Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess

Pannonibacter phragmitetus is a bioremediation reagent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs) while it rarely infects healthy populations. However, infection by the opportunistic pathogen P. phragmitetus complicates diagnosis and treatments, and poses a serious threat to immunocompromised patients owing to its multidrug resistance. Unfortunately, genome features, antimicrobial resistance, and virulence potentials in P. phragmitetus have not been reported before. A predominant colony (31801) was isolated from a liver abscess patient, indicating that it accounted for the infection. To investigate its infection mechanism(s) in depth, we sequenced this bacterial genome and tested its antimicrobial resistance. Average nucleotide identity (ANI) analysis assigned the bacterium to the species P. phragmitetus (ANI, >95%). Comparative genomics analyses among Pannonibacter spp. representing the different living niches were used to describe the Pannonibacter pan‐genomes and to examine virulence factors, prophages, CRISPR arrays, and genomic islands. Pannonibacter phragmitetus 31801 consisted of one chromosome and one plasmid, while the plasmid was absent in other Pannonibacter isolates. Pannonibacter phragmitetus 31801 may have a great infection potential because a lot of genes encoding toxins, flagellum formation, iron uptake, and virulence factor secretion systems in its genome. Moreover, the genome has 24 genomic islands and 2 prophages. A combination of antimicrobial susceptibility tests and the detailed antibiotic resistance gene analysis provide useful information about the drug resistance mechanisms and therefore can be used to guide the treatment strategy for the bacterial infection.
Protein Tyrosine Phosphatase Nonreceptor Type 2 Regulates Autophagosome Formation in Human Intestinal Cells

Background: Autophagy is a process of central importance for maintaining cell homeostasis, survival, and the regulation of inflammation. Recent studies associated variants within the gene loci, encoding protein tyrosine phosphatase nonreceptor type 2 (PTPN2), and autophagy genes, such as autophagy‐related 16‐like 1 (ATG16L1), with chronic inflammatory disorders, such as Crohn's disease (CD). We show that PTPN2 regulates autophagy in human intestinal epithelial cells (IEC) and primary colonic lamina propria fibroblasts (CLPF). Methods: Protein analysis in IEC and CLPF was performed by western blotting. Autophagososme formation was assessed by LC3B immunofluorescence or immunohistochemistry. Human intestinal tissue samples were obtained from noninflammatory bowel disease (IBD) control or from CD patients and genotyped for disease‐associated PTPN2 or ATG16L1 variations. Results: Knockdown of PTPN2 causes impaired autophagosome formation and dysfunctional autophagy resulted in increased levels of intracellular Listeria monocytogenes (LM) and elevated IEC apoptosis in response to tumor necrosis factor (TNF) and interferon gamma (IFN‐&ggr;). Similar findings were observed in primary CLPF derived from CD patients carrying the CD‐associated PTPN2 variant. Presence of the ATG16L1 variant prevented the cytokine‐induced rise in PTPN2 protein, finally resulting in impaired LC3B‐II levels in IEC. Actively inflamed intestinal biopsies from CD patients carrying either ATG16L1 or PTPN2 genetic variants revealed aberrant LC3B expression patterns when compared with samples from non‐IBD control patients. Conclusions: Our results demonstrate that PTPN2 regulates autophagosome formation in human intestinal cells. We provide a model of how a dysfunction of the CD susceptibility genes, PTPN2 and/or ATG16L1, may contribute to the onset and perpetuation of chronic intestinal inflammation. (Inflamm Bowel Dis 2011;)
Quantitative evaluation of Parkinson's disease using sensor based smart glove

Parkinson's disease (PD) is a chronic neurodegenerative movement disorder. The motor status of patients with PD can be characterized by the Unified Parkinson's disease rating scale (UPDRS). However, the UPDRS evaluates the movement disorders on a descriptive level only. Diagnosis and therapy of PD could be augmented if a quantitative assessment could be implemented. Thus, a wireless wearable sensor system for the evaluation of severity of motor dysfunction in PD was developed. The system was integrated into a smart glove1. This glove has two touch sensors, two 3D-accelerometers and a force sensor to assess the cardinal motor symptoms of PD (bradykinesia, tremor and rigidity of hand and arm). In this paper we describe the setup of the glove and initial results.
Optimized speed controller for induction motor drive using quantum lightning search algorithm

This paper presents an improve proportional-integral-derivative (PID) controller design technique for controlling a three-phase induction motor (TIM) speed drive using quantum lightning search algorithm (QLSA). This proposed controller avoids the exhaustive conventional trial- and-error procedure for obtaining PID parameters. Objective function using in the proposed controller is mean absolute error (MAE) to enhance the TIM speed performance under sudden change of the speed and load conditions. The QLSA is used to improve two controller system PID and PI controllers in the TIM drive. Moreover, the QLSA algorithm comperes with three optimization algorithms, namely, lightning search algorithm (LSA), the backtracking search algorithm (BSA), the particle swarm optimization (PSO). Designed and validated the simulation model by using a MATLAB/Simulink environment. Results show that the QLSA-based PID and PI speed controller is achieved better results than the other optimization controllers through reduce of damping capability, enhance the transient response, minimize the MAE, root mean square error (RMSE) and standard division (SD) of the speed response.
Do blood collection methods influence whole-blood platelet function analysis?

Pre-analytical variables interact with standard coagulation parameters. How these variables affect the platelet function analysis is not completely known. How collection site and puncture method affect multiple electrode aggregometry (MEA) and platelet function analyzer (PFA-100®) was compared regarding contact activation. First, volunteers scheduled for elective cardiac surgery had blood collected from four lines: venous, arterial, central venous and by venipuncture. MEA and PFA-100® were analysed blinded for site origin. Second, two samples (citrate, Corn Trypsin Inhibitor, CTI) were collected in syringe or vacuum tubes. Thrombin generation (TG) was determined. MEA was triggered by adenosine diphosphate (ADP, 6.4 µM), arachidonic acid (ASPI, 0.5 mM), collagen (Col, 3.2 µg/ml), ristocetin (Risto, 0.2 mg/ml) and thrombin receptor-activating peptide (TRAP, 32 µM). PFA-100® was triggered by collagen/epinephrine and collagen/ADP. TG was assessed in platelet-poor plasma with 1 pM tissue factor and 4 µM phospholipids and without trigger. Data were analysed using a two-way mixed-effects model for the intraclass correlation (ICC) and by the Mann–Whitney U-test. MEA and PFA-100® revealed good correlation (ICC) between the sites. CTI inhibited TG significantly more effective than citrate. Contact activation was independent of the collection method. Only the MEA ASPI test revealed significant differences between the two collection methods. Blood sampling from all lines for MEA and PFA-100® assays is justified. Contact activation is always present. Apparently this does not influence platelet function test results. Collection methods do not seem relevant, although, one should always consider using a standardized method.
Board diversity and corporate social responsibility in Jordan

Purpose - This study aims to investigate the impact of board diversity characteristics, namely, independence, gender, age and nationality of directors on the level of corporate social responsibility (CSR) disclosures. Design/methodology/approach - Content analysis was used to determine CSR disclosure. This study used panel data analysis to investigate the influence of board diversity characteristics on CSR disclosures. Findings - Panel data analysis show that the level of CSR disclosure has increased over the period of study. Results also reveal a positive and significant association between the level of CSR disclosure and board diversity variables. Research limitations/implications - This study examined only companies listed on Amman Stock Exchange. Therefore, the generalisation of the results might be limited to the listed companies only. Practical implications - Findings are relevant to policymakers, professional organisations and practitioners in Jordan and in other Arab countries. Social implications - The role of women in the boardroom is important to ensure more CSR activities by the listed companies. Jordan being a Muslim country should take the initiative to introduce laws to increase the number of women to the board. Originality/value - This study offers significant contributions to existing CSR literature in Jordan and in other Arab countries by introducing female directors. Findings are important to policymakers. They should implement quotas for women in the boardroom, and adopting such a policy will increase the participation of women in the decision-making process of the companies and reduce gender bias.
Real Practice of Hepatocellular Carcinoma in Japan: Conclusions of the Japan Society of Hepatology 2009 Kobe Congress

This article presents the current consensus on the management of hepatocellular carcinoma (HCC) formed at the 45th Annual Meeting of the Japan Society of Hepatology (June 4–5, 2009) and the 3rd International Kobe Liver Symposium (June 6–7, 2009) held in Kobe. Concluded important consensuses, which were well accepted by Japanese HCC specialists, are as follows. (1) Patients with type B or type C liver cirrhosis, who are an ultrahigh-risk group of liver cancer, should be screened every 3–4 months by ultrasonography and measurement of AFP and PIVKA-II. (2) Gd-EOB-MRI is useful for the diagnosis of early HCC. (3) The JIS score is more useful for the staging of liver cancer than the BCLC staging system, which is a global standard. (4) The TNM staging system by the Liver Cancer Study Group of Japan is superior to the TNM stage by the AJCC/UICC. (5) The therapeutic algorithm in the Japanese guidelines for the management of liver cancer is superior to the BCLC treatment algorithm. (6) Early stage. Liver cancers should be treated by radiofrequency ablation if they are ≤2 cm, and by surgical resection if they are Child-Pugh A solitary lesions. (7) Liver transplantation is only indicated for Child-Pugh C patients within Milan Criteria. In conclusion, these consensuses seem to well reflect the real practice pattern of the management of HCC in Japan and provide valuable information for other countries as well.
Occurrence of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia in progressive adult periodontitis.

BACKGROUND Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia are the major periodontal bacteria species in most forms of progressive periodontitis in Scandinavia and the United States. The occurrence of periodontal pathogens appears to be different in subjects of different ethnic origin, and geographical factors may influence the distribution of these species. METHODS The occurrence of A. actinomycetemcomitans, P. gingivalis, and P. intermedia was determined using a DNA probe in progressive adult periodontitis in Chileans. Sixty patients (mean age 43.6 +/- 8 years) who had not previously received any type of periodontal therapy were selected. Bleeding on probing, probing depth, and clinical attachment level measurements were made with an automated probe. Patients were monitored at 2-month intervals until at least 2 sites exhibited > or =2 mm attachment loss. Two subgingival plaque samples from active sites were taken in 56 subjects and matched with 2 plaque samples from inactive sites in the same individuals. RESULTS P. gingivalis was found in 75% of active sites and in 59.7% of inactive sites in 96% of the patients (P = 0.022). P. gingivalis at high levels of detection was significantly more frequent in active sites (48.2%) than in inactive sites (31.2%) (P = 0.014). A. actinomycetemcomitans was detected in 6.25% of active sites and in 12.5% of inactive sites in 11.6% of patients. P. intermedia was found in 33% of patients and at a significantly higher proportion in active sites (49.1%) than in inactive sites (30.3%) (P = 0.006). There was a significantly higher proportion of inactive sites (34.8%) than active sites (19.6%) without any of the 3 pathogens (P = 0.016). Bleeding on probing was significantly more associated with active sites with high levels of P. gingivalis and with active sites with P. intermedia than with inactive sites. CONCLUSIONS A high prevalence of P. gingivalis and P. intermedia was found in adult periodontitis, and the occurrence of these bacteria appears to be higher in Chileans than in other populations. No apparent association exists between A. actinomycetemcomitans and progressive adult periodontitis in Chileans.
Visual tracking using quantum-behaved particle swarm optimization

Visual tracking is one of the most important applications in computer vision. Since the tracking process can be formed as a dynamic optimization problem. PSO, an effective algorithm to solve optimization problem, has been used in tracking widely. However, it has been proved that the traditional PSO is easy to converge to local optimum. In this paper, we adopt quantum-behaved particle swarm optimization (QPSO) for visual tracking. QPSO has better global convergence compared with the PSO, and can overcome the shortcomings of PSO algorithm. In order to achieve better tracking performance, we improve the traditional tracking framework based on PSO and propose a sequential QPSO based tracking algorithm in this paper. We conduct numerous experiments, and the results have shown the effectiveness of our method, even when the object undergoes abrupt motion or large changes in illumination, scale and appearance.
Automated fuzzy logic based skull stripping in neonatal and infantile MR images

Automated morphometric analysis using human brain magnetic resonance (MR) images is an effective approach to investigate the morphological changes of the brain. However, even though many methods for adult brain have been studied, there are few studies for infantile brain. Same as the adult brain, it is effective to measure cerebral surface and for quantitative diagnosis of neonatal and infantile brain diseases. This article proposes a skull stripping method that can be applied to the neonatal and infantile brain. The proposed method can be applied to both of T1 weighted and T2 weighted MR images. First, the proposed method estimates intensity distribution of white matter, gray matter, cerebrospinal fluid, fat, and others using a priori knowledge based Bayesian classification with Gaussian mixture model. The priori knowledge is embedded by representing them with fuzzy membership functions. Second, the proposed method optimizes the whole brain by using fuzzy active surface model, which evaluates the deforming model with fuzzy rules. The proposed method was applied to 26 neonatal and infantile subjects between −4 weeks and 4 years 1 month old. The results showed that the proposed method stripped skull well from any neonatal and infantile MR images.
Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O‐GlcNAc in the DNA damage response pathway

The modification of intracellular proteins by monosaccharides of O‐linked β‐N‐acetylglucosamine (O‐GlcNAc) is an essential and dynamic PTM of metazoans. The addition and removal of O‐GlcNAc is catalyzed by the O‐GlcNAc transferase (OGT) and O‐GlcNAcase, respectively. One mechanism by which O‐GlcNAc is thought to mediate proteins is by regulating phosphorylation. To provide insight into the pathways regulated by O‐GlcNAc, we have utilized SILAC‐based quantitative proteomics to carry out comparisons of site‐specific phosphorylation in OGT wild‐type and Null cells. Quantitation of the phosphoproteome demonstrated that of 5529 phosphoserine, phosphothreonine, and phosphotyrosine sites, 232 phosphosites were upregulated and 133 downregulated in the absence of O‐GlcNAc. Collectively, these data suggest that deletion of OGT has a profound effect on the phosphorylation of cell cycle and DNA damage response proteins. Key events were confirmed by biochemical analyses and demonstrate an increase in the activating autophosphorylation event on ATM (Ser1987) and on ATM's downstream targets p53, H2AX, and Chk2. Together, these data support widespread changes in the phosphoproteome upon removal of O‐GlcNAc, suggesting that O‐GlcNAc regulates processes such as the cell cycle, genomic stability, and lysosomal biogenesis. All MS data have been deposited in the ProteomeXchange with identifier PXD001153 (http://proteomecentral.proteomexchange.org/dataset/PXD001153).
EPEC effector EspF promotes Crumbs3 endocytosis and disrupts epithelial cell polarity

Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system to inject effector proteins into host intestinal epithelial cells causing diarrhoea. EPEC infection redistributes basolateral proteins β1‐integrin and Na+/K+ ATPase to the apical membrane of host cells. The Crumbs (Crb) polarity complex (Crb3/Pals1/Patj) is essential for epithelial cell polarisation and tight junction (TJ) assembly. Here, we demonstrate that EPEC displaces Crb3 and Pals1 from the apical membrane to the cytoplasm of cultured intestinal epithelial cells and colonocytes of infected mice. In vitro studies show that EspF, but not Map, alters Crb3, whereas both effectors modulate Pals1. EspF perturbs polarity formation in cyst morphogenesis assays and induces endocytosis and apical redistribution of Na+/K+ ATPase. EspF binds to sorting nexin 9 (SNX9) causing membrane remodelling in host cells. Infection with ΔespF/pespFD3, a mutant strain that ablates EspF binding to SNX9, or inhibition of dynamin, attenuates Crb3 endocytosis caused by EPEC. In addition, infection with ΔespF/pespFD3 has no impact on Na+/K+ ATPase endocytosis. These data support the hypothesis that EPEC perturbs apical–basal polarity in an EspF‐dependent manner, which would contribute to EPEC‐associated diarrhoea by disruption of TJ and altering the crucial positioning of membrane transporters involved in the absorption of ions and solutes.
Desensitization of the Platelet Aggregation Response to ADP: Differential Down-regulation of the P2Y1 and P2cyc Receptors

Summary Platelets activated by ADP become refractory to restimulation, but the mechanism of this process is not well understood. A normal platelet response to ADP requires coactivation of the P2Y1 receptor responsible for shape change and the P2cyc receptor, responsible for completion and amplification of the response. The aim of the present study was to characterize the desensitization of platelets to ADP and to determine whether or not these two receptors are desensitized simultaneously through identical pathways when platelets become refractory to ADP. It was found that full inhibition of platelet aggregation in response to restimulation by ADP required the presence of ADP in the medium or use of a high concentration (1 mM) of its non-hydrolysable analogue ADP β S. Platelets incubated for 1 h at 37° C with 1 mM ADP β S and resuspended in Tyrode’s buffer containing apyrase displayed a stable refractory state characterized by the inability to aggregate or change shape in response to ADP. ADP β S treated platelets loaded with fura2/AM showed complete blockade of the calcium signal in response to ADP, whereas the capacity of ADP to inhibit PGE1 stimulated cAMP accumulation in these platelets was only diminished. Consequently, serotonin was able to promote ADP induced aggregation through activation of the Gq coupled 5HT2A receptor while adrenaline had no such effect. These results suggested that the refractory state of ADP β S treated platelets was entirely due to desensitization of the P2Y1 receptor, the P2cyc receptor remaining functional. Binding studies were performed to determine whether the P2Y1 and/or P2cyc binding sites were modified in refractory platelets. Using selective P2Y1 and P2cyc antagonists (A3P5P and AR-C66096 respectively), we could demonstrate that the decrease in [33P]2MeSADP binding sites on refractory platelets corresponded to disappearance of the P2Y1 sites with no change in the number of P2cyc sites, suggesting internalization of the P2Y1 receptor. This was confirmed by flow cytometric analysis of Jurkat cells expressing an epitope-tagged P2Y1 receptor, where ADP β S treatment resulted in complete loss of the receptor from the cell surface. We conclude that the P2Y1 and P2cyc receptors are differently regulated during platelet activation.
School start time effects on adolescent learning and academic performance, emotional health and behaviour

Purpose of review The investigation of the relationship between the time of day that school begins and the effects it could have on students began in the mid-1990s. Since that time, many articles have been written either for the medical literature or the educational literature. This review is intended to bridge that gap by examining together the findings for both academic and health outcomes, exploring what we know and what is needed in further investigation. Recent findings Teens who are sleep deficient (defined as obtaining less than 8 h per night) because of early starting time for their school are much more likely to engage in risky behaviours, such as drug, cigarette and alcohol use, have significant feelings of depression, get lower grades and are at greater risk for car crashes. Many studies of academic performance and later school start time indicate benefits, although further research is needed to understand the related mechanisms that contribute to improvements in achievement. Recent research in adolescent sleep and outcomes is being shaped by not only measuring sleep duration, but also examining the timing in which sleep occurs. Summary Early school starting time for middle and high students has a clear, deleterious effect on their health and well being. Most recently, sleep deficit in teens is being viewed as a public health issue that needs a wider discussion about its impact and it necessitates improved public education about the sleep phase shift that occurs during adolescence.