Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Concentrating Periods of Physical Activity on the Risk of Injury in Organized Sports in a Pediatric Population

Background:The trend in pediatric sport organizations is to regroup activities into tournaments. Sports-related injuries in children are a public concern. Objective:To evaluate the association between sport injuries and consolidation of physical activity in children. Design:A case-crossover study. Setting:The emergency department of a tertiary care hospital for approximately 1 year in 2006. Participants:Eligible participants had to be between 8 to 16 years of age, presenting to the emergency department for an acute injury that occurred during a timed organized sport event. Assessment of risk factors:A standardized questionnaire was used to evaluate the number of hours of organized physical activity, which was defined as a supervised exercise leading to competitions. The number of hours of activity was compared between case periods (48 hours and 7 days) and control periods of same length. Main outcome measurements:An injury was defined as any acute problem with organic tissue that occurred during a sport. Results:On average, participants performed 136 minutes of organized sport activity in the 48 hours preceding the injury for a mean difference of 8 ± 18 min. They also performed 356 minutes of organized sports in the 7 days prior the injury. This represented an increase of 40 ± 31 minutes compared to the control periods. Conclusions:More injuries were observed if the athletes had increased the concentration of activity in the 7 days prior. Although small, this difference reflected a minor clinical effect. In our study, we failed to disclose an association for the period of 48 hours.
The kinetics of x-ray survival of mammalian cells in vitro.

SummaryThe shapes of the x-ray survival-curves of two tissue-cultured mammalian cell-lines have been studied, using machine methods for data fitting. It was found that the survival data fit a ‘multi-process’ cell-killing model better than the ‘single-process’ model proposed by other workers. In addition, the effects of the mode of plating and the time of irradiation were studied. Although both affect the sensitivity of the cells, no effect on the shapes of the survival-curves was demonstrated.
A mammalian factor that binds telomeric TTAGGG repeats in vitro

We have identified a DNA-binding activity with specificity for the TTAGGG repeat arrays found at mammalian telomeres. This factor, called TTAGGG repeat factor (TRF), is present in nuclear extracts of human, mouse, and monkey cells. TRF from HeLa cells was characterized in detail by electrophoretic mobility shift assays. It binds double-stranded TTAGGG repeats in linear and circular DNAs. Single-stranded repeats are not recognized. The optimal site for TRF appears to contain more than six contiguous TTAGGG repeats. Tandem arrays of TAGGG, TTTAGGG, TTTTAGGG, TTGGGG, and TTAGGC repeats do not bind TRF well, indicating that TRF preferentially recognizes the telomeric repeat sequence present at mammalian chromosome ends. The apparent molecular mass of this factor, based on recovery of TRF from sodium dodecyl sulfate-polyacrylamide gels, is approximately 50 kDa. We suggest that TRF binds along the length of mammalian telomeres.
Correlation of overall survival with gene expression profiles in a prospective study of resectable esophageal cancer.

PURPOSE Preoperative chemotherapy has demonstrated a survival benefit for patients with potentially resectable esophageal cancer; however, currently it is not possible to predict the benefit of this treatment for an individual patient. This prospective study was designed to correlate gene expression profiles with clinical outcome in this setting. PATIENTS AND METHODS Eligible patients were deemed to have resectable disease after staging by computed tomography, endoscopic ultrasound, and laparoscopy as indicated and following discussion at the multidisciplinary team meeting. All patients received neoadjuvant platinum and fluoropyrimidine-based chemotherapy; and clinical data were entered prospectively onto a study-specific database. Total RNA was isolated from pretreatment tumor biopsies obtained at baseline endoscopy and analyzed using a cDNA array consisting of 22,000 cDNA clones. RESULTS Of the patients with adequate follow-up accrued between 2002 and 2005, 35 satisfied the quality control measures for the microarray profiling. Median follow-up was 938 days. Supervised hierarchical clustering of normalized data revealed 165 significantly differentially expressed genes based on overall survival (OS; P < .01) with 2 distinct clusters: a poor outcome group: N = 17 (1 year OS 46.2%) and a good outcome group: N = 18 (1 year OS 100%). Genes identified included those previously associated with esophageal cancer and, interestingly, a group of genes encoding proteins involved in the regulation of the TOLL receptor-signaling pathway. CONCLUSION This initial study has highlighted groups of tumors with distinct gene expression profiles based on survival and warrants further validation in a larger cohort. This approach may further our understanding of individual tumor biology and thus facilitate the development of tailored treatment.
Serine 18 Phosphorylation of RAX, the PKR Activator, Is Required for PKR Activation and Consequent Translation Inhibition*

It is now apparent that the double-stranded (ds)RNA-dependent protein kinase, PKR, is a regulator of diverse cellular responses to stress. Recently, the murine dsRNA-binding protein RAX and its human ortholog PACT were identified as cellular activators of PKR. Previous reports demonstrate that following stress, RAX/PACT associates with and activates PKR resulting in eIF2α phosphorylation, consequent translation inhibition, and cell death via apoptosis. Although RAX/PACT is phosphorylated during stress, any regulatory role for this post-translational modification has been uncertain. Now we have discovered that RAX is phosphorylated on serine 18 in both human and mouse cells. The non-phosphorylatable form of RAX, RAX(S18A), although still able to bind dsRNA and associate with PKR, fails to activate PKR following stress. Furthermore, stable expression of RAX(S18A) results in a dominant-negative effect characterized by deficiency of eukaryotic initiation factor 2 α subunit phosphorylation, delay of translation inhibition, and failure to undergo rapid apoptosis following removal of interleukin-3. We propose that the ability of RAX to activate PKR is regulated by a sequential mechanism featuring RAX association with PKR, RAX phosphorylation at serine 18, and activation of PKR.
Multispectral Imaging Autofluorescence Microscopy for the Analysis of Lymph-Node Tissues

Abstract Although histochemical and immunohistochemical methods are the standard procedures in diagnosis of lymphoproliferative disorders, useful improvements in evidencing histopathologic manifestations can be obtained with the introduction of tissue autofluorescence analyses. We used microspectrofluorometry and a Multispectral Imaging Autofluorescence Microscopy (MIAM) technique to analyze lymph-node biopsies from patients with lymphoadenopathy of different origins. Images of tissue autofluorescence were obtained by excitation at 365 nm of lymph-node sections and sequential detection with interference filters (50 nm bandwidth) peaked at 450, 550 and 658 nm. Monochrome images were combined together in a single red–green–blue color image. Most of the fluorescence was observed within the blue spectral band because of large contributions from extracellular collagen and elastin fibers as well as from reduced form of intracellular nicotinamide adenine dinucleotide (phosphate). Autofluorescence imaging shows morphological differences between neoplastic and non-neoplastic tissues. The reactive hyperplasia samples show the typical lymph-node organization with weak fluorescent follicles separated by high fluorescent connective trabeculae. In the neoplastic lymph nodes the loss of follicle organization is observed. Consequently, MIAM permits to discriminate between non-neoplastic and neoplastic tissues on the basis of their autofluorescence pattern. Multispectral imaging of tissue autofluorescence may present some advantages with respect to standard histochemical microscopy since it (1) does not require any chemical manipulation of samples; (2) gives real-time results performing the analysis immediately upon specimen resection; and (3) supplies a representation of the biological structure organization linked to endogenous fluorophores.
Phenotypic spectrum associated with de novo mutations in QRICH1 gene

Rare de novo mutations represent a significant cause of idiopathic developmental delay (DD). The use of next‐generation sequencing (NGS) has boosted the identification of de novo mutations in an increasing number of novel genes. Here we present 3 unrelated children with de novo loss‐of‐function (LoF) mutations in QRICH1, diagnosed through trio‐based exome sequencing. QRICH1 encodes the glutamine‐rich protein 1, which contains 1 caspase activation recruitment domain and is likely to be involved in apoptosis and inflammation. All 3 children had speech delay, learning difficulties, a prominent nose and a thin upper lip. In addition, 2 of them had mildly raised creatine kinase (CK) and 1 of them had autism. Despite their small number, the patients had a relatively consistent pattern of clinical features suggesting the presence of a QRICH1‐associated phenotype. LoF mutations in QRICH1 are suggested as a novel cause of DD.
The Electrodermal Activity in Rats with Sleep Deprivation

Sleep deprivation causes a wide range of cognitive deficits like impairments in vigilance, memory and physiological processes. To our knowledge, few chronic sleep deprivation studies have related the possible electrodermal activity (EDA) changes that show sympathetic activation. In this study, we aimed to investigate the effects of a 21-days sleep deprivation on EDA and neurobehavioral changes in open field area. The study was occurred with young and young adult Wistar Albino rats in Physiology laboratoryof Erciyes University Medical Faculty. The rats were randomly divided in six groups in total as a sleep deprivation group, pedestal control group and cages control group, and three of aged-matched groups. The skin resistance levels (SRL) and skin resistance response (SRR) were significantly decreased in substantive level in young and young adults sleep deprivation groups according to control groups. In open field test evaluations in young and young adult sleep deprivation groups significant increase in the number of crossline, rear and defecation. Sleep deprivation caused a decline in the electrodermal activity due to giving rise to increase in sympathetic tonus and anxiety in young and young adult rats.
Integrative Analysis Workflow for Untargeted Metabolomics in Translational Research

Background: Metabolomics is an emerging ‘omics’ science that has demonstrated its fast gaining importance as a powerful profiling tool for determining an individual’s response to a foreign stimulus such as a drug, toxin, or environmental change; or as an indicator of disease progression. Such small molecule profiles can used as biological markers of disease, and provide an indicator of drug efficacy or toxicity.Several studies have demonstrated that the results of any single ‘omics’ analysis may not be sufficient to decode extremely complex biological mechanisms. Methods: We have developed a translational research workflow to enable researchers to perform cutting-edge integrative analysis of metabolomics data with transcriptomics (gene expression) data using knowledge-driven networks. This network based view of interconnected functional partners can provide valuable new insight about the underlying biochemical processes and pathways associated with the phenotype of interest. To enhance and simplify metabolomics annotation we built a fully cross-referenced database called MetPlus DB, which integrates data from the three most comprehensive metabolite databases tailored largely towards mammalian metabolomics: HMDB, HUAMNCYC, and LIPID MAPS.Cross-referencing information is provided for linking to several other mainstream cheminformatics/bioinformatics repositories including KEGG, METLIN, ChEBI, FooDB, Pubchem, and Chemspider to provide unambiguous knowledge on clinically and physiologically relevant metabolites. We have made the integrated database available freely to the research community (https://github.com/ICBI/MetPlus-DB). Results: To demonstrate the usefulness and strength of our methodology, we have tested it on a multi-omics profiling dataset from NCI-60 breast cancer cell lines to explore the biological dynamics of breast cancer. Conclusions: Our results demonstrate a streamlined approach for the comprehensive annotation of metabolites using MetPlus DB, and the subsequent integration of metabolomics and transcriptomics data to explore potentially relevant biological interactions and candidate biomarkers associated with disease phenotype.
Cytosolic Prion Protein (PrP) Is Not Toxic in N2a Cells and Primary Neurons Expressing Pathogenic PrP Mutations*

Inherited prion diseases are linked to mutations in the prion protein (PrP) gene, which favor conversion of PrP into a conformationally altered, pathogenic isoform. The cellular mechanism by which this process causes neurological dysfunction is unknown. It has been proposed that neuronal death can be triggered by accumulation of PrP in the cytosol because of impairment of proteasomal degradation of misfolded PrP molecules retrotranslocated from the endoplasmic reticulum (Ma, J., Wollmann, R., and Lindquist, S. (2002) Science 298, 1781–1785). To test whether this neurotoxic mechanism is operative in inherited prion diseases, we evaluated the effect of proteasome inhibitors on the viability of transfected N2a cells and primary neurons expressing mouse PrP homologues of the D178N and nine octapeptide mutations. We found that the inhibitors caused accumulation of an unglycosylated, aggregated form of PrP exclusively in transfected N2a expressing PrP from the cytomegalovirus promoter. This form contained an uncleaved signal peptide, indicating that it represented polypeptide chains that had failed to translocate into the ER lumen during synthesis, rather than retrogradely translocated PrP. Quantification of N2a viability in the presence of proteasome inhibitors demonstrated that accumulation of this form was not toxic. No evidence of cytosolic PrP was found in cerebellar granule neurons from transgenic mice expressing wild-type or mutant PrPs from the endogenous promoter, nor were these neurons more susceptible to proteasome inhibitor toxicity than neurons from PrP knock-out mice. Our analysis fails to confirm the previous observation that mislocation of PrP in the cytosol is neurotoxic, and argues against the hypothesis that perturbation of PrP metabolism through the proteasomal pathway plays a pathogenic role in prion diseases.
Cross-Domain Interference Costs during Concurrent Verbal and Spatial Serial Memory Tasks are Asymmetric

Some evidence suggests that memory for serial order is domain-general. Evidence also points to asymmetries in interference between verbal and visual–spatial tasks. We confirm that concurrently remembering verbal and spatial serial lists provokes substantial interference compared with remembering a single list, but we further investigate the impact of this interference throughout the serial position curve, where asymmetries are indeed apparent. A concurrent verbal order memory task affects spatial memory performance throughout the serial positions of the list, but performing a spatial order task affects memory for the verbal serial list only for early list items; in the verbal task only, the final items are unaffected by a concurrent task. Adding suffixes eliminates this asymmetry, resulting in impairment throughout the list for both tasks. These results suggest that domain-general working memory resources may be supplemented with resources specific to the verbal domain, but perhaps not with equivalent spatial resources.
The Effect of Sunlight on Postoperative Analgesic Medication Use: A Prospective Study of Patients Undergoing Spinal Surgery

Objective: Exposure to natural sunlight has been associated with improvement in mood, reduced mortality among patients with cancer, and reduced length of hospitalization for patients who have experienced myocardial infarction. Our aim was to evaluate whether the amount of sunlight in a hospital room modifies a patient’s psychosocial health, the quantity of analgesic medication used, and the pain medication cost. Methods: A prospective study of pain medication use was conducted in 89 patients undergoing elective cervical and lumbar spinal surgery where they were housed on either the “bright” or “dim” side of the same hospital unit. Analgesic medication was converted to standard morphine equivalents for interpatient comparison. The intensity of sunlight in each hospital room was measured daily and psychologic questionnaires were administered on the day after surgery and at discharge. Results: Patients staying on the bright side of the hospital unit were exposed to 46% higher-intensity sunlight on average (p = .005). Patients exposed to an increased intensity of sunlight experienced less perceived stress (p = .035), marginally less pain (p = .058), took 22% less analgesic medication per hour (p = .047), and had 21% less pain medication costs (p = .047). Age quartile was the only other variable found to be a predictor of analgesic use, with a significant negative correlation (p <.001). However, patients housed on the bright side of the hospital consistently used less analgesic medications in all age quartiles. Conclusion: The exposure postoperatively of patients who have undergone spinal surgery to increased amounts of natural sunlight during their hospital recovery period may result in decreased stress, pain, analgesic medication use, and pain medication costs. ACCF = anterior cervical corpectomy and fusion; ACDF = anterior cervical discectomy and fusion; AEDET = Achieving Excellence Design Evaluation Toolkit; CES-D = Center for Epidemiological Studies–Depression Scale; CNS = central nervous system; DS = degenerative spondylolisthesis; LOS = length of stay; LOT-R = Life Orientation Test-Revised; LS = lumbar stenosis; MPQ = McGill Pain Questionnaire; OR = operating room; PACU = postanesthesia care unit; PCA = patient-controlled analgesia; PFI = Private Finance Initiative; POMS = Reduced POMS–Anxiety Scale; PRN = as needed; PSS = Perceived Stress Scale; SAD = seasonal affective disorder; TCAs = tricyclic antidepressants; UK = United Kingdom.
Soil-surface CO2 flux and growth in a boreal Norway spruce stand

Global warming is predicted to affect the carbon balance of forests. A change in the carbon balance would give a positive or negative feedback to the greenhouse effect, which would affect global warming. The effects of long-term soil warming on growth, nutrient and soil-surface CO2 flux (R) dynamics were studied in irrigated (I) and irrigated-fertilised (IL) stands of Norway spruce in northern Sweden. Soil temperature on heated plots (Ih and ILh) was maintained 5 oC above that on unheated plots (Ic and ILc) from May to October, by heating cables. After six years' soil warming, stemwood production increased by 100% and 50% in the I and IL treatment, respectively. The main production increase occurred at the beginning of the season, probably as an effect of the earlier increase in soil temperature. In the Ih treatment, however, the growth increase was evident during the entire season. The effect of increased nitrogen (N), mineralisation on annual growth appeared to be stronger than the direct effect of warming. From 1995−2000, the total amount of N stored in aboveground tree parts increased by 100 and 475 kg N ha-1 on Ic and ILc plots, respectively. During the same period, 450 kg N fertiliser was added to the ILc plot. Soil warming increased the total amount of N stored in aboveground tree parts by 50 kg N ha-1, independently of nutrient treatment. Soil warming did not significantly increase R, except in early spring, when R was 30−50% higher on heated compared to unheated plots. The extended growing season, however, increased annual respiration (RA) by 12−30% throughout. RA losses were estimated to be 0.6−0.7 kg C ha-1 a-1. Use of relationships between R and soil temperature, derived from unheated plots, overestimated RA on heated plots by 50−80%. These results suggest that acclimation of root or microbial respiration or both to temperature had occurred, but the exact process(es) and their relative contribution are still unclear. In conclusion, the study showed that soil warming stimulated tree growth, but resulted in only a minor increase of annual R, suggesting an increased carbon sink for boreal forests in a warmer climate.
Selection of knowledge acquisition techniques based upon the problem domain characteristics of production and operations management expert systems

The application of expert systems to various problem domains in business has grown steadily since their introduction. Regardless of the chosen method of development, the most commonly cited problems in developing these systems are the unavailability of both the experts and knowledge engineers and difficulties with the process of acquiring knowledge from domain experts. Within the field of artificial intelligence, this has been called the ‘knowledge acquisition’ problem and has been identified as the greatest bottleneck in the expert system development process. Simply stated, the problem is how to acquire the specific knowledge for a well‐defined problem domain efficiently from one or more experts and represent it in the appropriate computer format. Given the ‘paradox of expertise’, the experts have often proceduralized their knowledge to the point that they have difficulty in explaining exactly what they know and how they know it. However, empirical research in the field of expert systems reveals that certain knowledge acquisition techniques are significantly more efficient than others in helping to extract certain types of knowledge within specific problem domains. In this paper we present a mapping between these empirical studies and a generic taxonomy of expert system problem domains. In so doing, certain knowledge acquisition techniques can be prescribed based on the problem domain characteristics. With the production and operations management (P/OM) field as the pilot area for the current study, we first examine the range of problem domains and suggest a mapping of P/OM tasks to a generic taxonomy of problem domains. We then describe the most prominent knowledge acquisition techniques. Based on the examination of the existing empirical knowledge acquisition research, we present how the empirical work can be used to provide guidance to developers of expert systems in the field of P/OM.