gebhart/patrepeval huggingface dataset:
Preparation and Properties of a Novel Class of Polyhydroxyalkanoate Copolymers (2005)

Polyhydroxyalkanoates (PHAs) are biodegradable aliphatic polyesters, known to be produced by many common microorganisms. Nodax is a recently introduced family of PHA copolymers comprising 3-hydroxybutyrate units and a relatively small amount of other medium chain length 3-hydroxyalkanoate (mcl-3HA) comonomers with side groups of at least three carbon units or more. There are several different grades of copolymers available, depending on the average molecular weight, average mcl-3HA content within the copolymer, and side group chain length of the chosen mcl-3HA unit. PHA copolymers with different mcl-3HA types and contents can be made either by bacterial fermentation or by chemical synthesis. The incorporation of mcl-3HA units into PHAs effectively lowers the crystallinity and T(m) in a manner similar to the effect of alpha-olefins in linear low-density polyethylene. The T(m) can be lowered well below the thermal decomposition temperature of PHAs to make this material much easier to process. The reduced crystallinity provides the ductility and toughness required for many practical applications. The mcl-3HA content regulates the T(m) and crystallinity of copolymer almost independently of the branch size, as long as more than three carbons are present in the side group. On the other hand, the side group chain length of the mcl-3HA has a profound effect on the flexibility of copolymer.
Recognizing human action in time-sequential images using hidden Markov model (2003)

A human action recognition method based on a hidden Markov model (HMM) is proposed. It is a feature-based bottom-up approach that is characterized by its learning capability and time-scale invariability. To apply HMMs, one set of time-sequential images is transformed into an image feature vector sequence, and the sequence is converted into a symbol sequence by vector quantization. In learning human action categories, the parameters of the HMMs, one per category, are optimized so as to best describe the training sequences from the category. To recognize an observed sequence, the HMM which best matches the sequence is chosen. Experimental results for real time-sequential images of sports scenes show recognition rates higher than 90%. The recognition rate is improved by increasing the number of people used to generate the training data, indicating the possibility of establishing a person-independent action recognizer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optically Stimulated Luminescence Dosimetry Using Doped Fused Quartz (1999)

Optically stimulated luminescence (OSL) dosimetry measurements using Cu1+-doped fused quartz are reported. The OSL sensitivity of this material to 60Co ? rays was found to be about twenty times greater than that measured previously for related Cu1+-doped glasses that exhibit OSL sensitivity. The dose-response was measured from 0.13 to 51.6 �C.kg-1 (0.5 mR to 300 mR) and is linear over this range. Spectral measurements of the photoluminescence, thermoluminescence and optically stimulated luminescence reveal that the Cu1+ ions serve as the luminescence centres for recombination of both the TL and OSL traps. The results indicate that the TL and OSL traps in the Cu1+-doped fused quartz are in some way related.
Mitochondrial oxidative stress drives tumor progression and metastasis: should we use antioxidants as a key component of cancer treatment and prevention? (2011)

The functional role of oxidative stress in cancer pathogenesis has long been a hotly debated topic. A study published this month in BMC Cancer by Goh et al., directly addresses this issue by using a molecular genetic approach, via an established mouse animal model of human breast cancer. More specifically, alleviation of mitochondrial oxidative stress, via transgenic over-expression of catalase (an anti-oxidant enzyme) targeted to mitochondria, was sufficient to lower tumor grade (from high-to-low) and to dramatically reduce metastatic tumor burden by >12-fold. Here, we discuss these new findings and place them in the context of several other recent studies showing that oxidative stress directly contributes to tumor progression and metastasis. These results have important clinical and translational significance, as most current chemo-therapeutic agents and radiation therapy increase oxidative stress, and, therefore, could help drive tumor recurrence and metastasis. Similarly, chemo- and radiation-therapy both increase the risk for developing a secondary malignancy, such as leukemia and/or lymphoma. To effectively reduce mitochondrial oxidative stress, medical oncologists should now re-consider the use of powerful anti-oxidants as a key component of patient therapy and cancer prevention. Please see related research article: http://www.biomedcentral.com/1471-2407/11/191.
Intracellular Free Magnesium Deficiency Plays a Key Role in Increased Platelet Reactivity in Type II Diabetes Mellitus (1992)

These results suggest that type II diabetic patients have intracellular Mg2+ deficiency and that Mg deficiency may be a key factor in leading to enhanced platelet reactivity in type II diabetes. Therefore, Mg supplementation may provide a new therapeutic approach to reducing vascular disease in patients with diabetes.
CTLA-4 Regulates Tolerance Induction and T Cell Differentiation In Vivo (1998)

Cytotoxic T lymphocyte Ag-4 (CTLA-4; CD152) is an important T cell regulatory molecule. In vitro experiments have shown that the blockade of signals through CTLA-4 augments T cell expansion, while CTLA-4 cross-linking results in decreased T cell proliferation due to decreased IL-2 production. However, less is known about the role of CTLA-4 in regulating an ongoing immune response. In this study, we examined the role of CTLA-4 in the expansion, decline, tolerization, and differentiation of T cells following treatment with staphylococcal enterotoxin B (SEB). Anti-CTLA-4 treatment resulted in increased numbers of SEB-reactive T cells and blockade of subsequent tolerance induction. Further examination of the SEB-reactive cells from anti-CTLA-4-treated mice demonstrated that both the CD4+ and CD8+ Vbeta8+ T cells produced IL-4, providing evidence that not only do signals through CTLA-4 regulate T cell-tolerizing events, but they also play an important role in the differentiation of T cells in vivo.
Is CD137 Ligand (CD137L) Signaling a Fine Tuner of Immune Responses? (2015)

Now, it has been being accepted that reverse signaling through CD137 ligand (CD137L) plays an important role in vivo during hematopoiesis and in immune regulation. However, due to technical difficulty in dissecting both directional signaling events simultaneously in vivo, most biological activities caused by CD137-CD137L interactions are considered as results from signaling events of the CD137 receptor. To make the story more complex, CD137(-/-) and CD137L(-/-) mice have increased or decreased immune responses in a context-dependent manner. In this Mini review, I will try to provide a plausible explanation for how CD137L signaling is controlled during immune responses.
Regulation of V(D)J Recombination Activator Protein RAG-2 by Phosphorylation (1993)

Antigen receptor genes are assembled by site-specific DNA rearrangement. The recombination activator genes RAG-1 and RAG-2 are essential for this process, termed V(D)J rearrangement. The activity and stability of the RAG-2 protein have now been shown to be regulated by phosphorylation. In fibroblasts RAG-2 was phosphorylated predominantly at two serine residues, one of which affected RAG-2 activity in vivo. The threonine at residue 490 was phosphorylated by p34cdc2 kinase in vitro; phosphorylation at this site in vivo was associated with rapid degradation of RAG-2. Instability was transferred to chimeric proteins by a 90-residue portion of RAG-2. Mutation of the p34cdc2 phosphorylation site of the tumor suppressor protein p53 conferred a similar phenotype, suggesting that this association between phosphorylation and degradation is a general mechanism.
A longitudinal study of sex differences in how physicians relate to dying patients. (1993)

The authors were interested in whether or not there were sex differences in the way physicians respond to the needs of dying patients and their families at the time they graduate from medical school versus ten years later. A 71% return rate was received from a questionnaire mailed in 1976 to 1,540 graduates of five selected medical schools; the return rate for the follow-up study in 1986 was 58%. Ten percent of the respondents were female. The 1976 findings provided some evidence to support the argument that there are differences between male and female physicians' attitudes toward dying patients soon after graduation. The 1986 data, gathered after a decade of practicing medicine, showed even more striking differences. Perhaps "feminine characteristics" lend themselves to better communication with dying patients and their families than "masculine traits" do.
Statistical Analysis of Character Correlations in Brewer's Blackbirds (1971)

&lt;it&gt;Power, D. M. (Dept. of Ornithology, Royal Ontario Museum and Dept. of Zoology, University of Toronto, Toronto, Ontario, Canada) 1971. Statistical analysis of character correlations in Brewer's Blackbirds. Syst. Zool., 20:186–203&lt;/it&gt;.—Character correlations among 37 skin and skeletal characters within a statistically homogeneous sample of Brewer's blackbirds (&lt;it&gt;Euphagus cyanocephalus&lt;/it&gt;) were analyzed by component analysis and average linkage cluster analysis in order to isolate structural and/or functional character sets. Associations were assessed using product-moment correlation coefficients, partial correlations that corrected for a general size factor, and a subset of special partial correlations that corrected for a group factor defining high intercorrelations among limb bone length measurements. With ordinary correlations separate associations were identified for limb bone length, flight feather length, bill length, sternum size, bill width, and limb bone thickness. Some characters were predominantly independent. Partial correlations that corrected for covariation due to the group limb bone length factor indicated special associations among wing bones. An overall size factor is defined as that component which accounts for most of the covariation among all characters. Partial correlations correcting for this factor were analyzed and several size-independent associations emerged. The limb bone length assemblage is in part size-dependent. Size-independent associations include wing bone length, flight feather length, bill length, bill width, and limb bone thickness assemblages, and possibly a partial leg bone length set. Association of three sternal characters appears size-dependent, however a special size-independent association between sternum length and keel height was found. In addition, low-level, size-independent associations are found for pelvis width and bill height characters, as well as between the scapula and coracoid in the pectoral girdle. Results suggest the existence of selective factors that affect the development of functional complex as a whole. Comments are given concerning redundant characters in systematic studies and a temporary solution is offered concerning the problem of adequate sample size in studies of character correlations.
Mapping the phosphorylation sites of proteins using on-line immobilized metal affinity chromatography/capillary electrophoresis/electrospray ionization multiple stage tandem mass spectrometry (2000)

On-line immobilized metal affinity chromatography/capillary electrophoresis/electrospray ionization-mass spectrometry (IMAC/CE/ESI-MS) offers selective preconcentration of phosphorylated peptides with identification of the phosphorylated amino acid(s). The preconcentration provides low concentration limits of detection and capillary electrophoresis separates the peptides. Recently, we reported a fast, simple, and sensitive on-line IMAC/CE/ESI-MS/MS method for the determination of phosphopeptides at low-pmole levels. That work is expanded here by use of multiple stage tandem mass spectrometry (MS(n), n = 2,3) to isolate and fragment target ions to provide more reliable assignments of phosphorylated residues. The application of IMAC/CE/ESI-MS(n) is demonstrated by the analysis of tryptic digests of alpha- and beta-casein and in-gel tryptic digests of beta-casein.
Docosahexaenoic and Eicosapentaenoic Acids Inhibit Human Lymphoproliferative Responses In Vitro but not the Expression of T Cell Surface Activation Markers (1996)

The effects of polyunsaturated fatty acids (PUFAs: docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids) on induced lymphocyte proliferation and expression of CD25alpha chain of interleukin-2 receptor, CD71 and HLA-DR were investigated. PUFAs had no effect on phytohaemagglutinin (PHA)-induced lymphocyte agglutination, but they strongly inhibited the lymphoproliferative response to PHA. This inhibitory effect is PUFA dose-dependent and seems to be more potent with DHA than EPA, Pre-incubation experiments showed that lymphocytes cultured with PUFAs for 6 h then washed and exposed to PHA, still inhibited lymphocyte proliferation. The authors also showed that this inhibitory activity was time dependent but became nonsignificant when PUFAs were added after 48 h lymphocyte culture. The addition of excess exogenous human recombinant rIL-2 partly restored PHA-lymphocyte proliferation inhibited by EPA but not by DHA. On the other hand, the authors showed that PUFAS did not inhibit IL-2 stimulated lymphocyte proliferation. The addition of PUFAs to cell culture medium had no inhibitory action on the PHA-induced lymphocyte expression of CD25, CD71 and HLA-DR. Furthermore, this effect appeared independent of eicosanoid synthesis or peroxide formation. Indeed, the inclusion of aspirin and vitamin E in the culture medium did not prevent the inhibitory effects of PUFAs on lymphocyte proliferation. Regardless of the mechanism of action, the inhibitory effect of PUFAs on activated lymphocytes may explain why some clinical trials of fish oil supplemented diets containing high amounts of DHA and EPA have been successful in improving the health status of patients suffering from inflammatory and autoimmune disorders.
Methylated DNA as a possible screening marker for neoplastic disease in several body fluids (2003)

Early detection appears to be one of the most important approaches to reducing mortality caused by neoplasia. Changes in DNA methylation have been recognized as one of the most common molecular alterations in human tumors. Due to the ubiquity of DNA methylation changes and the possibility to detect methylated DNA in several body fluids, this specifically altered DNA may serve as a potential new screening marker for neoplastic disease.
Interaction of Intraleukocytic Bacteria and Antibiotics (1973)

Bacteria that survive inside polymorphonuclear neutrophils (PMN) following phagocytosis are protected from the bactericidal action of most antibiotics. Two possible explanations are altered metabolism by intraleukocytic bacteria or failure of antibiotics to enter the phagosome. The oxygen consumption of intraleukocytic and extraleukocytic bacteria was measured as an index of bacterial metabolism. PMN respiration and bactericidal activity were suppressed with large doses of hydrocortisone and extraleukocytic bacterial oxygen consumption was abolished by the addition of lysostaphin. Intraleukocytic bacterial continued to consume oxygen suggesting that surviving ingested micro-organisms are metabolically active. Neither penicillin (which cannot kill intraleukocytic bacteria) nor rifampin (which can kill intraleukocytic bacteria) was bactericidal for staphylococci at 5 degrees C. Thus, rifampin is not uniquely able to kill "resting" bacteria.Intraleukocytic or extraleukocytic Staphylococcus aurens were incubated with [benzyl-(14)C]penicillin for 2 h at 37 degrees C. Live intraleukocytic bacteria bound only 13% as much penicillin as live bacteria incubated with killed PMN. To measure the penetration of antibiotics into PMN, [(14)C]rifampin and [(14)C]penicillin were measured in leukocyte pellets and in the supernatant fluid. The total water space in the pellets was quantitated using tritium water and the extracellular water space was measured using Na(235)SO(4). All penicillin associated with the cell pellet could be accounted for in extracellular water. Thus penicillin was completely excluded from the leukocytes. Rifampin was concentrated in the cell pellet 2.2 times when compared with the supernatant concentration. These studies suggest that a likely explanation for the survival of phagocytized bacteria in the presence of high concentrations of most antibiotics is the inability of the antibiotic to enter the phagocyte. Rifampin, which is highly lipid soluble, can enter leukocytes and kill intracellular bacteria.
The Molecular Cell Biology of Interferon-Gamma and Its Receptor (1993)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Interdicting protease-activated receptor-2-driven inflammation with cell-penetrating pepducins (2011)

Protease-activated receptor-2 (PAR2), a cell surface receptor for trypsin-like proteases, plays a key role in a number of acute and chronic inflammatory diseases of the joints, lungs, brain, gastrointestinal tract, and vascular systems. Despite considerable effort by the pharmaceutical industry, PAR2 has proven recalcitrant to targeting by small molecule inhibitors, which have been unable to effectively prevent the interaction of the protease-generated tethered ligand with the body of the receptor. Here, we report the development of first-in-class cell-penetrating lipopeptide "pepducin" antagonists of PAR2. The design of the third intracellular (i3) loop pepducins were based on a structural model of a PAR2 dimer and by mutating key pharmacophores in the receptor intracellular loops and analogous pepducins. Individual pharmacophores were identified, which controlled constitutive, agonist, and antagonist activities. This approach culminated in the identification of the P2pal-18S pepducin which completely suppressed trypsin and mast cell tryptase signaling through PAR2 in neutrophils and colon cancer cells. The PAR2 pepducin was highly efficacious in blocking PAR2-dependent inflammatory responses in mouse models. These effects were lost in PAR2-deficient and mast-cell-deficient mice, thereby validating the specificity of the pepducin in vivo. These data provide proof of concept that PAR2 pepducin antagonists may afford effective treatments of potentially debilitating inflammatory diseases and serve as a blueprint for developing highly potent and specific i3-loop-based pepducins for other G protein-coupled receptors (GPCRs).
Occurrence of multiple types of human papillomavirus in genital tract lesions. Analysis by in situ hybridization and the polymerase chain reaction. (1991)

More than 22 types of human papillomavirus (HPV) have been detected in genital tract squamous cell intraepithelial lesions. Seven of two hundred eighty-six (2.4%) genital tract tissues in which HPV DNA was detected by in situ hybridization contained two or more different HPV types. When analyzed by site, 5 of 204 (2.4%) of cervical intraepithelial lesions were infected by more than one type, compared with 2 of 82 (2.4%) of vulvar lesions. The rate for low-grade lesions was similar (5/218; 2.3%) to that for high-grade lesions (2/68; 2.9%). In contrast, two different HPV types were detected in 6/33 (18%) of tissues by the polymerase chain reaction (PCR) using type-specific primers for eight HPV types. It is concluded that infection by one HPV type is rarely associated with concurrent 'active' infection by a second HPV type, even though DNA of a different viral type can be detected by PCR in about one fifth of such cases. Further study is required to determine if an existing HPV infection can inhibit replication by a different HPV type.
High Cellular Concentration of Peripheral Blood Progenitor Cells During Cryopreservation Adversely Affects CFU-GM but Not Hematopoietic Recovery (1996)

The effects of bone marrow (BM) and peripheral blood progenitor (PBPC) concentration during cryopreservation on subsequent hematopoietic engraftment following high-dose chemotherapy were studied in 24 patients. Seventeen BM harvests and 71 PBPC collections were performed between July 1991 and June 1994. The PBPC were frozen at significantly higher cellular concentrations than the BM (medians of 243 x 10(6)/ml versus 73 x 10(6)/ml respectively, p = 0.0003). The recovery of committed progenitor cell colonies (CFU-GM) was significantly lower from PBPC frozen at concentrations above the median, compared with 116% from those frozen at concentrations below the median (p = 0.0467). This phenomenon was not seen in BM, which was generally frozen at a threefold lower concentrations. Despite the lower recovery of CFU-GM when PBPC were frozen at a higher concentration, the patients receiving these grafts achieved good hematopoietic recovery. The higher number of PBPC probably compensated for the loss, and the patients still received a substantial number of clonogenic hematopoietic precursors.
A STATISTICAL INTERPRETATION OF TERM SPECIFICITY AND ITS APPLICATION IN RETRIEVAL (1972)

Abstract The exhaustivity of document descriptions and the specificity of index terms are usually regarded as independent. It is suggested that specificity should be interpreted statistically, as a function of term use rather than of term meaning. The effects on retrieval of variations in term specificity are examined, experiments with three test collections showing in particular that frequently‐occurring terms are required for good overall performance. It is argued that terms should be weighted according to collection frequency, so that matches on less frequent, more specific, terms are of greater value than matches on frequent terms. Results for the test collections show that considerable improvements in performance are obtained with this very simple procedure.
Relationship between plasma and red cell biopterins in acute and chronic hyperphenylalaninaemia (1989)

Biopterin concentrations in red blood cells were higher in patients with chronic hyperphenylalaninaemia than following a single oral dose of phenylalanine, although the plasma concentrations were similar. These findings suggest that tetrahydrobiopterin is synthesized in immature red blood cells in response to hyperphenylalaninaemia. The less marked increase in plasma biopterin suggests slow release from a tissue reservoir. The maintenance of a differential between erythrocyte and plasma biopterin concentrations suggests that some mechanism retains biopterin intracellularly.