gebhart/patrepeval huggingface dataset:
Measurement of intrinsic fluorescence to probe the conformational flexibility and thermodynamic stability of a single tryptophan protein entrapped in a sol–gel derived glass matrix (1998)

In this study techniques based on measurement of intrinsic tryptophan (Trp) fluorescence were used to monitor the stability and conformational flexibility of the single tryptophan protein monellin which was entrapped in sol–gel derived glass monoliths formed from tetraethylorthosilicate. The monoliths were aged either in buffer (wet-aged) or in air (dry-aged). The steady-state fluorescence spectra, steady-state anisotropy and acrylamide quenching behaviour of the single Trp at position 3 were monitored during chemical denaturation with guanidine hydrochloride, and during thermal denaturation. These studies indicated that there were no significant improvements in either chemical or thermal stability when the protein was present in wet-aged monoliths. However, the long-term stability of the protein was improved six-fold when such monoliths were stored at 4 °C. The encapsulation of monellin into dry-aged monoliths caused the thermal unfolding transition to broaden and shift upward by 10 °C, and caused the long-term stability to improve by 12-fold (compared to solution). Chemical stability studies also showed a broader transition for the unfolding of the protein in dry-aged monoliths, and suggested that the protein was present in a distribution of environments, each with a slightly different thermodynamic stability. The steady-state fluorescence responses obtained during denaturation and the accessibility of native and denatured protein to quencher provided clear evidence that the entrapped protein had a smaller range of conformational motions compared to the protein in solution, and that the entrapped protein was not able to unfold completely. The restriction of conformational motion, along with the increased structural order of the internal environment of the monoliths, play a role in the improvements in thermal and long-term stability that were observed.
Sulfation, the Up-and-Coming Post-Translational Modification:  Its Role and Mechanism in Protein−Protein Interaction (2007)

Tyrosine sulfation is a post-translational modification entailing covalent attachment of sulfate to tyrosine residues. It takes place in the trans-Golgi, is necessary for the bioactivity of some proteins, and improves their ability to interact with other proteins. In the present work, we show that a protein containing a sulfated tyrosine with a delocalized negative charge forms a salt bridge with another protein if it has two or more adjacent arginine residues containing positive delocalized charges. These noncovalent complexes are so stable that, when submitted to collision induced dissociation, the peptides forming the complex dissociate. Just one covalent bond fragments, the covalent bond between the tyrosine oxygen and the SO3 sulfur, and is represented by the appearance of a new peak (basic peptide + SO3), suggesting that in some instances covalent bonds will break down before the noncovalent bonds between the arginine guanidinium and SO3 dissociate. The data implies that the dissociation pathway is preferred; however, fragmentation between tyrosine and the sulfate residue is a major pathway.
Per-symbol-based digital back-propagation approach for PDM-CO-OFDM transmission systems (2013)

For polarization-division-multiplexing coherent optical orthogonal frequency division multiplexing (PDM-CO-OFDM) systems, we propose a per-symbol-based digital back-propagation (DBP) approach which, after cyclic prefix removal, conducts DBP for each OFDM symbol. Compared with previous DBP, this new proposal avoids the use of inefficient overlap-and-add operation and saves one fast Fourier transform (FFT) module, therefore simplifying the hardware implementation. Transmitting a 16-QAM, 42.8-Gb/s PDM-CO-OFDM signal over 960-km standard single mode fiber (SSMF), we compare the previous and the proposed DBP approaches with different receiver's sampling rates and different step lengths in each DBP iteration, and found that the proposed DBP can achieve a similar performance as that of the previous DBP while enjoying a simpler implementation. We have also specifically introduced a small self-phase modulation (SPM) model for DBP and demonstrated its feasibility with the same experimental setup.
The Catecholamine, Cortisol, and Hemodynamic Responses to Mild Perioperative Hypothermia (1995)

Compared with patients in the forced-air warming group, patients receiving routine thermal care had lower core temperatures, a greater degree of peripheral vasoconstriction, higher norepinephrine concentrations, and higher arterial blood pressures in the early postoperative period. These findings suggest a possible mechanism for hypothermia-related cardiovascular morbidity in the perioperative period.
Expression of LeY and extended LeY blood group-related antigens in human malignant, premalignant, and nonmalignant colonic tissues. (1986)

The LeY determinant, a difucosylated type 2 blood group-related antigen, is a positional isomer of the Leb blood group antigen and a fucosylated derivative of the LeX antigen. The LeX antigen behaves like an oncodevelopmental tumor-associated antigen in human colon cancer, and extended polyfucosyl LeX antigens are more specific for colon cancer tissues than are simple, monofucosyl LeX antigens. The present investigation compared the expression of simple and extended LeY antigens in a variety of malignant and nonmalignant human colonic tissues to gain insight into the normal distribution and cancer-associated expression of these antigens. Monoclonal antibody AH-6, which recognizes the LeY epitope irrespective of its carrier carbohydrate chain, stained the majority of specimens regardless of malignant potential or location within the colon. In contrast, CC-1 and CC-2 monoclonal antibodies, which recognize extended LeY structures, and KH-1, which is specific to trifucosyl LeY, preferentially stained malignant colonic tissues and rarely stained normal colonic mucosae. Mucosa immediately adjacent to cancer usually stained with AH-6 but not with KH-1, CC-1, or CC-2. Extended or trifucosyl LeY antigen expression was limited exclusively to premalignant (adenomatous) polyps and was invariably absent from nonpremalignant (hyperplastic) polyps. Moreover, among adenomatous polyps, extended LeY antigen expression tended to correlate with three parameters of malignant potential: larger polyp size; villous histology, and severe dysplasia. AH-6 failed to distinguish between hyperplastic and adenomatous polyps. In second-trimester fetal colonic mucosa, AH-6 bound to both proximal and distal segments whereas KH-1, CC-1, and CC-2 bound only to proximal segments. We conclude that in human colon, the LeY hapten is an oncodevelopmental cancer-associated antigen and extended LeY antigens are highly specific markers for malignancy and premalignancy.
A SEROLOGICAL DIFFERENTIATION OF SPECIFIC TYPES OF BOVINE HEMOLYTIC STREPTOCOCCI (GROUP B) (1934)

Under uniform diet conditions the normal bile fistula dog will eliminate pretty constant amounts of cholesterol-about 0.5 to 1.0 mg. cholesterol per kilo per 24 hours. Diets rich in cholesterol (egg yolk) will raise the cholesterol output in the bile but compared to the diet intake (1.5 gm. cholesterol) the output increase in the bile is trivial (5-15 mg.). Calves' brains in the diet are inert. Bile salt alone will raise the cholesterol output in the bile as much and often more than a cholesterol rich diet. Bile salt plus egg yolk plus whole bile give maximal output figures for bile cholesterol-60 mg. per 24 hours. Liver injury (chloroform) decreases both bile salt and cholesterol elimination in the bile. Blood destruction (hydrazine) fails to increase the bile cholesterol output and this eliminates the red cell stroma as an important contributing factor. Certain cholagogues (isatin and decholin) will increase the bile flow but cause no change in cholesterol elimination. The ratio of cholesterol to bile salt in the bile normally is about 1 to 100 but the bile salts are more labile in their fluctuations. The ratio is about reversed in the circulating blood plasma where the cholesterol is high (150-300 mg. per cent) and the bile salt concentration very low. Cholesterol runs so closely parallel to bile salt in the bile that one may feel confident of a physical relationship. In addition there is a suspicion that the bile cholesterol is in some obscure fashion linked with the physiological activity of hepatic epithelium.
Cloning and heterologous expression of a broad specificity aminotransferase ofLeishmania mexicanapromastigotes (2003)

We have previously reported that Leishmania mexicana promastigotes possess a broad substrate specificity aminotransferase (BSAT), able to transaminate aspartate, aromatic amino acids, methionine and leucine. We have confirmed now this unusual substrate specificity by cloning its gene and expressing in Escherichia coli the recombinant active protein. The amino acid sequence of BSAT shares over 40% identity with other eukaryotic and prokaryotic aspartate aminotransferases, thus showing that the enzyme belongs to the subfamily Ialpha of aminotransferases, and has only 6% identity with the tyrosine aminotransferase from Trypanosoma cruzi, which has a similar substrate specificity. The production of recombinant active enzyme in good yields opens up the possibility of obtaining its 3D-structure, in order to investigate the structural basis of the broad substrate specificity.
c-Jun Regulates the Stability and Activity of the p53 Homologue, p73 (2004)

Chemotherapeutic drugs and stress signals activate p73, the structural and functional homologue of p53, both by transcriptional activation and post-translational modifications. However, cisplatin, a DNA damage-inducing chemotherapeutic agent, is thought to regulate p73 only by affecting its stability through mechanisms involving the MLH-1/c-Abl signaling cascade. Here we show that c-Jun, a component of the AP-1 family of transcription factors, contributes to p73 induction by cisplatin. c-jun(-/-) cells are defective in p73 induction, and ectopic c-Jun expression augments p73 levels. c-Jun-mediated accumulation of p73 requires the transactivation activity of c-Jun and occurs in a c-Abl- and Mdm2-independent manner. c-Jun expression increases p73 half-life by preventing it from proteasome-mediated degradation, resulting in the potentiation of p73-mediated transcriptional activity. Moreover, mouse fibroblasts lacking c-Jun are resistant to cisplatin-induced apoptosis, and reintroduction of c-Jun restores p73 activation and sensitivity to cisplatin. Furthermore, p73-mediated apoptosis is abrogated in c-jun(-/-) cells. Together, these findings demonstrate a possible role for c-Jun in regulating p73 function and highlight the importance of the cooperativity between transcription factors in potentiating apoptosis.
Learning Dictionaries for Named Entity Recognition using Minimal Supervision (2014)

This paper describes an approach for automatic construction of dictionaries for Named Entity Recognition (NER) using large amounts of unlabeled data and a few seed examples. We use Canonical Correlation Analysis (CCA) to obtain lower dimensional embeddings (representations) for candidate phrases and classify these phrases using a small number of labeled examples. Our method achieves 16.5% and 11.3% F-1 score improvement over co-training on disease and virus NER respectively. We also show that by adding candidate phrase embeddings as features in a sequence tagger gives better performance compared to using word embeddings.
Complete nucleotide sequence of mouse 18 S rRNA gene: comparison with other available homologs (1984)

We present the complete sequence of mouse 18 S rRNA. As indicated by comparison with yeast, Xenopus and rat, the conservation of eukaryotic 18 S rRNA sequences is extensive. However, this conservation is far from being uniform along the molecule: most of the base changes and the size differences between species are concentrated at specific locations. Two distinct classes of divergent traces can be detected which differ markedly in their rates of nucleotide substitution during evolution, and should prove valuable in additional comparative analyses, both for eukaryotic taxonomy and for rRNA higher order organization. Mouse and rat 18 S rRNA sequences differ by only 14 point changes over the 1869 nucleotides of the molecule.
NSAID induced gastrointestinal complications: the ARAMIS perspective--1997. Arthritis, Rheumatism, and Aging Medical Information System. (1998)

Gastrointestinal (GI) complications related to nonsteroidal antiinflammatory drug (NSAID) therapy are the most prevalent category of adverse drug reactions. Patients with arthritis are among the most frequent users of NSAID and are therefore particularly at risk for these side effects. To evaluate the nature of NSAID related GI complications and to determine how their frequency can be reduced, a series of studies of such complications in patients with rheumatic disease has been carried out based on data from the Arthritis, Rheumatism, and Aging Medical Information System (ARAMIS). We review the literature and present findings from the ARAMIS studies. This report addresses whether GI side effects such as dyspepsia can serve as warning symptoms for serious GI complications and describes the risk factors for these life threatening complications. It also describes differences among NSAID with regard to their GI toxicity and describes a study that investigated whether H2-receptor antagonists and antacids affect the development of serious GI complications. In addition, ongoing research and topics to be addressed in future studies are described.
The role of remote sensing data in near-surface seismic characterization (2007)

Andreas Laake and Andrew Cutts, WesternGeco, UK show how remote sensing data can enhance seismic-based near-surface model building. The characterization of the near-surface is among the most significant challenges in onshore surface seismic technology. Advanced seismic techniques such as point source and point receiver based methods have revealed the impact the near-surface has on the coupling of sources and receivers and on the generation and propagation of seismic noise modes. Modern seismic data acquisition and processing techniques require corrections for coupling perturbation and surface wave noise to provide correct data for the characterization of hydrocarbon reservoir. Seismic acquisition can only provide local information about the near-surface properties in the vicinity of the sources and the receivers due to the common practice of recording the seismic data along source and receiver lines. The resulting near-surface model is based on spatially limited information.
Langmuir-Blodgett Films (1996)

This book provides a multidisciplinary introduction to the subject of Langmuir–Blodgett films. These films are the focus of intense current worldwide interest, as the ability to deposit organic films of nanometre thicknesses has many implications in materials science, and in the development of new electronic and opto-electronic devices. Beginning with the application of simple thermodynamics to the common bulk phases of matter, the book outlines the nature of the phases associated with floating monolayer films. The Langmuir–Blodgett deposition process itself is described in some detail and contrasted with other thin film techniques. Monolayer-forming materials and the structural, electrical and optical properties of Langmuir–Blodgett films are discussed separately. Each chapter is comprehensive, easy to understand and generously illustrated. Appendices are provided for the reader wishing to delve deeper into the physics and chemistry background.
Sickle Cell Anemia, a Molecular Disease (1949)

The erythrocytes of certain individuals possess the capacity to undergo reversible changes in shape in response to changes in the partial pressure of oxygen. When the oxygen pressure is lowered, these cells change their forms from the normal biconcave disk to crescent, holly wreath, and other forms. This process is known as sickling. About 8 percent of American Negroes possess this characteristic; usually they exhibit no pathological consequences ascribable to it. These people are said to have sicklemia, or sickle cell trait. However, about 1 in 40 (4) of these individuals whose cells are capable of sickling suffer from a severe chronic anemia resulting from excessive destruction of their erythrocytes; the term sickle cell anemia is applied to their condition.
Wires that, Usually, We Never Notice (2010)

Richard stopped our car partwayup our drive and did heever have a puzzled look:whye's my wife just standing there,exiled and outside? I pointed in replyto the wires running overhead,wires that, usually, we never notice,and motioned to their juncture with our housewhere a little fire had started.
Two members of the mouse mdr gene family confer multidrug resistance with overlapping but distinct drug specificities. (1990)

We report the cloning and functional analysis of a complete clone for the third member of the mouse mdr gene family, mdr3. Nucleotide and predicted amino acid sequence analyses showed that the three mouse mdr genes encode highly homologous membrane glycoproteins, which share the same length (1,276 residues), the same predicted functional domains, and overall structural arrangement. Regions of divergence among the three proteins are concentrated in discrete segments of the predicted polypeptides. Sequence comparison indicated that the three mouse mdr genes were created from a common ancestor by two independent gene duplication events, the most recent one producing mdr1 and mdr3. When transfected and overexpressed in otherwise drug-sensitive cells, the mdr3 gene, like mdr1 and unlike mdr2, conferred multidrug resistance to these cells. In independently derived transfected cell clones expressing similar amounts of either MDR1 or MDR3 protein, the drug resistance profile conferred by mdr3 was distinct from that conferred by mdr1. Cells transfected with and expressing MDR1 showed a marked 7- to 10-fold preferential resistance to colchicine and Adriamycin compared with cells expressing equivalent amounts of MDR3. Conversely, cells transfected with and expressing MDR3 showed a two- to threefold preferential resistance to actinomycin D over their cellular counterpart expressing MDR1. These results suggest that MDR1 and MDR3 are membrane-associated efflux pumps which, in multidrug-resistant cells and perhaps normal tissues, have overlapping but distinct substrate specificities.
Small Animals Are Not Susceptible to Human Immunodeficiency Virus Infection (1987)

Several species of small animals were inoculated at birth or as adults with blood components from patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related disorders, or with the human immunodeficiency virus (HIV). No ill effects were noted in rats, hamsters, guinea-pigs, rabbits or musk shrews. Mice inoculated with clinical specimens had a significant incidence of mortality as compared with control groups (18.7% against 5.9%, P less than 0.025). Mice receiving HIV showed an increase in mortality, but it was not statistically significant. Infection of the animals by HIV could not be detected by virological or immunological studies. We concluded that none of these animal species provided a useful model for evaluating HIV infection.
Derivation of Three Clones from Human Embryonic Stem Cell Lines by FACS Sorting and Their Characterization (2006)

Here we describe the first report of three human embryonic stem cell (hESC) clones, hES 3.1, 3.2, and 3.3, derived from the parent line hES3 by sorting of single-cell preparations by flow cytometry. The viability of single-cell preparations before and after cell sorting remained >98%. The hESC were selected by size gating and forward-angle light scatter and were dispersed directly as single cell/ well into 96-well plates containing human fetal fibroblasts as feeder layers. Single stem cell dispersion into 96-well plates was confirmed by using cells from a hES3 line that constitutively expressed green fluorescence protein (eGFP) under similar conditions of flow cytometry. Three clones were obtained from the parent line hES3 -- hES3.1, 3.2, and 3.3 -- and they have been in continuous culture for more than 1 year. The cloning efficiency was less than <0.5%. These hESC clones show normal stem cell characteristics, such as undifferentiated growth, high nucleocytoplasmic ratio, the same karyotype as that of the parent line (46 XX), stem cell surface markers (i.e., SSEA3, SSEA4, OCT4, TRA-1-60, and TRA-1-81), and gene expression for pluripotency (Oct-4 and nanog). They all formed embryoid bodies in suspension cultures, and after seeding in culture plates they showed pluripotency in vitro by forming cell lineages derived from all three germ layers as indicated by expression of the ectodermal marker nestin, the mesodermal marker renin, and the endodermal markers alpha-fetoprotein and GATA6. All clones showed normal expression of alkaline phosphatase activity, a marker of in vitro pluripotency. When hESC clones (1-2 x 10(6) total) were injected into nonobese diabetic-severe combined immunodeficiency (NOD-SCID) mice under the kidney capsule, all formed teratomas within 6-8 weeks. Analysis of the stem cell surface marker TRA-1-160 by flow cytometry showed nonsignificant (p < 0.05) differences between the clones and the parent line. The clones also differed in their expression of genes, with only one, hES 3.2, expressing the endodermal markers, i.e., alpha-fetoprotein and GATA6. The ability to produce clones from a parent hESC line rapidly by FACS sorting will help provide a homogeneous population of cells for achieving uniformed lineage specifications for future transplantation therapies and biomedical research.
Phase I clinical and pharmacokinetic study of a novel schedule of flavopiridol in relapsed or refractory acute leukemias (2010)

Flavopiridol as a single agent given by intravenous bolus/continuous intravenous infusion causes marked, immediate cytoreduction in relapsed/refractory acute leukemias, but objective clinical responses were uncommon. With this schedule, the dose is limited by secretory diarrhea.
Chlamydia pneumoniae, strain TWAR and atherosclerosis. (1993)

Infection with Chlamydia pneumoniae, strain TWAR, has been associated with atherosclerotic cardiovascular disease in two types of investigations, seroepidemiological and morphological-molecular. A series of seroepidemiological studies from Finland and the United States have shown a statistically significant association between several types of TWAR antibody, including immune complexes, and atherosclerotic disease of the coronary and carotid arteries. The morphological-molecular studies have shown the C. pneumoniae organism in atheroma of the coronary arteries, and aorta but not in normal arteries. The presence of the organism in atheroma has been demonstrated by electron-microscopy, immunocytochemical staining with TWAR-specific monoclonal antibody and by the polymerase chain reaction for TWAR-specific DNA. The aetiological or pathogenic significance of the association of C. pneumoniae and atherosclerotic disease remains to be determined.