gebhart/patrepeval huggingface dataset:
Development and evaluation of a PCR-based immunoassay for the rapid detection of methicillin-resistant Staphylococcus aureus (1998)

A multiplex polymerase chain reaction (PCR), involving detection of the mecA and femB genes, was combined with a novel immunoassay system capable of detecting specific PCR products. The resulting PCR-immunoassay was evaluated in comparison with conventional microbiological techniques used in the routine diagnostic laboratory for the rapid identification of methicillin-resistant Staphylococcus aureus (MRSA), either in pure culture or in overnight broth cultures obtained following enrichment of patient screening swabs. Among the 480 purified isolates of staphylococci and 246 enrichment broths examined, only one 'false-negative' result was obtained by PCR, compared with 18 'false-negative' results obtained by conventional methodology and demonstrated by further conventional examination. Five demonstrable 'false-positive' results were obtained by conventional methodology, compared with a possible 10 by the PCR-immunoassay, although it was not certain that these 10 PCR results were true 'false positives' as, by definition, MRSA could not be isolated by conventional methodology. The results indicated that the routine diagnostic laboratory was encountering difficulties in identifying MRSA correctly, and that the conventional microbiological techniques lacked sensitivity. Overall, the PCR technique was more accurate and sensitive than conventional methodology in detecting MRSA, and results were available within 24 h of screening swabs arriving in the laboratory, compared with a minimum of 48-72 h by conventional techniques. The immunoassay system added to the usefulness of the method by allowing the detection of specific PCR products within 5 min of completing the PCR, without the normal additional step of agarose gel electrophoresis.
Tumor-specific antigen of murine T-lymphoma defined with monoclonal antibody. (1982)

A panel of hybridomas was constructed by fusion of P3X63Ag8 myeloma cells with spleen cells from a BALB/c mouse that had been immunized with a C57BL/Ka x-ray-induced lymphoma, C6XL. One of forty-three hybridomas secreting antibodies reactive with the tumor cells was found to be unreactive with normal spleen cells in a radioimmunometric assay. This antibody, designated 124-40, was unreactive with normal adult thymus, spleen, lymph node, or bone marrow cells, or with fetal spleen or thymus cells in radioimmunometric or radioimmunoprecipitation assays. Flow microfluorometric analysis of these nonmalignant lymphoid cells failed to reveal subpopulations reactive with MAb 124-40. The antibody was highly specific for the lymphoma cells used for immunization and did not react with a panel of other spontaneous or x-ray-induced or chemically induced lymphomas. The antigen reactive with MAb 124-40 was isolated by radioimmunoprecipitation and found to be a glycoprotein composed of disulfide-bonded subunits of 39,000 m.w. and 41,000 m.w. A cell surface component of similar structure, but not reactive with MAb 124-40 could be detected by two-dimensional electrophoresis in extracts of purified T cells, but not B cells. These results suggest that the apparently individually specific lymphoma antigen reactive with MAb 124-40 might be a clonally expressed epitope carried by a T cell surface component.
A 128-Channel 6 mW Wireless Neural Recording IC With Spike Feature Extraction and UWB Transmitter (2009)

This paper reports a 128-channel neural recording integrated circuit (IC) with on-the-fly spike feature extraction and wireless telemetry. The chip consists of eight 16-channel front-end recording blocks, spike detection and feature extraction digital signal processor (DSP), ultra wideband (UWB) transmitter, and on-chip bias generators. Each recording channel has amplifiers with programmable gain and bandwidth to accommodate different types of biological signals. An analog-to-digital converter (ADC) shared by 16 amplifiers through time-multiplexing results in a balanced trade-off between the power consumption and chip area. A nonlinear energy operator (NEO) based spike detector is implemented for identifying spikes, which are further processed by a digital frequency-shaping filter. The computationally efficient spike detection and feature extraction algorithms attribute to an auspicious DSP implementation on-chip. UWB telemetry is designed to wirelessly transfer raw data from 128 recording channels at a data rate of 90 Mbit/s. The chip is realized in 0.35 mum complementary metal-oxide-semiconductor (CMOS) process with an area of 8.8 x 7.2 mm(2) and consumes 6 mW by employing a sequential turn-on architecture that selectively powers off idle analog circuit blocks. The chip has been tested for electrical specifications and verified in an ex vivo biological environment.
AidH, an Alpha/Beta-Hydrolase Fold Family Member from an Ochrobactrum sp. Strain, Is a Novel N -Acylhomoserine Lactonase (2010)

N-acylhomoserine lactones (AHLs) are signaling molecules in many quorum-sensing (QS) systems that regulate interactions between various pathogenic bacteria and their hosts. Quorum quenching by the enzymatic inactivation of AHLs holds great promise in preventing and treating infections, and several such enzymes have been reported. In this study, we report the characterization of a novel AHL-degrading protein from the soil bacterium Ochrobactrum sp. strain T63. This protein, termed AidH, shares no similarity with any of the known AHL degradases but is highly homologous with a hydrolytic enzyme from Ochrobactrum anthropi ATCC 49188 that contains the alpha/beta-hydrolase fold. By liquid chromatography-mass spectrometry (MS) analysis, we demonstrate that AidH functions as an AHL-lactonase that hydrolyzes the ester bond of the homoserine lactone ring of AHLs. Mutational analyses indicate that the G-X-Nuc-X-G motif or the histidine residue conserved among alpha/beta-hydrolases is critical for the activity of AidH. Furthermore, the AHL-inactivating activity of AidH requires Mn(2+) but not several other tested divalent cations. We also showed that AidH significantly reduces biofilm formation by Pseudomonas fluorescens 2P24 and the pathogenicity of Pectobacterium carotovorum, indicating that this enzyme is able to effectively quench QS-dependent functions in these bacteria by degrading AHLs.
Distinct Signaling Cascades Elicited by Different Formyl Peptide Receptor 2 (FPR2) Agonists (2013)

The formyl peptide receptor 2 (FPR2) is a remarkably versatile transmembrane protein belonging to the G-protein coupled receptor (GPCR) family. FPR2 is activated by an array of ligands, which include structurally unrelated lipids and peptide/proteins agonists, resulting in different intracellular responses in a ligand-specific fashion. In addition to the anti-inflammatory lipid, lipoxin A4, several other endogenous agonists also bind FPR2, including serum amyloid A, glucocorticoid-induced annexin 1, urokinase and its receptor, suggesting that the activation of FPR2 may result in potent pro- or anti-inflammatory responses. Other endogenous ligands, also present in biological samples, include resolvins, amyloidogenic proteins, such as beta amyloid (Aβ)-42 and prion protein (Prp)106-126, the neuroprotective peptide, humanin, antibacterial peptides, annexin 1-derived peptides, chemokine variants, the neuropeptides, vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase activating polypeptide (PACAP)-27, and mitochondrial peptides. Upon activation, intracellular domains of FPR2 mediate signaling to G-proteins, which trigger several agonist-dependent signal transduction pathways, including activation of phospholipase C (PLC), protein kinase C (PKC) isoforms, the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway, the mitogen-activated protein kinase (MAPK) pathway, p38MAPK, as well as the phosphorylation of cytosolic tyrosine kinases, tyrosine kinase receptor transactivation, phosphorylation and nuclear translocation of regulatory transcriptional factors, release of calcium and production of oxidants. FPR2 is an attractive therapeutic target, because of its involvement in a range of normal physiological processes and pathological diseases. Here, we review and discuss the most significant findings on the intracellular pathways and on the cross-communication between FPR2 and tyrosine kinase receptors triggered by different FPR2 agonists.
Construction of Combinatorial Antibody Expression Libraries in Escherichia Coli (2007)

A lambda vector system has been developed for the construction and coexpression of diverse populations of heavy and light chain cDNA sequences. Heavy and light chain sequences within the immunological repertoire are generated by the polymerase chain reaction using primers directed to conserved regions within the variable region framework. Two lambda vectors are employed for the independent construction of heavy and light chain cDNA libraries. The libraries are randomly combined to produce a population of lambda phage with each containing one heavy and one light chain cDNA sequence. The vectors direct the synthesis and secretion of functional Fab antibody fragments from a dicistronic operon. Libraries of up to 1 x 10(7) recombinants can be obtained with a diversity approaching in vivo estimates. Analysis of the heavy and light chain combinations reveals that the complete antibody repertoire can be generated by subsequent reshuffling of heavy and light chain cDNAs within an initial Fab-producing library. Inherent bias found in vivo toward certain heavy and light chain combinations can be virtually eliminated.
Gas-Assisted Thin-Film Evaporation from Confined Spaces for Dissipation of High Heat Fluxes (2009)

A new cooling scheme utilizing evaporation from an ultrathin, spatially confined liquid film is described and analyzed for thermal management of hot spots with local heat fluxes in excess of 600 W/cm2. This is achieved by a stable monolayer of liquid maintained on the surface and using fully dry sweeping gas (e.g., air) blown at high velocity (50–100 m/s) above this liquid monolayer. We also demonstrate how dielectric coolants like FC72 can outperform water as an evaporative coolant for this scheme. This work presents the conceptual system design, the results of performance analysis supporting the feasibility of the proposed cooling scheme, and experimental results that demonstrate the idea as well as validate the computational results. The analysis allows one to elucidate the salient physical features of evaporative cooling from spatially confined thin films subjected to a sweeping gas and to identify the key parameters resulting enhanced performance. The simplified model provides results in a form suitable for designing a full-scale cooling device (perspiration nanopatch) that exploits the unique advantages of the proposed cooling scheme.
Targeted metabolic labeling of yeast N-glycans with unnatural sugars (2010)

Metabolic labeling of glycans with synthetic sugar analogs has emerged as an attractive means for introducing nonnatural chemical functionality into glycoproteins. However, the complexities of glycan biosynthesis prevent the installation of nonnatural moieties at defined, predictable locations within glycoproteins at high levels of incorporation. Here, we demonstrate that the conserved N-acetyglucosamine (GlcNAc) residues within chitobiose cores of N-glycans in the model organism Saccharomyces cerevisiae can be specifically targeted for metabolic replacement by unnatural sugars. We introduced an exogenous GlcNAc salvage pathway into yeast, allowing cells to metabolize GlcNAc provided as a supplement to the culture medium. We then rendered the yeast auxotrophic for production of the donor nucleotide-sugar uridine-diphosphate-GlcNAc (UDP-GlcNAc) by deletion of the essential gene GNA1. We demonstrate that gna1Delta strains require a GlcNAc supplement and that expression plasmids containing both exogenous components of the salvage pathway, GlcNAc transporter NGT1 from Candida albicans and GlcNAc kinase NAGK from Homo sapiens, are required for rescue in this context. Further, we show that cells successfully incorporate synthetic GlcNAc analogs N-azidoacetyglucosamine (GlcNAz) and N-(4-pentynoyl)-glucosamine (GlcNAl) into cell-surface glycans and secreted glycoproteins. To verify incorporation of the nonnatural sugars at N-glycan core positions, endoglycosidase H (endoH)-digested peptides from a purified secretory glycoprotein, Ygp1, were analyzed by mass spectrometry. Multiple Ygp1 N-glycosylation sites bearing GlcNAc, isotopically labeled GlcNAc, or GlcNAz were identified; these modifications were dependent on the supplement added to the culture medium. This system enables the production of glycoproteins that are functionalized for specific chemical modifications at their glycosylation sites.
Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure (2006)

Our results provide the first evidence that specific TFs identified in murine models (MEF2, NKX, NFAT, and GATA) are associated with human heart failure. Moreover, these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. These findings provide a crucial link between animal models and human disease and suggest a specific role for FOX signaling in modulating the hypertrophic response of the heart to stress in humans.
Depression and Suicidal Behavior in Acne Patients Treated With Isotretinoin: A Systematic Review (2005)

Isotretinoin (13-cis retinoic acid) is an effective treatment for severe cystic or recalcitrant acne vulgaris; however, concerns have been raised regarding its potential association with depression and suicidal behavior. We sought to explore the proposed relationship between isotretinoin use and the risk of depression and attempted and completed suicide in patients with acne vulgaris by performing a systematic literature search for studies reporting primary data on depression and suicidal behavior in patients treated with isotretinoin for acne vulgaris. Nine studies met the qualifying criteria for our analysis. Rates of depression among isotretinoin users ranged from 1% to 11% across studies, with similar rates in oral antibiotic control groups. Overall, studies comparing depression before and after treatment did not show a statistically significant increase in depression diagnoses or depressive symptoms. Some, in fact, demonstrated a trend toward fewer or less severe depressive symptoms after isotretinoin therapy. This decrease was particularly evident in patients with pretreatment scores in the moderate or clinical depression range. No correlation between isotretinoin use and suicidal behavior was reported, although only one retrospective study presented data on this topic. Although the current literature does not support a causative association between isotretinoin use and depression, there are important limitations to many of the studies. The available data on suicidal behavior during isotretinoin treatment are insufficient to establish a meaningful causative association.
Dissection of the multiple mechanisms of TNF‐α‐induced apoptosis in liver injury (2004)

Tumor necrosis factor (TNF)-alpha-induced hepatocyte apoptosis is implicated in a wide range of liver diseases including viral hepatitis, alcoholic hepatitis, ischemia/reperfusion liver injury, and fulminant hepatic failure. TNF-alpha exerts a variety of effects that are mediated mainly by TNF-receptor 1 (TNF-R1) in cell death. The activation of TNF-R1 leads to the activation of multiple apoptotic pathways involving the activation of the pro-death Bcl-2 family proteins, reactive oxygen species, C-Jun NH2-terminal kinase, cathepsin B, acidic sphingomyelinase and neutral sphingomyelinase. These pathways are closely interlinked and mainly act on mitochondria, which release the apoptogenic factors and other events, resulting in apoptosis. This article reviews the recent progress in the molecular mechanisms of TNF-alpha-induced apoptosis in hepatocytes, and discusses how these molecular findings are shaping our understanding of the pathogenesis of liver diseases and our strategy to develop novel therapeutics.
Power Electronics Cooling Effectiveness Versus Thermal Inertia (2005)

Today, the popularity of power electronics integration is increasing. Despite the prospect of fully integrated module, including features like driving and control electronics, protection, power integration has not taken-off for medium to high power electronics applications. Manufacturing issues such as yield, reliability and return-on-investment for a new fabrication line are the major blocking points. As a first step toward integrated modules, integration of the cooling system appears realistic and cost effective. Increasing the cooling effectiveness could double the output current of an inverter while using the same amount of silicon. On the other hand, integrated cooling leads to small thermal inertia, which can generate high temperature variation under load cycling condition. This paper highlights the relationship between cooling effectiveness and thermal inertia. Typical performances of several cooling systems are compared under load cycling condition to explain how to take into account the variation of the losses in the choice of a cooling technique at the design stage. As an example, a standard liquid cooled plate performed similar to an integrated microchannel network for specific load variation frequencies.
57.3: Invited Paper : Head‐worn Displays ‐ Lens Design (2010)

Abstract There is a growing and sometimes critical need to ubiquitously process, visualize, and merge information with the world around us, in real‐time. This need has created a renewed interest in see‐ through (as opposed to look‐at) augmented mobile viewing systems that are compact, low cost, and convenient, with resolution that approaches that of the human visual system extending into the peripheral field of view. We will review key technology paths that build on historical highlights and discuss some market barriers to the emergence of eyewear format head‐ worn displays (HWDs). Finally, we will focus on freeform approaches and feature emerging solutions in freeform combiners that build on a novel description of freeform surfaces and provide a key competitive advantage in the ability to separate the see‐ through scene and the user by a seamless thin plastic window.
Relaxin (1984)

The past decade has seen major advances in understanding the chemistry of relaxin. Sensitive radioimmunoassays have allowed description of the secretion patterns of relaxin in several species. It is likely that technical advances in the near future will provide significant quantities of human relaxin as well as monoclonal antibodies to various relaxins. These tools should clarify the physiological roles of relaxin, elucidate its mechanisms of action, and enable testing of human relaxin as a potentially useful pharmacological agent.
Natural Genetic Exchanges between Vaccine and Wild Poliovirus Strains in Humans (2000)

In a previous study of poliovirus vaccine-derived strains isolated from patients with vaccine-associated paralytic poliomyelitis (VAPP) (9, 11), we reported that a high proportion (over 50%) of viruses had a recombinant genome. Most were intertypic vaccine/vaccine recombinants. However, some had restriction fragment length polymorphism (RFLP) profiles different from those of poliovirus vaccine strains. We demonstrate here that five such recombinants, of 88 VAPP strains examined, carried sequences of wild (nonvaccine) origin. To identify the parental wild donor of these sequences, we used RFLP profiles and nucleotide sequencing to look for similarity in the 3D polymerase-coding region of 61 wild, cocirculating poliovirus isolates (43 type 1, 16 type 2, and 2 type 3 isolates). In only one case was the donor identified, and it was a wild type 1 poliovirus. For the other four vaccine/wild recombinants, the wild parent could not be identified. The possibility that the wild sequences were of a non-poliovirus-enterovirus origin could not be excluded. Another vaccine/wild recombinant, isolated in Belarus from a VAPP case, indicated that the poliovirus vaccine/wild recombination is not an isolated phenomenon. We also found wild polioviruses (2 of 15) carrying vaccine-derived sequences in the 3' moiety of their genome. All these results suggest that genetic exchanges with wild poliovirus and perhaps with nonpoliovirus enteroviruses, are also a natural means of evolution for poliovirus vaccine strains.
Differential Effects of Superoxide Dismutase Mimetics after Mechanical Overload of Articular Cartilage (2017)

Post-traumatic osteoarthritis can develop as a result of the initial mechanical impact causing the injury and also as a result of chronic changes in mechanical loading of the joint. Aberrant mechanical loading initiates excessive production of reactive oxygen species, oxidative damage, and stress that appears to damage mitochondria in the surviving chondrocytes. To probe the benefits of increasing superoxide removal with small molecular weight superoxide dismutase mimetics under severe loads, we applied both impact and overload injury scenarios to bovine osteochondral explants using characterized mechanical platforms with and without GC4403, MnTE-2-PyP, and MnTnBuOE-2-PyP. In impact scenarios, each of these mimetics provides some dose-dependent protection from cell death and loss of mitochondrial content while in repeated overloading scenarios only MnTnBuOE-2-PyP provided a clear benefit to chondrocytes. These results support the hypothesis that superoxide is generated in excess after impact injuries and suggest that superoxide production within the lipid compartment may be a critical mediator of responses to chronic overload. This is an important nuance distinguishing roles of superoxide, and thus superoxide dismutases, in mediating damage to cellular machinery in hyper-acute impact scenarios compared to chronic scenarios.
Delaying forever: Uniaxial strained silicon transistors in a 90nm CMOS technology (2004)

We describe the device physics of uniaxial strained silicon transistors. Uniaxial strain is more effective, less costly and easier to implement. The highest PMOS drive current to date is reported: 0.72mA/ /spl mu/m. Pattern sensitivity and mobility/Rext partitioning are discussed. Finally we measure inverter delays as low as 4.6pS, and show 50Mb SRAMs operational at 0.65V.
Entity Synonyms for Structured Web Search (2011)

Nowadays, there are many queries issued to search engines targeting at finding values from structured data (e.g., movie showtime of a specific location). In such scenarios, there is often a mismatch between the values of structured data (how content creators describe entities) and the web queries (how different users try to retrieve them). Therefore, recognizing the alternative ways people use to reference an entity, is crucial for structured web search. In this paper, we study the problem of automatic generation of entity synonyms over structured data toward closing the gap between users and structured data. We propose an offline, data-driven approach that mines query logs for instances where content creators and web users apply a variety of strings to refer to the same webpages. This way, given a set of strings that reference entities, we generate an expanded set of equivalent strings (entity synonyms) for each entity. Our framework consists of three modules: candidate generation, candidate selection, and noise cleaning. We further study the cause of the problem through the identification of different entity synonym classes. The proposed method is verified with experiments on real-life data sets showing that we can significantly increase the coverage of structured web queries with good precision.