gebhart/patrepeval huggingface dataset:
Performance of Kiestra Total Laboratory Automation Combined with MS in Clinical Microbiology Practice (2014)

The requisite 24 hr incubation time for microbial pathogens to reach sufficient growth for susceptibility testing and identification would be shortened by the implementation of Kiestra TLA in combination with MS, compared to the use of CM. Not only can this method optimize workflow and reduce costs, but it can allow potentially life-saving switches in antibiotic regimen to be initiated sooner.
Immune and inflammatory processes in cutaneous tissues. Mechanisms and speculations. (1990)

Epithelial tissues in general (and skin in particular) define boundaries between inside and outside, host and environment. Mammalian skin and its appendages are poised at the critical interface between the delicately balanced internal milieu ofthe host and the mercurial forces of the outside world. Human skin diseases characterized by histopathologically distinct pat- terns of infiltration by T cells, B cells, monocytes, and granu- locytes (referred to collectively as leukocytes) number quite literally in the hundreds. To state that the pathophysiologic mechanisms involved in the evolution of such unique inflam- matory infiltrates are poorly understood is to euphamize; yet, recent advances have begun to allow for the construction of hypothetical paradigms that address the issue of mechanism in cutaneous immune and inflammatory processes.
Potential for cellular stress response to hepatic factor VIII expression from AAV vector (2016)

Hemophilia A and B are coagulation disorders resulting from the loss of functional coagulation factor VIII (FVIII) or factor IX proteins, respectively. Gene therapy for hemophilia with adeno-associated virus vectors has shown efficacy in hemophilia B patients. Although hemophilia A patients are more prevalent, the development of therapeutic adeno-associated virus vectors has been impeded by the size of the F8 cDNA and impaired secretion of FVIII protein. Further, it has been reported that over-expression of the FVIII protein induces endoplasmic reticulum stress and activates the unfolded protein response pathway both <i>in vitro</i> and in hepatocytes <i>in vivo</i>, presumably due to retention of misfolded FVIII protein within the endoplasmic reticulum. Engineering of the F8 transgene, including removal of the B domain (BDD-FVIII) and codon optimization, now allows for the generation of adeno-associated virus vectors capable of expressing therapeutic levels of FVIII. Here we sought to determine if the risks of inducing the unfolded protein response in murine hepatocytes extend to adeno-associated virus gene transfer. Although our data show a mild activation of unfolded protein response markers following <i>F8</i> gene delivery at a certain vector dose in C57BL/6 mice, it was not augmented upon further elevated dosing, did not induce liver pathology or apoptosis, and did not impact FVIII immunogenicity.
Real-time scene stabilization and mosaic construction (2002)

We describe a real-time system designed to construct a stable view of a scene through aligning images of an incoming video stream and dynamically constructing an image mosaic. This system uses a video processing unit developed by the David Sarnoff Research Center called the Vision Front End (VFE-100) for the pyramid-based image processing tasks required to implement this process. This paper includes a description of the multiresolution coarse-to-fine image registration strategy, the techniques used for mosaic construction, the implementation of this process on the VFE-100 system, and experimental results showing image mosaics constructed with the VFE-100.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prevention of clindamycin-induced colitis in hamsters by Clostridium sordellii antitoxin. (1979)

Toxins produced by Clostridium difficile have been implicated in the etiology of antibiotic-induced colitis. Clostridium difficile antitoxin is not available, but recent studies have shown that toxins present in the feces of patients with this disease are neutralized by Clostridium sordellii antitoxin. We found that C. sordellii antitoxin neutralized toxins produced in broth cultures of either C. sordellii or C. difficile and that passive immunization with C. sordellii antitoxin before challenge with clindamycin prevented colitis in hamsters. Significantly fewer antitoxin-treated animals than unimmunized controls developed diarrhea and died with hemorrhagic colitis. Administration of 300 U of antitoxin parenterally either on the day of challenge with clindamycin or 24 hr later provided significant protection (25% mortality vs. 100% mortality in controls, P less than 0.01). None of eight animals given antitoxin (300 U) both on the day of challenge and 24 hr later died. Filtrates prepared from cecal contents of dead or killed hamsters were tested for toxicity by intraperitoneal injection into hamsters and by addition to monolayers of monkey kidney cells. Fecal filtrates from antitoxin-protected animals were not toxic in these assays, but filtrates from control animals were uniformly toxic. Passive immunization against clostridial toxins was protective against clindamycin-associated colitis in this model. This finding further substantiates the importance of these toxins in the pathogenesis of antibiotic-induced colitis.
Privileged Phosphine-Based Metal–Organic Frameworks for Broad-Scope Asymmetric Catalysis (2014)

A robust and porous Zr metal-organic framework (MOF) based on a BINAP-derived dicarboxylate linker, BINAP-MOF, was synthesized and post-synthetically metalated with Ru and Rh complexes to afford highly enantioselective catalysts for important organic transformations. The Rh-functionalized MOF is not only highly enantioselective (up to >99% ee) but also 3 times as active as the homogeneous control. XAFS studies revealed that the Ru-functionalized MOF contains Ru-BINAP precatalysts with the same coordination environment as the homogeneous Ru complex. The post-synthetically metalated BINAP-MOFs provide a versatile family of single-site solid catalysts for catalyzing a broad scope of asymmetric organic transformations, including addition of aryl and alkyl groups to α,β-unsaturated ketones and hydrogenation of substituted alkene and carbonyl compounds.
The Intrusion Detection Message Exchange Format (IDMEF) (2007)

The purpose of the Intrusion Detection Message Exchange Format (IDMEF)
is to define data formats and exchange procedures for sharing
information of interest to intrusion detection and response systems
and to the management systems that may need to interact with them.
This document describes a data model to represent information exported
by intrusion detection systems and explains the rationale for using
this model. An implementation of the data model in the Extensible
Markup Language (XML) is presented, an XML Document Type Definition is
developed, and examples are provided. This memo defines an
Experimental Protocol for the Internet community.
Volumetric photoacoustic endoscopy of upper gastrointestinal tract: ultrasonic transducer technology development (2011)

We have successfully implemented a focused ultrasonic transducer for photoacoustic endoscopy. The photoacoustic endoscopic probe's ultrasound transducer determines the lateral resolution of the system. By using a focused ultrasonic transducer, we significantly improved the endoscope's spatial resolution and signal-to-noise ratio. This paper describes the technical details of the ultrasonic transducer incorporated into the photoacoustic endoscopic probe and the experimental results from which the transducer's resolution is quantified and the image improvement is validated.
Large-scale reconfigurable computing in a microsoft datacenter (2014)

Presents a collection of slides that address the topic of large-scale reconfigurable computing in Microsoft data centers. Some of the following topics are addressed: increased efficiencies with hardware specialization; current data center environments; the relationship between efficiency versus specialization; the integration of FPGAs in data centers; and new models for improved data centers.
Soluble class I MHC with beta2-microglobulin covalently linked peptides: specific binding to a T cell hybridoma. (1999)

Soluble forms of the mouse MHC class I molecule, Dd, were produced in which the peptide binding groove was uniformly occupied by peptides attached via a covalent flexible peptide linker to the N terminus of the associated beta2-microglobulin. The MHC heavy chain and beta2-microglobulin were firmly associated, and the molecules displayed an Ab epitope requiring proper occupancy of the peptide binding groove. Soluble Dd containing a covalent version of a well-characterized Dd-binding peptide from HIV stimulated a T cell hybridoma specific for this combination. Furthermore, a tetravalent version of this molecule bound specifically with apparent high avidity to this hybridoma.
Sakrale Neuromodulation als Zweitlinien-Therapie bei therapierefraktären irritativen Symptomen des unteren Harntrakts verschiedener Ätiologie: Erfahrungen einer deutschen Anwender-Klinik (2012)

In the selected patient groups SNM is a promising and, in experienced hands, a low-complication second-line therapy for the treatment of LUTS of idiopathic aetiology. However, the general recommendation of SNM for multiple sclerosis and chronic pelvic pain syndrome patients cannot be given on the basis of our results. Further prospective, randomised multicentre studies are need to further refine the indications for SNM in LUTS of neurogenic and non-neurogenic origins.
Osteopontin activation of c-src in human melanoma cells requires the cytoplasmic domain of the integrin alpha v-subunit. (1996)

In human melanoma cells, expression of the alpha v beta 3 integrin is correlated with the metastatic potential. The expression of osteopontin (OPN or OP), a protein ligand for the integrin alpha v beta 3, also correlates with metastatic potential of some tumors. Analysis of signal transduction, stimulated by OPN/alpha v beta 3 in human melanoma cells (M21), revealed activation of pp60c-src associated with the integrin. pp60c-src stimulation by OPN was dose dependent, and it was inhibited in vitro by a tyrosine kinase inhibitor, herbimycin-A. To determine the need for the cytoplasmic domain of the alpha v-subunit, in the association of pp60c-src with alpha v beta 3, a cell line expressing truncated alpha v was studied. M21-L cells lacked alpha v expression but stably transfected with complementary DNAs encoding alpha v full length protein alpha v 1018 or alpha v 995 (lacking 23 carboxyl-terminal amino acids), and a fibroblast cell line (FG) expressing alpha v beta 5 but not alpha v beta 3, were used. Western analysis and immune complex kinase assays of anti- alpha v immunoprecipitates demonstrated that M21-L/alpha v995 cells did not exhibit pp60c-src association with alpha v, whereas the alpha v1018 complementary DNA transfected cells and FG cells had pp60c-src associated with the alpha v integrins. Immunofluorescence analysis revealed pp60c-src, alpha v beta 3 integrin, and actin distribution along the plasma membrane of M21 cells. 35S-labeling of cells and analysis of complexes immunoprecipitated by a monoclonal antibody against alpha v beta 3 demonstrated association of actin with the immune complexes. We conclude that OPN stimulates pp60c-src kinase activity associated with the alpha v beta 3 integrin and that the association requires the cytoplasmic tail of the alpha v chain.
Seq2SQL: Generating Structured Queries from Natural Language using Reinforcement Learning (2017)

A significant amount of the world's knowledge is stored in relational databases. However, the ability for users to retrieve facts from a database is limited due to a lack of understanding of query languages such as SQL. We propose Seq2SQL, a deep neural network for translating natural language questions to corresponding SQL queries. Our model leverages the structure of SQL queries to significantly reduce the output space of generated queries. Moreover, we use rewards from in-the-loop query execution over the database to learn a policy to generate unordered parts of the query, which we show are less suitable for optimization via cross entropy loss. In addition, we will publish WikiSQL, a dataset of 80654 hand-annotated examples of questions and SQL queries distributed across 24241 tables from Wikipedia. This dataset is required to train our model and is an order of magnitude larger than comparable datasets. By applying policy-based reinforcement learning with a query execution environment to WikiSQL, our model Seq2SQL outperforms attentional sequence to sequence models, improving execution accuracy from 35.9% to 59.4% and logical form accuracy from 23.4% to 48.3%.
Pathogenesis of systemic lupus erythematosus (2003)

The exact patho-aetiology of systemic lupus erythematosus (SLE) remains elusive. An extremely complicated and multifactorial interaction among various genetic and environmental factors is probably involved. Multiple genes contribute to disease susceptibility. The interaction of sex, hormonal milieu, and the hypothalamo-pituitary-adrenal axis modifies this susceptibility and the clinical expression of the disease. Defective immune regulatory mechanisms, such as the clearance of apoptotic cells and immune complexes, are important contributors to the development of SLE. The loss of immune tolerance, increased antigenic load, excess T cell help, defective B cell suppression, and the shifting of T helper 1 (Th1) to Th2 immune responses leads to B cell hyperactivity and the production of pathogenic autoantibodies. Finally, certain environmental factors are probably required to trigger the disease.
Bcl-2 overexpression blocks caspase activation and downstream apoptotic events instigated by photodynamic therapy (1998)

Treatment with the photosensitizer benzoporphyrin derivative monoacid ring A (BPD-MA, verteporfin) followed by irradiation with visible light induces apoptosis in human acute myelogenous leukaemia HL-60 cells. Photoactivation of BPD-MA induces procaspase 3 (CPP32/Yama/apopain) and procaspase 6 (Mch2) cleavage into their proteolytically active subunits in these cells. The Bcl-2 proto-oncogene product has been shown to protect cells from a number of proapoptotic stimuli. In the present study, the influence of Bcl-2 overexpression on cellular resistance to photoactivation of BPD-MA was studied. Overexpression of Bcl-2 in HL-60 cells prevented apoptosis-related events including caspase 3 and 6 activation, poly(ADP-ribose) polymerase cleavage and the formation of hypodiploid DNA produced by BPD-MA (0-200 ng ml(-1)) and light. However, Bcl-2 overexpression was less effective at preventing cell death that occurred after photoactivation at high levels (50-100 ng ml(-1)) compared with lower doses (10-25 ng ml(-1)) of BPD-MA. These results indicate that caspase 3 and 6 activation and their regulation by Bcl-2 may play important roles in photodynamic therapy (PDT)-induced cell killing.
Fast-track applications: The potential for direct delivery of proteins and nucleic acids to plant cells for the discovery of gene function (2005)

In animal systems, several methods exist for the direct delivery of nucleic acids and proteins into cells for functional analysis. Until recently, these methods have not been applied to plant systems. Now, however, several preliminary reports suggest that both nucleic acids and proteins can also be delivered into plant cells by very simple, direct application. This promises to open the way for high-throughput screening for gene function in a range of plant species.
Enhancement source-coupled logic for mixed-mode VLSI circuits (1992)

Low-noise enhancement source-coupled logic (ESCL) is proposed for applications in high-precision mixed-mode integrated circuits (ICs). The differential ESCL topology offers potential low-power supply noise advantages over conventional CMOS logic for mixed-mode ICs by steering a constant current to perform the logic operation and it requires a smaller logic swing ( Delta V/sub L/<0.2 V/sub dd/) compared to static CMOS logic ( Delta V=V/sub dd/). For mixed-mode ICs, ESCL reduces the digital switching noise by approximately two orders of magnitude ('20-30 mu A/gate) compared to conventional static logic spikes (0.5-1 mA/gate) which is essential to the development of sensitive on-chip analog circuitry. Results from several ESCL circuits implemented in a 2- mu m p-well CMOS technology are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Exploiting predicate-window semantics over data streams (2006)

The continuous sliding-window query model is used widely in data stream management systems where the focus of a continuous query is limited to a set of the most recent tuples. In this paper, we show that an interesting and important class of queries over data streams cannot be answered using the sliding-window query model. Thus, we introduce a new model for continuous window queries, termed the predicate-window query model that limits the focus of a continuous query to the stream tuples that qualify a certain predicate. Predicate-window queries have some distinguishing characteristics, e.g., (1) The window predicate can be defined over any attribute in the stream tuple (ordered or unordered). (2) Stream tuples qualify and disqualify the window predicate in an out-of-order manner. In this paper, we discuss the applicability of the predicate-window query model. We will show how the existing sliding-window query models fail to answer some of the predicate-window queries. Finally, we discuss the challenges in supporting the predicate-window query model in data stream management systems.
Overview of Extracellular Vesicles, Their Origin, Composition, Purpose, and Methods for Exosome Isolation and Analysis (2019)

The use of extracellular vesicles, specifically exosomes, as carriers of biomarkers in extracellular spaces has been well demonstrated. Despite their promising potential, the use of exosomes in the clinical setting is restricted due to the lack of standardization in exosome isolation and analysis methods. The purpose of this review is to not only introduce the different types of extracellular vesicles but also to summarize their differences and similarities, and discuss different methods of exosome isolation and analysis currently used. A thorough understanding of the isolation and analysis methods currently being used could lead to some standardization in the field of exosomal research, allowing the use of exosomes in the clinical setting to become a reality.
Optical Fiber Probe for Biomedical Raman Spectroscopy (2004)

In vitro experiments have demonstrated the ability of Raman spectroscopy to diagnose a wide variety of diseases. Recent in vivo investigations performed with optical fiber probes were promising but generally limited to easily accessible organs, often requiring relatively long collection times. We have implemented an optical design strategy to utilize system throughput fully by characterizing the Raman distribution from tissue. This scheme optimizes collection efficiency, minimizes noise, and has resulted in small-diameter, highly efficient Raman probes that are capable of collecting high-quality data in 1 s. Performance has been tested through simulations and experiments with tissue models and several in vitro tissue types, demonstrating that this new design can advance Raman spectroscopy as a clinically practical technique.
Static and Dynamic Solvation at the Air/Water Interface (2000)

The electronic excited-state solvation dynamics of coumarin 314 (C314) adsorbed at the air/water interface was investigated by femtosecond time-resolved second-harmonic generation (TRSHG). The second-harmonic spectrum of C314 at the air/water interface was determined using a tunable optical parametric generator, giving a spectral peak at 419 ± 3 nm. The solvatochromic shift is in good agreement with the recently proposed interfacial polarity scale, which predicts that the empirical polarity parameter of the interface is the arithmetic mean of the two bulk phases. The time-resolved second-harmonic response to the excited-state solvation was measured at two fundamental wavelengths (840 and 900 nm) and with two pump polarizations (S and P). The results indicate that the static spectral peaks of the S- and P-pumped distributions are offset ∼5 nm, while the dynamic interfacial solvation proceeds with two time constants, τ1 = ∼200 fs and τ2 = 1.2 ps, which are independent of C314 interfacial orientation. The slight blue shift of the C314 molecules closer to the normal incidence indicates that the electronic spectra of species at the air/water interface is inhomogeneously broadened by orientation, an effect which had not been observed previously. This can be described by a static solvation that depends on the orientation of the molecule's dipole moment at the interface. The dynamic solvation times are consistent with bulk experiment, as well as theory, which indicates that the air/water relaxation times, which are controlled by water/water interactions, should not be different from the bulk values.
The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins. (1994)

The hnRNP C proteins (C1/C2) are tenacious nuclear pre-mRNA-binding proteins that belong to the large RNP motif family of RNA-binding proteins. This motif identifies an RNA-binding domain (RBD) that consists of a four-stranded antiparallel beta-sheet packed against two alpha-helices. Despite considerable information on the structure of the hnRNP C RBD, little is known about its RNA-binding properties. To address this we used in vitro selection/amplification from pools of random sequence RNA to determine the RNA-binding specificity of hnRNP C1. After 8 rounds of selection/amplification nearly all RNAs contained contiguous stretches of at least 5 U residues, and filter-binding assays demonstrated that this sequence constitutes a high-affinity (Kd = 170 nM) binding site for hnRNP C1. The highest affinity we measured for hnRNP C1 was for r(U)14 (Kd = 14 nM). An RBD-containing peptide fragment of hnRNP C1 (amino acids 2-94) bound oligoribonucleotides containing an hnRNP C1 high-affinity binding site with nearly equal affinity to that of hnRNP C1. Unlike hnRNP C1, however, this peptide also bound oligoribonucleotides that do not contain high-affinity hnRNP C1-binding sites. We identified a region of 10 amino acids, immediately COOH-terminal to the RNP motif (amino acids 95-104), that prevents the minimal RBD from binding nonspecific RNA ligands. We propose that the highly conserved beta alpha beta beta alpha beta core structure of the RNP motif RBD confers a general RNA binding activity to RNP motif RBDs and that the determinants of RNA-binding specificity reside in the most variable regions, the loops connecting the beta-strands and/or the contiguous NH2 and COOH termini of the RBD.
Induction of a Highly Specific Antiviral State in Transgenic Plants: Implications for Regulation of Gene Expression and Virus Resistance (1993)

John A. Lindbo, Laura Silva-Rosales, William M. Proebsting, William G. Dougherty, Induction of a Highly Specific Antiviral State in Transgenic Plants: Implications for Regulation of Gene Expression and Virus Resistance, The Plant Cell, Vol. 5, No. 12 (Dec., 1993), pp. 1749-1759
Spectral Beam Combining of 2 μm Tm Fiber Laser Systems (2010)

We report spectral beam combining of three 2-μm Tm fiber lasers each locked to slightly different wavelengths, using a new spectral-limiting device, providing a path forward to beam–combining at the multi-kW level.
Continuous Glucose Sensing with a Fluorescent Thin‐Film Hydrogel (2003)

Sweetness and light: A fluorescent thin-film hydrogel that contains a covalently bound boronic-acid-functional quencher (Q) and a fluorescent dye (F; see Figure) continuously senses glucose under physiological conditions through binding of the sugar (S) to a labeled receptor (R).