Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered expression of goblet cell‐ and mucin glycosylation‐related genes in the intestinal epithelium during infection with the nematode Nippostrongylus brasiliensis in rat

Intestinal nematode infection induces marked goblet cell hyperplasia and mucus secretion, but the mechanisms of regulation of the changes still remain to be elucidated. In the present study, epithelial cells were isolated from the rat small intestine at various times after Nippostrongylus brasiliensis infection, and the levels of expression of goblet cell‐ and mucin glycosylation‐related genes were estimated by semi‐quantitative reverse transcription (RT)‐PCR. Among the genes investigated, mucin core peptide (MUC) 2, sialyltransferase (Siat) 4c and trefoil factor family (TFF) 3 were upregulated as early as 2–4 days post‐infection, suggesting that they are associated with an early innate protective response. Seven days post‐infection and thereafter, when the nematodes reached maturity, significant upregulation of MUC3, MUC4, resistin‐like molecule β (Relmβ) and 3O‐sulfotransferase (3ST)1 was observed, while 3ST2 expression levels increased after the majority of the worms were expelled from the intestine. Similar alterations of glycosylation‐related gene expression were also observed in mast‐cell‐deficient Ws/Ws rats, suggesting that mast cells in the epithelium are not relevant to the upregulation of these genes. The present finding that the expression level of each goblet cell‐ or glycosylation‐related gene was altered differently during the time course of infection indicates the progression of sequential qualitative changes in the mucus layer after infection.
AVPR1A and SLC6A4 Polymorphisms in Choral Singers and Non-Musicians: A Gene Association Study

Amateur choral singing is a common pastime and worthy of study, possibly conferring benefits to health and social behaviour. Participants might be expected to possess musical ability and share some behavioural characteristics. Polymorphisms in genes concerned with serotonergic neurotransmission are associated with both behaviour and musical aptitude. Those investigated previously include the variable number tandem repeats RS1, RS3 and AVR in the AVPR1A (arginine vasopressin receptor 1a) gene and STin2 in the SLC6A4 (solute carrier family 6 [neurotransmitter transporter, serotonin], member 4) gene, as well as the SLC6A4 promoter region polymorphism, 5-HTTLPR. We conducted a genetic association study on 523 participants to establish whether alleles at these polymorphisms occur more commonly in choral singers than in those not regularly participating in organised musical activity (non-musicians). We also analysed tagging single nucleotide polymorphisms (SNPs) for AVPR1A and SLC6A4 to determine whether other variants in these genes were associated with singer/non-musician status. At the STin2 polymorphism, overall association with singer/non-musician status was evident at P = 0.006. The 9-repeat (P = 0.04) and 12-repeat (P = 0.04) alleles were more common in singers and the 10-repeat allele less so (P = 0.009). Odds ratios were 0.73 (95% CI 0.57–0.94) for the 10-repeat allele and 2.47 (95% CI 0.88–6.94) for the rarer 9-repeat allele. No overall association was detected at P<0.05 between any other polymorphism and singer/non-musician status. Our null findings with respect to RS3, RS1 and AVR, polymorphisms associated with musical ability by other authors, suggest that choir membership may depend partly on factors other than musical ability. In a related musical project involving one participating choir, a new 40-part unaccompanied choral work, “Allele”, was composed and broadcast on national radio. In the piece, each singer's part incorporated their personal RS3 genotype.
Plasma Extracellular Vesicles Enriched for Neuronal Origin: A Potential Window into Brain Pathologic Processes

Our team has been a pioneer in harvesting extracellular vesicles (EVs) enriched for neuronal origin from peripheral blood and using them as a biomarker discovery platform for neurological disorders. This methodology has demonstrated excellent diagnostic and predictive performance for Alzheimer's and other neurodegenerative diseases in multiple studies, providing a strong proof of concept for this approach. Here, we describe our methodology in detail and offer further evidence that isolated EVs are enriched for neuronal origin. In addition, we present evidence that EVs enriched for neuronal origin represent a more sensitive and accurate base for biomarkers than plasma, serum, or non-enriched total plasma EVs. Finally, we proceed to investigate the protein content of EVs enriched for neuronal origin and compare it with other relevant enriched and non-enriched populations of plasma EVs. Neuronal-origin enriched plasma EVs contain higher levels of signaling molecules of great interest for cellular metabolism, survival, and repair, which may be useful as biomarkers and to follow response to therapeutic interventions in a mechanism-specific manner.
Eliciting Societal Preferences for Weighting QALYs for Burden of Illness and End of Life

Objectives . Recent proposals for value-based assessment, made by the National Institute of Health and Care Excellence (NICE) in the United Kingdom, recommended that burden of illness (BOI) should replace end of life (EOL) as a factor for consideration when deciding on new health technologies. This article reports on a study eliciting societal preferences for 1) BOI from a medical condition, defined as quality-adjusted life year (QALY) loss due to premature mortality and prospective morbidity, and 2) EOL, defined as expected life expectancy of less than 2 years and expected life expectancy gain from new treatment of 3 months or more. Methods . A discrete choice experiment survey was conducted with an online UK general population sample. Respondents chose whether they thought the health service should treat patient group A or B: life expectancy and health-related quality of life (HRQOL) with current treatment or life expectancy and HRQOL gains from new treatment, respectively. These attributes were used to derive BOI, QALY gain, and EOL. The respondents’ choices were analyzed using conditional logistic regression with a range of specifications examined, including BOI or EOL, QALY gain and QALY gain squared, and robustness. QALY weights were estimated. Results . The sample of 3669 respondents was representative of the UK population for age and sex. QALY gain had a positive and significant coefficient across all models. QALY gain squared term was negative and significant across all models, indicating a diminishing marginal social value from QALY gains. When included, the BOI coefficient was generally small, positive, and significant, but this was not consistent across the different life expectancy variants. EOL was always positive and significant. Conclusions . The social value of a QALY gain is not equal between recipients but depends on whether they are end of life, and it may depend on the prospective burden of illness.
The expression of plakoglobin is a potential prognostic biomarker for patients with surgically resected lung adenocarcinoma

Purpose This study aimed to explore the relationship between plakoglobin expression and clinical data in the patients with surgically resected lung adenocarcinoma. Results With follow-up of median 50.14 months, the average PFS and OS were 16.82 and 57.92 months, respectively. In 147 patients, recurrence or death was observed in 131 patients. According to the log-rank test, low plakoglobin expression was a significant predictor for favorable DFS (P=0.006) and OS (P=0.043). For the analyses within subgroups, high plakoglobin expression was an independent factor for reducing DFS in non-metastatic patients with resected lung adenocarcinoma (P < 0.05). Moreover, high plakoglobin expression was associated with poor DFS even receiving adjuvant chemotherapy (P =0.028) and with a shorter DFS (HR, 2.01, 95%CIs, 1.35 to 2.97, P=0.001) and OS (HR, 1.94, 95%CIs, 1.12 to 3.37, P=0.019). Patients and methods The expression of plakoglobin in 147 primary tumor tissues was examined by using immunohistochemistry and clinical data were collected. The optimal cutoff value of immunoreactivity score (IRS) was calculated and used to divide all the patients into two groups: low-level group (IRS: 0-3, n=59) and high-level group (IRS: 4-12, n=88). Kaplan–Meier curves were applied to assess the plakoglobin expression and clinical variables. The univariate and multivariate Cox model analyses were performed to evaluate the effects of clinical factors and plakoglobin expression on disease-free survival (DFS) and overall survival (OS). Conclusion High plakoglobin expression is an independent negative prognostic factor for patients with surgically resected lung adenocarcinoma.
Ultrasound guided cytological aspiration of supraclavicular lymph nodes in patients with suspected lung cancer

Background: Lung cancer is the leading cause of death from cancer in the UK. Pathological diagnosis traditionally requires invasive procedures such as bronchoscopy, mediastinoscopy, or image guided biopsy. Ultrasound of the neck with fine needle aspiration cytology (FNAC) of enlarged but impalpable supraclavicular nodes has been used in patients with suspected lung cancer who have N2 or N3 disease on staging computed tomography (CT). If positive, this technique helps to both stage the patient and provide a cytological diagnosis. Methods: 101 patients were enrolled prospectively over a 1 year period. FNAC was performed on all supraclavicular nodes over 5 mm in size using the capillary aspiration technique. Results: Sixty one of the 101 patients had enlarged supraclavicular nodes and underwent FNAC. The overall malignant yield was 45.5% of patients scanned and 75.4% of patients sampled. As a result of FNAC, 43 patients (42.6%) avoided more invasive procedures. Conclusion: Ultrasound guided FNAC is a promising, relatively non-invasive technique for the staging and diagnosis of patients with lung cancer.
The French Organ Transplant Data System

The Agence de la Biomédecine is a state agency dealing with Public Health issues related, among others, to organ, tissue and cell transplantation in France. The Agence maintains a national information system used to coordinate and administer organ procurement and transplant activities and to perform the evaluation of organ transplantation activities. This paper describes the core uses and functional requirements of Cristal, the donor, recipient and allocation software of the information system and its evolution in the new system.
Subversion and Utilization of Host Innate Defense by Leishmania amazonensis

Infection with Leishmania amazonensis and other members of the Leishmania mexicana complex can lead to diverse clinical manifestations, some of which are relatively difficult to control, even with standard chemotherapy. Diffuse cutaneous leishmaniasis (CL) is a rare but severe form, and its clinical hallmark is excessive parasitic growth in infected cells accompanied by profound impairments in host immune responses to the parasites. Since these parasites also cause non-healing CL in most inbred strains of mice, these animals are valuable models for dissecting the mechanisms of persistent infection and disease pathogenesis. In comparison to other Leishmania species, L. amazonensis infections are most remarkable for their ability to repress the activation and effector functions of macrophages, dendritic cells, and CD4+ T cells, implying discrete mechanisms at work. In addition to this multilateral suppression of host innate and adaptive immunity, the activation of types I and II interferon-mediated responses and autophagic/lipid metabolic pathways actually promotes rather than restrains L. amazonensis infection. These seemingly contradictory findings reflect the remarkable adaptation of the parasites to the ancient defense machinery of the host, as well as the complex parasite–host interactions at different stages of infection, which collectively contribute to non-healing leishmaniasis in the New World. This review article highlights new evidence that reveals the strategies utilized by L. amazonensis parasites to subvert or modulate host innate defense machinery in neutrophils and macrophages, as well as the regulatory roles of host innate responses in promoting parasite survival and replication within the huge parasitophorous vacuoles. A better understanding of unique features in host responses to these parasites at early and late stages of infection is important for the rational design of control strategies for non-healing leishmaniasis.
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB—the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon–intron architectures, syntenic orthologs and parent–child trees. The interactive web interface allows navigation along the species phylogenies, complex queries with various identifiers, annotation keywords and phrases, as well as with gene copy-number profiles and sequence homology searches. With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups.
Space‐Time Database for Standardization of Adult Magnetocardiogram‐Making Standard MCG Parameters

Background: The magnetocardiogram (MCG) is a promising medical tool for detecting and visualizing abnormal cardiac electrical activation in heart‐disease patients. However, there is no large‐scale MCG database of healthy subjects, and there is little knowledge of gender‐ and age‐related influences on MCG data.
Insulin plus a sulfonylurea agent for treating type 2 diabetes.

PURPOSE To review the recent literature on the efficacy of combined insulin and sulfonylurea therapy in patients with type 2 diabetes. DATA SOURCES Pertinent articles were obtained through an English-language MEDLINE search from 1979 to 1990 and from the references of these articles. STUDY SELECTION We reviewed the studies in which patients with poorly controlled diabetes received insulin and a sulfonylurea agent and in which insulin treatment alone (usually given in conjunction with a placebo) was compared with insulin plus sulfonylurea therapy. DATA EXTRACTION Pre- and post-treatment insulin doses, blood glucose levels, glycated hemoglobin values, C-peptide levels, and insulin levels were analyzed. Other data were analyzed separately. RESULTS OF DATA SYNTHESIS Data from similar trials were compared. Data from concurrent trials were analyzed separately from data derived from cross-over trials. Weighted mean fasting blood glucose levels, glycated hemoglobin levels, insulin dosage, and fasting C-peptide concentrations were determined for insulin plus placebo and insulin plus sulfonylurea agent groups for both types of studies. In concurrent trials, the weighted mean post-treatment glycated hemoglobin level was 11.1% after insulin plus placebo compared with 10.0% after insulin plus a sulfonylurea agent. In cross-over trials, the corresponding values were 10.6% and 9.8%. CONCLUSIONS Combination therapy with insulin and a sulfonylurea agent only slightly improved glycemic control in patients with type 2 diabetes. When a sulfonylurea agent was used, less exogenous insulin was needed, but fasting serum insulin levels were not different between the treatment groups. Such therapy did not produce nearly normal blood glucose concentrations and therefore should not be used in patients with poorly controlled type 2 diabetes receiving insulin.
Effect of an amine fluoride dentifrice on dental caries used in a community-based oral health education program.

OBJECTIVES The purpose of this study was to investigate the caries-reducing effect of an amine fluoride toothpaste when used under real-life conditions in a community preventive program. METHODS Approximately 12,500 children 3-12 years of age were provided with toothpaste (four tubes or 360 grams annually during three years) to be used in kindergartens or schools and once a day at home. The teachers supervised daily toothbrushing sessions. Random samples of children in each of the ages 3, 6, 9, and 12 years were selected from the intervention and the reference communities at both the start of the study and after three years, and examined for dental caries experience. RESULTS Amine fluoride dentifrice seemed to provide a reduction in dental caries prevalence compatible to the most commonly used fluoride dentifrice compounds. CONCLUSIONS The implemented fluoride toothpaste program is a feasible and practical method of improving the oral health status of children.
A NEW SURVEY FOR GIANT ARCS

We . ˢ . ͫ report on the first results of an imaging survey to detect strong gravitational lensing targeting the richest clusters selected from the photometric data of the Sloan Digital Sky Survey (SDSS) with follow-up deep imaging observations from the Wisconsin–Indiana–Yale NOAO (WIYN) 3.5 m telescope and the University of Hawaii 88 inch telescope (UH88). The clusters are selected from an area of 8000 deg2 using the red cluster sequence technique and span the redshift range 0.1 ≲ z ≲ 0.6, corresponding to a comoving cosmological volume of ∼2 Gpc3. Our imaging survey thus targets a volume more than an order of magnitude larger than any previous search. A total of 240 clusters were imaged of which 141 had sub-arcsecond image quality. Our survey has uncovered 16 new lensing clusters with definite giant arcs, an additional 12 systems for which the lensing interpretation is very likely, and 9 possible lenses which contain shorter arclets or candidate arcs which are less certain and will require further observations to confirm their lensing origin. Among these new systems are several of the most dramatic examples of strong gravitational lensing ever discovered, with multiple bright arcs at large angular separation. These will likely become “poster-child” gravitational lenses similar to Abell 1689 and CL0024+1654. The new lenses discovered in this survey will enable future systematic studies of the statistics of strong lensing and their implications for cosmology and our structure formation paradigm.
Neuroprotective Strategies for the Neonatal Brain

Injury to the perinatal brain is a leading cause of childhood mortality and lifelong disability. Cerebral palsy and cognitive impairment are usually related to periventricular white matter damage, which is seen chiefly in babies born before 32 wk gestational age, and to corticosubcortical lesions, which occur mainly in full-term infants. Despite recent improvements in neonatal care, no effective treatment for perinatal brain lesions is available. Several interventions, such as magnesium sulfate in preterm newborns and hypothermia in term newborns, are the focus of completed or continuing clinical trials. Improved understanding of the pathophysiological mechanisms involved in perinatal brain lesions helps to identify potential targets for neuroprotective interventions, as discussed in this review.
NETASA: neural network based prediction of solvent accessibility

MOTIVATION Prediction of the tertiary structure of a protein from its amino acid sequence is one of the most important problems in molecular biology. The successful prediction of solvent accessibility will be very helpful to achieve this goal. In the present work, we have implemented a server, NETASA for predicting solvent accessibility of amino acids using our newly optimized neural network algorithm. Several new features in the neural network architecture and training method have been introduced, and the network learns faster to provide accuracy values, which are comparable or better than other methods of ASA prediction. RESULTS Prediction in two and three state classification systems with several thresholds are provided. Our prediction method achieved the accuracy level upto 90% for training and 88% for test data sets. Three state prediction results provide a maximum 65% accuracy for training and 63% for the test data. Applicability of neural networks for ASA prediction has been confirmed with a larger data set and wider range of state thresholds. Salient differences between a linear and exponential network for ASA prediction have been analysed. AVAILABILITY Online predictions are freely available at: http://www.netasa. org. Linux ix86 binaries of the program written for this work may be obtained by email from the corresponding author.
Overproduction of l-Lysine from Methanol by Methylobacillus glycogenes Derivatives Carrying a Plasmid with a Mutated dapA Gene

ABSTRACT The dapA gene, encoding dihydrodipicolinate synthase (DDPS) partially desensitized to inhibition by l-lysine, was cloned from an l-threonine- andl-lysine-coproducing mutant of the obligate methylotrophMethylobacillus glycogenes DHL122 by complementation of the nutritional requirement of an Escherichia coli dapAmutant. Introduction of the dapA gene into DHL122 and AL119, which is the parent of DHL122 and an l-threonine producing mutant, elevated the specific activity of DDPS 20-fold andl-lysine production 2- to 3-fold with concomitant reduction of l-threonine in test tube cultures. AL119 containing thedapA gene produced 8 g of l-lysine per liter in a 5-liter jar fermentor from methanol as a substrate. Analysis of the nucleotide sequence of the dapA gene shows that it encodes a peptide with an Mr of 30,664 and that the encoded amino acid sequence is extensively homologous to those of other organisms. In order to study the mutation that occurred in DHL122, the dapA genes of the wild type and AL119 were cloned and sequenced. Comparison of the nucleotide sequences of the dapA genes revealed that the amino acid at residue 88 was F in DHL122 whereas it was L in the wild type and AL119, suggesting that this amino acid alteration that occurred in DHL122 caused the partial desensitization of DDPS to the inhibition byl-lysine. The similarity in the amino acid sequences of DDPS in M. glycogenes and other organisms suggests that the mutation of the dapA gene in DHL122 is located in the region concerned with interaction of the allosteric effector,l-lysine.
Investigation of structural, tribological and corrosion properties of electroless Ni–B coating deposited on 316L stainless steel

The AISI 316L type of stainless steel is a popular steel material, as it has excellent corrosion resistance in aqueous solutions at ambient temperatures. However, the application of the AISI 316L stainless steel is limited by its relatively low hardness and low wear resistance. In this study, the electroless Ni–B coating was deposited on the AISI 316L stainless steel, and its structural, tribological and corrosion properties were characterised. Microstructural analysis showed that the electroless Ni–B coating deposited on the AISI 316L steel substrate exhibited a typical cauliflower-like structure exhibits an amorphous growth. From this study, it may be concluded that this process cannot only improve the hardness and wear resistance of the 316L stainless steel, but can also provide cathodic protection without losing or sacrificing the original properties of the 316L stainless steel.