Miracle-dz/UniFAR-FTUs huggingface dataset:
Duplex Real-Time PCR Assay for Detection of Streptococcus pneumoniae in Clinical Samples and Determination of Penicillin Susceptibility

ABSTRACT We have developed a duplex real-time PCR for the rapid diagnosis of Streptococcus pneumoniae infection from culture-negative clinical samples with the simultaneous determination of penicillin susceptibility. The assay amplifies a lytA gene target and a penicillin binding protein 2b (pbp2b) gene target in penicillin-susceptible organisms. The assay was shown to be sensitive (detects 0.5 CFU per PCR) and specific for the detection of S. pneumoniae DNA. The assay was validated by comparing pbp2b PCR results with MIC data for 27 S. pneumoniae isolates. All 5 isolates with penicillin MICs of >1.0 mg/liter were pbp2b real-time PCR negative, as were 9 of the 10 isolates with penicillin MICs of 0.12 to 1.0 mg/liter. One isolate with a penicillin MIC of 0.12 to 1.0 mg/liter gave an equivocal pbp2b real-time PCR result. Twelve isolates were penicillin susceptible (MICs of ≤0.06 mg/liter) and pbp2b real-time PCR positive. These data were used to establish an algorithm for the interpretation of penicillin susceptibility from the duplex PCR result. pbp2b real-time PCR results were also compared to an established PCR-restriction fragment length polymorphism (RFLP) method previously applied to these 27 isolates and 46 culture-negative clinical samples (containing S. pneumoniae DNA by broad-range 16S rRNA gene PCR). Discordant results were seen for four isolates and six culture-negative clinical samples, as PCR-RFLP could not reliably detect penicillin MICs of 0.12 to 1.0 mg/liter. We report prospective application of the duplex PCR assay to the diagnosis of S. pneumoniae infection from 200 culture-negative clinical specimens sent to the laboratory for diagnostic broad-range 16S rRNA gene PCR. One hundred six were negative in the duplex PCR. Ninety-four were lytA PCR positive, and 70 of these were also pbp2b PCR positive and interpreted as penicillin susceptible. Fourteen were pbp2b PCR negative and interpreted as having reduced susceptibility to penicillin. For the remaining 10 samples, susceptibility to penicillin was not determined.
Global Scale Analysis of Martian Landslide Mobility and Paleoenvironmental Clues

The mobility of landslides on Mars is studied based on a database of 3,118 events. To establish the volume of the landslides for the whole data set based on the deposit area, a new volume‐area relationship based on a representative data set of 222 landslides is used. By plotting the H/L ratio between fall height H and runout L versus volume, the landslide mobility is analyzed and compared with existing empirical relationships for Martian and terrestrial landslides. By analyzing the mobility in terms of normalized residuals, that is, the relative deviation of the H/L ratio from the data set best‐fit line, mobility is found to depend on both the landslide location on Mars and the landslide typology. This allows us to identify four different types of high‐mobility (hypermobile) landslides. Three classes of high‐mobility landslides are associated respectively to meteoroid impact, the Olympus Mons aureoles, and landslides with Toreva‐block failure style, and their mobility can be explained by the peculiar flow mechanics. The fourth class includes landslides associated with isolated craters, those in the regions wetted by the putative Oceanus Borealis, and the ones at high latitudes. We suggest that the common factor behind all the hypermobile landslides of this fourth kind is the presence of ice. This is confirmed by our data showing that landslides increase in mobility with latitude. The latitudinal trend mirrors the distribution of ice as detected by radar, neutron probes, and the presence of glacial and layered ejecta morphologies. Because the overall landslide distribution supports the presence of ice‐lubricated conditions, two ice lubrication models are presented showing how ice melting within or underneath the landslides could enhance mobility. By proper analysis in terms of apparent friction residuals, we find that the mobility of landslides in Valles Marineris with the largest landslide concentration is lower than average. We explain this circumstance partly from the smaller role of ice in equatorial Valles Marineris and partly because the collapses from high slope relief imply high‐speed impact with the floor valley confinement, loss of momentum, and decrease in mobility. Environmental consequences imply that the present subsurface ice distribution may have been persistent throughout the Amazonian period.
HP0197 Contributes to CPS Synthesis and the Virulence of Streptococcus suis via CcpA

Streptococcus suis serotype 2 (SS2), a major swine pathogen and an emerging zoonotic agent, has greatly challenged global public health. The encoding proteins with unknown functions the bacterium encodes are an obstruction to studies of the pathogenesis. A novel surface protective antigen HP0197 is one of these proteins which have no sequence homology to any known protein. In the present study, the protein was determined to be involved in bacterial virulence through an evaluation of the isogenic mutant (Δhp0197) in both mice and pigs. The experimental infection also indicated that Δhp0197 could be cleared easily during infection, which could be attributed to the reduced thickness of the capsular polysaccharides (CPS) and the significantly reduced phagocytotic resistance. Microarrays-based comparative transcriptome analysis suggested that the suppressed expression of the operon responsible for CPS synthesis might be reversed by CcpA activity, which controlled global regulation of carbon catabolite through the binding of the CcpA and HPr-Ser-46-P to the catabolite-responsive elements (cre) of the target operons. The hypothesis was approved by the fact that the purified FLAG-tagged HPr from WT stain exhibited a higher binding activity to cre with CcpA compared to the Δhp0197 by the Electrophoretic Mobility Shift Assay, suggesting lower level of phosphorylation of the phosphocarrier protein HPr at residue Ser-46 (HPr-Ser-46P) in Δhp0197. These indicated that HP0197 could enhance CcpA activity to control the expression of genes involved in carbohydrate utilization and CPS synthesis, thus contributing to the virulence of S. suis.
Traffic flow analysis of tor pluggable transports

Tor provides the users the ability to use the Internet anonymously. On the Tor network, the users connect to three relays run by volunteers. The addresses of these relays are publicly available. Some organizations prevent access to Tor by blocking the addresses of these relays. To mitigate this, Tor has introduced the concept of bridges and pluggable transports. Bridges are relays that do not have publicly available addresses so that they can evade the blocking. Pluggable transports are used to obfuscate the connection to these bridges. In this paper, we investigate the robustness of these pluggable transports in evading the flow based traffic analysis and blocking systems.
Simple Method for Shiga Toxin 2e Purification by Affinity Chromatography via Binding to the Divinyl Sulfone Group

Here we describe a simple affinity purification method for Shiga toxin 2e (Stx2e), a major causative factor of edema disease in swine. Escherichia coli strain MV1184 transformed with the expression plasmid pBSK-Stx2e produced Stx2e when cultivated in CAYE broth containing lincomycin. Stx2e bound to commercial D-galactose gel, containing α-D-galactose immobilized on agarose resin via a divinyl sulfone linker, and was eluted with phosphate-buffered saline containing 4.5 M MgCl2. A small amount of Stx2e bound to another commercial α-galactose-immobilized agarose resin, but not to β-galactose-immobilized resin. In addition, Stx2e bound to thiophilic adsorbent resin containing β-mercaptoethanol immobilized on agarose resin via a divinyl sulfone, and was purified in the same manner as from D-galactose gel, but the Stx2e sample contained some contamination. These results indicate that Stx2e bound to D-galactose gel mainly through the divinyl sulfone group on the resin and to a lesser extent through α-D-galactose. With these methods, the yields of Stx2e and attenuated mutant Stx2e (mStx2e) from 1 L of culture were approximately 36 mg and 27.7 mg, respectively, and the binding capacity of the D-galactose gel and thiophilic adsorbent resin for Stx2e was at least 20 mg per 1 ml of resin. In addition, using chimeric toxins with prototype Stx2 which did not bind to thiophilic adsorbent resin and some types of mutant Stx2e and Stx2 which contained inserted mutations in the B subunits, we found that, at the least, asparagine (amino acid 17 of the B subunits) was associated with Stx2e binding to the divinyl sulfone group. The mStx2e that was isolated exhibited vaccine effects in ICR mice, indicating that these methods are beneficial for large-scale preparation of Stx2e toxoid, which protects swine from edema disease.
Effect of reverse flow on the pattern of wall shear stress near arterial branches

Atherosclerotic lesions have a patchy distribution within arteries that suggests a controlling influence of haemodynamic stresses on their development. The distribution near aortic branches varies with age and species, perhaps reflecting differences in these stresses. Our previous work, which assumed steady flow, revealed a dependence of wall shear stress (WSS) patterns on Reynolds number and side-branch flow rate. Here, we examine effects of pulsatile flow. Flow and WSS patterns were computed by applying high-order unstructured spectral/hp element methods to the Newtonian incompressible Navier–Stokes equations in a geometrically simplified model of an aorto-intercostal junction. The effect of pulsatile but non-reversing side-branch flow was small; the aortic WSS pattern resembled that obtained under steady flow conditions, with high WSS upstream and downstream of the branch. When flow in the side branch or in the aortic near-wall region reversed during part of the cycle, significantly different instantaneous patterns were generated, with low WSS appearing upstream and downstream. Time-averaged WSS was similar to the steady flow case, reflecting the short duration of these events, but patterns of the oscillatory shear index for reversing aortic near-wall flow were profoundly altered. Effects of reverse flow may help explain the different distributions of lesions.
The prevalence of metabolic syndrome and insulin resistance according to the phenotypic subgroups of polycystic ovary syndrome in a representative sample of Iranian females*

BACKGROUND: Polycystic ovary syndrome (PCOS) is associated with metabolic abnormalities which are also parts of metabolic syndrome (MetS). It is debated whether all women with PCOS should be screened for MetS and Insulin resistance (IR), since they may vary in terms of PCOS phenotype, ethnicity and age. This large scale study aimed to determine the prevalence of MetS among Iranian women diagnosed with different phenotypic subgroups of PCOS based on the Rotterdam criteria. METHODS: This study was conducted from January 2006 to June 2008 in Isfahan, Iran. The study population comprised females diagnosed with PCOS referred to the infertility clinic. The subjects were divided into for subgroups according to different phenotypes of PCOS based on the Rotterdam criteria. They underwent metabolic screening according to NCEP ATP III guidelines and IR screening based on homeostasis model assessment (HOMA) of insulin resistance. RESULTS: The prevalence of MetS and IR were 24.9% and 24.3%, respectively. A significant difference in the prevalence of MetS was documented between anovulatory women having PCOS with or without hyperandrogenism (23.1% and 13.9%, respectively; P = 0.001). Likewise, in PCOS women with hyperandrogenism, the MetS prevalence differed among those with or without polycystic ovary (23.1% and 63.8%, respectively; P = 0.001). CONCLUSIONS: The prevalence of MetS and IR varies between the phenotypic subgroups of PCOS. Hyperandrogenemia PCOS phenotypes of Iranian women, in particular those without sonographic polycystic ovary, are highly at risk of MetS and IR.
Genome-wide RNAi selection identifies a regulator of transmission stage-enriched gene families and cell-type differentiation in Trypanosoma brucei

Trypanosoma brucei, causing African sleeping-sickness, exploits quorum-sensing (QS) to generate the ‘stumpy forms’ necessary for the parasite’s transmission to tsetse-flies. These quiescent cells are generated by differentiation in the bloodstream from proliferative slender forms. Using genome-wide RNAi selection we screened for repressors of transmission stage-enriched mRNAs in slender forms, using the stumpy-elevated ESAG9 transcript as a model. This identified REG9.1, whose RNAi-silencing alleviated ESAG9 repression in slender forms and tsetse-midgut procyclic forms. Interestingly, trypanosome surface protein Family 5 and Family 7 mRNAs were also elevated, which, like ESAG9, are T. brucei specific and stumpy-enriched. We suggest these contribute to the distinct transmission biology and vector tropism of T. brucei from other African trypanosome species. As well as surface family regulation, REG9.1-depletion generated QS-independent development to stumpy forms in vivo, whereas REG9.1 overexpression in bloodstream forms potentiated spontaneous differentiation to procyclic forms in the absence of an external signal. Combined, this identifies REG9.1 as a regulator of developmental cell fate, controlling the expression of Trypanosoma brucei-specific molecules elevated during transmission.
Comparison of the effectiveness of lidocaine and salbutamol on coughing provoked by intravenous remifentanil during anesthesia induction

Background Coughing is a side effect of opioids that is rarely studied. Here, we evaluated the incidence of remifentanil induced coughing during anesthesia induction in an attempt to identify its risk factors and to examine the preventive effects of lidocaine and salbutamol. Methods A total of 237 patients scheduled to undergo general anesthesia were allocated randomly into three groups. Group C received no medication, while Group L received 2% lidocaine at 0.5 mg/kg intravenously 1 minute prior to remifentanil infusion and Group S inhaled one metered aerosol puff of salbutamol 15 minutes prior to entering the operating room. Remifentanil was infused at 5 ng/ml by target controlled infusion and coughing was measured for five minutes and graded as none, mild, moderate, or severe based on the number of coughs. Results The incidences of coughing were 30.4%, 25.3%, and 35.4% in Groups C, L, and S, respectively. The incidences, onset times, and severity of coughing did not differ significantly among groups. In addition, multivariate analysis showed that non-smoking and a lower body weight were risk factors of remifentanil-induced coughing (odds ratio, 8.13; P = 0.024, 1.11, and 0.004, respectively). Conclusions The incidence of remifentanil-induced coughing was 30%. A total of 0.5 mg/kg lidocaine and 1 metered aerosol puff of salbutamol did not prevent coughing. Non-smoking and low body weight were found to be risk factors of remifentanil-induced coughing.
Genetic Complexity of Fusidic Acid-Resistant Small Colony Variants (SCV) in Staphylococcus aureus

FusE mutants are fusidic acid-resistant small colony variants (SCVs) of Staphylococcus aureus that can be selected with aminoglycosides. All FusE SCVs have mutations in rplF, encoding ribosomal protein L6. However, individual FusE mutants including some with the same mutation in rplF display auxotrophy for either hemin or menadione, suggesting that additional mutations are involved. Here we show that FusE SCVs can be divided into three genetic sub-groups and that some carry an additional mutation, in one of the genes required for hemin biosynthesis, or in one of the genes required for menadione biosynthesis. Reversion analysis and genome sequencing support the hypothesis that these combinations of mutations in the rplF, hem, and/or men genes can account for the SCV and auxotrophic phenotypes of FusE mutants.
Environmental Exposure and Leptospirosis, Peru

Human infection by leptospires has highly variable clinical manifestations, which range from subclinical infection to fulminant disease. We conducted a population-based, cross-sectional seroepidemiologic study in Peru to determine potential relationships of environmental context to human exposure to Leptospira and disease associated with seroconversion. Three areas were studied: a flooded, urban slum in the Peruvian Amazon city of Iquitos; rural, peri-Iquitos villages; and a desert shantytown near Lima. Seroprevalence in Belen was 28% (182/650); in rural areas, 17% (52/316); and in a desert shantytown, 0.7% (1/150). Leptospira-infected peridomestic rats were found in all locales. In Belen, 20 (12.4%) of 161 patients seroconverted between dry and wet seasons (an incidence rate of 288/1,000). Seroconversion was associated with history of febrile illness; severe leptospirosis was not seen. Human exposure to Leptospira in the Iquitos region is high, likely related both to the ubiquity of leptospires in the environment and human behavior conducive to transmission from infected zoonotic sources.
A Longitudinal Study Examining Adherence to Guidelines in Diabetes Care According to Different Definitions of Adequacy and Timeliness

Background Performance indicators assessing quality of diabetes care often look at single processes, e.g. whether an HbA1c test was conducted. Adequate care, however, consists of consecutive processes which should be taken in time (clinical pathways). We assessed quality of diabetes care by looking at single processes versus clinical pathways. In addition, we evaluated the impact of time period definitions on this quality assessment. Methodology We conducted a cohort study in 2007–2008 using the GIANTT (Groningen Initiative to Analyse type 2 diabetes Treatment) database. Proportions of patients adequately managed for HbA1c, systolic blood pressure (SBP), LDL-cholesterol (LDL-C), and albumin/creatinin ratio (ACR) were calculated for the pathway of (1) risk factor level testing, (2) treatment intensification when indicated, (3) response to treatment evaluation. Strict and wide time periods for each step were defined. Proportions of patients adequately managed regarding the overall pathway and single steps, using strict or wide time periods were compared using odds ratios (OR) with 95% confidence intervals. Findings Of 11176 patients diagnosed with type 2 diabetes, 9439 with complete follow-up were included. The majority received annual examination of HbA1c (86%) and SBP (86%), whereas this was 67% for LDL-C and 49% for ACR. Adequate management regarding the three-step pathway was observed in 73%, 53%, 46%, 41% of patients for HbA1c, SBP, LDL-C, and ACR respectively. Quality scores reduced significantly due to the second step (OR 0.43, 0.18, 0.44, 0.74), but were not much further reduced by the third step. Timely treatment evaluation occurred in 88% for HbA1c, 87% for SBP, 83% for LDL-C, and 76% for ACR. The overall score was not significantly changed by using strict time windows. Conclusion Quality estimates of glycemic, blood pressure and cholesterol management are substantially reduced when looking at clinical pathways as compared to estimates based on commonly used simple process measures.
A Self-Organized Localization-Free Clustering Approach for Redundancy Exploitation in Large Wireless Sensor Networks

This paper investigates organization problems of large wireless sensor networks. In spite of their random deployment, nodes have to organize themselves as energy efficient as possible to avoid redundant sensor and transceiver tasks. In addition to energy awareness, the network has to guarantee complete sensor coverage and connectivity as long as possible. This paper presents a novel clustering algorithm, which allows building up clusters without knowledge about their position. Next to the advantage that only one node per cluster has to be active at each time, also no node has to localize itself. We compared our developed algorithm with former clustering and redundancy detection approaches in terms of nodes per cluster and coverage abilities.
Seeing without Knowing: Neural Signatures of Perceptual Inference in the Absence of Report

Every day, we experience a rich and complex visual world. Our brain constantly translates meaningless fragmented input into coherent objects and scenes. However, our attentional capabilities are limited, and we can only report the few items that we happen to attend to. So what happens to items that are not cognitively accessed? Do these remain fragmentary and meaningless? Or are they processed up to a level where perceptual inferences take place about image composition? To investigate this, we recorded brain activity using fMRI while participants viewed images containing a Kanizsa figure, an illusion in which an object is perceived by means of perceptual inference. Participants were presented with the Kanizsa figure and three matched nonillusory control figures while they were engaged in an attentionally demanding distractor task. After the task, one group of participants was unable to identify the Kanizsa figure in a forced-choice decision task; hence, they were “inattentionally blind. ” A second group had no trouble identifying the Kanizsa figure. Interestingly, the neural signature that was unique to the processing of the Kanizsa figure was present in both groups. Moreover, within-subject multivoxel pattern analysis showed that the neural signature of unreported Kanizsa figures could be used to classify reported Kanizsa figures and that this cross-report classification worked better for the Kanizsa condition than for the control conditions. Together, these results suggest that stimuli that are not cognitively accessed are processed up to levels of perceptual interpretation.