gebhart/patrepeval huggingface dataset:
Incidence of Bloodstream Infections Due to <i>Candida</i> Species and In Vitro Susceptibilities of Isolates Collected from 1998 to 2000 in a Population-Based Active Surveillance Program (2004)

To determine the incidence of Candida bloodstream infections (BSI) and antifungal drug resistance, population-based active laboratory surveillance was conducted from October 1998 through September 2000 in two areas of the United States (Baltimore, Md., and the state of Connecticut; combined population, 4.7 million). A total of 1,143 cases were detected, for an average adjusted annual incidence of 10 per 100,000 population or 1.5 per 10,000 hospital days. In 28% of patients, Candida BSI developed prior to or on the day of admission; only 36% of patients were in an intensive care unit at the time of diagnosis. No fewer than 78% of patients had a central catheter in place at the time of diagnosis, and 50% had undergone surgery within the previous 3 months. Candida albicans comprised 45% of the isolates, followed by C. glabrata (24%), C. parapsilosis (13%), and C. tropicalis (12%). Only 1.2% of C. albicans isolates were resistant to fluconazole (MIC, > or = 64 microg/ml), compared to 7% of C. glabrata isolates and 6% of C. tropicalis isolates. Only 0.9% of C. albicans isolates were resistant to itraconazole (MIC, > or = 1 micro g/ml), compared to 19.5% of C. glabrata isolates and 6% of C. tropicalis isolates. Only 4.3% of C. albicans isolates were resistant to flucytosine (MIC, > or = 32 microg/ml), compared to < 1% of C. parapsilosis and C. tropicalis isolates and no C. glabrata isolates. As determined by E-test, the MICs of amphotericin B were > or = 0.38 microg/ml for 10% of Candida isolates, > or =1 microg/ml for 1.7% of isolates, and > or = 2 microg/ml for 0.4% of isolates. Our findings highlight changes in the epidemiology of Candida BSI in the 1990s and provide a basis upon which to conduct further studies of selected high-risk subpopulations.
Real-time computational photon-counting LiDAR (2017)

The availability of compact, low-cost, and high-speed MEMS-based spatial light modulators has generated widespread interest in alternative sampling strategies for imaging systems utilizing single-pixel detectors. The development of compressed sensing schemes for real-time computational imaging may have promising commercial applications for high-performance detectors, where the availability of focal plane arrays is expensive or otherwise limited. We discuss the research and development of a prototype light detection and ranging (LiDAR) system via direct time of flight, which utilizes a single high-sensitivity photon-counting detector and fast-timing electronics to recover millimeter accuracy three-dimensional images in real time. The development of low-cost real time computational LiDAR systems could have importance for applications in security, defense, and autonomous vehicles.
Genome-Wide Transcriptional Variation within and between Steady States for Continuous Growth of the Hyperthermophile<i>Thermotoga Maritima</i> (2005)

Maltose-limited, continuous growth of the hyperthermophile Thermotoga maritima at different temperatures and dilution rates (80 degrees C/0.25 h(-1), 80 degrees C/0.17 h(-1), and 85 degrees C/0.25 h(-1)) showed that transcriptome-wide variation in gene expression within mechanical steady states was minimal compared to that between steady states, supporting the efficacy of chemostat-based approaches for functional genomics studies.
A Guided Mashup Framework for Rapid Software Analysis Service Composition (2012)

Historical data about software projects is stored in repositories such as version control, bug tracking and mailing lists. Analyzing such data is vital to discover unthought-of-yet-interesting insights of a software project. Even though a wide range of software analysis techniques are already available, integration of such analyses is yet to be systematically addressed. Inspired from the recently introduced concept of Software as a Service, our research group investigated the concept of Software Analysis as a Service (SOFAS), a distributed and collaborative software analysis platform. SOFAS allows software analyses to be accessed, composed into workflows, and executed over the Internet. However, traditional service composition is a complex, time consuming and error-prone process, which requires experts in both composition languages and existing standards. In this paper, we propose a mashup platform to address the problem of software analysis composition in a light-weight, programming-free process-centric way. Our proposed mashup platform provides design-time guidance to the users throughout the mashup design by integrating a continuous feedback mechanism. It requires exploiting semantic web technologies and Software Engineering Ontologies (SEON).
Comparison of Different Tests to Diagnose Feline Infectious Peritonitis (2003)

Clinical data from 488 cats (1979-2000) with histopathologically confirmed feline infectious peritonitis (FIP) and 620 comparable controls were evaluated retrospectively to assess the value of several diagnostic tests frequently used in the evaluation of cats with suspected FIP. Diagnostic utility of serum albumin to globulin ratio for the diagnosis of FIP was greater than of the utility of serum total protein and gamma-globulin concentrations. Diagnostic utility of these variables was higher when performed on effusion. On effusion, positive and negative predictive values of Rivalta's test, a test that distinguishes between exudates and transudates (0.86 and 0.97), anti-coronavirus antibody detection (0.90 and 0.79), and immunofluorescence staining of coronavirus antigen in macrophages (1.00 and 0.57) were investigated. The positive and negative predictive values of presence of anti-coronavirus antibodies were 0.44 and 0.90, respectively, antibody concentrations (1:1,600) were 0.94 and 0.88. presence of immune complexes measured by a competitive enzyme-linked immunosorbent assay were 0.67 and 0.84, and detection of viral RNA by serum reverse-transcriptase polymerase chain reaction (RT-PCR) were 0.90 and 0.47. Effusion RT-PCR was performed in 6 cats; it was positive in all 5 cats with FIP and negative in the cat with another disease. Diagnostic assays on the fluid in cats with body effusion had good predictive values. Definitive diagnosis of FIP on the basis of measurement of various variables in serum was not possible. Serum tests can only be used to facilitate the decision for more invasive diagnostic methods.
Adoção de inovações : o uso do e-learning por colaboradores de uma empresa de telecomunicações (2008)

The expected benefits of e-learning for an organization depend upon its employees adopting this innovation. Therefore, understanding how individuals adopt e-learning, or resist doing so, can identify potential barriers to acceptance, and suggest actions which can be taken to maximize both e-learning's acceptance and its frequency of use. The main goal of this research is to analyze the factors which influence individual adoption of e-learning by the organization's employees, based on the Technology Acceptance Model -TAM, proposed by DAVIS et al (1989). Initial bibliographical research on individual and organizational adoption of innovation and of e-learning implementation was used to develop the theoretical framework. The conceptual model was tested through empirical research using interviews with e-learning specialists. In the second stage, a large organization from the telecommunication sector in Brazil was chosen to be studied through a multiple methods approach, including interviews with the organization's e-learning team, employee survey and document analysis. Factor analysis, non-parametric tests and logistic regression were conducted on the 312 valid questionnaires answered by the company's employees. The results show TAM is adequate for understanding the factors influencing e-learning adoption. The inclusion of the factor, Favorable Learning Environment, in the analytical framework proved to be an important contribution of the present study. The results confirmed that experience with this innovation and the survey participant's profile both can impact employees' perceptions regarding e-learning. The Favorable Learning Environment factor surpasses the others, since it influences both the e-learning Intention and Use Behavior factors in a positive way, and reinforces the relevance of the organization's environment in innovation adoption. The Perceived Usefulness factor is the most important in explaining Intention to Use; at the same time, it can be a negative influence for Use Behavior, which could be explained by possible frustration related to e-learning courses. Among the suggestions given to increase the e-learning adoption in the researched organization, the following could be mentioned: match the e-learning content with both employees' and organizational needs, innovate e-learning methodology, increase leadership involvement and support, encourage e-learning participation during work hours, give better information on available technical support, and improve e-learning communication and quality of system navigation.
Characterization and engineering of the bifunctional <i>N</i> - and <i>O</i> -glucosyltransferase involved in xenobiotic metabolism in plants (2007)

The glucosylation of pollutant and pesticide metabolites in plants controls their bioactivity and the formation of subsequent chemical residues. The model plant Arabidopsis thaliana contains >100 glycosyltransferases (GTs) dedicated to small-molecule conjugation and, whereas 44 of these enzymes catalyze the O-glucosylation of chlorinated phenols, only one, UGT72B1, shows appreciable N-glucosylating activity toward chloroanilines. UGT72B1 is a bifunctional O-glucosyltransferase (OGT) and N-glucosyltransferase (NGT). To investigate this unique dual activity, the structure of the protein was solved, at resolutions up to 1.45 A, in various forms including the Michaelis complex with intact donor analog and trichlorophenol acceptor. The catalytic mechanism and basis for O/N specificity was probed by mutagenesis and domain shuffling with an orthologous enzyme from Brassica napus (BnUGT), which possesses only OGT activity. Mutation of BnUGT at just two positions (D312N and F315Y) installed high levels of NGT activity. Molecular modeling revealed the connectivity of these residues to H19 on UGT72B1, with its mutagenesis exclusively defining NGT activity in the Arabidopsis enzyme. These results shed light on the conjugation of nonnatural substrates by plant GTs, highlighting the catalytic plasticity of this enzyme class and the ability to engineer unusual and desirable transfer to nitrogen-based acceptors.
Crime Mapping in India: A GIS Implementation in Chennai City Policing (2004)

Abstract In India, though the Police agencies of Bangalore, Hyderabad, Goa, Mumbai, Delhi, Kolkata, Chennai and Trivandrum use customized GIS, its application is still in a rudimentary stage. There is a felt need for the fullest application of this potent technology in Indian policing. Hence, researchers in the University of Madras collaborated with the Chennai Police department and developed this study. This research work was submitted to the Police Commissioner, Chennai city and was implemented. The findings of this study showed that, using GIS is a much more compatible means of crime pattern analysis than current processes because of its geographic referencing capabilities. This research has provided valuable information concerning property crimes in Chennai city, including data on the social and physical characteristics of these areas that contribute to localized criminal activity.
Sensor Data Collection Through Gateways in a Highly Mobile Mesh Network (2007)

Widely distributed sensors must discover paths back to data collection points possibly through sparsely connected and mobile networks. Current addressing and service discovery schemes in mobile networks are not well-suited to multihop disconnected networks. This paper describes an architecture and protocol for sensor data collection through highly mobile ad-hoc network (MANET) that may never experience end-to-end connectivity. Special gateway nodes are described which are responsible for intelligently routing messages to their intended destination(s). These gateway nodes qualify their links and announce their status to the MANET, a simple approach to service discovery that is effective in this implementation. The protocol is implemented and tested in a laboratory and outdoor environment.
Toward Big Data Analytics (2015)

Diabetes is one of the top priorities in medical science and health care management, and an abundance of data and information is available on these patients. Whether data stem from statistical models or complex pattern recognition models, they may be fused into predictive models that combine patient information and prognostic outcome results. Such knowledge could be used in clinical decision support, disease surveillance, and public health management to improve patient care. Our aim was to review the literature and give an introduction to predictive models in screening for and the management of prevalent short- and long-term complications in diabetes. Predictive models have been developed for management of diabetes and its complications, and the number of publications on such models has been growing over the past decade. Often multiple logistic or a similar linear regression is used for prediction model development, possibly owing to its transparent functionality. Ultimately, for prediction models to prove useful, they must demonstrate impact, namely, their use must generate better patient outcomes. Although extensive effort has been put in to building these predictive models, there is a remarkable scarcity of impact studies.
Time-scale modification in medium to low rate speech coding (2005)

Time-scale modification (TSM) of speech is one potential method for speech data reduction at medium to low bit rates. In this application, the speech waveform is compressed in time prior to coding, then expanded to its original speed at the receiver. In this paper, we apply the synchronized-overlap-add (SOLA) method of TSM, developed at BBN, to speech coding at 9.6 and 4.8 kbits/s. These systems were obtained by combining TSM with other established speech coding methods.
General Anesthetic Action at an Internal Protein Site Involving the S4-S5 Cytoplasmic Loop of a Neuronal K+Channel (2000)

The structural bases of general anesthetic action on a neuronal K(+) channel were investigated using the series of homologous 1-alkanols, electrophysiology, and mutational analysis. Domain swapping between dShaw2 (alkanol-sensitive) and hKv3.4 (alkanol-resistant) and site-directed mutagenesis demonstrated that a 13-amino acid cytoplasmic loop (S4-S5) determines the selective inhibition of native dShaw2 channels by 1-alkanols. The S4-S5 loop may contribute to a receptor for both 1-alkanols and the inactivation particle, because the enhanced 1-alkanol sensitivity of hKv3.4 channels hosting S4-S5 mutations correlates directly with disrupted channel inactivation. Evidence of a discrete protein site was also obtained from the analysis of the relationship between potency and alkyl chain length, which begins to level off after 1-hexanol. Rapid application to the cytoplasmic side of inside-out membrane patches shows that the interaction between dShaw2 channels and 1-alkanols equilibrates in <200 ms. By contrast, the equilibration time is >1000-fold slower when the drug is applied externally to outside-out membrane patches. The data strongly favor a mechanism of inhibition involving a discrete internal site for 1-alkanols in dShaw2 K(+) channels. A new working hypothesis proposes that 1-alkanols lock dShaw2 channels in their closed conformation by a direct interaction at a crevice formed by the S4-S5 loop.
An iterative algorithm for decomposition of speech signals into periodic and aperiodic components (1998)

The speech signal may be considered as the output of a time-varying vocal tract system excited with quasiperiodic and/or random sequences of pulses. The quasiperiodic part may be considered as the deterministic or periodic component and the random part as the stochastic or aperiodic component of the excitation. We discuss issues involved in identifying and separating the periodic and aperiodic components of the source. The decomposition is performed on an approximation to the excitation signal, instead of decomposing the speech signal directly. The linear prediction residual signal is used as an approximation to the excitation signal of the vocal tract system. Speech is first analyzed to determine the voiced and unvoiced parts of the signal. Decomposition of the voiced part into periodic and aperiodic components is then accomplished by first identifying the frequency regions of harmonic and noise components in the spectral domain. The signal corresponding to the noise regions is used as a first approximation to the aperiodic component. An iterative algorithm is proposed which reconstructs the aperiodic component in the harmonic regions. The periodic component is obtained by subtracting the reconstructed aperiodic component signal from the residual signal. The individual components of the residual are then used to excite the derived all-pole model of the vocal tract system to obtain the corresponding components of the speech signal. Experiments were conducted using synthetic speech. They demonstrated the ability of the algorithm for decomposition of a synthetic speech signal made of a mixture of periodic and aperiodic components. Application to natural speech is also discussed.
CD4−CD8αα Subset of CD1d-Restricted NKT Cells Controls T Cell Expansion (2004)

Valpha24 invariant (Valpha24i) CD1d-restricted NKT cells are widely regarded to have immune regulatory properties. They are known to have a role in preventing autoimmune diseases and are involved in optimally mounted immune responses to pathogens and tumor cells. We were interested in understanding how these cells provide protection in autoimmune diseases. We first observed, using EBV/MHC I tetrameric complexes, that expansion of Ag-specific cells in human PBMCs was reduced when CD1d-restricted NKT cells were concomitantly activated. This was accompanied by an increase in a CD4(-)CD8alphaalpha(+) subset of Valpha24i NKT cells. To delineate if a specific subset of NKT cells was responsible for this effect, we generated different subsets of human CD4(-) and CD4(+) Valpha24i NKT clones and demonstrate that a CD4(-)CD8alphaalpha(+) subset with highly efficient cytolytic ability was unique among the clones in being able to suppress the proliferation and expansion of activated T cells in vitro. Activated clones were able to kill CD1d-bearing dendritic or target cells. We suggest that one mechanism by which CD1d-restricted NKT cells can exert a regulatory role is by containing the proliferation of activated T cells, possibly through timely lysis of APCs or activated T cells bearing CD1d.
ElevatederbB-2 oncoprotein levels in preoperative and follow-up serum samples define an aggressive disease course in patients with breast cancer (1994)

The study's results suggest that assay serum erbB-2 levels may be valuable in the follow-up and monitoring of patients with breast cancer whose primary tumors show erbB-2 overexpression by immunohistochemistry.
Round-to-flat transformation of angular-momentum-dominated beams (2003)

A study of round-to-flat configurations, and vice versa, of angular-momentum-dominated beams is presented. The beam propagation in an axial magnetic field is described in terms of the familiar Courant-Snyder formalism by using a rotating coordinate system. The discussion of the beam transformation is based on the general properties of a cylindrically symmetric beam matrix and the existence of two invariants for a symplectic transformation in 4D phase space.
<title>Spatiotemporal model of human vision for digital video compression</title> (1997)

We propose a new model for the prediction of distortion visibility in digital image sequences, which is aimed at use in digital video compression algorithms. The model is an extension of our spatial vision model with a spatio-temporal contrast sensitivity function and an eye movement estimation algorithm. Due to the importance of smooth pursuit eye movements when viewing image sequences, eye movements cannot be neglected in a spatio-temporal vision model. Although eye movements can be incorporated by motion compensation of the contrast sensitivity function, the requirements for this motion compensation are different than those for motion compensated prediction in video coding. We propose an algorithm for the estimation of smooth pursuit eye movements, under the worst-case assumption that the observer is capable of tracking all objects in the image.
Comparative genomic sequencing reveals a strikingly similar architecture of a conserved syntenic region on human chromosome 11p15.3 (including gene ST5) and mouse chromosome 7 (2001)

Comparative genomics is a superior way to identify phylogenetically conserved features like genes or regions involved in gene regulation. The comparison of extended orthologous chromosomal regions should also reveal other characteristic traits essential for chromosome or gene function. In the present study we have sequenced and compared a region of conserved synteny from human chromosome 11p15.3 and mouse chromosome 7. In human, this region is known to contain several genes involved in the development of various disorders like Beckwith-Wiedemann overgrowth syndrome and other tumor diseases. Furthermore, in the neighboring chromosome region 11p15.5 extensive imprinting of genes has been reported which might extend to region 11p15.3. The analysis of approximately 730 kb in human and 620 kb in mouse led to the identification of eleven genes. All putative genes found in the mouse DNA were also present in the same order and orientation in the human chromosome. However, in the human DNA one putative gene of unknown function could be identified which is not present in the orthologous position of the mouse chromosome. The sequence similarity between human and mouse is higher in transcribed and exon regions than in non-transcribed segments. Dot plot analysis, however, reveals a surprisingly well-conserved sequence similarity over the entire analyzed region. In particular, the positions of CpG islands, short regions of very high GC content in the 5' region of putative genes, are similar in human and mouse. With respect to base composition, two distinct segments of significantly different GC content exist as well in human as in the mouse. With a GC content of 45% the one segment would correspond to "isochore H1" and the other segment (39% GC in human, 40% GC in mouse) to "isochore L1/L2". The gene density (one gene per 66 kb) is slightly higher than the average calculated for the complete human genome (one gene per 90 kb). The comparison of the number and distribution of repetitive elements shows that the proportion of human DNA made up by interspersed repeats (43.8%) is significantly higher than in the corresponding mouse DNA (30.1%). This partly explains why the human DNA is longer between the landmark genes used to define the orthologous positions in human and mouse.
Concentric Circular Antenna Array synthesis using a differential Invasive Weed Optimization algorithm (2010)

Concentric Circular Antenna Array (CCAA) has several interesting features that makes it indispensable in mobile and communication applications. Here we have considered a uniform arrangement of elements where the inter-element spacing is kept half a wavelength. The main aim is to reduce the sidelobe levels and the primary lobe beamwidth as much as possible. Central to our design is a hybridization of two prominent metaheuristics of current interest namely the Invasive Weed Optimization (IWO) and Differential Evolution (DE). The results of the DIWO algorithm have been shown to perform better then other state-of-the-art metaheuristics like the Particle Swarm Optimization (PSO), DE and IWO.