Miracle-dz/UniFAR-FTUs huggingface dataset:
New Real-Time PCR Assay for Rapid Detection of Methicillin- Resistant Staphylococcus aureus Directly from Specimens Containing a Mixture of Staphylococci

ABSTRACT Molecular methods for the rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) are generally based on the detection of an S. aureus-specific gene target and the mecA gene. However, such methods cannot be applied for the direct detection of MRSA from nonsterile specimens such as nasal samples without the previous isolation, capture, or enrichment of MRSA because these samples often contain both coagulase-negative staphylococci (CoNS) and S. aureus, either of which can carry mecA. In this study, we describe a real-time multiplex PCR assay which allows the detection of MRSA directly from clinical specimens containing a mixture of staphylococci in <1 h. Five primers specific to the different staphylococcal cassette chromosome mec (SCCmec) right extremity sequences, including three new sequences, were used in combination with a primer and three molecular beacon probes specific to the S. aureus chromosomal orfX gene sequences located to the right of the SCCmec integration site. Of the 1,657 MRSA isolates tested, 1,636 (98.7%) were detected with the PCR assay, whereas 26 of 569 (4.6%) methicillin-susceptible S. aureus (MSSA) strains were misidentified as MRSA. None of the 62 nonstaphylococcal bacterial species or the 212 methicillin-resistant or 74 methicillin-susceptible CoNS strains (MRCoNS and MSCoNS, respectively) were detected by the assay. The amplification of MRSA was not inhibited in the presence of high copy numbers of MSSA, MRCoNS, or MSCoNS. The analytical sensitivity of the PCR assay, as evaluated with MRSA-negative nasal specimens containing a mixture of MSSA, MRCoNS, and MSCoNS spiked with MRSA, was ∼25 CFU per nasal sample. This real-time PCR assay represents a rapid and powerful method which can be used for the detection of MRSA directly from specimens containing a mixture of staphylococci.
Multiangle, multiscale inversion of migrated seismic data

The relation between the angle‐dependent reflectivity of an interface in a target zone and the amplitude‐variation‐with‐offset (AVO) effects observed in the seismic data at the earth’s surface is complicated by many factors, as was pointed out in Ostrander’s classic paper (Geophysics, 1984). Some factors are “reflection related” (such as thin‐bed tuning, reflector curvature), others “propagation related” (such as geometrical spreading, transmission and/or anelastic losses), or “acquisition related” (such as source/receiver directivity, geophone coupling). Amplitude‐versus‐angle (AVA) inversion in a target zone can be carried out successfully only when these effects are taken into account, either by forward modeling or by stepwise processing prior to AVA inversion. In the Delphi research program, we opt for the latter. For example, by decomposing multicomponent ocean‐bottom measurements into P- and S-wave responses, the effects of receiver directivity are implicitly suppressed. Furthermore, the geometrical.
The Effects of Multiple Infections on the Expression And Evolution Of Virulence in a Daphnia-Endoparasite System

Abstract Multiple infections of a host by different strains of the same microparasite are common in nature. Although numerous models have been developed in an attempt to predict the evolutionary effects of intrahost competition, tests of the assumptions of these models are rare and the outcome is diverse. In the present study we examined the outcome of mixed-isolate infections in individual hosts, using a single clone of the waterflea Daphnia magna and three isolates of its semelparous endoparasite Pasteuria ramosa. We exposed individual Daphnia to single- and mixed-isolate infection treatments, both simultaneously and sequentially. Virulence was assessed by monitoring host mortality and fecundity, and parasite spore production was used as a measure of parasite fitness. Consistent with most assumptions, in multiply infected hosts we found that the virulence of mixed infections resembled that of the more virulent competitor, both in simultaneous multiple infections and in sequential multiple infections in which the virulent isolate was first to infect. The more virulent competitor also produced the vast majority of transmission stages. Only when the less virulent isolate was first to infect, the intrahost contest resembled scramble competition, whereby both isolates suffered by producing fewer transmission stages. Surprisingly, mixed-isolate infections resulted in lower fecundity-costs for the hosts, suggesting that parasite competition comes with an advantage for the host relative to single infections. Finally, spore production correlated positively with time-to-host-death. Thus, early-killing of more competitive isolates produces less transmission stages than less virulent, inferior isolates. Our results are consistent with the idea that less virulent parasite lines may be replaced by more virulent strains under conditions with high rates of multiple infections.
A Classification of SQL-Injection Attacks and Countermeasures

SQL injection attacks pose a serious security threat to Web applications: they allow attackers to obtain unrestricted access to the databases underlying the applications and to the potentially sensitive information these databases contain. Although researchers and practitioners have proposed various methods to address the SQL injection problem, current approaches either fail to address the full scope of the problem or have limitations that prevent their use and adoption. Many researchers and practitioners are familiar with only a subset of the wide range of techniques available to attackers who are trying to take advantage of SQL injection vulnerabilities. As a consequence, many solutions proposed in the literature address only some of the issues related to SQL injection. To address this problem, we present an extensive review of the different types of SQL injection attacks known to date. For each type of attack, we provide descriptions and examples of how attacks of that type could be performed. We also present and analyze existing detection and prevention techniques against SQL injection attacks. For each technique, we discuss its strengths and weaknesses in addressing the entire range of SQL injection attacks.
Public Participation in Analytic-Deliberative Decision Making: Evaluating a Large-Group Online Field Experiment

This article reports an evaluation of the quality and scale of interactions during an online field experiment. A large number of individuals (n= 179) worked with an online public participation geographic information system (PPGIS) platform during a month-long field experiment about regional transportation improvement decision making in the central Puget Sound area of Washington. The system platform logged more than 120,000 client–server interaction events. We developed a geovisual analytic technique called a grapevine to evaluate the quality and scale of public participation using event log data. The grapevine 4D space–time geographic information system (GIS) visualization helps distinguish productive clusters of analytic-deliberative process and for guiding content analysis of the user-generated discussion. Comparison of the nature and content of participant message exchanges before and after GIS-based analytic activities revealed a significant shift in focus. We characterize this shift in the focus of deliberation as the result of participants sharing their lay expertise, in the form of simplifying assumptions, to cope with the technical details of the GIS-based analysis and move the large group toward agreeing on a transportation package for the region. The article concludes by extending the implications of the research with a three-part framework called participatory interaction modeling, wherein geographically distributed networks of designers and developers, participant users, and social and behavioral science evaluators learn how to create PPGIS capabilities that can better address societal goals.
Gingival Biotype Assessment in a Healthy Periodontium: Transgingival Probing Method.

BACKGROUND Gingival biotype is the thickness of the gingiva in the faciopalatal dimension. It has a significant impact on the outcome of the restorative, regenerative and implant therapy. It has been suggested that a direct co-relation exists with the susceptibility of gingival recession followed by any surgical procedure. So, the study was aimed to assess gingival biotype in different age groups of males and females using transgingival probing method. MATERIALS AND METHODS Gingival thickness (GT) was evaluated in 336 patients including males and females of different age groups. The latter was based on the transparency of the periodontal probe through the gingival margin while probing the buccal sulcus. Final data collected was then used for statistical analysis. RESULTS A significant difference was found between males and females with males showing thick biotype. Out of the total samples 76.9% of males showed thick biotype compared to 13.3 % of females which was statistically significant. CONCLUSION This was probably one of the few attempts to correlate gingival biotype with different age groups in males and females. A clear thick gingiva was found in more than two-third of the male subjects whereas majority of female subjects showed thin biotype. Also, it was seen that in females, the gingival biotype varies with age unlike in male.
On the use of a deep pressure gradient constraint for estimating the steady state ocean circulation from hydrographic data

Estimating unobserved quantities such as velocities and transports indirectly from temperature and salinity measurements is one of the best studied problems in physical oceanography. It is ill posed. The ill posedness is traditionally removed by adding prior information such as a level of no motion or a set of conservation principles. We propose to use the deep pressure gradient taken from a prognostic integration of an ocean general circulation model in primitive equations as a weak constraint when using the stationary inverse of the same model to derive transports. First results for the western boundary currents in the North Atlantic compare well with previous estimates from several studies including direct measurements.
Wealth Effects of Banks' Rights to Market and Originate Annuities

We examine wealth effects, for banks and insurers, of bank rights to sell and underwrite annuities. The stock-price reactions to four court and regulatory decisions are consistent with expectations of bank gains at insurers’ expense. Cross-sectionally, smaller, riskier insurers with higher distribution costs and substantial annuity business sustain larger wealth losses. Larger, riskier bank holding companies with fee-based and consumer business gain most, consistent with the extension of federal safety-net guarantees as a source of gains. Banking stock-price reactions to the Supreme Court’s decision are opposite other findings, possibly reflecting unfulfilled expectations of a broader mandate for expanded bank rights.
Fully Distributed Algorithms for Convex Optimization Problems

We describe a distributed algorithm for convex constrained optimization in networks without any consistent naming infrastructure. The algorithm produces an approximately feasible and near-optimal solution in time polynomial in the network size, the inverse of the permitted error, and a measure of curvature variation in the dual optimization problem. It blends, in a novel way, gossip-based information spreading, iterative gradient ascent, and the barrier method from the design of interior-point algorithms.
Developments in Oklahoma in 1954

Exploratory drilling, as well as development drilling, increased very slightly in Oklahoma during 1954. As has been the case in the several past years, exploratory activity has failed to uncover any fields of major importance during the past year. Secondary-recovery projects recovered more than 36,000,000 barrels of oil in 1954 or one-fifth of the oil produced during the year. This is about a 3% increase over the previous year. Leasing activity decreased while geophysical activity increased very slightly over the previous year.
Effects of vitamin E on lipid peroxidation in healthy persons.

CONTEXT Oxidative stress may play a role in the development or exacerbation of many common diseases. However, results of prospective controlled trials of the effects of antioxidants such as vitamin E are contradictory. OBJECTIVE To assess the effects of supplemental vitamin E on lipid peroxidation in vivo in healthy adults. DESIGN Randomized, double-blind, placebo-controlled trial conducted March 1999 to June 2000. SETTING A general clinical research center in a tertiary referral academic medical center. PARTICIPANTS Thirty healthy men and women aged 18 to 60 years. INTERVENTIONS Participants were randomly assigned to receive placebo or alpha-tocopherol dosages of 200, 400, 800, 1200, or 2000 IU/d for 8 weeks (n = 5 in each group), followed by an 8-week washout period. MAIN OUTCOME MEASURES Three indices of lipid peroxidation, urinary 4-hydroxynonenal (4-HNE) and 2 isoprostanes, iPF(2alpha)-III and iPF(2alpha)-VI, measured by gas chromatography/mass spectrometry and compared among the 6 groups at baseline, 2, 4, 6, and 8 weeks, and 1, 3, and 8 weeks after discontinuation. RESULTS Circulating vitamin E levels increased in a dose-dependent manner during the study. No significant effect of vitamin E on levels of urinary 4-HNE or either isoprostane was observed. Mean (SEM) baseline vs week 8 levels of iPF(2alpha)-III were 154 (20.1) vs 168 (22.3) pg/mg of creatinine for subjects taking placebo; 165 (19.6) vs 234 (30.1) pg/mg for those taking 200 IU/d of vitamin E; and 195 (26.7) vs 213 (40.6) pg/mg for subjects taking 2000 IU/d. Corresponding iPF(2alpha)-VI levels were 1.43 (0.6) vs 1.62 (0.4) ng/mg of creatinine for subjects taking placebo; 1.64 (0.3) vs 1.24 (0.8) ng/mg for those taking 200 IU/d of vitamin E; and 1.83 (0.3) vs 1.94 (0.9) ng/mg for those taking 2000 IU/d. Baseline vs week 8 levels of 4-HNE were 0.5 (0.04) vs 0.4 (0.05) ng/mg of creatinine for subjects taking placebo; 0.4 (0.06) vs 0.5 (0.02) ng/mg with 200 IU/d of vitamin E; and 0.2 (0.02) vs 0.2 (0.1) ng/mg with 2000 IU/d. CONCLUSIONS Our results question the rationale for vitamin E supplementation in healthy individuals. Specific quantitative indices of oxidative stress in vivo should be considered as entry criteria and for dose selection in clinical trials of antioxidant drugs and vitamins in human disease.
Diagnosis of Adrenal Insufficiency

The recent survey' of endocrine function testing recommended a review of standards and the need for guidelines describing an adequate response to a short synacthen test (SST). A survey of British laboratories' and endocrinologists? demonstrated a lack of consensus. This may be in part due to the original work having used the fluorimetric method for cortisol. Consensus guidelines need to be sufficiently robust to include patients investigated as outpatients and those who are critically ill. Our standards for an inadequate response to SST are a basal cortisol > 250 nmoljL between 0800 hand 0900 h, peak response > 550 nrnol/L' and an increment usually > 200 nmoljL, and they did not agree with the proposed consensus guidelines that the serum cortisol at 30 min should be double the basal and greater than 650 nmol/L;' Comparisons of insulin tolerance tests and SST gave an adequate response for SST to be a 30 min cortisol > 495 nmol/L," > 550 nmol/L" and > 700 nrnol/L. " The predominant patient group studied were those with hypothalamic-pituitary disease and not with primary adrenal disease. A recent review of the laboratory assessment of adrenal insufficiency stated that the rise in cortisol during a SST was inversely proportional to the basal cortisol with smaller increases in the morning and concluded that the cortisol increase was an unreliable index. " Studies of SST in acute hospital admissions recommended that the peak cortisol should be > 600 nmoljL8 and in critically ill patients, the absence of an increase in plasma cortisol may indicate adrenal insufficiency. A consensus guideline for the SST may prove difficult because of the heterogeneous group of patients and different time of day to which it will be applied. There is the need to study the SST in the different subgroups of adrenal insufficiency, with cortisol determined by immunoassay.
Short‐wave directional properties in the vicinity of atmospheric and oceanic fronts

[1] The author estimated and investigated mean wave directions and directional spread parameters of 0.505 Hz ocean waves using data from 24.5 MHz-HF ocean radar. The author described temporal and spatial variabilities of the short-wave field. The short-wave direction is a good indication of wind direction. The spread parameter was related to the variability of wind direction. The author examined the case that an atmospheric front or an oceanic front exists in the HF ocean radar observation area. In the case of an atmospheric front the short-wave direction changed with the passage of the atmospheric front. Furthermore, the complicated frontal structure, which cannot be verified from a weather chart, was revealed. Narrow directional spread was observed in the vicinity of the convergent front, which was reproduced using a simplified model based on the wave action conservation law. The result shows that wave refraction associated with a frontal convergent zone is important in determining the spatial variability of short-wave directional properties.
Assessing the safety of a velocity sourced series elastic actuator using the head injury criterion

The Velocity Sourced Series Elasic Actuator has been proposed as a method for providing safe force or torque based acutation for robots without compromsing the actuator performance. In this paper we assess the safety of Velocity Sourced Series Elastic Actuators by measuring the Head Injury Criterion scores for collisions with a model head. The study makes a comparitive analysis against stiff, high impedance actuation using the same motor without the series elastic component, showing that the series elastic component brings about a massive reduction in the chance of head injury. The benefits of a collision detection and safe reaction system are shown to be limited to collisions at low speeds, providing greater interaction comfort but not necessarily contributing to safety from injury.
The effect of collapse structures on ground deformations in calderas

Ground deformations related to unrest episodes in calderas are generally interpreted, like in other volcanic environments, in terms of increased pressure within a magma chamber embedded in a continuous, elastic medium, In this framework, the depth of the pressure source is inferred from the size of the deformed area. This scheme works quite well for individual volcanoes (for instance Hawaiian shields) where a good correspondence between inflation events and eruptive episodes has been observed. Ground deformation in calderas, however, show unusual features that are difficult to interpret within such a scheme, because considerable positive deformation (in the order of several meters) and microfracturing (i.e. intense seismicity) may occur without eruptions, altough the estimated depth for the magma source is sometime very shallow (less than 1–2 km). It has been recently suggested that the contact zones at the border of collapsed calderas, could act as stress‐strain discontinuity zones and thus bias modeling results obtained for continuous elastic media. We use both observations and theoretical modeling based on 3‐D finite element techniques to show that ground deformations in collapsed calderas are strongly influenced by the caldera structure, giving a new perspective in related geological and geophysical observations in such areas.
Coexistence of Interacting Opinions in a Generalized Sznajd Model

The Sznajd model is a sociophysics model that mimics the propagation of opinions in a closed society, where the interactions favor groups of agreeing people. It is based in the Ising and Potts ferromagnetic models and, although the original model used only linear chains, it has since been adapted to general networks. This model has a very rich transient, which has been used to model several aspects of elections, but its stationary states are always consensus states. In order to model more complex behaviors, we have, in a recent work, introduced the idea of biases and prejudices to the Sznajd model by generalizing the bounded confidence rule, which is common to many continuous opinion models, to what we called confidence rules. In that work we have found that the mean field version of this model (corresponding to a complete network) allows for stationary states where noninteracting opinions survive, but never for the coexistence of interacting opinions. In the present work, we provide networks that allow for the coexistence of interacting opinions for certain confidence rules. Moreover, we show that the model does not become inactive; that is, the opinions keep changing, even in the stationary regime. This is an important result in the context of understanding how a rule that breeds local conformity is still able to sustain global diversity while avoiding a frozen stationary state. We also provide results that give some insights on how this behavior approaches the mean field behavior as the networks are changed.
Guided tour of handoff steering for bandwidth in indoor venues

With the advancement and development for more than two decades, WiFi has become an indispensable infrastructure in most of indoor venues. Indoor localization using this pre-existing infrastructure has been studied in the literature and is proven practically feasible, which mostly relies on WiFi fingerprints and the corresponding radiomap database. Since the radiomap essentially tells which APs are available and how strong their signals are at positions in the venue, this information can usefully utilized to “steer” to a better AP for the purpose of increasing the user throughput, which we call Guided Tour of Handoff Steering (GUT) in this paper. This steering is not much different from a conventional handoff, but it does not need an expensive scanning process owing to the radiomap, thus some additional handoffs are allowed than conventional handoffs. This leads to higher throughput, because a client can switch to a better AP whenever available. Based on an extensive experiment in a large-scale indoor venue of 119,685m2 with 1,734 APs, it is observed that GUT achieves as much as 84% higher throughput, but the number of handoffs increases only a few. This result supports that the handoff steering is not as expensive as the conventional handoff in terms of latency and traffic.
ALL-SOURCE NAVIGATION FOR ENHANCING UAV OPERATIONS IN GPS-DENIED ENVIRONMENTS

The drive towards utilizing small, cheap, autonomous aerial vehicles for military operations means that navigation systems that are robust to GPS denial must be employed. The simplest option available is to increase the accuracy of the inertial measurement unit (IMU), but this can substantially increase the price per operational unit. This paper presents an overview of the All-Source Navigation system developed by BAE Systems Australia based on inexpensive MEMS IMUs and a supporting image processing unit. The navigation system is capable of sustaining the operational flight capability of the vehicle for prolonged periods of time compared to the pure inertial solution. At its core, All-Source Navigation makes use of SLAM techniques. A variety of additional aiding sources are fused into the inertial navigation solution to give improved navigational accuracy during flight. The system is capable of performing both conventional static, as well as in-flight alignment. All-Source Navigation is demonstrated on the Kingfisher 2 UAV platform at the West Sale test facility.