gebhart/patrepeval huggingface dataset:
Safety and immunogenicity of investigational Shigella conjugate vaccines in Israeli volunteers (1996)

The safety and immunogenicity of investigational conjugates, composed of the O-specific polysaccharides of Shigella sonnei and Shigella flexneri type 2a covalently bound to Pseudomonas aeruginosa recombinant exoprotein A (rEPA), were evaluated in 192 Israeli soldiers. None had significant local reactions or fever. Fourteen days after injection, 90% of S. sonnei-rEPA recipients and 73 to 77% of S. flexneri-rEPA recipients had a fourfold or greater increase in serum immunoglobulin G (IgG) and IgA anti-lipopolysaccharide (anti-LPS) levels; at 2 years, these remained higher than at prevaccination (P < 0.01). There was a fourfold or greater increase in IgM anti-LPS in 20% of vaccinees at 2 weeks, but levels returned to prevaccination values at 6 to 12 months. IgG was the highest and most sustained class of LPS antibodies. Reinjection at day 42 did not boost antibody levels. Eighteen of 23 (78%) who received S. sonnei-rEPA and 13 of 19 (68%) who received S. flexneri-rEPA. had significant IgA-secreting cell responses. Significant IgG antibody-secreting cell responses were detected in 19 of 23 (83%) and 11 of 19 (58%) volunteers following vaccination with S. sonnei-rEPA and S. flexneri 2a-rEPA, respectively. On the basis of these data, further evaluation of the Shigella conjugates for protective efficacy in field trials in Israel was started.
A Subset of Mixed Simulations: Augmented Physical Simulations with Virtual Underlays (2012)

Most of us have appreciated Mixed Reality (MR) in the form of the virtual “yellow first down line” when watching football on TV. However, MR technology was previously confined to a few pioneering groups and was not readily available. Simply defined, MR integrates the virtual and physical worlds to generate new environments where real and virtual objects are collocated (share the same space) while augmenting our capabilities to interpret, understand, practice, learn, train or teach. MR technology is becoming affordable and finding its way into simulation giving rise to a new field we call Mixed Simulation. We present in this paper five new mixed simulators with physical exteriors and virtual underlays: central venous access (CVA), ventriculostomy, radio frequency lesion, spinal instrument implantation and regional anesthesia. We exploited advances in the capabilities, cost and/or sensor miniaturization in medical imaging, tracking technology, 3D printing (rapid prototyping) and 3D graphic cards to develop and deploy compact, inexpensive mixed simulators that are anatomically authentic, i.e., exact physical and/or virtual replicas of the actual individuals used as models. Sub-millimeter accuracy, miniaturized tracking sensors monitor and record every move, twist and turn of a tracked needle during the simulated procedures, facilitating after action review or even self-debriefing (when instructors are unavailable) and automated scoring algorithms (immune to inter-rater variability) that include tracking and grading of near misses. Mixed simulators offer the potential for improved training and debriefing for military and civilian applications; e.g., the CVA simulator improves learning outcome in residents and can provide civilian reservists unfamiliar with subclavian venous access (common in military trauma medicine and combat casualty care) training prior to frontline deployment to care for warfighters.
Cutting Edge: In Situ Tetramer Staining of Antigen-Specific T Cells in Tissues (2000)

Staining Ag-specific T cells with fluorescently labeled tetrameric MHC/peptide complexes has provided a powerful experimental approach to characterizing the immune response. In this report, we describe an extension of this method to directly visualize Ag-specific T cells in tissues. We successfully stained transgenic T cells with MHC tetramers in spleen sections from both 2C and OT-1 TCR transgenic mice. In addition, with the in situ tetramer staining technique, we detected a very small population of Ag-specific T cells in tissue after adoptive transfer of transgenic TCR T cells to a syngeneic nontransgenic mouse. We also show that the in situ tetramer technique can be applied to lightly fixed as well as frozen tissue, thus extending the method to archived tissue collections. This in situ tetramer staining technique offers a general approach to tracking the Ag-specific T cells in tissues.
Subconjunctival biocompatibility of a viscous bioerodable poly(ortho ester) (1998)

The biocompatibility of a viscous poly(ortho ester) (POE) intended for prolonged intraocular drug delivery was studied. This hydrophobic and bioerodable carrier was subconjunctivally injected in rabbits and evaluated both clinically and histologically. To assess the cause of the triggered transient acute inflammatory reaction, the two monomers, the intermediate and final degradation products, and the local toxicity of different solvents used during the polymer preparation were tested. Since the two initial monomers and the intermediate degradation products induced only moderate inflammation, the main acute inflammatory reaction is attributed to the formation of an acidic by-product which has been monitored in vitro by measuring the progressive decrease of the environmental pH. The influence of the sterilization procedure on tissue biocompatibility was established by comparing two polymers of similar molecular weight: one after gamma-sterilization, and an aseptically synthesized one. The biocompatibility was significantly improved by avoiding irradiation of the polymer.
Reconstruction of C3 and C4 metabolism in Methylobacterium extorquens AM1 using transposon mutagenesis (2003)

The growth of Methylobacterium extorquens AM1 on C(1) compounds has been well-studied, but little is known about how this methylotroph grows on multicarbon compounds. A Tn5 transposon mutagenesis procedure was performed to identify genes involved in the growth of M. extorquens AM1 on succinate and pyruvate. Of the 15000 insertion colonies screened, 71 mutants were found that grew on methanol but either grew slowly or were unable to grow on one or both of the multicarbon substrates. For each of these mutants, the chromosomal region adjacent to the insertion site was sequenced, and 55 different genes were identified and assigned putative functions. These genes fell into a number of predicted categories, including central carbon metabolism, carbohydrate metabolism, regulation, transport and non-essential housekeeping functions. This study focused on genes predicted to encode enzymes of central heterotrophic metabolism: 2-oxoglutarate dehydrogenase, pyruvate dehydrogenase and NADH : ubiquinone oxidoreductase. In each case, the mutants showed normal growth on methanol and impaired growth on pyruvate and succinate, consistent with a role specific to heterotrophic metabolism. For the first two cases, no detectable activity of the corresponding enzyme was found in the mutant, verifying the predictions. The results of this study were used to reconstruct multicarbon metabolism of M. extorquens AM1 during growth on methanol, succinate and pyruvate.
Construction of recombinant neisserial Hsp60 proteins and mapping of antigenic domains (1995)

Here we report the cloning and expression, in Escherichia coli, of PCR-amplified DNA encoding the 63-kDa stress-inducible protein of Neisseria gonorrhoeae strains VP1 and PID2, Neisseria meningitidis 2996 and the commensal Neisseria flavescens. DNA sequence analysis revealed in all cases one open reading frame of 541-544 amino acids corresponding to a protein of approximately 57,000 Da. The various neisserial proteins were > 96% identical at the amino acid level and showed extensive homology with proteins belonging to the Hsp60 heat-shock-protein family. We constructed defined glutathione S-transferase fusion polypeptides of the gonococcal Hsp60 homologue to locate antigenic domains on the recombinant protein. Variation in the immunoreactivity of two monoclonal antibodies recognizing a conserved and a neisseria-unique antigenic Hsp60 determinant, respectively, could thus be deduced to result from single amino acid substitutions. Analysis of the antibody response in patients' sera demonstrated reactivity with the same fusion polypeptides in six out of nine sera, indicating that neisserial Hsp60 is expressed during the natural infection and that distinct domains on the protein are immunodominant in vivo.
Quality Enhancement Research Initiative in Stroke (2000)

Stroke is the third leading cause of death and a leading cause of adult disability in the United States. Both within and outside of the Veterans Health Administration (VHA), the lack of a systematic approach to stroke prevention and treatment may have contributed to reduced rates of compliance with recommended practices and increased rates of stroke. Gaps in the knowledge base inhibit a systematic approach to high-quality care within the veteran population. Initial recommendations for closing those gaps are proposed. In some cases (eg, systematic anticoagulation management), the VHA is perceived as a leader in applied research; therefore, a systematic national policy for implementing these clinics may significantly reduce stroke rates. In other areas (eg, carotid endarterectomy), databases exist that would help advance quality and outcomes, but short-term studies are necessary to establish their utility. To promote strategic improvement in prevention, treatment, and rehabilitation for veterans who may be at risk or have had a stroke, specific objectives are proposed to (1) identify best practices for the effective delivery of long-term anticoagulation and enhance veterans' access to these services, (2) develop risk-adjusted models for the surgical preventive procedure carotid endarterectomy to understand facility variation in outcomes so practices can be improved, (3) define a systematic acute stroke management system so that high-quality stroke-related care can be generalizable to a variety of VHA settings, and (4) assess the impact of poststroke rehabilitation on risk adjustment and the location of outcomes so as to facilitate the implementation of best rehabilitation practices.
2′-C-Methyl Branched Pyrimidine Ribonucleoside Analogues: Potent Inhibitors of RNA Virus Replication (2007)

RNA viruses are the agents of numerous widespread and often severe diseases. Their unique RNA-dependent RNA polymerase (RDRP) is essential for replication and, thus, constitutes a valid target for the development of selective chemotherapeutic agents. In this regard, we have investigated sugar-modified ribonucleoside analogues as potential inhibitors of the RDRP. Title compounds retain 'natural' pyrimidine bases, but possess a beta-methyl substituent at the 2'-position of the D- or L-ribose moiety. Evaluation against a broad range of RNA viruses, either single-stranded positive (ssRNA+), single-stranded negative (ssRNA-) or double-stranded (dsRNA), revealed potent activities for D-2'-C-methyl-cytidine and -uridine against ssRNA+, and dsRNA viruses. None of the L-enantiomers were active. Moreover, the 5'-triphosphates of the active D-enantiomers were found to inhibit the bovine virus diarrhoea virus polymerase. Thus, the 2'-methyl branching of natural pyrimidine ribonucleosides transforms physiological molecules into potent, broad-spectrum antiviral agents that merit further development.
Siloxane-Terminated Solubilizing Side Chains: Bringing Conjugated Polymer Backbones Closer and Boosting Hole Mobilities in Thin-Film Transistors (2011)

We introduce a novel siloxane-terminated solubilizing group and demonstrate its effectiveness as a side chain in an isoindigo-based conjugated polymer. An average hole mobility of 2.00 cm(2) V(-1) s(-1) (with a maximum mobility of 2.48 cm(2) V(-1) s(-1)), was obtained from solution-processed thin-film transistors, one of the highest mobilities reported to date. In contrast, the reference polymer with a branched alkyl side chain gave an average hole mobility of 0.30 cm(2) V(-1) s(-1) and a maximum mobility of 0.57 cm(2) V(-1) s(-1). This is largely explained by the polymer packing: our new polymer exhibited a π-π stacking distance of 3.58 Å, while the reference polymer showed a distance of 3.76 Å.
Optical imaging of skin pathology with a polarized light camera (2003)

A hand-held camera uses polarized light to reject multiply scattered photons and create an image based on photons scattered from the superficial layers of skin. Roughly, the upper 300 um of skin are imaged. Images of melanoma are shown. More information can be found at http://www.bme.ogi.edu/biomedicaloptics/.
Translocation of c-myc in the hereditary renal cell carcinoma associated with a t(3;8)(p14.2;q24.13) chromosomal translocation. (1985)

A translocation between chromosomes 3 and 8, t(3;8)(p14.2;q24.13), has been reported in a family with hereditary renal cell carcinoma. Using somatic cell hybrids, we have isolated, separately, both derivative chromosomes. We find that the c-myc oncogene (8q24.1) has been translocated to the derivative 3 [der(3)]. We have not detected a rearrangement within an approximately equal to 21-kilobase region around the c-myc gene using restriction enzyme digestion and Southern blot hybridization analysis. The translocated c-myc gene should provide a probe to the chromosome 3p14 region, which appears to be important not only in renal cell carcinoma but also in small cell carcinoma of the lung. These hybrids have also been useful for the regional mapping of the Chinese hamster ovary cell Gly-B defect to 8q22.1----q24.13 and support the regional assignment of acylase I to 3p21.
Specificity of binding of a strain of uropathogenic Escherichia coli to Gal alpha 1—-4Gal-containing glycosphingolipids. (1985)

A strain of Escherichia coli originally isolated from urine of a patient with acute pyelonephritis was studied in detail for binding to glycosphingolipids. Bacteria labeled metabolically with [14C]glucose were layered over a glycolipid chromatogram and bound bacteria were detected by autoradiography. The detection was down to a few ng of glycolipid (pmol level) under these assay conditions. At a test level of 500 ng all glycolipids (more than a dozen molecular species analyzed) with Gal alpha 1----4Gal as an internal or terminal part bound the bacteria strongly while glycolipids known to lack this sequence were negative. Conformational analysis using hard sphere calculations including the exo-anomeric effect showed a bend in the saccharide chain at this disaccharide with a largely hydrophobic surface of the convex side, probably being part of the binding epitope. Mixtures of glycolipids isolated from a human ureter scraping and from urinary sediments bound bacteria in the 2- to 7-sugar interval. Thus, this infectious strain of E. coli recognizes glycolipids being present in epithelial cells lining the urinary tract.
Microfluidics and photonics for Bio‐System‐on‐a‐Chip: A review of advancements in technology towards a microfluidic flow cytometry chip (2008)

Microfluidics and photonics come together to form a field commonly referred to as 'optofluidics'. Flow cytometry provides the field with a technology base from which both microfluidic and photonic components be developed and integrated into a useful device. This article reviews some of the more recent developments to familiarize a reader with the current state of the technologies and also highlights the requirements of the device and how researchers are working to meet these needs.
Low cost electroless copper metallization of BCB for high-density wiring systems (1999)

A fully additive and selective metallization process for structured Cu metallization of BCB was evaluated. BCB was used as the polymeric dielectric due to its excellent electrical and mechanical properties. BCB surface pretreatment by RIE is necessary as a first step to achieve sufficient adhesion of electrolessly deposited Cu on BCB. In a second step, the BCB surface is coated by a precursor layer consisting of palladium acetate and a photoactivator. Precursor layer structuring is by standard i-line lithography followed by wet development with an organic solvent that dissolves unexposed precursor layer areas (negative working photolithography). The remaining pattern consists of Pd/sup 2+/ in an organic matrix which is not yet catalytically active for electroless plating. An alkaline solution of KBH/sub 4/ in water activates the Pd/sup 2+/ by reducing it to Pd/sup 0/. Pd/sup 0/ is highly active for electroless Cu deposition. The metallization process uses commercial electroless Cu baths. The electrical resistance of the electrolessly metallized vias is comparable to sputter metallization. The possibility of thin film multilayer metallization was evaluated by via metallization. The reliability of the deposited Cu was checked by air-to-air thermal cycling (-55/spl deg/C/+125/spl deg/C). The application of this process could be in the area of high density substrates such as the one used for MCM-D/L.
Turbo Codes: Principles and Applications (2000)

This book grew out of our research, industry consulting and con­ tinuing education courses. Turbo coding initially seemed to belong to a restricted research area, while now has become a part of the mainstream telecommu­ nication theory and practice. The turbo decoding principles have found widespread applications not only in error control, but in de­ tection, interference suppression and equalization. Intended for use by advanced students and professional engi­ neers, involved in coding and telecommunication research, the book includes both basic and advanced material. The chapters are se­ quenced so that the knowledge is acquired in a logical and progres­ sive way. The algorithm descriptions and analysis are supported by examples throughout the book. Performance evaluations of the presented algorithms are carried out both analytically and by sim­ ulations. Basic material included in the book has been taught to students and practicing professionals over the last four years in the form of senior undergraduate or graduate courses, lecture series and short continuing education courses
Host DNA released in response to aluminum adjuvant enhances MHC class II-mediated antigen presentation and prolongs CD4 T-cell interactions with dendritic cells (2013)

Many vaccines include aluminum salts (alum) as adjuvants despite little knowledge of alum's functions. Host DNA rapidly coats injected alum. Here, we further investigated the mechanism of alum and DNA's adjuvant function. Our data show that DNase coinjection reduces CD4 T-cell priming by i.m. injected antigen + alum. This effect is partially replicated in mice lacking stimulator of IFN genes, a mediator of cellular responses to cytoplasmic DNA. Others have shown that DNase treatment impairs dendritic cell (DC) migration from the peritoneal cavity to the draining lymph node in mice immunized i.p. with alum. However, our data show that DNase does not affect accumulation of, or expression of costimulatory proteins on, antigen-loaded DCs in lymph nodes draining injected muscles, the site by which most human vaccines are administered. DNase does inhibit prolonged T-cell-DC conjugate formation and antigen presentation between antigen-positive DCs and antigen-specific CD4 T cells following i.m. injection. Thus, from the muscle, an immunization site that does not require host DNA to promote migration of inflammatory DCs, alum acts as an adjuvant by introducing host DNA into the cytoplasm of antigen-bearing DCs, where it engages receptors that promote MHC class II presentation and better DC-T-cell interactions.
Time‐domain whole‐field fluorescence lifetime imaging with optical sectioning (2001)

A whole-field time-domain fluorescence lifetime imaging (FLIM) microscope with the capability to perform optical sectioning is described. The excitation source is a mode-locked Ti:Sapphire laser that is regeneratively amplified and frequency doubled to 415 nm. Time-gated fluorescence intensity images at increasing delays after excitation are acquired using a gated microchannel plate image intensifier combined with an intensified CCD camera. By fitting a single or multiple exponential decay to each pixel in the field of view of the time-gated images, 2-D FLIM maps are obtained for each component of the fluorescence lifetime. This FLIM instrument was demonstrated to exhibit a temporal discrimination of better than 10 ps. It has been applied to chemically specific imaging, quantitative imaging of concentration ratios of mixed fluorophores and quantitative imaging of perturbations to fluorophore environment. Initially, standard fluorescent dyes were studied and then this FLIM microscope was applied to the imaging of biological tissue, successfully contrasting different tissues and different states of tissue using autofluorescence. To demonstrate the potential for real-world applications, the FLIM microscope has been configured using potentially compact, portable and low cost all-solid-state diode-pumped laser technology. Whole-field FLIM with optical sectioning (3D FLIM) has been realized using a structured illumination technique.
Detection and recognition of correction utterances on misrecognition of spoken dialog system (2005)

Abstract When we communicate with computers through a speech interface, misrecognition is inevitable. Detection of repetition by users is helpful for the system to detect the error and recover. In this paper, we assume that the utterance includes repetitions for correction and propose a method to detect correction utterances in spontaneously spoken dialog. We combined a word spotting method based on dynamic time warping (DTW) and an N ‐best hypothesis overlap measure for the purpose. We obtained a recall rate of 92.7% and a precision of 89.1%. We next used the detection of correction utterances to improve recognition accuracy. © 2005 Wiley Periodicals, Inc. Syst Comp Jpn, 36(11): 24–33, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/scj.20341
Early Dental Epithelial Transcription Factors Distinguish Ameloblastoma from Keratocystic Odontogenic Tumor (2014)

The aim of the study was to characterize the molecular relationship between ameloblastoma and keratocystic odontogenic tumor (KCOT) by means of a genome-wide expression analysis. Total RNA from 27 fresh tumor samples of 15 solid/multicystic intraosseous ameloblastomas and 12 sporadic KCOTs was hybridized on Affymetrix whole genome arrays. Hierarchical clustering separated ameloblastomas and KCOTs into 2 distinct groups. The gene set enrichment analysis based on 303 dental genes showed a similar separation of ameloblastomas and KCOTs. Early dental epithelial markers PITX2, MSX2, DLX2, RUNX1, and ISL1 were differentially overexpressed in ameloblastoma, indicating its dental identity. Also, PTHLH, a hormone involved in tooth eruption and invasive growth, was one of the most differentially upregulated genes in ameloblastoma. The most differentially overexpressed genes in KCOT were squamous epithelial differentiation markers SPRR1A, KRTDAP, and KRT4, as well as DSG1, a component of desmosomal cell-cell junctions. Additonally, the epithelial stem cell marker SOX2 was significantly upregulated in KCOT when compared with ameloblastoma. Taken together, the gene expression profile of ameloblastoma reflects differentiation from dental lamina toward the cap/bell stage of tooth development, as indicated by dental epithelium-specific transcription factors. In contrast, gene expression of KCOT indicates differentiation toward keratinocytes.