Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of methicillin-resistant Staphylococcus aureus and methicillin-resistant coagulase-negative Staphylococcus spp. isolated from US West Coast public marine beaches.

OBJECTIVES The aim of this study was to isolate and characterize methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococcus spp. (MRCoNS) from marine water and intertidal beach sand from public beaches in Washington State, USA. METHODS Fifty-one staphylococci from Washington State beaches were characterized using antimicrobial susceptibility testing, carriage of acquired tetracycline and/or macrolide resistance genes, staphylococcal cassette chromosome mec (SCCmec) typing, the BBL Crystal Gram-Positive ID System and/or 16S rRNA sequencing, coagulase test and multilocus sequence typing (MLST) for MRSA. RESULTS Five multidrug-resistant MRSA SCCmec type I, of which three were MLST type ST45, one ST59 and one a new MLST type, ST1405, plus one susceptible non-typeable (NT) MRSA ST30 were characterized. Thirty-three MRCoNS isolates, representing 21 strains from 9 Staphylococcus spp. , carried a range of SCCmec types [I (2), II (6), III (3), V (2), I/II (1) and NT (7)] and varied in their antibiotic susceptibility to other antibiotic classes and carriage of acquired tetracycline/macrolide resistance gene(s). MRSA and MRCoNS donors co-transferred tet(M) and erm(A) genes to an Enterococcus faecalis recipient at a frequency of 10(-8). CONCLUSIONS This is the first report of MRSA and MRCoNS isolated from marine water and intertidal beach sand. The MLST types and antibiotic carriage of five MRSA isolates were similar to hospital MRSA isolates rather than US community-acquired MRSA isolates. Our results suggest that public marine beaches may be a reservoir for transmission of MRSA to beach visitors as well as an ecosystem for exchange of antibiotic resistance genes among staphylococci and related genera.
Crystal structures and kinetic properties of enoyl‐acyl carrier protein reductase I from Candidatus Liberibacter asiaticus

Huanglongbing (HLB) is a destructive citrus disease. The leading cause of HLB is Candidatus Liberibacter asiaticus. Fatty acid biosynthesis is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterial agents. Enoyl−acyl carrier protein reductase (also called ENR or FabI and a product of the fabI gene) is an enzyme required in a critical step of bacterial fatty acid biosynthesis and has attracted attention as a target of novel antimicrobial agents. We determined the crystal structures of FabI from Ca. L. asiaticus in its apoform as well as in complex with b‐nicotinamide adenine dinucleotide (NAD) at 1.7 and 2.7 Å resolution, respectively, to facilitate the design and screening of small molecule inhibitors of FabI. The monomeric ClFabI is highly similar to other known FabI structures as expected; however, unlike the typical tetramer, ClFabI exists as a hexamer in crystal, whereas as dimer in solution, on the other hand, the substrate binding loop which always disordered in apoform FabI structures is ordered in apo‐ClFabI. Interestingly, the structure of ClFabI undergoes remarkable conformational change in the substrate‐binding loop in the presence of NAD. We conclude that the signature sequence motif of FabI can be considered as Gly‐(Xaa)5‐Ser‐(Xaa)n‐Val‐Tyr‐(Xaa)6‐Lys‐(Xaa)n‐Thr instead of Tyr‐(Xaa)6‐Lys. We have further identified isoniazid as a competitive inhibitor with NADH.
Analysis of Bilingual Children’s Performance on the English and Spanish Versions of the Woodcock-Muñoz Language Survey-R (WMLS-R)

The purpose of this study was to investigate the way in which items on the Woodcock-Muñoz Language Survey Revised (WMLS-R) Spanish and English versions function for bilingual children from different ethnic subgroups who speak different dialects of Spanish. Using data from a sample of 324 bilingual Hispanic families and their children living on the United States mainland, differential item functioning (DIF) was conducted to determine if test items in English and Spanish functioned differently for Mexican, Cuban, and Puerto Rican bilingual children. Data on child and parent language characteristics and children’s scores on Picture Vocabulary and Story Recall subtests in English and Spanish were collected. DIF was not detected for items on the Spanish subtests. Results revealed that some items on English subtests displayed statistically and practically significant DIF. The findings indicate that there are differences in the difficulty level of WMLS-R English-form test items depending on the examinees’ ethnic subgroup membership. This outcome suggests that test developers need to be mindful of potential differences in performance based on ethnic subgroup and dialect when developing standardized language assessments that may be administered to bilingual students.
Muscular Force Patterns during Level Walking in ACL-Deficient Patients with a Concomitant Medial Meniscus Tear

Background The abnormal knee joint motion patterns caused by anterior cruciate ligament (ACL) deficiency are thought to be associated with articular cartilage degeneration. High rates of meniscus tear combined with ACL rupture are observed, and these knees suffer a higher risk of early cartilage degeneration. Research Question This study investigated lower limb muscular force patterns of ACL-deficient knees with a concomitant medial meniscus tear. Methods 12 volunteers and 22 patients were recruited, including 12 patients with isolated ACL deficiency (ACLD) and 10 ACL-deficient patients with a concomitant medial meniscus tear (ACLDM). Level walking data at a self-selected speed were collected before surgery. Then, a musculoskeletal dynamic analysis system, AnyBody, was applied to simulate tibiofemoral flexion moments and muscle forces. Results Our results indicate that the tibiofemoral peak flexion and extension moments in ACLDM patients are significantly lower than in controls. The rectus femoris force in ACLDM patients was significantly lower than in isolated ACL-deficient patients and the controls during mid and terminal stance phase, while no significant difference was found in hamstring and vastus force. Additionally, the gastrocnemius force in ACL-deficient patients both with and without a medial meniscus tear was lower than in controls during mid-stance phase. Significance The ACLDM patients had lower peak tibiofemoral flexion moment, lower gastrocnemius force in mid-stance phase, and lower rectus femoris force during the mid and terminal stance phase. These results may help clinicians to better understand the muscle function and gait pattern in ACL-deficient patients with a concomitant medial meniscus tear.
Acts of control in schizophrenia: dissociating the components of inhibition

Background. Inhibitory deficits have been frequently reported in schizophrenia. Such deficits are usually associated with activities of prefrontal cortex and related networks. An understanding of intentional inhibitory control requires knowledge of how actions are planned and initiated and the components involved in stopping these actions. Methods. Patients with schizophrenia, a psychosis comparison group and a healthy control group participated in a visual choice reaction time (go) task and attempted to inhibit their responses to the go task when an auditory ‘stop’ signal was heard. Results. Schizophrenia patients demonstrated significantly slower response execution but the estimated speed of inhibition was not significantly different from that of healthy controls. Both patient groups were impaired in their ability to inhibit a response across a range of stop-signal delays. The poorer performance of schizophrenia patients only was related to a difficulty in reliably triggering the inhibitory response. Conclusions. Impaired response inhibition is not unique to schizophrenia. However, the nature of their problem is markedly different from that of other psychopathological groups. Possible neural mechanisms underpinning difficulties in triggering inhibitory responses and in the voluntary initiation of actions in schizophrenia are considered.
Multilayer etch masks for 3-dimensional fabrication of robust silicon carbide microstructures

This paper details the creation of 3-dimensional (3-D) microstructures in 4H-silicon carbide (4H-SiC) substrates with a plasma etch process that utilizes multilayer etch masks. An inductively coupled plasma (ICP) etch process (SF6/O2) for SiC was developed and etch rates as high as ~1 μm/min, a selectivity of 60:1 (SiC to Ni), and aspect ratio dependent etch characteristics were demonstrated. In addition, the selectivity of atomic layer deposited (ALD) Al2O3 etch masks to 4H-SiC is reported for the first time. Using this unique process, the microfabrication of complex microstructures (mechanical gears, Lego®-like bricks, and poker chips) is presented. The use of 4H-SiC as the structural material enables such microstructures to be utilized under high cycles of wear, within elevated temperatures, and within chemically corrosive environments.
Content-based analysis to detect Arabic web spam

Search engines are important outlets for information query and retrieval. They have to deal with the continual increase of information available on the web, and provide users with convenient access to such huge amounts of information. Furthermore, with this huge amount of information, a more complex challenge that continuously gets more and more difficult to illuminate is the spam in web pages. For several reasons, web spammers try to intrude in the search results and inject artificially biased results in favour of their websites or pages. Spam pages are added to the internet on a daily basis, thus making it difficult for search engines to keep up with the fast-growing and dynamic nature of the web, especially since spammers tend to add more keywords to their websites to deceive the search engines and increase the rank of their pages. In this research, we have investigated four different classification algorithms (naïve Bayes, decision tree, SVM and K-NN) to detect Arabic web spam pages, based on content. The three groups of datasets used, with 1%, 15% and 50% spam contents, were collected using a crawler that was customized for this study. Spam pages were classified manually. Different tests and comparisons have revealed that the Decision Tree was the best classifier for this purpose.
A2A Adenosine Receptor May Allow Expansion of T Cells Lacking Effector Functions in Extracellular Adenosine-Rich Microenvironments1

Immunosuppressive signaling via the A2A adenosine receptor (A2AR) provokes a mechanism that protects inflamed tissues from excessive damage by immune cells. This mechanism is desirable not only for preventing uncontrolled tissue destruction by overactive immune responses, but also for protecting tumor tissues from antitumor immune responses. In aforementioned circumstances, T cell priming may occur in an environment containing high concentrations of extracellular adenosine. To examine qualitative changes in T cells activated in the presence of adenosine, we asked whether different functional responses of T cells are equally susceptible to A2AR agonists. In this study, we demonstrate that A2AR signaling during T cell activation strongly inhibited development of cytotoxicity and cytokine-producing activity in T cells, whereas the inhibition of T cell proliferation was only marginal. Both CD8+ and CD4+ T cells proliferated well in the presence of A2AR agonists, but their IFN-γ-producing activities were susceptible to inhibition by cAMP-elevating A2AR. Importantly, the impaired effector functions were maintained in T cells even after removal of the A2AR agonist, reflecting T cell memory of the immunoregulatory effect of adenosine. Thus, although the adenosine-rich environment may allow for the expansion of T cells, the functional activation of T cells may be critically impaired. This physiological mechanism could explain the inefficiency of antitumor T cells in the tumor microenvironment.
A new covalent peroxidase conjugation method using bis(sulfosuccinimidyl) suberate as cross-linking reagent in a two-step procedure

ABSTRACT A new method has been developed to prepare horseradish peroxidase (HRP) conjugates using bis(sulfosuccinimidyl)suberate (BS3) as cross-linking reagent in a two-step procedure. The enzyme is reacted with BS3, introducing active ester molecules into the enzyme itself, and it is then used directly to label amino-containing compounds without further treatment. The proteins involved in the conjugation undergo minimal modifications. The reaction conditions are evaluated, as well as studies on the conservation of the biological activities of the conjugated proteins and the stability of the conjugates in time. These conjugates are found to be significantly improved compared with similar products prepared by conventional methods.
CHARACTERISING THE SPECRTAL SIGNAL OF DISCHARGE ZONES AT THE MARGIN OF THE GREAT ARTESIAN BASIN

Diffuse discharge along the southwest margin of the Great Artesian Basin is thought to be an important, but currently poorly understood, component of the Basin’s water budget. Remote sensing data are being investigated as a tool for mapping the salt and soil moisture variations associated with diffuse discharge zones, in order to assist in scaling up of field based discharge measurements to regional diffuse discharge estimates. The discharge zones have been segregated into four conceptual discharge scenarios which relate subsurface processes and variation in discharge rates, with expected observable surface characteristics. A handheld soil moisture probe (“Hydraprobe”) was used to collect surface soil moisture and conductivity data from the top 5 cm soil layer to ground-truth a number of processing methods applied to the satellite data. The Hydraprobe data were analysed to investigate the relationship between soil moisture and salinity at the ground surface. Hydraprobe data showed areas non-saline areas exhibited a uniformly low soil moisture content, consistent with the conceptual model of the discharge zones. Average field soil moisture and salinity data generally correlated well with landforms. Landsat TIR data showed a correlation with field data over the discharge area. This response was inconsistent between satellite images and it is presently unclear what the response in TIR data relates to. The Landsat Band7/Band1 salt ratio showed the strongest correlation to landforms characterised by salt at the surface and results suggest the salt ratio will be useful in distinguishing discharge zones. Introduction The Great Artesian Basin (GAB) is Australia’s largest groundwater system, and one of the largest in the world, underlying approximately 22% of the continent (Habermehl, 1980). The GAB is the only reliable source of water for agriculture and industry in parts of arid and semi arid central and eastern Australia. Discharge from the basin is thought to be concentrated along its south west margin, where the aquifer is either outcropping or brought close to the surface by folding and faulting. In these areas higher rates of water are lost from the GAB than in deeper aquifer settings. In shallow settings the vertical leakage feeds local water tables, and is then lost to evaporation.
rs12603332 is associated with male asthma patients specifically in urban areas of Lahore, Pakistan

ABSTRACT Objective: rs12603332, an important regulatory site variant, is known to alter the regulatory motif E2A that is involved in the maturation of B-lymphocytes. The study was designed to check whether different environmental exposures alter its risk allele association with asthma or not. Methods: 200 Physician-diagnosed asthma patients and 108 healthy individuals were enrolled from hospitals of Lahore. After quantitation of DNA extracted from peripheral blood, amplification of genomic region with rs12603332, followed by single base extension (SBE), was performed. Allele and genotype frequencies were calculated by SHEsis and Haploview software packages. Statistical analyses on PLINK were also performed, taking different factors as covariates. HaploReg analysis was done to predict the effect of risk allele on different regulatory motifs. Results: Risk allele for rs12603332 i.e., “C” allele was found to be significantly associated with male patients residing in urban localities. Conclusion: The finding suggests that on exposure with urban environment, risk allele carriers tend to develop asthma symptoms via epigenetic regulation of motif associated with maturation of B-lymphocytes.
The benefits of using semi-continuous and continuous models to analyze binge eating data: A Monte Carlo investigation.

OBJECTIVE Change in binge eating is typically a primary outcome for interventions targeting individuals with eating pathology. A range of statistical models exist to handle these types of frequency distributions, but little empirical evidence exists to guide the appropriate choice of statistical model. METHOD Monte Carlo simulations were used to investigate the utility of semi-continuous models relative to continuous models in various situations relevant to binge eating treatment studies. RESULTS Semi-continuous models yielded more accurate estimates of the population, while continuous models were higher powered when higher levels of missing data were present. DISCUSSION The present findings generally support the use of semi-continuous models applied to binge eating data, with total sample sizes of roughly 200 being adequately powered to detect moderate treatment effects. However, models with a significant amount of missing data yielded more favorable power estimates for continuous models.
Dated Plant Phylogenies Resolve Neogene Climate and Landscape Evolution in the Cape Floristic Region

In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions show remarkable consistency across all 12 clades with regard to both the types of environments identified as ancestral, and the timing of shifts to alternative conditions. They reveal that Early Miocene land surfaces of the CFR were wetter than at present and were dominated by quartzitic substrata. These conditions continue to characterize the higher-elevation settings of the Cape Fold Belt, where they have fostered the persistence of ancient fynbos lineages. The Middle Miocene (13–17 Ma) saw the development of perennial to weakly-seasonal arid conditions, with the strongly seasonal rainfall regime of the west coast arising ~6.5–8 Ma. Although the Late Miocene may have seen some exposure of the underlying shale substrata, the present-day substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene events. Particularly important was renewed erosion, following the post-African II uplift episode, and the reworking of sediments on the coastal platform as a consequence of marine transgressions and tectonic uplift. These changes facilitated adaptive radiations in some, but not all, lineages studied.
Brachial flow-mediated dilation predicts subclinical target organ damage progression in essential hypertensive patients: a 3-year follow-up study

Objectives: We found impaired brachial flow-mediated dilation (FMD) was associated with the number of target organ damage (TOD) in 2007. The present study investigated whether FMD predicted TOD progression in essential hypertension. Methods and results: Endothelium-dependent FMD was measured in 280 adults in 2007. At the third year of examination, 199 patients (mean age 62.5 ± 9.5, men 59.3%) were approached for participation in our study. Patients were divided into two groups: normal FMD group (FMD ≥10) and impaired FMD group (FMD <10). In patients with 0–1 TOD at baseline, impaired FMD group (n = 65) led to thicker intima–media thickness (P = 0.02), increased carotid-to-femoral pulse wave velocity (P = 0.03), increased urinary albumin/creatinine ratio (P = 0.04) and increased TOD number (P = 0.02), as compared with the normal FMD group (n = 59) at the end of the follow-up, even after adjusting for age and sex, whereas the relationship did not exist in 2–4 TOD group at baseline. TOD number increase was associated with the prevalence of diabetes mellitus (&bgr; = 0.180, P = 0.035), blood pressure control (&bgr; = −0.277, P = 0.001), low-density lipoprotein cholesterol (&bgr; = 0.234, P = 0.006) and baseline FMD (&bgr; = −0.168, P = 0.043) in stepwise multivariate regression analysis. FMD remained a significant predictor of TOD number increase in multiple logistic regression analysis after adjustment for several known risk factors (relative risk 0.92, 95% confidence interval 0.85–0.99, P = 0.042, for each 1% increase in FMD). Conclusion: FMD is a predictor of future TOD progression in low-risk essential hypertensive patients, but has little predictive value in the late stage of TOD.
How do Students Conceptualise Health and its Risk Factors? A Study among Iranian Schoolchildren.

BACKGROUND To assess the concept of children concerning their health and its risk factors, a group of primary and middle school students were asked to draw a few relevant pictures in order to deeply explore the comprehension of this key group. METHODS In this cross-sectional study 1165 students, aged 7-15 years old, selected through random stratified sampling, were asked to draw a number of eight paintings, four paintings on health concepts, and the other four on health risk factors. The paintings were then assessed by two independent observers, and their themes and contents were abstracted and analysed. RESULTS The students drew a total of 2330 paintings, 1165 paintings on the concept of health, and 1165 paintings on health risk factors. The most and least expressed health concepts concerned "mental health" and "healthy diet" (73.3% and 4.8%, respectively). Considering health risk factors, "unhealthy diet" and the two concepts of "environmental hazards" and "neglected personal hygiene" had the most (95%) and least (1.4% each) frequencies. Students in public schools, primary level and girls drew more pictures about health concept or/and its risk factors (P<0.05). The association between parents' education level and the numbers of pictures were not statistically significant. CONCLUSION Although students had a broad view about health and its risk factors, generally little attention had been paid to some of the main aspects such as physical activity, healthy diet, mental and oral health, and environmental hazards. In addition, it seems that parents' educational level, as one of the main socio-economic factors, did not have any significant impact on their concepts.
Isolation and characterization of microsatellite markers for Hypochaeris incana (Asteraceae) and close relatives1

Premise of the study: We developed microsatellite markers to study clonal growth and interspecific hybridization in the Patagonian and subantarctic plant Hypochaeris incana (Asteraceae) and its closest relatives. Methods and Results: We developed primers for microsatellite loci from 454 sequence reads of genomic DNA of H. incana. We tested them on individuals of H. acaulis, H. hookeri, H. incana, H. palustris, and H. tenuifolia. We selected 15 polymorphic microsatellite loci, which delivered clearly scorable fragments in most or all species. With mean values between 0.7 and 0.8, the expected heterozygosity in populations of H. incana is high. Conclusions: Due to high levels of polymorphism, the developed markers make it possible to distinguish between genets and ramets in H. incana. In some markers, null alleles complicate the scoring of genotypes in tetraploids. All of the developed markers are suitable to study interspecific hybridization among this group of closely related species.