Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp.

The relatedness of Brucella spp. and Ochrobactrum anthropi was studied by protein profiling, Western blot, immunoelectrophoresis and 16S rRNA analysis. Whole-cell and soluble proteins of brucellae and O. anthropi showed serological cross-reactivities quantitatively and qualitatively more intense than those existing with similar extracts of Agrobacterium spp. Numerical analysis of Western blot profiles of whole-cell extracts showed that O. anthropi LMG 3301 was closer to Brucella spp. than to O. anthropi LMG 3331T, a result not obtained by protein profiling. These differences were not observed by Western blot with soluble fractions, and immunoelectrophoretic analyses suggested that this was due to destruction of conformational epitopes in Western blot procedures with the subsequent simplification of antigenic profile. Analysis of the 16S rRNA sequences of strains previously used in the species definition confirmed that strain LMG 3301, and also LMG 3306, were closer to the brucellae, and that LMG 3331T was in a separate cluster. The LMG 3301 and the LMG 3331T clusters could also be separated by their different colistin sensitivity and by PCR with 16S rRNA Brucella primers, and both methods showed strains of both clusters among clinical isolates classified as O. anthropi by conventional tests. These results and those of previous DNA-DNA hybridization studies [Holmes, B. , Popoff, M. , Kiredjian, M. & Kersters, K. (1988). Int J Syst Bacteriol 38, 406-416] show that the LMG 3301 cluster and related clinical isolates should be given a new species status for which the name Ochrobactrum intermedium sp. nov. is proposed (type strain is LMG 3301T=NCTC 12171T = CNS 2-75T).
Delamination Growth and Residual Strength of Compressively Loaded Sandwich Panels with Stiffness Tailored Face Sheets

This study shows that a simple approach to stiffness tailoring of composite face sheets can improve the performance of sandwich panels under compressive loading when delaminations are present. The simple stiffness tailoring concept used here is to reposition of all 08 material (aligned with the loading direction) into regions of certain width near the edges of the sandwich panel. This concept has been shown to improve the buckling and postbuckling performance of solid plates and to offer control of delamination growth. To evaluate this tailoring design concept in sandwich panels, numerical simulations of onset and propagation of the delamination growth were conducted with uniform face sheets and tailored face sheets. The delamination front tracing method previously developed by the authors was used to perform the delamination growth analysis. The interfacial elements, which allow the growth of the delamination front to be traced, are placed at the interface between the top face sheet and the core in the undelaminated region. They enable calculation of the strain energy release rates and application of a fracture mechanics delamination growth criterion. Gap elements were used to avoid interfacial overlap. Based on the numerical study, the improvement in the ultimate load provided by the simple stiffness tailoring concept ranges from 80% to 100%, depending on the extent of tailoring. Substantial improvements in the residual strength and stiffness, after significant delamination growth, can also be observed. Therefore, this article provides a potential design concept that can improve the damage tolerance of sandwich panels without adding weight.
Akt1 Stimulates Homologous Recombination Repair of DNA Double-Strand Breaks in a Rad51-Dependent Manner

Akt1 is known to promote non-homologous end-joining (NHEJ)-mediated DNA double-strand break (DSB) repair by stimulation of DNA-PKcs. In the present study, we investigated the effect of Akt1 on homologous recombination (HR)-dependent repair of radiation-induced DSBs in non-small cell lung cancer (NSCLC) cells A549 and H460. Akt1-knockdown (Akt1-KD) significantly reduced Rad51 protein level, Rad51 foci formation and its colocalization with γH2AX foci after irradiation. Moreover, Akt1-KD decreased clonogenicity after treatment with Mitomycin C and HR repair, as tested by an HR-reporter assay. Double knockdown of Akt1 and Rad51 did not lead to a further decrease in HR compared to the single knockdown of Rad51. Consequently, Akt1-KD significantly increased the number of residual DSBs after irradiation partially independent of the kinase activity of DNA-PKcs. Likewise, the number of residual BRCA1 foci, indicating unsuccessful HR events, also significantly increased in the irradiated cells after Akt1-KD. Together, the results of the study indicate that Akt1 seems to be a regulatory component in the HR repair of DSBs in a Rad51-dependent manner. Thus, based on this novel role of Akt1 in HR and the previously described role of Akt1 in NHEJ, we propose that targeting Akt1 could be an effective approach to selectively improve the killing of tumor cells by DSB-inducing cytotoxic agents, such as ionizing radiation.
High rate of A2142G point mutation associated with clarithromycin resistance among Iranian Helicobacter pylori clinical isolates

This study aimed to investigate the clarithromycin resistance and its associated molecular mechanisms among Helicobacter pylori isolates from dyspeptic patients in Shiraz, Iran. From January to May 2014, 100 H. pylori strains were isolated from patients with gastroduodenal disorders. The resistance to clarithromycin was quantitatively evaluated, using Epsilometer (E‐test) method. Polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) was performed on all the isolates to detect A2143G and A2142G mutations in 23S rRNA gene. The H. pylori isolation rate was found to be 31.4%. E‐test showed that 20% of isolates were resistant to clarithromycin (MIC ≥ 1 mg/L). MIC of clarithromycin ranged between 0.016 and 24 mg/L. Findings of PCR‐RFLP showed that the A2142G was the most (90%) frequently point mutation, followed by the A2143G (10%). No statistically significant difference was found between H. pylori clarithromycin resistance point mutations and patients’ gender or age. To the best of our knowledge, this is the first report of high frequency of A2142G point mutation in Iran and probably in other regions of the world. Considering the increasing trend of H. pylori resistance to clarithromycin due to these mutations, it is crucial to investigate the new therapeutic approaches against H. pylori infection.
Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules

Autism spectrum disorder (ASD) is marked by a strong genetic heterogeneity, which is underlined by the low overlap between ASD risk gene lists proposed in different studies. In this context, molecular networks can be used to analyze the results of several genome-wide studies in order to underline those network regions harboring genetic variations associated with ASD, the so-called “disease modules. ” In this work, we used a recent network diffusion-based approach to jointly analyze multiple ASD risk gene lists. We defined genome-scale prioritizations of human genes in relation to ASD genes from multiple studies, found significantly connected gene modules associated with ASD and predicted genes functionally related to ASD risk genes. Most of them play a role in synapsis and neuronal development and function; many are related to syndromes that can be in comorbidity with ASD and the remaining are involved in epigenetics, cell cycle, cell adhesion and cancer.
Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet–Induced Obesity and Diabetes in Mice

OBJECTIVE—Diabetes and obesity are characterized by a low-grade inflammation whose molecular origin is unknown. We previously determined, first, that metabolic endotoxemia controls the inflammatory tone, body weight gain, and diabetes, and second, that high-fat feeding modulates gut microbiota and the plasma concentration of lipopolysaccharide (LPS), i.e., metabolic endotoxemia. Therefore, it remained to demonstrate whether changes in gut microbiota control the occurrence of metabolic diseases. RESEARCH DESIGN AND METHODS—We changed gut microbiota by means of antibiotic treatment to demonstrate, first, that changes in gut microbiota could be responsible for the control of metabolic endotoxemia, the low-grade inflammation, obesity, and type 2 diabetes and, second, to provide some mechanisms responsible for such effect. RESULTS—We found that changes of gut microbiota induced by an antibiotic treatment reduced metabolic endotoxemia and the cecal content of LPS in both high-fat–fed and ob/ob mice. This effect was correlated with reduced glucose intolerance, body weight gain, fat mass development, lower inflammation, oxidative stress, and macrophage infiltration marker mRNA expression in visceral adipose tissue. Importantly, high-fat feeding strongly increased intestinal permeability and reduced the expression of genes coding for proteins of the tight junctions. Furthermore, the absence of CD14 in ob/ob CD14−/− mutant mice mimicked the metabolic and inflammatory effects of antibiotics. CONCLUSIONS—This new finding demonstrates that changes in gut microbiota controls metabolic endotoxemia, inflammation, and associated disorders by a mechanism that could increase intestinal permeability. It would thus be useful to develop strategies for changing gut microbiota to control, intestinal permeability, metabolic endotoxemia, and associated disorders.
Descriptional complexity of nfa of different ambiguity

In this paper, we study the tradeoffs in descriptional complexity of NFA (nondeterministic finite automata) of various amounts of ambiguity. We say that two classes of NFA are separated if one class can be exponentially more succinct in descriptional sizes than the other. New results are given for separating DFA (deterministic finite automata) from UFA (unambiguous finite automata), UFA from MDFA (DFA with multiple initial states) and UFA from FNA (finitely ambiguous NFA). We present a family of regular languages that we conjecture to be a good candidate for separating FNA from LNA (linearly ambiguous NFA).
Antibody responses to Haemophilus influenzae type b conjugate vaccine in sickle cell disease.

OBJECTIVE: To investigate the immunogenicity of Haemophilus influenzae type b (Hib) conjugate vaccines in children with sickle cell disease. DESIGN: Open study. SETTING: Haemoglobinopathy clinic. SUBJECTS: Children with homozygous haemoglobin SS disease (HbSS), sickle haemoglobin C disease (HbSC), and sickle-beta thalassaemia disease (HbS-beta Thal). INTERVENTIONS: Children over the age of 2 years received a single dose of Hib-tetanus toxoid conjugate vaccine (PRP-T). MAIN OUTCOME MEASURES: Antibody response to Hib polysaccharide (PRP) approximately one month after vaccination. RESULTS: 77 children over the age of 2 years were studied,, 55 with HbSS, 16 with HbSC, and six with HbS-beta Thal. Before vaccination, 44% had anti-PRP IgG titres less than the level associated with long term protection (1.0 microgram/ml). After a single dose of PRP-T all children mounted an antibody titre > 1 microgram/ml. Geometric mean anti-PRP IgG titre achieved postvaccination (45.2 micrograms/ml 95% confidence interval (CI) 31.6 to 64.8) was comparable to that of a healthy population. Children with HbSC, however, had a significantly higher antibody titre postvaccination (91.1 micrograms/ml; 95% CI 32.7 to 254.4) than the children with HbSS (36.7 micrograms/ml; 95% CI 25.1 to 52.9). CONCLUSIONS: Children with a diagnosis of sickle cell disease who are over the age of 2 years make a vigorous antibody response to a single dose of PRP-T vaccine and hence we suggest unimmunised individuals in this group should receive a single dose of a Hib conjugate vaccine.
Test-Retest Reliability of Computational Network Measurements Derived from the Structural Connectome of the Human Brain

Structural magnetic resonance (MR) connectomics holds promise for the diagnosis, outcome prediction, and treatment monitoring of many common neurodevelopmental, psychiatric, and neurodegenerative disorders for which there is currently no clinical utility for MR imaging (MRI). Before computational network metrics from the human connectome can be applied in a clinical setting, their precision and their normative intersubject variation must be understood to guide the study design and the interpretation of longitudinal data. In this work, the reproducibility of commonly used graph theoretic measures is investigated, as applied to the structural connectome of healthy adult volunteers. Two datasets are examined, one consisting of 10 subjects scanned twice at one MRI facility and one consisting of five subjects scanned once each at two different facilities using the same imaging platform. Global graph metrics are calculated for unweighed and weighed connectomes, and two levels of granularity of the connectome are evaluated: one based on the 82-node cortical and subcortical parcellation from FreeSurfer and one based on an atlas-free parcellation of the gray-white matter boundary consisting of 1000 cortical nodes. The consistency of the unweighed and weighed edges and the module assignments are also computed for the 82-node connectomes. Overall, the results demonstrate good-to-excellent test-retest reliability for the entire connectome-processing pipeline, including the graph analytics, in both the intrasite and intersite datasets. These findings indicate that measurements of computational network metrics derived from the structural connectome have sufficient precision to be tested as potential biomarkers for diagnosis, prognosis, and monitoring of interventions in neurological and psychiatric diseases.
Activity and Interactions of Liposomal Antibiotics in Presence of Polyanions and Sputum of Patients with Cystic Fibrosis

Background To compare the effectiveness of liposomal tobramycin or polymyxin B against Pseudomonas aeruginosa in the Cystic Fibrosis (CF) sputum and its inhibition by common polyanionic components such as DNA, F-actin, lipopolysaccharides (LPS), and lipoteichoic acid (LTA). Methodology Liposomal formulations were prepared from a mixture of 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine (DMPC) or 1,2-Dipalmitoyl-sn-Glycero-3-Phosphocholine (DPPC) and Cholesterol (Chol), respectively. Stability of the formulations in different biological milieus and antibacterial activities compared to conventional forms in the presence of the aforementioned inhibitory factors or CF sputum were evaluated. Results The formulations were stable in all conditions tested with no significant differences compared to the controls. Inhibition of antibiotic formulations by DNA/F-actin and LPS/LTA was concentration dependent. DNA/F-actin (125 to 1000 mg/L) and LPS/LTA (1 to 1000 mg/L) inhibited conventional tobramycin bioactivity, whereas, liposome-entrapped tobramycin was inhibited at higher concentrations - DNA/F-actin (500 to 1000 mg/L) and LPS/LTA (100 to 1000 mg/L). Neither polymyxin B formulation was inactivated by DNA/F-actin, but LPS/LTA (1 to 1000 mg/L) inhibited the drug in conventional form completely and higher concentrations of the inhibitors (100 to 1000 mg/L) was required to inhibit the liposome-entrapped polymyxin B. Co-incubation with inhibitory factors (1000 mg/L) increased conventional (16-fold) and liposomal (4-fold) tobramycin minimum bactericidal concentrations (MBCs), while both polymyxin B formulations were inhibited 64-fold. Conclusions Liposome-entrapment reduced antibiotic inhibition up to 100-fold and the CFU of endogenous P. aeruginosa in sputum by 4-fold compared to the conventional antibiotic, suggesting their potential applications in CF lung infections.
Konrad-Zuse-Zentrum für Informationstechnik Berlin

This report presents the final realization and implementation of a global inexact Newton method proposed by Deuflhard. In order to create a complete piece of software, a recently developed iterative solver (program GBIT) due to Deuflhard, Freund, Walter is adapted and serves as the standard iterative linear solver. Alternative linear iterative solvers may be adapted as well, e.g. the widely distributed code GMRES. The new software package GIANT (Global Inexact Affine Invariant Newton Techniques) allows an efficient and robust numerical solution of very large scale highly nonlinear systems. Due to the user friendly interface and its modular design, the software package is open for an easy adaptation to specific problems. Numerical experiments for some selected problems illustrate performance and usage of the package.
Safety and biodistribution of 111In-amatuximab in patients with mesothelin expressing cancers using Single Photon Emission Computed Tomography-Computed Tomography (SPECT-CT) imaging

Amatuximab is a chimeric high-affinity monoclonal IgG1/k antibody targeting mesothelin that is being developed for treatment of mesothelin-expressing cancers. Considering the ongoing clinical development of amatuximab in these cancers, our objective was to characterize the biodistribution, and dosimetry of 111Indium (111In) radiolabelled amatuximab in mesothelin-expressing cancers. Between October 2011 and February 2013, six patients including four with malignant mesothelioma and two with pancreatic adenocarcinoma underwent Single Photon Emission Computed Tomography-Computed Tomography (SPECT/CT) imaging following administration of 111In amatuximab. SPECT/CT images were obtained at 2–4 hours, 24–48 hours and 96–168 hours after radiotracer injection. In all patients, tumor to background ratios (TBR) consistently met or exceeded an uptake of 1.2 (range 1.2–62.0) which is considered the minimum TBR that can be visualized. TBRs were higher in tumors of patients with mesothelioma than pancreatic adenocarcinoma. 111In-amatuximab uptake was noted in both primary tumors and metastatic sites. The radiotracer dose was generally well-tolerated and demonstrated physiologic uptake in the heart, liver, kidneys and spleen. This is the first study to show tumor localization of an anti-mesothelin antibody in humans. Our results show that 111In-amatuximab was well tolerated with a favorable dosimetry profile. It localizes to mesothelin expressing cancers with a higher uptake in mesothelioma than pancreatic cancer.
Whole-Plasma and High-Density Lipoprotein Subtraction Surface Lipid Composition in IDDM Men

To determine whether compositional abnormalities are present in high-density lipoprotein (HDL) in patients with insulin-dependent diabetes mellitus (IDOM) that might negate its putatively protective cardiovascular effects, we studied the plasma lipoproteins of 12 men with varying degrees of clinical control (mean fasting glucose 193 ± 10 mg/dl, mean glycoalbumin > 73% above control mean). The diabetic patients' basal plasma triglyceride, total- and free- (unesterified) cholesterol, HDL cholesterol (HDL-chol), and apolipoprotein Al, All, and B concentrations were similar to those of control subjects, but the freecholesterol- to-lecithin ratio, a new index of cardiovascular disease risk, was significantly increased in their plasma (0.97 ± 0.14 vs. 0.88 ± 0.07, P < .02) and their very-low-density lipoprotein (VLDL)-low-density lipoprotein (LDL) subfraction (1.50 ± 0.51 vs. 1.08 ± 0.15, P < .005). Although HDL2-chol was similar in diabetic and control groups, the HDL2-chol-to-free-cholesterol ratio (diabetic vs. control, 4.64 ± 1.7 vs. 1.96 ± 1.0 μmol/ml, P < .025) and the sphingomyelin-to-lecithin ratio (0.23 ± 0.08 vs. 0.20 ± 0.09, P < .025) were both significantly increased in the IDDM group. HDL3-chol was higher in the IDDM than in the control subjects (diabetic vs. control, 38.6 ± 5.2 vs. 32.7 ± 2.7 mg/dl, P < .005). In contrast to whole plasma and the VLDL + LDL subfraction, the freecholesterol- to-lecithin ratio of IDDM and control HDL subfractions were similar. These results demonstrate that men with IDDM have both qualitative and quantitative changes in lipoprotein surface lipid composition involving VLDL + LDL and HDL2 plasma subfractions. Because changes in the amounts of free cholesterol and phospholipid in lipoproteins have been shown to influence the directional fluxes of cholesterol, these compositional alterations suggest that IDDM may adversely affect both lipoproteinlipoprotein and lipoprotein-cell interactions.
Decision-making impairment in obsessive-compulsive disorder as measured by the Iowa Gambling Task.

OBJECTIVE This study aims to evaluate the process of decision-making in patients with obsessive-compulsive disorder (OCD) using the Iowa Gambling Task (IGT). In addition, we intend to expand the understanding of clinical and demographic characteristics that influence decision-making. METHOD Our sample consisted of 214 subjects (107 diagnosed with OCD and 107 healthy controls) who were evaluated on their clinical, demographic and neuropsychological features. Moreover, the Iowa Gambling Task (IGT), a task that detects and measures decision-making impairments, was used. RESULTS We found that OCD patients performed significantly worse on the IGT. Furthermore, features such as symptoms of anxiety did not influence IGT performance. CONCLUSION Impaired decision-making seems to be a key feature of OCD. Given that OCD is a complex heterogeneous disorder, homogeneous groups are necessary for an accurate characterization of our findings.
Do existing measures of Poincare plot geometry reflect nonlinear features of heart rate variability?

Heart rate variability (HRV) is concerned with the analysis of the intervals between heartbeats. An emerging analysis technique is the Poincare plot, which takes a sequence of intervals and plots each interval against the following interval. The geometry of this plot has been shown to distinguish between healthy and unhealthy subjects in clinical settings. The Poincare plot is a valuable HRV analysis technique due to its ability to display nonlinear aspects of the interval sequence. The problem is, how does one quantitatively characterize the plot to capture useful summary descriptors that are independent of existing HRV measures? Researchers have investigated a number of techniques: converting the two-dimensional plot into various one-dimensional views; the fitting of an ellipse to the plot shape; and measuring the correlation coefficient of the plot. The authors investigate each of these methods in detail and show that they are all measuring linear aspects of the intervals which existing HRV indexes already specify. The fact that these methods appear insensitive to the nonlinear characteristics of the intervals is an important finding because the Poincare plot is primarily a nonlinear technique. Therefore, further work is needed to determine if better methods of characterizing Poincare plot geometry can be found.
Formation of Giant Planets by Concurrent Accretion of Solids and Gas inside an Anticyclonic Vortex

We study the formation of a giant gas planet by the core accretion and gas capture process, with numerical simulations, under the assumption that the planetary core forms in the center of an anticyclonic vortex. The presence of the vortex concentrates centimeter- to meter-sized particles from the surrounding disk and speeds up the core formation process. Assuming that a planet of Jupiter mass is forming at 5 AU from the star, the vortex enhancement results in considerably shorter formation times than are found in standard core-accretion gas-capture simulations. Also, formation of a gas giant is possible in a disk with mass comparable to that of the minimum mass solar nebula.