gebhart/patrepeval huggingface dataset:
Amyloid-β(1−42) Rapidly Forms Protofibrils and Oligomers by Distinct Pathways in Low Concentrations of Sodium Dodecylsulfate (2007)

Alzheimer's disease (AD) is characterized by large numbers of senile plaques in the brain that consist of fibrillar aggregates of 40- and 42-residue amyloid-beta (Abeta) peptides. However, the degree of dementia in AD correlates better with the concentration of soluble Abeta species assayed biochemically than with histologically determined plaque counts, and several investigators now propose that soluble aggregates of Abeta are the neurotoxic agents that cause memory deficits and neuronal loss. These endogenous aggregates are minor components in brain extracts from AD patients and transgenic mice that express human Abeta, but several species have been detected by gel electrophoresis in sodium dodecylsulfate (SDS) and isolated by size exclusion chromatography (SEC). Endogenous Abeta aggregation is stimulated at cellular interfaces rich in lipid rafts, and anionic micelles that promote Abeta aggregation in vitro may be good models of these interfaces. We previously found that micelles formed in dilute SDS (2 mM) promote Abeta(1-40) fiber formation by supporting peptide interaction on the surface of a single micelle complex. In contrast, here we report that monomeric Abeta(1-42) undergoes an immediate conversion to a predominant beta-structured conformation in 2 mM SDS which does not proceed to amyloid fibrils. The conformational change is instead rapidly followed by the near quantitative conversion of the 4 kDa monomer SDS gel band to 8-14 kDa bands consistent with dimers through tetramers. Removal of SDS by dialysis gave a shift in the predominant SDS gel bands to 30-60 kDa. While these oligomers resemble the endogenous aggregates, they are less stable. In particular, they do not elute as discrete species on SEC, and they are completed disaggregated by boiling in 1% SDS. It appears that endogenous oligomeric Abeta aggregates are stabilized by undefined processes that have not yet been incorporated into in vitro Abeta aggregation procedures.
Improving Readability for Automatic Speech Recognition Transcription (2020)

Modern Automatic Speech Recognition (ASR) systems can achieve high performance in terms of recognition accuracy. However, a perfectly accurate transcript still can be challenging to read due to grammatical errors, disfluency, and other errata common in spoken communication. Many downstream tasks and human readers rely on the output of the ASR system; therefore, errors introduced by the speaker and ASR system alike will be propagated to the next task in the pipeline. In this work, we propose a novel NLP task called ASR post-processing for readability (APR) that aims to transform the noisy ASR output into a readable text for humans and downstream tasks while maintaining the semantic meaning of the speaker. In addition, we describe a method to address the lack of task-specific data by synthesizing examples for the APR task using the datasets collected for Grammatical Error Correction (GEC) followed by text-to-speech (TTS) and ASR. Furthermore, we propose metrics borrowed from similar tasks to evaluate performance on the APR task. We compare fine-tuned models based on several open-sourced and adapted pre-trained models with the traditional pipeline method. Our results suggest that finetuned models improve the performance on the APR task significantly, hinting at the potential benefits of using APR systems. We hope that the read, understand, and rewrite approach of our work can serve as a basis that many NLP tasks and human readers can benefit from.
The use of electrophysiological monitoring in the intraoperative management of intracranial aneurysms (1999)

SSEPs and BAEPs are useful in preventing clinical neurological injury during surgery for intracranial aneurysms and in predicting which patients will have unfavourable outcomes.
Optical methods for sensing glucose (2011)

This critical review covers the present state of the art in optical sensing of glucose. Following an introduction into the significance of (continuous) sensing of glucose and a brief look back, we discuss methods based on (a) monitoring the optical properties of intrinsically fluorescent or labeled enzymes, their co-enzymes and co-substrates; (b) the measurement of the products of enzymatic oxidation of glucose by glucose oxidase; (c) the use of synthetic boronic acids; (d) the use of Concanavalin A; and (e) the application of other glucose-binding proteins. We finally present an assessment in terms of the advantages and disadvantages of the various methods (237 references).
Combining Next-Generation Sequencing and Immune Assays: A Novel Method for Identification of Antigen-Specific T Cells (2013)

In this study, we combined a novel sequencing method, which can identify individual clonotypes based on their unique T cell receptor (TCR) rearrangement, with existing immune assays to characterize antigen-specific T cell responses. We validated this approach using three types of assays routinely used to measure antigen-specific responses: pentamers which enable identification of T cells bearing specific TCRs, activation marker expression following antigen stimulation and antigen-induced proliferation to identify cytomegalovirus (CMV) specific clonotypes. In one individual, 8 clonotypes were identified using a pentamer reagent derived from the CMV pp65 protein. The same 8 clonotypes were also identified following sequencing of cells that upregulated an activation marker following incubation with an identical peptide derived from pp65. These 8 and an additional 8 clonotypes were identified using a more sensitive CFSE-based proliferation assay. We found clear sequence homology among some of the clonotypes identified, and the CDR3 region in one clonotype was identical to a previously published pp65-specific clonotype sequence. Many of these CMV-specific clonotypes were present at frequencies below 10(-5) which are undetectable using standard flow-cytometric methods. These studies suggest that an immune response is comprised of a diverse set of clones, many of which are present at very low frequencies. Thus, the combination of immune assays and sequencing depicts the richness and diversity of an immune response at a level that is not possible using standard immune assays alone. The methods articulated in this work provide an enhanced understanding of T cell-mediated immune responses at the clonal level.
<title>Software implementation of MPEG-II video encoding using socket programming in LAN</title> (1994)

This contribution will examine the parallel characteristics of MPEG video encoding and explore the feasibility of using a group of workstations under a LAN to perform MPEG-II encoding. An analysis of partitioning the MPEG algorithm into several tasks is presented. This is followed by the details of implementation by using socket programming as a means to coordinate the workstations. The following conclusions have been reached: (1) Since each slice header has a start code which is byte-aligned, each slice is a good basic unit for parallel processing. This is the case for I- P- and B-pictures. (2) All the most computationally expensive operations, such as Motion Estimation and DCT, can be conducted in parallel. (3) The quantization parameter is processed in a sequential manner since it should be derived from the history of the encoding. Computer simulations have been conducted, and the bitstreams generated are the same as those of a sequential encoder and can be decoded by an MPEG-II decoder.
Growth promotion of canola (rapeseed) seedlings by a strain of Pseudomonas putida under gnotobiotic conditions (1987)

Inoculation of canola (Brassica campestris) seeds with a nitrogen-fixing strain of Pseudomonas putida (GR12-2) drastically increased the root length of seedlings grown in sterile growth pouches. Seed inoculation with inactive bacteria did not affect root lengths. Root elongation capacity was retained by nonnitrogen-fixing mutants of strain GR12-2. On the other hand, two other wild-type pseudomonads that do not fix nitrogen also increased root elongation. The addition of mineral nitrogen to the growth solution at concentrations of 1 mM or higher significantly inhibited root elongation of either inoculated or noninoculated seedlings. On the other hand, the addition of phosphate to the growth solution at similar concentrations stimulated root elongation of inoculated and noninoculated seedlings. The combined effects of bacterial inoculation and addition of phosphate on root and shoot elongation and on root and shoot weight were additive. Seed inoculation with P. putida GR12-2 increased the uptake of labelled phosphorus ( 32 P) by seedlings grown in growth pouches and also enhanced the shoot elongation of seedlings grown in sterile soil. The capacity of P. putida GR12-2 to enhance phosphate uptake and to promote plant growth under gnotobiotic conditions may open the door to a new direction in the development of plant growth promoting inoculants.
Effect of vaccination with a monovalent Leptospira interrogans serovar hardjo type hardjo-bovis vaccine on type hardjo-bovis infection of cattle (1991)

Effectiveness of 2 concentrations of a monovalent vaccine containing Leptospira interrogans serovar hardjo type hardjo-bovis was evaluated for protection of heifers from infection with type hardjo-bovis. Nine heifers were given 2 doses of low-dose vaccine (8.32 x 10(8) cells/dose); 9 heifers were given 2 doses of high-dose vaccine (8.32 x 10(9) cells/dose); and 1 steer and 1 heifer were maintained as nonvaccinated controls. Groups of vaccinated cattle were challenge-exposed with serovar hardjo type hardjo-bovis at 7 (n = 6), 11 (n = 6), or 15 (n = 6) weeks after completion of vaccination. All cattle were challenge-exposed by conjunctival instillation of 1 x 10(5) hardjo-bovis cells on 3 consecutive days. Both control and all vaccinated cattle became infected and shed serovar hardjo type hardjo-bovis in their urine. Leptospires were detected in 15 of 16 (94%) urine samples from control cattle and in 124 of 143 (87%) samples from vaccinated cattle. Leptospires were detected in kidneys of 17 of 18 vaccinated cattle and 2 of 2 control cattle and in the uterus or oviducts of 13 of 18 vaccinates and the 1 control heifer.
High thermal and chemical stability in pyrazolate-bridged metal–organic frameworks with exposed metal sites (2011)

Reactions between the tritopic pyrazole-based ligand 1,3,5-tris(1H-pyrazol-4-yl)benzene (H3BTP) and transition metal acetate salts in DMF afford microporous pyrazolate-bridged metal–organic frameworks of the type M3(BTP)2·xsolvent (M = Ni (1), Cu, (2), Zn (3), Co (4)). Ab-initioX-ray powder diffraction methods were employed in determining the crystal structures of these compounds, revealing 1 and 2 to exhibit an expanded sodalite-like framework with accessible metal cation sites, while 3 and 4 possess tetragonal frameworks with hydrophobic surfaces and narrower channel diameters. Compounds 1–4 can be desolvated without loss of crystallinity by heating under dynamic vacuum, giving rise to microporous solids with BET surface areas of 1650, 1860, 930 and 1027 m2 g−1, respectively. Thermogravimetric analyses and powder X-ray diffraction measurements demonstrate the exceptional thermal and chemical stability of these frameworks. In particular, 3 is stable to heating in air up to at least 510 °C, while 1 is stable to heating in air to 430 °C, as well as to treatment with boiling aqueous solutions of pH 2 to 14 for two weeks. Unexpectedly, 2 and 3 are converted into new crystalline metal–organic frameworks upon heating in boiling water. With the combination of stability under extreme conditions, high surface area, and exposed metal sites, it is anticipated that 1 may open the way to testing metal–organic frameworks for catalytic processes that currently employ zeolites.
Structure-function analysis of the human papillomavirus type 16 E7 oncoprotein (1992)

The E7 gene of human papillomavirus type 16 encodes a multifunctional nuclear phosphoprotein that is functionally and structurally similar to the adenovirus (Ad) E1A proteins and the T antigens of other papovaviruses. E7 can cooperate with an activated ras oncogene to transform primary rodent cells, trans activate the Ad E2 promoter, and abrogate transforming growth factor beta-mediated repression of c-myc. Recent studies suggest that these functions may in part be a consequence of the ability of E7 to associate with the product of the retinoblastoma tumor suppressor gene (pRB). In this study, a series of site-specific mutations of the human papillomavirus type 16 E7 gene product were constructed and assessed for their effects on intracellular protein stability, ras cooperativity, transcriptional trans activation, pRB association, and phosphorylation. The results of these studies indicate that the transforming and trans-activating domains extensively overlap within a region of the protein analogous to conserved region 2 of Ad E1A, suggesting that pRB binding is necessary for both activities. Deletion of sequences in conserved region 1 abrogates cellular transformation but has only a marginal effect on trans activation. These data suggest that E7 trans activation and cellular transformation are interrelated but separable functions.
Role of Protein Kinase C Isoforms in Phorbol Ester-induced Vascular Endothelial Growth Factor Expression in Human Glioblastoma Cells (1999)

Aberrant expression of the potent angiogenic cytokine, vascular endothelial growth factor (VEGF), has been demonstrated to be associated with most human solid tumors. Both transcriptional and post-transcriptional mechanisms have been shown to modulate VEGF expression in a multitude of cell types. Here we report that when protein kinase C (PKC) pathways were activated in human glioblastoma U373 cells by phorbol 12-myristate 13-acetate (PMA), VEGF mRNA expression was up-regulated via a post-transcriptional mRNA stabilization mechanism. PMA treatment exhibited no increase in VEGF-specific transcriptional activation as determined by run-off transcription assays and VEGF promoter-luciferase reporter assays. However, PMA increased VEGF mRNA half-life from 0.8 to 3.6 h which was blocked by PKC inhibitors but not by protein kinase A or cyclic nucleotide-dependent protein kinase inhibitors. When U373 cells were transfected with antisense oligonucleotide sequences to the translation start sites of PKC-alpha, -beta, -gamma, -delta, -epsilon, or -zeta isoforms, both PKC-alpha and -zeta antisense oligonucleotides showed substantial inhibition of PMA-induced VEGF mRNA. In addition, overexpression of PKC-zeta resulted in a strong constitutive up-regulation of VEGF mRNA expression. This study demonstrates for the first time that specific PKC isoforms regulate VEGF mRNA expression through post-transcriptional mechanisms.
Characterization of a Cloned Temperature-Sensitive Construct of the Diphtheria Toxin A Domain (2005)

Our goal was to determine how the DTM mutant construct of the A domain of diphtheria toxin (DTx) causes temperature-sensitive effects in Drosophila and yeast [Bellen, H. J., D'Evelyn, D., Harvey, M., Elledge, S. J. (1992) Development 114, 787-796]. Because DTM fortuitously bears the same point mutation as found in the A chain of CRM197, an ADP-ribosyltransferase (ADPrT)-deficient form of DTx, we hypothesized that the dramatic low-temperature-sensitive effects did not stem from ADP-ribosylation of elongation factor 2 (EF-2). To rule out acquisition of ADPrT activity at low temperatures, we assayed mutant forms of the A domain of DTx produced by in vitro transcription/translation and found that DTM has no ability to ADP-ribosylate EF-2 at 18 or 30 degrees C. Because the DTM gene results in a protein with a 23-amino acid missense carboxy-terminal extension, we also constructed a form without this extension. Assays for nuclease activity revealed that nuclease activity comigrated with the two distinguishable E. coli-cloned mutant proteins DTM and DTM-23, regardless of whether electrophoresis was conducted under denaturing or nondenaturing conditions in gels embedded with DNA. Studies with CRM197 showed that Ca(2+) and Mg(2+) promote single-strand DNA nicks, whereas Mn(2+) promotes double-strand DNA breaks. Evidence that the cation-dependent nuclease and NAD-dependent ADPrT enzymic sites are distinct is that NAD protected only the A domain of DTx from proteolytic cleavage, whereas DNA protected the A domains of both DTx and CRM197. We conclude that the nuclease activity of DTM is responsible for the temperature-sensitive effects associated with its expression in both yeast and Drosophila.
Isolation of Escherichia coli mutants defective in enzymes of membrane lipid synthesis. (1975)

A new method has been developed which permits the rapid screening of E. coli colonies for mutants with defective enzymes of phospholipid metabolism. In this procedure, a disc of filter paper is pressed down on an agar plate containing several hundred colonies of mutagen-treated cells, after which the paper is lifted off. In the process the colonies are transferred to the paper, giving rise to a replica print of the master plate. The few cells from each colony left on the master keep growing in the original pattern. The pattern of colonies is also retained on the filter paper, even after the cells are rendered permeable with lysozyme and EDTA. Colonies treated in this manner remain absorbed to the paper, where they can convert sn-(U-14-C)glycero-3-P to phosphatidyl(U-14-C)glycerophosphate, dependent on added CDP-diglyceride. Unrelated reactions of sn-(U-14-C)glycero-3-P that may obscure the synthesis of phosphatidyl-glycerophosphate are inhibited by the addition of reagents poisoning energy generation. The radioactive phospholipid that forms around each colony on the paper is precipitated in situ with trichloroacetic acid, and unreacted sn-(U-14-C)glycero-3-P is washed away. After autoradiography, the colonies on the filter paper are stained with Coomassie blue. When the autoradiogram is superimposed on the strained paper, mutants are identified as blue colonies lacking a black halo. With this method, 20,000 colonies were screened in several days. Four mutants were identified with low levels of CDP-diglyceride:snglycero-3-P phosphatidyl transferase (EC 2.7.8.5, GLYCEROL-PHOSPHATE PHOSPHATIDYLTRANSFERASE, PHOSPHATIDYLGLYCEROPHOSPHATE SYNTHETASE) IN EXTRACTS. With a similar assay, 10,000 additional colonies were screened for mutants with altered CDP-diglyceride:L-serine O-phosphatidyltransferase (EC 2.7.8.8, phosphatidylserine synthetase), and four strains were found in which the enzyme is thermolabile. The screening technique described here is termed replica printing and should be applicable not only to studies of phospholipid metabolism but also to nucleic acid and protein synthesis.
Intelligent Software Agents on the Internet: Chapters 1-3 (1997)

Software agents are a rapidly developing area of research. However, to many it is unclear what agents are and what they can (and maybe cannot) do. In the first part, this thesis will provide an overview of these, and many other agent-related theoretical and practical aspects. Besides that, a model is presented which will enhance and extend agents' abilities, but will also improve the way the Internet can be used to obtain or offer information and services on it. The second part is all about trends and developments. On the basis of past and present developments of the most important, relevant and involved parties and factors, future trends and developments are extrapolated and predicted.
Preventing intense false positive and negative reactions attributed to the principle of ELISA to re-investigate antibody studies in autoimmune diseases (2014)

To study the possible involvement of potential environmental pathogens in the pathogenesis of autoimmune diseases, it is essential to investigate antibody responses to a variety of environmental agents and autologous components. However, none of the conventional ELISA buffers can prevent the false positive and negative reactions attributed to its principal, which utilizes the high binding affinity of proteins to plastic surfaces. The aims of this study are to reveal all types of non-specific reactions associated with conventional buffer systems, and to re-investigate antibody responses to potential environmental pathogenic and autologous antigens in patients with autoimmune diseases using a newly developed buffer system "ChonBlock™" by ELISA. Compared to conventional buffers, the new buffer was highly effective in reducing the most intense false positive reaction caused by hydrophobic binding of immunoglobulin in sample specimens to plastic surfaces, "background (BG) noise reaction", and other non-specific reactions without interfering with antigen-antibody reactions. Applying this buffer, we found that IgG antibody responses to Escherichia coli O111:B4, E. coli lipopolysaccharide (LPS) and peptidoglycan polysaccharide (PG-PS) were significantly lower or tended to be lower in patients with rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), whereas IgA antibody responses to these antigens were equal or tended to be higher compared to normal controls. As a consequence, the IgA/IgG antibody ratios against these agents were significantly higher in patients with RA and SLE, except for Crohn's disease, which showed significantly higher IgG responses to these antigens. To assay antibodies in human sera, it is indispensable to eliminate false positive and negative reactions by using an appropriate buffer system, and to include antigen non-coated blank wells to determine BG noise reactions of invidual samples. Finally, based on our preliminary analysis in this study, we propose that low IgG antibody responses to potential pathogenic environmental factors may be the fundamental disorder in autoimmune diseases.
Identification of the yeast TOP3 gene product as a single strand-specific DNA topoisomerase. (1992)

The TOP3 gene of the yeast Saccharomyces cerevisiae was postulated to encode a DNA topoisomerase, based on its sequence homology to Escherichia coli DNA topoisomerase I and the suppression of the poor growth phenotype of top3 mutants by the expression of the E. coli enzyme (Wallis, J.W., Chrebet, G., Brodsky, G., Golfe, M., and Rothstein, R. (1989) Cell 58, 409-419). We have purified the yeast TOP3 gene product to near homogeneity as a 74-kDA protein from yeast cells lacking DNA topoisomerase I and overexpressing a plasmid-borne TOP3 gene linked to a phosphate-regulated yeast PHO5 gene promoter. The purified protein possesses a distinct DNA topoisomerase activity: similar to E. coli DNA topoisomerases I and III, it partially relaxes negatively but not positively supercoiled DNA. Several experiments, including the use of a negatively supercoiled heteroduplex DNA containing a 29-nucleotide single-stranded loop, indicate that the activity has a strong preference for single-stranded DNA. A protein-DNA covalent complex in which the 74-kDa protein is linked to a 5' DNA phosphoryl group has been identified, and the nucleotide sequences of 30 sites of DNA-protein covalent complex formation have been determined. These sequences differ from those recognized by E. coli DNA topoisomerase I but resemble those recognized by E. coli DNA topoisomerase III. Based on these results, the yeast TOP3 gene product can formally be termed S. cerevisiae DNA topoisomerase III. Analysis of supercoiling of intracellular yeast plasmids in various DNA topoisomerase mutants indicates that yeast DNA topoisomerase III has at most a weak activity in relaxing negatively supercoiled double-stranded DNA in vivo, in accordance with the characteristics of the purified enzyme.