gebhart/patrepeval huggingface dataset:
RLC - A Reliable Approach to Fast and Efficient Live Migration of Virtual Machines in the Clouds (2014)

Today, IaaS cloud providers are dynamically minimizing the cost of data centers operations, while maintaining the Service Level Agreement (SLA). Currently, this is achieved by the live migration capability, which is an advanced state-of-the-art technology of Virtualization. However, existing migration techniques suffer from high network bandwidth utilization, large network data transfer, large migration time as well as the destination's VM failure during migration. In this paper, we propose Reliable Lazy Copy (RLC) - a fast, efficient and a reliable migration technique. RLC provides a reasonable solution for high-efficiency and less disruptive migration scheme by utilizing the three phases of the process migration. For effective network bandwidth utilization and reducing the total migration time, we introduce a learning phase to estimate the writable working set (WWS) prior to the migration, resulting in an almost single time transfer of the pages. Our approach decreases the total data transfer by 1.16 x - 12.21x and the total migration time by a factor of 1.42x - 9.84x against the existing approaches, thus providing a fast and an efficient, reliable VM migration of the VMs in the cloud.
A practical entry to β-aryl-β-alkyl amino alcohols: application to the synthesis of a potent BACE1 inhibitor (2012)

The 1,2-addition of alkyl Grignard reagents to readily available N-tert-butanesulfinyl ketimines, bearing an α-silyloxy substituent, proceeds in high yields and excellent diastereocontrol. The utility of the present method was demonstrated by the synthesis, in enantiomerically pure form, of one recently disclosed β-secretase (BACE1) inhibitor.
Synthesis and characteristics of the poly(carboxybetaine)s and the corresponding cationic polymers (1997)

Two types of carboxybetaines and their corresponding cationic monomers and polymers are synthesized in this study. Comparing the chemical shifts of the methylene groups in the cationic monomers and carboxybetaines in both 1H- and 13C-NMR spectra reveal that the respective methylene groups are clearly distinguished from their chemical shifts in 1H- and 13C-NMR spectra. The solubilities, moisture regain properties, and solution properties of the poly(carboxybetaine)s and cationic polymers are investigated in relation to their molecular structures. Because the cationic polymers were ionized in an aqueous solution, the cationic polymers were more soluble than the poly(carboxybetaine). For the various functional groups of poly(carboxybetaine)s and cationic polymers, the order of tendency for moisture regain is COO > CONH. Results obtained from the reduced viscosity for cationic poly(TMMPAMS) are reversed from that for zwitterionic poly(DMAEAPL). © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 3527–3536, 1997
A Cloned DNA Fragment for Identification of Mycobacterium tuberculosis (1989)

The identification of Mycobacterium tuberculosis is a lengthy process. Attempts were made to develop a more rapid, specific, and sensitive assay for identifying tubercle bacilli in biologic specimens by differentially screening plasmid libraries of Sau3AI-digested M. tuberculosis H37Rv (ATCC 25618) DNA with homologous and heterologous DNA for clones that hybridized strongly with M tuberculosis DNA alone. Three clones, pMTB1, pMTb2, and pMTb3, were selected for further study. Southern analysis indicated that these clones reacted strongly with DNA from strains of M. tuberculosis isolated in different parts of the world, weakly with DNA from other mycobacterial species, and not at all with Escherichia coli or human DNA. Smaller fragments of mycobacterial DNA contained in plasmid pMTb3 were sub cloned into pBR322 (pMTb4) or pUC12 (pMTb5). These recombinant plasmids hybridized with DNA from M. tuberculosis, Mycobacterium bovis, and Mycobacterium bovis BCG (bacille Calmette-Guérin) Montreal and may provide the reagents needed for the development of new methods for rapid diagnosis of M. tuberculosis infections.
Photoaffinity labeling of the porcine brain alpha 2-adrenergic receptor using a radioiodinated arylazide derivative of rauwolscine: identification of the hormone-binding subunit. (1986)

A functionalized derivative of the alpha 2-selective antagonist rauwolscine formed the basis for a photoaffinity adduct that has allowed identification of the hormone-binding subunit of the brain alpha 2-adrenergic receptor protein. Rauwolscine carboxylate underwent reaction with 4-N-t-butyloxycarbonyl-aminoaniline, leading to the synthesis of rauwolscine 4-aminophenyl carboxamide (Rau-AmPC). Rau-AmPC was radioiodinated and converted to the arylazide derivative, 17 alpha-hydroxy-20 alpha-yohimban-16 beta-[N-(4-azido-3-[125I]iodo)phenyl] carboxamide (125I-Rau-AzPC), via a diazonium salt intermediate. The characterization of 125I-Rau-AzPC as a photolabile probe employed alpha 2-adrenergic receptors, which were first solubilized from porcine brain membranes and partially purified by affinity chromatography utilizing a yohimbine-agarose affinity matrix. In the partially purified receptor preparation incubated with 125I-Rau-AzPC, photolysis resulted in covalent labeling of a major (Mr, 62,000) peptide as determined by NaDodSO4/PAGE and autoradiography. Labeling of this peptide was inhibited by the alpha 2-selective antagonist, yohimbine, and the non-subtype-selective alpha-antagonist, phentolamine, but not by the alpha 1-antagonist, prazosin, or the beta-receptor antagonist, (-)-alprenolol. The alpha-adrenergic agonist epinephrine also inhibited labeling in a stereoselective manner. These data indicate that the photolabeled Mr 62,000 peptide is the hormone-binding subunit of the alpha 2-adrenergic receptor protein. The availability of this radioiodinated photoaffinity probe for the alpha 2-adrenergic receptor should facilitate further structural and biophysical characterization of the receptor protein.
Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region (2011)

Non-reciprocal genetic rearrangements associated with large duplicate sequence blocks could substantially contribute to the IGHV region diversity. Since the resulting polymorphisms may affect the number, composition and organization of the gene segments in this region, it may have significant impact on the function of the IGHV gene segment repertoire, antibody diversity, and therefore, the immune system. Because one of the gene segments, 3-30 (1.9III), is associated with autoimmune diseases, it could be of diagnostic significance to learn about the variants in the haplotypes by using the multiplex haplotype analysis system used in the present study with DNA sequence tags specific for the variants of all gene segments in this region.
Assessing Hydration Status: The Elusive Gold Standard (2007)

Acknowledging that total body water (TBW) turnover is complex, and that no measurement is valid for all situations, this review evaluates 13 hydration assessment techniques. Although validated laboratory methods exist for TBW and extracellular volume, no evidence incontrovertibly demonstrates that any concentration measurement, including plasma osmolality (P(osm)), accurately represents TBW gain and loss during daily activities. Further, one blood or urine sample cannot validly represent fluctuating TBW and fluid compartments. Future research should (a) evaluate novel techniques that assess hydration in real time and are precise, accurate, reliable, non-invasive, portable, inexpensive, safe, and simple; and (b) clarify the relationship between P(osm) and TBW oscillations in various scenarios.
Mechanism of the spinal cord injury and the cervical spondylotic myelopathy: new approach based on the mechanical features of the spinal cord white and gray matter (2003)

These differences in mechanical properties between the white and gray matter constitute different mechanisms contributing to the development of tissue damage and clinical symptoms.
Fusion Protein Vaccine by Domains of Bacterial Exotoxin Linked with a Tumor Antigen Generates Potent Immunologic Responses and Antitumor Effects (2005)

Antigen-specific immunotherapy represents an attractive approach for cancer treatment because of the capacity to eradicate systemic tumors at multiple sites in the body while retaining the requisite specificity to discriminate between neoplastic and nonneoplastic cells. It has been shown that certain domains of bacterial exotoxins facilitate translocation from extracellular and vesicular compartments into the cytoplasm. This feature provides an opportunity to enhance class I and/or II presentation of exogenous antigen to T lymphocytes. We investigated previously whether the translocation domain (domain II) of Pseudomonas aeruginosa exotoxin A with a model tumor antigen, human papillomavirus type 16 E7, in the context of a DNA vaccine could enhance vaccine potency. We then attempted to determine whether this chimeric molecule could also generate strong antigen-specific immunologic responses and enhance the potency of cancer vaccine in the protein format. Our results show that vaccination with the PE(DeltaIII)-E7-KDEL3 fusion protein enhances MHC class I and II presentation of E7, leading to dramatic increases in the number of E7-specific CD8+ and CD4+ T-cell precursors and markedly raised titers of E7-specific antibodies. Furthermore, the PE(DeltaIII)-E7-KDEL3 protein generates potent antitumor effects against s.c. E7-expressing tumors and preestablished E7-expressing metastatic lung tumors. Further, mice immunized with PE(DeltaIII)-E7-KDEL3 protein vaccine also retained long-term immunologic responses and antitumor effects. Our results indicate that retrograde-fusion protein via the delivery domains of exotoxins with an antigen greatly enhances in vivo antigen-specific immunologic responses and represents a novel strategy to improve cancer vaccine potency.
Notch Inhibition Prevents Differentiation of Human Limbal Stem/Progenitor Cells in vitro (2019)

Notch signaling has been shown to regulate the homeostasis and wound healing of the corneal epithelium. We investigated the effect of Notch inhibition in the human limbal stem/progenitor cells (LSCs) in vitro by using small molecules. Treatment of the LSCs with DAPT and SAHM1 reduced the proliferation rate and maintained the undifferentiated state of the LSCs in a concentration dependent manner. Stratification and differentiation of the corneal epithelium were not reduced after Notch inhibition, indicating that the function of the corneal basal cells is retained. Our findings suggest that Notch signaling plays a role in the proliferation and maintenance of LSCs.
Mechanism of Amyloid Removal in Patients With Alzheimer Disease Treated With Gantenerumab (2011)

Gantenerumab treatment resulted in a dose-dependent reduction in brain amyloid level, possibly through an effector cell-mediated mechanism of action.
Efficient and Specific Removal of Albumin from Human Serum Samples (2003)

Patient serum or plasma is frequently monitored for biochemical markers of disease or physiological status. Many of the rapidly evolving technologies of proteome analysis are being used to find additional clinically informative protein markers. The unusually high abundance of albumin in serum can interfere with the resolution and sensitivity of many proteome profiling techniques. We have used monoclonal antibodies against human serum albumin (HSA) to develop an immunoaffinity resin that is effective in the removal of both full-length HSA and many of the HSA fragments present in serum. This resin shows markedly better performance than dye-based resins in terms of both the efficiency and specificity of albumin removal. Immunoglobulins are another class of highly abundant serum protein. When protein G resin is used together with our immunoaffinity resin, Ig proteins and HSA can be removed in a single step. This strategy could be extended to the removal of any protein for which specific antibodies or affinity reagents are available.
CD3+4-8- alpha beta T cell population with biased T cell receptor V gene usage. Presence in bone marrow and possible involvement of IL-3 for their extrathymic development (1992)

Analysis of TCR of a series of CD4-8- (double negative; DN) alpha beta T cell lines induced with IL-3 revealed that their V gene usage was biased for V alpha 4 and V beta 2. This has been confirmed in the primary short-term cultures. Thus, IL-3 induced the generation of DN alpha beta T cells with predominant V beta 2 gene expression from the CD4+/CD8+ T cell-depleted spleen or bone marrow (BM) cells of both normal and nude BALB/c mice within 10 days. It was further indicated that the V beta 2+ beta-chain genes contained few junctional N regions in both IL-3-induced primary DN alpha beta T cells and continuous lines. Search for the in vivo counterpart of in vitro IL-3-induced DN alpha beta T cells revealed that BM, but not spleens, of normal BALB/c and B6 mice did contain a significant proportion of DN alpha beta T cells, and that the majority of them expressed V beta 2+ beta-chain genes with few junctional N regions. The presence of V beta 2+ DN alpha beta T cells was similarly observed in the BM of BALB/c nude mice, but their proportion varied markedly among various strains of mice, which was not linked to H-2 haplotypes. The results indicated that V beta 2+ DN alpha beta T cells in the BM represented one of the thymus-independent T cell populations, whose development was under the major histocompatibility Ag complex-unlinked genetic control. TCR of these T cells were shown to be functional as judged by the proliferative response to anti-V beta 2 antibody. Taken together, present results suggested that IL-3 could induce differentiation and/or proliferation of DN alpha beta T cells with uniquely limited repertoire, which existed preferentially in BM in vivo, and implied the possible involvement of extrathymic endogenous ligands as a positive selection force.
Polishable and Renewable DNA Hybridization Biosensors (1998)

Routine applications of DNA hybridization biosensors are often restricted by the need for regenerating the single-stranded (ss) probe for subsequent reuse. This note reports on a viable alternative to prolonged thermal or chemical regeneration schemes through the mechanical polishing of oligonucleotide-bulk-modified carbon composite electrodes. The surface of these biocomposite hybridization biosensors can be renewed rapidly and reproducibly by a simple extrusion/polishing protocol. The immobilized probe retains its hybridization activity on confinement in the interior of the carbon paste matrix, with the use of fresh surfaces erasing memory effects and restoring the original target response, to allow numerous hybridization/measurement cycles. We expect that such reusable nucleic acid modified composite electrodes can be designed for a wide variety of biosensing applications.
Rat Cortical Oligodendrocyte–Embryonic Motoneuron Co-Culture: An <I>In Vitro</I> Axon-Oligodendrocyte Interaction Model (2012)

Mechanisms that control the differentiation and function of oligodendrocytes in the central nervous system are complex and involve multiple inputs from the surrounding environment, including localized concentrations of growth factors and the extracellular matrix. Dissection and analysis of these inputs are key to understanding the pathology of central nervous system demyelinating diseases such as multiple sclerosis, where the differentiation of myelinating oligodendrocytes from their precursors underlies the remission phase of the disease. <i>In vitro</i> co-culture models provide a mechanism for the study of factors that regulate differentiation of oligodendrocyte precursors but have been difficult to develop due to the complex nature of central nervous system myelination. This study describes development of an <i>in vitro</i> model that merges a defined medium with a chemically modified substrate to study aspects of myelination in the central nervous system. We demonstrate that oligodendrocyte precursors co-cultured with rat embryonic motoneurons on non-biological substrate (diethylenetriamine trimethoxy-silylpropyldiethylenetriamine), can be induced to differentiate into mature oligodendrocytes that express myelin basic protein, using a serum-free medium. This defined and reproducible model of <i>in vitro</i> myelination could be a valuable tool for the development of treatments for demyelinating diseases such as multiple sclerosis.
Generation of Natural pH Gradients in Microfluidic Channels for Use in Isoelectric Focusing (2000)

As a part of an ongoing investigation of the use of isoelectric focusing (IEF) in microfluidic devices, pH gradients were electrochemically formed and optically quantified in microfluidic channels using acid-base indicators. The microchannels consisted of two parallel 40-mm-long electrodes with an interelectrode gap of 2.54 mm; top and bottom transparent windows were separated by 0.2 mm. Gradients in pH were formed as a result of the electrochemical decomposition of water at an applied potential not higher than 2.5 V to avoid generation of gas bubbles. Solutions contained low concentrations of a single buffer. The stability of the pH gradients and their sensitivity to changes in initial conditions were investigated under static (nonflow) conditions. Isoelectric focusing of sample biological analytes, bovine hemoglobin and bovine serum albumin, was performed to illustrate the potential of "microfluidic transverse IEF" for use in continuous concentration and separation systems.
Purification of polyethylenimine polyplexes highlights the role of free polycations in gene transfer (2004)

This study presents an efficient method to remove free PEI from PEI polyplexes by SEC. Our results from transfection experiments demonstrate that free PEI substantially contributes to efficient gene expression but also mediates toxic effects in a dose-dependent manner. Purified polyplexes without free PEI have to be applied at increased concentrations to achieve high transfection levels, but exhibit a greatly improved toxicity profile.
Pregnancy-related mortality surveillance--United States, 1991--1999. (2003)

Continued surveillance and additional studies should be conducted to monitor the magnitude of pregnancy-related mortality, to identify factors that contribute to the continuing racial disparity in pregnancy-related mortality, and to develop effective strategies to prevent pregnancy-related mortality for all women. In addition, CDC is working with state health departments, researchers, health-care providers, and other stakeholders to improve the ascertainment and classification of pregnancy-related deaths.
Alkali-Urea Extraction of Demineralized Bone Matrix Removes Noggin, an Inhibitor of Bone Morphogenetic Proteins (2004)

Demineralized bone matrix (DBM) and native bone morphogenetic protein (nBMP) are complex mixtures of non-collagenous bone proteins. These mixtures contain many of the BMPs that are available as recombinant molecules. Information regarding the presence in these materials of molecules that may affect the availability and activity of the BMPs is very limited. We have devised a simple chemical extraction of DBM using alkali-urea that produces a water soluble extractate that inhibits the osteogenic activity of DBM. We have demonstrated the presence of noggin, an extracellular BMP ligand antagonist, in this material. We conclude that differential chemical extraction may be a useful means of removing inhibitory molecules from DBM and nBMP.
Evaluation of Streck Tissue Fixative, a Nonformalin Fixative for Preservation of Stool Samples and Subsequent Parasitologic Examination (1999)

We undertook a study to evaluate Streck tissue fixative (STF) as a substitute for formalin and polyvinyl alcohol (PVA) in fecal preservation. A comparison of formalin, PVA, (mercuric chloride based), and STF was done by aliquoting fecal samples into each fixative. Stool specimens were collected in Haiti, and parasites included Cyclospora cayetanensis, Giardia intestinalis, Entamoeba coli, Iodamoeba butschlii, Endolimax nana, Ascaris lumbricoides, Trichuris trichiura, Strongyloides stercoralis, and Necator americanus. Preserved stools were examined at various predetermined times (1 week, 1 month, and 3 months) to establish the quality of the initial preservation as well as the suitability of the fixative for long-term storage. At each time point, stool samples in fixatives were examined microscopically as follows: (i) in wet mounts (with bright-field and epifluorescence microscopy), (ii) in modified acid-fast-, trichrome-, and safranin-stained smears, and (iii) with two commercial test kits. At the time points examined, morphologic features remained comparable for samples fixed with 10% formalin and STF. For comparisons of STF- and 10% formalin-fixed samples, specific findings showed that Cyclospora oocysts retained full fluorescence, modified acid-fast- and safranin-stained smears of Cryptosporidium and Cyclospora oocysts were equal in staining quality, and results were comparable in the immunofluorescence assay and enzyme immunoassay commercial kits. Stool fixed in STF and stained with trichrome showed less-than-acceptable staining quality compared with stool fixed in PVA. STF provides an excellent substitute for formalin as a fixative in routine examination of stool samples for parasites. However, modifications to the trichrome staining procedures will be necessary to improve the staining quality for protozoal cysts fixed in STF to a level comparable to that with PVA.
Adaptive EAP Estimation of Ability in a Microcomputer Environment (1982)

Expected a posteriori (EAP) estimation of ability, based on numerical evaluation of the mean and variance of the posterior distribution, is shown to have unusually good properties for computerized adaptive testing. The calculations are not complex, precede noniteratively by simple summation of log likelihoods as items are added, and require only values of the response function obtainable from precalculated tables at a limited number of quadrature points. Simulation studies are reported showing the near equivalence of the posterior standard deviation and the standard error of measurement. When the adaptive testings terminate at a fixed posterior standard deviation criterion of .90 or better, the regression of the EAP estimator on true ability is virtually linear with slope equal to the reliability, and the measurement error homogeneous, in the range ± 2.5 standard deviations.
Towards Better Decoding and Language Model Integration in Sequence to Sequence Models (2017)

The recently proposed Sequence-to-Sequence (seq2seq) framework advocates replacing complex data processing pipelines, such as an entire automatic speech recognition system, with a single neural network trained in an end-to-end fashion.In this contribution, we analyse an attention-based seq2seq speech recognition system that directly transcribes recordings into characters.We observe two shortcomings: overconfidence in its predictions and a tendency to produce incomplete transcriptions when language models are used.We propose practical solutions to both problems achieving competitive speaker independent word error rates on the Wall Street Journal dataset: without separate language models we reach 10.6% WER, while together with a trigram language model, we reach 6.7% WER.
A Th1-Inducing Adjuvant, MPL<sup>®</sup>, Enhances Antibody Profiles in Experimental Animals Suggesting It Has the Potential to Improve the Efficacy of Allergy Vaccines (2001)

Immunisation of mice with two different antigens adsorbed to L-tyrosine induced a Th1-skewed primary response when in conjunction with MPL adjuvant which also generally enhances a specific IgG response. Incorporation of MPL adjuvant in the immunisation of rats prevented a secondary specific IgE response. These results suggest that the employment of this new adjuvant in clinical allergy vaccination formulations may result in an improved efficacy which could be utilised in various ways to improve compliance.