gebhart/patrepeval huggingface dataset:
Wavelet Feature Extraction from Neurophysiological Signals (2010)

<P>This chapter contains sections titled: <UL> <LI> <P>Introduction</P> </LI> <LI> <P>Wavelet Transforms</P> </LI> <LI> <P>Signal-to-Noise Ratio</P> </LI> <LI> <P>Wavelet Spectral Division</P> </LI> <LI> <P>Variance</P> </LI> <LI> <P>Spectral Features in the Wavelet Extrema and Zero-Crossings</P> </LI> <LI> <P>Computation</P> </LI> <LI> <P>Experimental Results</P> </LI> <LI> <P>Discussion</P> </LI> </UL> </P> <P>This chapter contains sections titled: <UL> <LI> <P>Acknowledgments</P> </LI> <LI> <P>Appendix: Expected Number of Zero Crossings</P> </LI> <LI> <P>References</P> </LI> </UL> </P>
Changes in activity of fructose-1,6-bisphosphate aldolase in livers of fasted rabbits and accumulation of crossreacting immune material. (1979)

The activity of fructose-1,6-bisphosphate aldolase (D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase, EC 4.1.2.13) in livers of fasted rabbits decreases to less than one-half the value found in livers of fed rabbits. However, the concentration of aldolase protein in the liver extracts, measured with a specific antibody, remains unchanged. More than twice as much antibody is required to neutralize the aldolase activity in liver extracts from fasted compared with fed rabbits. The results suggest that modification of liver aldolase occurs during fasting, resulting in loss of catalytic activity without loss of immunoreactivity.
A Small Scale Method for the Production of Soymilk and Silken Tofu (1997)

Interest in traditional Asian foods such as tofu and soymilk has developed in the USA during the past few years. Lacking, however, is a small scale, rapid test that will permit plant breeders and food technologists to evaluate the potential of various soybean [( Glycine max L.(Merr)] cultivars and breeding lines to produce these foods. A procedure is described in which 80 g of ground soybean is used to make silken tofu. Glucono‐δ‐1actone serves as the coagulant in the procedure. The method results in tofu whose characteristics are reproducible among different preparations, and whose quality compares favorably with imported Japanese silken tofu that is available commercially in the USA. To evaluate the method, soymilk and tofu were made from 182 experimental, public, and private soybean cultivars grown in Indiana in 1990. Differences were observed among cultivars for soymilk yield, tofu whiteness, and texture (tofu fracturability and hardness). Significant correlations were found between soybean protein content, soymilk protein content, and tofu fracturability. The same correlations have previously been established in the literature based on comparisons of material made by traditional large scale manufacturing methods. A correlation between soymilk solids content and fracturability was also observed when the ratio of water used to process the ground soybean was varied. The small scale method will be useful to evaluate soybean lines from breeding programs.
TNF-α is a critical negative regulator of type 1 immune activation during intracellular bacterial infection (2004)

TNF-α has long been regarded as a proimmune cytokine involved in antimicrobial type 1 immunity. However, the precise role of TNF-α in antimicrobial type 1 immunity remains poorly understood. We found that TNF-α–deficient (TNF(–/–)) mice quickly succumbed to respiratory failure following lung infection with replication-competent mycobacteria, because of apoptosis and necrosis of granuloma and lung structure. Tissue destruction was a result of an uncontrolled type 1 immune syndrome characterized by expansion of activated CD4 and CD8 T cells, increased frequency of antigen-specific T cells, and overproduction of IFN-γ and IL-12. Depletion of CD4 and CD8 T cells decreased IFN-γ levels, prevented granuloma and tissue necrosis, and prolonged the survival of TNF(–/–) hosts. Early reconstitution of TNF-α by gene transfer reduced the frequency of antigen-specific T cells and improved survival. TNF-α controlled type 1 immune activation at least in part by suppressing T cell proliferation, and this suppression involved both TNF receptor p55 and TNF receptor p75. Heightened type 1 immune activation also occurred in TNF(–/–) mice treated with dead mycobacteria, live replication-deficient mycobacteria, or mycobacterial cell wall components. Our study thus identifies TNF-α as a type 1 immunoregulatory cytokine whose primary role, different from those of other type 1 cytokines, is to keep an otherwise detrimental type 1 immune response in check.
Studies on syntheses of 1-alkyl-2-substitutedthiazolylbenzimidazoles (2003)

Studies on syntheses of 1-alkyl-2-substitutedthiazolyl-benzimidazoles 4 starting from 2-acetylbenzimidazoles 1 have been reported. Alkylation of 1 leads to 1-alkyl-2-acetyl-benzimidazoles 2, which on bromination yield theknown 1-alkyl-2-(α-bromoacetyl)benzimidazoles 3. The latter on treatment with thioureas yield 4.
Purification and characterization of a rice cysteine proteinase inhibitor. (1987)

A proteinaceous substance that inhibited the activity of papain (EC 3.4.22.2) was found in seeds of rice, Oryza saliva L. japonica. This cysteine proteinase inhibitor (CPI) was purified by a series of purification procedures including CM-Sephadex C-50, Sephadex G-75, and DEAE-Sephadex A-50 chromatography. The CPI was a single polypeptide with a molecular weight of about 12, 000, with an isoelectric point at pH 5.3. The CPI was stable below 100°C and between pH 2.2-9.0. The inhibition of papain by the CPI was non-competitive, with a Ki value of 2.44 × 10-8 M. The complete inhibition of papain was reached by an equimolar concentration of the CPI.
Negative selection systems for transgenic barley (Hordeum vulgare L.): comparison of bacterial codA‐ and cytochrome P450 gene‐mediated selection (1999)

Efficient negative selection systems are increasingly needed for numerous applications in plant biology. In recent years various counter-selectable genes have been tested in six dicotyledonous species, whereas there are no data available for the use of negative selection markers in monocotyledonous species. In this study, we compared the applicability and reliability of two different conditional negative selection systems in transgenic barley. The bacterial codA gene encoding cytosine deaminase, which converts the non-toxic 5-fluorocytosine (5-FC) into the toxic 5-fluorouracil (5-FU), was used for in vitro selection of germinating seedlings. Development of codA-expressing seedlings was strongly inhibited by germinating the seeds in the presence of 5-FC. For selecting plants in the greenhouse, a bacterial cytochrome P450 mono-oxygenase gene, the product of which catalyses the dealkylation of a sulfonylurea compound, R7402, into its cytotoxic metabolite, was used. T1 plants expressing the selectable marker gene showed striking morphological differences from the non-transgenic plants. In experiments with both negative selectable markers, the presence or absence of the transgene, as predicted from the physiological appearance of the plants under selection, was confirmed by PCR analysis. We demonstrate that both marker genes provide tight negative selection; however, the use of the P450 gene is more amenable to large-scale screening under greenhouse or field conditions.
Murein Lipoprotein Is a Critical Outer Membrane Component Involved inSalmonella entericaSerovar Typhimurium Systemic Infection (2005)

Lipopolysaccharide (LPS) and Braun (murein) lipoprotein (Lpp) are major components of the outer membrane of gram-negative enteric bacteria that function as potent stimulators of inflammatory and immune responses. In a previous paper, we provided evidence that two functional copies of the lipoprotein gene (lppA and lppB) located on the chromosome of Salmonella enterica serovar Typhimurium contributed to bacterial virulence. In this study, we characterized lppA and lppB single-knockout (SKO) mutants and compared them with an lpp double-knockout (DKO) mutant using in vitro and in vivo models. Compared to the lpp DKO mutant, which was nonmotile, the motility of the lpp SKO mutants was significantly increased (73 to 77%), although the level of motility did not reach the level of wild-type (WT) S. enterica serovar Typhimurium. Likewise, the cytotoxicity was also significantly increased when T84 human intestinal epithelial cells and RAW264.7 murine macrophages were infected with the lpp SKO mutants compared to the cytotoxicity when cells were infected with the lpp DKO mutant. The level of interleukin-8 (IL-8) in polarized T84 cells infected with the lppB SKO mutant was significantly higher (two- to threefold higher), reaching the level in cells infected with WT S. enterica serovar Typhimurium, than the level in host cells infected with the lppA SKO mutant. The lpp DKO mutant induced minimal levels of IL-8. Similarly, sera from mice infected with the lppB SKO mutant contained 4.5- to 10-fold-higher levels of tumor necrosis factor-alpha and IL-6; the levels of these cytokines were 1.7- to 3.0-fold greater in the lppA SKO mutant-infected mice than in animals challenged with the lpp DKO mutant. The increased cytokine levels observed with the lppB SKO mutant in mice correlated with greater tissue damage in the livers and spleens of these mice than in the organs of animals infected with the lppA SKO and lpp DKO mutants. Moreover, the lppB SKO mutant-infected mice had increased susceptibility to death. Since the lpp DKO mutant retained intact LPS, we constructed an S. enterica serovar Typhimurium triple-knockout (TKO) mutant in which the lppA and lppB genes were deleted from an existing msbB mutant (msbB encodes an enzyme required for the acylation of lipid A). Compared to the lpp DKO and msbB SKO mutants, the lpp-msbB TKO mutant was unable to induce cytotoxicity and to produce cytokines and chemokines in vitro and in vivo. These studies provided the first evidence of the relative contributions of Lpp and lipid A acylation to Salmonella pathogenesis.
The importance of tumor necrosis factor and lipoproteins in the pathogenesis of chronic heart failure. (2001)

Elevated levels of proinflammatory cytokines, such as tumor necrosis factor (TNF) and interleukin-6 (IL-6), have been demonstrated in patients with chronic heart failure (CHF). Evidence suggests that cytokines such as these may play a central role in the pathogenesis of this syndrome. TNF has several properties that are particularly detrimental in CHF, such as negatively inotropic effects, the promotion of left ventricular remodelling, and the induction of dilated cardiomyopathy in humans. Furthermore, TNF can cause skeletal muscle wasting and apoptosis, and, therefore, may be important in the development of cardiac cachexia. Although the precise stimulus for immune activation in CHF is unknown, one hypothesis is that endotoxin may be a significant trigger for cytokine release. This is supported by the finding that decompensated CHF patients have elevated endotoxin levels that normalize on diuretic therapy. The factors that influence endotoxin responsiveness in patients with CHF, in particular the potential importance of serum lipoproteins, will be discussed in this review.
The diagnostic accuracy of pleural effusion and plasma samples versus tumour tissue for detection of EGFR mutation in patients with advanced non-small cell lung cancer: comparison of methodologies (2013)

MPE and plasma are valid surrogates for NSCLC tumour EGFR mutation detection when tissue is not available. ARMS is most suitable for mutation detection in tissue and MPE cell blocks; however, mutant-specific IHC could be a complementary method when DNA-based molecular testing is unavailable.
Involvement of Sialoadhesin in Entry of Porcine Reproductive and Respiratory Syndrome Virus into Porcine Alveolar Macrophages (2003)

Porcine reproductive and respiratory syndrome virus (PRRSV) shows a very restricted tropism for cells of the monocyte/macrophage lineage. It enters cells via receptor-mediated endocytosis. A monoclonal antibody (MAb) that is able to block PRRSV infection of porcine alveolar macrophages (PAM) and that recognizes a 210-kDa protein (p210) was described previously (MAb41D3) (X. Duan, H. Nauwynck, H. Favoreel, and M. Pensaert, J. Virol. 72:4520-4523, 1998). In the present study, the p210 protein was purified from PAM by immunoaffinity using MAb41D3 and was subjected to internal peptide sequencing after tryptic digestion. Amino acid sequence identities ranging from 56 to 91% with mouse sialoadhesin, a macrophage-restricted receptor, were obtained with four p210 peptides. Using these peptide data, the full p210 cDNA sequence (5,193 bp) was subsequently determined. It shared 69 and 78% amino acid identity, respectively, with mouse and human sialoadhesins. Swine (PK-15) cells resistant to viral entry were transfected with the cloned p210 cDNA and inoculated with European or American PRRSV strains. Internalized virus particles were detected only in PK-15 cells expressing the recombinant sialoadhesin, demonstrating that this glycoprotein mediated uptake of both types of strains. However, nucleocapsid disintegration, like that observed in infected Marc-145 cells as a result of virus uncoating after fusion of the virus with the endocytic vesicle membrane, was not observed, suggesting a block in the fusion process. The ability of porcine sialoadhesin to mediate endocytosis was demonstrated by specific internalization of MAb41D3 into PAM. Altogether, these results show that sialoadhesin is involved in the entry process of PRRSV in PAM.
Fully Human CD38 Antibodies Efficiently Trigger ADCC of Multiple Myeloma Cell Lines and Primary Tumor Cells. (2005)

Abstract Although new treatment modalities have recently been added to the standard regimens for multiple myeloma, the clinical outcome for patients with advanced disease is often limited. Monoclonal antibodies are increasingly used for tumor therapy, and may also represent interesting options for multiple myeloma patients. CD38 is one of the most promising target antigens on malignant plasma cells, which are evaluated in preclinical and early clinical studies as targets for antibody therapy. CD38 is a type II transmembrane protein with ectoenzymatic activity, which is involved in calcium mobilization. Human CD38 is predominantly expressed by bone marrow precursor cells and by terminally differentiated plasma cells. Multiple myeloma cells show moderate to high expression levels - making CD38 a potential candidate as target for immunotherapy. A panel of 42 fully human CD38 antibodies was generated by immunizing human Ig transgenic mice. Immunofluorescence studies with CD38 transfected cells demonstrated antigen-specific, high affinity binding, and cross-blocking experiments revealed four distinct epitope groups. Seven antibodies, representing each of the four groups, were selected for further analyses. ADCC and CDC activity against CD38-positive myeloma cell lines (AMO-1 and JK6), and against freshly-isolated primary multiple myeloma cells was investigated. Human whole blood served as effector source, which was then fractionated into plasma (containing human complement), mononuclear (MNC) or granulocytic (PMN) effector cells. All antibodies mediated concentration-dependent killing of both multiple myeloma cell lines - using human mononuclear cells as effector source. Also complement-dependent killing of freshly isolated myeloma cells was observed. However, none of the antibodies recruited PMN for tumor cell lysis. Importantly, CD38 antibodies also killed freshly isolated tumor cells from a rare patient with a CD38/138- positive plasma cell leukemia, which was chemotherapy- refractory at the time of analysis. Furthermore, CD38 antibodies effectively prevented outgrowth of CD38-positive tumor cells in SCID mouse xenograft models. Antibody 005 was significantly more effective in these assays compared to the remaining panel of CD38 antibodies. In conclusion, CD38 antibodies efficiently mediated killing of multiple myeloma cell lines as well as freshly isolated tumor cells and prevented tumor outgrowth in xenografted SCID mice. Antibody 005 was superior in mediating CDC and ADCC via MNC - particularly at low antibody concentrations.
Sources of Resistance to Pepino mosaic virus in Tomato Accessions (2007)

Pepino mosaic virus (PepMV) is an emerging disease on greenhouse tomato. This highly contagious disease is difficult to control. The best disease management strategy is likely through the use of disease resistance. A major tomato germplasm core collection was evaluated for its resistance against PepMV. These accessions included 23 Solanum lycopersicum, 8 S. pimpinellifolium, 33 S. peruvianum, 18 S. chilense, and 27 S. habrochaites. The results showed that all plants in the accessions corresponding to S. lycopersicum and S. pimpinellifolium were susceptible to PepMV-US infection. On the other hand, two accessions of S. peruvianum (LA107 and LA1305) and S. chilense (LA1971 and LA2748) appeared to have some levels of moderate resistance. However, the most promising resistance segregated in three S. habrochaites accessions (LA1731, LA2156, and LA2167). Resistant plants from these three S. habrochaites accessions were saved for selection. A secondary screening was carried out with progenies generated from the selected plants. These tests showed the segregation of broad-spectrum resistance from the selected S. habrochaites plants against PepMV, especially in LA1731. The segregated LA1731 plants were resistant to not only the U.S. type isolate but also the European type isolate.
Platelet-Rich Plasma and Bone Graft Materials: A Review and a Standardized Research Protocol (2004)

Since the introduction of platelet-rich plasma (PRP), several authors (clinicians and researchers) have investigated its efficacy using different bone grafting materials. There have been various research protocols and different types of clinical cases. This position paper suggests a standardized research protocol for the use of, and evaluation of PRP and bone grafts.
State of the Art Review on Hypermedia Issues And Applications (1999)

Machine (HAM) [Consens &amp;amp; Mendelzon, 1989]. It addresses the following issues raised by Halasz: Search and query mechanisms, augmentation of the basic node and link model, virtual structures, computation over the hypertext network, and versioning. Using GraphLog, queries are formulated by drawing graph patterns. These patterns are then searched for in the hypertext network to yield subgraphs. GraphLog is highly expressive and it uses the notions of deductive database theory and descriptive complexity. The language is powerful enough to allow the specification and manipulation of arbitrary subsets of the network and supports the computation of aggregate functions on the subgraphs of the hypertext document. It can support dynamically defined structures as well as inference capabilities. GraphLog is an extension of the graph-based query language called G+. G+ was extended by adding the notions of negation, aggregation, and improved semantics to make it simple, yet powerful. It can express ...
Identification of chondrocyte‐binding peptides by phage display (2013)

As an initial step toward targeting cartilage tissue for potential therapeutic applications, we sought cartilage-binding peptides using phage display, a powerful technology for selection of peptides that bind to molecules of interest. A library of phage displaying random 12-amino acid peptides was iteratively incubated with cultured chondrocytes to select phage that bind cartilage. The resulting phage clones demonstrated increased affinity to chondrocytes by ELISA, when compared to a wild-type, insertless phage. Furthermore, the selected phage showed little preferential binding to other cell types, including primary skin fibroblast, myocyte and hepatocyte cultures, suggesting a tissue-specific interaction. Immunohistochemical staining revealed that the selected phage bound chondrocytes themselves and the surrounding extracellular matrix. FITC-tagged peptides were synthesized based on the sequence of cartilage-binding phage clones. These peptides, but not a random peptide, bound cultured chondrocytes, and extracelluar matrix. In conclusion, using phage display, we identified peptide sequences that specifically target chondrocytes. We anticipate that such peptides may be coupled to therapeutic molecules to provide targeted treatment for cartilage disorders.
Integrin α6A splice variant regulates proliferation and the Wnt/β-catenin pathway in human colorectal cancer cells (2014)

The integrin α6 subunit pre-messenger RNA undergoes alternative splicing to generate two different splice variants, named α6A and α6B, having distinct cytoplasmic domains. In the human colonic gland, these splice variants display different patterns of expression suggesting specific functions for each variant. We have previously found an up-regulation of the α6β4 integrin in colon adenocarcinomas as well as an increase in the α6A/α6B ratio, but little is known about the involvement of α6Aβ4 versus α6Bβ4 in this context. The aim of this study was to elucidate the function of the α6Aβ4 integrin in human colorectal cancer (CRC) cells. Expression studies on a panel of primary CRCs confirmed that the up-regulation of the α6 subunit in CRC is a direct consequence of the increase of the α6A variant. To investigate the functional significance of an α6A up-regulation in CRC, we specifically knocked down its expression in well-established CRC cell lines using a small-hairpin RNA approach. Results showed a growth rate reduction in all α6A knockdown CRC cell lines studied. The α6A silencing was also found to be associated with a significant repression of a number of Wnt/β-catenin pathway end points. Moreover, it was accompanied by a reduction in the capacity of these cells to develop tumours in xenografts. Taken together, these results demonstrate that the α6A variant is a pro-proliferative form of the α6 integrin subunit in CRC cells and appears to mediate its effects through the Wnt/β-catenin pathway.
Regioselective Deiodination of Thyroxine by Iodothyronine Deiodinase Mimics: An Unusual Mechanistic Pathway Involving Cooperative Chalcogen and Halogen Bonding (2012)

Iodothyronine deiodinases (IDs) are mammalian selenoenzymes that catalyze the conversion of thyroxine (T4) to 3,5,3'-triiodothyronine (T3) and 3,3',5'-triiodothyronine (rT3) by the outer- and inner-ring deiodination pathways, respectively. These enzymes also catalyze further deiodination of T3 and rT3 to produce a variety of di- and monoiodo derivatives. In this paper, the deiodinase activity of a series of peri-substituted naphthalenes having different amino groups is described. These compounds remove iodine selectively from the inner-ring of T4 and T3 to produce rT3 and 3,3'-diiodothyronine (3,3'-T2), respectively. The naphthyl-based compounds having two selenols in the peri-positions exhibit much higher deiodinase activity than those having two thiols or a thiol-selenol pair. Mechanistic investigations reveal that the formation of a halogen bond between the iodine and chalcogen (S or Se) and the peri-interaction between two chalcogen atoms (chalcogen bond) are important for the deiodination reactions. Although the formation of a halogen bond leads to elongation of the C-I bond, the chalcogen bond facilitates the transfer of more electron density to the C-I σ* orbitals, leading to a complete cleavage of the C-I bond. The higher activity of amino-substituted selenium compounds can be ascribed to the deprotonation of thiol/selenol moiety by the amino group, which not only increases the strength of halogen bond but also facilitates the chalcogen-chalcogen interactions.