Miracle-dz/UniFAR-FTUs huggingface dataset:
The immunoglobulin superfamily in cell surface recognition.

Vers le milieu des annees 1960 on a propose que l'evolution des genes des chaines legeres (L) et lourdes (H) des immunoglobulines (Ig) resultaient de la duplication d'un segment de gene primordial codant environ une centaine d'acides amines. Les domaines variable et constant etaient ainsi apparentes a la fois par leur structure et par leur evolution. Cette hypothese a ete confortee dans les annees 70 grâce a la resolution cristallographique des structures des chaines L et des fragments Fab. On a pu ainsi identifier une unite structurale commune aux domaines V et C, a savoir le domaine immunoglobulinique (domaine Ig)
Ligand-Signaled Upregulation of Enterococcus faecalis ace Transcription, a Mechanism for Modulating Host-E. faecalis Interaction

ABSTRACT Enterococcus faecalis, the third most frequent cause of bacterial endocarditis, appears to be equipped with diverse surface-associated proteins showing structural-fold similarity to the immunoglobulin-fold family of staphylococcal adhesins. Among the putative E. faecalis surface proteins, the previously characterized adhesin Ace, which shows specific binding to collagen and laminin, was detectable in surface protein preparations only after growth at 46°C, mirroring the finding that adherence was observed in 46°C, but not 37°C, grown E. faecalis cultures. To elucidate the influence of different growth and host parameters on ace expression, we investigated ace expression using E. faecalis OG1RF grown in routine laboratory media (brain heart infusion) and found that ace mRNA levels were low in all growth phases. However, quantitative reverse transcription-PCR showed 18-fold-higher ace mRNA amounts in cells grown in the presence of collagen type IV compared to the controls. Similarly, a marked increase was observed when cells were either grown in the presence of collagen type I or serum but not in the presence of fibrinogen or bovine serum albumin. The production of Ace after growth in the presence of collagen type IV was demonstrated by immunofluorescence microscopy, mirroring the increased ace mRNA levels. Furthermore, increased Ace expression correlated with increased collagen and laminin adhesion. Collagen-induced Ace expression was also seen in three of three other E. faecalis strains of diverse origins tested, and thus it appears to be a common phenomenon. The observation of host matrix signal-induced adherence of E. faecalis may have important implications on our understanding of this opportunistic pathogen.
Evaluation of Biexponential Relaxation Processes by Magnetic Resonance Imaging

Despite the complexity of biologic tissues, a monoexponential behaviour is usually assumed when estimating relaxation processes in vivo by magnetic resonance imaging (MRI). This study was designed to evaluate the potential of biexponential decomposition of T1 and T2 relaxation curves obtained at 1.5 tesla (T). Measurements were performed on a phantom of bicompartmental perspex boxes with combinations of different CuSO4 concentrations. T1 determination was based on a 12-points partial saturation inversion recovery pulse sequence. T2 determination was provided by a multiple spin echo sequence with 32 echoes. Applying biexponential curve analysis, a significant deviation from a monoexponential behaviour was recognized at a ratio of corresponding relaxation rates of about 3 and 2, estimating T1 and T2 relaxation, respectively (p<0.01, F-test). Requiring an SD≤10 per cent for each set of parameters, the biexponential model was accepted when this ratio exceeded a factor of 5 and 8, respectively. Referring to ‘expected’ T1 and T2 values, however, an accuracy within 20 per cent only was observed at ratios of at least 6 and 15. It is concluded that quantitative estimation of individual and specific relaxation components in complex biologic tissues by MRI may prove very difficult.
Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution

Significance Photolyases repair UV-B–induced DNA lesions. They form a large protein family together with cryptochrome photoreceptors (cryptochrome/photolyase family, CPF). A more recently discovered CPF subclade consists of DASH (Drosophila, Arabidopsis, Synechocystis, Human)-type cryptochromes (cry-DASH), present in bacteria, plants, animals, and fungi. Cry-DASH are considered as photoreceptors with residual repair activity for DNA lesions in single-stranded DNA. Canonical photolyases repair such lesions in single-stranded and double-stranded DNA. Here, we show that mucoromycotina fungi except Umbelopsis ramanniana, which is an early diverging lineage within the mucoralean fungi, encode only cry-DASH. They possess the full spectrum of DNA repair activity as canonical photolyases as exemplified for the Phycomyces CryA. This finding is a unique example of CPF evolution where a canonical CPD-photolyase was lost but its function was maintained by cry-DASH. DASH (Drosophila, Arabidopsis, Synechocystis, Human)-type cryptochromes (cry-DASH) belong to a family of flavoproteins acting as repair enzymes for UV-B–induced DNA lesions (photolyases) or as UV-A/blue light photoreceptors (cryptochromes). They are present in plants, bacteria, various vertebrates, and fungi and were originally considered as sensory photoreceptors because of their incapability to repair cyclobutane pyrimidine dimer (CPD) lesions in duplex DNA. However, cry-DASH can repair CPDs in single-stranded DNA, but their role in DNA repair in vivo remains to be clarified. The genome of the fungus Phycomyces blakesleeanus contains a single gene for a protein of the cryptochrome/photolyase family (CPF) encoding a cry-DASH, cryA, despite its ability to photoreactivate. Here, we show that cryA expression is induced by blue light in a Mad complex-dependent manner. Moreover, we demonstrate that CryA is capable of binding flavin (FAD) and methenyltetrahydrofolate (MTHF), fully complements the Escherichia coli photolyase mutant and repairs in vitro CPD lesions in single-stranded and double-stranded DNA with the same efficiency. These results support a role for Phycomyces cry-DASH as a photolyase and suggest a similar role for cry-DASH in mucoromycotina fungi.
CAMA Centre for Applied Macroeconomic Analysis Asset Prices , Business Cycles , and Markov-Perfect Fiscal Policy when Agents are Risk-Sensitive CAMA Working Paper 69 / 2013 October 2013

We study a business cycle model in which a benevolent fiscal authority must determine the optimal provision of government services, while lacking credibility, lump-sum taxes, and the ability to bond finance deficits. Households and the fiscal authority have risk sensitive preferences. We find that outcomes are affected importantly by the household’s risk sensitivity, but not by the fiscal authority’s. Further, while household risk-sensitivity induces a strong precautionary saving motive, which raises capital and lowers the return on assets, its effects on fluctuations and the business cycle are generally small, although more pronounced for negative shocks. Holding the stochastic steady state constant, increases in household risk-sensitivity lower the risk-free rate and raise the return on equity, increasing the equity premium. Finally, although risk-sensitivity has little effect on the provision of government services, it does cause the fiscal authority to lower the income tax rate. An additional contribution of this paper is to present a method for computing Markov-perfect equilibria in models where private agents and the government are risk-sensitive decision makers. | T H E A U S T R A L I A N N A T I O N A L U N I V E R S I T Y
HCV inhibits antigen processing and presentation and induces oxidative stress response in gastric mucosa

Productive hepatitis C virus (HCV) infection appears to be primarily confined to the liver. However, a wide variety of extrahepatic disease manifestations are associated with the infection and HCV RNA has been frequently detected in gastric mucosa. The present study aims to determine molecular alterations present in vivo in the stomach where HCV expression does not induce a carcinoma but a lymphoma, thus extending the knowledge of alterations in intracellular pathways consequent to HCV infection. We compared, by 2‐D DIGE, the gastric protein expression profile from six HCV positive and six HCV negative samples lacking neoplastic or dysplastic conditions. In HCV positive tissue we observed a down regulation of proteins involved in MHC maturation and assembly, antigen processing and presentation and ER stress, in addition to an up regulation of proteins involved in cellular oxidative stress responses. Ubiquinol‐cytochrome‐C‐reductase (UQCRFS1), part of the mitochondrial respiratory chain complex‐III, was identified as the most up regulated protein. Data were confirmed by Western blot and immunohistochemistry. Our results demonstrate a HCV negative influence on the different pathways that determine antigen processing and presentation via MHC‐I and the cellular attempts to counteract HCV induced oxidative stress. Both these processes facilitate immune escape and cell survival and probably contribute to HCV chronicization.
Phase I trial of recombinant fusion protein PIXY321 for mobilization of peripheral-blood cells.

PURPOSE Mobilization of peripheral-blood cells (PBC) with cytokines alone results in rapid hematopoietic recovery and avoids the potential morbidity associated with mobilization by chemotherapy. PIXY321, a fusion protein that consists of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-3 (IL-3), has enhanced hematopoietic colony-forming activity as compared with individual or equimolar combinations of the two cytokines. A phase I trial of PIXY321 for mobilization of PBC in patients with malignant lymphoma was performed. PATIENTS AND METHODS Thirteen patients with malignant lymphoma who were eligible for high-dose therapy (HDT) were enrolled onto the trial. All patients were ineligible for autologous bone marrow transplantation due to overt metastatic disease in the marrow or to severe marrow hypocellularity. PIXY321 was administered at three dose levels of 250, 500, and 750 micrograms/m2/d by continuous infusion until completion of PBC collections. Collections were initiated when the WBC count was greater than 10 x 10(9)/L or 4 days after the initiation of PIXY321, whichever came first. Collections were continued until a minimum of 6.5 x 10(8) mononuclear cells (MNC)/kg patient weight were obtained. RESULTS PIXY321 was generally well tolerated. Side effects associated with PIXY321 administration did not exceed grade 2 and included fever (85%), chills/sweats (54%), myalgias (38%), fatigue (31%), nausea/vomiting (31%), headache (31%), edema (23%), and rhinorrhea (23%). The median numbers of colony-forming units-granulocyte/macrophage (CFU-GM) in the graft products for the three dose levels were 0.31, 2.94, and 2.88 x 10(4)/kg, respectively; the median numbers of burst-forming units-erythroid (BFU-e) were 0.20, 6.94, and 12.78 x 10(4)/kg, and the median numbers of CD34+ cells were 2.30, 0.74, and 0.39 x 10(6)/kg. Following transplantation, the median times to an absolute neutrophil count (ANC) > 0.5 x 10(9)/L were 12, 15, and 12 days, respectively, and the median times to platelet transfusion independence were 30, 19, and 15 days. CONCLUSION PIXY321 can be safely administered and effectively mobilizes PBC in patients with bone marrow defects. PIXY321-mobilized PBC autotransplants result in rapid and sustained hematopoietic recovery.
Fractional Discrete Processes: Compound and Mixed Poisson Representations

We consider two fractional versions of a family of nonnegative integer-valued processes. We prove that their probability mass functions solve fractional Kolmogorov forward equations, and we show the overdispersion of these processes. As particular examples in this family, we can define fractional versions of some processes in the literature as the Pólya-Aeppli process, the Poisson inverse Gaussian process, and the negative binomial process. We also define and study some more general fractional versions with two fractional parameters.
Role of Rhipicephalus Annulatus Tick in Transmission of Lumpy Skin Disease Virus in Naturally Infected Cattle in Egypt

| Lumpy skin disease (LSD) is an infectious viral disease of cattle that results in serious economic and international trade consequences. Recently, hard ticks have been incriminated in lumpy skin disease virus (LSDV) transmission. The present study attempted to investigate the role of Rhipicephalus annulatus ticks, collected from naturally infected animals, in the transmission of LSDV. A total of 300 naturally infected cattle exhibiting the acute signs of LSD were clinically examined. Skin nodules and R. annulatus stages were collected from the diseased cattle. Samples were examined by PCR for the P32 gene and positive samples were confirmed by direct gene sequencing. Female engorged ticks were incubated for eggs deposition. LSDV infections in eggs and larvae that hatched from these eggs were screened by virus isolation on the chorioallontoic membrane (CAM) of embryonated chicken egg (ECE) and confirmed by PCR. Characteristic pock lesions were observed on the inoculated CAM. Positive PCR results were obtained from skin lesions, eggs, larvae and pock lesions of the CAM. Sequence analysis of the terminal 174bp of the P32 gene of LSDV sequences revealed a high degree of similarity to LSDV sequences available in Genbank database. The obtained results are highly suggestive for the possibility of the vertical transmission of LSDV in Rhipicephalus annulatus female ticks.
Effects of DDT and triclosan on tumor‐cell binding capacity and cell‐surface protein expression of human natural killer cells

1,1,1‐trichloro‐2,2‐bis(4‐chlorophenyl)ethane (DDT) and triclosan (TCS) are organochlorine (OC) compounds that contaminate the environment, are found in human blood and have been shown to decrease the tumor‐cell killing (lytic) function of human natural killer (NK) cells. NK cells defend against tumor cells and virally infected cells. They bind to these targets, utilizing a variety of cell surface proteins. The present study examined concentrations of DDT and TCS that decrease lytic function for alteration of NK binding to tumor targets. Levels of either compound that caused loss of binding function were then examined for effects on expression of cell‐surface proteins needed for binding. NK cells exposed to 2.5 μM DDT for 24 h (which caused a greater than 55% loss of lytic function) showed a decrease in NK binding function of about 22%, and a decrease in CD16 cell‐surface protein of 20%. NK cells exposed to 5 μM TCS for 24 h showed a decrease in ability to bind tumor cells of 37% and a decrease in expression of CD56 of about 34%. This same treatment caused a decrease in lytic function of greater than 87%. These results indicated that only a portion of the loss of NK lytic function seen with exposures to these compounds could be accounted for by loss of binding function. They also showed that loss of binding function is accompanied by a loss of cell‐surface proteins important in binding function. Copyright © 2012 John Wiley & Sons, Ltd.
OntoPair : Towards a Collaborative Game for Building OWL-Based Ontologies

Collective Intelligence takes advantage of collaboration, competition and integration. It often uses mixed groups of humans and computers to research in new unexplored ways. Ontologies, which are the main building block of the Semantic Web, are usually prepared by domain experts. We introduce a novel approach, which employs Collective Intelligence, towards building simple domain ontologies through a game called OntoPair, an entertaining web-based game that is able to build simple OWL-based ontologies based on collected information from players. The game collects properties and common-sense facts regarding an object by means of some fixed templates and translates them into OWL representation by aid of a mediator/mapper and builds simple domain ontologies after refinement in several iterations. We define the game and preform a small experiment that proves our idea.
Lay People's Perceptions of Sexually Transmitted Infections in Uganda

In order to understand lay people's perceptions of sexually transmitted infections (STIs) focus group discussions and semi-structured interviews were held with community members and patients with STIs in Mbarara and Kampala, Uganda. Symptoms of common STIs and the modes of transmission methods were known. STIs were perceived as naturalistic diseases caused by a tiny insect called akakoko or akawuka, although female infertility, one of the common complications of STIs, was perceived as a supernatural ailment. There was no stigma towards people with AIDS, although stigma towards people with other STIs was high. There were also strong negative attitudes towards the use of condoms. More than 60% of the patients interviewed had received treatment from the informal sector which included self-treatment and traditional healers. To reduce the incidence and complications of STIs, there may be a need to collaborate with the informal sector, to further evaluate the beliefs and practices identified in this study and to target them for health education.
Sudoku: Strategy versus Structure

Sudoku puzzles, and their variants, have become extremely popular in the last decade, and can now be found daily in most major U.S. newspapers. In addition to the countless books of Sudoku puzzles, there are many guides to Sudoku strategy and logic. (Some good references are the books [1, 3], and the web pages [5, 6]. The reader is also directed to these for explanations of some of the terms mentioned throughout this discussion.) The purpose of this paper is to relate a common class of strategies, used to solve the vast majority of Sudoku puzzles, to the formulation of Sudoku puzzles as assignment problems and as linear programs. In particular, we give a simple characterization of this class, using a well-known graph theorem, and show further how the ability of this set of strategies to solve a Sudoku puzzle also implies that the solution can be represented as the unique nonnegative solution to a system of linear equations. These results provide excellent applications of principles commonly presented in introductory classes in finite mathematics and combinatorial optimization, and point as well to some interesting open research problems in the area.
Lack of genetic association between the angiotensin-converting enzyme gene insertion/deletion polymorphism and longevity in a Han Chinese population

Introduction. The insertion/deletion polymorphism of the angiotensin-converting enzyme (ACE) gene has been reported to associate with human longevity. However, little information is available in a Han Chinese longevity population.Therefore, we investigated the association of the ACE gene insertion/ deletion polymorphism with longevity in a Han Chinese population. Materials and methods. We compared the distribution of ACE insertion/deletion genotype and allele frequencies in two groups: a longevity group (399 subjects) aged over 90 years and a control group (302 subjects) aged less than 60 years. Results. No difference in genotype and allele frequencies of the ACE gene insertion/deletion polymorphism was observed between the longevity group and the control group.When adjusting for gender, the difference between the longevity group and the control group was also not significant regarding the frequencies of the genotypes (male, p=0.994 and female, p=0.797) as well as allele frequencies (male, p=0.969 and female, p=0.884). Conclusions. No association of the ACE gene insertion/deletion polymorphism with longevity was observed in our Han Chinese population.
Effect of Delay to Definitive Surgical Fixation on Wound Complications in the Treatment of Closed, Intra-articular Calcaneus Fractures

Background: There are conflicting data regarding the benefits of delaying operative fixation of calcaneus fractures to decrease wound complication rates. The purpose of this study was to examine the effect of delaying fixation on wound complication rates as well as to identify other risk factors. Methods: A retrospective review at 4 institutions, including 24 surgeons, identified 405 closed, operatively treated, intra-articular calcaneus fractures. We compared fractures with and without wound complications with regards to patient demographics, medical risk factors, fracture severity, time to fixation, operative approach, primary subtalar arthrodesis, and surgeon experience. Results: Wound complications were observed in 21% (87/405) of fractures, of which 33% (29/87) required operative intervention. Male sex (P = .032), smoking (P = .028), and the extensile lateral approach (P < .001) were associated with higher complication rates. Fractures treated with an extensile lateral approach had an overall wound complication rate of 32.1%, while those treated with a sinus tarsi or percutaneous approach had an overall wound complication rate of 8.3% (odds ratio [OR], 5.3; 95% confidence interval [CI], 2.9-9.5; P < .001). Among patients treated with an extensile lateral approach, delayed operative fixation did not decrease wound complication rates despite comparable fracture severity across time points. In contrast, among fractures treated with less invasive approaches, delayed fixation beyond 2 weeks resulted in a significantly increased wound complication rate of 15.2% as compared to a wound complication rate of only 2.1% among fractures treated within a week of injury (OR, 3.2; 95% CI, 1.3-9.5; P = .01). This was observed despite similar fracture severity across time points. Primary subtalar arthrodesis did not impact complication rates. A higher wound complication rate among senior surgeons was likely secondary to their predilection for the extensile lateral approach. Conclusion: Delaying definitive fixation of closed, intra-articular calcaneus fractures did not decrease wound complication rates when using the extensile lateral approach, and we found an increased wound complication rate when using less invasive approaches. Level of Evidence: Level III, observational study.
Pseudo-oscillator Analysis of Scalar Nonlinear Time-Delay Systems Near a Hopf bifurcation

In this paper, a novel method named pseudo-oscillator analysis is developed for the local dynamics near a Hopf bifurcation of scalar nonlinear dynamical systems with time delays. For this purpose, a pseudo-oscillator that is slightly perturbed from an undamped oscillator is firstly constructed, its fundamental frequency is the same as the frequency at the bifurcation point, and the disturbance is associated with the original system. Next, the pseudo-power function, defined as the power function of the pseudo-oscillator, is estimated along a harmonic function. Then we conclude that the local dynamics near the Hopf bifurcation can be justified from the variation of the averaged pseudo-power function. The new method features a clear physical intuition and easy computation, and it yields very accurate prediction for the periodic solution resulted from the Hopf bifurcation, as shown in three illustrative examples.