Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of environmental enrichment exposure on neuronal morphology of streptozotocin-induced diabetic and stressed rat hippocampus

Background: Environmental enrichment (EE) exposure is known to influence the structural changes in the neuronal network of hippocampus. In the present study, we evaluated the effects of EE exposure on the streptozotocin (STZ)-induced diabetic and stressed rat hippocampus. Methods: Male albino rats of Wistar strain (4-5 weeks old) were grouped into normal control (NC), vehicle control (VC), diabetes (DI), diabetes + stress (DI + S), diabetes + EE (DI + E), and diabetes + stress + EE (DI + S + E) groups (n = 8 in each group). Rats were exposed to stress and EE after inducing diabetes with STZ (40 mg/kg). Rats were sacrificed on Day 30 and brain sections were processed for cresyl violet staining to quantify the number of surviving neurons in the CA1, CA3, and dentate hilus (DH) regions of hippocampus. Results: A significant (p < 0.001) decrease in the number of survived neurons was noticed in DI (CA1, 34.06 ± 3.2; CA3, 36.1 ± 3.62; DH, 9.83 ± 2.02) as well as DI + S (CA1, 14.03 ± 3.12; CA3, 20.27 ± 4.09; DH, 6.4 ± 1.21) group rats compared to NC rats (CA1, 53.64 ± 2.96; CA3, 62.1 ± 3.34; DH, 21.11 ± 1.03). A significant (p < 0.001) increase in the number of survived neurons was observed in DI + E (CA1, 42.3 ± 3.66; CA3, 46.73 ± 4.74; DH, 17.03 ± 2.19) and DI + S + E (CA1, 29.69 ± 4.47; CA3, 36.73 ± 3.89; DH, 12.23 ± 2.36) group rats compared to DI and DI + S groups, respectively. Conclusions: EE exposure significantly reduced the amount of neuronal damage caused by complications of diabetes and stress to the neurons of hippocampus.
T Cells Activation and Interferon-γ/Nitric Oxide Production during Behçet Disease: A Study in Algerian Patients

The aim of the current study is to situate CDs expression (CD3+, CD4+, CD8+) and their relationship with IFNγ and NO production in Algerian patients with Behçet disease (n = 34 ). Our results revealed an elevated expression of T cells markers tested in patients in active stage of the disease in relation to IFNγ and NO increase levels. Most interestingly, we noted that CD4+/CD8+ expression correlated with IFNγ and NO production in active stage. In contrast, we observed a decrease of these mediators in inactive stage. Collectively, our results indicate a dependent relation between these parameters and inflammatory response associated with the evolutionary stage of the disease.
Subchronic toxicity of Baltic herring oil and its fractions in the rat II: Clinical observations and toxicological parameters.

This study aimed to increase the knowledge about the toxicity of fish-derived organohalogen pollutants in mammals. The strategy chosen was to separate organohalogen pollutants derived from Baltic herring (Clupea harengus) fillet, in order to obtain fractions with differing proportions of identified and unidentified halogenated pollutants, and to perform a subchronic toxicity study in rats, essentially according to the OECD guidelines, at three dose levels. Nordic Sea lodda (Mallotus villosus) oil, with low levels of persistent organohalogen pollutants, was used as an additional control diet. The toxicological examination showed that exposure to Baltic herring oil and its fractions at dose levels corresponding to a human intake in the range of 1.6 to 34.4 kg Baltic herring per week resulted in minimal effects. The spectrum of effects was similar to that, which is observed after low-level exposure to pollutants such as chlorinated dibenzo-p-dioxins and dibenzofurans (CDD/F) and chlorinated biphenyls, despite the fact that these contaminants contribute to a minor part of the extractable organically bound chlorine (EOCI). The study confirmed previous findings that induction of hepatic ethoxyresorufin deethylase (EROD) activity takes place at daily intake levels 0.15 ng fish-derived CDD/F-TEQs/kg body weight. The study also demonstrated that hepatic vitamin A reduction takes place at somewhat higher daily exposure levels, i.e. 0.16-0.30 ng fish-derived CDD/F-TEQs/kg body weight. Halogenated fatty acids, the major component of EOCI, could not be linked to any of the measured effects. From a risk management point of view, the study provides important new information of effect levels for Ah-receptor mediated responses following low level exposure to organohalogen compounds from a matrix relevant for human exposure.
Genes Involved in Formation of Structured Multicellular Communities by Bacillus subtilis

ABSTRACT The spore-forming bacterium Bacillus subtilis is capable of assembling multicellular communities (biofilms) that display a high degree of spatiotemporal organization. Wild strains that have not undergone domestication in the laboratory produce particularly robust biofilms with complex architectural features, such as fruiting-body-like aerial projections whose tips serve as preferential sites for sporulation. To discover genes involved in this multicellular behavior and to do so on a genome-wide basis, we took advantage of a large collection of mutants which have disruptions of most of the uncharacterized genes in the B. subtilis genome. This collection, which was generated with a laboratory strain, was screened for mutants that were impaired in biofilm formation. This subset of mutated genes was then introduced into the wild strain NCIB 3610 to study their effects on biofilm formation in liquid and solid media. In this way we identified six genes that are involved in the development of multicellular communities. These are yhxB (encoding a putative phosphohexomutase that may mediate exopolysaccharide synthesis), sipW (encoding a signal peptidase), ecsB (encoding an ABC transporter subunit), yqeK (encoding a putative phosphatase), ylbF (encoding a regulatory protein), and ymcA (a gene of unknown function). Further analysis revealed that these six genes play different roles in B. subtilis community development.
Mortality in England and Wales attributable to current alcohol consumption

STUDY OBJECTIVE To estimate the number of deaths attributable to current alcohol consumption levels in England and Wales by age and sex. DESIGN Epidemiological approach using published relative risks and population data. SETTING England and Wales. MAIN OUTCOME MEASURES Numbers of deaths by age and sex and years of life lost for alcohol related conditions. RESULTS Because of the cardioprotective properties of alcohol, it is estimated that there are approximately 2% fewer deaths annually in England and Wales than would be expected in a non-drinking population. This proportion varies greatly by age and sex and only among men aged over 55 years and women aged over 65 years is there likely to be found a net favourable mortality balance. It is also estimated that there were approximately 75 000 premature years of life lost in England and Wales in 1996 attributable to alcohol consumption. The main causes of alcohol attributable mortality among the young include road traffic fatalities, suicide and alcoholic liver disease. CONCLUSIONS At a population level, current alcohol consumption in England and Wales may marginally reduce mortality. However, the benefit is disproportionately found among the elderly. Estimating alcohol attributable mortality by age and sex may be a useful indicator for developing alcohol strategies. More research into the possible effect modifications of pattern of consumption, beverage type, age and gender will enable these estimates to be improved.
Hypersomnia subtypes, sleep and relapse in bipolar disorder

Background. Though poorly defined, hypersomnia is associated with negative health outcomes and new-onset and recurrence of psychiatric illness. Lack of definition impedes generalizability across studies. The present research clarifies hypersomnia diagnoses in bipolar disorder by exploring possible subgroups and their relationship to prospective sleep data and relapse into mood episodes. Method. A community sample of 159 adults (aged 18–70 years) with bipolar spectrum diagnoses, euthymic at study entry, was included. Self-report inventories and clinician-administered interviews determined features of hypersomnia. Participants completed sleep diaries and wore wrist actigraphs at home to obtain prospective sleep data. Approximately 7 months later, psychiatric status was reassessed. Factor analysis and latent profile analysis explored empirical groupings within hypersomnia diagnoses. Results. Factor analyses confirmed two separate subtypes of hypersomnia (‘long sleep’ and ‘excessive sleepiness’) that were uncorrelated. Latent profile analyses suggested a four-class solution, with ‘long sleep’ and ‘excessive sleepiness’ again representing two separate classes. Prospective sleep data suggested that the sleep of ‘long sleepers’ is characterized by a long time in bed, not long sleep duration. Longitudinal assessment suggested that ‘excessive sleepiness’ at baseline predicted mania/hypomania relapse. Conclusions. This study is the largest of hypersomnia to include objective sleep measurement, and refines our understanding of classification, characterization and associated morbidity. Hypersomnia appears to be comprised of two separate subgroups: long sleep and excessive sleepiness. Long sleep is characterized primarily by long bedrest duration. Excessive sleepiness is not associated with longer sleep or bedrest, but predicts relapse to mania/hypomania. Understanding these entities has important research and treatment implications.
Therapeutic Antibodies to KIR3DL2 and Other Target Antigens on Cutaneous T-Cell Lymphomas

KIR3DL2 is a member of the killer cell immunoglobulin-like receptor (KIR) family that was initially identified at the surface of natural killer (NK) cells. KIR3DL2, also known as CD158k, is expressed as a disulfide-linked homodimer. Each chain is composed of three immunoglobulin-like domains and a long cytoplasmic tail containing two immunoreceptor tyrosine-based inhibitory motifs. Beside its expression on NK cells, it is also found on rare circulating T lymphocytes, mainly CD8+. Although the KIR gene number varies between haplotype, KIR3DL2 is a framework gene present in all individuals. Together with the presence of genomic regulatory sequences unique to KIR3DL2, this suggests some particular functions for the derived protein in comparison with other KIR family members. Several ligands have been identified for KIR3DL2. As for other KIRs, binding to HLA class I molecules is essential for NK development by promoting phenomena such as licensing and driving NK cell maturation. For KIR3DL2, this includes binding to HLA-A3 and -A11 and to the free heavy chain form of HLA-B27. In addition, KIR3DL2 binds to CpG oligonucleotides (ODN) and ensures their transport to endosomal toll-like receptor 9 that promotes cell activation. These characteristics have implicated KIR3DL2 in several pathologies: ankylosing spondylitis and cutaneous T-cell lymphomas such as Sézary syndrome, CD30+ cutaneous lymphoma, and transformed mycosis fungoides. Consequently, a new generation of humanized monoclonal antibodies (mAbs) directed against KIR3DL2 has been helpful in the diagnosis, follow-up, and treatment of these diseases. In addition, preliminary clinical studies of a novel targeted immunotherapy for cutaneous T-cell lymphomas using the anti-KIR3DL2 mAb IPH4102 are now underway. In this review, we discuss the various aspects of KIR3DL2 on the functions of CD4+ T cells and how targeting this receptor helps to develop innovative therapeutic strategies.
Efficient use of accessibility in microRNA target prediction

Considering accessibility of the 3′UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by the sum of the opening and hybridization energies, used in currently available algorithms, is not an efficient way to rank predictions. Instead, we describe an algorithm which also considers only the accessible binding sites but which ranks predictions according to over-representation. When compared with experimentally validated and refuted targets in the fruit fly and human, our algorithm shows a remarkable improvement in precision while significantly reducing the computational cost in comparison with other free energy based methods. In the human genome, our algorithm has at least twice higher precision than other methods with their default parameters. In the fruit fly, we find five times more validated targets among the top 500 predictions than other methods with their default parameters. Furthermore, using a common statistical framework we demonstrate explicitly the advantages of using the canonical ensemble instead of using the minimum free energy structure alone. We also find that ‘naïve’ global folding sometimes outperforms the local folding approach.
An International Comparison of Attitudes Toward Traditional and Modern Medicine in a Chinese and an American Clinic Setting

Introduction. International comparative research on traditional medicine (TM) offers a useful method for examining differences in patient characteristics and can provide insight into: (i) more universal characteristics which may cross cultures and international borders; (ii) unique characteristics influenced by regional/national factors; and (iii) cultural values of immigrant populations. To explore these issues TM patients from the United States and China were compared. Methods. Data collection took place at two TM college clinics. A convenience sample of 128 patients in China and 127 patients in the United States completed a 28-item questionnaire. Results. There was a marked similarity between the two patient groups in terms of the biological characteristics of age and gender. Musculoskeletal issues were the most common presenting complaints in the United States; while in China TM was used for a more diverse array of conditions. The majority of patients in both countries had initially used allopathic medicine (AM); significantly, more of the United States respondents stopped allopathic treatment after beginning traditional treatment. In comparing the two countries, patients in China were significantly more satisfied with AM and American patients significantly more satisfied with TM. In comparing the two medicines, the patient samples in both countries were significantly more satisfied with TM than AM. Discussion. Although treatment often originated with allopathic providers, many patients sought alternatives presumably to find the best solution to their problems. This tendency toward self-assignment suggests that a pluralistic healthcare system may provide the greatest satisfaction resulting from personal choice and improved outcomes.
Carotid plaque classification: Defining the certainty with which plaque components can be differentiated

Multicontrast‐weighted MRI has the potential to become a powerful tool for assessment of atherosclerotic plaque. However, similarities in MR properties across plaque components limit the certainty with which these components can be differentiated. An understanding of MRI's underlying limitations in distinguishing atherosclerotic plaque components, and optimization of key parameters (including the set of components investigated and contrast weightings used) are required. In this study we analyzed endarterectomy specimens using multicontrast MRI and compared the results with matching histological findings to determine the probability of error, an unbiased measure of the underlying error caused by similarity in the spectral characteristics of components. The total error was >40% when five distinct components were investigated, but this was halved when components with similar functions and intensities were grouped together. When three contrast weightings were used to view plaque, diffusion‐weighted imaging (DWI) proved valuable for separating hemorrhage from necrotic core, and “hemorrhage + necrotic” from “loose connective tissue + fibrous tissue. ” A two‐way interaction between contrast weightings and components demonstrated that the value of a contrast can be exploited or marginalized depending on the choice of contrast weightings used. Magn Reson Med 57:874–880, 2007. © 2007 Wiley‐Liss, Inc.
Genotypic Evolution of Azole Resistance Mechanisms in Sequential Candida albicans Isolates

ABSTRACT TAC1 (for transcriptional activator of CDR genes) is critical for the upregulation of the ABC transporters CDR1 and CDR2, which mediate azole resistance in Candida albicans. While a wild-type TAC1 allele drives high expression of CDR1/2 in response to inducers, we showed previously that TAC1 can be hyperactive by a gain-of-function (GOF) point mutation responsible for constitutive high expression of CDR1/2. High azole resistance levels are achieved when C. albicans carries hyperactive alleles only as a consequence of loss of heterozygosity (LOH) at the TAC1 locus on chromosome 5 (Chr 5), which is linked to the mating-type-like (MTL) locus. Both are located on the Chr 5 left arm along with ERG11 (target of azoles). In this work, five groups of related isolates containing azole-susceptible and -resistant strains were analyzed for the TAC1 and ERG11 alleles and for Chr 5 alterations. While recovered ERG11 alleles contained known mutations, 17 new TAC1 alleles were isolated, including 7 hyperactive alleles with five separate new GOF mutations. Single-nucleotide-polymorphism analysis of Chr 5 revealed that azole-resistant strains acquired TAC1 hyperactive alleles and, in most cases, ERG11 mutant alleles by LOH events not systematically including the MTL locus. TAC1 LOH resulted from mitotic recombination of the left arm of Chr 5, gene conversion within the TAC1 locus, or the loss and reduplication of the entire Chr 5. In one case, two independent TAC1 hyperactive alleles were acquired. Comparative genome hybridization and karyotype analysis revealed the presence of isochromosome 5L [i(5L)] in two azole-resistant strains. i(5L) leads to increased copy numbers of azole resistance genes present on the left arm of Chr 5, among them TAC1 and ERG11. Our work shows that azole resistance was due not only to the presence of specific mutations in azole resistance genes (at least ERG11 and TAC1) but also to their increase in copy number by LOH and to the addition of extra Chr 5 copies. With the combination of these different modifications, sophisticated genotypes were obtained. The development of azole resistance in C. albicans is therefore a powerful instrument for generating genetic diversity.
Discovering Interesting Association Rules: A Multi-objective Genetic Algorithm Approach

Association rule mining is considered as one of the important tasks of data mining intended towards decision making process. It has been mainly developed to identify interesting associations and/or correlation relationships between frequent itemsets in datasets. A multi-objective genetic algorithm approach is proposed in this paper for the discovery of interesting association rules with multiple criteria i.e. support, confidence and simplicity (comprehensibility). With Genetic Algorithm (GA), a global search can be achieved and system automation is developed, because the proposed algorithm could identify interesting association rules from a dataset without having the user-specified thresholds of minimum support and minimum confidence. The experimental results on various types of datasets show the usefulness and effectiveness of the proposed algorithm. General Terms Knowledge Discovery in Databases (KDD), Data Mining, Genetic Algorithm, Optimization.
On Cross-Stack Configuration Errors

Today's web applications are deployed on powerful software stacks such as MEAN (JavaScript) or LAMP (PHP), which consist of multiple layers such as an operating system, web server, database, execution engine and application framework, each of which provide resources to the layer just above it. These powerful software stacks unfortunately are plagued by so-called cross-stack configuration errors (CsCEs), where a higher layer in the stack suddenly starts to behave incorrectly or even crash due to incorrect configuration choices in lower layers. Due to differences in programming languages and lack of explicit links between configuration options of different layers, sysadmins and developers have a hard time identifying the cause of a CsCE, which is why this paper (1) performs a qualitative analysis of 1,082 configuration errors to understand the impact, effort and complexity of dealing with CsCEs, then (2) proposes a modular approach that plugs existing source code analysis (slicing) techniques, in order to recommend the culprit configuration option. Empirical evaluation of this approach on 36 real CsCEs of the top 3 LAMP stack layers shows that our approach reports the misconfigured option with an average rank of 2.18 for 32 of the CsCEs, and takes only few minutes, making it practically useful.
Herpes Simplex Virus Type 1 Vector-Mediated Expression of Nerve Growth Factor Protects Dorsal Root Ganglion Neurons from Peroxide Toxicity

ABSTRACT Nerve growth factor β subunit (β-NGF) transgene delivery and expression by herpes simplex virus type 1 (HSV-1) vectors was examined in a cell culture model of neuroprotection from hydrogen peroxide toxicity. Replication-competent (tk− K mutant background) and replication-defective (ICP4−;tk− S mutant background) vectors were engineered to contain the murine β-NGF cDNA under transcriptional control of either the human cytomegalovirus immediate-early gene promoter (HCMV IEp) (e.g., KHN and SHN) or the latency-active promoter 2 (LAP2) (e.g., KLN and SLN) within the viral thymidine kinase (tk) locus. Infection of rat B103 and mouse N2A neuronal cell lines, 9L rat glioma cells, and Vero cells with the KHN or SHN vectors resulted in the production of β-NGF-specific transcripts and β-NGF protein reaching a maximum at 3 days postinfection (p.i.). NGF protein was released into the culture media in amounts ranging from 10.83 to 352.86 ng/ml, with the highest levels being achieved in B103 cells, and was capable of inducing neurite sprouting of PC-12 cells. The same vectors produced high levels of NGF in primary dorsal root ganglion (DRG) cultures at 3 days. In contrast to HCMV IEp-mediated expression, the LAP2-NGF vectors showed robust expression in primary DRG neurons at 14 days. The neuroprotective effect of vector produced NGF was assessed by its ability to inhibit hydrogen peroxide-induced neuron toxicity in primary DRG cultures. Consistent with the kinetics of vector-mediated NGF expression, HCMV-NGF vectors were effective in abrogating the toxic effects of peroxide at 3 but not 14 days p.i. whereas LAP2-NGF vector transduction inhibited apoptosis in DRG neurons at 14 days p.i. but was ineffective at 3 days p.i. Similar kinetics of NGF expression were observed with the KHN and KLN vectors in latently infected mouse trigeminal ganglia, where high levels of β-NGF protein expression were detected at 4 wks p.i. only from the LAP2; HCMV-NGF-driven expression peaked at 3 days but could not be detected during HSV latency at 4 weeks. Together, these results indicate that (i) NGF vector-infected cells produce and secrete mature, biologically active β-NGF; (ii) vector-synthesized NGF was capable of blocking peroxide-induced apoptosis in primary DRG cultures; and (iii) the HCMV-IEp functioned to produce high levels of NGF for several days; but (iv) only the native LAP2 was capable of long-term expression of a therapeutic gene product in latently infected neurons in vivo.
Evaluation of Collaborative Prediction Algorithm

This project investigates the collaborative prediction al gorithm focusing on the recently proposed promising method Maximum-Margin M atrix Factorization (MMMF). Several experiments were conducted with actual datasets, and quantitative results showed a good predictio n performance of MMMF. Also, the significant variance of computational tim e were observed in the experiments.