gebhart/patrepeval huggingface dataset:
Biotemplated nanostructures: directed assembly of electronic and optical materials using nanoscale complementarity (2007)

The worlds of biology and materials engineering have traditionally been quite distinct. The spontaneous assembly of biological materials presents a stark contrast to the rational fabrication conventionally required for high-performance materials. The merger of these diverse fields represents a tremendous opportunity, given that biomolecules can organize into intricate, functionally sophisticated structures—exactly the sort of precise control urgently needed to make the next generation of materials for medicine, computing, communications, energy, and the environment. In the last several years, tremendous advances have been made towards using the structures of biomolecules as scaffolds and templates for nanomaterials. This overview discusses how the sequence and structural information encoded within proteins and nucleic acids can be used to program the synthesis of nanomaterials.
Chromosomal Abnormalities in Cancer (2008)

This review gives an account of chromosomal aberrations in cancer cells. Such abnormalities have typically been associated with hematologic cancers, but recent work has shown a variety of chromosomal changes in solid tumors, including prostate cancer and non–small-cell lung cancer. The authors point out that some of the chromosomal abnormalities have revealed targets for cancer treatment, and others have clinical application in the diagnosis of certain types of neoplasms and in the formulation of a prognosis.
TCR and CD3 antibody cross‐reactivity in 44 species (2007)

The production of monoclonal antibodies is very costly, and antibodies are only available for a limited number of species. Until a more cost effective method of antibody production is found, identification of cross-reactive antibodies is an alternative approach that can provide investigators studying immunity in minor species with valuable antibody reagents. Flow cytometry was used to test 21 monoclonal antibodies (mAb), raised against alphabeta and gammadelta T cell receptors and CD3 from human and five animal species, for cross-reactivity in 44 different species including 16 species of nonhuman primates, marsupials, carnivores, lagomorphs, rodents, ruminants, swine, cetacean, horse, birds, a reptile, and fish. Fifteen of the mAbs cross-reacted with orthologous molecules in one or more species. Two antibodies, anti-human TCR gammadelta (B1.1), and anti-human CD3 (SP34) were found to costain in 13 species of nonhuman primates. This study has identified valuable new reagents for studying T cell populations in different animal species and for the first time characterized antibodies useful for studying gammadelta T cell populations in many species of primates. These antibodies may be used for further immunity research in species with less well-characterized immune systems.
Circulating Fetal Cell-Free DNA Fractions Differ in Autosomal Aneuploidies and Monosomy X (2013)

MPS tag-count data can be used to determine FF directly and accurately. Compared with male euploid fetuses, the FF is higher in maternal plasma when the fetus has trisomy 21 and is lower when the fetus has trisomy 18, 13, or monosomy X. The different biologies of these aneuploidies have practical implications for the determination of cutoff values, which in turn will affect the diagnostic sensitivity and specificity of the test.
Oxidative stress induces cell cycle-dependent Mre11 recruitment, ATM and Chk2 activation and histone H2AX phosphorylation (2008)

DNA damage response recruits complex molecular machinery involved in DNA repair, arrest of cell cycle progression, and potentially in activation of apoptotic pathway. Among the first responders is the Mre11- (MRN) complex of proteins (Mre11, Rad50, Nbs1), essential for activation of ATM; the latter activates checkpoint kinase 2 (Chk2) and phosphorylates histone H2AX. In the present study the recruitment of Mre11 and phosphorylation of ATM, Chk2 and H2AX (gammaH2AX) detected immunocytochemically were measured by laser scanning cytometry to assess kinetics of these events in A549 cells treated with H(2)O(2). Recruitment of Mre11 was rapid, peaked at 10 min of exposure to the oxidant, and was of similar extent in all phases of the cell cycle. ATM and Chk2 activation as well as H2AX phosphorylation reached maximum levels after 30 min of treatment with H(2)O(2); the extent of phosphorylation of each was most prominent in S-, less in G(1)-, and the least in G(2)M- phase cells. A strong correlation between activation of ATM and Chk2, measured in the same cells, was seen in all phases of the cycle. In untreated cells activated Chk2 and Mre11 were distinctly present in centrosomes while in interphase cells they had characteristic punctate nuclear localization. The punctate expression of activated Chk2 both in untreated and H(2)O(2) treated cells was accentuated when measured as maximal pixel rather than integrated value of immunofluorescence (IF) per nucleus, and was most pronounced in G(1) cells, likely reflecting the function of Chk2 in activating Cdc25A. Subpopulations of G(1) and G(2)M cells with strong maximal pixel of Chk2-Thr68(P) IF in association with centrosomes were present in untreated cultures. Cytometric multiparameter assessment of the DNA damage response utilizing quantitative image analysis that allows one to measure inhomogeneity of fluorochrome distribution (e.g., maximal pixel) offers unique advantage in studies of the response of different cell constituents in relation to cell cycle position.
Restoration of Defective Oxygen-transport Function of Stored Red Blood Cells by Addition of Inosine (1968)

During storage of acid-citrate-dextrose-blood the oxygen affinity of the haemoglobin is increased; i.e. the oxygen dissociation curve is shifted to the left. In the meantime the red cell ATP and 2,3-diphospho-glycerate levels are decreased. In the present investigation it is shown that these changes are reversed by addition of inosine. Thus the oxygen-transport function of stored blood seems to be related to the intracorpuscular ATP and 2,3-diphosphoglycerate levels.
Vaccinia virus A17L gene product is essential for an early step in virion morphogenesis (1995)

Vaccinia virus (VV) A17L gene encodes a 23-kDa protein that is proteolytically cleaved to generate a 21-kDa product that is incorporated into the viral particles. We have previously shown that the 21-kDa protein forms a stable complex with the VV 14-kDa envelope protein and suggested that the 21-kDa protein may serve to anchor the 14-kDa protein to the envelope of the virion (D. Rodríguez, J. R. Rodríguez, and M. Esteban, J. Virol. 67:3435-3440, 1993). To study the role of the 21-kDa protein in virion assembly, in this investigation we generated a VV recombinant, VVindA17L, that contains an inducible A17L gene regulated by the E. coli repressor/operator system. In the absence of the inducer, shutoff of the A17L gene was complete, and this shutoff correlated with a reduction in virus yields of about 3 log units. Although early and late viral polypeptides are normally synthesized in the absence of the A17L gene product, proteolytic processing of the major p4a and p4b core proteins was clearly impaired under these conditions. Electron microscopy examination of cells infected in the absence of isopropylthiogalactopyranoside (IPTG) revealed that virion morphogenesis was completely arrested at a very early stage, even prior to the formation of crescent-shaped membranes, which are the first distinguishable viral structures. Only electron-dense structures similar to rifampin bodies, but devoid of membranes, could be observed in the cytoplasm of cells infected with VVindA17L under nonpermissive conditions. Considering the most recent assembly model presented by Sodeik et al. (B. Sodeik, R. W. Doms, M. Ericsson, G. Hiller, C. E. Machamer, W. van't Hof, G. van Meer, B. Moss, and G. Griffiths, J. Cell Biol. 121:521-541, 1993), we propose that this protein is targeted to the intermediate compartment and is involved in the recruitment of these membranes to the viral factories, where it forms the characteristic crescent structures that subsequently result in the formation of virions.
Inhibition of fibroblast cell adhesion on substrate by coating with 2-methacryloyloxyethyl phosphorylcholine polymers (1999)

Fibroblast adhesion and growth behavior were examined on various polymers coated on a poly(ethylene telephthalate) (PET) substrate. The polymers are poly[2-methacryloyloxyethyl phosphorylcholine (MPC)-co-n-butyl methacrylatel copolymer (PMB)s with different MPC unit compositions, and poly(2-hydroxyethyl methacrylate). Surface analysis by dynamic contact angle measurement revealed that the mobility of the polymer chain on the PET substrate depended on the MPC unit composition, but there was no significant difference between the PMBs with 3-10 mol% MPC units and poly(HEMA). Fibronectin adsorption on the polymer surface from a cell culture medium was determined by immunoassay. The adsorbed fibronection was evenly distrubuted in every polymer, however, the amount was reduced with an increase in the MPC unit composition in the PMB. This result suggested that the MPC unit could weaken the interaction between the polymer surface and proteins. When fibroblast L-929 cells, were cultured on the polymers, the cells adhered and the number of cells increased on not only the hydrophobic poly(BMA) but also on the hydrophilic poly(HEMA). However, the number of cells that adhered on the PMB surface decreased with an increase in the MPC unit composition. This was a result of the fibronectin adsorption behavior. Thus, it could be concluded that since the PMB could suppress cell adhesion proteins e.g. fibronectin, the PMB showed excellent cell adhesive resistance properties.
Clinical nutrition: 7. Functional foods--more than just nutrition. (2002)

Case 

Mr. B is a well-educated, nonsmoking, 48-year-old, sedentary businessman with type 2 diabetes mellitus that is well controlled with metformin. He has no renal or other complications of his disease, and his body weight is normal. His lipid profile, however, is abnormal with the low-density
Expression of mutated epidermal growth factor receptor by non-small cell lung carcinomas. (1993)

The development of novel immunotherapy strategies for non-small cell lung cancer (NSCLC) will be facilitated by the identification of tumor-specific targets. Although the epidermal growth factor receptor (EGFR) is overexpressed in many cases of NSCLC, its wide distribution in normal tissue may limit its suitability as an immunotherapeutic target. However, mutations within the EGFR that are unique to malignancies may provide specific targets for immunotherapeutic intervention. For example, one mutant form, the type III deletion mutant of the EGFR, that has been identified in glioblastomas contains a novel peptide sequence in its extracellular domain which is detectable by anti-peptide antisera. In this study, the prevalence of this type of mutation of the EGFR in NSCLC was determined. Thirty-two frozen sections of primary NSCLC were examined by immunocytochemistry to determine the presence of native and mutated EGFR. Native EGFR was overexpressed in 12 of the 32 sections and a diffuse cellular distribution of the EGFR type III deletion mutation was identified in five (16%) of the specimens (2 of 13 squamous, 2 of 2 mixed, 0 of 10 adenocarcinoma, and 1 of 7 undifferentiated). This mutated EGFR was not detected in sections of normal breast, lung, skin, ovary, colon, kidney, endometrium, and placenta. The type III EGFR deletion mutant, expressed in some cases of NSCLC, may be a molecularly defined, tumor-specific antigen in lung cancer.
Eosinophils and atopic dermatitis (2004)

In spite of the progress regarding the description of immunological phenomena associated with atopic dermatitis (AD), the pathogenesis of this disease still remains unclear. The presence of eosinophils in the inflammatory infiltrate of AD has long been established. Eosinophil numbers as well as eosinophil granule protein levels in peripheral blood are elevated in most AD patients and appear to correlate with disease activity. Moreover, eosinophil granule proteins, which possess cytotoxic activity, are deposited in the skin lesions. These observations indicate a role of eosinophils in the pathogenesis of AD. Furthermore, AD is associated with increased production of T helper 2 cytokines including interleukin (IL)-5, which specifically acts on eosinophils, resulting in accelerated eosinophilopoiesis, chemotaxis, cell activation, and delayed apoptosis. Therefore, IL-5 is an interesting target for experimental therapy in this inflammatory disorder of the skin. Such studies might result in new insights into the pathogenetic role of eosinophils in AD.
Recommended guidelines for uniform reporting of data from out-of-hospital cardiac arrest: the Utstein Style. A statement for health professionals from a task force of the American Heart Association, the European Resuscitation Council, the Heart and Stroke Foundation of Canada, and the Australian Resuscitation Council. (1991)

esuscitation has become an important multi- disciplinary branch of medicine, demanding a spectrum of skills and attracting a plethora of specialties and organizations, each of which claims a legitimate interest in the science and prac- tice of resuscitation. This complex background has hindered the development of a uniform pattern or set of definitions for reporting results. Different systems cannot readily be compared or contrasted because data are rarely compatible. Representatives from the American Heart Association, the European Resusci- tation Council, the Heart and Stroke Foundation of Canada, and the Australian Resuscitation Council recently met to establish uniform terms and defini- tions for out-of-hospital resuscitation.
Synthesis and secretion of bacterial antigens by attenuated Salmonella via the Escherichia coli hemolysin secretion system. (1994)

We describe a plasmid system which allows the secretion of foreign antigens in attenuated Salmonella aroA strains by the secretion apparatus of E. coli hemolysin. The gene (or gene fragment) encoding the antigen is inserted in frame into a residual position of the hlyA gene, encoding the HlyA secretion signal (HlyAs). Generally, the fused gene is efficiently expressed and the synthesized antigen is in part secreted into the culture supernatant and in part exposed on the surface of the producing Salmonella strain. The successful use of this approach is demonstrated with two antigens of Salmonella typhimurium, PagC and SlyA, both of which are potent virulence factors but produced only in small amounts under in vitro culture conditions and two virulence proteins of Listeria monocytogenes, p60 and listeriolysin. Interestingly the listeriolysin fusion protein proved to be cytolytically active and allowed, when expressed in Salmonella, the escape of these bacteria into the cytoplasm of infected macrophages.
Structure and ionic conductivity in lithium garnets (2010)

Garnets are capable of accommodating an excess of lithium cations beyond that normally found in this prototypical structure. This excess lithium is found in a mixture of coordination environments with considerable positional and occupational disorder and leads to ionic conductivity of up to 4 × 10−4 S cm−1 at room temperature. This high value for total conductivity, combined with excellent thermal and (electro)chemical resistance makes these candidate materials for operation in all solid-state batteries. This review looks at garnets with a wide range of stoichiometries and lithium concentrations and the impact of complex lithium distributions and crystallographic order/disorder transitions on the transport properties of these materials.
Proton/peptide cotransporter (PEPT 2) from human kidney: Functional characterization and chromosomal localization (1995)

We report here on the functional characterization of the H+/peptide cotransporter PEPT 2 cloned from human kidney and on the chromosomal localization of the PEPT 2 gene. PEPT 2, when functionally expressed in HeLa cells, induces the transport of the neutral dipeptide glycylsarcosine. The induced transport activity is markedly influenced by extracellular pH. The optimum pH for the transport process is 6.0-7.0. Kinetic analysis has revealed that PEPT 2 is a high-affinity transporter, the Michaelis-Menten constant for glycylsarcosine being 74 +/- 14 microM. The human intestinal H+/peptide cotransporter PEPT 1 has 4-fold less affinity for the dipeptide under identical experimental conditions. Studies with other chemically diverse dipeptides have established that PEPT 2 possesses higher affinity than PEPT 1 not only for neutral peptides but also for peptides consisting of anionic and/or cationic amino acids. Somatic cell hybrid analysis and in situ hybridization have shown that the gene encoding PEPT 2 maps to human chromosome 3q13.3-q21.
Quarterly Economic Commentary Research Notes, Autumn 2015 (2015)

The pace of the Irish recovery would appear to be increasing; the latest National Accounts indicate that output in the economy grew by over 5 per cent in 2014 and by almost 2 per cent in Q2 2015 alone. Use of the nowcasting model (summarised in the Appendix) suggests the economy is growing through Q3 by approximately 1.5 per cent per quarter in 2015. Accordingly, we now update our forecast for GDP in 2015 to 6 per cent, with GNP expected to grow marginally less at 5.9 per cent. One significant consequence of this is that Irish income per capita, which fell significantly post-2007, is now back to the peak level prior to the financial crisis.
[Expression of p15 and p16 proteins in tongue squamous cell carcinoma and their significances]. (2003)

The expression of p15 and p16 protein are closely associated with clinical stages and cervical lymph node metastasis of TSCC. p15 deletion, or both p15 and p16 co-deletion in TSCC can also predict a poor prognosis. p15 and p16 expression can be used as parameters for evaluating clinical stages and metastatic potential as well as prognosis of TSCC.
The localized expression of extracellular matrix components in healing tendon insertion sites: an in situ hybridization study (2002)

The localized expression of a number of extracellular matrix genes was evaluated over time in a novel rat rotator cuff injury model. The supraspinatus tendons of rats were severed at the bony insertion and repaired surgically. The healing response was evaluated at 1, 2, 4, and 8 weeks post-injury using histologic and in situ hybridization techniques. Expression patterns of collagens (I, II, III, IX, X, XII), proteoglycans (decorin, aggrecan, versican, biglycan, fibromodulin), and other extracellular matrix proteins (elastin, osteocalcin, alkaline phosphatase) were evaluated at the healing tendon to bone insertion site. Histologic results indicate a poor healing response to the injury, with only partial recreation of the insertion site by 8 weeks. In situ hybridization results indicate a specific pattern of genes expressed in each zone of the insertion site (i.e., tendon, fibrocartilage, mineralized cartilage, bone). Overall, expression of collagen types I and XII, aggrecan, and biglycan was increased, while expression of collagen type X and decorin was decreased. Expression of collagen type I, collagen type XII, and biglycan decreased over time, but remained above normal at 8 weeks. Results indicate that the rat supraspinatus tendon is ineffective in recreating the original insertion site, even at 8 weeks post-injury, in the absence of biological or biomechanical enhancements.
Structural Characterization and High‐Temperature Behavior of Silicon Oxycarbide Glasses Prepared from Sol‐Gel Precursors Containing Si‐H Bonds (1995)

Silicon oxycarbide glasses have been synthesized by inert atmosphere pyrolysis at 1000°C of gel precursors obtained by cohydrolysis of triethoxysilane, HSi(OEt) 3 , and methyl‐diethoxysilane, HMeSi(OEt) 2 . The oxycarbide structures have been carefully characterized by means of different techniques such as 29 Si magic angle spinning nuclear magnetic resonance (MAS‐NMR) and Raman spectroscopies, X‐ray diffraction (XRD), and chemical analysis. Experimental results clearly indicate that, depending on the composition of the starting gels, the resulting oxycarbide glass either is formed by a pure oxycarbide phase or contains an extra carbon or silicon phase. By increasing the temperature up to 1500°C, the oxycarbide glasses display compositional and weight stability; however, the amorphous network undergoes structural rearrangements that lead to the precipitation of nano‐sized β‐SiC crystallites into amorphous silica. Crystallization of metallic silicon is also clearly observed at 1500°C for the samples in which the presence of Si‐Si bonds was postulated at 1000°C.
Stromal‐Cell and Cytokine‐Dependent Lymphocyte Clones Which Span the Pre‐B‐ to B‐Cell Transition (1990)

Five stromal-cell-dependent lymphocyte clones are described that correspond to late pre-B or early B-cell stages of differentiation. They are useful for determining the molecular requirements for pre-B replication, for studying the stromal cells that supply those factors, and for delineating the final sequence of differentiation events as newly formed lymphocytes prepare to exit the bone marrow. The efficiency of lymphocyte growth at limiting dilution varied substantially on different stromal-cell clones and may reflect functional heterogeneity of stromal cells. Most lymphocyte clones were similar to uncloned lymphocytes from Whitlock-Witte cultures in that they responded only transiently to interleukin-7 (IL-7) and then died, unless maintained on a stromal-cell clone. One unusual lymphocyte clone (2E8) was propagated for more than 1 year in IL-7 alone and was selectively responsive to that cytokine. Most of the lymphocyte clones were not tumorigenic in immunodeficient mice. However, one pre-B clone (1A9) grew autonomously in culture when held at high density, responded to conditioned medium from a number of cell lines, and was tumorigenic. Tumors derived from this clone were infiltrated by stromal cells and lymphocytes taken from the tumors' retained characteristics of the original clone. Ly-6 antigens were inducible on 2E8 and 1A9 cells, but the lymphocytes were otherwise arrested in differentiation. The 2E8 cells had rearranged and expressed kappa light-chain genes but displayed them on the surface along with surrogate light chains and mu heavy chains. Thus, expression of authentic light chain need not coincide with termination of surrogate light-chain utilization in newly formed B cells. Several glycoproteins have recently been demonstrated to be associated with surface immunoglobulin (Ig) on mature B-lineage cells and plasma-cell tumors. We now show that one member of this family (approximately 33 kD) was associated with the mu+surrogate light-chain complex on the 1A9 pre-B-cell clone. When compared to mature B lymphomas, fewer bands coprecipitated with the surface-labeled Ig isolated from pre-B- and early B-cell lines, suggesting that components of the antigen receptor are sequentially acquired during development. The normal replication and differentiation of pre-B cells is probably regulated by complex interactions with multiple cytokines and matrix components of the marrow microenvironment. Cloned lymphocyte lines that are dependent on stromal cells should continue to be important tools for molecular definition of those interactions.