gebhart/patrepeval huggingface dataset:
Sequences in the Cytoplasmic Tail of the Gibbon Ape Leukemia Virus Envelope Protein That Prevent Its Incorporation into Lentivirus Vectors (2001)

Pseudotyping retrovirus and lentivirus vectors with different viral fusion proteins is a useful strategy to alter the host range of the vectors. Although lentivirus vectors are efficiently pseudotyped by Env proteins from several different subtypes of murine leukemia virus (MuLV), the related protein from gibbon ape leukemia virus (GaLV) does not form functional pseudotypes. We have determined that this arises because of an inability of GaLV Env to be incorporated into lentivirus vector particles. By exploiting the homology between the GaLV and MuLV Env proteins, we have mapped the determinants of incompatibility in the GaLV Env. Three modifications that allowed GaLV Env to pseudotype human immunodeficiency virus type 1 particles were identified: removal of the R peptide (C-terminal half of the cytoplasmic domain), replacement of the whole cytoplasmic tail with the corresponding MuLV region, and mutation of two residues upstream of the R peptide cleavage site. In addition, we have previously proposed that removal of the R peptide from MuLV Env proteins enhances their fusogenicity by transmitting a conformational change to the ectodomain of the protein (Y. Zhao et al., J. Virol. 72:5392-5398, 1998). Our analysis of chimeric MuLV/GaLV Env proteins provides further evidence in support of this model and suggests that proper Env function involves both interactions within the cytoplasmic tail and more long-range interactions between the cytoplasmic tail, the membrane-spanning region, and the ectodomain of the protein.
Bone Marrow Stem Cells Prevent Left Ventricular Remodeling of Ischemic Heart Through Paracrine Signaling (2006)

In this study, we hypothesized that bone marrow stem cells (BMSCs) protect ischemic myocardium through paracrine effects that can be further augmented with preconditioning. In in vitro experiments, cell survival factors such as Akt and eNOS were significantly increased in BMSCs following anoxia. In the second series of experiments following coronary ligation in mice, left ventricles were randomly injected with the following: DMEM (G-1), BMSCs (G-2), and preconditioned BMSCs (G-3). Four days after myocardial infarction, BMSCs were observed within injured myocardium in G-2 and G-3. Apoptotic cardiomyocytes within periinfarct area were significantly reduced in G-3. Four weeks after myocardial infarction, smaller left ventricular (LV) dimension and increased LV ejection fraction were observed in G-3. Infarct area was significantly reduced in G-3. However, GFP+ cardiomyocytes were observed in low numbers within periinfarct area in G-2 and G-3. In conclusion, BMSCs secreted cell survival factors under ischemia, and they prevented apoptosis in cardiomyocytes adjacent to the infarcted area. Preconditioning of BMSCs enhanced their survival and ability to attenuate LV remodeling, which was attributable, in part, to paracrine effects.
Human endogenous retrovirus (HERV)‐K transcripts in germ cell and trophoblastic tumours (1998)

Prompted by the observation of retroviral particle formation in teratocarcinoma cell lines and the consistent finding of antibodies against Gag and Env proteins encoded by human endogenous retrovirus (HERV)-K genomes in the sera of patients with classical seminoma, we studied ovarian and testicular germ cell tumours, their precursor lesions, dysgenetic gonads, and trophoblast lesions for expression of HERV-K sequences by in situ hybridization using radioactive and non-radioactive probes. HERV-K transcripts were detected in all testicular and ovarian germ cell tumours with the exception of teratomas and spermatocytic seminomas. HERV-K expression was also common to testicular carcinoma in situ as well as gonocytes of dysgenetic gonads. Among gestational trophoblastic lesions, HERV-K expression was regularly found in choriocarcinomas, but not in molar lesions. The patterns of HERV-K expression suggest a common molecular pathogenesis of most germ cell tumour entities and malignant gestational trophoblastic disease. They furthermore support the concept of carcinoma in situ as a precursor lesion common to most testicular germ cell neoplasms. The detection of HERV-K gene products in body fluids and tissues may aid diagnosis and monitoring of germ cell tumours and related lesions.
Mass spectrometric characterization of a high-field asymmetric waveform ion mobility spectrometer (1998)

Ion mobility spectrometry (IMS) has become an important method for the detection of many compounds because of its high sensitivity and amenability to miniaturization for field-portable monitoring; applications include detection of narcotics, explosives, and chemical warfare agents. High-field asymmetric waveform ion mobility spectrometry (FAIMS) differs from IMS in that the electric fields are applied using a high-frequency periodic asymmetric waveform, rather than a dc voltage. Furthermore, in FAIMS the compounds are separated by the difference in the mobility of ions at high electric field relative to low field, rather than by compound to compound differences in mobility at low electric field (IMS). We report here the first cylindrical-geometry-FAIMS interface with mass spectrometry (FAIMS-MS) and the MS identification of the peaks observed in a FAIMS compensation voltage (CV) spectrum. Using both an electrometer-based-FAIMS (FAIMS-E) and FAIMS-MS, several variables that affect the sensitivity of ion detection were examined for two (polarity reversed) asymmetric waveforms (modes 1 and 2) each of which yields a unique spectrum. An increase in the dispersion voltage (DV) was found to improve the sensitivity and separation observed in the FAIMS CV spectrum. This increase in sensitivity and the unexpected dissimilarity in modes 1 and 2 suggest that atmospheric pressure ion focusing is occurring in the FAIMS analyzer. The sensitivity and peak locations in the CV spectra were affected by temperature, gas flow rates, operating pressure, and analyte concentration.
Plastic electronics based on semiconducting polymers (2002)

Plastic electronics are set to be one of the next applications of semiconducting polymers appearing on the market. The electronics are constructed from integrated plastic circuits (IPC) based on organic field effect transistors (OFETs). The aim of this technology is to create low cost electronics using inexpensive standard polymer technologies in combination with laser and/or printing technologies which allow mass production for low cost mass products like ident tags, electronic watermarks, smart cards, electronic labels. Although many improvements have been achieved during the last few years, numerous problems still must be solved. The authors present recent results for OFETs with conjugated polymers like polythiophenes as active semiconducting material. The performance of the OFETs strongly depends on the quality of the semiconducting layer, i.e. molecular ordering, homogeneity, purity and doping level. Several aspects of preparing OFETs with special emphasis on the effect of the properties of the semiconducting polymer on the transistor parameters are discussed.
A significant proportion of normal resting B cells are induced to secrete immunoglobulin through contact with anti‐receptor antibody‐activated helper T cells in clonal cultures (1988)

This report describes single-cell techniques to address the nature of a cellular interaction in which activated T lymphocytes stimulate small resting B cells to develop into antibody-forming cell clones in the absence of any surface immunoglobulin ligand or an antigen bridge. The cloned T helper cell line E9.D4 was stimulated with the anti-V beta 8 antibody F23.1 bound to the plastic of Terasaki 10-ul culture wells. When an excess of T helper lymphocytes was used (1,000 X-irradiated or 600 unirradiated, stimulated E9.D4 cells), 10-25% of B cells responded by antibody formation as judged by an enzyme-linked immunosorbent assay performed after 5 days of culture. When one of a very small number of B cells were present, the rate-limiting step to antibody-forming cell formation was the number of T cells present. Far fewer T cells sufficed for stimulation when culture trays were tilted to force T and B cells into proximity at the sulcus formed at the bottom edge of the culture wells. When T cell numbers were limiting, unirradiated T cells out-performed irradiated T cells. Some cell clones held for 7 days switched to IgG antibody production. E9.D4 supernatants were virtually ineffective in causing B cell stimulation, even when 3T3 filler cells were added to support cultures. The results suggest that cell contact, and perhaps conjugate formation, with a strongly activated T cell can cause changes in the adjacent resting B cells akin to those of Ig receptor cross-linking, following which a lymphokine flux (even one not involving IL 4 and 5) promotes antibody-forming cell development.
Single-electron transistors in heterostructure nanowires (2003)

Semiconductor-based single-electron transistors have been fabricated using heterostructure nanowire growth, by introducing a double barrier of InP into InAs nanowires. From electrical measurements, we observe a charging energy of 4 meV for the approximately 55 nm diameter and 100 nm long InAs islands between the InP barriers. The Coulomb blockade can be periodically lifted as a function of gate voltage for all devices, which is a typical signature of single-island transistors. Homogeneous InAs nanowires show no such effect for the corresponding voltage ranges.
Imaging cyclophosphamide-induced intramedullary apoptosis in rats using 99mTc-radiolabeled annexin V. (2001)

Radiolabeled annexin V can be used to detect and directly quantify the degree of intramedullary and splenic apoptosis in a noninvasive fashion using current clinical radionuclide imaging equipment. Annexin V imaging may be useful clinically in the diagnosis and management of myelodysplastic syndrome.
Effect of threading dislocations on mobility in selectively doped heterostructures grown on Si substrates (1994)

We studied the effect of threading dislocation scattering on the mobility of a two-dimensional electron gas. To verify our theory, we grew Si-doped AlGaAs/GaAs selectively doped heterostructures with different dislocation densities by changing the number of thermal annealing cycles. The theory agreed well with our experimental results. Previous work on high electron mobility transistors (HEMTs) fabricated on Si indicated that the device characteristics are insensitive to the dislocation density. Our theory states that the room temperature mobility reduction by dislocations with a density below 108 cm−3 does not affect HEMT device performance, which is consistent with empirically known results.
Immunogenicity and protection against genital Chlamydia infection and its complications by a multisubunit candidate vaccine. (2007)

These results underscore the potential, albeit moderate, vaccine advantage of the multisubunit formulation.
Prediction of protein antigenic determinants from amino acid sequences. (1981)

A method is presented for locating protein antigenic determinants by analyzing amino acid sequences in order to find the point of greatest local hydrophilicity. This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging these values along the peptide chain. The point of highest local average hydrophilicity is invariably located in, or immediately adjacent to, an antigenic determinant. It was found that the prediction success rate depended on averaging group length, with hexapeptide averages yielding optimal results. The method was developed using 12 proteins for which extensive immunochemical analysis has been carried out and subsequently was used to predict antigenic determinants for the following proteins: hepatitis B surface antigen, influenza hemagglutinins, fowl plague virus hemagglutinin, human histocompatibility antigen HLA-B7, human interferons, Escherichia coli and cholera enterotoxins, ragweed allergens Ra3 and Ra5, and streptococcal M protein. The hepatitis B surface antigen sequence was synthesized by chemical means and was shown to have antigenic activity by radioimmunoassay.
Plaque composition in plexogenic and thromboembolic pulmonary hypertension: the critical role of thrombotic material in pultaceous core formation (2002)

Chronic thromboembolic pulmonary hypertension is associated with atherosclerotic plaques with glycophorin-rich pultaceous cores, and plexogenic pulmonary hypertension with fibrous plaques. Thromboembolic material thus plays a critical role in the formation of pultaceous cores, of which erythrocyte membrane derived glycophorin is a major component.
Pseudomonas putida KT2442 cultivated on glucose accumulates poly(3-hydroxyalkanoates) consisting of saturated and unsaturated monomers (1992)

The biosynthesis of poly(3-hydroxyalkanoates) (PHAs) by Pseudomonas putida KT2442 during growth on carbohydrates was studied. PHAs isolated from P. putida cultivated on glucose, fructose, and glycerol were found to have a very similar monomer composition. In addition to the major constituent 3-hydroxydecanoate, six other monomers were found to be present: 3-hydroxyhexanoate, 3-hydroxyoctanoate, 3-hydroxydodecanoate, 3-hydroxydodecenoate, 3-hydroxytetradecanoate, and 3-hydroxytetradecenoate. The identity of all seven 3-hydroxy fatty acids was established by gas chromatography-mass spectrometry, one-dimensional 1H-nuclear magnetic resonance, and two-dimensional double-quantum filtered correlation spectroscopy 1H-nuclear magnetic resonance. The chemical structures of the monomer units are identical to the structure of the acyl moiety of the 3-hydroxyacyl-acyl carrier protein intermediates of de novo fatty acid biosynthesis. Furthermore, the degree of unsaturation of PHA and membrane lipids is similarly influenced by shifts in the cultivation temperature. These results strongly indicate that, during growth on nonrelated substrates, PHA monomers are derived from intermediates of de novo fatty acid biosynthesis. Analysis of a P. putida pha mutant and complementation of this mutant with the cloned pha locus revealed that the PHA polymerase genes necessary for PHA synthesis from octanoate are also responsible for PHA formation from glucose.
High‐efficiency cloning of Arabidopsis full‐length cDNA by biotinylated CAP trapper (1998)

Full-length cDNAs are essential for functional analysis of plant genes. We constructed high-content, full-length cDNA libraries from Arabidopsis thaliana plants based on chemical introduction of a biotin group into the diol residue of the CAP structure of eukaryotic mRNA, followed by RNase I treatment, to select full-length cDNA. More than 90% of the total clones obtained were of full length; recombinant clones were obtained with high efficiency (2.2 x 10(6)/9 micrograms starting mRNA). Sequence analysis of 111 randomly picked clones indicated that 32 isolated cDNA groups were derived from novel genes in the A. thaliana genome.
High level monocyte chemoattractant protein-1 expression in transgenic mice increases their susceptibility to intracellular pathogens (1995)

We have constructed transgenic mice in which the mouse mammary tumor virus long terminal repeat controls the expression of murine monocyte chemoattractant protein-1 (MCP-1). Several independently derived lines of transgenic mice constitutively expressed MCP-1 protein in a variety of organs. Protein extracts from these organs had substantial in vitro monocyte chemoattractant activity that was neutralized by an anti-MCP-1 Ab, indicating that transgenic MCP-1 protein is biologically active. However, no transgenic mouse at any age displayed monocyte infiltrates in MCP-1-expressing organs. Two transgenic lines had circulating MCP-1 levels of 13 to 26 ng/ml, which is a concentration sufficient to induce maximal monocyte chemotaxis in vitro. These transgenic lines showed a 1 to 1.5 log greater sensitivity to infection with Listeria monocytogenes and Mycobacterium tuberculosis. A third transgenic line had lower serum levels of MCP-1 and was resistant to L. monocytogenes. The results suggest that this transgenic model is one of monocyte nonresponsiveness to locally produced MCP-1 due to either receptor desensitization or neutralization of a chemoattractant gradient by high systemic concentrations of MCP-1. Regardless of the mechanism, the data indicate that constitutively high levels of MCP-1 expression do not induce monocytic infiltrates, and that MCP-1 is involved in the host response to intracellular pathogens.
Chronic Inflammatory Disorders and Their Redox Control: From Molecular Mechanisms to Therapeutic Opportunities (2011)

A chronic inflammatory disease is a condition characterized by persistent inflammation. A number of human pathologies fall into this category, and a great deal of research has been conducted to learn more about their characteristics and underlying mechanisms. In many cases, a genetic component has been identified, but also external factors like food, smoke, or environmental pollutants can significantly contribute to worsen their symptoms. Accumulated evidence clearly shows that chronic inflammatory diseases are subjected to a redox control. Here, we shall review the identity, source, regulation, and biological activity of redox molecules, to put in a better perspective their key-role in cancer, diabetes, cardiovascular diseases, atherosclerosis, chronic obstructive pulmonary diseases, and inflammatory bowel diseases. In addition, the impact of redox species on autoimmune disorders (rheumatoid arthritis, systemic lupus erythematosus, psoriasis, and celiac disease) and neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis) will be discussed, along with their potential therapeutic implications as novel drugs to combat chronic inflammatory disorders.
Turning On Cell Migration with Electroactive Substrates (2001)

A dynamic surface can “turn on” the migration of adherent cells. This dynamic property is based on a self-assembled monolayer that presents hydroquinone groups. Electrochemical oxidation converts the hydroquinone into the corresponding benzoquinone, which then undergoes a Diels–Alder reaction with a conjugate of cyclopentadiene and a peptide ligand. This in situ modification of the substrate gives a surface that promotes cell migration (see scheme).
Surface-Directed Liquid Flow Inside Microchannels (2001)

Self-assembled monolayer chemistry was used in combination with either multistream laminar flow or photolithography to pattern surface free energies inside microchannel networks. Aqueous liquids introduced into these patterned channels are confined to the hydrophilic pathways, provided the pressure is maintained below a critical value. The maximum pressure is determined by the surface free energy of the liquid, the advancing contact angle of the liquid on the hydrophobic regions, and the channel depth. Surface-directed liquid flow was used to create pressure-sensitive switches inside channel networks. The ability to confine liquid flow inside microchannels with only two physical walls is expected to be useful in applications where a large gas-liquid interface is critical, as demonstrated here by a gas-liquid reaction.
SHEAR‐WAVE VELOCITY ESTIMATION IN POROUS ROCKS: THEORETICAL FORMULATION, PRELIMINARY VERIFICATION AND APPLICATIONS1 (1992)

A bstract Shear‐wave velocity logs are useful for various seismic interpretation applications, including bright spot analyses, amplitude‐versus‐offset analyses and multicomponent seismic interpretations. Measured shear‐wave velocity logs are, however, often unavailable. We developed a general method to predict shear‐wave velocity in porous rocks. If reliable compressional‐wave velocity, lithology, porosity and water saturation data are available, the precision and accuracy of shear‐wave velocity prediction are 9% and 3%, respectively. The success of our method depends on: (1) robust relationships between compressional‐ and shear‐wave velocities for water‐saturated, pure, porous lithologies; (2) nearly linear mixing laws for solid rock constituents; (3) first‐order applicability of the Biot–Gassmann theory to real rocks. We verified these concepts with laboratory measurements and full waveform sonic logs. Shear‐wave velocities estimated by our method can improve formation evaluation. Our method has been successfully tested with data from several locations.
Synthesis of Multimeric MR Contrast Agents for Cellular Imaging (2008)

We have prepared a series of molecular multimeric MR contrast agents for cell labeling that are easy to synthesize, relatively low molecular weight, and biocompatible. The relaxivities of the agents range from 17 to 85 mM(-1) s(-1). Cellular uptake is concentration dependent and viability is excellent. MR images of cell pellets reveal a marked increase in observed signal intensity.
Current diagnosis and treatment of gastrointestinal carcinoids in a series of 101 patients: the significance of serum chromogranin-A, somatostatin receptor scintigraphy and somatostatin analogues. (2005)

a) Tumor size (especially in appendiceal and gastric carcinoids) and, also, the dispersion of disease, highly predict the evolution of the patients; b) serum Chromogranin-A seems to be a very useful tumor marker for the diagnosis and follow-up of pts with GI carcinoids; c) the introduction of new imaging techniques and especially OCTREOSCAN contributes to a better localization of the primary tumors and their metastases, as well as, to the right decision of the appropriate medical treatment; d) surgical excision is the treatment of choice in nonmetastatic tumors; and e) in pts with metastatic disease, the administration of Somatostatin analogues improves their quality of life.
A field guide for cancer diagnostics using cell‐free DNA: From principles to practice and clinical applications (2017)

Recently, many genome-wide profiling studies provided insights into the molecular make-up of major cancer types. The deeper understanding of these genetic alterations and their functional consequences led to the discovery of novel therapeutic opportunities improving clinical management of cancer patients. While tissue-based molecular patient stratification is the gold standard for precision medicine, it has certain limitations: Tissue biopsies are invasive sampling procedures carrying the risk of complications and may not represent the entire tumor due to underlying genetic heterogeneity. In this context, complementary characterization of genetic information in the blood of cancer patients can serve as minimal-invasive 'liquid biopsy'. Fragments of circulating cell-free DNA (cfDNA) are released from tissues of healthy individuals as well as cancer patients. The fraction of cfDNA that is released from primary tumors or metastases (i.e. circulating tumor DNA, ctDNA) represents genetic aberrations in cancer cells, which are a potential source for diagnostic, prognostic, and predictive biomarkers. Recent studies have demonstrated technical feasibility and clinical applications including detection of drug targets and resistance mutations as well as longitudinal monitoring of tumors under therapy. To this end, a variety of pre-analytical procedures for blood processing, isolation and quantification of cfDNA are being employed and several analytical methods and technologies ranging from PCR-based single locus assays to genome-wide approaches are available, which considerably differ in sensitivity, specificity, and throughput. However, broad implementation of ctDNA analysis in daily clinical practice requires a thorough understanding of theoretical, technical, and biological concepts and necessitates standardization and validation of pre-analytical and analytical procedures across different technologies. Here, we review the pertinent literature and discuss the advantages and limitations of available methodologies and their potential applications in molecular diagnostics.