gebhart/patrepeval huggingface dataset:
Comprehensive Study of the Evolution of Gas−Liquid Partitioning of Aroma Compounds during Wine Alcoholic Fermentation (2010)

Calculating the gas-liquid partitioning of aromatic molecules during winemaking fermentation is essential to minimize the loss of aroma and to optimize the fermentation conditions. In this study, the effect of the main fermentation parameters on the partition coefficients (ki) of higher alcohols (2-methylpropan-1-ol and 3-methyl butan-1-ol) and esters (ethyl acetate, 3-methyl-1-butyl acetate, and 2-ethyl hexanoate) was assessed. The values of ki were first determined in synthetic media simulating must and wine. They varied considerably with both the hydrophobicity of the compound and the composition of the medium. Then, the effect of temperature on ki was quantified. The absence of any effect of gas composition was also established by replacing air with CO2. Finally, the impact of CO2 stripping was assessed by running specific fermentations in which the rate of CO2 production was kept constant by perfusion with assimilable nitrogen. These fermentations showed that in contrast to temperature and must composition, CO2 stripping did not change the gas-liquid partitioning of higher alcohols and esters.
Thromboembolic complications in patients with arrhythmogenic right ventricular dysplasia/cardiomyopathy (2006)

(i) ARVD/C may be complicated by thrombosis. Annual incidence of such complications is significantly lower than reported for left ventricle failure. (ii) Anticoagulation should be used in ARVD/C patients with large, hypokinetic RV and slow blood flow. (iii) Patients with severe forms of ARVD/C, thrombus formation in the RV and/or spontaneous echocardiographic contrast are at higher risk of a poor outcome.
Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance (2001)

Tetracyclines were discovered in the 1940s and exhibited activity against a wide range of microorganisms including gram-positive and gram-negative bacteria, chlamydiae, mycoplasmas, rickettsiae, and protozoan parasites. They are inexpensive antibiotics, which have been used extensively in the prophlylaxis and therapy of human and animal infections and also at subtherapeutic levels in animal feed as growth promoters. The first tetracycline-resistant bacterium, Shigella dysenteriae, was isolated in 1953. Tetracycline resistance now occurs in an increasing number of pathogenic, opportunistic, and commensal bacteria. The presence of tetracycline-resistant pathogens limits the use of these agents in treatment of disease. Tetracycline resistance is often due to the acquisition of new genes, which code for energy-dependent efflux of tetracyclines or for a protein that protects bacterial ribosomes from the action of tetracyclines. Many of these genes are associated with mobile plasmids or transposons and can be distinguished from each other using molecular methods including DNA-DNA hybridization with oligonucleotide probes and DNA sequencing. A limited number of bacteria acquire resistance by mutations, which alter the permeability of the outer membrane porins and/or lipopolysaccharides in the outer membrane, change the regulation of innate efflux systems, or alter the 16S rRNA. New tetracycline derivatives are being examined, although their role in treatment is not clear. Changing the use of tetracyclines in human and animal health as well as in food production is needed if we are to continue to use this class of broad-spectrum antimicrobials through the present century.
Developmental patterning of the carbohydrate antigen FC10.2 during early embryogenesis in the chick (1990)

An oligosaccharide antigen (FC10.2), formerly described only in mammalian cells and secreted glycoproteins, has been detected and found to display striking temporal and spatial patterning in the chick during early embryonic development. This antigen is expressed on type 1 chains, which are isomers of oligosaccharides of the poly-N-acetyllactosamine series (type 2 chains). Immunoreactivities before and after neuraminidase treatment of serial sections of chick embryos during the first 17 stages of development indicate that the FC10.2 structure occurs predominantly in the sialylated form (S-FC10.2). The FC10.2 and S-FC10.2 antigens are prominent markers of the primordial germ cells, being strongly expressed by these cells from the pre-primitive streak stage onwards. S-FC10.2 is also a clear marker of the pronephric duct from its first appearance. Initially present over the entire apical surface of the ectoderm, antigenicity diminishes in an antero-posterior direction as neurulation proceeds. A unique pattern for a carbohydrate antigen is displayed by cells of the primitive streak; antigenicity is lost with de-epithelialisation and ingression, but is regained in a pericellular distribution on the mesoderm cells that emerge from the primitive streak. Thereafter, successive changes in expression and distribution of FC10.2 and S-FC10.2 are features of mesodermal tissues, particularly during somitogenesis. These antigens are prominent components of the extracellular matrix around the notochord and sclerotome cells. They are also prominent posteriorly in the subectodermal region, ceasing abruptly at the lateral limits of the embryo proper. Although no absolute correlations can yet be made, several features of the distribution of these antigens suggest that they may be integral components of, or ligands for, cell adhesion molecules.
Congenital-Infantile Fibrosarcoma (2001)

Congenital-infantile fibrosarcoma (CIFS) is a relatively indolent sarcoma that should be distinguished from more aggressive spindle cell sarcomas of childhood. CIFSs have been found to have a novel recurrent reciprocal translocation t(12;15)(p13;q25) resulting in the gene fusion ETV6-NTRK3 (ETS variant gene 6; neurotrophic tyrosine kinase receptor type 3). We studied immunohistochemical expression of NTRK3, and conducted a reverse transcription-polymerase chain reaction (RT-PCR) assay to detect the ETV6-NTRK3 fusion transcripts using archival formalin-fixed paraffin-embedded tissues from 10 CIFSs. Thirty-eight other spindle cell tumors were included as controls. The ETV6-NTRK3 fusion transcripts were identified in 7 (70%) of 10 CIFSs. Nucleotide sequence analysis showed that the fusion occurred between ETV6 exon 5 and NTRK3 exon 13. The 38 control tumors were negative for the fusion transcript. Immunohistochemically, CIFSs consistently expressed NTRK3. But the expression of NTRK3 also was observed in 22 of 38 control tumors. These results show the diagnostic usefulness of RT-PCR methods to detect ETV6-NTRK3 fusion transcripts in archival formalin-fixed paraffin-embedded tissue and the important role of NTRK3 in the development of CIFS, despite its being a protein of little importance in differential diagnosis.
Desorption Electrospray Ionization-Mass Spectrometry of Proteins (2007)

Desorption electrospray ionization-mass spectrometry (DESI-MS) was evaluated for the detection of proteins ranging in molecular mass from 12 to 66 kDa. Proteins were uniformly deposited on a solid surface without pretreatment and analyzed with a DESI source coupled to a quadrupole ion trap mass spectrometer. DESI-MS parameters optimized for protein detection included solvent flow rate, temperature of heated capillary tube, incident and reflection angle, sheath gas pressure, and ESI voltage. Detection limits were obtained for all protein standards, and they were found to decrease with decreasing protein molecular mass: for cytochrome c (12.3 kDa) and lysozyme (14.3 kDa) a detection limit of 4 ng/mm2 was obtained; for apomyoglobin (16.9 kDa) 20 ng/mm2; for beta-lactoglobulin B (18.2 kDa) 50 ng/mm2; and for chymotrypsinogen A (25.6 kDa) 100 ng/mm2. The DESI-MS analysis of higher molecular mass proteins such as ovalbumin (44.4 kDa) and bovine serum albumin (66.4 kDa) yielded mass spectra of low signal-to-noise ratio, making their detection and molecular weight determination difficult. In this study, DESI-MS proved to be a rapid and robust method for accurate MW determination for proteins up to 17 kDa under ambient conditions. Finally, we demonstrated the DESI-MS detection of the bacteriophage MS2 capsid protein from crude samples with minimal sample preparation.
Troponin subunit stoichiometry and content in rabbit skeletal muscle and myofibrils. (1983)

The quantity and molar ratio of the three troponin subunits to actin were determined in rabbit psoas muscle, muscle homogenates (800 X g pellet), and purified myofibrils. Proteins were separated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The quantities of the separated proteins were determined directly from the gel slices by amino acid analysis after correction for losses and background. The molar ratio of actin, troponin T, troponin I, and troponin C was found to be 6.99:1:05:1:04:0.92 in purified myofibrils and was not significantly different (p greater than 0.05) from those obtained from 800 X g pellets of muscle homogenates or intact muscle tissue. Isolated troponin purified by several different procedures also had a 1:1:1 subunit ratio although the variability was much greater than that found in myofibrils. The troponin content of rabbit psoas muscle and myofibrils was 91 +/- 16 and 770 +/- 110 pmol/mg, respectively.
Establishment of a novel human megakaryoblastic leukemia cell line, MEG- 01, with positive Philadelphia chromosome (1985)

A megakaryoblastic cell line, designated MEG-01, was established from the bone marrow of a patient with blast crisis of Philadelphia (Ph1) chromosome-positive chronic myelogenous leukemia. MEG-01 cells grew in single-cell suspension with a doubling time of 36 to 48 hours. Under the usual culture conditions, approximately half of the cells adhered to the culture flask with extention of pseudopods. MEG-01 cells were positive for the periodic acid-Schiff reaction, alpha-naphthyl acetate esterase, and acid phosphatase, and negative for myeloperoxidase, alpha-naphthyl butyrate esterase, naphthol AS-D chloroacetate esterase, and alkaline phosphatase. Ultrastructural platelet peroxidase was positive in MEG-01 cells. Cytoplasmic factor VIII (FVIII)-related antigen was weakly positive in larger MEG-01 cells by both an indirect immunofluorescent technique with monoclonal antibodies and a direct immunoperoxidase technique using horseradish peroxidase-conjugated conventional rabbit anti-human FVIII antibody. Platelet glycoprotein (GP) IIb/IIIa antigen was uniformly demonstrated on the surface of MEG-01 cells by both indirect immunofluorescent and immunoperoxidase techniques using antiplatelet GP IIb/IIIa monoclonal antibodies; platelet GP lb antigen was demonstrated only in the cytoplasm of larger MEG-01 cells. MEG-01 cells possessed no markers for B or T lymphocytes or for myeloid cells. Chromosome analysis of this cell line revealed a human male hyperdiploid karyotype with a modal chromosome number of 56 to 58. The Ph1 chromosome was observed in all karyotypes analyzed. This novel human megakaryoblastic cell line may provide a useful model for the study of human megakaryopoiesis and of the biosynthetic mechanisms of proteins unique to megakaryocytic lineage.
Stretching DNA Using the Electric Field in a Synthetic Nanopore (2005)

The mechanical properties of DNA over segments comparable to the size of a protein-binding site (3-10 nm) are examined using an electric-field-induced translocation of single molecules through a nanometer diameter pore. DNA, immersed in an electrolyte, is forced through synthetic pores ranging from 0.5 to 1.5 nm in radius in a 10 nm thick Si(3)N(4) membrane using an electric field. To account for the stretching and bending, we use molecular dynamics to simulate the translocation. We have found a threshold for translocation that depends on both the dimensions of the pore and the applied transmembrane bias. The voltage threshold coincides with the stretching transition that occurs in double-stranded DNA near 60 pN.
Ultralow-Density Nanostructured Metal Foams:  Combustion Synthesis, Morphology, and Composition (2006)

The synthesis of low-density, nanoporous materials has been an active area of study in chemistry and materials science dating back to the initial synthesis of aerogels. These materials, however, are most often limited to metal oxides, e.g., silica and alumina, and organic aerogels, e.g., resorcinol/formaldehyde, or carbon aerogels, produced from the pyrolysis of organic aerogels. The ability to form monolithic metallic nanocellular porous materials is difficult and sometimes elusive using conventional methodology. Here we report a relatively simple method to access unprecedented ultralow-density, nanostructured, monolithic, transition-metal foams, utilizing self-propagating combustion synthesis of novel transition-metal complexes containing high nitrogen energetic ligands. During the investigation of the decomposition behavior of the high-nitrogen transition metal complexes, it was discovered that nanostructured metal monolithic foams were formed in a post flame-front dynamic assembly having remarkably low densities down to 0.011 g cm(-3) and extremely high surface areas as high as 270 m(2) g(-1). We have produced monolithic nanoporous metal foams via this method of iron, cobalt, copper, and silver metals. We expect to be able to apply this to many other metals and to be able to tailor the resulting structure significantly.
Knee Injury and Osteoarthritis Outcome Score (KOOS)—Development of a Self-Administered Outcome Measure (1998)

There is broad consensus that good outcome measures are needed to distinguish interventions that are effective from those that are not. This task requires standardized, patient-centered measures that can be administered at a low cost. We developed a questionnaire to assess short- and long-term patient-relevant outcomes following knee injury, based on the WOMAC Osteoarthritis Index, a literature review, an expert panel, and a pilot study. The Knee injury and Osteoarthritis Outcome Score (KOOS) is self-administered and assesses five outcomes: pain, symptoms, activities of daily living, sport and recreation function, and knee-related quality of life. In this clinical study, the KOOS proved reliable, responsive to surgery and physical therapy, and valid for patients undergoing anterior cruciate ligament reconstruction. The KOOS meets basic criteria of outcome measures and can be used to evaluate the course of knee injury and treatment outcome.
Real‐time markerless lung tumor tracking in fluoroscopic video: Handling overlapping of projected structures (2015)

This study shows that in case of tumor overlapping with dense structures, multiple-template tracking provides more accurate results than a single-template approach. The developed algorithm shows promising results in terms of suitability for real-time application and robustness against frequently changing overlapping.
Invited Review: Mechanochemical signal transduction in the fetal lung (2000)

Growth and maturation of fetal lungs are regulated by both humoral and physical factors. Mechanical stretch stimulates fetal lung cell proliferation and affects fetal lung maturation by influencing the production of extracellular matrix molecules and the expression of specific genes of fetal lung cells. These effects are mediated through special signal transduction pathways in fetal lung cells. Various in vivo and in vitro model systems have been developed to investigate the mechanotransduction process. The diversity and discrepancy of these studies have raised many questions. We will briefly summarize mechanical force-induced signals in fetal lung cell proliferation and differentiation and then discuss several important issues related to these studies.
Topical Review (1999)

Transepithelial transducing cells, particularly the gastrin (G) cell, co-ordinate gastric acid secretion with the arrival of food in the stomach. Recent work suggests that multiple active products are generated from the gastrin precursor, and that there are multiple control points in gastrin biosynthesis. Biosynthetic precursors and intermediates (progastrin and Gly-gastrins) are putative growth factors; their products, the amidated gastrins, regulate epithelial cell proliferation, the differentiation of acid-producing parietal cells and histamine-secreting enterochromaffin-like (ECL) cells, and the expression of genes associated with histamine synthesis and storage in ECL cells, as well as acutely stimulating acid secretion. Gastrin also stimulates the production of members of the epidermal growth factor (EGF) family, which in turn inhibit parietal cell function but stimulate the growth of surface epithelial cells. Plasma gastrin concentrations are elevated in subjects with Helicobacter pylori, who are known to have increased risk of duodenal ulcer disease and gastric cancer. Studies of the physiology of gastrin may therefore contribute to an understanding of the mechanisms relevant to major upper gastrointestinal tract disease.
An apparatus for the study of airborne infection (1952)

A relatively simple and safe apparatus for the study of airborne infection is described. Cloud sampling and assessment techniques are described and critically discussed. Evidence is given concerning the satisfactory reproducibility of in vitro and in vivo assays. Limitations to the usefulness of the apparatus are noted.
Approaches for gene targeting and targeted gene expression in plants (2011)

Transgenic science and technology are fundamental to state-of-the-art plant molecular genetics and crop improvement. The new generation of technology endeavors to introduce genes 'stably' into 'site-specific' locations and in 'single copy' without the integration of extraneous vector 'backbone' sequences or selectable markers and with a 'predictable and consistent' expression. Several similar strategies and technologies, which can push the development of 'smart' genetically modified plants with desirable attributes, as well as enhance their consumer acceptability, are discussed in this review.
CD19-Targeted T Cells for Hematologic Malignancies (2015)

Recently, immunotherapy for cancer has begun to garner traction with encouraging results in a number of malignancies. Included within this arena has been the genetic engineering of autologous T cells with chimeric antigen receptors (CARs) against tumor target. The majority of this experience has included the use of CAR T cells directed against CD19 for B-cell hematologic malignancies. The most striking efficacy to date with CAR T cells directed against CD19 has been in relapsed and refractory B-cell acute lymphoblastic leukemia, with the overwhelming majority of patients experiencing complete remissions. In addition, single-center and largely early-phase studies have demonstrated responses in patients with varying histologic findings of relapsed and refractory B-cell non-Hodgkin lymphoma. The favorable response rates seen with this technology have been tempered by the high risk of toxicity, particularly in the form of cytokine-release syndrome and neurotoxicity. Agents such as tocilizumab and corticosteroids have been used to treat these toxicities. The current state of the science includes strategies to circumvent and treat toxicity, manufacturing, and study of later-generation CAR constructs with the intention of improving efficacy and development of CARs against other tumor targets for both hematologic and solid tumor malignancies. The observation of an early efficacy ensures further integration and development of this modality into future immunotherapeutic strategies for various cancers.
CRISPR-Cas (2013)

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR-associated genes) is an adaptive immunity system in bacteria and archaea that functions via a distinct self-non-self recognition mechanism that is partially analogous to the mechanism of eukaryotic RNA interference (RNAi). The CRISPR-Cas system incorporates fragments of virus or plasmid DNA into the CRISPR repeat cassettes and employs the processed transcripts of these spacers as guide RNAs to cleave the cognate foreign DNA or RNA. The Cas proteins, however, are not homologous to the proteins involved in RNAi and comprise numerous, highly diverged families. The majority of the Cas proteins contain diverse variants of the RNA recognition motif (RRM), a widespread RNA-binding domain. Despite the fast evolution that is typical of the cas genes, the presence of diverse versions of the RRM in most Cas proteins provides for a simple scenario for the evolution of the three distinct types of CRISPR-cas systems. In addition to several proteins that are directly implicated in the immune response, the cas genes encode a variety of proteins that are homologous to prokaryotic toxins that typically possess nuclease activity. The predicted toxins associated with CRISPR-Cas systems include the essential Cas2 protein, proteins of COG1517 that, in addition to a ligand-binding domain and a helix-turn-helix domain, typically contain different nuclease domains and several other predicted nucleases. The tight association of the CRISPR-Cas immunity systems with predicted toxins that, upon activation, would induce dormancy or cell death suggests that adaptive immunity and dormancy/suicide response are functionally coupled. Such coupling could manifest in the persistence state being induced and potentially providing conditions for more effective action of the immune system or in cell death being triggered when immunity fails.
Intestinal distribution of hyaluronan in small bowel allografting in the rat (1993)

Abstract Hyaluronan (hyaluronic acid; HA) was demonstrated and quantified in small bowel tissue at different times after small bowel transplantation. Semiallogeneic or semisyngeneic rat models were used to elicit either unidirectional graft rejection or graft-versus-host disease (GVHD). In normal rat small bowel, HA was present in the villous lamina propria and around medium-sized vessels in the interstitium of the crypt area. During graft rejection a cellular infiltrate and edema appeared in the lamina propria in the crypt area where an accumulation of HA was also demonstrated. There was progressive accumulation of HA in the small bowel during rejection, and on day 6 there was a threefold increase compared to the values in syngeneic grafts. The increase in tissue HA was paralleled by an increase in the total water content of the rejecting graft. In specimens from animals suffering from GVHD, no significant changes in water or HA content and distribution were observed until day 12. The data suggest that accumulation of HA might contribute to the pathophysiology of the transplantation edema and that HA might be of potential diagnostic value in differentiating between graft rejection and GVHD.
Singularity-matching peaks in a superconducting single-electron transistor (1997)

We report the experimental observation of the recently predicted peaks on the $I\ensuremath{-}V$ curve of a superconducting single-electron transistor at relatively high temperatures. The peaks are due to the matching of singularities in the quasiparticle density of states in two electrodes of a tunnel junction. The energy shift due to Coulomb blockade provides the matching at finite voltage.