gebhart/patrepeval huggingface dataset:
Discovery of AMG 853, a CRTH2 and DP Dual Antagonist (2011)

Prostaglandin D2 (PGD2) plays a key role in mediating allergic reactions seen in asthma, allergic rhinitis, and atopic dermatitis. PGD2 exerts its activity through two G protein-coupled receptors (GPCRs), prostanoid D receptor (DP or DP1), and chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2 or DP2). We report the optimization of a series of phenylacetic acid derivatives in an effort to improve the dual activity of AMG 009 against DP and CRTH2. These efforts led to the discovery of AMG 853 (2-(4-(4-(tert-butylcarbamoyl)-2-(2-chloro-4-cyclopropylphenyl sulfonamido)phenoxy)-5-chloro-2-fluorophenyl)acetic acid), which is being evaluated in human clinical trials for asthma.
Identification of genes expressed in premalignant breast disease by microscopy-directed cloning. (1994)

Histopathologic study of human breast biopsy samples has identified specific lesions which are associated with a high risk of development of invasive breast cancer. Presumably, these lesions (collectively termed premalignant breast disease) represent the earliest recognizable morphologic expression of fundamental molecular events that lead to the development of invasive breast cancer. To study molecular events underlying premalignant breast disease, we have developed a method for isolating RNA from histologically identified lesions from frozen human breast tissue. This method specifically obtains mRNA from breast epithelial cells and has identified three genes which are differentially expressed in premalignant breast epithelial lesions. One gene identified by this method is overexpressed in four of five noncomedo ductal carcinoma in situ lesions and appears to be the human homologue of the gene encoding the M2 subunit of ribonucleotide reductase, an enzyme involved in DNA synthesis.
Enhanced Production of Insulin-Like Growth Factor I Fusion Protein in Escherichia coli by Coexpression of the Down-Regulated Genes Identified by Transcriptome Profiling (2003)

The transcriptome profiles of recombinant Escherichia coli producing human insulin-like growth factor I fusion protein (IGF-I(f)) during the high-cell-density fed-batch culture were analyzed using DNA microarrays. The expression levels of 529 genes were significantly altered after induction. About 200 genes were significantly down-regulated during the production of IGF-I(f) after induction. Among these down-regulated genes, we rationally selected and coexpressed in E. coli producing IGF-I(f) the prsA gene (encoding a phosphoribosyl pyrophosphate synthetase) and the glpF gene (encoding a glycerol transporter), which are involved in an early key step in the biosynthetic pathway of nucleotides and amino acids (Trp and His) and the first step in glycerol utilization, respectively. As a result, the production of IGF-I(f) could be increased from 1.8 +/- 0.13 (+/- standard deviation) to 4.3 +/- 0.24 g/liter. The volumetric productivity was also increased from 0.36 +/- 0.027 to 0.82 +/- 0.048 g/liter/h. These results demonstrate that transcriptome profiling can provide invaluable information in designing engineered strains showing enhanced performance.
프로골프선수들의 심리기술 훈련 프로그램 개발 (2003)

본 연구의 목적은 국내 프로골프선수들이 경험하는 심리기술 요인을 심층면접 방법을 이용하여 탐색하고, 이를 기초로 프로골프선수들의 심리기술훈련 프로그램을 개발하여 궁극적으로 프로골프선수들의 최적 수행에 효과적으로 적용할 수 있도록 기초자료를 제공함에 그 목적이 있었다. 본 연구에는 국내 KPGA, KLPGA에 소속되어 있으며 최소 2년간 지속적으로 경기에 참여하고 있는 9명의 연구대상자가 참여하였다. 이에 연구절차를 통하여 도출된 결과는 다음과 같다. 먼저 심층면접을 통하여 도출된 국내 프로골프선수들의 심리 기술 요인은 각성 및 불안조절, 집중력, 목표설정, 자신감, 루틴(자동화), 자기관리의 총6개 요인이 도출되었다. 이를 기초로 5명의 전문가 회의를 통하여 심리기술이해, 목표설정, 자기관리, 루틴, 심상훈련, 자신감, 이완훈련, 주의집중, 심리기술종합로 구성된 총12주 프로골프선수들의 심리기술훈련 프로그램이 개발되었다. 이에 프로골프선수들의 심리기술훈련 프로그램은 다시 심리기술, Drive Shot, Putting의 골프수행능력 검사의 타당성 검증 절차를 통하여 최종 심리기술훈련 프로그램이 개발되었다.
CSF proteome analysis in multiple sclerosis patients by two‐dimensional electrophoresis (2008)

We found an overexpression of IgG free kappa light chain protein in both CIS and RR-MS patients, compared with control subjects and an increased expression of an apolipoprotein E isoform in RR-MS patients, compared with CIS and control groups. Our results confirm the presence of CSF proteome changes in MS patients. Future research should be aimed to investigate the role of these candidate CSF markers in larger cohorts of CIS and MS patients.
Human major histocompatibility complex class II invariant chain is expressed on the cell surface. (1990)

Class II major histocompatibility complex antigens are intracellularly associated with a nonpolymorphic polypeptide referred to as the invariant chain. Before the class II heterodimer appears on the cell surface, the invariant chain dissociates but it has so far been unclear as to whether or not a proportion of the invariant chain also appears on the plasma membrane. We describe a study with three monoclonal antibodies which recognize an extracytoplasmic determinant present on all forms of the invariant chain and use them to demonstrate its presence on the surface of the intact cells. The determinants recognized by two of the antibodies were found to be located within the 60 amino acids at the extreme C-terminal (extracytoplasmic) end of the invariant chain. The invariant chain-specific monoclonal antibody, VIC-Y1, was found to bind a determinant located between amino acids 1 and 73, which correspond to mainly cytoplasmic residues. Using the C-terminal specific antibodies, the number of antibody binding sites on the surface of two B lymphoma lines was estimated to be 10(5) per cell. The results of this study appear to resolve the highly disputed question of whether or not the invariant chain can appear as a plasma membrane protein. The results are discussed in the context of a possible role for the invariant chain in antigen processing and presentation.
Donnan Exclusion – Ion Exclusion Chromatography (1982)

Abstract A review of Donnan exclusion and ion exclusion chromatography is presented by extracting the phenomena of ‘‘pure'’ ionic exclusion by ion-exchangers from literature and by giving its theoretical background in terms of Donnan equilibrium distribution, not intending a complete collection of the literature on conventional ion-exclusion chromatography.
GPR56 and TG2: Possible Roles in Suppression of Tumor Growth by the Microenvironment (2007)

Metastasis is a complex process that involves multiple levels of cell-cell interaction. Among these interactions, tumor-stroma interactions are being actively investigated. Metastatic cells are hypothesized to show gene expression changes that contribute to their survival and growth at the distant site. Such changes could contribute either to enhancement of growth or to evasion of growth inhibition by the normal tissue environment thus allowing growth as metastases. Our recent report that tumors from highly metastatic melanoma derivatives express low levels of a suppressor of tumor progression, GPR56, is consistent with such a model. GPR56 associates in a complex with Gaq and the tetraspanin protein CD81. We further identified a ligand that interacts with GPR56 in the extracellular matrix (ECM) as TG2, a major crosslinking enzyme in the matrix. TG2 also binds to fibronectin and integrins and affects their cell adhesion functions. TG2 itself has been implicated in suppression of tumor progression; therefore TG2 might serve as a host defense against the invading metastatic cells. The highly metastatic cells may escape from this inhibition by down-regulation of GPR56. Much future work will be needed to test this hypothesis and further our understanding of metastasis in general.
Differentially Private Federated Learning: A Client Level Perspective (2017)

Federated learning is a recent advance in privacy protection. In this context, a trusted curator aggregates parameters optimized in decentralized fashion by multiple clients. The resulting model is then distributed back to all clients, ultimately converging to a joint representative model without explicitly having to share the data. However, the protocol is vulnerable to differential attacks, which could originate from any party contributing during federated optimization. In such an attack, a client's contribution during training and information about their data set is revealed through analyzing the distributed model. We tackle this problem and propose an algorithm for client sided differential privacy preserving federated optimization. The aim is to hide clients' contributions during training, balancing the trade-off between privacy loss and model performance. Empirical studies suggest that given a sufficiently large number of participating clients, our proposed procedure can maintain client-level differential privacy at only a minor cost in model performance.
Comprehensive, Quantitative Mapping of T Cell Epitopes in Gluten in Celiac Disease (2010)

Celiac disease is a genetic condition that results in a debilitating immune reaction in the gut to antigens in grain. The antigenic peptides recognized by the T cells that cause this disease are incompletely defined. Our understanding of the epitopes of pathogenic CD4(+ )T cells is based primarily on responses shown by intestinal T-cells in vitro to hydrolysates or polypeptides of gluten, the causative antigen. A protease-resistant 33-amino acid peptide from wheat alpha-gliadin is the immunodominant antigen, but little is known about the spectrum of T cell epitopes in rye and barley or the hierarchy of immunodominance and consistency of recognition of T-cell epitopes in vivo. We induced polyclonal gluten-specific T cells in the peripheral blood of celiac patients by feeding them cereal and performed a comprehensive, unbiased analysis of responses to all celiac toxic prolamins, a class of plant storage protein. The peptides that stimulated T cells were the same among patients who ate the same cereal, but were different after wheat, barley and rye ingestion. Unexpectedly, a sequence from omega-gliadin (wheat) and C-hordein (barley) but not alpha-gliadin was immunodominant regardless of the grain consumed. Furthermore, T cells specific for just three peptides accounted for the majority of gluten-specific T cells, and their recognition of gluten peptides was highly redundant. Our findings show that pathogenic T cells in celiac disease show limited diversity, and therefore suggest that peptide-based therapeutics for this disease and potentially other strongly HLA-restricted immune diseases should be possible.
Review of Mid- to High-Temperature Solar Selective Absorber Materials (2002)

This report describes the concentrating solar power (CSP) systems using solar absorbers to convert concentrated sunlight to thermal electric power. It is possible to achieve solar absorber surfaces for efficient photothermal conversion having high solar absorptance (a) for solar radiation and a low thermal emittance (e) at the operational temperature. A low reflectance (?'' 0) at wavelengths (?) 3 mm and a high reflectance (?'' 1) at l 3 mm characterize spectrally selective surfaces. The operational temperature ranges of these materials for solar applications can be categorized as low temperature (T< 100 C), mid-temperature (100 C< T< 400 C), and high-temperature (T> 400 C). High- and mid-temperature applications are needed for CSP applications. For CSP applications, the ideal spectrally selective surface would be low-cost and easy to manufacture, chemically and thermally stable in air at elevated operating temperatures (T= 500 C), and have a solar absorptance= 0.98 and a thermal emittance= 0.05 at 500 C.
Representation Learning Using Multi-Task Deep Neural Networks for Semantic Classification and Information Retrieval (2015)

Xiaodong Liu, Jianfeng Gao, Xiaodong He, Li Deng, Kevin Duh, Ye-yi Wang. Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2015.
Gamma delta T lymphocyte regeneration after T lymphocyte-depleted bone marrow transplantation from mismatched family members or matched unrelated donors. (1996)

The recovery of gamma delta T lymphocytes was studied in 31 recipients of T cell-depleted allogeneic bone marrow (BMT) to determine if the dynamics of reconstitution could be related to graft-versus-host disease (GVHD) or other complications of marrow transplantation. Two distinct patterns of regeneration were apparent. In 12 patients, there was a progressive rise in both the percentage and the absolute number of peripheral blood gamma delta T cells over the first year post-transplantation, but these increases never breached levels found in 14 healthy donors. Each of the 19 remaining patients had abnormally high proportions and numbers of gamma delta T cells on at least two occasions following transplantation. The clinical factor that best explained these observations was the frequency of intercurrent infections. Of 19 patients with abnormally increased percentages and numbers of gamma delta T lymphocytes, 18 had one or more episodes of confirmed viral or fungal infection, contrasted with only two of 12 in the comparison group (P < 0.001). There was no significant association of gamma delta T cell recovery patterns with the presence of GVHD (P = 0.33). We conclude that the recovery of gamma delta T lymphocytes after marrow transplantation may vary. Supranormal levels of this T cell subset are associated with infection and may contribute significantly to cellular immune defenses against fungal or viral disease.
siRNA Conjugates Carrying Sequentially Assembled Trivalent N-Acetylgalactosamine Linked Through Nucleosides Elicit Robust Gene Silencing In Vivo in Hepatocytes (2015)

Asialoglycoprotein receptor (ASGPR) mediated delivery of triantennary N-acetylgalactosamine (GalNAc) conjugated short interfering RNAs (siRNAs) to hepatocytes is a promising paradigm for RNAi therapeutics. Robust and durable gene silencing upon subcutaneous administration at therapeutically acceptable dose levels resulted in the advancement of GalNAc-conjugated oligonucleotide-based drugs into preclinical and clinical developments. To systematically evaluate the effect of display and positioning of the GalNAc moiety within the siRNA duplex on ASGPR binding and RNAi activity, nucleotides carrying monovalent GalNAc were designed. Evaluation of clustered and dispersed incorporation of GalNAc units to the sense (S) strand indicated that sugar proximity is critical for ASGPR recognition, and location of the clustered ligand impacts the intrinsic potency of the siRNA. An array of nucleosidic GalNAc monomers resembling a trivalent ligand at or near the 3' end of the S strand retained in vitro and in vivo siRNA activity, similar to the parent conjugate design. This work demonstrates the utility of simple, nucleotide-based, cost-effective siRNA-GalNAc conjugation strategies.
Why are proteins marginally stable? (2001)

Most globular proteins are marginally stable regardless of size or activity. The most common interpretation is that proteins must be marginally stable in order to function, and so marginal stability represents the results of positive selection. We consider the issue of marginal stability directly using model proteins and the dynamical aspects of protein evolution in populations. We find that the marginal stability of proteins is an inherent property of proteins due to the high dimensionality of the sequence space, without regard to protein function. In this way, marginal stability can result from neutral, non-adaptive evolution. By allowing evolving protein sub-populations with different stability requirements for functionality to complete, we find that marginally stable populations of proteins tend to dominate. Our results show that functionalities consistent with marginal stability have a strong evolutionary advantage, and might arise because of the natural tendency of proteins towards marginal stability.
Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation (2009)

The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. Salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). The expression of genes involved in carbon metabolism, cell growth, and phage structures was decreased. Transcriptome profiles of D. vulgaris responses to salt adaptation were compared with transcriptome profiles of D. vulgaris responses to salt shock (short-term NaCl exposure). Metabolite assays showed that glutamate and alanine accumulated under salt adaptation conditions, suggesting that these amino acids may be used as osmoprotectants in D. vulgaris. Addition of amino acids (glutamate, alanine, and tryptophan) or yeast extract to the growth medium relieved salt-related growth inhibition. A conceptual model that links the observed results to currently available knowledge is proposed to increase our understanding of the mechanisms of D. vulgaris adaptation to elevated NaCl levels.
Characterization of a human teratocarcinoma cell assay for inhibitors of metabolic cooperation (1985)

Although a Chinese hamster V79 cell-based assay for inhibitors of metabolic cooperation is currently available, the development of a human cell-based assay is desirable in order to avoid inappropriate extrapolation from animal cells to human cells. Cells derived from a human teratocarcinoma cell line (designated PA-1), which has a stable pseudodiploid karyotype and excellent in vitro growth properties, were used in a metabolic cooperation assay. The assay was based on the metabolic isolation of hypoxanthine-guanine phosphoribosyltransferase (HGPRT)-deficient variants in the presence of HGPRT-proficient cells and 6-thioguanine. Chemicals which inhibit the transfer of the lethal metabolite of 6-thioguanine from HGPRT-proficient to HGPRT-deficient cells will allow for recovery of the 6-thioguanine-resistant (HGPRT-deficient) cells. Chemicals tested included 12-O-tetradecanoylphorbol-13-acetate and related analogues phorbol-12,13-didecanoate, mezerein, and 4-phorbol-12,13-didecanoate. Concurring with results previously obtained in V79 cells, 12-O-tetradecanoylphorbol-13-acetate and phorbol-12,13-didecanoate strongly inhibited metabolic cooperation, whereas mezerein was moderately inhibitory and 4 alpha-phorbol-12,13-didecanoate was inactive. These cells thus hold promise as a human cell-based assay for inhibitors of metabolic cooperation.
Data Manipulating Functions in Parallel Processors and Their Implementations (1974)

This paper shows that there exists a class of functions called data manipulating functions (DMF's), in sequential as well as paralel processors. The circuits used to achieve these functions can be considered to form an independent functional block, called a data manipulator. A basic organization applicable to both sequential and parallel processors is then suggested. The main deviation of a parallel processor orgaization from the conventional Von Neumann organization is seen to be in the bit-slice (bis) manipulating functions. A comprehensive set of bis manipulating functions from the categories of permuting, replicating, spacing and masking is given. Implementation of the last category, the masking functions, is usually through a mask register by defining its content (mask pattern). It is found that for many operations the required mask patterns are periodic and/or monotonic. The upper bounds of generating these patterns are found. The techniques and designs of two data manipulators for the first three categories of DMF's (permuting, replicating, spacing) are given. Periodic and monotonic mask patterns are also used to help in implementing some of these functions. In addition, it is shown that the data manipulator designs presented in this paper are extremely flexible to suit the requirements of various parallel processors.
Robust denoising and moving shadows detection in traffic scenes (2001)

This paper presents a work we have done on the motion detection in the context of an outdoor traffic scene for visual surveillance purposes. Our motion detection algorithm is based both on background subtraction and three frame difference. We propose quite innovative solutions for denoising, blobs filling and shadow detection without exploiting any a priori knowledge. Actually, methods presented here have been fully setup only for the former technique. Target sequence is made of 8-bits grey level still images, taken at 30 fps. This application works off line at 8 fps on a 800 MHz Pentium III computer. 1.
Imaging of melanoma with L-131-labeled monoclonal antibodies. (1983)

Mouse monoclonal antibodies and Fab fragments specific for p97, a melanoma-associated antigen, were used to image metastatic human melanoma. Preclinical studies in athymic mice showed antigen-specific uptake in melanoma xenografts, and toxicity tests in rabbits gave no evidence for tissue damage after injection of up to 100 times the amount of antibody used in humans. Six patients received 1 mg labeled antibody, and one patient received 1 mg of labeled Fab. No. toxic side effects were observed. All of the six patients had positive scans, visualizing 22 of 25 (88%) of lesions larger than 1.5 cm. In tumors from two patients, greater uptake of p97-specific, versus control IgG and Fab, respectively, was documented by biopsy. Antibodies to mouse immunoglobulin appeared in three patients receiving 1 mg or more of radiolabeled mouse antibody.
Cloning and characterization of a Chlamydia trachomatis L3 DNA fragment that codes for an antigenic region of the major outer membrane protein and specifically hybridizes to the C- and C-related-complex serovars (1989)

Chlamydia trachomatis L3 DNA was cloned and expressed in lambda gt11. A recombinant plaque that expressed an antigen that reacted with rabbit polyclonal antichlamydial L3 serum and with two monoclonal antibodies specific for serovars L3 and I was selected from this Chlamydia genomic library. The beta-galactosidase Chlamydia fusion protein was purified by immunoaffinity chromatography and injected into mice to produce monoclonal antibodies. These monoclonal antibodies reacted by Western (immuno-) blot with both the fusion protein and the major outer membrane protein from purified L3 elementary bodies. The chlamydial DNA fragment was shown by DNA sequence analysis to be 168 base pairs in length and to correspond to the constant regions 1 and 2 and the variable segment 1 of the major outer membrane protein gene. The recombinant chlamydial DNA fragment hybridized under stringent conditions by Southern and dot blot analysis exclusively with the DNA from the C- and C-related-complex C. trachomatis serovars.