gebhart/patrepeval huggingface dataset:
Array-to-Array Transfer of an Artificial Nose Classifier (2001)

This paper describes the use of a microsphere sensor technology that allows simple fabrication of vapor sensor arrays with reproducible response patterns. Microsphere sensor fabrication protocols are uncomplicated and yield billions of highly reproducible sensors. Microsphere sensor arrays combined with a generalized Whitney-Mann-Wilcoxen (GWMW) classifier were used to discriminate between the presence and absence of nitroaromatic compounds in high background vapor mixtures. The classifier was trained on one sensor array and then used to obtain 98.2 and 93.7% correct classification rates with data collected using two subsequent arrays made up to six months after the initial training was performed. These results represent an advance in the ability to transfer training data between multiple sensor arrays with a fluorescence-based artificial nose.
Mapping of mutations associated with neurovirulence in monkeys infected with Sabin 1 poliovirus revertants selected at high temperature (1990)

Poliovirus type 1 neurovirulence is difficult to analyze because of the 56 mutations which differentiate the neurovirulent Mahoney strain from the attenuated Sabin strain. We have isolated four neurovirulent mutants which differ from the temperature-sensitive parental Sabin 1 strain by only a few mutations, using selection for temperature resistance: mutant S(1)37C1 was isolated at 37.5 degrees C, S(1)38C5 was isolated at 38.5 degrees C, and S(1)39C6 and S(1)39C10 were isolated at 39.5 degrees C. All four mutants had a positive reproductive capacity at supraoptimal temperature (Rct+ phenotype). Mutant S(1)37C1 induced paralysis in two of four cynomolgus monkeys, and the three other mutants induced paralysis in four of four monkeys. The lesion score increased from the S(1)37C1 mutant to the S(1)39 mutants. To map the mutations associated with thermoresistance and neurovirulence, we sequenced all regions in which the Sabin 1 genome differs from the Mahoney genome. The S(1)37C1 mutant had one mutation in the 5' noncoding region and another in the 3' noncoding region. Mutant S(1)38C5 had these mutations plus another mutation in the 3D polymerase gene. The S(1)39 mutants had three additional mutations in the capsid protein region. The mutations were located at positions at which the Sabin 1 and Mahoney genomes differ, except for the mutation in the 5' noncoding region. The noncoding-region mutations apparently confer a low degree of neurovirulence. The 3D polymerase mutation, which distinguishes S(1)38C5 and S(1)39 mutants from S(1)37C1, is probably responsible for the high neurovirulence of S(1)38C5 and S(1)39 mutants. The capsid region mutations may contribute to the neurovirulence of the S(1)39 mutants, which was the highest among the mutants.
Comparative Analysis of Total Body and Dermatoscopic Photographic Monitoring of Nevi in Similar Patient Populations at Risk for Cutaneous Melanoma (2010)

In our experience with both approaches, monitoring patients at risk for melanoma using TB photography was associated with lower biopsy rates and lower nevus-to-melanoma ratios than using DELM and facilitated detection of new and changing lesions. In both cohorts, the majority of melanomas detected on follow-up arose de novo.
Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples (2010)

Our results demonstrate that this novel approach for cDNA synthesis has valuable utility for application of ultra-high throughput technologies, such as whole transcriptome sequencing using 454 technology, to very small biological samples comprised of tens of cells as might be obtained via approaches like laser microdissection.
Functional replacement of the hemolysin A transport signal by a different primary sequence. (1993)

Secretion of the 107-kDa hemolysin A (HlyA) from Escherichia coli is mediated by the membrane proteins hemolysin B and hemolysin D. Hemolysin B is a member of the so-called ATP binding cassette transporter superfamily, which includes the multidrug resistance P-glycoprotein, the cystic fibrosis CFTR protein, and the major histocompatibility complex-associated transporter of antigenic peptides. Recognition of HlyA by the hemolysin B/D transporter is dependent on a signal sequence mapped to the C-terminal 50 or so amino acids of the HlyA molecule. We show that the C-terminal 70 amino acids of leukotoxin from Pasteurella hemolytica can substitute functionally for the HlyA signal sequence. This 70-amino acid sequence contains no primary sequence similarity to the HlyA signal sequence; however, structural motifs of helix-turn-helix followed by strand-loop-strand can be deduced for both sequences. We also demonstrate by site-directed mutagenesis that changes to these predicted motifs affect transport function. It thus appears that the transport signal of HlyA may be defined by a higher-order structure and that the hemolysin transporter may recognize a much wider diversity of primary sequences than previously anticipated. This finding may have implications for understanding the basis of substrate specificity of other ATP binding cassette transporters.
Epithelial Cell Mitochondrial Dysfunction and PINK1 Are Induced by Transforming Growth Factor- Beta1 in Pulmonary Fibrosis (2015)

TGF-β1 induces lung epithelial cell mitochondrial ROS and depolarization and stabilizes the key mitophagy initiating protein, PINK1. PINK1 ameliorates epithelial cell death and may be necessary to limit fibrogenesis.
In vivo inhibition of CD44 limits intra-abdominal spread of a human ovarian cancer xenograft in nude mice: a novel role for CD44 in the process of peritoneal implantation. (1997)

Ovarian cancer cells frequently metastasize by implanting onto the peritoneal mesothelial lining of the abdominal cavity. Data obtained from in vitro adhesion studies have suggested a possible role for the CD44 molecule in this process. The purpose of the present study was to determine the in vivo role of CD44 in ovarian cancer metastasis by using a nude mouse xenograft model of peritoneal implantation. Three groups of 10 athymic female nude mice each received an i.p. inoculum of 10 x 10(6) cells from a CD44-positive human ovarian cancer cell line (36M2) in the presence of either anti-D144 antibody (Ab; nonreactive IgG1), anti-DF3 Ab (reactive IgG1 Ab that does not inhibit in vitro binding), or neutralizing anti-CD44 Ab (IgG1). The number of peritoneal and diaphragmatic implants at 5 weeks for anti-D144 and anti-DF3-treated groups was 103 +/- 17 and 120 +/- 20, respectively (mean +/- SE; P > 0.2). In contrast, animals treated with anti-CD44 Ab experienced a significant reduction in the number of tumor implants (35 +/- 4; P < 0.002). Anti-CD44 Ab was not inhibitory to the growth of 36M2 cells in vitro and did not inhibit s.c. tumor growth in vivo, suggesting that the observed effect was related to inhibition of peritoneal implantation. These data suggest that the CD44 molecule plays an important in vivo role in ovarian cancer cell implantation and that strategies to inhibit CD44 function may represent a novel approach to limiting the intra-abdominal spread of this highly lethal tumor.
Transforming growth factor beta-activated kinase 1 (TAK1)-dependent checkpoint in the survival of dendritic cells promotes immune homeostasis and function (2012)

Homeostatic control of dendritic cell (DC) survival is crucial for adaptive immunity, but the molecular mechanism is not well defined. Moreover, how DCs influence immune homeostasis under steady state remains unclear. Combining DC-specific and -inducible deletion systems, we report that transforming growth factor beta-activated kinase 1 (TAK1) is an essential regulator of DC survival and immune system homeostasis and function. Deficiency of TAK1 in CD11c(+) cells induced markedly elevated apoptosis, leading to the depletion of DC populations, especially the CD8(+) and CD103(+) DC subsets in lymphoid and nonlymphoid tissues, respectively. TAK1 also contributed to DC development by promoting the generation of DC precursors. Prosurvival signals from Toll-like receptors, CD40 and receptor activator of nuclear factor-κB (RANK) are integrated by TAK1 in DCs, which in turn mediated activation of downstream NF-κB and AKT-Foxo pathways and established a gene-expression program. TAK1 deficiency in DCs caused a myeloid proliferative disorder characterized by expansion of neutrophils and inflammatory monocytes, disrupted T-cell homeostasis, and prevented effective T-cell priming and generation of regulatory T cells. Moreover, TAK1 signaling in DCs was required to prevent myeloid proliferation even in the absence of lymphocytes, indicating a previously unappreciated regulatory mechanism of DC-mediated control of myeloid cell-dependent inflammation. Therefore, TAK1 orchestrates a prosurvival checkpoint in DCs that affects the homeostasis and function of the immune system.
Cross table lateral radiography for measurement of acetabular cup version (2016)

Our study shows that cross table radiography provides acceptable information for clinical use, but has limited use for precise analysis of acetabular cup version.
Heparin-Induced Thrombocytopenia: New Insights Into the Impact of the FcγRIIa-R-H131 Polymorphism (1998)

Heparin-induced thrombocytopenia (HIT), a severe complication of heparin treatment, can be associated with new thrombotic complications. HIT antibodies activate platelets via the platelet Fcgamma-receptor (FcgammaRIIa), which carries a functionally relevant polymorphism (FcgammaRIIa-R-H131). The effect of this polymorphism on the clinical manifestations of HIT is controversial. We determined prospectively the FcgammaRIIa-R-H131 genotypes in 389 HIT patients, in 351 patients with thrombocytopenia or thrombosis due to causes other than HIT and without detectable HIT antibodies, and in 256 healthy blood donors. For this purpose, a novel nested sequence-specific primer-polymerase chain reaction (SSP-PCR) was developed. FcgammaRIIa-R/R131 was found to be overrepresented in the HIT patients (27%) compared with the control groups (non-HIT patients [21%] and blood donors [20%]). In a subgroup of 122 well-characterized HIT patients, the genotype distribution in patients presenting with thrombocytopenia only was compared with that of patients who developed thromboembolic complications. The frequency of FcgammaRIIa-R/R131 among patients with thrombotic events was significantly elevated (37% v 17%; P = .036). Our results indicate that genotype distribution can be correlated to the clinical outcome of patients with HIT. We speculate that the reduced clearance of immune complexes in patients with the FcgammaRIIa-R/R131 allotype causes prolonged activation of endothelial cells and platelets, thus increasing the risk for thrombotic complications.
Surface-enhanced Raman scattering and biophysics (2002)

Surface-enhanced Raman scattering (SERS) is a spectroscopic technique which combines modern laser spectroscopy with the exciting optical properties of metallic nanostructures, resulting in strongly increased Raman signals when molecules are attached to nanometre-sized gold and silver structures. The effect provides the structural information content of Raman spectroscopy together with ultrasensitive detection limits, allowing Raman spectroscopy of single molecules. Since SERS takes place in the local fields of metallic nanostructures, the lateral resolution of the technique is determined by the confinement of the local fields, which can be two orders of magnitude better than the diffraction limit. Moreover, SERS is an analytical technique, which can give information on surface and interface processes.
CIR, a corepressor linking the DNA binding factor CBF1 to the histone deacetylase complex (1999)

CBF1 is a member of the CSL family of DNA binding factors, which mediate either transcriptional repression or transcriptional activation. CSL proteins play a central role in Notch signaling and in Epstein-Barr virus-induced immortalization. Notch is a transmembrane protein involved in cell-fate decisions, and the cytoplasmic domain of Notch (NotchIC) targets CBF1. The Epstein-Barr virus-immortalizing protein EBNA2 activates both cellular and viral gene expression by targeting CBF1 and mimicking NotchIC. We have examined the mechanism of CBF1-mediated repression and show that CBF1 binds to a unique corepressor, CBF1 interacting corepressor (CIR). A CIR homolog is encoded by Caenorhabditis elegans, indicating that CIR is evolutionarily conserved. Two CBF1 mutants that were unable to bind CIR did not function as repressors, suggesting that targeting of CIR to CBF1 is an important component of repression. When expressed as a Gal4 fusion protein, CIR repressed reporter gene expression. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex.
Design Resilient Modulus of Subgrade Soils from FWD Tests (2000)

The resilient modulus is a basic soil property governed by the elastic theory, and is a measure of the recoverable strain for a small, repetitive load. It is a required input in the AASHTO method of flexible pavement design. The resilient modulus of subgrade soils is a required input parameter for the AASHTO method of flexible pavement design and is also used to compute the modulus of subgrade reaction for the AASHTO rigid pavement design equations. This study analyzed subgrade resilient moduli, backcalculated from the Falling Weight Deflectometer deflection test results, on nine pavement subgrade projects of the Kansas Department of Transportation (KDOT). Laboratory resilient modulus test results were also reviewed for the fine-grained soils on these projects. The results show that the average "breakpoint" deviator stress for the fine-grained soils that displayed typical bi-linear behavior was 46 kPa. The design resilient modulus corresponding to this deviator stress value could be used in the instances when the "breakpoint" deviator stress is not distinct graphically. The average ratio of the laboratory-determined to the backcalculated resilient moduli was found to be 0.33. Backcalculated resilient moduli using the AASHTO algorithm and a nonlinear elastic analysis program were nearly identical for the soils that had slightly nonlinear characteristics. Results from either approaches can be used in design.
The Pathogenesis of Atherosclerosis (1976)

Atherosclerosis is an arterial disease that is recognized to be the chief cause of death in the United States and in Western Europe.1 Its importance as a principal cause of myocardial and cerebral infarction and thrombosis has been appreciated for many years. Nevertheless, its cause and pathogenesis remain unsolved. A major problem is that the disease progresses insidiously for many years before symptoms develop, making it difficult to follow the early development of the disease in individual patients, and to relate causally the several types of lesion that have been described. For the same reason, identification . . .
Immunogenicity and Protective Efficacy of Recombinant Human T-Cell Leukemia/Lymphoma Virus Type 1 NYVAC and Naked DNA Vaccine Candidates in Squirrel Monkeys (Saimiri sciureus) (2001)

We assessed the immunogenicities and efficacies of two highly attenuated vaccinia virus-derived NYVAC vaccine candidates encoding the human T-cell leukemia/lymphoma virus type 1 (HTLV-1) env gene or both the env and gag genes in prime-boost pilot regimens in combination with naked DNA expressing the HTLV-1 envelope. Three inoculations of NYVAC HTLV-1 env at 0, 1, and 3 months followed by a single inoculation of DNA env at 9 months protected against intravenous challenge with HTLV-1-infected cells in one of three immunized squirrel monkeys. Furthermore, humoral and cell-mediated immune responses against HTLV-1 Env could be detected in this protected animal. However, priming the animal with a single dose of env DNA, followed by immunization with the NYVAC HTLV-1 gag and env vaccine at 6, 7, and 8 months, protected all three animals against challenge with HTLV-1-infected cells. With this protocol, antibodies against HTLV-1 Env and cell-mediated responses against Env and Gag could also be detected in the protected animals. Although the relative superiority of a DNA prime-NYVAC boost regimen over addition of the Gag component as an immunogen cannot be assessed directly, our findings nevertheless show that an HTLV-1 vaccine approach is feasible and deserves further study.
A Review: Proteomics in Nasopharyngeal Carcinoma (2015)

Although radiotherapy is generally effective in the treatment of major nasopharyngeal carcinoma (NPC), this treatment still makes approximately 20% of patients radioresistant. Therefore, the identification of blood or biopsy biomarkers that can predict the treatment response to radioresistance and that can diagnosis early stages of NPC would be highly useful to improve this situation. Proteomics is widely used in NPC for searching biomarkers and comparing differentially expressed proteins. In this review, an overview of proteomics with different samples related to NPC and common proteomics methods was made. In conclusion, identical proteins are sorted as follows: Keratin is ranked the highest followed by such proteins as annexin, heat shock protein, 14-3-3σ, nm-23 protein, cathepsin, heterogeneous nuclear ribonucleoproteins, enolase, triosephosphate isomerase, stathmin, prohibitin, and vimentin. This ranking indicates that these proteins may be NPC-related proteins and have potential value for further studies.
Synthesis, characterization, redox kinetics, and assessment of DNA and thiol binding of a new class of platinum(II) and -(IV) pyrophosphato complexes (2008)

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Extended‐Core Discotic Liquid Crystals Based on the Intramolecular H‐Bonding in N‐Acylated 2,2′‐Bipyridine‐3,3′‐diamine Moieties (1997)

A new type of disc-shaped molecule (1 a-c) has been synthesised and characterised. The molecules were built up by linking three lipophilic, N-monoacylated 2,2'-bipyridine-3,3'-diamine wedges to a central 1,3,5-benzenetricarbonyl unit. They show liquid crystalline behaviour, as shown by DSC, polarisation microscopy and X-ray diffraction. In all cases the mesophase was characterised as a Dho phase. From (1) H NMR results it was shown that the interior of compounds 1 a-c preferentially adopts a C3 symmetrical conformation owing to strong intramolecular H-bonding, which gives rise to an extended core. This large core induces strong interactions between molecules, leading to mesophases of enhanced thermal stability.
Developing bioinformatics computer skills (2001)

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Punish/Reward: Learning with a Critic in Adaptive Threshold Systems (1973)

An adaptive threshold element is able to "learn" a strategy of play for the game blackjack (twenty-one) with a performance close to that of the Thorp optimal strategy although the adaptive system has no prior knowledge of the game and of the objective of play. After each winning game the decisions of the adaptive system are "rewarded." After each losing game the decisions are "punished." Reward is accomplished by adapting while accepting the actual decision as the desired response. Punishment is accomplished by adapting while taking the desired response to be the opposite of that of the actual decision. This learning scheme is unlike "learning with a teacher" and unlike "unsupervised learning." It involves "bootstrap adaptation" or "learning with a critic." The critic rewards decisions which are members of successful chains of decisions and punishes other decisions. A general analytical model for learning with a critic is formulated and analyzed. The model represents bootstrap learning per se. Although the hypotheses on which the model is based do not perfectly fit blackjack learning, it is applied heuristically to predict adaptation rates with good experimental success. New applications are being explored for bootstrap learning in adaptive controls and multilayered adaptive systems.
Cryptochromes and Phytochromes Synergistically Regulate Arabidopsis Root Greening under Blue Light (2004)

To increase their fitness, plants sense ambient light conditions and modulate their developmental processes by utilizing multiple photoreceptors such as phytochrome, cryptochrome and phototropin. Even roots, which are normally not exposed to light, express photoreceptors and can respond to light by developing chloroplasts. In the present study, root greening was observed in Arabidopsis thaliana. Seedlings were grown under monochromatic light and chlorophyll levels in the roots were determined. It was found that blue light was far more effective at inducing chloroplast development in Arabidopsis roots than was red light, and this response was under the control of a strong synergistic interaction between phytochromes and cryptochromes. As expected, the cry1 mutant was deficient in this response. Interestingly, the phyAphyB double mutant failed to respond to blue light under these conditions. This strongly suggests that either phytochrome A or phytochrome B, in addition to cryptochrome, was required for this blue light response. It was further demonstrated that the expression of photosynthetic genes was regulated in the same way. Dichromatic irradiation experiments indicated that this interaction depends on the level of phyB P(FR). Analysis of the cop1, det1 and hy5 mutants indicated that the corresponding factors were involved in the response.
STUDIES ON METABOLIC FATE OF A NEW ANTIALLERGIC AGENT, AZELASTINE (4-(p-CHLOROBENZYL)-2-[N-METHYLPERHYDROAZEPINYL-(4)]-1-(2H)-PHTHALAZINONE HYDROCHLORIDE) (1980)

The metabolic fate of a new antiallergic agent, azelastine (4-(p-chlorobenzyl)-2-[N-methylperhydroazepinyl-(4)]-1-(2H)-phthalazinone hydrochloride) in rats and guinea pigs was investigated using its 14C-labelled compound. The blood level of radioactivity reached the maximum at 1-1.5 hr after oral administration, indicating the rapid absorption of the drug from gastrointestinal tract. A high concentration of radioactivity was detected in the lung of both species following either oral or intravenous administration. The major pathway of excretion of radioactivity was by way into feces, in both species. The radioactivity excreted in feces was attributable to that which was excreted in bile and exsorbed into gastrointegtinal tract. When the drug was given to pregnant rats, the concentration of radioactivity in the fetus was significantly lower than those in placenta and uterus, indicating the limited placental transfer of the drug. The successive oral administration of the drug in lower doses exerted no effect on the activity of microsomal drug-metabolizing enzymes of rat liver, while in higher doses, had a slight effect.
Peripheral arterial occlusive disease: Global gene expression analyses suggest a major role for immune and inflammatory responses (2008)

Lines of evidence revealed in this study not only support previous hypotheses, primarily based on studies of animal models and other types of arterial disease, that inflammatory responses may influence the development of PAD, but also permit the recognition of a wide spectrum of immune/inflammatory genes that can serve as signatures for disease progression in PAD. Further studies of these signature molecules may eventually allow us to develop more sophisticated protocols for pharmaceutical interventions.