Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Gemin5 as a Novel 7-Methylguanosine Cap-Binding Protein

Background A unique attribute of RNA molecules synthesized by RNA polymerase II is the presence of a 7-methylguanosine (m7G) cap structure added co-transcriptionally to the 5′ end. Through its association with trans-acting effector proteins, the m7G cap participates in multiple aspects of RNA metabolism including localization, translation and decay. However, at present relatively few eukaryotic proteins have been identified as factors capable of direct association with m7G. Methodology/Principal Findings Employing an unbiased proteomic approach, we identified gemin5, a component of the survival of motor neuron (SMN) complex, as a factor capable of direct and specific interaction with the m7G cap. Gemin5 was readily purified by cap-affinity chromatography in contrast to other SMN complex proteins. Investigating the underlying basis for this observation, we found that purified gemin5 associates with m7G-linked sepharose in the absence of detectable eIF4E, and specifically crosslinks to radiolabeled cap structure after UV irradiation. Deletion analysis revealed that an intact set of WD repeat domains located in the N-terminal half of gemin5 are required for cap-binding. Moreover, using structural modeling and site-directed mutagenesis, we identified two proximal aromatic residues located within the WD repeat region that significantly impact m7G association. Conclusions/Significance This study rigorously identifies gemin5 as a novel cap-binding protein and describes an unprecedented role for WD repeat domains in m7G recognition. The findings presented here will facilitate understanding of gemin5's role in the metabolism of non-coding snRNAs and perhaps other RNA pol II transcripts.
Accuracy of paediatric echocardiographic transmission via telemedicine

We evaluated the accuracy of realtime echocardiography studies conducted via telemedicine (at 384 kbit/s) and prerecorded video studies, by comparing the results with subsequent in-person echocardiography examination performed at follow-up. Between January 2002 and December 2004, there were 769 paediatric echo studies of patients aged one day to 19 years by telemedicine. There were three cases (0.4%) in which the study could not be successfully transmitted in realtime due to ISDN line or equipment failure. These were recorded, then transmitted and reviewed within 24 h. A normal heart was demonstrated in 272 studies (35%). A non-urgent congenital heart defect (CHD) was detected in 311 studies (41%). A critical cardiac abnormality was identified in 25 studies (3% of the total). Sixty-seven studies were repeated in person at the tertiary centre. All but one of the follow-up echocardiograms confirmed our initial telemedicine diagnosis (99% sensitivity). There were 655 videorecorded studies delivered to the tertiary centre between February 2002 and November 2003. Thirty-two patients had a repeated echocardiogram performed there. There were either discrepancies or lack of diagnostic clarity in 12 studies (38%) compared with on-site echo evaluations. This suggests that echocardiography evaluation using videorecordings may be less accurate than via realtime telemedicine.
The Kinase Domain of Titin Controls Muscle Gene Expression and Protein Turnover

The giant sarcomeric protein titin contains a protein kinase domain (TK) ideally positioned to sense mechanical load. We identified a signaling complex where TK interacts with the zinc-finger protein nbr1 through a mechanically inducible conformation. Nbr1 targets the ubiquitin-associated p62/SQSTM1 to sarcomeres, and p62 in turn interacts with MuRF2, a muscle-specific RING-B-box E3 ligase and ligand of the transactivation domain of the serum response transcription factor (SRF). Nuclear translocation of MuRF2 was induced by mechanical inactivity and caused reduction of nuclear SRF and repression of transcription. A human mutation in the titin protein kinase domain causes hereditary muscle disease by disrupting this pathway.
The Incidence and Short-term Outcomes of Acute Respiratory Illness with Cough in Children from a Socioeconomically Disadvantaged Urban Community in Australia: A Community-Based Prospective Cohort Study

Background Acute respiratory illnesses with cough (ARIwC) are predominant causes of morbidity in Australian Indigenous children; however, data on disease burden in urban communities are scarce. This study aimed to determine the incidence of ARIwC, the predictors of recurrent (≥4 episodes) ARIwC, and development of chronic cough following an ARIwC in urban, predominantly Indigenous, children aged <5 years from northern Brisbane, Australia. Methods Prospective cohort study of children aged <5 years registered with a primary healthcare center. ARIwC episodes and outcomes were collected for 12 months. Recurrent ARIwC was defined as ≥4 episodes in 12 months. Chronic cough was defined as cough lasting >4 weeks. Children who developed chronic cough were reviewed by a pediatric pulmonologist. Incidence densities per child-month of observation were calculated and predictors of recurrent ARIwC and chronic cough were evaluated in logistic regression models. Results Between February 2013 and November 2015, 200 children were enrolled; median age of 18.1 months, range (0.7–59.7 months) and 90% identified as Indigenous. A total of 1,722 child-months of observation were analyzed (mean/child = 8.58, 95% CI 8.18–9.0). The incidence of ARIwC was 24.8/100 child-months at risk (95% CI 22.3–27.5). Twenty-one children (10.5%) experienced recurrent ARIwC. Chronic cough was identified in 70/272 (25.7%) episodes of ARIwC. Predictors of recurrent ARIwC were presence of eczema, mold in the house, parent/carer employment status, and having an Aboriginal and Torres Strait Islander mother/non-Aboriginal and Torres Strait Islander father (compared to both parents being Aboriginal and Torres Strait Islander). Predictors of chronic cough included being aged <12 months, eczema, childcare attendance, previous history of cough of >4 weeks duration, having an Aboriginal and Torres Strait Islander mother/non-Aboriginal and Torres Strait Islander father (compared to both parents being Aboriginal and Torres Strait Islander), and a low income. Of those with chronic cough reviewed by a pediatric pulmonologist, a significant underlying disorder was found in 14 children (obstructive sleep apnea = 1, bronchiectasis = 2, pneumonia = 2, asthma = 3, tracheomalacia = 6). Discussion This community of predominantly Aboriginal and Torres Strait Islander and socially disadvantaged children bear a considerable burden of ARIwC. One in 10 children will experience more than three episodes over a 12-month period and 1 in five children will develop chronic cough post ARIwC, some with a serious underlying disorder. Further larger studies that include a broader population base are needed.
Text-dependent speaker recognition using PLDA with uncertainty propagation

In this paper, we apply and enhance the i-vector-PLDA paradigm to text-dependent speaker recognition. Due to its origin in text-independent speaker recognition, this paradigm does not make use of the phonetic content of each utterance. Moreover, the uncertainty in the i-vector estimates should be taken into account in the PLDA model, due to the short duration of the utterances. To bridge this gap, a phrase-dependent PLDA model with uncertainty propagation is introduced. We examined it on the RSR-2015 dataset and we show that despite its low channel variability, improved results over the GMM-UBM model are attained.
Hydrology and Earth System Sciences Discussions Water Accounting plus (wa+) – a Water Accounting Procedure for Complex River Basins Based on Satellite Measurements

This discussion paper is/has been under review for the journal Hydrology and Earth System Sciences (HESS). Please refer to the corresponding final paper in HESS if available. Abstract Coping with the issue of water scarcity and growing competition for water among different sectors requires proper water management strategies and decision processes. A prerequisite is a clear understanding of the basin hydrological processes, manageable and unmanageable water flows, the interaction with land use and opportunities to 5 mitigate the negative effects and increase the benefits of water depletion on society. Currently, water professionals do not have a common framework that links hydrological flows to user groups of water and their benefits. The absence of a standard hydrological and water management summary is causing confusion and wrong decisions. The non-availability of water flow data is one of the underpinning reasons for not having op-10 erational water accounting systems for river basins in place. In this paper we introduce Water Accounting Plus (WA+), which is a new framework designed to provide explicit spatial information on water depletion and net withdrawal processes in complex river basins. The influence of land use on the water cycle is described explicitly by defining land use groups with common characteristics. Analogous to financial accounting, WA+ 15 presents four sheets including (i) a resource base sheet, (ii) a consumption sheet, (iii) a productivity sheet, and (iv) a withdrawal sheet. Every sheet encompasses a set of indicators that summarize the overall water resources situation. The impact of external (e.g. climate change) and internal influences (e.g. infrastructure building) can be estimated by studying the changes in these WA+ indicators. Satellite measurements 20 can be used for 3 out of the 4 sheets, but is not a precondition for implementing WA+ framework. Data from hydrological models and water allocation models can also be used as inputs to WA+.
Preclinical Testing of Antihuman CD28 Fab′ Antibody in a Novel Nonhuman Primate Small Animal Rodent Model of Xenogenic Graft-Versus-Host Disease

Background Graft-versus-host disease (GVHD) is a severe complication of hematopoietic stem cell transplantation. Current therapies to prevent alloreactive T cell activation largely cause generalized immunosuppression and may result in adverse drug, antileukemia and antipathogen responses. Recently, several immunomodulatory therapeutics have been developed that show efficacy in maintaining antileukemia responses while inhibiting GVHD in murine models. To analyze efficacy and better understand immunological tolerance, escape mechanisms, and side effects of clinical reagents, testing of species cross-reactive human agents in large animal GVHD models is critical. Methods We have previously developed and refined a nonhuman primate (NHP) large animal GVHD model. However, this model is not readily amenable to semi-high throughput screening of candidate clinical reagents. Results Here, we report a novel, optimized NHP xenogeneic GVHD (xeno-GVHD) small animal model that recapitulates many aspects of NHP and human GVHD. This model was validated using a clinically available blocking, monovalent anti-CD28 antibody (FR104) whose effects in a human xeno-GVHD rodent model are known. Conclusions Because human-reactive reagents may not be fully cross-reactive or effective in vivo on NHP immune cells, this NHP xeno-GVHD model provides immunological insights and direct testing on NHP-induced GVHD before committing to the intensive NHP studies that are being increasingly used for detailed evaluation of new immune therapeutic strategies before human trials.
Multiword Expressions in Statistical Dependency Parsing

In this paper, we investigated the impact of extracting different types of multiword expressions (MWEs) in improving the accuracy of a data-driven dependency parser for a morphologically rich language (Turkish). We showed that in the training stage, the unification of MWEs of a certain type, namely compound verb and noun formations, has a negative effect on parsing accuracy by increasing the lexical sparsity. Our results gave a statistically significant improvement by using a variant of the treebank excluding this MWE type in the training stage. Our extrinsic evaluation of an ideal MWE recognizer (for only extracting MWEs of type named entities, duplications, numbers, dates and some predefined list of compound prepositions) showed that the preprocessing of the test data would improve the labeled parsing accuracy by 1.5%.
Electrophysiological characterization of Na+ currents in acutely isolated human hippocampal dentate granule cells

1 Properties of voltage‐dependent Na+ currents were investigated in forty‐two dentate granule cells (DGCs) acutely isolated from the resected hippocampus of twenty patients with therapy‐refractory temporal lobe epilepsy (TLE) using the whole‐cell patch‐clamp technique. 2 Depolarizing voltage commands elicited large, rapidly activating and inactivating Na+ currents (140 pS μm−2; 163 mm extracellular Na+) that were reduced in amplitude by lowering the Na+ gradient (43 mm extracellular Na+). At low temperatures (8‐12 °C), the time course of Na+ currents slowed and could be well described by the model of Hodgkin & Huxley. 3 Na+ currents were reversibly blocked by tetrodotoxin (TTX) and saxitoxin (STX) with a half‐maximal block of 4.7 and 2.6 nm, respectively. In order to reduce series resistance errors, the Na+ current was partially blocked by low toxin concentrations (10‐15 nm) in the experiments described below. Under these conditions, Na+ currents showed a threshold of activation of about ‐50 mV, and the voltages of half‐maximal activation and inactivation were ‐29 and ‐55 mV, respectively. 4 The time course of recovery from inactivation could be described with a double‐exponential function (time constants, 3‐20 and 60‐200 ms). The rapid and slow time constants showed a distinct voltage dependence with maximal values around ‐55 and ‐80 mV, respectively. These properties contributed to a reduction of the Na+ currents during repetitive stimulation that was more pronounced with higher stimulation frequencies and also showed a dependence on the holding potential. 5 In summary, the most striking features of DGC Na+ currents were the large current density and the presence of a current component showing a slow recovery from inactivation. Our data provide a basis for comparison with properties of Na+ currents in animal models of epilepsy, and for the study of drug actions in therapy‐refractory epilepsy.
Effect of Lowering the Glycemic Load With Canola Oil on Glycemic Control and Cardiovascular Risk Factors: A Randomized Controlled Trial

OBJECTIVE Despite their independent cardiovascular disease (CVD) advantages, effects of α-linolenic acid (ALA), monounsaturated fatty acid (MUFA), and low-glycemic-load (GL) diets have not been assessed in combination. We therefore determined the combined effect of ALA, MUFA, and low GL on glycemic control and CVD risk factors in type 2 diabetes. RESEARCH DESIGN AND METHODS The study was a parallel design, randomized trial wherein each 3-month treatment was conducted in a Canadian academic center between March 2011 and September 2012 and involved 141 participants with type 2 diabetes (HbA1c 6.5%–8.5% [48–69 mmol/mol]) treated with oral antihyperglycemic agents. Participants were provided with dietary advice on either a low-GL diet with ALA and MUFA given as a canola oil–enriched bread supplement (31 g canola oil per 2,000 kcal) (test) or a whole-grain diet with a whole-wheat bread supplement (control). The primary outcome was HbA1c change. Secondary outcomes included calculated Framingham CVD risk score and reactive hyperemia index (RHI) ratio. RESULTS Seventy-nine percent of the test group and 90% of the control group completed the trial. The test diet reduction in HbA1c units of −0.47% (−5.15 mmol/mol) (95% CI −0.54% to −0.40% [−5.92 to −4.38 mmol/mol]) was greater than that for the control diet (−0.31% [−3.44 mmol/mol] [95% CI −0.38% to −0.25% (−4.17 to −2.71 mmol/mol)], P = 0.002), with the greatest benefit observed in those with higher systolic blood pressure (SBP). Greater reductions were seen in CVD risk score for the test diet, whereas the RHI ratio increased for the control diet. CONCLUSIONS A canola oil–enriched low-GL diet improved glycemic control in type 2 diabetes, particularly in participants with raised SBP, whereas whole grains improved vascular reactivity.
Analysis of Inhomogeneous Thermofluiddynamical Processes in Short Time High Pressure Treatment of Liquid Foods

In high pressure processes pressure acts almost instantaneously. Due to inhomogeneous composition of high pressure systems, work of compression and subsequent heat transfer processes lead to inhomogeneous temperature fields in the vessel. In case of temperature sensitive reaction kinetics, heterogeneous conversion of matter can arise. In food and bio science, this can be of crucial importance for quality and safety. This contribution investigates temperature inhomogeneities in a vertically oriented cylindrical autoclave of 2.3 l during short time high pressure treatment of different sucrose solutions (ramp 400 MPa/s; holding time 120 s; pressure 700 MPa; mass fraction sucrose 0 – 0.5 kg/kg). Using analytical and numerical considerations, thermofluiddynamical non-uniformities are analyzed.
An evaluation of the anatomical basis of the Biceps Load tests I and II for superior labral anterior and posterior (SLAP) lesions

Both Biceps Load tests I and II rely on an increase in tension in the long head of biceps to identify a superior labral anterior and posterior (SLAP) lesion. This study aimed to evaluate the anatomical basis of Biceps Load tests I and II by measuring activity in the long head of biceps in the two clinical tests. Activity in the long head of biceps was measured in 12 healthy young participants using surface electromyography. Activity was only minimally increased in both Biceps Load I and II compared with the resting position. In the absence of convincing support for the anatomical basis of the test, investigations of diagnostic accuracy need to be replicated in order for the reported high accuracy of Biceps Load I and II tests to be supported with confidence. Clin. Anat. 21:647–651, 2008. © 2008 Wiley‐Liss, Inc.
Rapid diagnosis of Mycobacterium tuberculosis infection in children using interferon-gamma release assays (IGRAs)

Diagnosis of tuberculosis (TB) in children by the tuberculin skin test (TST) poses a diagnostic challenge for physicians due to its low specificity and cross-reactivity with nontuberculous mycobacteria and bacille Calmette-Guerin (BCG). Although interferon-gamma release assays (IGRAs) have been shown as novel TST alternatives for diagnosis of latent TB infection (LTBI) in adults, their effectiveness is less clear in children. The present study examined QuantiFERON-TB Gold (QFT-G) responses and IFN-gamma production capacity of TST-positive children, younger children ≤5 years. A total of 517 children of whom 434 were TST positive ranging in age from 1 month to 18 years were evaluated by the QFT-G. Of the 517 children, 434 (84%) were TST positive, 25 (5.8%) of whom were found to be QFT-G positive and 25 (5.4%) with an indeterminate response. Of the 517 children, 355 (68.7%) were previously BCG immunized and 310/355 (87.3%) were TST positive including 18/27 (66.7%) QFT-positive children. Adequate IFN-gamma production by purified TB peptides or mitogen was observed in 92.8% of children, 29.6% of whom were <5 years. This study shows that the QFT-G assay is useful for diagnosis of LTBI. The finding of 5.8% positive QFT-G in 434 TST-positive children underscores the superior specificity of the QFT-G than the TST and its greater cost effectiveness in preventing unnecessary and potentially toxic treatment in children. The study suggests that the majority of positive TST in children represent false-positive reactions and supports the use of IGRAs for diagnosis of LTBI in children, including those <5 years of age.
Analysis of word co-occurrence in human literature for supporting semantic correspondence discovery

Semantic similarity measurement aims to determine the likeness between two text expressions that use different lexicographies for representing the same real object or idea. In this work, we describe the way to exploit broad cultural trends for identifying semantic similarity. This is possible through the quantitative analysis of a vast digital book collection representing the digested history of humanity. Our research work has revealed that appropriately analyzing the co-occurrence of words in some periods of human literature can help us to determine the semantic similarity between these words by means of computers with a high degree of accuracy.
Homoarginine, heart failure, and sudden cardiac death in haemodialysis patients

Sudden cardiac death (SCD) is a major contributor to the excess mortality of patients on maintenance dialysis. Homoarginine deficiency may lead to decreased nitric oxide availability and endothelial dysfunction. Based on this rationale we assessed whether homoarginine deficiency is a risk factor for SCD in dialysis patients.
The Detection of Cotton Fiber Convolutions by the Reflection of Light

A device which allows the azimuthal monitoring of reflected light is described. The results of measuring the azimuthal angles between maximum reflected light and one-half of maximum reflected light are given for nineteen varieties of cotton of the G. barbadense and G. hirsutum species. This angle is shown to be a function of the induced convolutions in cotton fibers. These measurements by a new technique are compared separately with x-ray and microscopic orientation results. Also, comparisons are made between zero-gage tenacity versus 40% x-ray angle and zero-gage tenacity versus 50% optical angle.
The level of urinary IL-18 in acute kidney injury after cardiopulmonary bypass

This study investigated the diagnostic value of urinary interleukin-18 (uIL-18) in acute kidney injury (AKI) after cardiopulmonary bypass (CPB) in clinical practice. A total of 103 patients who underwent CPB were divided into the AKI group and non-AKI group according to the diagnostic criteria of AKI, and we collected the urine samples before and at 2, 4, 6, 8 and 12 h after CPB and the blood samples before and at 12, 24, 48 and 72 h after CPB for detection of the levels of uIL-18 and urinary neutrophil gelatinase-associated lipocalin (uNGAL) in urine samples and the levels of serum creatinine (Scr) in blood samples, respectively. With the results of detection, we measured the sensitivity and specificity of uIL-18 and uNGAL levels at 2 h after CPB in early diagnosis of AKI using the receiver operating characteristic (ROC) curve and area under curve (AUC). There were a total of 22 patients (21.4%) with AKI. From 12 h after CPB, the level of Scr in the AKI group was significantly elevated, and this increasing trend lasted for 60 h; comparisons with the levels before CPB and in non-AKI group showed that the differences had statistical significance (P<0.05). In AKI group, uIL-18 attained the peak level at 2 h after CPB, and the high level lasted for 10 h; comparisons with the levels before CPB and in non-AKI group showed that the differences had statistical significance (P<0.05); 2 h after CPB, the AUC was 90.48, and when the critical value was set as 1.6 µg/l, the sensitivity and specificity was 90.91 and 91.36%, respectively. Although there was a significant elevation in uNGAL level at 2 h after CPB in the AKI group, the level was dramatically decreased as soon as the peak level was attained at 4 h, and the high level only lasted for 8 h; difference between the level at 2 h after CPB and the level before CPB as well as that in the non-AKI group had statistical significance (P<0.05); at 2 h after CPB, the AUC was 83.25, and when the critical value was set as 100 µg/l, the sensitivity and specificity was, respectively 90.91 and 93.83%. The results indicated that after CPB, the level of uIL-18 shows a more promising diagnostic value in clinical practice than Scr and uNGAL in early diagnosis of AKI.