Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas aeruginosa Exhibits Frequent Recombination, but Only a Limited Association between Genotype and Ecological Setting

Pseudomonas aeruginosa is an opportunistic pathogen and an important cause of infection, particularly amongst cystic fibrosis (CF) patients. While specific strains capable of patient-to-patient transmission are known, many infections appear to be caused by unique and unrelated strains. There is a need to understand the relationship between strains capable of colonising the CF lung and the broader set of P. aeruginosa isolates found in natural environments. Here we report the results of a multilocus sequence typing (MLST)-based study designed to understand the genetic diversity and population structure of an extensive regional sample of P. aeruginosa isolates from South East Queensland, Australia. The analysis is based on 501 P. aeruginosa isolates obtained from environmental, animal and human (CF and non-CF) sources with particular emphasis on isolates from the Lower Brisbane River and isolates from CF patients obtained from the same geographical region. Overall, MLST identified 274 different sequence types, of which 53 were shared between one or more ecological settings. Our analysis revealed a limited association between genotype and environment and evidence of frequent recombination. We also found that genetic diversity of P. aeruginosa in Queensland, Australia was indistinguishable from that of the global P. aeruginosa population. Several CF strains were encountered frequently in multiple ecological settings; however, the most frequently encountered CF strains were confined to CF patients. Overall, our data confirm a non-clonal epidemic structure and indicate that most CF strains are a random sample of the broader P. aeruginosa population. The increased abundance of some CF strains in different geographical regions is a likely product of chance colonisation events followed by adaptation to the CF lung and horizontal transmission among patients.
Forming Impressions: Effects of Facial Expression and Gender Stereotypes

The present study of 138 participants explored how facial expressions and gender stereotypes influence impressions. It was predicted that images of smiling women would be evaluated more favorably on traits reflecting warmth, and that images of non-smiling men would be evaluated more favorably on traits reflecting competence. As predicted, smiling female faces were rated as more warm; however, contrary to prediction, perceived competence of male faces was not affected by facial expression. Participants' female stereotype endorsement was a significant predictor for evaluations of female faces; those who ascribed more strongly to traditional female stereotypes reported the most positive impressions of female faces displaying a smiling expression. However, a similar effect was not found for images of men; endorsement of traditional male stereotypes did not predict participants' impressions of male faces.
Two Additional Components of the Accessory Sec System Mediating Export of the Streptococcus gordonii Platelet-Binding Protein GspB

ABSTRACT The gspB-secY2A2 locus of Streptococcus gordonii strain M99 encodes the platelet-binding glycoprotein GspB, along with proteins that mediate its glycosylation and export. We have identified two additional components of the accessory Sec system (Asp4 and Asp5) encoded just downstream of gtfB in the gspB-secY2A2 locus. These proteins are required for GspB export and for normal levels of platelet binding by M99. Asp4 and Asp5 may be functional homologues of SecE and SecG, respectively.
Energy potential of a tidal fence deployed near a coastal headland

Enhanced tidal streams close to coastal headlands appear to present ideal locations for the deployment of tidal energy devices. In this paper, the power potential of tidal streams near an idealized coastal headland with a sloping seabed is investigated using a near-field approximation to represent a tidal fence, i.e. a row of tidal devices, in a two-dimensional depth-averaged numerical model. Simulations indicate that the power extracted by the tidal fence is limited because the flow will bypass the fence, predominantly on the ocean side, as the thrust applied by the devices increases. For the dynamic conditions, fence placements and headland aspect ratios considered, the maximum power extracted at the fence is not related in any obvious way to the local undisturbed kinetic flux or the natural rate of energy dissipation due to bed friction (although both of these have been used in the past to predict the amount of power that may be extracted). The available power (equal to the extracted power net of vertical mixing losses in the immediate wake of devices) is optimized for devices with large area and small centre-to-centre spacing within the fence. The influence of energy extraction on the natural flow field is assessed relative to changes in the M2 component of elevation and velocity, and residual bed shear stress and tidal dispersion.
Experimental study on current gain of BSIT

A means to improve the current gain hFSof the BSIT in a high drain current region has been derived from an experimental study about the dependency of the hFSversus drain current relationship on the channel width, the gate junction depth, and the impurity concentration in the n-high-resistivity drain region. The BSIT, designed in this manner and including 9000 channels in a chip of 7 × 10 mm2, exhibits a current gain over 100 and high switching speeds, a rise time of 200 ns, a storage time of 200 ns and a fall time of 25 ns at a drain current of 50 A.
Structure of a Neutral Glycosphingolipid Recognized by Human Antibodies in Polyagglutinable Erythrocytes from the Rare NOR Phenotype*

NOR is a rare inheritable polyagglutination phenomenon that has been described in two families. Our recent studies on these erythrocytes showed they contained at least two unique neutral glycosphingolipids, and based on their reactivity with Griffonia simplicifolia IB4 (GSL-IB4) isolectin (Kusnierz-Alejska, G., Duk, M., Storry, J. R., Reid, M. E., Wiecek, B., Seyfried, H., and Lisowska, E. (1999) Transfusion 39, 32–38), both oligosaccharide chains terminated with an α-galactose residue. The reactivity with GSL-IB4 suggested that these oligosaccharide chains terminated with a Galα1→3Gal- sequence and that anti-NOR agglutinins were common human anti-Galα1→3Gal xenoantibodies. In this report we describe the structure of one NOR component (NOR1) that migrated on thin-layer chromatographic plates in the region of pentaglycosylceramides. Treatment of this sample with α-galactosidase and β-N-acetylhexosaminidase was followed by high-performance thin-layer chromatography with product detection by lectins and the anti-Gb4 monoclonal antibody. The results suggested that NOR1 was an α-galactosylated Gb4Cer with a β-N-acetylhexosaminidase-resistant GalNAc residue. Gas phase disassembly by ion trap mass spectrometry analysis showed the sequence to be Hex1→4HexN1→3Hex1→4Hex1→4Hex linked to a ceramide composed of C18 sphingosine and a C24 monounsaturated fatty acid. Together these data indicate NOR1 to be a novel Galα1→4GalNAcβ1→3Galα1→4Galβ1→4 Glc-Cer structure. Additionally it has been shown that NOR glycolipids are recognized by human antibodies that were distinct from the known anti-Galα1→3Gal xenoantibodies.
Efficient Optimization of Multiple SPARQL Queries

A W3C standard for processing RDF data is a SPARQL query language, a technique that is used to encode data in meaningful manner. We investigate the foundations of SPARQL query optimization by grouping into individual clusters using common substructures in the multiple SPARQL queries, propose a comprehensive set of query rewriting rules for the clustered group and finally Query execution provide the final result of optimized query. The proposed technique is efficient and scalable for multiple SPARQL query.
Improving Adherence in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), the broad term encompassing both ulcerative colitis (UC) and Crohn’s disease (CD), represents a chronic inflammatory condition of various elements of the colon, small bowel and, in rare cases, the upper digestive tract. Characterized by episodes of relapse and remission, these diseases are unpredictable in course, debilitating in nature, and generally require lifelong treatment. Continued disease progression over time can lead to an increase in the number and severity of disease-related complications, as well as in increased risk for the development of colorectal cancer. As with other chronic illnesses, patient adherence to a prescribed course of medical treatment is paramount in the successful management of their disease burden. Unfortunately, it has been appropriately stated that “patient noncompliance thrives wherever and whenever medical recommendations are generated” (1). “Adherence” is a term used to describe the extent to which patients follow the advice of healthcare professionals regarding their medication and disease management, and is generally interchangeable with “compliance” (2). If one takes a more analytical perspective, adherence can be considered the sum of compliance (medication consumption as directed) and persistence (the duration of time over which medication is consumed). This distinction becomes important in chronic illnesses such as IBD, particularly given the overall variation in disease severity that occurs over the course of a patient’s lifetime. Prior to the twentieth century, adherence likely mattered little in the overall efficacy of a multitude of widely accepted treatments of the day. In fact, those who ignored their physician’s recommendations for dangerous treatments such as cupping, purging, trephening, bloodletting, and the ingestion of arsenic likely faired better for their skepticism. In modern times, however, the implications of medication nonadherence are far-reaching, including not only increased morbidity and disease-related complications, but economic and social impacts as well. This is particularly true of IBD, where prolonged periods of disINFLAMMATORY BOWEL DISEASE: A PRACTICAL APPROACH, SERIES #59
Survey of the methods and reporting practices in published meta‐analyses of test performance: 1987 to 2009

We performed a survey of meta‐analyses of test performance to describe the evolution in their methods and reporting. Studies were identified through MEDLINE (1966–2009), reference lists, and relevant reviews. We extracted information on clinical topics, literature review methods, quality assessment, and statistical analyses. We reviewed 760 publications reporting meta‐analyses of test performance, published between 1987 and 2009. Eligible reviews included a median of 18 primary studies that were used in quantitative analyses. Most common clinical areas were cardiovascular disease (21%) and oncology (25%); most common test categories were imaging (44%) and biomarker tests (28%). Assessment of verification and spectrum bias, blinding, prospective study design, and consecutive patient recruitment became more common over time (p < 0.001 comparing reviews published through 2004 vs 2005 onwards). These changes coincided with the increasing use of checklists to guide assessment of methodological quality. Heterogeneity tests were used in 58% of meta‐analyses; subgroup or regression analyses were used in 57%. Random effects models were employed in 57% of meta‐analyses (38% through 2004 vs 72% 2004–onwards; p < 0.001). Use of bivariate models of sensitivity and specificity increased in recent years (21% in 2008–2009 vs 7% in earlier years; p < 0.001). Methods employed in meta‐analyses of test performance have improved with the introduction of quality assessment checklists and the development of more sophisticated statistical methods. Copyright © 2013 John Wiley & Sons, Ltd.
Data Sparseness in Linear SVM

Large sparse datasets are common in many real-world applications. Linear SVM has been shown to be very efficient for classifying such datasets. However, it is still unknown how data sparseness would affect its convergence behavior. To study this problem in a systematic manner, we propose a novel approach to generate large and sparse data from real-world datasets, using statistical inference and the data sampling process in the PAC framework. We first study the convergence behavior of linear SVM experimentally, and make several observations, useful for real-world applications. We then offer theoretical proofs for our observations by studying the Bayes risk and PAC bound. Our experiment and theoretic results are valuable for learning large sparse datasets with linear SVM.
Analysis of Corynebacterium diphtheriae macrophage interaction: Dispensability of corynomycolic acids for inhibition of phagolysosome maturation and identification of a new gene involved in synthesis of the corynomycolic acid layer

Corynebacterium diphtheriae is the causative agent of diphtheria, a toxin mediated disease of upper respiratory tract, which can be fatal. As a member of the CMNR group, C. diphtheriae is closely related to members of the genera Mycobacterium, Nocardia and Rhodococcus. Almost all members of these genera comprise an outer membrane layer of mycolic acids, which is assumed to influence host-pathogen interactions. In this study, three different C. diphtheriae strains were investigated in respect to their interaction with phagocytic murine and human cells and the invertebrate infection model Caenorhabditis elegans. Our results indicate that C. diphtheriae is able to delay phagolysosome maturation after internalization in murine and human cell lines. This effect is independent of the presence of mycolic acids, as one of the strains lacked corynomycolates. In addition, analyses of NF-κB induction revealed a mycolate-independent mechanism and hint to detrimental effects of the different strains tested on the phagocytic cells. Bioinformatics analyses carried out to elucidate the reason for the lack of mycolates in one of the strains led to the identification of a new gene involved in mycomembrane formation in C. diphtheriae.
Associations of Domain-Specific Physical Activity With Leisure-Time Sedentary Behaviors in Chinese Professionals

Objective: To understand the association of domain-specific physical activity (PA) with leisure-time sedentary behavior (LTSB) among Chinese professionals. Methods: Totally, 3326 workers aged 35 to 64 years old from Beijing city and Zhejiang province were asked information on domain-specific PA with a revised Global Physical Activity Questionnaire (GPAQ). The association of domain-specific PA with LTSB-lifestyle (≥4 hours/day spent on LTSB) was examined with a binary logistic regression model. Results: Compared with sedentary occupational activity (OA), light-, moderate-, and vigorous-intensity OA were respectively associated with 55.3% (ORs, 0.447; 95%CI, 0.378 to 0.529), 63.5% (ORs, 0.365; 95%CI, 0.285 to 0.468), and 77.1% (ORs, 0.229; 95%CI, 0.126 to 0.417) less the odds of having LTSB-lifestyle. Those performing domestic activity (DA) are greater than and equal to 19.6 MET-hours/week had 30.1% (ORs, 0.699; 95%CI, 0.576 to 0.848) less the odds. Conclusions: Both non-sedentary occupations and DA were negatively associated with LTSB-lifestyle in these professionals.
Pulse Repetition Interval Detection using Statistical Modeling

Pulse Repetition Interval (PRI) Modulation Detection is an important subsystem of a typical electronic warfare support system. In this paper, a robust, fast, and well designed structure for detection of simple and complex PRI modulations based on statistical and sequential analysis of Pulse Repetition Interval (PRI) is proposed. Accuracy and robustness of the technique against electromagnetic noise are demonstrated via simulations.
Estimation of Annual Average Daily Traffic in a Florida County Using GIS and Regression

Accurate Annual Average Daily Traffic (AADT) information is important to many applications including roadway design, air quality compliance, travel model validation, etc. Yet complete or even extensive coverage of a network to collect traffic count data is impractical due to the cost involved. There have been studies to estimate AADT for interstate highways, expressways, urban roads, and rural roads. Such efforts are often hampered by the lack of relevant detailed information that adequately explains variations in the traffic counts. In this paper, a multiple linear regression model of AADT on local roadways in a large urban area is presented. By employing geographic information system (GIS) technology, a variety of land use and accessibility measurements are developed and tested. While most are statistically significant, few add enough explanatory power to be practical and useful. Four models are presented, which achieved R of 0.66 to 0.82. The predictive power of the models are also examined.
Arrhythmogenic left atrial cellular electrophysiology in a murine genetic long QT syndrome model.

AIMS Increasing evidence indicates that congenital long QT syndromes (LQTSs) promote atrial fibrillation. The atrial action potential (AP) has a short plateau, and whether LQTS atrial cardiomyocytes generate triggered activity via early afterdepolarizations (EADs) is unclear. Atrial cellular arrhythmia mechanisms have not been defined in congenital LQTS. Therefore, we studied atrial cardiomyocyte electrophysiology in mice with an LQTS3 SCN5A inactivation-impairing mutation (ΔKPQ heterozygotes). METHODS AND RESULTS Peak and late Na(+) current (I(NaP) and I(NaL)) were measured with whole-cell patch clamp in left atrial (LA) cardiomyocytes. APs were recorded in multicellular LA preparations with floating microelectrodes. I(NaL) was increased by 110% in LA cardiomyocytes of ΔKPQ mice, whereas I(NaP) was unchanged. AP duration (APD) was prolonged over all frequencies in ΔKPQ mice, but particularly at lower frequencies [e.g. APD(90) at 0.5 Hz: 197 ± 8 ms vs. wild-type (WT) 82 ± 2 ms, P< 0.001]. EADs occurred at 0.5 Hz in 10/18 ΔKPQ (56%) vs. 1/10 WT (10%) atria (P< 0.05). EADs immediately preceded premature APs in other LA regions, suggesting triggered activity. Ranolazine preferentially inhibited I(NaL) (50% inhibitory concentration: 12.5 vs. 151.8 µM for I(NaP)) in ΔKPQ myocytes. At 10 µM, ranolazine shortened APD (e.g. APD(90) at 0.5 Hz to 122 ± 4 ms, P= 0.01) without changing APD in WT and suppressed EAD occurrence and triggered activity (from 10/18 to 1/9 preparations, 11%, P< 0.05). CONCLUSION This study implicates increased I(NaL) in excessive atrial APD prolongation and arrhythmic EAD occurrence in a congenital LQTS3 mouse model. Our observations provide the first direct demonstration of atrial EADs and triggered activity in a genetically defined animal model of human LQTS and have potential clinically-relevant mechanistic and therapeutic implications.
Corn Cob Filled Chitosan Biocomposite Films

Recently, there has been renews interest in chitosan as materials in producing of biocomposite films. The chitosan (CS)/corn cob (CC) biocomposite films were prepared by solvent casting method. The effect of CC content on tensile properties of CS/CC biocomposite films was studied. The tensile strength and elongation at break of CS/CC biocomposite films decreased as increasing of CC content. However, the increasing of CC content was increased the tensile modulus of CS/CC biocomposite films. Scanning electron microscopy (SEM) was indicated that the deceasing of tensile properties was due to the poor interfacial adhesion between CC filler and CS matrix.
Associations of Maternal Prepregnancy Body Mass Index and Gestational Weight Gain With Adult Offspring Cardiometabolic Risk Factors: The Jerusalem Perinatal Family Follow-Up Study

Background— Accumulating evidence demonstrates that both maternal prepregnancy body mass index (mppBMI) and gestational weight gain (GWG) are associated with adult offspring adiposity. However, whether these maternal attributes are related to other cardiometabolic risk factors in adulthood has not been comprehensively studied. Methods and Results— We used a birth cohort of 1400 young adults born in Jerusalem who had extensive archival data and clinical information at 32 years of age to prospectively examine the associations of mppBMI and GWG with adiposity and related cardiometabolic outcomes. Greater mppBMI, independently of GWG and confounders, was significantly associated with higher offspring BMI, waist circumference, systolic and diastolic blood pressures, insulin, and triglycerides and with lower high-density lipoprotein cholesterol. For example, the effect sizes were translated to nearly 5 kg/m2 higher mean BMI, 8.4 cm higher waist circumference, 0.13 mmol/L (11.4 mg/dL) higher triglycerides, and 0.10 mmol/L (3.8 mg/dL) lower high-density lipoprotein cholesterol among offspring of mothers within the upper mppBMI quartile (mppBMI >26.4 kg/m2) compared with the lower quartile (mppBMI <21.0 kg/m2). GWG, independently of mppBMI, was positively associated with offspring adiposity; differences of 1.6 kg/m2 in BMI and 2.4 cm in waist were observed when offspring of mothers in the upper (GWG >14 kg) and lower (GWG <9 kg) quartiles of GWG were compared. Further adjustment for offspring adiposity attenuated the observed associations to the null. Conclusions— Maternal size both before and during pregnancy is associated with cardiometabolic risk factors in young adult offspring. The associations appear to be driven mainly by offspring adiposity. Future studies that explore mechanisms underlying the intergenerational cycle of obesity are warranted to identify potentially novel targets for cardiometabolic risk-reduction interventions.
Advancement of Compositional and Microstructural Design of Intermetallic γ-TiAl Based Alloys Determined by Atom Probe Tomography

Advanced intermetallic alloys based on the γ-TiAl phase have become widely regarded as most promising candidates to replace heavier Ni-base superalloys as materials for high-temperature structural components, due to their facilitating properties of high creep and oxidation resistance in combination with a low density. Particularly, recently developed alloying concepts based on a β-solidification pathway, such as the so-called TNM alloy, which are already incorporated in aircraft engines, have emerged offering the advantage of being processible using near-conventional methods and the option to attain balanced mechanical properties via subsequent heat-treatment. Development trends for the improvement of alloying concepts, especially dealing with issues regarding alloying element distribution, nano-scale phase characterization, phase stability, and phase formation mechanisms demand the utilization of high-resolution techniques, mainly due to the multi-phase nature of advanced TiAl alloys. Atom probe tomography (APT) offers unique possibilities of characterizing chemical compositions with a high spatial resolution and has, therefore, been widely used in recent years with the aim of understanding the materials constitution and appearing basic phenomena on the atomic scale and applying these findings to alloy development. This review, thus, aims at summarizing scientific works regarding the application of atom probe tomography towards the understanding and further development of intermetallic TiAl alloys.