gebhart/patrepeval huggingface dataset:
Inhibition of RICK/Nuclear Factor-κB and p38 Signaling Attenuates the Inflammatory Response in a Murine Model of Crohn Disease (2005)

Nuclear factor-kappaB (NF-kappaB) is the main target of anti-inflammatory therapies in human chronic inflammatory bowel diseases (IBD), Crohn disease, and ulcerative colitis. This study investigates the molecular anti-inflammatory mechanisms of SB203580, an inhibitor of the mitogen-activated protein kinase p38. The murine trinitrobenzene sulfonic acid (TNBS)-induced colitis was used as an established model of human Crohn disease. Here we show that SB203580 improved the clinical condition, reduced intestinal inflammation, and suppressed mRNA levels of pro-inflammatory cytokines elevated upon induction of colitis. Besides p38 kinase activity, the "classical" IkappaB-dependent NF-kappaB pathway was strongly up-regulated during colitis induction, whereas the "alternative" was not. SB203580 treatment resulted in a drastic down-regulation of p38 and NF-kappaB activity. The molecular analysis of NF-kappaB activation revealed that Rip-like interacting caspase-like apoptosis-regulatory protein kinase (RICK), a key component of a pathway leading to NF-kappaB induction, is also strongly inhibited by SB203580. In contrast, SB203580 had no effect on the colitis-induced activation of other potential NF-kappaB-activating kinases such as protein kinase C (PKC), mixed lineage kinase 3, and the oncogene product Cot/TPL2. Thus, the inhibitory effect of SB203580 on NF-kappaB activation is to a large extent mediated by RICK inhibition. RICK is the effector kinase of the intracellular receptor of bacterial peptidoglycan NOD. Because bacterial products are suggested to be the key pathogenic agents triggering IBD, inhibition of the NOD/RICK pathway may serve as a novel target of future therapies in human IBD.
Identification and Characterization of a Neutralizing Monoclonal Antibody Against Botulinum Neurotoxin, Serotype F, Following Vaccination With Active Toxin (1997)

Clostridium botulinum may produce any of seven known serotypes of neurotoxin (BoNT/A-/G), which are the most toxic bacterial proteins known. Efforts to develop a second-generation vaccine to these toxins would benefit from the isolation of hybridomas producing neutralizing monoclonal antibodies (MAbs). We hypothesized that previous efforts to isolate neutralizing MAbs against various BoNTs failed due to use of toxoided, chemically altered antigens. We employed a novel vaccination regimen employing native, active, single-chain BoNT/E (scBoNT/E). A number of the BoNT/E immunized mice were further vaccinated with lethal doses of fully active BoNT/F. MAb 7F8 consistently neutralized BoNT/F in three different assays: in vivo neutralization, passive neutralization, and neutralization of regional paralysis. There was no detectable recognition and essentially no neutralization of scBoNT/E. The epitope recognized by this MAb was denatured when treated with formalin, urea, guanidine chloride, or sodium dodecyl sulfate. Preliminary epitope mapping studies indicate that the MAb bound to a conformational epitope.
Scanning and Competition between AGs Are Involved in 3' Splice Site Selection in Mammalian Introns (1993)

In mammalian intron splicing, the mechanism by which the 3' splice site AG is accurately and efficiently identified has remained unresolved. We have previously proposed that the 3' splice site in mammalian introns is located by a scanning mechanism for the first AG downstream of the branch point-polypyrimidine tract. We now present experiments that lend further support to this model while identifying conditions under which competition can occur between adjacent AGs. The data show that the 3' splice site is identified as the first AG downstream from the branch point by a mechanism that has all the characteristics expected of a 5'-to-3' scanning process that starts from the branch point rather than the pyrimidine tract. Failure to recognize the proximal AG may arise, however, from extreme proximity to the branch point or sequestration within a hairpin. Once an AG has been encountered, the spliceosome can still see a limited stretch of downstream RNA within which an AG more competitive than the proximal one may be selected. Proximity to the branch point is a major determinant of competition, although steric effects render an AG less competitive in close proximity (approximately 12 nucleotides). In addition, the nucleotide preceding the AG has a striking influence upon competition between closely spaced AGs. The order of competitiveness, CAG congruent to UAG > AAG > GAG, is similar to the nucleotide preference at this position in wild-type 3' splice sites. Thus, 3' splice site selection displays properties of both a scanning process and competition between AGs based on immediate sequence context. This refined scanning model, incorporating elements of competition, is the simplest interpretation that is consistent with all of the available data.
Enhanced Immune Responses and Anti-Tumor Activity by Baculovirus Recombinant Carcinoembryonic Antigen (CEA) in Mice Primed with the Recombinant Vaccinia CEA (1994)

Carcinoembryonic antigen (CEA), a glycosylated protein of Mr 180, is one of the most widely studied oncofetal antigens. A majority of gastrointestinal cancers as well as breast and non-small-cell lung carcinomas express CEA. CEA thus represents a potential target for immunotherapy of several carcinoma types. A recombinant vaccinia-CEA virus (rV-CEA) was previously shown to induce anti-tumor activity in an experimental murine model after three rV-CEA inoculations. However, because the majority of cancer patients have received a previous smallpox vaccination, a long-lasting immune memory and/or induced anamnestic responses against vaccinia proteins may prevent repetitive boosting with the recombinant vaccinia virus expressing CEA. Therefore, other types of vaccines may be required to boost the anti-CEA immune response; one such schema would be the use of purified CEA as a boost in hosts given one administration of rV-CEA. Commercially available sources of CEA are usually derived from liver metastases extracts and are sometimes contaminated with nonspecific cross-reactive antigen. We have previously generated a recombinant source of full-length human CEA using a baculovirus expression system (bV-CEA). bV-CEA was shown to be glycosylated differently than native CEA, but it contains at least 10 epitopes found on native CEA (nCEA). Moreover, bV-CEA was able to induce a humoral response against CEA present on human colorectal cancer cell lines.(ABSTRACT TRUNCATED AT 250 WORDS)
Identification of Volatile Organic Compounds Produced by Bacteria Using HS-SPME-GC–MS (2013)

The analysis of volatile organic compounds (VOCs) as a tool for bacterial identification is reported. Headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography-mass spectrometry (GC-MS) was applied to the analysis of bacterial VOCs with the aim of determining the impact of experimental parameters on the generated VOC profiles. The effect of culture medium, SPME fiber type and GC column were fully evaluated with the Gram-negative bacteria Escherichia coli and Klebsiella pneumoniae and the Gram-positive species Staphylococcus aureus. Multivariate analysis, including cluster analysis and principal component analysis, was applied to VOC data to determine whether the parameters under investigation significantly affected bacterial VOC profiles. Culture medium, and to a lesser extent, SPME fiber type, were found to significantly alter detected bacterial VOC profiles. The detected VOCs varied little with the polarity of the GC column. The results indicate that the generated bacterial VOC profiles need careful evaluation if they are to be used for clinical diagnostics. The whole process is limited by the need to grow the bacteria in broth (18 h) before extraction and analysis (63 min).
Three-periodic nets and tilings: semiregular nets (2003)

Three-periodic semiregular nets are defined as those with just one kind of vertex and one kind of edge, but excluding the five regular and one quasiregular nets described earlier. Fourteen of these and their natural tilings are described and their importance in crystal chemistry is indicated.
Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era (2001)

Simple and complex carbohydrates have been described as ‘the last frontier of molecular and cell biology’. The enzymes that are required for the synthesis and degradation of these compounds provide an enormous challenge in the post-genomic era. This reflects both the extreme chemical and functional diversity of sugars and the difficulties in characterizing both the substrates and the enzymes themselves. The vast myriad of enzymes involved in the synthesis, modification and degradation of oligosaccharides and polysaccharides is only just being unveiled by genomic sequencing. These so-called ‘carbohydrate-active enzymes’ lend themselves to classification by sensitive sequence similarity detection methods. The modularity, often extremely complex, of these enzymes must first be dissected and annotated before high throughput characterization or ‘structural genomics’ approaches may be employed. Once achieved, modular analysis also permits collation of a detailed ‘census’ of carbohydrate-active enzymes for a whole organism or throughout an ecosystem. At the structural level, improvements in X-ray crystallography have opened up a three-dimensional understanding of the way these enzymes work. The mechanisms of many of the glycoside hydrolase families are becoming clearer, yet glycosyltransferases are only slowly revealing their secrets. What is clear from the genomic and structural data is that if we are to harness the latent power of glycogenomics, scientists must consider distant sequence relatives revealed by the sequence families or other sensitive detection methods.
Prospective Randomized Trial of an Anterior Surface Modified Prolate Intraocular Lens (2002)

The use of a modified prolate intraocular lens during cataract surgery has the potential to improve contrast sensitivity under both mesopic and photopic conditions.
The role of the novel adipocyte-derived hormone adiponectin in human disease (2003)

Adiponectin, also called GBP-28, apM1, AdipoQ and Acrp30, is a novel adipose tIssue-specific protein that has structural homology to collagen VIII and X and complement factor C1q, and that circulates in human plasma at high levels. It is one of the physiologically active polypeptides secreted by adipose tIssue, whose multiple functions have started to be understood in the last few Years.A reduction in adiponectin expression is associated with insulin resistance in some animal models. Administration of adiponectin has been accompanied by a reduction in plasma glucose and an increase in insulin sensitivity. In addition, thiazolidinediones, drugs that enhance insulin sensitivity through stimulation of the peroxisome proliferator-activated receptor-gamma, increase plasma adiponectin and mRNA levels in mice. On the other hand, this adipocyte protein seems to play a protective role in experimental models of vascular injury. In humans, adiponectin levels are inversely related to the degree of adiposity and positively associated with insulin sensitivity both in healthy subjects and in diabetic patients. Plasma adiponectin levels have been reported to be decreased in some insulin-resistant states, such as obesity and type 2 diabetes mellitus, and also in patients with coronary artery disease. On the contrary, chronic renal failure, type 1 diabetes and anorexia nervosa are associated with increased plasma adiponectin levels. Concentrations of plasma adiponectin have been shown to correlate negatively with glucose, insulin, triglyceride levels and body mass index, and positively with high-density lipoprotein-cholesterol levels and insulin-stimulated glucose disposal. Weight loss and therapy with thiazolidinediones increased endogenous adiponectin production in humans. Adiponectin increases insulin sensitivity by increasing tIssue fat oxidation, resulting in reduced circulating fatty acid levels and reduced intracellular triglyceride contents in liver and muscle. This protein also suppresses the expression of adhesion molecules in vascular endothelial cells and cytokine production from macrophages, thus inhibiting the inflammatory processes that occur during the early phases of atherosclerosis. In view of these data, it is possible that hypoadiponectinemia may play a role in the development of atherosclerotic vascular disease. In summary, the ability of adiponectin to increase insulin sensitivity in conjunction with its anti-inflammatory and anti-atherogenic properties have made this novel adipocytokine a promising therapeutic tool for the future, with potential applications in states associated with low plasma adiponectin levels.
Fermentative production of 1,4-butanediol from sugars by Bacillus sp. (1987)

Amongmicroorganisms screened from hundreds of soil samples, one bacterial strain was found to accumulate 1,4-BDO inside the cell. From its morphological and physiological characteristics, this strain was determined to belong to the genus Bacillus, and was named Bacillus sp.
Increased Efficacy of the Immunoglobulin G2a Subclass in Antibody-Mediated Protection against Lactate Dehydrogenase-Elevating Virus-Induced Polioencephalomyelitis Revealed with Switch Mutants (2002)

Immunoglobulin G1 (IgG1), IgG2a, and IgG2b switch variants were derived from an IgG3 monoclonal antibody directed against the VP3 envelope glycoprotein of lactate dehydrogenase-elevating virus (LDV). Among the four antibodies, IgG2a delayed the onset and progression of LDV-induced polioencephalomyelitis more than did the other subclasses. This suggests that the IgG2a predominance observed in many IgG antibody responses elicited by live viruses could, at least under some circumstances, correspond to the selection of the best protection for the infected host.
English dictionary searching with little extra space (1979)

When text is typeset using a computer-based system, it can also be checked for spelling errors automatically and efficiently. Several methods of spelling error detection have been proposed. Morris et al. [MORR75] study statistical properties of English words, and describe an algorithm to catch possible typos by examining the relative frequency of trigrams (3-letter combinations). Kernighan et al. [KERN78] report a more conventional approach which looks up each word in a machine readable spelling dictionary. 1 Knuth [KNUT73] comments on dictionary storage, and suggests an organization intended to reduce space requirements. Another, somewhat unsophisticated technique sorts all words in a document and prints those which occur infrequently. Of course, habitually misspelled words escape unnoticed in a frequency based system.
Flash memories: the best of two worlds (1989)

The use of flash memories, which are based on the technology of either erasable programmable ROMs (EPROMs) or electrically erasable programmable ROMs (EEPROMs), as an alternative to both of the latter is discussed. Their properties are compared to those of EPROMs and EEPROMs. Quality and reliability issues are considered. The future of all three memory types is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functional disorders of the sympathetic nervous system in mice lacking the α 1B subunit (Ca v 2.2) of N-type calcium channels (2001)

N-type voltage-dependent Ca(2+) channels (VDCCs), predominantly localized in the nervous system, have been considered to play an essential role in a variety of neuronal functions, including neurotransmitter release at sympathetic nerve terminals. As a direct approach to elucidating the physiological significance of N-type VDCCs, we have generated mice genetically deficient in the alpha(1B) subunit (Ca(v) 2.2). The alpha(1B)-deficient null mice, surprisingly, have a normal life span and are free from apparent behavioral defects. A complete and selective elimination of N-type currents, sensitive to omega-conotoxin GVIA, was observed without significant changes in the activity of other VDCC types in neuronal preparations of mutant mice. The baroreflex response, mediated by the sympathetic nervous system, was markedly reduced after bilateral carotid occlusion. In isolated left atria prepared from N-type-deficient mice, the positive inotropic responses to electrical sympathetic neuronal stimulation were dramatically decreased compared with those of normal mice. In contrast, parasympathetic nervous activity in the mutant mice was nearly identical to that of wild-type mice. Interestingly, the mutant mice showed sustained elevation of heart rate and blood pressure. These results provide direct evidence that N-type VDCCs are indispensable for the function of the sympathetic nervous system in circulatory regulation and indicate that N-type VDCC-deficient mice will be a useful model for studying disorders attributable to sympathetic nerve dysfunction.
Carbon Deposition and Hydrocarbon Formation on Group VIII Metal Catalysts (1998)

Carbon formed from CO in CO2 at around 500 °C deposited as nanotubes and encapsulating carbons on a supported Ni catalyst without H2 or as filaments if H2 was present. A thermodynamic model explains how hydrogen in low concentrations controls filament morphology and why equilibrium is shifted from that for graphite during carbon deposition. Carbon deposition reaction rates at low carbon activity in the absence of hydrogen are reported. A new concept of the rate limiting step for metal-catalyzed carbon formation is proposed, where conditions inside the bulk metal are at least as important as the surface chemistry. A mechanism with an unusual type of active site can qualitatively explain carbon formation rates through a broad range of reaction conditions. When hydrogen is present, a series of hydrocarbons are believed to form, as in fuel synthesis (Fischer−Tropsch) chemistry. Surface vinyl species that have been recently shown to be intermediates in Fischer−Tropsch chemistry also may polymerize to form graphene. The formation of vinyls from CO and H via surface alkyls occurs at a greater rate than methane formation when the supply of hydrogen is limited. Hydrogen from the bulk catalyst metal (not surface adsorbed) hydrogenates the surface alkyls, indicating that hydrogen solubility may control the metal-catalyzed formation of various hydrocarbons and eventually solid graphitic carbon.
Thermally Stable, Silica-Doped ε-WO3 for Sensing of Acetone in the Human Breath (2010)

Acetone in the human breath is a key marker for noninvasive diagnosis of diabetes. Here, sensing films of pure and SiO2-doped WO3 nanoparticles have been made, directly deposited and in situ annealed onto interdigitated electrodes by scalable flame aerosol technology. A unique innovation here is that these films consist of ε-WO3, a metastable phase that has a high selectivity to acetone. The effect of nontoxic Si doping on the ε-phase content and crystal and grain sizes was investigated and correlated to the acetone sensing performance of these films. The thermal stability of these materials was characterized as well, revealing a unique opportunity for reliable sensing of acetone and noninvasive diagnostics of diabetes. An optimal doping level with 10 mol % SiO2 resulted in highly sensitive and highly selective acetone sensors down to 20 ppb.
Differential Targeting of Viral Components by CD4+versus CD8+T Lymphocytes in Dengue Virus Infection (2012)

Dengue virus (DENV) is the principal arthropod-borne viral pathogen afflicting human populations. While repertoires of antibodies to DENV have been linked to protection or enhanced infection, the role of T lymphocytes in these processes remains poorly defined. This study provides a comprehensive overview of CD4(+) and CD8(+) T cell epitope reactivities against the DENV 2 proteome in adult patients experiencing secondary DENV infection. Dengue virus-specific T cell responses directed against an overlapping 15mer peptide library spanning the DENV 2 proteome were analyzed ex vivo by enzyme-linked immunosorbent spot assay, and recognition of individual peptides was further characterized in specific T cell lines. Thirty novel T cell epitopes were identified, 9 of which are CD4(+) and 21 are CD8(+) T cell epitopes. We observe that whereas CD8(+) T cell epitopes preferentially target nonstructural proteins (NS3 and NS5), CD4(+) epitopes are skewed toward recognition of viral components that are also targeted by B lymphocytes (envelope, capsid, and NS1). Consistently, a large proportion of dengue virus-specific CD4(+) T cells have phenotypic characteristics of circulating follicular helper T cells (CXCR5 expression and production of interleukin-21 or gamma interferon), suggesting that they are interacting with B cells in vivo. This study shows that during a dengue virus infection, the protein targets of human CD4(+) and CD8(+) T cells are largely distinct, thus highlighting key differences in the immunodominance of DENV proteins for these two cell types. This has important implications for our understanding of how the two arms of the human adaptive immune system are differentially targeted and employed as part of our response to DENV infection.
Detection of K-ras gene mutations in plasma DNA of patients with pancreatic adenocarcinoma: correlation with clinicopathological features. (1998)

We investigated the presence of K-ras gene mutation in plasma DNA and assessed its clinical value in patients with pancreatic adenocarcinoma. Mutations in codon 12 of the K-ras gene were examined by mutant allele-specific amplification method using DNA extracted from surgical specimens and plasma samples of 21 patients with pancreatic adenocarcinoma. K-ras gene mutation was detected in 15 of 21 (71%) primary tumors. In 9 of 15 (60%) patients with K-ras gene mutation-positive tumors, an identical mutation was detected in the plasma DNA. None of four patients with chronic pancreatitis or five healthy subjects had such mutations in plasma DNA. Tumors positive for K-ras gene mutation in plasma DNA were significantly larger (P = 0.04) and less likely to result in a curative cure after surgical resection (P = 0.09) than those negative for the mutation. Other clinicopathological features, including age, sex, histological type, mode of invasion, and metastasis, did not correlate with K-ras gene mutations in plasma DNA. Treatment resulted in disappearance of K-ras gene mutations in plasma DNA in six of nine (67%) patients. Three patients with a persistently positive K-ras gene mutation in pre- and post-treatment plasma samples were likely to show early recurrence or have a progressive disease. Our findings suggest that K-ras gene mutation can be detected in plasma DNA of patients with pancreatic adenocarcinoma. Detection of K-ras mutations in plasma may be clinically useful for evaluating tumor burden and efficacy of treatment.