Miracle-dz/UniFAR-FTUs huggingface dataset:
Eukaryotic Wobble Uridine Modifications Promote a Functionally Redundant Decoding System

ABSTRACT The translational decoding properties of tRNAs are modulated by naturally occurring modifications of their nucleosides. Uridines located at the wobble position (nucleoside 34 [U34]) in eukaryotic cytoplasmic tRNAs often harbor a 5-methoxycarbonylmethyl (mcm5) or a 5-carbamoylmethyl (ncm5) side chain and sometimes an additional 2-thio (s2) or 2′-O-methyl group. Although a variety of models explaining the role of these modifications have been put forth, their in vivo functions have not been defined. In this study, we utilized recently characterized modification-deficient Saccharomyces cerevisiae cells to test the wobble rules in vivo. We show that mcm5 and ncm5 side chains promote decoding of G-ending codons and that concurrent mcm5 and s2 groups improve reading of both A- and G-ending codons. Moreover, the observation that the mcm5U34- and some ncm5U34-containing tRNAs efficiently read G-ending codons challenges the notion that eukaryotes do not use U-G wobbling.
Adult Outcomes of Patients with Juvenile Idiopathic Arthritis

Background: Knowledge of the long-term outcomes of patients with juvenile idiopathic arthritis (JIA) has evolved during the past decade. Recent studies, using standardized classification criteria, new and reliable outcome measures and improved methods of statistical analyses, show that outcomes are still less than ideal. Approximately half of all young adults with JIA have ongoing active disease and over one third experience detectable degrees of disability and organ damage. These patients also show a distinctive pattern of growth disturbances. Most patients with general growth failure have systemic or polyarticular disease: significant short stature (final height standard deviation score <–2) has been noted in 41% of patients with systemic JIA and in 11% of patients with polyarticular JIA. In contrast, localized growth disturbances can be seen in patients with oligoarthritis. Conclusions: Despite its name, JIA can be a lifelong disorder. With early and more widespread use of biological and other innovative therapies, however, outcomes for patients with JIA should improve further.
West Nile Virus and High Death Rate in American Crows

We document effects of West Nile virus (WNV) on American Crows. More than two thirds of our crows died of WNV infection, peaking when the proportion of infected mosquitoes at roosts was greatest. WNV antibody prevalence in crows was low. Local ecologic effects can be dramatic as WNV inhabits new areas.
FACTORES CLAVE PARA LA BÚSQUEDA DEL APRENDIZAJE ORGANIZACIONAL EN LA CADENA DE SUMINISTRO: UNA APROXIMACIÓN TEÓRICA

Given the significant role played by subcontracting in recent years and the rise of supply chains, manage them efficiently is a key factor to consider for improving business performance. A good relationship with customers / suppliers increases the flow of communication and information between them, allowing them to learn from each other, making and organizational learning have come to obtain a cooperative advantage that is beneficial to both. However, despite being many advantages of this relationship, companies are reluctant to share information about your organization, meeting the controversy of losing control and protection of your organization. The objectives of this work are to analyze the influence of organizational learning within the supply chain because it improves the situation of the company, not only in terms of reducing costs but also optimize performance, consider some of the variables that influence this learning and suggest several proposals, laying the groundwork for future research.
Circadian variation of sleep during the follicular and luteal phases of the menstrual cycle.

STUDY OBJECTIVES Women experience insomnia more frequently than men. Menstrual cycle changes in reproductive hormones and circadian rhythms may contribute to sleep disruptions. Our aim, therefore, was to clarify the interaction between menstrual and circadian processes as it affects sleep. DESIGN Participants entered the laboratory during the mid-follicular (MF) and mid-luteal (ML) phases of their menstrual cycle for an ultra-rapid sleep-wake cycle (URSW) procedure, consisting of 36 cycles of 60-min wake episodes alternating with 60-min nap opportunities. This procedure concluded with an ad libitum nap episode. SETTING Time-isolation suite. PARTICIPANTS Eight unmedicated, physically and mentally healthy females with regular ovulatory menstrual cycles. INTERVENTIONS N/A. MEASUREMENTS Polysomnographic sleep from nocturnal sleep episodes and 60-min naps; subjective alertness; core body temperature (CBT); salivary melatonin; urinary estradiol; and urinary progesterone. RESULTS Increased CBT values at night and decreased CBT amplitude were observed during ML compared to MF. Circadian phase of CBT and the circadian melatonin profile were unaffected by menstrual phase. All analyzed sleep parameters showed a circadian variation throughout the URSW procedure, with no menstrual phase differences observed for most, including slow wave sleep (SWS). The circadian variation of REM sleep duration, however, was sensitive to menstrual phase, with reduced REM sleep during ML at circadian phase 0 degrees and 30 degrees. CONCLUSIONS Moderate but significant changes in REM sleep across the menstrual and circadian cycles were observed. These results support an interaction between circadian and menstrual processes in the regulation of REM sleep.
Understanding schizophrenia.

whatever route; in 1970 most doses would probably have been by injection. In the second study they distinguished between oral and intramuscular vitamin K. Only injected vitamin K was found to be significantly associated with cancer. This may be a dose effect. The preparation used is Konakion, which is phytomenadione (vitamin K,) in a vehicle of polyethoxylated castor oil, propylene glycol, and phenol. Though it was designed for intramuscular injection, it is also given orally in the United Kingdom. After a single injection blood concentrations in the newborn reach peak values at 12 hours of 350-1900 ng/l, while after a single oral dose the peak is reached at four hours and ranges from 20 to 330 ng/l.4 Vitamin K given orally is not as effective as injected vitamin K in preventing late onset haemorrhagic disease caused by vitamin K deficiency. It is breast fed infants who suffer from bleeding caused by vitamin K deficiency; the condition is rare in formula fed infants. Most infant formulas are now fortified with vitamin K, but even before they were they were reported to be protective. There is no evidence that formula fed babies are more likely to develop cancer than those who are breast fed. In the first 30 days of life infants fed on formula may receive as much as 1-5 mg of vitamin K, whereas breast fed infants receive a tenth of that amount.6 While we await confirmation or otherwise of the association between vitamin K and childhood cancer it seems reasonable to develop a programme of oral administration for all infants at birth, followed by vitamin K supplementation of breast fed infants over subsequent weeks. When the oral route is not available a small dose (100 Mtg) could be given by injection. There are, however, problems with the products available, and the British Paediatric Association and the Department of Health recently convened a meeting of experts to consider the issues in detail and make recommendations. Vitamin K is given to prevent haemorrhagic disease of the newborn (which occurs in infants aged up to 7 days) and late onset bleeding due to vitamin K deficiency (which occurs from 7 days to 6 months). Late onset bleeding is rare (4 to 8 cases per 100 000),7 but 30-50% of those affected die or are left with severe brain damage. This is certain; the risk of cancer is not. Before we change our practice we must be confident that any programme of oral administration will be as effective as injected vitamin K and that all infants who need it will receive it.
The direct and indirect costs among U.S. privately insured employees with hypogonadism.

INTRODUCTION While previous studies have noted that hypogonadism (HG) may pose a significant economic and quality-of-life burden, no studies have evaluated the impact of HG on healthcare utilization and costs in the United States. AIM Compare direct (health care) and indirect (disability leave or medical absence) costs between privately insured U.S. employees with HG and controls without HG. METHODS The study sample included 4,269 male employees, ages 35-64, with ≥ 2 HG diagnoses (International Classification of Diseases, Ninth Revision, Clinical Modification: 257.2x) or ≥ 1 HG diagnosis and ≥ 1 claim for testosterone therapy, 1/1/2005-3/31/2009, identified from a large, private insurance administrative database that includes medical, prescription drug, and disability claims data. The index date was the most recent HG diagnosis that had continuous eligibility for at least 1 year before (baseline period) and 1 year after (study period). Employees with HG were matched 1:1 on age, region, salaried vs. nonsalaried employment status, and index year to controls without HG. MAIN OUTCOME MEASURES Descriptive analyses compared demographic characteristics, comorbidities, resource utilization, direct and indirect costs inflated to USD 2009. Multivariate analyses adjusting for baseline characteristics were used to estimate risk-adjusted costs. RESULTS HG employees and controls had a mean age of 51 years. HG employees compared with controls had higher baseline comorbidity rates, including hyperlipidemia (50.2% vs. 25.3%), hypertension (37.7% vs. 21.1%), back/neck pain (32.0% vs. 15.7%), and human immunodeficiency virus/acquired immunodeficiency syndrome (7.1% vs. 0.3%) (all P < 0.0001). HG employees had higher mean study period direct ($10,914 vs. $3,823) and indirect costs ($3,204 vs. $1,450); HG-related direct costs were $832 (all P < 0.0001). Risk-adjusted direct ($9,291 vs. $5,248) and indirect ($2,729 vs. $1,840) costs were also higher for HG employees (all P < 0.0001). CONCLUSIONS Employees with HG had higher comorbidity rates and costs compared with controls. Given the low HG-related costs, a primary driver of costs among HG patients appears to be their comorbidity burden.
P85: a gag-mos Polyprotein Encoded by ts110 Moloney Murine Sarcoma Virus

Antibody to a synthetic peptide (anti-C3 serum) with the predicted sequence of the C terminus of the Moloney murine sarcoma virus (strain 124) v-mos gene was used in immunoprecipitation experiments with cytoplasmic extracts of a clone of NRK cells infected with ts110 Moloney murine sarcoma virus, termed 6m2 cells. ts110 Moloney murine sarcoma virus codes for two viral proteins of 85,000 and 58,000 Mr, termed P85 and P58, respectively, in nonproducer 6m2 cells maintained at 33°C. Anti-C3 serum specifically recognized [3H]leucine-labeled P85, but not P58, from infected cells maintained at 33°C, whereas antiserum prepared against murine leukemia virus p12 recognized both proteins. Normal serum and anti-C3 serum pretreated with excess C3 peptide did not precipitate P85. Immunoprecipitation experiments after metabolic labeling of 6m2 cells with 32Pi showed that P85 is phosphorylated. Both anti-C3 and anti-p12 sera specifically detected 32P-labeled P85. Cell-free translation of ts110 murine sarcoma virus/murine lukemia virus RNA produces P85, P58, and helper virus protein Pr63gag. Anti-C3 serum specifically precipitated P85 but neither P58 nor Pr63gag. We conclude from these studies that P85 is a product of both the gag and mos genes of ts110 murine sarcoma virus, and, therefore, it is referred to as P85gag-mos. We have not detected any other v-mos gene product in ts110-infected cells.
Generalized LDPC codes and generalized stopping sets

A generalized low-density parity check code (GLDPC) is a low-density parity check code in which the constraint nodes of the code graph are block codes, rather than single parity checks. In this paper, we study GLDPC codes which have BCH or Reed-Solomon codes as subcodes under bounded distance decoding (BDD). The performance of the proposed scheme is investigated in the limit case of an infinite length (cycle free) code used over a binary erasure channel (BEC) and the corresponding thresholds for iterative decoding are derived. The performance of the proposed scheme for finite code lengths over a BEC is investigated as well. Structures responsible for decoding failures are defined and a theoretical analysis over the ensemble of GLDPC codes which yields exact bit and block error rates of the ensemble average is derived. Unfortunately this study shows that GLDPC codes do not compare favorably with their LDPC counterpart over the BEC. Fortunately, it is also shown that under certain conditions, objects identified in the analysis of GLDPC codes over a BEC and the corresponding theoretical results remain useful to derive tight lower bounds on the performance of GLDPC codes over a binary symmetric channel (BSC). Simulation results show that the proposed method yields competitive performance with a good decoding complexity trade-off for the BSC.
Overestimation of the lipoprotein fractional catabolic rate (FCR) measured in short duration experiments.

The aim of the study was to compare two methods classically used in rats to determine the fractional catabolic rate (FCR) of labeled high or low density lipoproteins: constant infusion and single pulse. The FC of [14C]-sucrose HDL (High density lipoprotein) was studied. For the short term experiment (8 hours), both methods gave similar FCR determined 8 hours after HDL constant infusion (9.4%.h-1 +/- 0.6) or single pulse (8.5%.h-1 +/- 0.4), values significantly higher than those measured 24 hr after the single pulse (6.2%.h-1 +/- 0.3). The identification and simulation of the model representing HDL movements between an intravascular and extravascular pool, after single pulse and constant infusion methods, demonstrated that FCR of lipoproteins cannot be precisely measured with techniques involving excessively short observation periods.
Semipermeable membrane device–assisted desorption of pyrene from soils and its relationship to bioavailability

Desorption of pyrene from three different soils was studied using a semipermeable membrane device (SPMD)–assisted method to develop a new approach to predict bioavailability of hydrophobic organic compounds (HOCs) in soils. The results showed that pyrene desorption increased with reduction of soil organic matter content and elevation of pyrene concentration in unaged soils, and the 50‐d desorption percentage was 52.2 ± 3.6%, 76.3 ± 1.5%, and 99.4 ± 3.3% for soils 1, 2, and 3, respectively, at an initial pyrene concentration of 10 mg/kg and 73.6 ± 4.9%, 94.1 ± 4.1%, and 98.3 ± 4.9%, respectively, at an initial pyrene concentration of 100 mg/kg. Aging led to a reduction in SPMD–assisted desorption because of movement of pyrene molecules from easy‐desorbing to difficult‐desorbing sites. The pyrene 50‐d desorption percentage from 180‐d–aged soils reduced to 5.8 ± 0.6%, 18.8 ± 0.9%, and 34.2 ± 3.1% in soils 1, 2, and 3, respectively, at an initial pyrene concentration of 10 mg/kg and 43.9 ± 2.9%, 54.3 ± 4.7%, and 86.3 ± 3.5%, respectively, at an initial pyrene concentration of 100 mg/kg. Dry and wet conditions during aging had different effects on aging‐derived reduction of pyrene desorption, which was found, to our knowledge for the first time, to depend on pollutant concentration. The water to soil ratio during desorption had a significant effect on SPMD–assisted desorption dynamics. When this ratio changed from 10:1 to 1:1, desorption dynamics became more linear and slower, because when the ratio was low, the SPMD could not contact with soil particles well and the diffusion of pyrene from pore water into the SPMD might become the limiting step for SPMD accumulation of pyrene from soils. Good correlations were found between SPMD–assisted desorption and the biota–soil accumulation factor for both unaged and aged soils. The SPMD–assisted desorption is considered to be a reliable approach to predict the bioavailability of HOCs in soils.
Positive effect of IGF‐1 injection on gastrocnemius of rat during distraction osteogenesis

Distraction osteogenesis (DO) is used to form new bone between bone segments to lengthen the callus. Skeletal muscles frequently fail to adapt to distraction, which causes complications. Insulin‐like growth factor‐1 (IGF‐1) has been implicated as a central regulator of muscle repair. We hypothesized that IGF‐1 injection could reduce muscle complications in DO. A total of 102 Sprague‐Dawley rats received DO or did not were randomly assigned into saline, IGF‐1 and normal groups. On the day before the distraction, the rats in the IGF‐1 group were injected with IGF‐1. The gastrocnemius muscles of the rats were harvested at the 0, 1st, 4th, 7th, and 10th days of distraction. The weight of the muscles, cross‐sectional area (CSA) of the muscle fibers, collagen volume fraction (CVF), maximum limit load (MLL), maximum contraction forces, and gene expression of Akt, MyoD, myogenin, myostatin, and collagen I were analyzed. The results indicated that IGF‐1 injection had increased the weights, CSA of the muscle fibers, MLL and force generation of the gastrocnemius. Also, Akt, MyoD, and myogenin were upregulated, and myostatin was downregulated in the IGF‐1 group. Injection of IGF‐1 could attenuate the gastrocnemius atrophy, prevent fibrosis, increase MLL, and regulate the related mRNA. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:1424–1432, 2015.
Chinese alcoholic patients with esophageal cancer are genetically different from alcoholics with acute pancreatitis and liver cirrhosis

OBJECTIVE:It is a mystery why some alcoholic patients acquire certain organ-specific complications of alcoholism, whereas other alcoholic patients acquire different ones. The aim of this study was to investigate the differences among Chinese alcoholic patients with esophageal cancer, acute pancreatitis, and liver cirrhosis by studying the genetic polymorphisms of ADH2, ADH3, ALDH2, and P4502E1.METHODS:Liver alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), and cytochrome P4502E1 (P4502E1) are polymorphic at the ADH2, ADH3, and ALDH2 loci and the 5′-flanking region of the P4502E1. Using the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method, we determined the polymorphism of the above-mentioned alcohol metabolizing genes in 59 alcoholics with carcinoma of the esophagus (alcoholic esophageal Ca), 87 acute alcoholic pancreatitis patients, 116 alcoholics with liver cirrhosis (alcoholic cirrhosis), 19 alcoholics with both liver cirrhosis and acute pancreatitis (alcoholic P plus C), and 241 nonalcoholic patients.RESULTS:The results showed that the allele frequency of ALDH2*2 was significantly higher in the alcoholic esophageal Ca group than in the alcoholic pancreatitis and alcoholic cirrhosis groups. The allele frequency of ADH2*1 was significantly higher in the alcoholic esophageal Ca patients than in nonalcoholic control groups. The ALDH2*2 was significantly lower in alcoholic groups (except the alcoholic esophageal Ca group) than in nonalcoholic control groups. The allele frequencies of ADH2*1 and ALDH2*2 are higher in alcoholic patients with esophageal Ca than alcoholic patients without it. The genotype distribution of P4502E1, detected by RsaI and PstI, was not different among alcoholic patients with different organ diseases.CONCLUSIONS:The allele frequency of ADH2*1 and ALDH2*1 are different among subpopulations of alcoholics, suggesting that alcoholic patients with different specific types of organ damage are genetically different. The Chinese alcoholic patients with the ADH2*1 and ALDH2*2 allele are more susceptible to esophageal Ca.
SELDI-TOF-MS ProteinChip array profiling of tears from patients with dry eye.

PURPOSE Protein and peptides in tears play an important role in ocular surface diseases. In previous studies, changes have been demonstrated in the electrophoretic protein profiles of patients with dry eye. The purpose of this work was to determine the usefulness of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) ProteinChip Array (Ciphergen Biosystems, Inc., Fremont, CA) technology for the automated analysis of proteins and peptides in tear fluid. METHODS Patients with dry eye (DRY, n = 88) and healthy subjects (CTRL, n = 71) were examined. Their tear proteins were analyzed using SELDI-TOF-MS ProteinChip Arrays with three different chromatographic surfaces (CM10 cation exchange, Q10 anion exchange, and H50 reversed-phase) prepared by means of a laboratory liquid-handling robotic workstation. The data were analyzed by multivariate statistical techniques and artificial neural networks, and the most important biomarkers were purified and identified by tandem MS. RESULTS Complex patterns of tear proteins and peptides were detected. The different chromatographic surfaces revealed the selective enrichment of proteins such as lipocalin and lysozyme. Discriminant analysis demonstrated highly significant changes in the protein profiles in patients with dry eye (P < 0.001). With a seven-peptide multimarker panel, an artificial neural network could differentiate between patients with dry eye and healthy individuals with a specificity and sensitivity of 90%. The identification of biomarkers revealed an increase of inflammatory markers in patients with dry eye and a decrease of some proteins that may have protective functions. CONCLUSIONS The SELDI-TOF-MS technology seems to be ideally suitable for the mass screening of peptides and proteins in tears. This highly sensitive approach dramatically reduces the analysis time and provides protein profiles with great mass accuracy. Thus, it may become a very useful tool in the search for potential biomarkers for diagnosis and new therapeutics in ocular diseases such as dry eye.
Complete Genome Sequences of Edwardsiella tarda-Lytic Bacteriophages KF-1 and IW-1

ABSTRACT We report the complete genome sequences of two Edwardsiella tarda-lytic bacteriophages isolated from flounder kidney (KF-1) and seawater (IW-1). These newly sequenced phage genomes provide a novel resource for future studies on phage-host interaction mechanisms and various applications of the phages for control of edwardsiellosis in aquaculture.
Disruption of the PP1/GADD34 complex induces calreticulin exposure

In response to some chemotherapeutic agents, tumor cells can translocate calreticulin (CRT), which is usually contained in the lumen of the endoplasmic reticulum, to the surface of the plasma membrane. This effect requires the phosphorylation of the eukaryotic initiation factor 2a (eIF2a) by the eIF2a kinase PERK, yet may also be triggered by inhibition of the eIF2a phosphatase, which is composed by a catalytic subunit (PP1) and a regulatory subunit (GADD34). Here, we addressed the question whether the dissociation of the PP1/GADD34 complex would be sufficient to trigger CRT exposure. Molecular modeling led to the design of a GADD34-derived peptide that competitively disrupts the PP1/GADD34 complex. When added to intact cells, the GADD34-derived peptide fused to a plasma membrane translocation domain abolished the interaction between PP1 and GADD34, stimulated the phosphorylation of eIF2a, and triggered CRT exposure. However, the resolution of the PP1/GADD34 complex did not evoke apoptosis, allowing for the dissociation of CRT exposure and cell death. Anthracyclins, which are highly efficient in inducing CRT translocation to the cell surface also stimulated the dissociation of the PP1/GADD34 complex. These results suggest that the PP1/GADD34 complex plays a major role in the regulation of CRT exposure.