Miracle-dz/UniFAR-FTUs huggingface dataset:
Arsenic accumulating and transforming bacteria isolated from contaminated soil for potential use in bioremediation

Arsenic (As) is a metalloid and considered harmful due to its toxic and carcinogenic effects. Removal of arsenic is of great importance for human welfare. The main objective of this study was to isolate arsenic-resistant bacteria that are capable of removing arsenic from the environment. Soil samples were collected from an arsenic-affected area of West Bengal, India and 10 different bacterial strains were isolated. The minimum inhibitory concentration (MIC) values of the isolates varied widely in the range 50–125 mM (As) as arsenate and 10–100 mM (As) as arsenite. TEM and EDAX analysis were done to confirm intracellular accumulation of arsenic. The 16s RNA and phylogenetic analysis showed that seven isolates belonged to γ-proteobacterium, two isolates belonged to Firmicutes and one was identified as Kocuria genera. Some of these bacteria could oxidize arsenite to arsenate and all others could reduce arsenate to arsenite. The growth pattern of the bacterial strains in presence and absence of arsenic was also observed. All the 10 isolates exhibited multiple heavy metal (like Ni, Zn, Cu, Pb, Co, etc.) tolerances. Thus, these new bacterial strains could conveniently be used for bioremediation of soil and effluents and the enzymes produced by them may be used for commercial exploitation.
Langmuir Slip Model for Air Bearing Simulation Using the Lattice Boltzmann Method

The lattice Boltzmann method (LBM) is utilized to simulate the nanoscale flow physics of air bearings in the head-disk interface. In the high Knudsen number flow analysis of air bearings, the slip boundary model is very important to guarantee the accuracy of solution. In this paper, the Langmuir slip model for the rarefied gas flow was incorporated and its feasibility and accuracy was examined in nanoscale flow simulations. It was shown that our LBM can solve the fluid flow of air bearing with high efficiency due to its complex geometry handling capability and high accuracy comparable to the Boltzmann transport equation in the slip flow regime. The LBM model developed in this paper could serve as a powerful tool for the design of advanced air-bearing systems
Suicide Ideation Among Parents Bereaved by the Violent Deaths of Their Children

Suicidal behaviors of parents bereaved by a child's suicide have received considerable attention by researchers, but deaths by other violent causes have not. We observed 175 bereaved parents for five years following three types of violent death: accidents, homicides, and suicides. The results showed that the incidence of suicidal ideation (SI) among the study parents was 13% ( n = 34) over the 5 years and 9% ( n = 24) at the initial data collection four months after the death of an adolescent or young adult child. Comparisons of study parents grouped by the presence or absence of SI showed that after corrections were made for the number of t -tests conducted, statistically significant differences on three of four outcome variables remained (mental distress, depression, and posttraumatic stress disorder [PTSD], but not on acceptance of the child's death). The groups also differed significantly on four of seven mediating variables examined. The hypothesis that parents whose children died by suicide would report the highest incidence of suicidal ideation was not supported. Regression analyses showed that SI was a significant predictor of depression one year, but not five years, after the violent death of a child. The hypothesis that SI would predict both depression and PTSD one year postdeath was not supported. Clinical and policy recommendations are offered.
Algorithm for moving object detection and tracking in video sequence using color feature

In this paper we present an algorithm research on moving object detection and tracking in video sequence using color feature. In this algorithm we combine between the probability product kernels as a similarity measure, and the integral image to compute the histograms of all possible target regions of object tracking in data sequence. The objective of this algorithm is to associate target object in consecutive video frames. The association can be especially difficult when the objects are moving fast relative to the frame rate. Another situation that increases the complexity of the problem is when the tracked object changes orientation over time. For these situations the proposed algorithm is used to improve the tracking accuracy and decrease the tracking failures in the video tracking process, and usually employ a motion model which describes how the image of the target might change for different possible motions of the object.
Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS

ABSTRACT To examine phylogenetic identity and metabolic activity of individual cells in complex microbial communities, we developed a method which combines rRNA-based in situ hybridization with stable isotope imaging based on nanometer-scale secondary-ion mass spectrometry (NanoSIMS). Fluorine or bromine atoms were introduced into cells via 16S rRNA-targeted probes, which enabled phylogenetic identification of individual cells by NanoSIMS imaging. To overcome the natural fluorine and bromine backgrounds, we modified the current catalyzed reporter deposition fluorescence in situ hybridization (FISH) technique by using halogen-containing fluorescently labeled tyramides as substrates for the enzymatic tyramide deposition. Thereby, we obtained an enhanced element labeling of microbial cells by FISH (EL-FISH). The relative cellular abundance of fluorine or bromine after EL-FISH exceeded natural background concentrations by up to 180-fold and allowed us to distinguish target from non-target cells in NanoSIMS fluorine or bromine images. The method was optimized on single cells of axenic Escherichia coli and Vibrio cholerae cultures. EL-FISH/NanoSIMS was then applied to study interrelationships in a dual-species consortium consisting of a filamentous cyanobacterium and a heterotrophic alphaproteobacterium. We also evaluated the method on complex microbial aggregates obtained from human oral biofilms. In both samples, we found evidence for metabolic interactions by visualizing the fate of substrates labeled with 13C-carbon and 15N-nitrogen, while individual cells were identified simultaneously by halogen labeling via EL-FISH. Our novel approach will facilitate further studies of the ecophysiology of known and uncultured microorganisms in complex environments and communities.
Engineering a horseradish peroxidase C stable to radical attacks by mutating multiple radical coupling sites

Peroxidases have great potential as industrial biocatalysts. In particular, the oxidative polymerization of phenolic compounds catalyzed by peroxidases has been extensively examined because of the advantage of this method over other conventional chemical methods. However, the industrial application of peroxidases is often limited because of their rapid inactivation by phenoxyl radicals during oxidative polymerization. In this work, we report a novel protein engineering approach to improve the radical stability of horseradish peroxidase isozyme C (HRPC). Phenylalanine residues that are vulnerable to modification by the phenoxyl radicals were identified using mass spectrometry analysis. UV‐Vis and CD spectra showed that radical coupling did not change the secondary structure or the active site of HRPC. Four phenylalanine (Phe) residues (F68, F142, F143, and F179) were each mutated to alanine residues to generate single mutants to examine the role of these sites in radical coupling. Despite marginal improvement of radical stability, each single mutant still exhibited rapid radical inactivation. To further reduce inactivation by radical coupling, the four substitution mutations were combined in F68A/F142A/F143A/F179A. This mutant demonstrated dramatic enhancement of radical stability by retaining 41% of its initial activity compared to the wild‐type, which was completely inactivated. Structure and sequence alignment revealed that radical‐vulnerable Phe residues of HPRC are conserved in homologous peroxidases, which showed the same rapid inactivation tendency as HRPC. Based on our site‐directed mutagenesis and biochemical characterization, we have shown that engineering radical‐vulnerable residues to eliminate multiple radical coupling can be a good strategy to improve the stability of peroxidases against radical attack. Biotechnol. Bioeng. 2015;112: 668–676. © 2014 Wiley Periodicals, Inc.
Emotion and Efficacy Routes to Normative and Non-normative Collective Action 1 Explaining Radical Group Behaviour : Developing Emotion and Efficacy Routes to Normative and Non-normative Collective Action

A recent model of collective action distinguishes two distinct pathways; an emotional pathway whereby anger in response to injustice motivates action, and an efficacy pathway where the belief that issues can be solved collectively increases the likelihood that group members take action (van Zomeren, Spears, Fischer, & Leach, 2004). Research supporting this model has, however, focused entirely on relatively normative actions such as participating in demonstrations. The authors argue that the relations between emotions, efficacy and action differ for more extreme, non-normative actions and propose (1) that non-normative actions are often driven by a sense of low efficacy and (2) that contempt, which, unlike anger, entails psychological distancing and a lack of reconciliatory intentions, predicts non-normative action. These ideas are tested in three survey studies examining student protests against tuition fees in Germany (N = 332), Indian Muslims’ action support in relation to ingroup disadvantage (N = 156), and British Muslims’ responses to British foreign policy (N = 466). Results were generally supportive of predictions and indicated that (a) anger was strongly related to normative action but overall unrelated or less strongly related to non-normative action; (b) contempt was either unrelated or negatively related to normative action but significantly positively predicted nonnormative action; and (c) that efficacy was positively related to normative action and negatively to non-normative action. The implications of these findings for understanding and dealing with extreme intergroup phenomena such as terrorism are discussed.
Endovascular therapy for critical limb ischemia

Critical limb ischemia (CLI) represents an advanced disease state of peripheral arterial disease. It manifests as lower extremity ischemic rest pain or ischemic skin lesions leading to ulceration or gangrene. Patients with CLI often have multiple medical comorbidities and a 1-year mortality rate of 25% and a 1-year amputation rate of 25%. Historically, bypass surgery with autogenous veins for flow restoration has been the first-line therapy for CLI. However, advances in endovascular techniques and device technology have changed the treatment paradigm. Catheter-based technologies are rapidly evolving at a rate that is outpacing large-scale studies evaluating relevant clinical outcomes. Patients with CLI require a multidisciplinary management approach centered on aggressive medical therapies, wound care and prompt revascularization, with an emphasis on limb salvage. This review summarizes the contemporary endovascular therapies including balloon angioplasty, atherectomy and bare-metal stenting. In addition, we review emerging technologies, such as drug-eluting stents, drug-coated balloons and chronic total occlusion recanalization devices.
Comparison of Perturbed Pathways in Two Different Cell Models for Parkinson's Disease with Structural Equation Model

Increasing evidence indicates that different morphological types of cell death coexist in the brain of patients with Parkinson's disease (PD), but the molecular explanation for this is still under investigation. In this study, we identified perturbed pathways in two different cell models for PD through the following procedures: (1) enrichment pathway analysis with differentially expressed genes and the Reactome pathway database, and (2) construction of the shortest path model for the enriched pathway and detection of significant shortest path model with fitting time-course microarray data of each PD cell model to structural equation model. Two PD cell models constructed by the same neurotoxin showed different perturbed pathways. That is, one showed perturbation of three Reactome pathways, including cellular senescence, chromatin modifying enzymes, and chromatin organization, while six modules within metabolism pathway represented perturbation in the other. This suggests that the activation of common upstream cell death pathways in PD may result in various down-stream processes, which might be associated with different morphological types of cell death. In addition, our results might provide molecular clues for coexistence of different morphological types of cell death in PD patients.
Endoplasmic reticulum aminopeptidase 2 involvement in metastasis of oral cavity squamous cell carcinoma discovered by proteome profiling of primary cancer cells

Oral cavity squamous cell carcinoma (OSCC) is a leading cause of cancer-related deaths worldwide and associated with poor prognosis and mortality. Discovery of proteins that can improve OSCC treatment is needed. Using comparative proteome profiling of primary cells derived from OSCC and adjacent noncancerous epithelium, endoplasmic reticulum aminopeptidases 2 (ERAP2) has been identified as an OSCC-associated protein. Compared with the adjacent normal tissues, ERAP2 levels were determined to be significantly elevated in OSCC tissues using quantitative real-time PCR and immunohistochemistry. Importantly, overexpression of ERAP2 was associated with positive N stage, advanced overall stage, positive perineural invasion, and tumor depth (P = 0.041, 0.015, 0.010, and 0.032, respectively). The overall survival rates of patients without and with the ERAP2 overexpression were 71.9% and 56.0%, respectively (P = 0.029). Furthermore, knockdown of ERAP2 inhibited the migration and invasion abilities of OSCC cells. Our results collectively show that ERAP2 overexpression is associated with the cervical metastasis and poorer prognosis of OSCC.
Importance and limits of pre-hospital electrocardiogram in patients with ST elevation myocardial infarction undergoing percutaneous coronary angioplasty

Background: The purpose of this study is to present data on the effects of pre-hospital electrocardiogram (PH-ECG) on the outcome of ST elevation myocardial infarction (STEMI) patients treated with percutaneous coronary angioplasty (PCI) included in a registry undertaken in the Italian region of Lombardy. Pre-hospital 12-lead electrocardiogram is recommended by current guidelines in order to achieve faster times to reperfusion in patients with STEMI. Methods: The registry includes 3901 STEMI patients who underwent primary PCI over an 18-month period. Results: Mean age was 63 ± 12 years. Admission through the emergency medical system (EMS) occurred in 1603 patients (40%): they were older, more frequently had previous MI, TIMI flow = 0 at entry and were more frequently in Killip class >1 than patients who were not admitted through the EMS. Among the patients admitted through the EMS, PH-ECG was obtained in 475 patients (12%). These patients had less frequently an anterior MI, but more frequently had absence of TIMI flow at entry than patients whose ECG was not teletransmitted. Moreover, they had a significantly shorter first medical contact-to-balloon time and a trend toward a lower 30-day death rate (5.3% vs 7.9 %, p = 0.06). However, only patients in Killip class 2–3 had a significantly lower mortality when the diagnostic ECG was transmitted, whereas no difference was found in Killip class 1 or Killip class 4 patients. Conclusions: In this registry, PH-ECG significantly decreased first medical contact-to-balloon time. Attempts to achieve faster reperfusion times should be undertaken, as this may result in improved outcome, particularly in patients with mild to moderate symptoms of heart failure.
Staging and treatment with cyclophosphamide, vincristine and prednisone (CVP) in advanced cutaneous t‐cell lymphomas

Twenty‐three consecutive patients with cutaneous T‐cell lymphomas were submitted to staging procedures including lymphangiography, bone marrow biopsy and aspiration, peripheral blood morphological examination, peritoneoscopy with liver and spleen biopsy, and in selected patients lymph node biopsies. Extracutaneous disease (lymph nodes, bone marrow, liver and spleen) was detected in 12 patients. Bone marrow was involved in 25 per cent of the patients at presentation (all patients had lymph node involvement) and in two of nine patients with advanced disease during the follow‐up. Peripheral blood was involved in 65 per cent of the patients at presentation (ten patients with advanced disease) and in six of nine patients with advanced disease during the follow‐up. In 16 patients with advanced disease (T3‐T4 and/or extracutaneous disease), CVP was given with a 50 per cent objective response rate and four complete remissions of 47+, 12+, 19 and 19 months duration. Median survival of patients with advanced disease was 4 years.
Effect of Vascular Endothelial Growth Factor and Testis Tissue Culture on Spermatogenesis in Bovine Ectopic Testis Tissue Xenografts

Abstract Bovine ectopic testis tissue grafting is a technique that can be used to study bovine spermatogenesis and for the production of germ cells for a variety of applications. Approximately 10% of seminiferous tubule cross sections in testis grafts contain spermatids, providing a unique tool to investigate what regulates germ cell differentiation. We hypothesized that manipulation of testis tissue grafts would increase the percentage of seminiferous tubule cross sections undergoing complete germ cell differentiation. To test this hypothesis, bovine testis tissue was treated with vascular endothelial growth factor (VEGF) at the time of grafting or explant cultured for 1 wk prior to grafting. For the VEGF experiment, 8-wk donor tissue and graft sites were treated with 1 μg of VEGF in order to increase angiogenesis at the graft site. For the testis tissue culture experiment, 4-wk-old donor testis was cultured for 1 wk prior to grafting to stimulate spermatogonial stem cell proliferation. Testis tissue grafts were removed from the mice 24 wk after grafting. VEGF treatment increased graft weight and the percentage of seminiferous tubule cross sections with elongating spermatids at the time of graft removal. Cultured testis tissue grafts were smaller and had fewer seminiferous tubules per graft. However, there was no difference in the percentage of seminiferous tubule cross sections that contained any germ cell type between groups. These data indicate for the first time that bovine testis tissue can be manipulated to better support germ cell differentiation in grafted tissue.
Biodistribution study of phosphonolipids: a class of non‐viral vectors efficient in mice lung‐directed gene transfer

A multitude of cationic lipids have been synthesized since they were first proposed for use in gene therapy. Cationic lipids are able to efficiently transfect cells both in vitro and in vivo. Whereas most research groups have focused their investigations on the toxicity of these molecules, and on the location of expression of the DNA transferred by these vectors, little has been done to determine their biodistribution and elimination pathways. Our group has developed a family of cationic lipids termed phosphonolipids. Following a large in vitro screening experiment, we have selected several molecules for in vivo testing, with some of these phosphonolipids forming lipoplexes efficient in transfecting mouse lungs. It was thus of interest to study their fate after intravenous injection.
Replication errors may contribute to the generation of large deletions and duplications in the dystrophin gene

Frequent recurrent mutations of the human dystrophin gene lead to Duchenne and Becker muscular dystrophies. Although the ˜ 2.5 Mb size of the gene may form a large targe for mutations it is not clear to date which mechanisms promote the observed high frequency of spontaneous mutants (1 in 10,000 X‐chromosomes) of which a high percentage ( > 70%) are gross structural aberrations (deletions/duplications). In order to gain insight into possible molecular mechanisms we have cloned and sequenced the deletion junction fragments from two unrelated Duchenne patients. Our data, together with a short review on other cases from the literature, present evidence that errors of DNA replication may contribute to the generation of submicroscopic chromosome rearrangements. © 1992 Wiley‐Liss, Inc.
On the robust stability of uncertain discrete-time networked control systems over fading channels

This paper addresses the problem of establishing robust stability in the mean square sense of uncertain discrete-time networked control systems over fading channels for all admissible uncertainties. It is supposed that the plant is connected to the controller in closed-loop via a fading channel which is modeled through noise processes in multiplicative form. The uncertainty is constrained into a convex bounded polytope and affects the plant whose coefficients are allowed to depend polynomially on the uncertainty. It is shown that robust stability of the uncertain closed-loop system in the mean square sense for all admissible uncertainties is equivalent to the existence of suitable Lyapunov functions with polynomial dependence on the uncertainty. It is also shown that a sufficient and necessary condition for establishing the existence of such Lyapunov functions can be obtained through convex optimization.
Increased systolic blood pressure after mild cold and rewarming: relation to cold‐induced thermogenesis and age

Aim: Higher winter mortality in elderly has been associated with augmented systolic blood pressure (SBP) response and with impaired defense of core temperature. Here we investigated whether the augmented SBP upon mild cold exposure remains after a rewarming period, and whether SBP changes are linked to thermoregulation. Therefore, we tested the following hypotheses: cold‐induced increase in SBP (1) remains augmented after rewarming in elderly compared to young adults (2) is related to non‐shivering thermogenesis (NST) upon mild cold (3) is related to vasoconstriction upon mild cold.
UWB planar monopole antenna based on half-circular perturbations

In this paper, we investigated the radiation properties of novel planar monopole antenna with half-circular perturbations for ultra wideband (UWB) application. The proposed antenna, designed on low cost substrate material FR4, consists of a simple rectangular radiating patch with two half-circular cuts and a partial ground plane with a number of half-circular protuberances and cuts. The antenna is designed to operate from 1.85 GHz to 16.8 GHz and to achieve reflection of more than 10 dB. Good impedance matching, radiation pattern characteristics and constant efficiency are obtained in the frequency band of interest.