gebhart/patrepeval huggingface dataset:
Antigenic Equivalence of Human T-Cell Responses to Mycobacterium tuberculosis -Specific RD1-Encoded Protein Antigens ESAT-6 and Culture Filtrate Protein 10 and to Mixtures of Synthetic Peptides (2000)

The early secreted antigenic target 6-kDa protein (ESAT-6) and culture filtrate protein 10 (CFP-10) are promising antigens for reliable immunodiagnosis of tuberculosis. Both antigens are encoded by RD1, a genomic region present in all strains of Mycobacterium tuberculosis and M. bovis but lacking in all M. bovis bacillus Calmette-Guérin vaccine strains. Production and purification of recombinant antigens are laborious and costly, precluding rapid and large-scale testing. Aiming to develop alternative diagnostic reagents, we have investigated whether recombinant ESAT-6 (rESAT-6) and recombinant CFP-10 (rCFP-10) can be replaced with corresponding mixtures of overlapping peptides spanning the complete amino acid sequence of each antigen. Proliferation of M. tuberculosis-specific human T-cell lines in response to rESAT-6 and rCFP-10 and that in response to the corresponding peptide mixtures were almost completely correlated (r = 0.96, P < 0.0001 for ESAT-6; r = 0.98, P < 0.0001 for CFP-10). More importantly, the same was found when gamma interferon production by peripheral blood mononuclear cells in response to these stimuli was analyzed (r = 0.89, P < 0.0001 for ESAT-6; r = 0.89, P < 0.0001 for CFP-10). Whole protein antigens and the peptide mixtures resulted in identical sensitivity and specificity for detection of infection with M. tuberculosis. The peptides in each mixture contributing to the overall response varied between individuals with different HLA-DR types. Interestingly, responses to CFP-10 were significantly higher in the presence of HLA-DR15, which is the major subtype of DR2. These results show that mixtures of synthetic overlapping peptides have potency equivalent to that of whole ESAT-6 and CFP-10 for sensitive and specific detection of infection with M. tuberculosis, and peptides have the advantage of faster production at lower cost.
Cerebral blood flow and temporal lobe epileptogenicity (1996)

Long-term surface cerebral blood flow (CBF) monitoring was performed to test the hypothesis that temporal lobe epileptogenicity is a function of epileptic cortical perfusion. Forty-three bitemporal 2-hour periictal CBF studies were performed in 13 patients. Homotopic regions of temporal cortex maintained interictal epileptic cortical hypoperfusion and nonepileptic normal cortical CBF. At 10 minutes preictus, a statistically significant, sustained increase in CBF was detected on the epileptic temporal lobe. Two minutes preictus, there was approximation of CBF in the epileptic and nonepileptic temporal lobes. Thereafter, electrocorticographic (ECoG) and clinical seizure onset occurred. The linear relationship between CBF in the two hemispheres (epileptic and nonepileptic) was the inverse of normal (y = -0.347x + 62.767, r = 0.470, df = 95, p &lt; 0.05). The data indicated a direct linear correlation between epileptic cortical CBF and seizure interval (frequency-1), a clinical measure of epileptogenicity (r = 0.610, df = 49, p &lt; 0.05). Epileptogenicity was also found to be a logarithmic function of the difference between nonepileptic and epileptic cortical perfusion (r = 0.564, df = 58, t = 5.20, p &lt; 0.05). The results showed that progressive hypoperfusion of the epileptic focus correlated with a decreased seizure interval (increased epileptogenicity). Increased perfusion of the epileptic focus correlated with an increased seizure interval (decreased epileptogenicity). The fact that CBF alterations precede ECoG seizure activity suggests that vasomotor changes may produce electrical and clinical seizure onset.
Characterization of the electron mobility in the inverted &amp;lt;100&amp;gt; Si surface (1979)

The effective mobility of electrons in the inverted 〈100〉 Si surface was measured over a wide range of temperatures, gate voltages, and back-bias voltages. At a first glance the mobility appears to be strongly dependent on the channel surface doping. When the data were reanalyzed under a new approach where the mobility is plotted as a function of an effective perpendicular electric field experienced by the inversion layer, a universal curve has developed from the experimental data which indicates that the inversion layer mobility is not a function of doping density in the range (N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</inf> < 1.0 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> ) and not a function of nominal surface processing. Our model indicates that the MOSFET surface inversion layer mobility is a reproducible property associated with the Si/SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> system and not a parameter sensitive to nominal process variations encountered in the present n-channel Si-Gate Technology.
SpyAvidin Hubs Enable Precise and Ultrastable Orthogonal Nanoassembly (2014)

The capture of biotin by streptavidin is an inspiration for supramolecular chemistry and a central tool for biological chemistry and nanotechnology, because of the rapid and exceptionally stable interaction. However, there is no robust orthogonal interaction to this hub, limiting the size and complexity of molecular assemblies that can be created. Here we combined traptavidin (a streptavidin variant maximizing biotin binding strength) with an orthogonal irreversible interaction. SpyTag is a peptide engineered to form a spontaneous isopeptide bond to its protein partner SpyCatcher. SpyTag or SpyCatcher was successfully fused to the C-terminus of Dead streptavidin subunits. We were able to generate chimeric tetramers with n (0 ≤ n ≤ 4) biotin binding sites and 4-n SpyTag or SpyCatcher binding sites. Chimeric SpyAvidin tetramers bound precise numbers of ligands fused to biotin or SpyTag/SpyCatcher. Mixing chimeric tetramers enabled assembly of SpyAvidin octamers (8 subunits) or eicosamers (20 subunits). We validated assemblies using electrophoresis and native mass spectrometry. Eicosameric SpyAvidin was used to cluster trimeric major histocompatibility complex (MHC) class I:β2-microglobulin:peptide complexes, generating an assembly with up to 56 components. MHC eicosamers surpassed the conventional MHC tetramers in acting as a powerful stimulus to T cell signaling. Combining ultrastable noncovalent with irreversible covalent interaction, SpyAvidins enable a simple route to create robust nanoarchitectures.
Gentamicin distribution from a collagen carrier (1996)

Local delivery of antibiotics by a degradable carrier has the potential for high local antibiotic levels and avoids systemic toxicity. Intravenous access, renal function monitoring, and subsequent surgical removal may not be required when degradable local delivery modalities are used. This study examined the in vivo elution of gentamicin from processed bovine collagen (type I) in 66 adult White rabbits. Collagen impregnated with gentamicin (3 mg/kg) was implanted into the vastus lateralis, and data were collected from 15 minutes to 28 days after implantation. Local tissue biopsies were taken a minimum of 2 mm from the implantation site. The gentamicin was released into the local tissue and averaged more than 3,800 micrograms/ml during the initial 4 hours after implantation. Local levels fell to 6.90 +/- 5.22 micrograms/ml at 24 hours and subsequently were 2.70 +/- 1.75 micrograms/ml or more through day 28. Serum levels reached an average peak of 4.04 +/- 1.75 micrograms/ml at 5 hours after implantation, decreased after the initial 24 hours, and subsequently were less than 0.41 +/- 0.20 microgram/ml through day 28. Collagen impregnated with gentamicin proved to be an effective degradable carrier of gentamicin in the healthy rabbit; it provided local tissue concentrations above the minimum inhibitory concentration and serum concentrations below levels associated with systemic toxicity for 28 days after implantation.
Oral Steroid Treatment for Hearing Improvement in Ménière’s Disease and Endolymphatic Hydrops (2012)

The results of this and other studies would indicate that a Ménière's disease or endolymphatic hydrops patient is unlikely to experience an improvement in hearing from a short course of oral steroid. Clinically observed temporary improvement did not sustain over several months. Further work to elucidate the mechanisms underlying hearing loss in hydrops, perhaps focusing on the dendrite damage noted in animal models of hydrops, is warranted.
Predicting response to epigenetic therapy (2014)

Drugs targeting the epigenome are new promising cancer treatment modalities; however, not all patients receive the same benefit from these drugs. In contrast to conventional chemotherapy, responses may take several months after the initiation of treatment to occur. Accordingly, identification of good pretreatment predictors of response is of great value. Many clinical parameters and molecular targets have been tested in preclinical and clinical studies with varying results, leaving room for optimization. Here we provide an overview of markers that may predict the efficacy of FDA- and EMA-approved epigenetic drugs.
Discovering typical structures of documents (1998)

Article Discovering typical structures of documents: a road map approach Share on Authors: Ke Wang Department of Information Systems and Computer Science, National University of Singapore Department of Information Systems and Computer Science, National University of SingaporeView Profile , Huiqing Liu BioInformatics Center, National University of Singapore BioInformatics Center, National University of SingaporeView Profile Authors Info & Claims SIGIR '98: Proceedings of the 21st annual international ACM SIGIR conference on Research and development in information retrievalAugust 1998 Pages 146–154https://doi.org/10.1145/290941.290982Online:01 August 1998Publication History 82citation642DownloadsMetricsTotal Citations82Total Downloads642Last 12 Months9Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Studies on 1-Azabicyclo Compounds. XVI. Synthesis of 1'-Methylindan-2-spiro-2'-piperazine and Related Compounds (1973)

A new synthesis of the spirodiamines (IIIa-c) from the methiodides (Ia-c) via the spiroaminolactams (VIIa-c) by Stevens rearrangement is described.
Film stress-related vacancy supersaturation in silicon under low-pressure chemical vapor deposited silicon nitride films (1988)

The effect of stress in silicon nitride films, deposited by the low-pressure chemical vapor deposition process, on the point defect concentrations in silicon has been studied. The stress level in the nitride film is varied by controlling the ratio of flow rates of reactant gases R=fSiH2Cl2/fNH3, from 1/6 to 6. The stress in the nitride film is tensile and its magnitude increases with decreasing R. During anneals at 1100 °C in Ar with a high stress in the nitride, phosphorus diffusion in silicon is retarded, antimony diffusion is enhanced, and extrinsic stacking faults shrink faster than with a low stress. These results suggest that a vacancy supersaturation and a self-interstitial undersaturation exist under the nitride and that the deviation from the equilibrium point defect concentrations are closely related to the stress level in the silicon nitride film. From the phosphorus junction profiles with varying shape width, an effective vacancy diffusivity of 3×10−10 cm2/s has been obtained.
Recovery and Drift Dynamics of Resistance and Threshold Voltages in Phase-Change Memories (2007)

The electronic behavior of the chalcogenide material used in phase-change memory (PCM) plays a key role in defining the operation voltages and times of the memory cell. In particular, the threshold voltage for electronic switching of the amorphous chalcogenide determines the boundary between programming and readout operation, while its resistance allows the recognition of the bit status. This paper present a time-resolved analysis of threshold voltage and resistance in a PCM. Both dynamics of threshold voltage and resistance display a fast transient, named recovery behavior, in the first 30 ns after programming. A slower, nonsaturating drift transient is found for longer times. The two transients are discussed referring to electronic and structural rearrangements in the amorphous chalcogenide. Finally, the impact on the device level is considered
Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs (2007)

Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.
The role of primary varicose veins in venous ulceration. (1982)

"Venous" ulceration is usually ascribed to deep venous insufficiency. We record the cases of 20 patients with 23 ulcers without a history suggestive of deep vein disease who were found to have a normal deep venous system when evaluated by Doppler ultrasound, ambulatory venous pressures, and photoplethysmography. All had gross varicose veins present for many years (mean 24 years; range 10 to 35 years), and only 14 limbs had incompetent calf perforating veins. Effective treatment is facilitated by recognition of the relationship of varicose ulcer to superficial venous disease, usually incompetence of the saphenofemoral junction, with or without the presence of incompetent calf perforating veins.
Kinetic and Thermodynamic Basis of Promoter Strength:  Multiple Steps of Transcription Initiation by T7 RNA Polymerase Are Modulated by the Promoter Sequence (2002)

Transcription initiation by T7 RNA polymerase (T7 RNAP) is regulated by the specific promoter DNA sequence that is classically divided into two major domains, the binding domain (-17 to -5) and the initiation domain (-4 to +6). The occurrence of non-consensus bases within these domains is responsible for the diversity of promoter strength, the basis of which was investigated by studying T7 promoters with changes in the promoter specificity region (-13 to -6) of the binding domain and/or the melting region (-4 to -1) of the initiation domain. The transient state kinetics and thermodynamic studies revealed that multiple steps in the pathway of transcription initiation are modulated by the promoter DNA sequence. Three base changes in the promoter specificity region at -11, -12, and -13, found in the natural phi 3.8 promoter, reduced the overall affinity of the T7 RNAP for the promoter DNA by 2-3-fold and decreased the rate of pppGpG synthesis, the first RNA product. Promoter opening is thermodynamically driven in T7 RNAP, and a single base change in the melting region (TATA to TAAA) decreased the extent of open complex generated at equilibrium. This base change in the melting region also increased the K(d) of (+1) GTP and the dissociation rate of pppGpG. Thus, transcription initiation at various T7 promoters is differentially regulated by initiating GTP concentration. The specificity and melting regions of T7 promoter DNA act both independently and synergistically to affect distinct steps of transcription initiation. Although each step in the initiation pathway is affected to a small degree by promoter sequence variations, the cumulative effect dictates the overall promoter strength.
Autocrine regulation of rat chondrocyte proliferation by natriuretic peptide C and its receptor, natriuretic peptide receptor-B. (1994)

Natriuretic peptide receptor-B (NPR-B) was identified in rat chondrocytes, and its physiological functions were investigated. Rat tissues, including the xiphoid cartilage, brain, lung, liver, adrenal gland, and kidney, were screened for NPR-B activity, which we assayed by receptor guanylate cyclase activity specifically stimulated by C-type natriuretic peptide (CNP), a known selective activator of NPR-B. Cartilage showed distinctly higher NPR-B activity. Furthermore, exposure of cultured rat chondrocytes to CNP M) resulted in a large increase in intracellular cGMP production (376 38 pmoywell), with threshold responses occurring between and lo-@ M CNP. Atrial natriuretic peptide and brain natriuretic peptide also stimulated cGMP production in rat chondrocytes but with a potency that was at least 10 times less than that of CNP. Polymerase chain reaction analysis also demonstrated NPR-B gene expression in adult rat xiphisternum and cultured chondrocytes. These findings indicate that NPR-B is present in rat chondrocytes. In rat chondrocytes exposed to CNP, [SH]thymidine incorporation was inhibited in a dose-dependent manner (half-maximal response, lo-" M). However, much higher concentrations of atrial natriuretic peptide were required to induce the inhibition of thymidine incorporation. Interestingly, CNP-like immunoreactivity was detected in the conditioned medium from chondrocyte cultures. In addition, TGF-P1, a multifunctional cytokine, induced a marked increase in CNP secretion and CNP mRNA levels in chondrocytes. These results indicate that autocrine CNP inhibits mitogenesis in chondrocytes via NPR-B under the control of TGF-P1.
Role of T‐Cell Derived Cytokines in the Downregulation of Immune Responses in Parasitic and Retroviral Infection (1992)

Parasitic infection is frequently accompanied by a downregulation in host cell-mediated immunity. Recent studies suggest that this modulation of helper T cells and effector cell function can at least in part be attributed to the action of a set of inhibitory cytokines produced by T lymphocytes as well as by a number of other cell types. The best characterized of these inhibitory lymphokines are IL-4, IL-10 and TGF-beta. Interestingly, both IL-4 and IL-10 are produced by the Th2 but not the Th1 subset of CD4+ helper cells. The former subset dominates in many situations of chronic or exacerbated parasitic infection and is thought to suppress Th1 function as a consequence of the cross-regulatory activity of these two cytokines. The latter hypothesis is supported by recent experiments demonstrating that mAb-mediated neutralization of IL-10 reverses suppressed IFN-gamma responses and/or disease susceptibility in mice with parasitic infections. In vivo neutralization of TGF-beta has also been reported to increase host resistance to parasite challenge. In addition to suppressing T-cell differentiation, function or proliferation, IL-4, IL-10 and TGF-beta each inhibit the ability of IFN-gamma to activate macrophages for killing of both intracellular and extracellular parasites. Moreover, the three cytokines are able to synergize with each other in downregulating these parasiticidal effects. Interestingly, each of the cytokines inhibits the production of reactive nitrogen oxides, an effector mechanism previously demonstrated to play a major role in parasite killing by activated macrophages. In the case of IL-10, this suppression of nitrogen oxide production appears to result from an inhibition of TNF-alpha synthesis leading to defective macrophage stimulation. While distant from parasites in their biology and phylogeny, some retroviruses also appear to induce an over-production in downregulatory cytokines which is closely associated with the onset of immunodeficiency. Thus, in an animal model involving infection of mice with LP-BM5 MuLV and in human HIV infection, Th2 (IL-10 and/or IL-4) cytokine synthesis is increased while Th1 (IFN-gamma and/or IL-2) cytokine production is suppressed. These observations suggest that cytokine-mediated cross-regulation may play a role in the pathogenesis of acquired immune deficiency disease, contributing both to the progression of retroviral infection and the increase in susceptibility to opportunistic infections and malignancy. Observations of similar cytokine cross-regulatory activities in organisms as diverse as helminths, protozoa and retroviruses predict that comparable mechanisms may operate in a wide variety of infectious diseases.
Effects of dietary fat on metabolic disorders and reproductive performance of dairy cattle (1991)

Improved reproductive performance and reduced incidence of metabolic disorders have been postulated to be benefits of feeding supplemental fat to dairy cows. Increased plasma nonesterified fatty acid concentrations during fat supplementation may result from incomplete tissue uptake of fatty acids after lipoprotein lipase hydrolysis of very-low-density lipoprotein triglyceride; however, evidence suggests that net adipose tissue triglyceride hydrolysis may be increased during fat supplementation. Plasma 3-OH-butyrate concentrations remain relatively constant during fat supplementation but may have a tendency to be reduced if fat is supplemented to cows having relatively high basal plasma 3-OH-butyrate concentrations. Because plasma ketone levels usually increase when nonesterified fatty acid concentrations are elevated, it is hypothesized that potential antiketogenic effects of added fat are due to a glucose sparing effect. Supplemental fat does not seem to reduce hepatic lipid infiltration near the time of calving. Potential mechanisms by which supplemental fat may improve reproductive performance include stimulation of prostaglandin F2 a synthesis and secretion and enhanced utilization of blood cholesterol for progesterone synthesis. Days postpartum until first ovulation and luteal function of dairy cattle have been related to energy balance during the first 3 wk postpartum. Energy balance data for early lactation cows fed supplemental fat are not plentiful; however, slight but statistically nonsignificant increases have been observed when feeding fat. Cows fed supplemental fat that experience improved energy balance may begin to cycle sooner because of enhanced follicular growth and development. Applied studies examining the effects of supplemental fat on reproductive performance have provided inconsistent results.