gebhart/patrepeval huggingface dataset:
Autoreactive CD8+ T-cell responses to human myelin protein-derived peptides. (1994)

Identification of the targets of autoreactive T cells is important for understanding the pathogenesis of many autoimmune diseases. In multiple sclerosis, myelin proteins are thought to be the targets of autoreactive T-cell responses. To date only major histocompatibility complex class II-restricted CD4+ T-cell responses to myelin proteins have been investigated. In the present study, the ability of self peptides derived from human myelin proteins to induce autoreactive CD8+ T-cell responses has been assessed. Peptide sequences from human myelin basic protein (MBP), proteolipid protein (PLP), myelin-associated glycoprotein (MAG), and myelin oligodendrocyte glycoprotein have been identified that bind to and form stable complexes with HLA-A2. MBP 110-118, PLP 80-88, MAG 287-295, MAG 509-517, and MAG 556-564 were all able to induce peptide-specific HLA-A2-restricted CD8+ cytotoxic T-lymphocyte (CTL) responses in vitro in HLA-A2+ individuals. CTLs specific for MBP 110-118 and MAG 556-564 could recognize endogenously processed antigens presented by HLA-A2. CTL clones reactive to MBP 110-118 and MAG 556-564 produced tumor necrosis factor alpha and a subset of these clones also produced interferon gamma. These results demonstrate that (i) self peptides derived from human myelin proteins can induce autoreactive CD8+ CTLs and (ii) these CD8+ T cells produce cytokines thought to be important in mediating demyelinating disease. These studies provide an experimental approach for the assessment of CD8+ T-cell responses in such autoimmune diseases.
p16 INK4 Mutations and Altered Expression in Human Tumors and Cell Lines (1994)

Cell cycle arrest at the G(1) checkpoint allows completion of critical macromolecular events prior to S phase. Regulators of the G(1) checkpoint include an inhibitor of cyclin-dependent kinase, p16(INK4); two tumor-suppressor proteins, p53 and RB (the product of the retinoblastoma-susceptibility gene); and cyclin D1. Neither p16(INK4) nor the RB protein was detected in 28 of 29 tumor cell lines from human lung, esophagus, liver, colon, and pancreas. The presence of p16(INK4) protein is inversely correlated with detectable RB or cyclin D1 proteins and is not correlated with p53 mutations. Homozygous deletions of p16(INK4) were detected in several cell lines, but intragenic mutations of this gene were unusual in either cell lines or primary tumors. Transfection of the p16(INK4) cDNA expression vector into carcinoma cells inhibits their colony-forming efficiency and the p16(INK4) expressing cells are selected against with continued passage in vitro. These results are consistent with the hypothesis that p16(INK4) is a tumor-suppressor protein and that genetic and epigenetic abnormalities in genes controlling the G(1) checkpoint can lead to both escape from senescence and cancer formation.
A commented dictionary of techniques for genotyping (2001)

Several tools, differing in their technical and practical parameters, are available for the detection of point mutations as well as small deletions and insertions. In this article, a dictionary featuring over fifty methods for detection of mutation is presented. The distinguishing principle for each method is briefly explained. Sorting of and discussion on the methods give the reader a brief introduction to the field of genotyping.
Intranasal carbetocin reduces hyperphagia in individuals with Prader-Willi syndrome (2018)

ClinicalTrials.gov: NCT01968187FUNDING. The study was funded by Ferring Pharmaceuticals. Recruitment was aided by ongoing work in PWS performed through Eunice Kennedy Shriver National Institute of Child Health and Human Development grant U54 HD083211.
A patient homozygous for a mutation in the prothrombin gene 3??? -untranslated region associated with massive thrombosis (1997)

We describe the first reported case of a thrombophilia patient genetically homozygous for a recently described polymorphism in the 3'-UTR (untranslated region) of the prothrombin gene. It has previously been demonstrated that this genetic variant due to a G to A transition at nucleotide 20210 is common and associated with an almost threefold increased risk of venous thrombosis. This polymorphism was also shown to be associated with elevated plasma prothrombin (factor II) levels, which in itself was found to be a risk factor for venous thrombosis. The patient was a healthy young Mexican male who presented with a myocardial infarction and subsequent ileofemoral venous thrombosis and massive saddle pulmonary embolus. Testing done during his initial hospitalization suggested a congenital protein C deficiency. The patient was found to be homozygous for the prothrombin gene polymorphism as well as a carrier for factor V Leiden. This case strongly implies a clinically significant role for the factor II gene mutation in both arterial and venous thrombosis and demonstrates the need to perform diagnostic clotting based assays after resolution of acute thrombotic events. These findings further support the 'double hit' theory for thrombophilia in young patients.
Concentration of Circulating Rhodopsin mRNA in Diabetic Retinopathy (2004)

Diabetes mellitus is a major health problem throughout the world, and retinopathy is a serious and common complication of diabetes (1). Most individuals with diabetes will eventually develop diabetic retinopathy (DR). In the United States, up to 24 000 patients with diabetes become legally blind each year, and DR is the leading cause of blindness in adults 20–74 years of age (2). The United Kingdom Prospective Diabetes Study (UKPDS) showed that 39% of men and 35% of women had some degree of retinopathy at the time of diagnosis (3). With the incidence of diabetes mellitus increasing in many countries, the prevalence of DR as a major cause of blindness or visual impairment is also likely to increase. Factors influencing the development of retinopathy include type and duration of diabetes, degree of glycemic control, blood pressure, and serum lipids (3)(4)(5). Of these, duration of diabetes is the major factor related to the incidence of retinopathy.

Clinical trials such as the Diabetic Retinopathy Study (DRS) (6) and the Early Treatment Diabetic Retinopathy Study (ETDRS) (7) have shown that effective laser photocoagulation could reduce the loss of vision by 90%. To be effective, regular screening for DR is required. Current recommendations are for annual screening for DR (8). Although recent studies suggest that in the absence of risk factors such as insulin use or duration of diabetes >20 years, screening every 2 or 3 years is adequate in type 2 diabetes (9). Despite these guidelines, 30–50% of patients with diabetes still do not get any eye examinations (10). Screening for DR includes visual acuity assessment as well as fundal photographs through dilated pupils. This involves cooperation between various healthcare professionals, such as diabetologists, optometrists, general practitioners, and photographic screening clinics. Patient eye status is classified according to a scale …
Tyrosine phosphorylation of GAP and GAP-associated proteins in lymphoid and fibroblast cells expressing lck. (1991)

The Ras GTPase activating protein (GAP) is a strong candidate for the protein that links protein-tyrosine kinases to the Ras mitogenic pathway. GAP and two associated proteins, p62 and p190, were shown to be phosphorylated on tyrosine in the LSTRA thymoma cell line, in which the p56lck tyrosine kinase is overexpressed as a result of retroviral promoter insertion. In NIH3T3 fibroblasts expressing specific oncogenic and transformation-defective variants of p56lck, we found that the tyrosine phosphorylation of GAP complexes required both enzymatic activation and myristylation of p56lck, and correlated with lck transforming activity. The interaction between p62 and p190 from lck-transformed fibroblasts and GAP could be reconstituted in vitro using bacterial TrpE fusion proteins containing GAP Src homology 2 (SH2) domains. In vitro complex formation was insensitive to the prior denaturation of SH2 ligands, suggesting that SH2-binding sites are formed by linear peptide sequences. These results suggest that the tyrosine phosphorylation of GAP, and its interactions with SH2-binding proteins, may be involved in fibroblast transformation by activated lck, and may participate in signal transduction and cellular transformation in lymphoid cells.
Chiral separations in capillary electrophoresis using proteins as stereoselective binding agents (1997)

Proteins are receiving increased attention in capillary electrophoresis (CE) for use as ligands in chiral separations. This review examines the types of proteins that have been employed in CE for the analysis of chiral compounds and provides a summary of applications for such an approach. Several formats for this type of analysis are discussed, including methods that use immobilized proteins (i.e., affinity capillary electrochromatography and capillary gel affinity electrophoresis) or techniques that use proteins as running buffer additives (i.e., affinity capillary electrophoresis). The role of various experimental factors in these separations are considered, and a comparison is made between the general analytical properties of CE systems that use immobilized versus solution-phase proteins.
Urban/suburban out-of-sight propagation modeling (1992)

A model for the calculation of the path loss characteristics of a direct sequence (DS) spread spectrum signal which occurs when a mobile user is out-of-sight of the base station due to building blockage is presented. The environments studied are common throughout the world. Results for the experiments in which a base station antenna was set at heights of 6.6 m or 3.3 m, while the mobile antenna was fixed at a height of 1.5 m are presented. The goal of the experiments was to demonstrate the use of broadband DS spread spectrum code-division multiple-access (CDMA) as an efficient means of communication.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antibody-Directed Enzyme Prodrug Therapy (1995)

Antibody-directed enzyme prodrug therapy (ADEPT) is a new approach to the treatment of solid cancers. In ADEPT, an antibody (or antibody fragment) is conjugated to an enzyme and is used to localise the enzyme at the site of the tumour. Once localised, the enzyme is used to activate a noncytotoxic prodrug to an active cytotoxic form. Therapy can proceed in either 2 or 3 phases. In the 2-phase system, the nonlocalised unbound antibody-enzyme conjugate is allowed to clear naturally from the body, and then the prodrug is administered. In the 3-phase system, clearance of unbound conjugate is accelerated by a ‘clearance’ antibody.
CD3/Ti gamma A: a functional gamma -receptor complex expressed on human peripheral lymphocytes. (1988)

We have recently developed a mAb designated anti-Ti gamma A, which was found to immunoprecipitate from the well characterized CD3+ TCR alpha/beta- F6C7 fetal clone a CD3-associated disulfide-linked gamma-glycoprotein. This antibody recognizes approximately 3% of adult peripheral lymphocytes and delineates a CD2+ CD3+ TCR alpha/beta- CD4- NKH1- subset where expression of CD8 appears to vary widely from one individual to another. In the present study, we have used anti-Ti gamma A mAb to assess whether gamma-chains expressed on these adult lymphocytes are used as functional R. The two activities which have been associated thus far with TCR gamma+ cells, that is, IL-2-dependent proliferation and non-MHC-restricted cytotoxicity, were investigated here by using either resting or activated Ti gamma A+ lymphocytes. On the resting state, these cells (which appear as a very homogeneous population of granular lymphocytes) mediate little if any NK activity that could not be augmented by anti-Ti gamma A mAb. In contrast, after initial stimulation by PHA plus rIL-2 and subsequent culture in the presence of IL-2, activated Ti gamma A+ lymphocytes were strongly lytic against a series of conventional NK target cell lines. This cytotoxic function was either blocked or enhanced by anti-Ti gamma A mAb, depending upon experimental conditions. With respect to proliferation, it was possible to induce responses of resting Ti gamma A+ lymphocytes with antibody-coated CNBr beads only in the presence of exogenous IL-2, whereas, in culture, the same cells proliferated directly and secreted IL-2 after treatment by anti-Ti gamma A beads. Taken together, these data demonstrate that a major subset of circulating CD3+ TCR alpha/beta- lymphocytes use protein products of T cell gamma rearranging genes as functional R structures.
Principles and Practice of Clinical Pediatrics (1987)

Principles and Practice of Clinical Pediatrics is a primary care textbook written for office-based physicians, nurses, and students. The 107 chapters are divided into seven sections, including well-child care, assessing signs and symptoms, the ill or injured child, developmental disabilities, behavior problems, the primary care physician and the subspecialist, and talking with parents. The most unique aspect of this book is its section on assessing signs and symptoms. Common signs and sympcoms of illness are presented, first with a differential diagnosis, followed by a discussion of the differential diagnosis and recommendations for data gathering. An algorithmic decision tree is formulated for each sign and symptom, along with a discussion of the algorithm. This approach works well for most topics. However, for some topics the approach leads to fragmentation and redundancy; otitis media is partially discussed in the signs and symptoms chapter on earache and is then discussed in more detail
<title><emph type="1">f</emph>-information measures in medical image registration</title> (2001)

A much-used measure for registration of three-dimensional medical images is mutual information, which originates from information theory. However, information theory offers many more measures that may be suitable for image registration. Such measures denote the divergence of the joint grey value distribution of two images from the joint distribution for complete independence of the images. This paper compares the performance of mutual information as a registration measure with that of other information measures. The measures are applied to rigid registration of clinical PET/MR and MR/CT images, for 35 and 41 image pairs respectively. An accurate gold standard transformation is available for the images, based on implanted markers. Both registration performance and accuracy of the measures are studied. The results indicate that some information measures perform very poorly for the chosen registration problems, yielding many misregistrations, even when using a good starting estimate. Other measures, however, were shown to produce significantly more accurate results than mutual information.
Bacteriophages and their implications on future biotechnology: a review (2012)

Recently it has been recognized that bacteriophages, the natural predators of bacteria can be used efficiently in modern biotechnology. They have been proposed as alternatives to antibiotics for many antibiotic resistant bacterial strains. Phages can be used as biocontrol agents in agriculture and petroleum industry. Moreover phages are used as vehicles for vaccines both DNA and protein, for the detection of pathogenic bacterial strain, as display system for many proteins and antibodies. Bacteriophages are diverse group of viruses which are easily manipulated and therefore they have potential uses in biotechnology, research, and therapeutics. The aim of this review article is to enable the wide range of researchers, scientists, and biotechnologist who are putting phages into practice, to accelerate the progress and development in the field of biotechnology.
Network Configuration Protocol (NETCONF) (2011)

The Network Configuration Protocol (NETCONF) defined in this document
provides mechanisms to install, manipulate, and delete the
configuration of network devices. It uses an Extensible Markup
Language (XML)-based data encoding for the configuration data as well
as the protocol messages. The NETCONF protocol operations are realized
as remote procedure calls (RPCs). This document obsoletes RFC 4741.
[STANDARDS-TRACK]
Therapeutic cancer vaccines: are we there yet? (2010)

Enthusiasm for therapeutic cancer vaccines has been rejuvenated with the recent completion of several large, randomized phase III clinical trials that in some cases have reported an improvement in progression free or overall survival. However, an honest appraisal of their efficacy reveals modest clinical benefit and a frequent requirement for patients with relatively indolent cancers and minimal or no measurable disease. Experience with adoptive cell transfer-based immunotherapies unequivocally establishes that T cells can mediate durable complete responses, even in the setting of advanced metastatic disease. Further, these findings reveal that the successful vaccines of the future must confront: (i) a corrupted tumor microenvironment containing regulatory T cells and aberrantly matured myeloid cells, (ii) a tumor-specific T-cell repertoire that is prone to immunologic exhaustion and senescence, and (iii) highly mutable tumor targets capable of antigen loss and immune evasion. Future progress may come from innovations in the development of selective preparative regimens that eliminate or neutralize suppressive cellular populations, more effective immunologic adjuvants, and further refinement of agents capable of antagonizing immune check-point blockade pathways.
Study on mechanism of formaldehyde-induced DNA breakage and repair (2005)

The Formaldehyde-induced DNA breakage, its mechanism and repair was studied with single cell gel electrophoresis (SCGE) in the experiment. The results showed that formaldehyde could induce DNA breakage at low concentration(P0.01); the breakage could be inhibited markedly by mannitol, DMSO and SOD, which were the scavenger of ·OH and O~(.-)_2(P0.01). But the mannitol and DMSO was more powerful than SOD. It concluded that formaldehyde could assuredly induce DNA breakage through ROS, and the breakage could be repaired completely in 90 minutes.
Production of poly(3-hydroxybutyric acid) by recombinantEscherichia colistrains: genetic and fermentation studies (1995)

A number of Escherichia coli strains including K12, B, W, XL1-Blue, DH5 alpha, HB101, JM109, and C600 were transformed with the stable high-copy-number plasmid pSYL105 containing the Alcaligenes eutrophus polyhydroxyalkanoic acid biosynthesis genes, and were subsequently compared for their ability to synthesize and accumulate poly(3-hydroxybutyric acid) (PHB). The rate of PHB synthesis, the extent of PHB accumulation, and PHB yield from glucose varied considerably from one strain to another. Strains XL1-Blue and B harboring pSYL105 synthesized PHB at the highest rate to a final concentration of ca. 7 g/L in complex medium containing 20 g glucose/L. With an aim to reduce the cost of the medium, the effect on PHB accumulation of supplementing a defined medium with complex nitrogen sources was examined. A PHB concentration of 81 g/L could be obtained in 41 h from a pH-stat fed-batch culture of XL1-Blue(pSYL105) in a semidefined medium. When the availability of acetyl-CoA was increased by supplementing the medium with complex nitrogen sources, amino acids, or oleic acid, PHB synthesis by recombinant E. coli was enhanced.
Detection ofStaphylococcus aureusBiofilm on Tampons and Menses Components (2003)

Culturing has detected vaginal Staphylococcus aureus in 10%-20% of women. Because growth mode can affect virulence expression, this study examined S. aureus-biofilm occurrence in 44 paired-tampon and vaginal-wash-specimens from 18 prescreened women, using fluorescent in situ hybridization (FISH). All 44 specimens were also analyzed for S. aureus by standard culturing on mannitol salt agar, which produced positive results for 15 of the 44 specimens. FISH detected S. aureus cells in all 44 specimens, and S. aureus biofilm was observed in 37 of the 44 specimens. Independent confirmation of the presence of S. aureus in specimens from all 18 women was also obtained by amplification, via polymerase chain reaction, of an S. aureus-specific nuclease gene. The results of this study demonstrate that S. aureus biofilm can form on tampons and menses components in vivo. Additionally, the prevalence of vaginal S. aureus carriage may be more prevalent than what is currently demonstrated by standard culturing techniques.
Potentiating effects of nonactive/active vitamin D analogues and ketoconazole in parathyroid cells (2006)

The results support the idea that a non-1alpha-hydroxylated vitamin D analogue may elicit vitamin D receptor (VDR) effects in 1alpha-hydroxylase expressing parathyroid tumour cells. Further studies are warranted to elucidate whether precursor vitamin D analogues as well as inhibitors of 24-hydroxylase present therapeutic alternatives in patients suffering from HPT.
Identification of squash leaf curl virus (Egyptian isolate). (2009)

Squash leaf curl virus (SqLCV-Eg) was isolated from whiteflies-infected squash (Cucurbita pepo cv. Eskandrani) plants growing in Nubaria, El-Behera Governorate. The infected plants exhibited leaf curling, leaf crinkle, leaf narrowing, blistering, chlorosis, fruit malformation and stunting. SqLCVEg reacted positively with polyclonal antibodies specific to SqLCV using DAS-ELISA. It was transmitted by both syringe injection and whiteflies with transmission efficiency of about 35% and 100%, respectively. SqLCV-Eg isolate was transmitted from naturally infected squash to different species belonging to families Cucurbitaceae, Fabaceae, Solanaceae and Chenopodiaceae. SqLCV had TIP of 60oC, DEP of 10 and LIV of about 8 days. Electron micrograph of the partially purified -6 SqLCV revealed the presence of monomer and dimmer gemini particles with dimensions of 22 nm and 20 X 30 nm, respectively when negatively stained with uranyl acetate. Using degenerate oligonucleotide primers, the viral coat protein gene was amplified successfully by PCR, producing ~ 550 bp fragment from squash infected plants. The viral genome was detected by specific DNA probe using dot blot hybridization technique. Comparative nucleotide sequence analysis showed a similarity of 99% between SqLCV-Eg and other isolates.
The identification of a conserved binding motif within human papillomavirus type 16 E6 binding peptides, E6AP and E6BP. (1998)

A 16-mer peptide library was screened using the yeast two-hybrid system to identify peptides which specifically interact with the human papillomavirus type 16 (HPV-16) E6 protein. Four different peptides were identified, three of which contained an E-L-L/V-G motif. A fifth E6 binding peptide, derived from the putative tumour suppressor protein tuberin, was identified during a two-hybrid screen of a HeLa cDNA expression library. This peptide contained a D-I-L-G motif. Homology to the peptides was found within the E6 binding proteins E6-AP and E6-BP. A synthetic peptide containing the ELLG motif blocked the interaction of E6 with both E6-AP and E6-BP. The data suggest that E6 interacts through a structurally similar binding domain present within a number of cellular proteins.