gebhart/patrepeval huggingface dataset:
Eyes that Do Not Meet the Eligibility Criteria of Clinical Trials on Age-Related Macular Degeneration: Proportion of the Real-World Patient Population and Reasons for Exclusion (2021)

Among the included cases, 44.7% did not meet the eligibility criteria for VIEW study, suggesting that the conclusion derived from clinical trials may not directly reflect the real-world outcomes. Additionally, the reasons for ineligibility differed among the different subtypes of neovascular AMD.
Interactive procedural street modeling (2007)

This sketch presents a solution to efficiently model the street networks of large urban areas. Parish and Müller [2001] were the first to note that the street network is the key to create a large urban model. While this algorithm created a high quality solution, the method does not allow to incorporate user-control. To address this limitation we provide a rather different alternative to street modeling that allows to integrate a wide variety of user input. The key idea is to use tensor fields to guide the generation of street graphs. A user can interactively edit a street graph by either modifying the underlying tensor field or by changing the graph directly. This allows for efficient modeling, because we can combine high-level and low-level modeling operations, constraints, and procedural methods. The major contributions are as follows: (1) We are the first to introduce a procedural approach to model urban street networks that combines interactive user-guided editing operations and procedural methods. (2) We are introducing a new methodology to graph modeling in general. The idea of tensor-guided graph modeling together with the tight integration of interactive editing and procedural modeling has not been explored previously in related modeling problems, such as modeling of bark, cracks, fracture, or trees.
Targeted Genome Modification in Mice Using Zinc-Finger Nucleases (2010)

Homologous recombination-based gene targeting using Mus musculus embryonic stem cells has greatly impacted biomedical research. This study presents a powerful new technology for more efficient and less time-consuming gene targeting in mice using embryonic injection of zinc-finger nucleases (ZFNs), which generate site-specific double strand breaks, leading to insertions or deletions via DNA repair by the nonhomologous end joining pathway. Three individual genes, multidrug resistant 1a (Mdr1a), jagged 1 (Jag1), and notch homolog 3 (Notch3), were targeted in FVB/N and C57BL/6 mice. Injection of ZFNs resulted in a range of specific gene deletions, from several nucleotides to >1000 bp in length, among 20-75% of live births. Modified alleles were efficiently transmitted through the germline, and animals homozygous for targeted modifications were obtained in as little as 4 months. In addition, the technology can be adapted to any genetic background, eliminating the need for generations of backcrossing to achieve congenic animals. We also validated the functional disruption of Mdr1a and demonstrated that the ZFN-mediated modifications lead to true knockouts. We conclude that ZFN technology is an efficient and convenient alternative to conventional gene targeting and will greatly facilitate the rapid creation of mouse models and functional genomics research.
Generalized Multi-Protocol Label Switching (GMPLS) Signaling Functional Description (2003)

This document describes extensions to Multi-Protocol Label Switching (MPLS) signaling required to support Generalized MPLS. Generalized MPLS extends the MPLS control plane to encompass time-division (e.g., Synchronous Optical Network and Synchronous Digital Hierarchy, SONET/SDH), wavelength (optical lambdas) and spatial switching (e.g., incoming port or fiber to outgoing port or fiber). This document presents a functional description of the extensions. Protocol specific formats and mechanisms, and technology specific details are specified in separate documents.
Prognostic Factors in Follicular Lymphoma (2010)

Follicular lymphoma (FL) is one of the most common types of non-Hodgkin's lymphoma. It is usually diagnosed at an advanced stage, for which many treatment options exist, however, no curative standard therapy has been identified. The outcome is highly variable with a median survival of approximately 10 years. The life expectancy of patients with FL has been extended with the use of rituximab, a monoclonal antibody targeting the CD20 antigen on FL cells, but there remains a group of patients who fail to respond to chemoimmunotherapy and die early of their disease. Transformation of FL to an aggressive histology is an important event with high morbidity and mortality. The Follicular Lymphoma International Prognostic Index has become the clinically useful prognostic tool, but gives only a rough estimate of expected outcome. There is a need for useful biomarkers for prediction of the disease course of single patients to individualize therapy, especially in the new era of chemoimmunotherapy.
Control of Stereochemistry by σ-Participation of a Silyl Group. A Novel Method for Diastereoselective Polyol Synthesis (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTControl of Stereochemistry by σ-Participation of a Silyl Group. A Novel Method for Diastereoselective Polyol SynthesisKeiji Tanino, Naoei Yoshitani, Fumiko Moriyama, and Isao KuwajimaView Author Information Department of Chemistry, Tokyo Institute of Technology, Meguro, Tokyo 152, Japan Cite this: J. Org. Chem. 1997, 62, 13, 4206–4207Publication Date (Web):June 27, 1997Publication History Received25 February 1997Published online27 June 1997Published inissue 1 June 1997https://doi.org/10.1021/jo9703515Copyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views675Altmetric-Citations29LEARN 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 Read OnlinePDF (206 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Chemical reactions,Ethers,Molecular structure,Silicon,Substitution reactions Get e-Alerts
Synthesis and pharmacological properties of some 2-substituted 1-(3-pyridyl)-1,2,3,4-tetrahydro-beta-carbolines. (1987)

Six derivatives of 2-aminoacetyl-1,2,3,4-tetrahydro-beta-carboline (2a-f) were obtained, which yielded as a result of reduction with LiAlH4 six respective 2-aminoethyl-derivatives (3a-f). Pharmacological studies revealed that compounds 2f, 3e and 3f have sedative properties. None of the compounds possesses neuroleptic, antidepressive, anxiolytic, analgesic or anticonvulsant properties.
The Reactions of Phenylglyoxal and Related Reagents with Amino Acids1 (1977)

The reaction of phenylglyoxal (PGO), glyoxal (GO), and methylglyoxal (MGO) with amino acids were investigated at mild pH values at 25°. These aldehydes reacted most rapidly with arginine and the rate of reaction increased with increasing pH values. Histidine, cystine, glycine, tryptophan, asparagine, glutamine, and lysine reacted with these aldehydes at significant but various rates, depending on the pH and the kind of the reagent used. The reactions with these amino acids seemed to involve both the α-amino groups and the side chain groups, and no significant reaction appeared to occur with the side chain alone except with those of arginine, lysine, and cysteine. These reagents were similarly reactive with the guanidinium group of arginine, but PGO appeared to be much less reactive with the ε-amino group of lysine than MGO and GO. The other ordinary amino acids were very much less reactive or did not react at all with these reagents, with the exception of cysteine. D1-PGO-L-arginine was prepared from Nα-benzyloxycarbonyl-L-arginine, and di-PGO-methylguanidine from methylguanidine, and the stoichiometry of the reaction of two PGO molecules with one guanidino group was confirmed. A glyoxal derivative of L-arginine (GO-arginine) was prepared by reaction of glyoxal with arginine. GO-arginine was fairly unstable, especially at higher pH values. A similar derivative (MGO-arginine) was also found to be formed by reaction of MGO with L-arginine, and was similarly unstable. These derivatives, however, did not regenerate arginine upon acid hydrolysis.
Crystal Structures at 2.5 Angstrom Resolution of Seryl-tRNA Synthetase Complexed with Two Analogs of Seryl Adenylate (1994)

Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.
Differential expression of homeobox genes in functionally distinct CD34+ subpopulations of human bone marrow cells. (1994)

Class I homeobox (Hox) genes encode a major group of transcription factors controlling embryonic development and have been implicated in the continuing process of hematopoietic cell differentiation. They are clustered on four chromosomes and, in early development, exhibit spatially restricted expression with respect to their 3'-->5' chromosomal position. By using an improved PCR-based method for amplifying total cDNA derived from limited cell numbers, we now describe the expression of class I Hox genes in highly purified CD34+ cell subpopulations isolated from normal human bone marrow that represent functionally distinct stem and progenitor cell compartments. Our data indicate that at least 16 different Hox genes, mainly from the A and the B clusters, are expressed in one or more of these subpopulations of human hematopoietic cells. Moreover, markedly elevated expression of some of the Hox genes found at the 3' end of the A and B clusters (e.g., HoxB3) was a unique feature of the subpopulations that contained the most primitive functionally defined cells, whereas genes located in the 5' region of each cluster (e.g., HoxA10) were found to be expressed at nearly equal levels in the CD34+ subpopulations analyzed. In contrast to the findings for CD34+ cells, expression of two selected Hox genes, HoxB3 and HoxA10, was virtually extinguished in the CD34- fraction of bone marrow cells. These results demonstrate the expression of a broad range of Hox genes in primitive hematopoietic cells and point to the existence of a regulated program of Hox gene expression during their normal development.
Graft-versus-host disease: new directions for a persistent problem (1994)

Graft-versus-host disease (GVHD) continues to be a major complication after allogeneic bone marrow transplantation, especially with the increasing use of unrelated and mismatched donors. Recently there has been renewed scientific interest in GVHD because of the increasing appreciation of the complexity of the immune responses seen in GVHD. Two basic aspects of the immune response in GVHD, the immunologic target and the effector mechanisms, are now more completely understood. First, the target of the immune response in GVHD has long been felt to be histocompatibility antigens possessed by the host, but not the donor. Recently, recognition of self antigens in GVHD has been documented, showing that GVHD is more complex than simple alloreactivity. Second, the effector mechanism in GVHD was initially felt to be direct cytotoxicity by alloreactive T cells. It is now recognized that cytokines play a central role in mediating many of the clinical and experimental manifestations of GVHD. The development in these two areas will be reviewed and the implications for clinical transplantation discussed.
Mannose‐based inhibitors of Escherichia coli adhesion: design and applications (1007.2) (2014)

Structure‐thermodynamic relationships in protein‐carbohydrate interactions provide important decision makers in the design and maturation of bacterial ant‐adhesives. Many interactions in our innate defense depend on the specific recognition, of a high enough density of a glycan sequence, to evoke immune reaction. Bacteria hijack glycan receptors that are reminiscent of a physiological state of a mamalian cell that indicates a suitable habitat for the completion of their pathogenic cycle. The interruption of this process is envisioned using anti‐adhesives that selectively block bacterial adhesion but do not interfere with the immune system. The understanding of the biophysical basis of host‐pathogen interactions to empower intervention can be studied using purified adhesins and synthetic multivalent inhibitors. We measured affinities and stoichiometries using surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and dynamic light scattering (DLS). The geometry of a multivalent complex was determined using small angle X‐ray scattering (SAXS) and was found to agree with the stoichiometry and molecular size derived from ITC and DLS data respectively. Stunningly, a correlation could be found between the dispersion part of interaction energies (quantum chemical calculations), ITC‐derived entropies and crystal structure electron densities of inhibitors bound to FimH. Grant Funding Source : Supported by ANR‐12‐BSV5‐0016‐01
Assay of Plasma Insulin Activity by the Rat-diaphragm Method (1954)

Bornstein (1950) described a method for the assay of insulin in human plasma which was based on the fall of blood sugar of alloxan-diabetic hypophysectomized adrenalectomized rats (A.D.H.A. rats). Subsequently Bornstein and his colleagues determined the insulin content of plasma from various types of diabetic by this method (Bornstein and Trewhella, 1951 ; Bornstein and Lawrence, 1951a, 1951b). The published results of these workers were of such interest as to merit further study.
Real-time robot motion planning using rasterizing computer graphics hardware (1990)

We present a real-time robot motion planner that is fast and complete to a resolution. The technique is guaranteed to find a path if one exists at the resolution, and all paths returned are safe. The planner can handle any polyhedral geometry of robot and obstacles, including disjoint and highly concave unions of polyhedra.The planner uses standard graphics hardware to rasterize configuration space obstacles into a series of bitmap slices, and then uses dynamic programming to create a navigation function (a discrete vector-valued function) and to calculate paths in this rasterized space. The motion paths which the planner produces are minimal with respect to an L 1 (Manhattan) distance metric that includes rotation as well as translation.Several examples are shown illustrating the competence of the planner at generating planar rotational and translational plans for complex two and three dimensional robots. Dynamic motion sequences, including complicated and non-obvious backtracking solutions, can be executed in real time.
Effect of B(a)P on germ cells of male mice (2011)

Objective To study different concentrateions of B(a)P on enzyme activitiy,sperm abnormality rate,and DNA damage rate of mouse germ cells.Methods Lactate dehydrogenase(LDH),glucose-6-phosphate dehydrogenase(G-6-PD),sorbitol dehydrogenase(SDH) were measured with spectrophotometry;DNA damage was detected with single cell gel electrophoresis(SCGE),and sperm abnormality rate and sperm cells micronucleus rate were determined with sperm aberration test and micronucleus test,respectively.Results B(a)P affected activities of LDH,SDH,G-6-PD in mouse testicular cells.The activities of LDH in testicular cells decreased with the increasing of B(a)P exposure dose,and significant defference was observed between 20 mg/kg group and the negative control group(P0.05).DNA damage was observed in every exposure group,with the damage rate of 44%,79%,and 88%,respectively,and all of the rate were significantly different from that of negative control group(P0.05).Sperm abnormality rate and sperm cell micronucleus rate in each exposure group were 1.10%,2.24%,3.64%,and 11.00%,14.40%,17.40%,respectively,and were significantly different from that of the control group(P0.05).Conclusion B(a)P could influence enzyme activities of mouse sperm cell,cause DNA damage and have cytotoxicity to male mouse sperm cell within a certain dose range.
Antigen recognition by MHC-incompatible cells of a human mismatched chimera. (1988)

Tetanus toxin (TT)-specific T cell clones of donor origin were obtained from a patient with severe combined immunodeficiency (SCID) successfully reconstituted by transplantation of allogeneic fetal liver and thymus cells from two different donors performed 10 yr ago. A series of these clones recognized TT in the context of "allo" class II HLA determinants expressed by recipient APC. The restriction element of two T cell clones with the HLA phenotype of the first donor (HLA-DR1,8) and one T cell clone with the HLA phenotype of the second transplant (HLA-DR3,9) was HLA-DR4 of the recipient, whereas other T cell clones derived from the second transplant recognized TT in the context of HLA-DR5 of the recipient's APC. These latter T cell clones were not able to proliferate in response to TT when autologous APC were used. These data demonstrate that recipient and donor cells having different HLA phenotypes could cooperate across the allogeneic barrier and that MHC restriction of antigen (Ag) recognition is independent from the MHC genotype of the T cells but is influenced by the environment in which the T cells mature. We also isolated T cell clones that were able to recognize processed TT presented by all allogeneic EBV cell lines tested, indicating that the Ag specificity of these clones was not restricted by a particular class II MHC molecule. The Ag-specific proliferative response of one of these clones could be blocked by anti-class II MHC mAbs. These results demonstrate that in addition to Ag recognition in the context of specific class II MHC Ags, other types of Ag-specific responses may occur in this human chimera. It is not clear whether this "allo" plus Ag recognition is the result of education of transplanted fetal cells in the host thymus. Taking into consideration our previous findings indicating that alloreactive T cell clones specific for the recipient cells could be isolated in vitro from the PBL of the same patient, our data suggest that the mechanism for deletion of self-reactive clones and the generation of MHC-restricted responses are different.
Tumor-Associated Immune Parameters for Personalized Patient Care (2013)

The implementation of a robust technology adapted to clinical practice for the evaluation of the tumor-immune infiltrate is required to exploit its prognostic and theranostic value (Robins et al., this issue).
Exogenously provided peptides fail to complex with intracellular class II molecules for presentation by antigen-presenting cells (1997)

Exogenously supplied antigenic peptides can bind to and be presented by cell surface class II molecules of APCs without prior processing. However, it has been unclear whether peptide Ags exogenously supplied to APCs can also form complexes with nascent intracellular class II molecules that contribute to Ag presentation. We found that exogenously provided peptide Ags, unlike whole protein Ags, are presented as efficiently by fixed as by unfixed B lymphoblastoid APCs, suggesting that intracellular processes do not contribute to the presentation of exogenously supplied peptides by unfixed APCs. Consistent with this finding, exogenously provided peptides do not bind detectably to nascent intracellular class II molecules. We studied the basis for this failure. First, as compared with whole proteins, exogenously supplied peptides accumulate very poorly intracellularly. Second, peptides are more rapidly exocytosed. The limited ability of APCs to accumulate exogenously supplied peptides intracellularly provides a likely explanation for the failure of these peptides to associate with nascent intracellular class II molecules. Exogenously supplied peptides probably never reach the intracellular vesicles in which peptide loading of class II molecules occurs. These findings have implications for the use of peptides therapeutically to block presentation of autoantigens in autoimmune disease.
Primary structure of a cytochrome P-450: coding nucleotide sequence of phenobarbital-inducible cytochrome P-450 cDNA from rat liver. (1982)

We determined the coding nucleotide sequence of phenobarbital-inducible cytochrome P-450 mRNA of the rat by analysis of three cloned cDNAs and by primer extension methods. The deduced amino acid sequence of the cytochrome is composed of 491 amino acids, and its predicted molecular weight and amino acid composition concur with those determined with the purified protein. The sequence of one of the three cloned cDNAs is not identical with that of the other two. In their 922 overlapping nucleotides, 14 nucleotide substitutions occur, and 7 of them result in 6 amino acid changes, therefore indicating the presence of at least two similar but distinct mRNAs for phenobarbital-inducible cytochrome P-450. These substitutions occur in a limited portion of the sequence, apparently forming some sort of a "variable region."
CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses (2015)

Th17 responses are critical to a variety of human autoimmune diseases, and therapeutic targeting with monoclonal antibodies against IL-17 and IL-23 has shown considerable promise. Here, we report data to support selective bromodomain blockade of the transcriptional coactivators CBP (CREB binding protein) and p300 as an alternative approach to inhibit human Th17 responses. We show that CBP30 has marked molecular specificity for the bromodomains of CBP and p300, compared with 43 other bromodomains. In unbiased cellular testing on a diverse panel of cultured primary human cells, CBP30 reduced immune cell production of IL-17A and other proinflammatory cytokines. CBP30 also inhibited IL-17A secretion by Th17 cells from healthy donors and patients with ankylosing spondylitis and psoriatic arthritis. Transcriptional profiling of human T cells after CBP30 treatment showed a much more restricted effect on gene expression than that observed with the pan-BET (bromo and extraterminal domain protein family) bromodomain inhibitor JQ1. This selective targeting of the CBP/p300 bromodomain by CBP30 will potentially lead to fewer side effects than with the broadly acting epigenetic inhibitors currently in clinical trials.