gebhart/patrepeval huggingface dataset:
Characterization of an F1 Deletion Mutant of Yersinia pestis CO92, Pathogenic Role of F1 Antigen in Bubonic and Pneumonic Plague, and Evaluation of Sensitivity and Specificity of F1 Antigen Capture-Based Dipsticks (2011)

We evaluated two commercial F1 antigen capture-based immunochromatographic dipsticks, Yersinia Pestis (F1) Smart II and Plague BioThreat Alert test strips, in detecting plague bacilli by using whole-blood samples from mice experimentally infected with Yersinia pestis CO92. To assess the specificities of these dipsticks, an in-frame F1-deficient mutant of CO92 (Δcaf) was generated by homologous recombination and used as a negative control. Based on genetic, antigenic/immunologic, and electron microscopic analyses, the Δcaf mutant was devoid of a capsule. The growth rate of the Δcaf mutant generally was similar to that of the wild-type (WT) bacterium at both 26 and 37 °C, although the mutant's growth dropped slightly during the late phase at 37 °C. The Δcaf mutant was as virulent as WT CO92 in the pneumonic plague mouse model; however, it was attenuated in developing bubonic plague. Both dipsticks had similar sensitivities, requiring a minimum of 0.5 μg/ml of purified F1 antigen or 1 × 10(5) to 5 × 10(5) CFU/ml of WT CO92 for positive results, while the blood samples were negative for up to 1 × 10(8) CFU/ml of the Δcaf mutant. Our studies demonstrated the diagnostic potential of two plague dipsticks in detecting capsular-positive strains of Y. pestis in bubonic and pneumonic plague.
High current density "wired" quinoprotein glucose dehydrogenase electrode (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh current density "wired" quinoprotein glucose dehydrogenase electrodeLing. Ye, Martin. Haemmerle, Arjen J. J. Olsthoorn, Wolfgang. Schuhmann, Hans Ludwig. Schmidt, Johannis A. Duine, and Adam. HellerCite this: Anal. Chem. 1993, 65, 3, 238–241Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://doi.org/10.1021/ac00051a008Request reuse permissions Article Views685Altmetric-Citations149LEARN 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 (432 KB) Get e-Alertsclose Get e-Alerts
Block Copolymer Nanolithography: Translation of Molecular Level Control to Nanoscale Patterns (2009)

The self-asembly of block copolymers is a promising platform for the "bottom-up" fabrication of nanostructured materials and devices. This review covers some of the advances made in this field from the laboratory setting to applications where block copolymers are in use.
Polylysine Modification of Adenoviral Fiber Protein Enhances Muscle Cell Transduction (1999)

Adenoviral vectors (ADVs) are used widely for gene delivery to different tissues including muscle. One particularly promising use for ADVs is in the transfer of the dystrophin gene to the muscle of patients with Duchenne muscular dystrophy (DMD). However, studies in different animal models of DMD suggest that ADVs inefficiently transduce mature skeletal muscle. In this article we test whether AdZ.F(pK7), a genetically modified ADV that expresses a polylysine moiety on the end of the fiber protein, could enhance transduction of muscle cells and circumvent the maturation-dependent loss of muscle infectivity by ADVs. The efficiency of transduction was tested at different levels of muscle maturation. In vitro, AdZ.F(pK7) showed a higher level of transduction at all stages of differentiation including myoblasts, myotubes, and single muscle fibers. In vivo, mature skeletal muscle was transduced fourfold better by AdZ.F(pK7) than by the unmodifled vector (AdZ.F). Together, these observations demonstrate improved ADV transduction of skeletal muscle by modifying ADV tropism, and provide a proof-of-principle that modification of ADVs to target muscle-specific molecules could result in tissue-specific transfer of skeletal muscle tissue as well.
Analysis of Thermal Melting Curves (2003)

T(m) is defined as Temperature of melting or, more accurately, as temperature of midtransition. This term is often used for nucleic acids (DNA and RNA, oligonucleotides and polynucleotides). A thermal denaturation experiment determines the stability of the secondary structure of a DNA or RNA and aids in the choice of the sequences for antisense oligomers or PCR primers. Beyond a simple numerical value (the T(m)), a thermal denaturation experiment, in which the folded fraction of a structure is plotted vs. temperature, yields important thermodynamic information. We present the classic problems encountered during these experiments and try to demonstrate that a number of useful pieces of information can be extracted from these experimental curves.
Structural Elucidation of Post-Translational Modifications in Monoclonal Antibodies (2015)

Therapeutic proteins may undergo a series of modifications throughout their production, processing, and storage. These modifications can include the addition or replacement of functional groups, or structural changes such as folding, cleavage, and racemization. The presence of these modifications can affect therapeutic monoclonal antibody (mAb) biological activity, half-life, and immunogenicity. Post-translational modifications that arise during cellular expression and chemical modifications that may result during the biomanufacturing process and storage must be discovered, tracked, and evaluated for their impact on quality, safety, and efficacy. A review of the most common modifications encountered during therapeutic mAb development and their characterization using modern analytical approaches is presented, with an emphasis on mass spectrometry-based approaches. As a real-world example, a peptide mapping-based characterization study involving three independent laboratories was conducted using the reference mAb provided by the National Institute of Standards and Technology (NIST). Results from this study are discussed to provide a representative sampling of peptide mapping as it is currently applied to characterization of mAb modifications, as well as considerations to weigh when developing these experiments for qualitative and quantitative analysis.
Prevention of Detrimental Effect of Cyclosporin A on Vascular Ingrowth of Transplanted Pancreatic Islets With Verapamil (1989)

The revascularization of pancreatic islet clusters transplanted beneath the renal capsule was studied in a syngeneic mouse model. The degree of vascular ingrowth was visualized by in vivo fluorescence microscopy (fluorescein isothiocyanate-dextran) and judged by a semiquantitative method from coded video recordings. The recipients of isografts were divided into four groups, depending on their daily immunosuppressive treatment: 1) none (controls), 2) 15 mg/kg cyclosporin A (CsA), 3) 0.4 mg/kg verapamil + 15 mg/kg CsA, and 4) 20-30 mg/kg methylprednisolone. In control animals, capillary ingrowth was first demonstrated on day 6, followed by progressive vascularization up to day 34. After 6 mo, the vascular architecture was similar to that seen in normal islets in situ. CsA alone significantly decreased vascular ingrowth on day 14 compared with controls (P less than .02). Verapamil prevented the detrimental effect of CsA (P less than .01), probably by improving renal subcapsular blood flow. Methylprednisolone did not affect revascularization compared with control animals at day 14. We conclude that CsA inhibits vascular ingrowth into transplanted pancreatic islets, which is likely to have clinical implications. The prevention of CsA vascular ingrowth inhibition by a calcium antagonist indicates a possible approach to the correction of this problem, particularly when the renal capsule is used as the recipient's transplant site.
Solid-Phase and Solution-Phase Syntheses of Oligomeric Guanidines Bearing Peptide Side Chains (2005)

Synthetic strategies for preparing N,N‘-bridged oligomeric guanidines bearing peptide side chains both on solid support and in solution are presented. Monomers are prepared from common α-amino acids and therefore contain conventionally protected peptide side chains. The side chains include alkyl, aromatic, hydroxyl, amino, carboxylic acid, and amide functional groups. Oligomer elongation utilizes acid-sensitive sulfonyl activated thiourea through the formation of carbodiimide intermediate. With proper preparation of monomers, synthesis of oligomer can be performed in two directions (equivalent to N to C terminal or C to N terminal in a peptide sequence) with excellent efficiency.
Macroscopic cartilage formation with embryonic stem-cell-derived mesodermal progenitor cells (2003)

The totipotent embryonic stem cell generates various mesodermal cells when stimulated with BMP4. Among the resulting cells, those expressing flk-1 and/or PDGFRalpha displayed chondrogenic activity in the presence of TGFbeta3 and expressed cartilage-specific genes in 7 to 16 day pellet cultures. Depositions of cartilage matrix and type II collagen were detected by day 14. TGFbeta-stimulated chondrogenesis was synergistically enhanced by PDGF-BB, resulting in a larger cartilage particle filled with a cartilaginous area containing type II collagen, with a surface cell layer expressing type I collagen. In contrast, noggin inhibited both the TGFbeta- and TGFbeta+PDGF-stimulated cartilage formation, suggesting that a BMP-dependent pathway is involved. In fact, replacement of TGFbeta3 with BMP4 on days 10 to 12 markedly elevated the cartilage matrix deposition during the following 7 to 8 days. Moreover, culture with TGFbeta3 and PDGF-BB, followed by the incubation with BMP4 alone, resulted in a cartilage particle lacking type I collagen in the matrix and the surface layer, which suggests hyaline cartilage formation. Furthermore, such hyaline cartilage particles were mineralized. These studies indicate that the PDGFRalpha+ and/or flk-1+ cells derived from embryonic stem cells possess the full developmental potential toward chondrocytes, in common with embryonic mesenchymal cells.
Prognostic and predictive value of c-erbB2 overexpression in osteogenic sarcoma (2006)

Previous studies have shown that c-erbB-2/HER-2 is an independent prognostic factor in osteogenic sarcoma, but in the present study, its expression was not seen to be correlating with survival rate of the patients. Therefore, further studies are needed to reach a consensus regarding the reliability of c-erbB-2 as an independent prognostic factor in OS.
A universal combinatorial design of antibody framework to graft distinct CDR sequences: A bioinformatics approach (2011)

Antibody (Ab) humanization is crucial to generate clinically relevant biologics from hybridoma-derived monoclonal antibodies (mAbs). In this study, we integrated antibody structural information from the Protein Data Bank with known back-to-mouse mutational data to build a universal consensus of framework positions (10 heavy and 7 light) critical for the preservation of the functional conformation of the Complimentarity Determining Region of antibodies. On the basis of FR consensus, we describe here a universal combinatorial library suitable for humanizing exogenous antibodies by CDR-grafting. The six CDRs of the murine anti-human EGFR Fab M225 were grafted onto a distinct (low FR sequence similarity to M225) human FR sequence that incorporates at the 17 FR consensus positions the permutations of the naturally observed amino acid diversities. Ten clones were selected from the combinatorial library expressing phage-displayed humanized M225 Fabs. Surprisingly, 2 of the 10 clones were found to bind EGFR with stronger affinity than M225. Cell-based assays demonstrated that the 10 selected clones retained epitope specificity by blocking EGFR phosphorylation and thus hindering cellular proliferation. Our results suggest that there is a universal and structurally rigid near-CDR set of FR positions that cooperatively support the binding conformation of CDRs.
Implementing precise interrupts in pipelined processors (1988)

Five solutions to the precise interrupt problem in pipelined processors are described and evaluated. An interrupt is precise if the saved process state corresponds to a sequential model of program execution in which one instruction completes before the next begins. In a pipelined processor, precise interrupts are difficult to implement because an instruction may be initiated before its predecessors have completed. The first solution forces instructions to complete and modify the process state in architectural order. The other four solutions allow instructions to complete in any order, but additional hardware is used, so that a precise state can be restored when an interrupt occurs. All the methods are discussed in the context of a parallel pipeline structure. Simulation results for the Cray-1S scalar architecture are used to show that the first solution results in a performance degradation of at least 16%. The remaining four solutions offer better performance, and three of them result in as little as a 3% performance loss. Several extensions, including vector architectures, virtual memory, and linear pipeline structures, are briefly discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identification of Gas6, a putative ligand for Sky and Axl receptor tyrosine kinases, as a novel neurotrophic factor for hippocampal neurons (2002)

Sky (also known as "Tyro3" and "Rse") is a member of the Axl/Sky/Mer receptor tyrosine kinase family and has two immunoglobulin-like repeats and two fibronectin type III-like repeats in the extracellular domain. Gas6 is a ligand for all members of the Axl family, each of which (Axl, Sky, and c-Mer) has different affinities to Gas6. Physiological functions of Sky and Gas6 in the nervous system are not well understood, despite their importance, which is suggested by Sky structural features and its predominant expression in the brain. We found in the RNase protection assays that gas6 and sky mRNAs are expressed in the adult rat hippocampus and are similarly regulated during development. Expression levels were low during embryonic stages but gradually increased during development and reached the highest level in adulthood. Sky, but not Axl, immunoreactivity was observed in the adult hippocampus. Recombinant rat Gas6 attenuated hippocampal neuronal cell death that was caused by serum starvation in vitro, indicating that Gas6 is a novel neurotrophic factor for hippocampal neurons. Gas6 showed regulated expression in the sciatic nerve after nerve transection. Therefore, Sky and Gas6 have neurotrophic roles in the nervous system.
Adaptive runlength coding (2003)

Runlength coding is the standard coding technique for block transform-based image/video compression. A block of quantized transform coefficients is first represented as a sequence of RUN/LEVEL pairs that are then entropy coded-RUN being the number of consecutive zeros and LEVEL being the value of the following nonzero coefficient. We point out the inefficiency of conventional runlength coding and introduce a novel adaptive runlength (ARL) coding scheme that encodes RUN and LEVEL separately using adaptive binary arithmetic coding and simple context modeling. We aim to maximize compression efficiency by adaptively exploiting the characteristics of block transform coefficients and the dependency between RUN and LEVEL. Coding results show that with the same level of complexity, the proposed ARL coding algorithm outperforms the conventional runlength coding scheme by a large margin in the rate-distortion sense.
POLYMERIZATION OF METHYL METHACRYLATE INITIATED WITH VANILLIN (1978)

Abstract Vanillin was found to initiate the polymerization of methyl methacrylate(MMA) in benzene at 85 °C. The effects of the concentrations of vanillin and MMA on the rate of polymerization and on the degree of polymerization of poly-MMA were investigated. A probable initiation mechanism proposed. The polymerization is assumed to proceed through a radical mechanism. The polymeric effect of the polymer containing vanillin units was also studied.
A Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix Structures (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Novel Peptide Nucleic Acid Monomer for Recognition of Thymine in Triple-Helix StructuresAnne B. Eldrup, Otto Dahl, and Peter E. NielsenView Author Information Center for Biomolecular Recognition Department of Chemistry, University of Copenhagen Universitetsparken 5 DK-2100 Copenhagen Ø, Denmark Department of Biochemistry B The Panum Institute, Blegdamsvej 3 DK-2200 Copenhagen N, Denmark Cite this: J. Am. Chem. Soc. 1997, 119, 45, 11116–11117Publication Date (Web):November 12, 1997Publication History Received28 May 1997Published online12 November 1997Published inissue 1 November 1997https://pubs.acs.org/doi/10.1021/ja9717424https://doi.org/10.1021/ja9717424rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views737Altmetric-Citations66LEARN 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 InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Cytosine,Genetics,Monomers,Nucleobases,Thymine Get e-Alerts
Radiobiologic studies of low-dose—rate90y-lymphoma therapy (1994)

These results suggest that radiation-associated apoptosis may be important in the radiobiology of targeted radiopharmaceutical therapy.
Human immune response to botulinum pentavalent (ABCDE) toxoid determined by a neutralization test and by an enzyme-linked immunosorbent assay (1988)

To determine the immune status of persons receiving botulinum pentavalent (ABCDE) toxoid and to evaluate the effectiveness of the vaccine, we surveyed immunized individuals for neutralizing antibodies to type A and to type B botulinum toxins. After the primary series of three immunizations administered at 0, 2, and 12 weeks, 21 of 23 persons tested (91%) had a titer for type A that was greater than or equal to 0.08 international units (IU)/ml, and 18 (78%) had a titer for type B of greater than or equal to 0.02 IU/ml. (One international unit is defined as the amount of antibody neutralizing 10,000 mouse 50% lethal doses of type A or B botulinum toxin). Just before the first annual booster, 10 of 21 (48%) and 14 of 21 (67%) people lacked a detectable titer for type A and for type B, respectively. After the first booster, all individuals tested had a demonstrable titer to both types A and B. Of 77 persons who had previously received from one to eight boosts of the toxoid, 74 (96%) had an A titer of greater than or equal to 0.25 IU/ml and would not require an additional booster, according to the recommendations of the Centers for disease Control. However, only 44 of 77 (57%) had a B titer of greater than or equal to 0.25 IU/ml. In each group by booster number, even the group having had eight boosts, at least one person would require reimmunization on the basis of B titer. There was a wide range of antibody levels among individuals at the same point in the immunization scheme. Results from an enzyme linked immunosorbent assay, with purified type A or type B neurotoxin as the capture antigen, were compared with neutralization test results on 186 serum samples for type A and 168 samples for type B. Statistically, the correlation coefficients for results from the two assays were high (r = 0.69, P &lt; 0.0001, for type A and r = 0.77, P &lt; 0.0001, for type B). However, due to the wide dispersion of values obtained, using enzyme-linked immunosorbent assay results to predict neutralizing antibody levels is unwarranted.
Unnatural Selection in Chemical Systems (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnnatural Selection in Chemical SystemsLeslie E. OrgelCite this: Acc. Chem. Res. 1995, 28, 3, 109–118Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://doi.org/10.1021/ar00051a004RIGHTS & PERMISSIONSArticle Views1409Altmetric-Citations139LEARN 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