gebhart/patrepeval huggingface dataset:
Identification of Subdominant Cytotoxic T Lymphocyte Epitopes Encoded by Autologous HIV Type 1 Sequences, Using Dendritic Cell Stimulation and Computer-Driven Algorithm (2000)

Conventional analysis of the cytotoxic T lymphocyte (CTL) response to HIV-1 may underestimate the true breadth of CTL epitopes recognized. This underestimation could be due to several reasons, including (1) the use of laboratory-adapted stains of HIV or consensus sequences, which would lead to the identification of only highly conserved epitopes, (2) the use of EBV-transformed B cells (B-LCLs) and vaccinia virus constructs in standard assays that may obscure low level CTL responses due to high EBV or vaccinia reactivity, and (3) relatively insensitive assays wherein PBMCs instead of professional APCs are used to stimulate CTL responses. To address these problems, we first identified an immunodominant HLA-B7-restricted CTL epitope, by standard cloning methods, in a long-term nonprogressor (LTNP). To determine whether the patient had CTLs specific for autologous viral sequences other than the dominant epitope, proviral DNA was cloned and sequenced. A matrix-based epitope algorithm (EpiMatrix) was used to identify the top 2% of peptides from the viral sequences with the highest likelihood of binding to HLA-B7. These 55 peptides were synthesized and tested for HLA-B7 binding in a T2/B7 cell line; 10 peptides were able to stabilize HLA-B7 on the cell surface. By using peptide-pulsed autologous dendritic cells as a more sensitive method of CTL stimulation, we found three additional subdominant CTL epitopes.
Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages (2002)

The complete nucleotide sequence of ssRNA phage AP205 propagating in Acinetobacter species is reported. The RNA has three large ORFs, which code for the following homologues of the RNA coliphage proteins: the maturation, coat and replicase proteins. Their gene order is the same as that in coliphages. RNA coliphages or Leviviridae fall into two genera: the alloleviviruses, like Q(beta), which have a coat read-through protein, and the leviviruses, like MS2, which do not have this coat protein extension. AP205 has no read-through protein and may therefore be classified as a levivirus. A major digression from the known leviviruses is the apparent absence of a lysis gene in AP205 at the usual position, overlapping the coat and replicase proteins. Instead, two small ORFs are present at the 5' terminus, preceding the maturation gene. One of these might encode a lysis protein. The other is of unknown function. Other new features concern the 3'-terminal sequence. In all ssRNA coliphages, there are always three cytosine residues at the 3' end, but in AP205, there is only a single terminal cytosine. Distantly related viruses, like AP205 and the coliphages, do not have significant sequence identity; yet, important secondary structural features of the RNA are conserved. This is shown here for the 3' UTR and the replicase-operator hairpin. Interestingly, although AP205 has the genetic map of a levivirus, its 3' UTR has the length and RNA secondary structure of an allolevivirus. Sharing features with both MS2 and Q(beta) suggests that, in an evolutionary sense, AP205 should be placed between Q(beta) and MS2. A phylogenetic tree for the ssRNA phages is presented.
Cytogenetics and Molecular Genetics of Malignant Gliomas and Medulloblastoma (1990)

Malignant gliomas and medulloblastomas which are the most common primary malignant brain tumours of adult and children, respectively, resemble other neurogenic tumours as they frequently contain gene amplification and show non-random loss of specific chromosomal regions. In gliomas the gene which is most often amplified, is the epidermal growth factor receptor gene. In many cases the gene is rearranged as well, producing abnormally small epidermal growth factor receptor proteins. More than 80% of tumours have lost chromosome 10 and losses of 9p13, 17p and 22 occur in subgroups of cases. 17p loss is associated with point mutations of the p53 gene, but the relevant genes in the other chromosomal regions remain to be identified. For medulloblastoma the most frequent chromosomal abnormality is i(17q). Whether or not p53 gene mutations are the targets of 17p losses in these tumours remains to be determined. Approximately 5% of medulloblastoma biopsies contain gene amplification, although the incidence in medulloblastoma cell lines is more than 80%. c-myc is the gene which is most frequently amplified in this tumour type. The relationship of these various molecular genetic abnormalities to the biology of the tumours and the course of the patients remains largely unexplored.
Identification of pleckstrin-homology-domain-containing proteins with novel phosphoinositide-binding specificities (2000)

The second messenger phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] is generated by the action of phosphoinositide 3-kinase (PI 3-kinase), and regulates a plethora of cellular processes. An approach for dissecting the mechanisms by which these processes are regulated is to identify proteins that interact specifically with PtdIns(3,4,5)P3. The pleckstrin homology (PH) domain has become recognized as the specialized module used by many proteins to interact with PtdIns(3,4,5)P3. Recent work has led to the identification of a putative phosphatidylinositol 3,4,5-trisphosphate-binding motif (PPBM) at the N-terminal regions of PH domains that interact with this lipid. We have searched expressed sequence tag databases for novel proteins containing PH domains possessing a PPBM. Surprisingly, many of the PH domains that we identified do not bind PtdIns(3,4,5)P3, but instead possess unexpected and novel phosphoinositide-binding specificitiesin vitro. These include proteins possessing PH domains that interact specifically with PtdIns(3,4)P2 [TAPP1 (tandem PH-domain-containing protein-1) and TAPP2], PtdIns4P [FAPP1 (phosphatidylinositol-four-phosphate adaptor protein-1)], PtdIns3P [PEPP1 (phosphatidylinositol-three-phosphate-binding PH-domain protein-1) and AtPH1] and PtdIns(3,5)P2 (centaurin-β2). We have also identified two related homologues of PEPP1, termed PEPP2 and PEPP3, that may also interact with PtdIns3P. This study lays the foundation for future work to establish the phospholipid-binding specificities of these proteins in vivo, and their physiological role(s).
Remote Fiber-Optic Raman Analysis of Xylene Isomers in Mock Petroleum Fuels Using a Low-Cost Dispersive Instrument and Partial Least-Squares Regression Analysis (1995)

We report the use of a low-cost dispersive Raman instrument with charge-coupled-device (CCD) detection, near-infrared (near-IR) diode laser excitation, and remote fiber-optic sampling to analyze mock petroleum samples which contain high benzene, toluene, ethylbenzene, and xylene (BTEX) concentrations. Partial least-squares regression (PLSR) analysis is used to correlate the individual xylene isomer concentrations to the Raman spectral signal without the use of an internal standard. The resulting PLSR model is used to predict the concentration of individual xylene isomers, and it is found that, at a 95% confidence level, samples containing between ∼1.5 and 15% xylene isomer can be predicted to better than ±0.1% for meta- and para-xylene, and to ±0.15% for ortho-xylene. The use of PLS model leverage plots provides a facile statistical method by which to identify Raman spectra which involve diode laser mode hops or significant fiber backscatter.
The Amino‐Acid Sequence of Chicken Fast‐Skeletal‐Muscle Troponin I (1978)

The amino acid sequence of troponin I from chicken breast and leg muscle has been determined using tryptic and CNBr peptides. The protein contains 182 residues and has a molecular weight of 21136. The N-terminus is blocked and is probably acetylated. 35 of the residues have acidic and 45 have basic side chains giving an overall net positive charge of 9. The CNBr peptides from both breast and leg troponin I have been shown to be identical and no heterogeneity has been found in the tryptic peptides isolated from a mixture of the two proteins. It may thus be taken that the two proteins are identical. Comparison with the sequence of troponin I from rabbit fast skeletal muscle shows strong homology with 34 differences out of 182 residues. The major difference is in a deletion of three residues, from 152 to 154, in the rabbit protein.
Theoretical model for predicting rates of nitrosamine and nitrosamide formation in the human stomach (1988)

A mathematical model has been developed to estimate the rates of formation of nitrosamines and nitrosamides in the human stomach, under a variety of physiological and environmental conditions. The model combines a detailed description of the kinetics of N-nitrosation with mass balance equations which account for gastric emptying, dilution and absorption. The simulations were based on a typical schedule of dietary inputs, and included variations in gastric pH and in the volume of the stomach contents over a 24-h period. Consideration of these transient phenomena allowed a distinction to be made between amines or amides present in the diet and in gastric or salivary secretions. A comparison of the theoretical results with available data on the nitrosation of proline suggests that the model accurately predicts gastric rates of nitrosamine formation under control conditions, and correctly represents the strong catalytic effects of thiocyanate and the inhibitory effects of ascorbic acid or ascorbate ion. The results further suggest that nitrosoproline (NPro) excretion is not an accurate index of gastric nitrosation under physiological (low-dose) conditions, even when corrections are made for dietary intake of NPro. The predicted rates of formation of N-nitrosodimethylamine (NDMA), even for a diet high in dimethylamine, were found to be a factor of approximately 10(2) to 10(3) lower than published estimates of the dietary exposure to preformed NDMA. Thus, these findings do not support the hypothesis that gastric formation of NDMA from dietary dimethylamine poses a serious additional health risk. The results are presented in a graphical and tabular form which makes it possible to readily estimate the rates of formation of other nitrosamines or nitrosamides in the stomach, under various assumed conditions.
Zn–In–O based thin‐film transistors: Compositional dependence (2008)

Abstract The compositional dependence of sputter‐deposited Zn–In–O (ZIO) film properties and the TFT performance were studied by means of a combinatorial technique. Both the characteristics of ZIO‐TFTs and the ZIO film properties are very sensitive to the Zn:In ratio. The best TFT performances are obtained at Zn:In ∼60:40 at%, where the saturation mobility ( μ sat ), subthreshold swing (S.S.), on–off current ratio ( I on / I off ), and threshold voltage ( V th ) are 26.5 cm 2 /V s, 0.24 V/dec., 10 10 , and +2 V, respectively. The TFT characteristics peak at this compositional ratio. Specifically, μ sat , I on / I off and V th reach maximum, while S.S. reaches minimum at this ratio. The air stability of ZIO‐TFTs was also examined for active channel layers with different Zn:In ratios, which clarified that the TFTs with high stability are obtained around the same composition ratio where the best characteristics are obtained. It was confirmed by X‐ray diffraction and transmission electron microscopy that the ZIO films with this composition ratio have amorphous structure. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Using Agents for Generation and Maintenance of Mediators in a Data Integration System on the Web. (2001)

In this paper we present a system for data integration on the web, where an XML-based mediator plays a key role providing a homogeneous view of different data sources. One novelty of our approach is that we also propose solutions for the problems of generation and maintenance of mediators. Observe that, in dynamic environments, such as the Web, individual data sources may change not only their data but also their schemas. As a result, whenever a local schema changes, the mediator needs to be updated to reflect the modifications. The system uses agents to support mediator generation and maintenance. We specify a set of tasks that must be performed by the agents in order to support these two tasks. In our approach, we use correspondence assertions for specifying the semantics of XML-based mediators. We also discuss how this high-level specification of the mediator can be used to automate the generation and maintenance of mediators. 1.
Serum 25-hydroxyvitamin D in erythropoietic protoporphyria (2008)

This is the first report of significant levels of vitamin D deficiency and insufficiency in a large cohort of patients with a photodermatosis. Such individuals are at risk of associated adverse events. In future, clinicians should consider monitoring 25-hydroxyvitamin D levels and instigating oral supplementation or dietary advice if appropriate.
Specific Induction of Granzyme B in Human B Cells by Viral Antigens. (2008)

Abstract B cells are not currently known to produce granzyme B (GrB) in (patho-) physiological settings. We recently reported that B-chronic lymphocytic leukemia cells and normal B cells treated with interleukin-21 (IL-21) and anti-B cell receptor antibodies (anti-BCR) produce functional GrB. Here we demonstrate for the first time that viral antigens can also induce specific peripheral B lymphocytes to produce and secrete substantial amounts of active GrB. Using FACS, ELISpot, immunofluoresence and western blot we show that B cells from subjects recently vaccinated against tick-borne encephalitis virus (TBEV) but not unvaccinated subjects respond to viral TBEV antigens with GrB secretion in a dosedependent manner. This response is direct and occurs only in the presence of co-activation with certain IL-2 family cytokines such as IL-21. Similar results were found with other viruses including hepatitis B and rabies. GrB production in B cells required activation of JAK1 and STAT3 and inhibition of JAK1 by pyridone 6 completely abrogated GrB induction by viral antigens or anti-BCR. Our findings suggest GrB secretion by B cells may be part of a novel, anti-viral immune response mechanism. Further studies will elucidate whether or not granzyme B-secreting B cells can act as cytotoxic cells towards virus-infected cells.
Proliferation and differentiation of rat neuroepithelial precursor cells in vivo (1988)

Important features of adult neuronal number, location, and type are a consequence of early embryonic events that occur before neurons have differentiated. We have measured cell number during embryogenesis of the rat CNS. Markers that are expressed in the proliferating neuronal precursor are required to study the mechanisms controlling their proliferation and differentiation. By applying immunohistochemistry, fluorescence-activated cell sorting, and 3H-thymidine auto-radiography to dissociated rat CNS cells, we show that the monoclonal antibody Rat 401 recognizes a cell population with proliferative, temporal, and quantitative features expected of neuronal precursors.
Increasing the oscillation frequency of strong magnetic fields above 101 kHz significantly raises peripheral nerve excitation thresholds (2012)

The probability of PNS due to brief biphasic time-varying sinusoidal magnetic fields with magnetic excursions up to 0.4 T is shown to decrease significantly at and above 101 kHz. This phenomenon may have particular uses in dynamic scenarios (e.g., cardiac imaging) and in studying processes with short decay times (e.g., electron paramagnetic resonance imaging, bone and solids imaging). The study suggests the possibility of new designs for human and preclinical MRI systems that may be useful in clinical practice and scientific research.
Bioengineered Three-Layered Robust and Elastic Artery Using Hemodynamically-Equivalent Pulsatile Bioreactor (2008)

A robust and elastic small-diameter artery was engineered from three types of vascular cells using the physiological pulsatile bioreactor.
Antiproteases and Antioxidants: Strategies for the Pharmacologic Prevention of Lung Destruction (1986)

Proteolysis and oxidation are processes which play a central role in the pathogenesis of emphysema. Hereditary factors, including alpha 1-antitrypsin deficiency, and environmental exposures, such as to cigarette smoke, coal dust and bacteria, are associated with a high risk for the development of emphysema through their interactions with proteolytic and oxidative processes within the lung. Because of the key roles of oxidation and proteolysis, reasonable strategies for the prevention of lung destruction in high-risk individuals include such therapeutic interventions as augmentation of lung levels of alpha 1-antitrypsin and the administration of antioxidants.
Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium (2005)

Several human pathogens and the plant pathogen Agrobacterium tumefaciens use a type IV secretion system for translocation of effector proteins into host cells. How effector proteins are selected for transport is unknown, but a C-terminal transport signal is present in the proteins translocated by the A. tumefaciens VirB/D4 type IV secretion system. We characterized this signal in the virulence protein VirF by alanine scanning and further site-directed mutagenesis. The Cre recombinase was used as a reporter to measure the translocation efficiency of Cre-Vir fusions from A. tumefaciens to Arabidopsis. The data unambiguously showed that positive charge is an essential characteristic of the C-terminal transport signal. We increased the sensitivity of this translocation assay by modifying the Cre-induced readout in host cells from kanamycin resistance to GFP expression. This improvement allowed us to detect translocation of the VirD2 relaxase protein in the absence of transferred DNA, showing that attachment to the transferred DNA is not essential for transport by the VirB/D4 system. We also found another translocated effector protein, namely the VirD5 protein encoded by the tumor-inducing plasmid. According to secondary structure predictions, the C termini of all VirB/D4-translocated proteins identified so far are unstructured; however, they contain a characteristic hydropathic profile. Based on sequence alignments and mutational analysis of VirF, we conclude that the C-terminal transport signal for recruitment and translocation of effector proteins by the A. tumefaciens VirB/D4 system is hydrophilic and has a net positive charge with a consensus motif of R-X(7)-R-X-R-X-R-X-X(n)>.
Breast metastases after bone marrow transplantation for rhabdomyosarcoma. (1991)

Two adolescent females with metastatic alveolar rhabdomyosarcoma underwent intensive chemoradiotherapy and bone marrow transplantation, one autologous and one allogeneic. Recurrence was detected in the breasts of both patients, the first at autopsy and the other as the only site of treatment failure. Breast masses after bone marrow transplantation should be thoroughly investigated for metastatic disease in patients with rhabdomyosarcoma.
Emerging research logic devices (2005)

Presents an an assessment of new field-effect transistor, resonant tunnel device, single-electron transistor and quantum cellular automata technologies. The goal of this article is to provide technical assessments of new logic technologies. We attempt to "cast a broad net" to gather in one place alternative concepts for logic that would, if successful, substantially extend the International Technology Roadmap for Semiconductors (ITRS) beyond CMOS. The discussions provide some detail regarding device operation principles, advantages, challenges, maturity, and current and projected performance. The scaling of CMOS device and process technology, as it is known today, is projected to continue (7-nm physical channel length) by 2019. The grand challenge, then, is to invent and develop one or more new technologies that will extend the scaling of information-processing technologies through multiple generations beyond 2019. Such new technologies must meet certain fundamental requirements and possess certain compelling attributes to justify the very substantial investments that are necessary to build a new infrastructure.
Structural model of porcine factor VIII and factor VIIIa molecules based on scanning transmission electron microscope (STEM) images and STEM mass analysis. (1990)

Porcine plasma factor VIII (fVIII) molecules are heterodimers composed of a 76,000-mol wt light chain (-A3-C1-C2) and a heavy chain ranging in molecular weight from 82,000 (A1-A2) to 166,000 (A1-A2-B). Proteolytic activation of fVIII by thrombin results in fVIIIa heterotrimers lacking B domains (A1, A2, A3-C1-C2). In this study, immunoaffinity purified fVIII was further fractionated by mono S or mono Q chromatography to prepare heterodimers containing a light chain and an A1-A2-B heavy chain (fVIII 166/76) or an A1-A2 heavy chain (fVIII 82/76). Mass analysis of scanning transmission electron microscopic (STEM) images of fVIII 166/76 indicated that heterodimers (mass 237 +/- 20 kD) had irregularly globular core structures 10-12 nm across, and frequently displayed a diffuse, occasionally globular to ovoid satellite structure extending 5-14 nm from the core, and attached to it by a thin stalk. Factor VIII 82/76 molecules (mass 176 +/- 20 kD) had the same core structures as fVIII 166/76 molecules, but lacked the satellite structure. These findings indicate that A1-A2 domains of heavy chains and the light chains of the fVIII procofactor molecule are closely associated and constitute the globular core structure, whereas the B domainal portion of heavy chains comprises the peripheral satellite appendage. Factor VIII core structures commonly displayed a finger-like projection near the origin of the B domainal stalk that was also a consistent feature of the free heavy chains (mass 128-162 kD) found in fVIII 166/76 preparations. Factor VIII light chain monomers (mass, 76 +/- 16 kD) were globular to c-shaped particles 6-8 nm across. These chains commonly possessed a v-shaped projection originating from its middle region, that could also be observed at the periphery of fVIII core molecules. Factor VIIIa preparations contained heterotrimers (mass 162 +/- 13 kD) that had the same dimensions as fVIII core structures, lacked the B domainal appendage, and sometimes possessed the same core features as fVIII molecules. Molecular species corresponding to heterodimers (mass, 128 +/- 13 kD) and unassociated subunit chains (40-100 kD) were also observed in fVIIIa preparations, suggesting that heterotrimers have an appreciable tendency to dissociate, a phenomenon that could explain the decay of fVIIIa activity after thrombin activation of fVIII.