV DNA was detectable in plasma samples from 2 patients. The results of serologic analysis were consistent with past EBV infection. CONCLUSIONS SMTs in patients with AIDS typically arise in multiple and very unusual sites that are not often observed in SMTs among immunocompetent individuals. Our series also suggests association between EBV infection and SMTs in patients with AIDS. The exact role of EBV in smooth-muscle oncogenesis awaits further study.
Prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency in malaria endemic region of Iran (Sistan and Baluchestan Province): Epidemiological profile and trends over time

*Corresponding author: Hossein Ali Adineh, Department of Epidemiology and Biostatistics, Iranshahr University of Medical Sciences, Iranshahr, Iran; Health Promotion Research Center, Zahedan University of Medical Sciences, Zahedan, Iran. Tels: +98 9156388799, +98 5437222230 E-mail: Payam.health@yahoo.com This study protocol was performed according to the Helsinki Declaration and was assessed for ethic issues and approved by Ethical Committee of Zahedan University of Medical Sciences, Iran. Written informed consent was obtained from the heads of households. Foundation Project: Supported by World Health Organization (EMRO/TDR Small Grant with ID No. SGS 14/20), Deputies of Health and Research and Health Promotion Research Center in Zahedan University of Medical Sciences. The journal implements double-blind peer review practiced by specially invited international editorial board members.