gebhart/patrepeval huggingface dataset:
Vaccines for Pandemic Influenza (2006)

Recent outbreaks of highly pathogenic avian influenza in Asia and associated human infections have led to a heightened level of awareness and preparation for a possible influenza pandemic. Vaccination is the best option by which spread of a pandemic virus could be prevented and severity of disease reduced. Production of live attenuated and inactivated vaccine seed viruses against avian influenza viruses, which have the potential to cause pandemics, and their testing in preclinical studies and clinical trials will establish the principles and ensure manufacturing experience that will be critical in the event of the emergence of such a virus into the human population. Studies of such vaccines will also add to our understanding of the biology of avian influenza viruses and their behavior in mammalian hosts.
A Novel Approach to Characterize Clonality and Differentiation of Human Melanoma-Specific T Cell Responses: Spontaneous Priming and Efficient Boosting by Vaccination (2006)

Despite major progress in T lymphocyte analysis in melanoma patients, TCR repertoire selection and kinetics in response to tumor Ags remain largely unexplored. In this study, using a novel ex vivo molecular-based approach at the single-cell level, we identified a single, naturally primed T cell clone that dominated the human CD8(+) T cell response to the Melan-A/MART-1 Ag. The dominant clone expressed a high-avidity TCR to cognate tumor Ag, efficiently killed tumor cells, and prevailed in the differentiated effector-memory T lymphocyte compartment. TCR sequencing also revealed that this particular clone arose at least 1 year before vaccination, displayed long-term persistence, and efficient homing to metastases. Remarkably, during concomitant vaccination over 3.5 years, the frequency of the pre-existing clone progressively increased, reaching up to 2.5% of the circulating CD8 pool while its effector functions were enhanced. In parallel, the disease stabilized, but subsequently progressed with loss of Melan-A expression by melanoma cells. Collectively, combined ex vivo analysis of T cell differentiation and clonality revealed for the first time a strong expansion of a tumor Ag-specific human T cell clone, comparable to protective virus-specific T cells. The observed successful boosting by peptide vaccination support further development of immunotherapy by including strategies to overcome immune escape.
Identification of Flavor-Active Volatiles in Soy Protein Isolate via Gas Chromatography Olfactometry (2010)

Stir bar sorption and dynamic headspace purge techniques were used to recover the flavor volatiles from soy protein isolate and defatted soy flakes. Thirty-seven compounds were found to be the most flavor-active volatiles present in soy isolate by combining the results of both techniques. The majority of the volatiles are products of lipid oxidation, combined with a smaller number of amino acid degradation products. None of the individual components has a soy isolate flavor which is concluded to be a composite of them all. The full complement of flavor-active volatiles identified in soy protein isolate is also present in the defatted flake and a portion of these are carried through the isolate manufacturing process into the final product. Additionally, a significant amount of lipid remains bound to the soy protein and its continuing oxidation acts as a source of flavor volatiles throughout the manufacturing process. The flavor of the final product appears to be a composite of these two sources of volatiles.
Effector CD8 T cells transit to memory cells in the presence of tumor-associated antigen (85.17) (2007)

Abstract It is difficult to study the time frame and requirements for antigen removal as CD8 T effector cells transit to memory cells during an immune response because memory cells only readily appear after contraction of the effector response and clearance of antigen. To overcome these limitations, we have modeled the effector to memory transition in vitro and by the adoptive transfer of effector CTL to normal mice. When OVA-specific OT-I CTL were cultured in IL-15 without antigen, they acquired phenotypic and functional properties of memory cells 48 hr later. Such memory conversion occurred in the presence of 0.01 nM OVA peptide and APC, a dose that only induces a strong recall response, but not at a higher dose (0.1 nM) that readily activates naïve OT-I T cells. Following adoptive transfer of OT-I CTL to antigen-free normal mice, OT-I effector cells developed into central memory-like cells by 3 days post-transfer. Upon adoptive transfer to mice bearing the OVA-expressing E.G7 tumor, the OT-I CTL effector cells also readily converted to memory-like cells by day 3 post-transfer while the effector cells rejected the tumor. However, under conditions where the tumor was not cleared, memory production was impaired. Collectively, these data suggest that some CTL rapidly convert to memory cells concurrent with an effector response, without complete clearance of antigen, provided that antigen level is not too high. (Supported by the NIH)
His-391 of β-galactosidase (Escherichia coli) promotes catalyes by strong interactions with the transition state (2001)

His-391 of beta-galactosidase (Escherichia coli) was substituted by Phe, Glu, and Lys. Homogeneous preparations of the substituted enzymes were essentially inactive unless very rapid purifications were performed, and the assays were done immediately. The inactive enzymes were tetrameric, just like wild-type beta-galactosidase and their fluorescence spectra were identical to the fluorescence spectrum of wild-type enzyme. Analyses of two of the substituted enzymes that were very rapidly purified to homogeneity and rapidly assayed while they were still active (at only a few substrate concentrations so that the data could be rapidly obtained), showed that the kinetic values were very similar to the values obtained with the same enzymes that were only partially purified. This showed that the kinetics were not affected by the degree of purity and allowed kinetic analyses with partially purified enzymes so that large numbers of points could be used for accuracy. The data showed that His-391 is a very important residue. It interacts strongly with the transition state and promotes catalysis by stabilizing the transition state. Activation energy differences (deltadelta G(S) double dagger), as determined by differences in the kcat/Km values, indicated that substitutions for His-391 caused very large destabilizations (22.8-35.9 kJ/mol) of the transition state. The importance of His-391 for transition state stabilization was confirmed by studies that showed that transition state analogs are very poor inhibitors of the substituted enzymes, while inhibition by substrate analogs was only affected in a small way by substituting for His-391. The poor stabilities of the transition states caused significant decreases of the rates of the glycolytic cleavage steps (galactosylation, k2). Degalactosylation (k3) was not decreased to the same extent.
Drugs and drug delivery systems targeting amyloid-β in Alzheimer's disease (2015)

Alzheimer's disease (AD) is a devastating neurodegenerative disorder with no cure and limited treatment solutions that are unable to target any of the suspected causes. Increasing evidence suggests that one of the causes of neurodegeneration is the overproduction of amyloid beta (Aβ) and the inability of Aβ peptides to be cleared from the brain, resulting in self-aggregation to form toxic oligomers, fibrils and plaques. One of the potential treatment options is to target Aβ and prevent self-aggregation to allow for a natural clearing of the brain. In this paper, we review the drugs and drug delivery systems that target Aβ in relation to Alzheimer's disease. Many attempts have been made to use anti-Aβ targeting molecules capable of targeting Aβ (with much success in vitro and in vivo animal models), but the major obstacle to this technique is the challenge posed by the blood brain barrier (BBB). This highly selective barrier protects the brain from toxic molecules and pathogens and prevents the delivery of most drugs. Therefore novel Aβ aggregation inhibitor drugs will require well thought-out drug delivery systems to deliver sufficient concentrations to the brain.
Fundamentals of Anatomy and Physiology (1995)

This text is designed specifically to meet the needs of a diverse student population. It offers three ways of covering real-world applications: Clinical Discussion; Clinical Boxes (which provide more in-depth coverage of major diseases); and the Applications Manual. The artwork is unusual in that it falls into three categories: Compound Art combines Bill Ober's award-winning illustrations with photographs, micrographs, X-rays, and MRI images; Process Art shows how the successive stages of dynamic physiology processes unfold in time; and Large Illustrations Viewed from a Macro-Micro Level, in context, help students better understand anatomical structures. As for the pedagogy, the book has four main features: Concept Checks, which are interspersed questions that encourage students to stop and check their understanding of material before they move on; Concept Links, that have page references to help students review concepts discussed earlier in the text; Figure Reference Locators, red squares next to call out figures in the text that function as placeholders to make it easier to toggle between illustrations and the running narrative; and Three-Level Chapter Ending Material - this moves students through memorizing facts, to understanding concepts, to applying what they learn to solve problems. Level One questions review basic facts and terms. Level Two questions test the student's ability to comprehend and integrate the chapter's key concepts. Level Three exercises are real world scenarios designed to develop student's problem solving skills.
A computational study of off-target effects of RNA interference (2005)

RNA interference (RNAi) is an intracellular mechanism for post-transcriptional gene silencing that is frequently used to study gene function. RNAi is initiated by short interfering RNA (siRNA) of approximately 21 nt in length, either generated from the double-stranded RNA (dsRNA) by using the enzyme Dicer or introduced experimentally. Following association with an RNAi silencing complex, siRNA targets mRNA transcripts that have sequence identity for destruction. A phenotype resulting from this knockdown of expression may inform about the function of the targeted gene. However, 'off-target effects' compromise the specificity of RNAi if sequence identity between siRNA and random mRNA transcripts causes RNAi to knockdown expression of non-targeted genes. The complete off-target effects must be investigated systematically on each gene in a genome by adjusting a group of parameters, which is too expensive to conduct experimentally and motivates a study in silico. This computational study examined the potential for off-target effects of RNAi, employing the genome and transcriptome sequence data of Homo sapiens, Caenorhabditis elegans and Schizosaccharomyces pombe. The chance for RNAi off-target effects proved considerable, ranging from 5 to 80% for each of the organisms, when using as parameter the exact identity between any possible siRNA sequences (arbitrary length ranging from 17 to 28 nt) derived from a dsRNA (range 100-400 nt) representing the coding sequences of target genes and all other siRNAs within the genome. Remarkably, high-sequence specificity and low probability for off-target reactivity were optimally balanced for siRNA of 21 nt, the length observed mostly in vivo. The chance for off-target RNAi increased (although not always significantly) with greater length of the initial dsRNA sequence, inclusion into the analysis of available untranslated region sequences and allowing for mismatches between siRNA and target sequences. siRNA sequences from within 100 nt of the 5' termini of coding sequences had low chances for off-target reactivity. This may be owing to coding constraints for signal peptide-encoding regions of genes relative to regions that encode for mature proteins. Off-target distribution varied along the chromosomes of C.elegans, apparently owing to the use of more unique sequences in gene-dense regions. Finally, biological and thermodynamical descriptors of effective siRNA reduced the number of potential siRNAs compared with those identified by sequence identity alone, but off-target RNAi remained likely, with an off-target error rate of approximately 10%. These results also suggest a direction for future in vivo studies that could both help in calibrating true off-target rates in living organisms and also in contributing evidence toward the debate of whether siRNA efficacy is correlated with, or independent of, the target molecule. In summary, off-target effects present a real but not prohibitive concern that should be considered for RNAi experiments.
Self-Assembled Monolayers of Peptide Nucleic Acids on Gold Surfaces:  A Spectroscopic Study (2005)

We have characterized self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) chains adsorbed on gold surfaces by using reflection absorption infrared spectroscopy (RAIRS) and X-ray photoemission spectroscopy (XPS) techniques. We have found that the molecular orientation of PNAs strongly depends on surface coverage. At low coverage, PNA chains lie flat on the surface, while at high coverage, PNA molecules realign their molecular axes with the surface normal and form SAMs without the need of co-immobilization of spacers or other adjuvant molecules. The change in the molecular orientation has been studied by infrared spectroscopy and it has been confirmed by atomic force microscopy (AFM). PNA immobilization has been followed by analyzing the N(1s) XPS core-level peak. We show that the fine line shape of the N(1s) core-level peak at optimal concentration for biosensing is due to a chemical shift. A combination of the above-mentioned techniques allow us to affirm that the structure of the SAMs is stabilized by molecule-molecule interactions through noncomplementary adjacent nucleic bases.
Adjuvanted Intranasal Norwalk Virus‐Like Particle Vaccine Elicits Antibodies and Antibody‐Secreting Cells That Express Homing Receptors for Mucosal and Peripheral Lymphoid Tissues (2010)

The intranasal monovalent adjuvanted Norwalk VLP vaccine was well tolerated and highly immunogenic and is a candidate for additional study.
Gene silencing by cell-penetrating, sequence-selective and nucleic-acid hydrolyzing antibodies (2009)

Targeting particular mRNAs for degradation is a fascinating approach to achieve gene silencing. Here we describe a new gene silencing tool exploiting a cell-penetrating, nucleic-acid hydrolyzing, single-domain antibody of the light-chain variable domain, 3D8 VL. We generated a synthetic library of 3D8 VL on the yeast surface by randomizing residues located in one of two beta-sheets. Using 18-bp single-stranded nucleic acids as target substrates, including the human Her2/neu-targeting sequence, we selected 3D8 VL variants that had approximately 100-1000-fold higher affinity and approximately 2-5-fold greater selective hydrolyzing activity for target substrates than for off targets. 3D8 VL variants efficiently penetrated into living cells to be accumulated in the cytosol and selectively decreased the amount of target sequence-carrying mRNAs as well as the proteins encoded by these mRNAs with minimal effects on off-target genes. In particular, one 3D8 VL variant targeting the Her2 sequence showed more efficient downregulation of Her2 expression than a small-interfering RNA targeting the same Her2 sequence, resulting in apoptotic cell death of Her2-overexpressing breast cancer cells. Our results demonstrate that cell-penetrating 3D8 VL variants with sequence-selective, nucleic-acid-hydrolyzing activity can selectively degrade target mRNAs in the cytosol, providing a new gene silencing tool mediated by antibody.
Variable sequences in a mosaic-like domain of meningococcal tbp2 encode immunoreactive epitopes (1995)

Transferrin-binding proteins from Neisseria meningitidis vary among different isolates. We have identified and studied a hypervariable region adjacent to the carboxyl-end of the transferrin-binding domain of the Tbp2 molecule. The tbp2 genes from six strains of N. meningitidis were cloned and sequenced in this particular region. Sequence analysis of these regions along with five other sequences available from pathogenic Neisseria showed a common organisation of seven highly variable nucleotide stretches interspersed with six conserved nucleotide stretches. The variable regions correlated with the location of immunoreactive epitopes in polyclonal antisera raised to transferrin-binding proteins identified by peptide pin technology. Sequence analysis suggested a mosaic-like organisation of the tbp2 genes. Taken together, these data suggest that the antigenic variation in this part of the protein may result from a strong host immune pressure.
Automated assignment of charge states from resolved isotopic peaks for multiply charged ions (1995)

The recent proliferation of electrospray as an ionization method has greatly increased the ability to perform analyses of large biomolecules by using mass spectrometry. The major advantage of electrospray is the ability to produce multiply charged ions, which brings large molecules down to a mass-to-charge ratio range amenable to most instruments. Multiple charging is also a disadvantage because mass (m) becomes ambiguous unless charge (z) can be assigned. This is typically performed with simple algorithms that use multiple peaks of the same m and different z, but these methods are difficult to apply to complex mixtures and not applicable when only one z appears for each m. The use of mass analyzers with higher resolving powers, like the Fourier transform mass spectrometer, allows resolution of isotopic peaks, providing an internal 1-Da mass scale that can be used for unambiguous charge assignment. Manual assignment of charge state from the isotopic peaks is time consuming and becomes inaccurate when either the signal level or resolving power are low. For these cases, computer algorithms based on pattern recognition techniques have been developed to assist in assignment of charge states to isotopic clusters. These routines provide for more rapid analysis with higher accuracy than available manually.
Synthesis and Molecular Composites of Functionalized Polyisocyanates (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and Molecular Composites of Functionalized PolyisocyanatesChetan A. Khatri, Milind M. Vaidya, Kalle Levon, Salil K. Jha, and Mark M. GreenCite this: Macromolecules 1995, 28, 13, 4719–4728Publication Date (Print):June 1, 1995Publication History Published online1 May 2002Published inissue 1 June 1995https://doi.org/10.1021/ma00117a052RIGHTS & PERMISSIONSArticle Views223Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
Dual origin of mouse spleen macrophages. (1984)

The present study concerns the isolation, characterization, origin, and kinetics of spleen macrophages. The spleen was first perfused in situ to remove monocytes from the vascular bed and then dissected and treated with collagenase. The macrophages in the cell suspension thus obtained were characterized morphologically and cytochemically and then quantitated. The spleen cell suspension was incubated for 24 h in Leighton tubes to obtain an enriched glass-adherent population of macrophages for characterization and [3H]thymidine-labeling studies. Almost all of the adhering macrophages were esterase positive, had Fc and C3b receptors, and ingested EIgG and opsonized bacteria. In vitro labeling with [3H]thymidine showed that approximately 5% of the mononuclear phagocytes in the spleen synthesize DNA and must be considered to be dividing cells. The course of the number of labeled monocytes and macrophages after a single injection of [3H]thymidine indicates migration of monocytes into the spleen, where they become macrophages. Calculation of the influx of monocytes into the spleen and of the local production of macrophages by DNA-synthesizing mononuclear phagocytes showed that under steady-state conditions, 55% of the population of spleen macrophages is supplied by monocyte influx and 45% by local production. This means that there is a dual origin of spleen macrophages. The mean turnover time calculated with the value for the efflux of spleen macrophages is 6.0 d.
Screening for trisomy 21 by fetal tricuspid regurgitation, nuchal translucency and maternal serum free β-hCG and PAPP-A at 11 + 0 to 13 + 6 weeks (2005)

There is no relationship between tricuspid regurgitation and the levels of maternal serum free beta-hCG and PAPP-A in cases with trisomy 21. An integrated sonographic and biochemical test at 11 + 0 to 13 + 6 weeks can potentially identify about 90% of trisomy 21 fetuses for a false-positive rate of 2-3%.
Deep reactive ion etching of silicon using an aluminum etching mask (2003)

A method for fast and efficient deep etching of bulk silicon, using parallel capacitively coupled plasma is presented. The effects of the masking materials and RIE conditions are discussed. Based on the experimental results, a 1000 /spl Aring/ thick Al film sufficiently protects the unexposed substrate while allowing the etching of a 350 /spl mu/m deep hole with an area of 3/spl times/3mm/sup 2/ when etching with SF/sub 6//CHF/sub 3//O/sub 2/ plasma. A 2000 /spl mu/m long and 100 /spl mu/m wide (with layers of Al/SiO/sub 2//Si and thickness of 0.1/spl mu/m/2.2/spl mu/m/40/spl mu/m respectively) cantilever has been achieved. A silicon etch rate up to 2.5 to 2.8/spl mu/m/min has been obtained and an anisotropy of A = 0.5 (A=I-V/H, where V=horizontal undercut, H=etch depth) has been obtained. The technique was developed mainly for bulk micromachining of silicon or composite silicon cantilever structures.
The identification of a new alternative exon with highly restricted tissue expression in transcripts encoding the mouse Pgp-1 (CD44) homing receptor. Comparison of all 10 variable exons between mouse, human, and rat (1993)

The human CD44 cell surface glycoprotein family which has been implicated in lymphocyte homing, tumor metastasis, and extracellular matrix attachment consists of a large number of related isoforms that derive from the differential splicing of a single CD44 gene transcript. Recent mapping of the CD44 locus in man indicated the presence of at least nine alternative exons within the region of the gene encoding the variable membrane proximal extracellular domain. Here we report the identification of a 10th alternative exon (termed V1) in the mouse, human, and rat CD44 genes. We demonstrate tissue-specific patterns of expression for transcripts containing exons V1-V10 in the mouse and a highly restricted usage of exon V1 in transcripts from mouse gastric tissue. Close sequence homology between exons V1-V10 from mouse rat and human points to a specific functional role rather than a purely structural role for the membrane proximal extracellular domain of the CD44 molecule.