gebhart/patrepeval huggingface dataset:
Recognition of prostate-specific antigenic peptide determinants by human CD4 and CD8 T cells (1998)

It is now becoming accepted that one is not tolerant to all the determinants of self proteins: the T cell repertoire directed to some sequences in self proteins is intact and can be activated. When a self protein is exclusively expressed by tumour cells, the T cell repertoire directed to the particular self antigen can potentially be activated to attack the tumour: this would amount to induction of a beneficial autoimmune response. Prostate cancer offers a unique opportunity for activation of a tumour-specific immune response owing to the exclusive synthesis of prostate-specific antigen (PSA) and prostate-specific membrane antigen (PSM) by prostatic tissue and prostate tumour cells. In this study we examine the CD4 and CD8 T cell repertoires specific for peptides of PSA and PSM in normal human male individuals, using short-term, peptide antigen-driven CD4 and CD8 T cell lines. We show that short-term, CD4 T cell lines derived from six HLA-DR4 individuals showed strong proliferative responses to six of 10 tested peptides of PSA, selected as to contain a DR4 binding motif. Short-term, CD8 T cell lines from three HLA-A1 individuals showed specific cytolytic activity for autologous targets loaded with five of five tested peptides of PSA and PSM, selected to possess an HLA-A1 binding motif. One of the peptides chosen is termed a 'dual-motif' peptide, as it encodes determinants for both CD4 and CD8 T cells. These results, indicating the existence of CD4 and CD8 T cells against determinants of the self proteins, PSA and PSM, in healthy male individuals reveal the potential of the T cell repertoire from the typical prostate cancer patient to eradicate prostate tumours upon being appropriately activated.
Whole Blood Cells Loaded with Messenger RNA as an Anti‐Tumor Vaccine (2013)

The use of a cell-based vaccine composed of autologous whole blood cells loaded with mRNA is described. Mice immunized with whole blood cells loaded with mRNA encoding antigen develop anti-tumor immunity comparable to DC-RNA immunization. This approach offers a simple and affordable alternative to RNA-based cellular therapy by circumventing complex, laborious and expensive ex vivo manipulations required for DC-based immunizations.
Improved Ion Drag Pump (1962)

The measured characteristics (pressure-voltage, current-voltage, and efficiency) of an ion drag pump using razor edge emitters are reported and comparisons made with theory. The advantages of this pump over one using corona point emitters are discussed.
The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. (1995)

Chromosome I from the yeast Saccharomyces cerevisiae contains a DNA molecule of approximately 231 kbp and is the smallest naturally occurring functional eukaryotic nuclear chromosome so far characterized. The nucleotide sequence of this chromosome has been determined as part of an international collaboration to sequence the entire yeast genome. The chromosome contains 89 open reading frames and 4 tRNA genes. The central 165 kbp of the chromosome resembles other large sequenced regions of the yeast genome in both its high density and distribution of genes. In contrast, the remaining sequences flanking this DNA that comprise the two ends of the chromosome and make up more than 25% of the DNA molecule have a much lower gene density, are largely not transcribed, contain no genes essential for vegetative growth, and contain several apparent pseudogenes and a 15-kbp redundant sequence. These terminally repetitive regions consist of a telomeric repeat called W', flanked by DNA closely related to the yeast FLO1 gene. The low gene density, presence of pseudogenes, and lack of expression are consistent with the idea that these terminal regions represent the yeast equivalent of heterochromatin. The occurrence of such a high proportion of DNA with so little information suggests that its presence gives this chromosome the critical length required for proper function.
Measurement of Heart Rate Variability to Assess Pain in Sedated Critically Ill Patients: A Prospective Observational Study (2016)

ANI is effective in detecting pain in deeply sedated critically ill patients, including those patients treated with norepinephrine. No significant correlation was found between ANI and BPS.
RNA binding assays for Tat-derived peptides: implications for specificity (1992)

RNA recognition by the HIV Tat protein is mediated in part by an arginine- and lysine-rich basic subdomain implicated as a signature element in proteins that bind RNA. Relative RNA binding affinities for a 14-residue peptide derived from Tat that spans the basic region are determined using a competition protocol. Binding specificity is compared with complexation by a 38-residue model for the RNA binding domain of Tat using the same approach. Binding strength for the minimal (14 residue) peptide is correlated with that for the longer peptide: both peptides recognize a short, bulged duplex. However, the shorter peptide dissociates more rapidly from the wild-type site and discriminates less well between nonspecific (double-stranded RNA) and specific sites. Relative dissociation constants for 38-residue peptide determined from direct partition and competition assays differ; the former assay consistently predicts stronger discrimination against RNAs with mutations in the stems flanking the bulge. Differences between the two assays are reconciled in terms of contributions from labile binding which is unstable to native gel electrophoresis. Kinetic stability may constitute a major specificity determinant for basic subdomain-mediated recognition of RNA.
Isolation and Activity ofN-p-Coumaroyltyramine, anα-Glucosidase Inhibitor in Welsh Onion (Allium fistulosum) (1997)

A phenolic amide, N-p-coumaroyltyramine (1), was isolated as an α-glucosidase inhibitor from methanol extracts of Welsh onion (Allium fistulosum). The inhibitory activity of 1 against a yeast enzyme was as high as Ki 8.4 × 10−7 m. From a structure-activity relationship study of 1 and its related compounds, the occurrence of α-glucosidase inhibitory activity required a p-coumaramide structure, with an amide hydrogen and alkyl or aralkyl substituent on the amide part.
Oxidative damage and age-related macular degeneration. (1999)

This article provides current information on the potential role of oxidation in relation to age-related macular degeneration (AMD). The emphasis is placed on the generation of oxidants and free radicals and the protective effects of antioxidants in the outer retina, with specific emphasis on the photoreceptor cells, the retinal pigment epithelium and the choriocapillaris. The starting points include a discussion and a definition of what radicals are, their endogenous sources, how they react, and what damage they may cause. The photoreceptor/pigment epithelium complex is exposed to sunlight, is bathed in a near-arterial level of oxygen, and membranes in this complex contain high concentrations of polyunsaturated fatty acids, all considered to be potential factors leading to oxidative damage. Actions of antioxidants such as glutathione, vitamin C, superoxide dismutase, catalase, vitamin E and the carotenoids are discussed in terms of their mechanisms of preventing oxidative damage. The phototoxicity of lipofuscin, a group of complex autofluorescent lipid/protein aggregates that accumulate in the retinal pigment epithelium, is described and evidence is presented suggesting that intracellular lipofuscin is toxic to these cells, thus supporting a role for lipofuscin in aging and AMD. The theory that AMD is primarily due to a photosensitizing injury to the choriocapillaris is evaluated. Results are presented showing that when protoporphyric mice are exposed to blue light there is an induction in the synthesis of Type IV collagen synthesis by the choriocapillary endothelium, which leads to a thickened Bruch's membrane and to the appearance of sub-retinal pigment epithelial fibrillogranular deposits, which are similar to basal laminar deposits. The hypothesis that AMD may result from oxidative injury to the retinal pigment epithelium is further evaluated in experiments designed to test the protective effects of glutathione in preventing damage to cultured human pigment epithelial cells exposed to an oxidant. Experiments designed to increase the concentration of glutathione in pigment epithelial cells using dimethylfumarate, a monofunctional inducer, are described in relation to the ability of these cells to survive an oxidative challenge. While all these models provide undisputed evidence of oxidative damage to the retinal pigment epithelium and the choriocapillaris that is both light- and oxygen-dependent, it nevertheless is still unclear at this time what the precise linkage is between oxidation-induced events and the onset and progression of AMD.
Library Screen for Inhibitors Targeting Norovirus Binding to Histo-Blood Group Antigen Receptors (2006)

Human noroviruses (NVs) are a common cause of nonbacterial gastroenteritis. The disease is difficult to control due to its widespread nature and the lack of antivirals or vaccines against NVs. The recent identification of human histo-blood group antigens (HBGAs) as NV receptors opens a new way for the discovery and design of antivirals against NVs. A saliva-based enzyme immune assay (EIA) was used to screen a synthetic-compound library for inhibition of the binding of norovirus-like particles to HBGA receptors. Among 5,000 compounds tested in the first round of screening, 153 compounds exhibited >50% inhibition of the binding of VA387 (an NV that binds to A, B, and H epitopes) to the A antigen in saliva at approximately 50 mug/ml, and 14 of the 153 compounds revealed strong inhibition, with a 50% effective concentration of <15 muM. Ten and 11 of the 14 compounds also revealed inhibition of the binding of VA387 to the B and H antigens, respectively. Seven and 6 of the 14 compounds also blocked the binding of the prototype Norwalk virus (A and H binder) to the A and H antigens, respectively. One compound significantly inhibited the binding of MOH (A and B binder) to the A and B antigens, but no compound revealed any inhibitory effect on the binding of a Lewis binding strain (VA207) to the Lewis antigens. The EIA is a high-throughput method for large-scale library screening for antivirals against NVs. Studies to further characterize the lead compounds and to screen additional compounds for other NVs are ongoing in our laboratory.
Mechanisms of bone destruction in multiple myeloma: the importance of an unbalanced process in determining the severity of lytic bone disease. (1989)

In order to clarify the mechanisms involved in the occurrence of lytic bone lesions (BL) in multiple myeloma (MM), we have compared the presenting myeloma-induced histological bone changes of 14 previously untreated MM patients with lytic BL with those of seven MM patients lacking lytic BL at presentation despite similar myeloma cell mass. A major unbalanced bone remodeling (increased bone resorption with normal to low bone formation) was the characteristic feature of patients presenting lytic BL. Furthermore, this unbalanced process was associated with a significant reduction of bone mass. Unexpectedly, a balanced bone remodeling (increase of both bone resorption and bone formation, without bone mass reduction) rather than a true lack of an excessive bone resorption was the usual feature of patients lacking lytic BL. Our current work clearly shows that a majority (72%) of patients with MM present an important unbalanced bone remodeling at diagnosis, leading to bone mass reduction and bone destruction (unbalanced MM). Some patients (20%) retain a balanced bone remodeling with initial absence of bone destruction (balanced MM). Few (8%) patients have pure osteoblastic MM without bone destruction.
Lamotrigine derivatives and riluzole inhibit INa,P in cortical neurons (2002)

The persistent, slowly inactivating fraction of the sodium current is involved in key functions in the CNS such as dendritic integration of synaptic inputs and cellular excitability. We have studied whether established anti-epileptic drugs and neuroprotective agents target the persistent sodium current. Two lamotrigine derivatives (sipatrigine and 202W92) and riluzole inhibited the persistent sodium current at low, therapeutic concentrations. In contrast, lamotrigine and the classical antiepileptic agents phenytoin and valproic acid blocked the fast-inactivating sodium channel but failed to affect the persistent fraction. The ability to influence either mode of channel activity may represent a defining feature of each drug subclass, changing profoundly their clinical indications. Given the damaging role of a sustained influx of sodium in both pharmaco-resistant seizures or excitotoxic insults, we suggest the utilization of drugs that suppress the persistent conductance.
In vitro activity of LY146032 alone and in combination with other antibiotics against gram-positive bacteria (1988)

The antibacterial activity of LY146032 alone and in combination with other drugs was assayed against gram-positive isolates. Synergism was found when LY146032 was combined with netilmicin, amikacin, imipenem, and fosfomycin by both checkerboard and time-kill tests. Indifference predominated when LY146032 was combined with teicoplanin, vancomycin, and rifampin. Under no circumstances and with no combinations was an antagonistic effect detected.
Interdependence between Cytokines and Cell Adhesion Molecules to Induce Interleukin-6 Production by Stromal Cells in Myeloma (1998)

Bone marrow (BM) environment is thought to support the growth of myeloma cells and thus to play an important role in the pathogenesis of multiple myeloma (MM). Because interleukin-6 (IL-6) is an essential growth factor in MM, we have examined the effects of two myeloma cell lines (U266 and ARH-77) on the IL-6 production by BM stromal cells in a co-culture system. These cell lines strongly stimulate the IL-6 production and IL-6 triggering was partially dependent on physical contact between lines and stroma. The percentages of cell adhesion to stromal layers were 39 % and 25 % respectively for ARH77 and U266 cell lines. Inhibition studies with blocking monoclonal antibodies showed the importance of CD49d/CD106 and CD11a/CD54 interactions in the stimulation of IL-6 production by stromal cells. However, cell-to-cell contact was not an absolute requirement for IL-6 production. Cytokines, of which TNF-α and IL-1β produced by MM or accessory cells, were also able to stimulate IL-6 production by fibroblasts and show additive effects. In adhesion assays, TNF-a and IL-1β were able to increase the adhesion of MM cells to stromal cells. CD54 was upregulated by IL-1β, TNF-α or a contact with MM cells while CD 106 expression was not, suggesting only a functional change of this molecule. However, the role of monoclonal antibodies, directed against these factors, confirmed the role of TNF-α in the IL-6 production by stromal cells, while any IL-1β intervention was not shown in our co-culture system. IL-6 favoured and maintained adhesion of MM cells to stromal cells spontaneously since its rein-troduction in the favoured co-culture system restored their decreased adhesion observed on a glutaraldehyde fixed stromal layer. Overall our data suggest a functional overlap between cytokines and adhesion molecules for the paracrine IL-6 production.
Self‐report pain assessment tools for cognitively intact older adults: Integrative review (2017)

Examining the psychometric properties of comprehensive self-report pain assessment tools informs recommendations for the selection of tools to be used in clinical practice.
Differentiation of Ia-reactive CD8+ murine T cells does not require Ia engagement. Implications for the role of CD4 and CD8 accessory molecules in T cell differentiation. (1988)

The present study was undertaken to assess the Ia differentiation requirements of CD8+ class II-allospecific CTL, whose CD8+ phenotype is apparently "discordant" with their MHC class II reactivity. To do so, we compared the effect of in vivo anti-Ia blockade on the differentiation of Ia-reactive CD8+ CTL with its effect on the differentiation of CD4+ T cells. We found that anti-Ia blockade did not detectably interfere with the differentiation of CD8+ Ia-reactive CTL, even though it arrested the differentiation of CD4+ T cells. Thus, the differentiation of CD4+ T cells is strictly dependent upon Ia engagement, whereas the differentiation of CD8+ T cells, even those with reactivity against MHC class II alloantigens, does not require Ia engagement. These results support the concept that Ia-reactive CD8+ T cells are conventional CD8+ CTL, probably selected by self-class I MHC molecules during differentiation, whose receptors fortuitously crossreact on MHC class II alloantigens. Taken together, the present data indicate an intimate relationship between CD4/CD8 expression with MHC class specificity during T cell differentiation and selection. We suggest that an active triggering role for CD4 and CD8 accessory molecules in T cell differentiation is best able to explain these observations.
Sample Size Determination (2002)

Scientists who use animals in research must justify the number of animals to be used, and committees that review proposals to use animals in research must review this justification to ensure the appropriateness of the number of animals to be used. This article discusses when the number of animals to be used can best be estimated from previous experience and when a simple power and sample size calculation should be performed. Even complicated experimental designs requiring sophisticated statistical models for analysis can usually be simplified to a single key or critical question so that simple formulae can be used to estimate the required sample size. Approaches to sample size estimation for various types of hypotheses are described, and equations are provided in the Appendix. Several web sites are cited for more information and for performing actual calculations
Microlocal analysis and evolution equations (2008)

Lecture notes from 2008 CMI/ETH Summer School on Evolution Equations. These notes are an informal introduction to the applications of microlocal methods in the study of linear evolution equations and spectral theory. Calculi of pseudodifferential operators and Fourier integral operators are discussed and axiomatized, but not constructed: the focus is on how to apply these tools.
CsPbIBr2 Perovskite Solar Cell by Spray-Assisted Deposition (2016)

In this work, an inorganic halide perovskite solar cell using a spray-assisted solution-processed CsPbIBr2 film is demonstrated. The process allows sequential solution processing of the CsPbIBr2 film, overcoming the solubility problem of the bromide ion in the precursor solution that would otherwise occur in a single-step solution process. The spraying of CsI in air is demonstrated to be successful, and the annealing of the CsPbIBr2 film in air is also successful in producing a CsPbIBr2 film with an optical band gap of 2.05 eV and is thermally stable at 300 °C. The effects of the substrate temperature during spraying and the annealing temperature on film quality and device performance are studied. The substrate temperature during spraying is found to be the most critical parameter. The best-performing device fabricated using these conditions achieves a stabilized conversion efficiency of 6.3% with negligible hysteresis. Cesium metal halide perovskites remain viable alternatives to organic metal halide perovskites as the cesium-containing perovskites can withstand higher temperature.
Nonvalidation of Reported Genetic Risk Factors for Acute Coronary Syndrome in a Large-Scale Replication Study (2007)

Our null results provide no support for the hypothesis that any of the 85 genetic variants tested is a susceptibility factor for ACS. These results emphasize the need for robust replication of putative genetic risk factors before their introduction into clinical care.
Traditional Extractants in Nontraditional Solvents:  Groups 1 and 2 Extraction by Crown Ethers in Room-Temperature Ionic Liquids (2000)

The crown ethers 18-crown-6 (18C6), dicyclohexano-18-crown-6 (DCH18C6), and 4,4‘-(5‘)-di-(tert-butylcyclohexano)-18-crown-6 (Dtb18C6) were dissolved in 1-alkyl-3-methylimidazolium hexafluorophosphate ([Cnmim][PF6], n = 4, 6, 8) room-temperature ionic liquids (RTILs) and studied for the extraction of Na+, Cs+, and Sr2+ from aqueous solutions. In the absence of extractant, the distribution ratios for the metal ions indicate a strong preference for the aqueous phase. With the crown ethers as extractants in RTIL-based liquid/liquid separations, the resulting metal ion partitioning depends on the hydrophobicity of the crown ether and also on the composition of the aqueous phase (e.g., concentration of HNO3 vs Al(NO3)3). Aqueous solutions of HCl, Na3 citrate, NaNO3, and HNO3 (the latter at low concentrations) decrease the metal ion distribution ratios and also decrease the water content of the RTIL phase. High concentrations of HNO3 decompose PF6- and increase both the water content and the water solubility of the RTIL phase. Highly hydrated salts such as Al(NO3)3 and LiNO3 salt out both the RTIL ions and the crown ethers; thus, when the aqueous phase contains Al(NO3)3, the trend more closely resembles traditional solvent extraction behavior where DSr > DCs and the most hydrophobic extracting phase produces the highest partitioning. When [C8mim][PF6] is used as the extracting phase, the metal ions can be loaded from Al(NO3)3 and stripped using water. Dtb18C6 forms 1:1 complexes with Cs+ and Sr2+ and also yields the highest distribution ratios out of the three crowns examined. In comparison to traditional solvent extraction behavior, the metal ion partitioning in these systems exhibits exceptional behavior and, in certain instances, suggests a complicated partitioning mechanism, which necessitates a more thorough understanding of RTILs as solvents before interpretation of the results.
TLM-PSD model for optimization of energy and power density of vertically aligned carbon nanotube supercapacitor (2013)

Electrochemical capacitors with fast charging-discharging rates are very promising for hybrid electric vehicle industries including portable electronics. Complicated pore structures have been implemented in active materials to increase energy storage capacity, which often leads to degrade dynamic response of ions. In order to understand this trade-off phenomenon, we report a theoretical model based on transmission line model which is further combined with pore size distribution function. The model successfully explained how pores length, and pore radius of active materials and electrolyte conductivity can affect capacitance and dynamic performance of different capacitors. The powerfulness of the model was confirmed by comparing with experimental results of a micro-supercapacitor consisted of vertically aligned multiwalled carbon nanotubes (v-MWCNTs), which revealed a linear current increase up to 600 Vs(-1) scan rate demonstrating an ultrafast dynamic behavior, superior to randomly entangled singlewalled carbon nanotube device, which is clearly explained by the theoretical model.