gebhart/patrepeval huggingface dataset:
Functional analysis of DR17(DR3)-restricted mycobacterial T cell epitopes reveals DR17-binding motif and enables the design of allele-specific competitor peptides (1992)

We have previously shown that p3-13 (KTIAY-DEEARR) of the 65-kDa heat shock protein (hsp65) of Mycobacterium tuberculosis and Mycobacterium leprae is selected as an important T cell epitope in HLA-DR17+ individuals, by selectively binding to (a pocket in) DR17 molecules, the major subset of the DR3 specificity. We have now further studied the interaction between p3-13, HLA-DR17 and four different TCR (V beta 5.1, V beta 1, and V beta 4) by using T cell stimulation assays, direct peptide-DR binding assays, and a large panel (n = 240) of single amino acid substitution analogs of p3-13. We find that residues 5(I) and 8(D) of p3-13 are important DR17 binding residues, whereas the residues that interact with the TCR vary slightly for each DR17-restricted clone. By using N- and C-terminal truncated derivatives of p2-20 we defined the minimal peptide length for both HLA-DR17 binding and T cell activation: the minimal peptide that bound to DR17 was seven amino acids long whereas the minimal peptide that activated T cell proliferation was eight amino acids in length. Furthermore, two new DR17-restricted epitopes were identified on hsp70 and hsp18 of M. leprae. Alignment of the critical DR17-binding residues 5(I) and 8(D) of p3-13 with these two novel epitopes and two other DR17-binding peptides revealed the presence of highly conserved amino acids at positions n and n + 3 with I, L, and V at position n and D and E at position n + 3. D and E are particularly likely to interact with the DR17-specific, positively charged pocket that we have defined earlier. Based on these results, a set of single amino acid substituted analogs that failed to activate these T cell clones but still bound specifically to DR17 was defined and tested for their ability to inhibit T cell activation by p3-13 or other DR17-restricted epitopes. Those peptides were able to inhibit the response to p3-13 as well as other DR17-restricted mycobacterial epitopes in an allele-specific manner, and are anticipated to be of potential use for immunotherapeutic and vaccine design strategies.
The National Cancer Institute: cancer drug discovery and development program. (1992)

The discovery and development of novel therapeutic products for the treatment of malignancy is vitally important to those physicians responsible for the management of cancer patients. A description of the ongoing efforts at the National Cancer Institute (NCI) is intended to provide insight into those complex processes necessary to accomplish this mission. An update on the NCI's revised cancer screen is accompanied by a brief summary of those new agents scheduled to be entered into clinical investigation in the near future. The tremendous potential advantages and challenges associated with the use of a molecular approach to cancer drug design are discussed. Despite the differences of opinion that may exist regarding the optimal strategies for accomplishing the mission, there is no disagreement regarding the importance of the effort to find effective new therapies for cancer patients.
Modulated terahertz responses of split ring resonators by nanometer thick liquid layers (2008)

The terahertz responses of planar arrays of split ring resonators with 50nm thin liquid layers introduced in the interspaces between the metal structures have been studied using the terahertz-time domain spectroscopy technique. In our experimental configuration, both the circular current driven and linear polarization induced resonances show redshifted and enhanced transmission. The dielectric functions extracted from an effective medium model indicate that the behavior of the surface and interface charge oscillations is highly sensitive to the interface environment changes. The results suggest that this kind of device may be used for sensing applications.
Cold Adaptation in Budding Yeast (2004)

We have determined the transcriptional response of the budding yeast Saccharomyces cerevisiae to cold. Yeast cells were exposed to 10 degrees C for different lengths of time, and DNA microarrays were used to characterize the changes in transcript abundance. Two distinct groups of transcriptionally modulated genes were identified and defined as the early cold response and the late cold response. A detailed comparison of the cold response with various environmental stress responses revealed a substantial overlap between environmental stress response genes and late cold response genes. In addition, the accumulation of the carbohydrate reserves trehalose and glycogen is induced during late cold response. These observations suggest that the environmental stress response (ESR) occurs during the late cold response. The transcriptional activators Msn2p and Msn4p are involved in the induction of genes common to many stress responses, and we show that they mediate the stress response pattern observed during the late cold response. In contrast, classical markers of the ESR were absent during the early cold response, and the transcriptional response of the early cold response genes was Msn2p/Msn4p independent. This implies that the cold-specific early response is mediated by a different and as yet uncharacterized regulatory mechanism.
Measured versus Estimated Creatinine Clearance in Patients with Low Serum Creatinine Values (1993)

In patients with an SCr < 85 mumol/L, the actual measured SCr should be used when calculating Clcr (regardless of the patient's gender), by the Cockcroft-Gault method.
I n s i t u cleaning of GaAs surfaces using hydrogen dissociated with a remote noble-gas discharge (1990)

I n situ cleaning of GaAs surfaces has been achieved at 350 °C with a novel technique employing hydrogen that is excited and dissociated using a remote Ar discharge. Reconstructed surfaces characteristic of clean, As-stabilized GaAs surfaces have been observed with reflection high-energy electron diffraction following the cleaning treatment. Auger electron spectroscopy analyses confirm that such a treatment removes both carbon and oxygen contamination from the surface. X-ray photoelectron spectroscopy shows the removal of oxygen bonded to both Ga and As on the surface. Emission spectroscopy shows evidence of excited molecular and atomic hydrogen with the downstream-excitation process.
Specific features of glycogen metabolism in the liver (1998)

Although the general pathways of glycogen synthesis and glycogenolysis are identical in all tissues, the enzymes involved are uniquely adapted to the specific role of glycogen in different cell types. In liver, where glycogen is stored as a reserve of glucose for extrahepatic tissues, the glycogen-metabolizing enzymes have properties that enable the liver to act as a sensor of blood glucose and to store or mobilize glycogen according to the peripheral needs. The prime effector of hepatic glycogen deposition is glucose, which blocks glycogenolysis and promotes glycogen synthesis in various ways. Other glycogenic stimuli for the liver are insulin, glucocorticoids, parasympathetic (vagus) nerve impulses and gluconeogenic precursors such as fructose and amino acids. The phosphorolysis of glycogen is mainly mediated by glucagon and by the orthosympathetic neurotransmitters noradrenaline and ATP. Many glycogenolytic stimuli, e.g. adenosine, nucleotides and NO, also act indirectly, via secretion of eicosanoids from non-parenchymal cells. Effectors often initiate glycogenolysis cooperatively through different mechanisms.
Cross-linked protein crystals for vaccine delivery (1999)

The progress toward subunit vaccines has been limited by their poor immunogenicity and limited stability. To enhance the immune response, subunit vaccines universally require improved adjuvants and delivery vehicles. In the present paper, we propose the use of cross-linked protein crystals (CLPCs) as antigens. We compare the immunogenicity of CLPCs of human serum albumin with that of soluble protein and conclude that there are marked differences in the immune response to the different forms of human serum albumin. Relative to the soluble protein, crystalline forms induce and sustain over almost a 6-month study a 6- to 10-fold increase in antibody titer for highly cross-linked crystals and an approximately 30-fold increase for lightly cross-linked crystals. We hypothesize that the depot effect, the particulate structure of CLPCs, and highly repetitive nature of protein crystals may play roles in the enhanced production of circulating antibodies. Several features of CLPCs, such as their remarkable stability, purity, biodegradability, and ease of manufacturing, make them highly attractive for vaccine formulations. This work paves the way for a systematic study of protein crystallinity and cross-linking on enhancement of humoral and T cell responses.
Transport Protocol Requirements for Distributed Multimedia Information Systems (1989)

Typical Distributed Multimedia Information Systems are made up of clusters of workstations connected by local area networks. Such systems allow users to exchange information in the form of ‘documents’ containing text, graphics and voice; some systems support both store-and-forward and real-time material. Here we consider various transport protocol requirements and conclude that some essential features are not available with existing protocols. The main objective of the work described here is to investigate the use of transport protocols which support the notion of multicast logical connectivity, both within a single network and in an internet environment. In this paper we show that protocols with multicasting capabilities can yield a substantial performance improvement over protocols which support only unicast logical connectivity. We propose ways in which multicasting can be exploited to suit our application. A prototype implementation of a multicast communication facility based on these requirements is presented, and an application model is used to measure the transport protocol performance under various possible system configurations and loads. Results of performance measurements are presented, based on experiments carried out on an Ethernet-based internet.
Corneal Sensation After Corneal Refractive Surgery with Small Incision Lenticule Extraction (2013)

The findings of the study revealed that, although both F-LASIK and SMILE procedures changed the corneal sensation 1 week, 1 month, and 3 months after surgery, they did not affect the dry eye parameters at any point.
A Device-Independent Evaluation of Carbonyl Emissions from Heated Electronic Cigarette Solvents (2017)

We developed a device-independent test method to investigate carbonyl emissions from different e-cigarette liquids under precisely controlled temperatures. PG and GL were identified to be the main sources of toxic carbonyl compounds from e-cigarette use. GL produced much more formaldehyde than PG. Besides formaldehyde and acetaldehyde, measurable amounts of acrolein were also detected at ≥270°C but only when GL was present in the e-liquid. At 215°C, the estimated daily exposure to formaldehyde from e-cigarettes, exceeded United States Environmental Protection Agency (USEPA) and California Office of Environmental Health Hazard Assessment (OEHHA) acceptable limits, which emphasized the need to further examine the potential cancer and non-cancer health risks associated with e-cigarette use.
Indirect recognition of donor HLA-DR peptides in organ allograft rejection. (1996)

To determine whether indirect allorecognition is involved in heart allograft rejection T cells obtained from peripheral blood and graft biopsy tissues were expanded in the presence of IL-2 and tested in limiting dilution analysis (LDA) for reactivity to synthetic peptides corresponding to the hypervariable regions of the mismatched HLA-DR antigen(s) of the donor. Serial studies of 32 patients showed that T cell reactivity to donor allopeptides was strongly associated with episodes of acute rejection. The frequency of allopeptide reactive T cells was 10-50-fold higher in the graft than in the periphery indicating that T cells activated via the indirect allorecognition pathway participate actively in acute allograft rejection. In recipients carrying a graft differing by two HLA-DR alleles the response appeared to target only one of the mismatched antigens of the donor. Indirect allorecognition was restricted by a single HLA-DR antigen of the host and directed against one immunodominant peptide of donor HLA-DR protein. However, intermolecular spreading was demonstrated in patients with multiple rejection episodes by showing that they develop allopeptide reactivity against the second HLA-DR antigen. These data imply that early treatment to suppress T cell responses through the indirect pathway of allorecognition, such as tolerance induction to the dominant donor determinant, may be required to prevent amplification and perpetuation of the rejection process.
T-Epitope Designer: A HLA-peptide binding prediction server (2005)

http://www.bioinformation.net/ted/
Polyphosphate blocks tumour metastasis via anti-angiogenic activity (2007)

PolyP (inorganic polyphosphate) is a linear polymer of many tens or hundreds of orthophosphate residues found in a wide range of organisms, including bacteria, fungi, insects, plants and vertebrates. Despite its wide distribution in mammalian tissues and plasma, the biological functions of polyP on tumour metastasis and angiogenesis have not been previously examined. In the present study, we have shown that polyP effectively blocked in vivo pulmonary metastasis of B16BL6 cells by suppression of neovascularization, whereas it did not affect proliferation or adhesion to extracellular matrix proteins. PolyP not only inhibited bFGF (basic fibroblast growth factor)-induced proliferation and ERK (extracellular-signal-regulated kinase)/p38 MAPK (mitogen-activated protein kinase) activation of human endothelial cells, but also blocked the binding of bFGF to its cognate cell-surface receptor. Furthermore, polyP inhibited bFGF-induced in vitro and in vivo angiogenesis, suggesting that polyP possesses an anti-angiogenic activity. Since neovascularization is essential for tumour metastasis, our present findings clearly indicate that polyP has an in vivo anti-metastatic activity via its anti-angiogenic activity. Taken together with the fact that angiogenesis occurs under various normal and pathological conditions, our observations suggest that endogenous polyP may play a critical role during embryonic development, wound healing and inflammation, as well as in the progress of pathological diseases such as rheumatoid arthritis and cancer.
Design of a Catalytic Active Site for Electrochemical CO2 Reduction with Mn(I)-Tricarbonyl Species (2015)

The design, synthesis, and assessment of a new manganese-centered catalyst for the electrochemical reduction of CO2 is described. The reported species, MnBr(6-(2-hydroxyphenol)-2,2'-bipyridine)(CO)3, includes a ligand framework with a phenolic proton in close proximity to the CO2 binding site, which allows for facile proton-assisted C-O bond cleavage. As a result of this modification, seven times the electrocatalytic current enhancement is observed compared to MnBr(2,2'-bipyridine)(CO)3. Moreover, reduction is possible at only 440 mV of overpotential. Theoretical computations suggest that the entropic contribution to the activation free energy is partially responsible for the increased catalytic activity. Experimental work, including voltammetry and product quantification from controlled potential electrolysis, suggests a key mechanistic role for the phenolic proton in the conversion of CO2 to CO.
Retinoids as Anti-Cancer Agents (1996)

Abstract: Retinoids, synthetic and natural analogs of retinoic acid, exhibit potent growth inhibitory and cell differentiation activities which account for their beneficial effects in cancer in ex vivo and in vivo models. These simple molecules with pleiotropic effects have shown potential as therapeutic agents for the treatment of cancer either alone or in combination with other agents. Retinoids regulate the growth of various cell types by directly modulating the expression of responsive genes through nuclear retinoid receptors (RARs and RXRs), which are ligand dependent transcription factors. The translo­ cation of RARCX in acute pro-myelocytic leukemia, decreased expression of RARP and reduced activity of the •RARP promoter in various tumors and cancer cell lines, and restoration of retinoid sensitivity to cancer cells by RAR expression vector transfection, are all indicative of the direct involvement of RAR malfunction in the process of tumorigenesis and also suggest a role for RARs as ligand dependent tumor suppressors. The current use of retinoids in cancer is limited because of their associated toxicities and lack of efficacy at tolerated doses. In order to improve the therapeutic index of retinoids, various strategies are currently being employed, e.g., receptor selective retinoids, anti-AP! selective retinoids and combination therapies. The development of novel retinoids along with an increased understanding of the biological functions and mechanisms of action of retinoid receptors are likely to usher in a new era of retinoid therapy of cancers.
Roles of endothelin signaling in melanocyte development and melanoma (2010)

Endothelin (Edn) signaling via the G-coupled, Edn receptor type B (Ednrb) is essential for the development of melanocytes from the neural crest (NC) and has been associated with melanoma progression. Edn3 plays varying roles during melanocyte development, promoting the proliferation and self-renewal of NC-derived multi- and bi-potential precursors as well as the survival, proliferation, differentiation and migration of committed melanocyte precursors. Melanocyte differentiation is achieved via the interaction of Ednrb and Kit signaling, with Ednrb being specifically required in the final differentiation step, rather than in the initial specification of melanocytic fate. Ednrb has also been implicated in the de-differentiation of mature melanocytes, a process that takes place during the malignant transformation of these cells. Ednrb was found to be upregulated in melanoma metastases and was shown to alter tumor-host interactions leading to melanoma progression. Antagonists to this receptor were shown to inhibit melanoma cell growth and increase the apoptotic rate of these cells, and to lead to disease stabilization in melanoma patients. Thus, Edn signaling inhibition may prove useful in the treatment of certain types of melanoma.
Automated method for detection and segmentation of liver metastatic lesions in follow-up CT examinations (2015)

This paper presents a fully automated method for detection and segmentation of liver metastases in serial computed tomography (CT) examinations. Our method uses a given two-dimensional baseline segmentation mask for identifying the lesion location in the follow-up CT and locating surrounding tissues, using nonrigid image registration and template matching, in order to reduce the search area for segmentation. Adaptive region growing and mean-shift clustering are used to obtain the lesion segmentation. Our database contains 127 cases from the CT abdomen unit at Sheba Medical Center. Development of the methodology was conducted using 22 of the cases, and testing was conducted on the remaining 105 cases. Results show that 94 of the 105 lesions were detected, for an overall matching rate of 90% making the correct RECIST 1.1 assessment in 88% of the cases. The average Dice index was [Formula: see text], the average sensitivity was [Formula: see text], and the positive predictive value was [Formula: see text]. In 92% of the rated cases, the results were classified by the radiologists as acceptable or better. The segmentation performance, matching rate, and RECIST assessment results hence appear promising.
Photo-Removable Protecting Groups for in Situ DNA Microarray Synthesis (2004)

try has great potential as a rapid, cost-effective, and sensitive assay when antibody-coated, high-specific-activity europium(III) nanoparticles are used as labels. We believe that the analytical approach is applicable to various analytes and sample matrixes. Furthermore, this simple and rapid assay format could be beneficial, e.g., when time is critical concerning the life of a patient, such as for cardiac diagnostics.
Integrated polarization-analyzing CMOS image sensor for detecting incoming light ray direction (2010)

A CMOS image sensor with an integrated wire grid polarizer to sense the polarization of light is presented. The chip consists of an array of 128 by 128 pixels, it occupies an area of 5×4 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and it has been designed and fabricated in a CMOS 180nm process. The integrated grid polarizer is oriented in various directions to compute the Stokes parameters which can be used to determine the degree of polarization of the incoming light ray.
Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection (2014)

Traits associated with response to PRRSV infection in growing pigs are largely controlled by genomic regions with relatively small effects, with the exception of SSC4. Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome. These results show that selection for the SSC4 region could potentially reduce the effects of PRRS in growing pigs, ultimately reducing the economic impact of this disease.
Role of the Adrenal Gland and Adrenal-Mediated Chemosignals in Suppression of Estrus in the House Mouse: The Lee-Boot Effect Revisited1 (1998)

Mature female mice, grouped in the absence of a male stimulus, exhibit a suppressed estrous cycle (the so-called Lee-Boot effect). We have designed a series of experiments to elucidate the involvement of the adrenal gland in this phenomenon. Our initial results indicate that adrenalectomized mice exhibit a regular estrous cycle in either isolated or grouped conditions. A single, intact mouse caged with five adrenalectomized females showed repeated normal cycles. When the urine samples from group-caged intact mice or group-caged adrenalectomized mice were applied to the external nares of singly caged females, estrous cycles were inhibited in the animals receiving urine from the intact mice but not from the adrenalectomized mice. In addition, corticosterone therapy restored the function of estrus suppression in grouped, adrenalectomized mice. We had previously shown that the urinary excretion of several volatile compounds (2-heptanone, trans-5-hepten-2-one, trans-4-hepten-2-one, pentyl acetate, cis-2-penten-1-yl acetate, and 2,5-dimethylpyrazine) was adrenal mediated (Science 1986; 231:722-725). A further testing of these compounds in relation to estrus suppression has now revealed that a mixture of these compounds is effective, but removing 2, 5-dimethylpyrazine from the mixture abolished the biological response. The overall results of this study show conclusively an important role of the adrenal gland and adrenal-mediated urinary metabolites in estrus suppression.
Morphologic and Management Characteristics of Individuals with Unilateral Cleft Lip and Palate Who Required Maxillary Advancement (2008)

Maxillary hypoplasia that will require a Le Fort I advancement can be determined as early as age 10. Multiple missing maxillary teeth, secondary palate procedures including pharyngeal flaps, and inconsistent team care with delayed orthodontic intervention are contributing factors to maxillary underdevelopment.