Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of nodular bacteria of Scorpiurus muricatus in western Algeria and their impact on plant growth.

A total of 51 bacterial strains were isolated from root nodules of Scorpiurus muricatus sampled from 6 regions of western Algeria. Strain diversity was assessed by rep-PCR amplification fingerprinting, which grouped the isolates into 28 different clusters. Partial nucleotide sequencing of the 16S rRNA gene and BLAST analysis revealed that root nodules of S. muricatus were colonized by different species close to Rhizobium vignae, Rhizobium radiobacter, Rhizobium leguminosarum, Phyllobacterium ifriqiyense, Phyllobacterium endophyticum, Starkeya sp. , and Pseudomonas sp. However, none of these strains was able to form nodules on its host plant; even nodC was present in a single strain (SMT8a). The inoculation test showed a great improvement in the growth of inoculated plants compared with noninoculated control plants. A significant amount of indole acetic acid was produced by some strains, but only 2 strains could solubilize phosphate. In this report we described for the first time the diversity of bacteria isolated from root nodules of S. muricatus growing in different regions in western Algeria and demonstrated their potential use in promoting plant growth.
Role of receptor binding specificity in influenza A virus transmission and pathogenesis

The recent emergence of a novel avian A/H7N9 influenza virus in poultry and humans in China, as well as laboratory studies on adaptation and transmission of avian A/H5N1 influenza viruses, has shed new light on influenza virus adaptation to mammals. One of the biological traits required for animal influenza viruses to cross the species barrier that received considerable attention in animal model studies, in vitro assays, and structural analyses is receptor binding specificity. Sialylated glycans present on the apical surface of host cells can function as receptors for the influenza virus hemagglutinin (HA) protein. Avian and human influenza viruses typically have a different sialic acid (SA)‐binding preference and only few amino acid changes in the HA protein can cause a switch from avian to human receptor specificity. Recent experiments using glycan arrays, virus histochemistry, animal models, and structural analyses of HA have added a wealth of knowledge on receptor binding specificity. Here, we review recent data on the interaction between influenza virus HA and SA receptors of the host, and the impact on virus host range, pathogenesis, and transmission. Remaining challenges and future research priorities are also discussed.
Effectiveness of Postinoculation (R)-9-(2-Phosphonylmethoxypropyl)Adenine Treatment for Prevention of Persistent Simian Immunodeficiency Virus SIVmne Infection Depends Critically on Timing of Initiation and Duration of Treatment

ABSTRACT (R)-9-(2-Phosphonylmethoxypropyl)adenine (PMPA), an acyclic nucleoside phosphonate analog, is one of a new class of potent antiretroviral agents. Previously, we showed that PMPA treatment for 28 days prevented establishment of persistent simian immunodeficiency virus (SIV) infection in macaques even when therapy was initiated 24 h after intravenous virus inoculation. In the present study, we tested regimens involving different intervals between intravenous inoculation with SIV and initiation of PMPA treatment, as well as different durations of treatment, for the ability to prevent establishment of persistent infection. Twenty-four cynomolgus macaques (Macaca fascicularis) were studied for 46 weeks after inoculation with SIV. All mock-treated control macaques showed evidence of productive infection within 2 weeks postinoculation (p.i.). All macaques that were treated with PMPA for 28 days beginning 24 h p.i. showed no evidence of viral replication following discontinuation of PMPA treatment. However, extending the time to initiation of treatment from 24 to 48 or 72 h p.i. or decreasing the duration of treatment reduced effectiveness in preventing establishment of persistent infection. Only half of the macaques treated for 10 days, and none of those treated for 3 days, were completely protected when treatment was initiated at 24 h. Despite the reduced efficacy of delayed and shortened treatment, all PMPA-treated macaques that were not protected showed delays in the onset of cell-associated and plasma viremia and antibody responses compared with mock controls. These results clearly show that both the time between virus exposure and initiation of PMPA treatment as well as the duration of treatment are crucial factors for prevention of acute SIV infection in the macaque model.
Reliability-based hybrid MMSE/subspace-max-log-APP MIMO detector

We present an algorithm which is a flexible and scalable trade-off both in complexity and performance between unbiased MMSE and Max-Log-APP MIMO detection. In a first step, LLRs are generated based on linear detection (Max-Log per stream). A predefined number of LLRs is chosen as 'reliable' based on LLR magnitude. For the remaining 'unreliable' subspace we compute the joint Max-Log-APP solution. The algorithm contains unbiased MMSE detection as well as full Max-Log-APP detection as special cases and is suited for iterative detection-decoding.
Recurrent fetal hydrocephalus: Two rare cases of non-familial hydrocephalus recurring in consecutive pregnancies

Objectives: To assess the effect of Evidence Based Medicine (EBM) workshop on knowledge and skills of physicians towards EBM use in the near future as well as in the long run. Methods: This is a randomized controlled trial conducted in the primary health care administration center in Dammam, Saudi Arabia between October and November 2008. Fifty-nine primary care physicians in the intervention group participated in the EBM workshops while 89 physicians from the control group attended other primary health care activities other than EBM workshop. The main outcome was to measure the change in the participants’ level of awareness and competencies in EBM components (including formulation of questions, literature searching, critical thinking and appraisal) using a pre-designed questionnaire before, immediately after, and 4 months after the workshop. Results: Evidence Based Medicine workshops improved physician’s scores in all components of EBM, from 38.9%±20.0% at pre-test to 81.4%±10.6% post-test, and sustained this improvement to a lesser degree to 66.8%±10.0% 4 months post-intervention test ( p <0.001 for the differences in all scores). Conclusion: Participating in EBM workshop significantly enhanced physicians’ ability to formulate questions, performed literature search, critical appraisal, and applied best-evidence in clinical practice, which retained up to 4 months post-test.
A mapping study on bayesian networks for software quality prediction

Bayesian Networks (BN) have been used for decision making in software engineering for many years. We investigate the current status of BNs in predicting software quality in three aspects: 1) techniques used for parameter learning, 2) techniques used for structure learning, and 3) type of variables that represent BN nodes. We performed a systematic mapping study on 38 primary studies that employed BNs to predict software quality. The most popular technique for building the final structure of BNs is the use of expert knowledge with different inference algorithms. Variables in BNs are treated as categorical in more than 70% of studies. Compared to other domains, the usage of BNs is still very limited due to high dependency on expert knowledge and tools.
Lost Letter Measure of Variation in Altruistic Behaviour in 20 Neighbourhoods

Altruistic behaviour varies across human populations and this variation is likely to be partly explained by variation in the ecological context of the populations. We hypothesise that area level socio-economic characteristics will determine the levels of altruism found in individuals living in an area and we use a lost letter experiment to measure altruism across 20 neighbourhoods with a wide range of income deprivation scores in London, UK. The results show a strong negative effect of neighbourhood income deprivation on altruistic behaviour, with letters dropped in the poorest neighbourhoods having 91% lower odds of being returned than letters dropped in the wealthiest neighbourhoods. We suggest that measures of altruism are strongly context dependant.
A Comparative Genomic Analysis of Energy Metabolism in Sulfate Reducing Bacteria and Archaea

The number of sequenced genomes of sulfate reducing organisms (SRO) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. In this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii) are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H+-pyrophosphatases, complex I homologs, Rnf, and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases, and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H2, formate, pyruvate, NAD(P)H, β-oxidation, and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.
Small Airways Involvement in Patients with Rheumatoid Arthritis

Objectives: One of the common causes of morbidity in patients with RA is pulmonary involvement. Some studies have shown that the possible abnormal results of pulmonary function tests in rheumatoid disease are higher than usual. We aimed to evaluate the prevalence of spirometric abnormalities in patients with RA. Materials & Methods: This case-control study was conducted on 99 patients with RA who referred to a rheumatology clinic in Qazvin, northwest Iran. Sixty five age- and sex-matched healthy controls were recruited as well. History taking, physical examination, laboratory tests and spirometry were performed for the participants. RA severity was assessed according to Disease Activity Score 28 (DAS28). The data were processed using SPSS software version 16. Chi square and student's t test and multiple logistic regressions were used as appropriated. Results: The mean (±SD) age of the patients was 46 (±10.5) years. The mean (±SD) duration of disease was 4.8 (±5.4) years, and the mean (±SD) DAS28 was 2.5 (±1.1). Dyspnea was the most common respiratory complaint (6.1%). Three (3%) patients had mild restrictive, 2 (2%) patients mild obstructive, and one (1%) patient moderate obstructive diseases. In the control group, only one participant had mild restrictive pulmonary disease (P<0.05). A significant decrease of FEF25 [OR=3.2; 95%CI (1.9-4.5)], FEF50 [OR=2.5; 95% CI (1.7-3.1)], FEF75 [OR=2.3; 95% CI (1.4-2.7)] and FEF25-75 [OR=2.7; 95% CI (1.7-3.5)] was observed in patients compared with the control group. We found no correlation between the patients’ age, duration and severity of the disease, and laboratory tests with spirometric indices. Conclusion: It is recommended that patients with RA be visited on a regular basis and PFT be done for them for the early diagnosis of pulmonary involvement.
Spontaneous Autoimmune Diabetes in Monoclonal T Cell Nonobese Diabetic Mice

It has been established that insulin-dependent diabetes mellitus (IDDM) in nonobese diabetic (NOD) mice results from a CD4+ and CD8+ T cell–dependent autoimmune process directed against the pancreatic beta cells. The precise roles that beta cell–reactive CD8+ and CD4+ T cells play in the disease process, however, remain ill defined. Here we have investigated whether naive beta cell–specific CD8+ and CD4+ T cells can spontaneously accumulate in pancreatic islets, differentiate into effector cells, and destroy beta cells in the absence of other T cell specificities. This was done by introducing Kd– or I-Ag7–restricted beta cell–specific T cell receptor (TCR) transgenes that are highly diabetogenic in NOD mice (8.3- and 4.1-TCR, respectively), into recombination-activating gene (RAG)-2–deficient NOD mice, which cannot rearrange endogenous TCR genes and thus bear monoclonal TCR repertoires. We show that while RAG-2−/− 4.1-NOD mice, which only bear beta cell–specific CD4+ T cells, develop diabetes as early and as frequently as RAG-2+ 4.1-NOD mice, RAG-2−/− 8.3-NOD mice, which only bear beta cell–specific CD8+ T cells, develop diabetes less frequently and significantly later than RAG-2+ 8.3-NOD mice. The monoclonal CD8+ T cells of RAG-2−/− 8.3-NOD mice mature properly, proliferate vigorously in response to antigenic stimulation in vitro, and can differentiate into beta cell–cytotoxic T cells in vivo, but do not efficiently accumulate in islets in the absence of a CD4+ T cell–derived signal, which can be provided by splenic CD4+ T cells from nontransgenic NOD mice. These results demonstrate that naive beta cell– specific CD8+ and CD4+ T cells can trigger diabetes in the absence of other T or B cell specificities, but suggest that efficient recruitment of naive diabetogenic beta cell–reactive CD8+ T cells to islets requires the assistance of beta cell–reactive CD4+ T cells.
An augmented Lagrangian coordination-decomposition algorithm for solving distributed non-convex programs

A novel augmented Lagrangian method for solving non-convex programs with nonlinear cost and constraint couplings in a distributed framework is presented. The proposed decomposition algorithm is made of two layers: The outer level is a standard multiplier method with penalty on the nonlinear equality constraints, while the inner level consists of a block-coordinate descent (BCD) scheme. Based on standard results on multiplier methods and recent results on proximal regularised BCD techniques, it is proven that the method converges to a KKT point of the non-convex nonlinear program under a semi-algebraicity assumption. Efficacy of the algorithm is demonstrated on a numerical example.
Clinical potential of pulsating aerosol for sinus drug delivery

There is a high incidence of nasal disorders including chronic rhinosinusitis (CRS), affecting ∼ 14% of the total population. However, a topical treatment regimen shows only modest efficacy, and drug delivery to the posterior nose, osteomeatal area, and paranasal sinuses is still a challenge. Therefore, the primary treatment option of CRS is functional endonasal sinus surgery (FESS). Most nasally administered aerosolized drugs are efficiently filtered by the nasal valve and do not reach the sinuses, the site of chronic inflammation. Sinus ventilation, nasal and paranasal aerosol deposition can be achieved by using a pulsating airflow, offering new topical treatment options for nasal disorders. Inhalation studies in nasal casts and in healthy volunteers have shown up to 8% of the nasally deposited drug within the sinuses, which could not be achieved using nasal pump sprays. In addition, compared with nasal pump sprays, retention kinetics of the radiolabel deposit in the nose was prolonged by about a factor of five. With this efficiency, topical aerosol therapies of sinus disorders can be achieved and, owing to the prolonged retention, reduced application modes are possible. This offers new treatment options of sinus-nasal disorders in comparison with or after FESS.
Molecular Mechanisms That Underlie the Dynamic Adaptation of Innate Monocyte Memory to Varying Stimulant Strength of TLR Ligands

In adaptation to rising stimulant strength, innate monocytes can be dynamically programed to preferentially express either pro- or anti-inflammatory mediators. Such dynamic innate adaptation or programing may bear profound relevance in host health and disease. However, molecular mechanisms that govern innate adaptation to varying strength of stimulants are not well understood. Using lipopolysaccharide (LPS), the model stimulant of toll-like-receptor 4 (TLR4), we reported that the expressions of pro-inflammatory mediators are preferentially sustained in monocytes adapted by lower doses of LPS, and suppressed/tolerized in monocytes adapted by higher doses of LPS. Mechanistically, monocytes adapted by super-low dose LPS exhibited higher levels of transcription factor, interferon regulatory factor 5 (IRF5), and reduced levels of transcriptional modulator B lymphocyte-induced maturation protein-1 (Blimp-1). Intriguingly, the inflammatory monocyte adaptation by super-low dose LPS is dependent upon TRAM/TRIF but not MyD88. Similar to LPS, we also observed biphasic inflammatory adaptation and tolerance in monocytes challenged with varying dosages of TLR7 agonist. In sharp contrast, rising doses of TLR3 agonist preferentially caused inflammatory adaptation without inducing tolerance. At the molecular level, the differential regulation of IRF5 and Blimp-1 coincides with unique monocyte adaptation dynamics by TLR4/7 and TLR3 agonists. Our study provides novel clue toward the understanding of monocyte adaptation and memory toward distinct TLR ligands.
Biopsy vs. superficial scraping: detection of human papillomavirus 6, 11, 16, and 18 in potentially malignant and malignant oral lesions.

BACKGROUND Several epidemiologic studies have shown a broad variation in the prevalence of human papillomavirus (HPV) in oral precancerous tissues and oral carcinomas. METHODS Biopsies and superficial scrapes of lesions, clinically suspected of HPV infection, were taken from patients with potentially malignant and malignant oral lesions, and subject to HPV DNA detection by PCR-Southern blot analysis. RESULTS From 22 patients with potentially malignant and malignant lesions analyzed, 41% of the biopsies were HPV DNA positive, whereas 95-100% of the superficial scrapes were positive (McNemar, P < 0.0001). Clinical presumption of HPV infection detected 67% (P < 0.0001) of the HPV DNA positive cases compared with 48% (P < 0.0001) determined by cytology and histopathology. The prevalence of HPV 6, 11, 16 and 18 in the oral mucosa was studied in 59 individuals. While 9% of normal controls were HPV DNA positive, 100% of the patients with potentially malignant and malignant lesions were HPV DNA positive, and the prevailing genotype was HPV 16 followed by HPV 18. CONCLUSIONS The higher HPV DNA detection rate in superficial oral scrapes than in biopsies suggests that accurate epidemiological information on oral HPV infection/oral carcinogenesis depends not only on the DNA detection technique, but also on the tissue/cell sampling procedure.
Bioreducible Liposomes for Gene Delivery: From the Formulation to the Mechanism of Action

Background A promising strategy to create stimuli-responsive gene delivery systems is to exploit the redox gradient between the oxidizing extracellular milieu and the reducing cytoplasm in order to disassemble DNA/cationic lipid complexes (lipoplexes). On these premises, we previously described the synthesis of SS14 redox-sensitive gemini surfactant for gene delivery. Although others have attributed the beneficial effects of intracellular reducing environment to reduced glutathione (GSH), these observations cannot rule out the possible implication of the redox milieu in its whole on transfection efficiency of bioreducible transfectants leaving the determinants of DNA release largely undefined. Methodology/Principal Findings With the aim of addressing this issue, SS14 was here formulated into binary and ternary 100 nm-extruded liposomes and the effects of the helper lipid composition and of the SS14/helper lipids molar ratio on chemical-physical and structural parameters defining transfection effectiveness were investigated. Among all formulations tested, DOPC/DOPE/SS14 at 25∶50∶25 molar ratio was the most effective in transfection studies owing to the presence of dioleoyl chains and phosphatidylethanolamine head groups in co-lipids. The increase in SS14 content up to 50% along DOPC/DOPE/SS14 liposome series yielded enhanced transfection, up to 2.7-fold higher than that of the benchmark Lipofectamine 2000, without altering cytotoxicity of the corresponding lipoplexes at charge ratio 5. Secondly, we specifically investigated the redox-dependent mechanisms of gene delivery into cells through tailored protocols of transfection in GSH-depleted and repleted vs. increased oxidative stress conditions. Importantly, GSH specifically induced DNA release in batch and in vitro. Conclusions/Significance The presence of helper lipids carrying unsaturated dioleoyl chains and phosphatidylethanolamine head groups significantly improved transfection efficiencies of DOPC/DOPE/SS14 lipoplexes. Most importantly, this study shows that intracellular GSH levels linearly correlated with transfection efficiency while oxidative stress levels did not, highlighting for the first time the pivotal role of GSH rather than oxidative stress in its whole in transfection of bioreducible vectors.
Characterization and modelling of spectrum for dynamic spectrum access with spatial statistics and random fields

There is need to develop better models and characterization methods for spectrum usage and radio environments of cognitive radios. Currently different theoretical and simulation based approaches towards enabling dynamic spectrum access would greatly benefit from the possibility to generate synthetic data for testing purposes. Such Radio Environment Maps must statistically exhibit the characteristics of realistic environments. Previous and on-going spectrum measurement campaigns are generating a vast amount of such data. In this paper we provide a partial answer to the spectrum modelling problem by showing how one can characterize and model spectrum maps with spatial statistics and random fields. We present the basic mathematical premises for building models and also through examples outline how one can generate useful statistics from real measurement data.
Structural SCOP Superfamily Level Classification Using Unsupervised Machine Learning

One of the major research directions in bioinformatics is that of assigning superfamily classification to a given set of proteins. The classification reflects the structural, evolutionary, and functional relatedness. These relationships are embodied in a hierarchical classification, such as the Structural Classification of Protein (SCOP), which is mostly manually curated. Such a classification is essential for the structural and functional analyses of proteins. Yet a large number of proteins remain unclassified. In this study, we have proposed an unsupervised machine learning approach to classify and assign a given set of proteins to SCOP superfamilies. In the method, we have constructed a database and similarity matrix using P-values obtained from an all-against-all BLAST run and trained the network with the ART2 unsupervised learning algorithm using the rows of the similarity matrix as input vectors, enabling the trained network to classify the proteins from 0.82 to 0.97 f-measure accuracy. The performance of ART2 has been compared with that of spectral clustering, Random forest, SVM, and HHpred. ART2 performs better than the others except HHpred. HHpred performs better than ART2 and the sum of errors is smaller than that of the other methods evaluated.