Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeography and Population Structure of the Japanese Wild Boar Sus scrofa leucomystax: Mitochondrial DNA Variation

Abstract Phylogeographic characteristics and population structure of Japanese wild boar (Sus scrofa leucomystax) were investigated using mitochondrial DNA (mtDNA) sequence data. Sixteen Japanese wild boar haplotypes detected from partial sequences of the mtDNA control region (574-bp) from 180 Japanese wild boar specimens from 10 local populations on Honshu, Shikoku, and Kyushu islands and 41 haplotypes from other S. scrofa were analyzed using the neighbor-joining method. The Japanese wild boars were more closely related to Northeast Asian wild boars from Mongolia than to the other Asian continental S. scrofa. The Japanese and Northeast Asian wild boars were not significantly distinguished by corrected average pairwise difference analysis. The ancestors of Japanese wild boars are suggested to have been part of the continental S. scrofa population that spread from Southeast to Northeast Asia during the Middle to Late Pleistocene. The Japanese wild boar mtDNA haplotype cladogram shows 95% parsimoniously plausible branch connections supporting three sympatric clades. Nested clade analysis indicates that these three clades are the result of distinct historical events or gene flow. The present population of Japanese wild boars may have been formed by a few independent migrations of distinct clades from the continent with subsequent mixing on the Japanese Islands.
A three-layer model of source code comprehension

In this paper we first propose a source code comprehension model built as a hierarchy of three abstraction levels from the source code to the purpose (goal) of the program. The elements belonging to each layer have been precisely defined as well as their links to the elements in the adjacent layers. Consequently this model allows to bridge the semantic gap between the purpose of the program defined in business terms and the code that implements it. The model leverages two ontologies: an action ontology, which is specific to our approach, and a domain concept ontology. Next this model has been implemented as a tool under Eclipse and two experiments have been performed to assess the relevance of our approach in the maintenance of a large-scale program. The results of this experiment are very encouraging. The contribution of the paper is the presentation of our program comprehension model built on a novel approach based on an action ontology, the description of the tool we developed to assess the relevance of model and the testing of the latter with two controlled experiments.
Daptomycin Is Effective for Treatment of Experimental Endocarditis Due to Methicillin-Resistant and Glycopeptide-Intermediate Staphylococcus epidermidis

ABSTRACT This study evaluated the daptomycin activity against two methicillin-resistant Staphylococcus epidermidis (MRSE) clinical isolates with different vancomycin susceptibilities: MRSE-375, with a vancomycin MIC of 2 μg/ml, and NRS6, a glycopeptide-intermediate S. epidermidis (GISE) strain with a vancomycin MIC of 8 μg/ml. The in vivo activity of daptomycin at two different doses (standard dose [SD-daptomycin], 6 mg/kg of body weight/day intravenously [i.v.]; high dose [HD-daptomycin], 10 mg/kg/day i.v.) was evaluated in a rabbit model of infective endocarditis and compared with that of a standard dose of vancomycin (SD-vancomycin; 1 g i.v. every 12 h) for 2 days. For the MRSE-375 strain, high-dose vancomycin (HD-vancomycin; 1 g i.v. every 6 h) was also studied. For MRSE-375, SD- and HD-daptomycin therapy sterilized significantly more vegetations than SD-vancomycin therapy (9/15 [60%] and 11/15 [73%] vegetations, respectively, versus 3/16 [19%] vegetations; P = 0.02 and P = 0.002, respectively). HD-daptomycin sterilized more vegetations than HD-vancomycin (11/15 [73%] versus 5/15 [33%] vegetations; P = 0.03) and was more effective than SD- and HD-vancomycin in reducing the density of bacteria in valve vegetations (0 log10 CFU/g vegetation [interquartile range {IQR}, 0 to 1 log10 CFU/g vegetation] versus 2 log10 CFU/g vegetation [IQR, 2 to 2 log10 CFU/g vegetation] and 2 log10 CFU/g vegetation [IQR, 0 to 2.8 log10 CFU/g vegetation]; P = 0.002 and P = 0.01, respectively). For the NRS6 strain, SD- and HD-daptomycin were significantly more effective than vancomycin in reducing the density of bacteria in valve vegetations (3.7 log10 CFU/g vegetation [IQR, 2 to 6 log10 CFU/g vegetation] versus 7.1 log10 CFU/g vegetation [IQR, 5.2 to 8.5 log10 CFU/g vegetation]; P = 0.02). In all treatment arms, isolates recovered from vegetations remained susceptible to daptomycin and vancomycin and had the same MICs. In conclusion, daptomycin at doses of 6 mg/kg/day or 10 mg/kg/day is more effective than vancomycin for the treatment of experimental endocarditis due to MRSE and GISE.
An Efficient Wake-Up Strategy Considering Spurious Glitches Phenomenon for Power Gating Designs

During the power mode transition, simultaneously turning on sleep transistors provides a sufficiently large surge current, which may cause a large IR drop in the power networks. The IR drop in turn causes errors in the retention sequential elements of the sleep modules or errors of the nonsleep modules. One efficient way to control the surge current is to schedule the turn-on sequences of sleep transistors. In this paper, we introduce several important properties of the surge current during the power mode transition for the distributed sleep transistor network (DSTN) design, which is a popular power gating design style. Based on these properties, we propose an accurate estimation of the surge current and provide efficient schedules on the DSTN structure. Our methods achieved significantly better results than previous works-on average, 261 times wake-up time reduction and 30% less energy loss during the power mode transition.
Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome Proceeds Via High Specificity*

Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4+ T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides, i.e. the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, because of the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly poor correlation between the source proteins identified in the HLA class II ligandome and the DC cellular proteome. Important selective sieving from the sampled proteome to the ligandome was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4+ T cell epitopes relevant in health and disease.
[Fear of childbirth].

Background: About 20 percent of all women suffer from fear of childbirth. Fear of childbirth refers to anxiety and/or fear before, during and/or after the birth, that affect a woman's everyday life negatively. Women with fear of childbirth often wish for caesarean section to avoid confrontation with their fears during a vaginal delivery. Caesarean section on the woman's request stands for 8 percent of today ́s cesarean sections. It is of great importance that women with fear of childbirth is captured early in pregnancy and offered an individualized care. Aim: To study the impact of treatment given to women with fear of childbirth during pregnancy. Method: Systematic literature review based on 14 quantitative scientific articles. Results: Caesarean section outcome and requests for caesarean section decreased among women with fear of childbirth who received some form of intervention to reduce the fear. Women with fear of childbirth also valued their birth experience as more positive and had a lower degree of fear of childbirth after receiving the intervention. Conclusion: Research shows that different treatment such as psychoeducative group therapy with relaxation, extra support, cognitive therapy, psychosomatic support, intensive therapy, group psychoeducation with relaxation, exercise program, mindfulness course and psycho educative phone support for fear of childbirth has effect, but there is no research on which method is most effective. To compare or measure the effect of a treatment further randomized controlled trials are
Evaluation of Bufadienolides as the Main Antitumor Components in Cinobufacin Injection for Liver and Gastric Cancer Therapy

Background Cinobufacin injection, also known as huachansu, is a preparation form of Cinobufacini made from Cinobufacin extract liquid. Despite that Cinobufacin injection is shown to shrink liver and gastric tumors, improving patient survival and life quality, the effective components in Cinobufacin remain elusive. In this study, we aim to screen antitumor components from Cinobufacin injection to elucidate the most effective antitumor components for treatment of liver and gastric cancers. Materials and Methods High performance liquid chromatography (HPLC) and LC-MS/MS analysis were used to separate and determine the components in Cinobufacin injection. Inhibition rates of various components in Cinobufacin injection on liver and gastric cancer cells were determined with MTT assay; Hepatocellular carcinoma and gastric cancer models were used to assess the antitumor effect of the compounds in vivo. Results The major constituents in Cinobufacin injection include peptides, nucleic acids, tryptamines and bufotalins. MTT assay revealed that bufadienolides had the best antitumor activity, with peptides being the second most effective components. Bufadienolides showed significant inhibition rates on gastric and hepatocellular tumour growth in vivo. Conclusion Bufadienolides are the most effective components in Cinobufacini injection for the treatment of liver and gastric cancers. This discovery can greatly facilitate further research in improving the therapeutic effects of Cinobufacin injection, meanwhile reducing its adverse reaction.
Influence of oscillating positive expiratory pressure and the forced expiratory technique on sputum cell counts and quantity of induced sputum in patients with asthma or chronic obstructive pulmonary disease.

OBJECTIVE To evaluate whether respiratory therapy techniques influence the number of cells within and quantity of induced sputum in patients with asthma or chronic obstructive pulmonary disease (COPD). METHODS Randomized clinical trial, in which patients with asthma or COPD under intervention (n = 16 and 10, respectively) were compared with control groups (n = 16 and 10). Patients in the asthma/intervention (A/I) and COPD/intervention (C/I) groups were submitted to oscillating positive expiratory pressure maneuvers for 5 min, followed by 10 forced expiratory technique sequences. These patients were also submitted to an induced sputum protocol with inhaled hypertonic saline (3%, 4% or 5%; A/I group) or inhaled isotonic saline (C/I group). The asthma/control (A/C) and COPD/control (C/C) groups were submitted only to the standard induced sputum protocol. RESULTS The final mean weight of the sputum samples was significantly greater in the A/I group than in the A/C group (2,767.25 +/- 998.08 mg vs. 1,689.17 +/- 1,189.96 mg; p = 0.03). The mean/median total cell counts (x10(6)/mL) were higher in the A/I and C/I groups than in the A/C and C/C groups (4.06/0.95 and 0.63/0.39, p = 0.05, vs. 5.08/1.77 and 0.64/0.40, p = 0.02). There were no statistically significant differences among the groups in terms of cell viability. CONCLUSIONS The use of respiratory therapy techniques can increase sputum sample weight in asthma patients, as well as increasing total cell counts in patients with asthma or COPD.
Status of Primary Liver Cancer Found through Routine Health Check-up

This study aimed to investigate the status of primary liver cancers found through a routine health check-up. The data of subjects who were diagnosed with primary liver cancer for the first time through a routine health check-up during a period of 8-yr were analyzed. Primary liver cancers were detected for the first time in 34 subjects among 91,219 routine health check-up subjects. Only 11.8% of primary liver cancer subjects had been under previous surveillance. Of them, 55.8% were positive for HBsAg, 17.7% were positive for anti-HCV, and 8.8% were heavy alcohol comsumers. However, 17.7% of the subjects were neither heavy alcohol consumers nor positive for both HBsAg and anti-HCV. Of the subjects, 50.0% had a single nodular tumor, 23.5% had multi-nodular tumors, and 26.5% had an infiltrative tumor. A routine health check-up may provide beneficial opportunities to detect a liver cancer in a very early stage. It is beneficial to start surveillance in high-risk subjects for liver cancer or to detect any liver cancer in subjects without risk factors of chronic viral hepatitis or heavy alcohol consumption.
Neuronal fiber tracts connecting the brain and ventral nerve cord of the early Drosophila larva

By using a combination of dye injections, clonal labeling, and molecular markers, we have reconstructed the axonal connections between brain and ventral nerve cord of the first‐instar Drosophila larva. Out of the approximately 1,400 neurons that form the early larval brain hemisphere, less than 50 cells have axons descending into the ventral nerve cord. Descending neurons fall into four topologically defined clusters located in the anteromedial, anterolateral, dorsal, and basoposterior brain, respectively. The anterolateral cluster represents a lineage derived from a single neuroblast. Terminations of descending neurons are almost exclusively found in the anterior part of the ventral nerve cord, represented by the gnathal and thoracic neuromeres. This region also contains small numbers of neurons with axons ascending into the brain. Terminals of the ascending axons are found in the same basal brain regions that also contain descending neurons. We have mapped ascending and descending axons to the previously described scaffold of longitudinal fiber tracts that interconnect different neuromeres of the ventral nerve cord and the brain. This work provides a structural framework for functional and genetic studies addressing the control of Drosophila larval behavior by brain circuits. J. Comp. Neurol. 515:427–440, 2009. © 2009 Wiley‐Liss, Inc.
Human T-cell leukemia virus type I Tax induces the expression of dendritic cell markers associated with maturation and activation

Human T-cell leukemia virus type I (HTLV-I) is the etiologic agent of both adult T-cell leukemia (ATL) and HTLV-I—associated myelopathy/tropical spastic paraparesis (HAM/TSP). Although the genesis of HAM/TSP likely involves several steps, the generation of a highly specific and effective population of Tax-specific CD8+ cytotoxic T lymphocytes (CTLs) that migrate to the central nervous system (CNS) is of pivotal importance in this neuropathologic process. Presentation of Tax peptides by activated dendritic cells (DCs) to naïve CD8+ T cells likely plays an important role in the induction of a Tax-specific CTL response and the eventual neurologic dysfunction observed in HAM/TSP. The immune response mounted during HTLV-I infection is primarily targeted against Tax with both Tax-specific antibodies and CTLs found in HTLV-I-infected individuals, indicating that Tax is available for immune recognition. Studies have suggested that Tax may be secreted from HTLV-I—infected cells and act as an extracellular cytokine, be internalized and processed for presentation, or be transported to the nucleus where it may act as a transcriptional activator. The authors report in this article that purified Tax induces DC activation involving an increase in the production of CD80 and CD86 mRNA in the absence of corresponding protein synthesis. Furthermore, intracellular Tax down-regulates the protein expression of molecules involved in antigen presentation. This implies a difference in the mechanism of Tax activity depending upon its location. Additionally, treatment of JAWS II DCs with extracellular Tax decreases the ability of DCs to present a major histocompatibility complex (MHC) class I-restricted peptide, indicating that Tax likely matures the DCs to the point where presentation of a secondary antigen is restricted. The implication of the experimental results with respect to the generation of a Tax-specific CTL compartment that participates in the genesis of HAM/TSP is discussed.
Noise-based testing and analysis of multi-threaded C/C++ programs on the binary level

This paper aims at allowing noise-based testing and dynamic analysis of multi-threaded C/C++ programs on the binary level. First, several problems of monitoring multi-threaded C/C++ programs on the binary level are discussed together with their possible solutions. Next, a brief overview of noise injection techniques is provided along with a proposal of improving them using a fine-grained combination of several noise injection techniques within a single program. The proposed ideas have been implemented in a prototype way using the PIN framework for Intel binaries and tested on a~set of multi-threaded C/C++ programs. The obtained experimental evidence justifying the proposed solutions and illustrating the effect of various noise settings in the context of multi-threaded C/C++ programs is discussed.
Molecular modulation of airway epithelial ciliary response to sneezing

Our purpose was to evaluate the effect of the mechanical force of a sneeze on sinonasal cilia function and determine the molecular mechanism responsible for eliciting the ciliary response to a sneeze. A novel model was developed to deliver a stimulation simulating a sneeze (55 mmHg for 50 ms) at 26°C to the apical surface of mouse and human nasal epithelial cells. Ciliary beating was visualized, and changes in ciliary beat frequency (CBF) were determined. To interrogate the molecular cascades driving sneeze‐induced changes of CBF, pharmacologic manipulation of intra‐ and extracellular calcium, purinergic, PKA, and nitric oxide (NO) signaling were performed. CBF rapidly increases by ≥150% in response to a sneeze, which is dependent on the release of adenosine triphosphate (ATP), calcium influx, and PKA activation. Furthermore, apical release of ATP is independent of calcium influx, but calcium influx and subsequent increase in CBF are dependent on the ATP release. Lastly, we observed a blunted ciliary response in surgical specimens derived from patients with chronic rhinosinusitis compared to control patients. Apical ATP release with subsequent calcium mobilization and PKA activation are involved in sinonasal ciliary response to sneezing, which is blunted in patients with upper‐airway disease. —Zhao, K. ‐Q. , Cowan, A. T. , Lee, R. J., Goldstein, N. , Droguett, K. , Chen, B. , Zheng, C. , Villalon, M. , Palmer, J. N. , Kreindler, J. L. , Cohen, N. A. Molecular modulation of airway epithelial ciliary response to sneezing. FASEB J. 26, 3178–3187 (2012). www.fasebj. org
Romanized Arabic and Berber detection using prediction by partial matching and dictionary methods

Arabic is one of the Semitic languages written in Arabic script in its standard form. However, the recent rise of social media and new technologies has contributed considerably to the emergence of a new form of Arabic, namely Arabic written in Latin scripts, often called Romanized Arabic or Arabizi. While Romanized Arabic is an informal language, Berber or Tamazight uses Latin script in its standard form with some orthography differences depending on the country it is used in. Both these languages are under-resourced and unknown to the state-of-the-art language identiüers. In this paper, we present a language automatic identifier for both Romanized Arabic and Romanized Berber. We also describe the built linguistic resources (large dataset and lexicons) including a wide range of Arabic dialects (Algerian, Egyptian, Gulf, Iraqi, Levantine, Moroccan and Tunisian dialects) as well as the most popular Berber varieties (Kabyle, Tashelhit, Tarifit, Tachawit and Tamzabit). We use the Prediction by Partial Matching (PPM) and dictionary-based methods. The methods reach a macro-average F-Measure of 98.74% and 97.60% respectively.
In Vitro Metabolic and Mitogenic Signaling of Insulin Glargine and Its Metabolites

Background Insulin glargine (Lantus®) is a long-acting basal insulin analog that demonstrates effective day-long glycemic control and a lower incidence of hypoglycemia than NPH insulin. After subcutaneous injection insulin glargine is partly converted into the two main metabolites M1 ([GlyA21]insulin) and M2 ([GlyA21,des-ThrB30]insulin). The aim of this study was to characterize the glargine metabolites in vitro with regard to their insulin receptor (IR) and IGF-1 receptor (IGF1R) binding and signaling properties as well as their metabolic and mitogenic activities. Methods The affinity of human insulin, insulin glargine and its metabolites to the IR isoforms A and B or IGF1R was analyzed in a competitive binding assay using SPA technology. Receptor autophosphorylation activities were studied via In-Cell Western in CHO and MEF cells overexpressing human IR-A and IR-B or IGF1R, respectively. The metabolic response of the insulins was studied as stimulation of lipid synthesis using primary rat adipocytes. Thymidine incorporation in Saos-2 cells was used to characterize the mitogenic activity. Conclusions The binding of insulin glargine and its metabolites M1 and M2 to the IR were similar and correlated well with their corresponding autophosphorylation and metabolic activities in vitro. No differences were found towards the two IR isoforms A or B. Insulin glargine showed a higher affinity for IGF1R than insulin, resulting in a lower EC50 value for autophosphorylation of the receptor and a more potent stimulation of thymidine incorporation in Saos-2 cells. In contrast, the metabolites M1 and M2 were significantly less active in binding to and activation of the IGF1R and their mitogenicity in Saos-2 cells was equal to human insulin. These findings strongly support the idea that insulin glargine metabolites contribute with the same potency as insulin glargine to blood glucose control but lead to significantly reduced growth-promoting activity.