gebhart/patrepeval huggingface dataset:
Alternative Splicing Due to an Intronic SNP Defines a Novel HLA-B44-Restricted-Hematopoiesis-Restricted Minor Histocompatibility Antigen. (2006)

Abstract Minor histocompatibility antigens (mHAgs) with expression limited to hematopoietic cells represent attractive targets for immunotherapy to induce selective graft-versus-leukemia (GVL) reactions. Here we report the identification of a novel mHAg which is recognized by an HLA-B*4403-restricted CTL clone. Microsatellite allele image analysis of two DNA pools generated from CTL-defined mHAg positive and mHAg negative groups was performed using microsatellite markers set at 100 kb intervals within the segment initially mapped by two-point genetic linkage analysis and detailed mapping of the chromosomal recombinant points. This approach defined a 0.53 Mbp region of chromosome 18q21–22 containing 12 candidate genes potentially encoding the mHAg, although the target gene could not be identified. Subsequently, cDNA expression cloning studies demonstrated that the CTL epitope of interest was encoded by a novel allelic splice variant of XM_209104, hereafter designated as XM_209104-av. Indeed, this gene was found to lie within the region predicted by microsatellite allele image analysis. The immunogenicity of the epitope was generated by differential protein expression due to alternative splicing, which was completely controlled by one intronic single nucleotide polymorphism (SNP) located in the consensus 5′ splice site adjacent to an exon. To our knowledge, this is the first example of a mHAg controlled by a SNP located in a region other than coding sequences. Because the CTL lysed also HLA-B*4402 positive, mHAg positive B-LCLs, this novel epitope peptide can bind to not only HLA-B*4403 but also HLA-B*4402 which is a relatively common HLA-B allele in Caucasian populations. Finally, the finding that the novel XM_209104-av showed low or no expression in normal tissues including resting hematopoietic cells, but significantly higher expression in primary acute leukemia cells, especially those of myeloid lineage, suggest that this novel epitope may be an attractive therapeutic target for immunotherapy not only as a minor H antigen but also as a leukemia-associated antigen.
Using Monolingual Clickthrough Data to Build Cross-lingual Search Systems (2006)

A major portion of the World Wide Web(WWW) is still dominated by a few languages, with English being on the top. Monolingual information retrieval systems have been setup for such languages and are widely in use. To cater to a wider and diverse language speaking web users, we need Cross Lingual Information Retrieval (CLIR) systems that are capable of receiving a query in one language and returning results from a different language. To our knowledge not much work has been done in creating CLIR systems on the WWW. This is partly due to the unavailability of bilingual resources required for a major portion of the languages that are still a minority language in terms of the documents present on the WWW. Another important reason being the time and effort required to create a practical and useful CLIR system. In this paper, we address the problem of creating CLIR systems for language pairs in which the source language is a minority language and the target language is a majority language with existing search engines. We use clickthrough data from a monolingual search engine to learn translation models that could be used to perform cross lingual search. This approach has enabled us to generate practical CLIR systems on a large scale with less effort and with bilingual resources. We experiment and report the evaluation of our approach by creating CLIR systems for an Indian language and a few other European Languages.
Implementation of nondestructive Young's modulus measurement by miniature optical sensors (2005)

Accurate real time nondestructive modulus measurement is one of the principal requirements in service life monitoring of smart structures. However, most current measurement methods, such as tension and/or compression testing are inappropriate for such applications. For one thing, the force load may damage the casting. For another, the test process is not trivial and inconvenient for real-time modulus monitoring. This paper describes an acoustic-based measurement mechanism using two separated miniature optical sensors. The sensor features miniature size (<500μm), high resolution and accuracy, high temperature and pressure survivability, electromagnetic interference immunity (EMI), electrically non- conductivity, and chemical erosion inertness. This technique offers future potential for real-time measurement for in-service monitoring, particularly in applications involving such environments as high temperatures or high pressure.
Treatment of a Patient with Advanced Esophageal Cancer with a Combination of Mitomycin C and Capecitabine: Activation of the Thymidine Phosphorylase as Active Principle? (2003)

Background: Both capecitabine, an oral prodrug of 5-fluorouracil (5-FU), and mitomycin C (MMC) have demonstrated activity as single agents in patients with gastrointestinal cancer. Furthermore, a combination of MMC with infusional 5-FU can induce tumor remission even in patients pretreated with 5-FU. Capecitabine and MMC act synergistically due to an upregulation of the thymidine phosphorylase activity by MMC in a human xenograft model. Patient: We sought to exploit these preclinically observed effects in a patient with esophageal cancer who was progressive after a first-line radiochemotherapy with 5-FU and cisplatin. He was treated with a combination of MMC and capecitabine on a compassionate use basis. A rapid remission lasting for about 6 months was observed. Conclusion: This is the first report on a combination therapy with capecitabine and MMC. The remission observed in our patient suggests that the preclinically observed synergy has clinical impact. This combination should be further investigated in prospective clinical trials.
Profiling networks of distinct immune-cells in tumors (2016)

This integrative bioinformatics approach demonstrates that capturing the protein network signatures and ratios of distinct immune-cell in the tumor microenvironment maybe an important factor in predicting response to therapy. This may serve as a computational strategy to define network signatures of distinct immune-cells to guide immuno-pathological discovery.
Traffic Signals on Endothelium for Lymphocyte Recirculation and Leukocyte Emigration (1995)

The circulatory and migratory properties of white blood cells have evolved to allow efficient surveillance of tissues for infectious pathogens and rapid accu­ mulation at sites of injury and infection. Lymphocytes continually patrol the body for foreign antigen by recirculating from blood, through tissue, into lymph, and back to blood. Lymphocytes acquire a predilection, based on the environment in which they first encounter foreign antigen, to home to or recirculate through that same environment (39, 40). Granulocytes and mono­ cytes cannot recirculate, but emigrate from the bloodstream in response to molecular changes on the surface of blood vessels that signal injury or infec­ tion. Lymphocytes can similarly accumulate in response to inflammatory stim­ uli. The nature of the inflammatory stimulus determines whether lymphocytes. monocytes, neutrophils, or eosinophils predominate, and thus exercises spec­ ificity in the molecular or codes that are displayed on endothe­ lium and control of particular leukocyte classes. Recent findings show that the traffic signals for lymphocyte recirculation and for neutrophil and monocyte localization in inflammation are strikingly similar at the molecular level. These signal or area code molecules are
Detection of African horse sickness virus by reverse transcription-PCR (1994)

Reverse transcription-PCR (RT-PCR) was used to detect African horse sickness virus (AHSV). A single primer pair which amplified a 423-bp fragment of the S8 gene which encodes the NS2 protein of AHSV was identified. Amplification of this fragment from all nine serotypes of AHSV was achieved with these primers. Between 10(1) and 10(2) copies of AHSV genomic double-stranded RNA could be detected by RT-PCR followed by agarose gel electrophoresis and ethidium bromide staining. Application of RT-PCR to blood samples from AHSV-infected horses resulted in earlier detection of viremia than virus isolation did. Furthermore, viremia was detected by RT-PCR in blood samples from horses infected with an avirulent isolate of AHSV which were negative by virus isolation. AHSV was also detected by RT-PCR in spleen and lung samples from horses which died of AHSV infection. These results indicate that RT-PCR is a rapid and sensitive method for the identification of horses infected with AHSV.
Total synthesis of (±)-5β,8α- androst-9(11)-ene-3,17-dione (1979)

A total synthesis of (±)-5β,8α- androst-9(11)-ene-3,17-dione is described. The key step is a ring C forming SnCl 4 -catalyzed Diels–Alder reaction in which the geometry of the diene controls syn–anti stereochemistry while the catalyst guides the addition to the desired endo orientation. A preparation of ethyl E-2-methyl-4-oxo-2-butenoate and the dehydration of a tertiary allylic alcohol by the pyrolysis of the corresponding tosyl carbamate are also described.
Immunization of Six-Month-Old Infants with Different Doses of Edmonston–Zagreb and Schwarz Measles Vaccines (1990)

Because measles causes an estimated 2 million deaths per year among children in developing countries, including a substantial proportion of infants less than nine months old--the age at which vaccination is recommended--there has been interest in using different strains of vaccine and higher doses to achieve immunization of younger infants. We conducted a randomized trial of three different doses of Edmonston-Zagreb and of Schwarz measles vaccines in infants to evaluate the effect of the strain and dose of vaccine on the serologic response and acute adverse reactions to vaccination. Six-month-old infants received a standard, medium, or high dose of one of the vaccines, and nine-month-old infants received a standard dose. Antibody levels were measured before and after vaccination, by means of a plaque-reduction neutralization assay, in 1061 six-month-olds and 299 nine-month-olds. Edmonston-Zagreb vaccine produced higher rates of seroconversion and seropositivity than comparable doses of Schwarz vaccine. Among the six-month-old infants, the seroconversion rate 18 weeks after vaccination with the standard dose of Edmonston-Zagreb vaccine was 92 percent, that with the medium dose was 96 to 97 percent, and that with the high dose was 98 percent; the rates for the corresponding doses of Schwarz vaccine were 66 percent, 76 percent, and 91 percent, respectively. Higher seroconversion rates were observed with an increase in the dose of either Edmonston-Zagreb (P less than 0.01) or Schwarz (P less than 0.001) vaccine. The seroconversion rates produced by high and medium doses of Edmonston-Zagreb vaccine in six-month-olds were equal to or significantly higher than the rate produced by a standard dose of Schwarz vaccine in nine-month-olds (87 percent). Clinical adverse reactions were not associated with the strain or dose of a vaccine. We conclude that Edmonston-Zagreb vaccine is more immunogenic than Schwarz vaccine in infants and can induce effective immunization against measles at six months of age.
Electroluminescence from a Mixed Red−Green−Blue Colloidal Quantum Dot Monolayer (2007)

We demonstrate light emitting devices (LEDs) with a broad spectral emission generated by electroluminescence from a mixed-monolayer of red, green, and blue emitting colloidal quantum dots (QDs) in a hybrid organic/inorganic structure. The colloidal QDs are reproducibly synthesized and yield high luminescence efficiency materials suitable for LED applications. Independent processing of the organic charge transport layers and the QD luminescent layer allows for precise tuning of the emission spectrum without changing the device structure, simply by changing the ratio of different color QDs in the active layer. Spectral tuning is demonstrated through fabrication of white QD-LEDs that exhibit external quantum efficiencies of 0.36% (Commission Internationale de l'Eclairage) coordinates of (0.35, 0.41) at video brightness, and color rendering index of 86 as compared to a 5500 K blackbody reference.
Differentially Private Release of the Distribution of Clustering Coefficients across Communities (2019)

Aiming to provide more information about the behaviors between groups or patterns between clusters in social networks, we propose a two-step differentially private method to release the distribution of clustering coefficients across communities. The DPLM algorithm improves a Louvain method to partition one network using an exponential mechanism. We introduce an absolute gain of modularity to sanitize neighboring communities. Otherwise, the algorithm is difficult to converge due to the randomness introduced. The DPCC algorithm charts the noisy distribution of clustering coefficients as a histogram, which presents the results in an intuitive manner. We conduct experiments on three real-world datasets to evaluate the proposed method. The experimental results indicate that the proposed method provides valuable distribution results while guaranteeing <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi mathvariant="normal">ε</mml:mi></mml:mrow></mml:math>-differential privacy. Moreover, the DPLM algorithm can obtain better modularity for the networks.
A Mycobacterium leprae‐specific gene encoding an immunologically recognized 45 kDa protein (1993)

By screening a Mycobacterium leprae lambda gt11 expression library with a serum from an Ethiopian lepromatous leprosy (LL) patient a clone was isolated (LL4) belonging to hybridization group III of a panel of previously isolated M. leprae clones. Members of this hybridization group encode a serologically recognized 45 kDa protein. The complete DNA sequences of the partially overlapping clones LL4 and L1 (hybridization group III) are presented and these revealed the presence of an open reading frame (ORF) predicting a protein with a molecular size of 42,448 Da. Southern hybridizations on total genomic DNA of M. leprae, Mycobacterium tuberculosis and eight atypical mycobacteria showed that the LL4 DNA fragment is specific for M. leprae DNA even under low-stringency conditions. The M. leprae specificity of LL4 DNA was further confirmed by the polymerase chain reaction using four different sets of primers. Western blotting analyses showed that the M. leprae 45 kDa protein is frequently recognized by antibodies from leprosy patients and that this recognition is specific since no antibodies could be detected in sera of tuberculosis patients. T-cell proliferation assays also demonstrated T-cell recognition by leprosy patients and healthy contacts of the M. leprae 45 kDa protein. The specificity of the LL4 DNA region and the 45 kDa antigen that is encoded by hybridization group III could provide unique tools for the development of M. leprae-specific immunological and DNA reagents.
Intestinal lipid absorption and transport (2001)

The purpose of this review is to update the reader on our current knowledge of the digestion, uptake, and transport of dietary lipid. In particular, it discusses how intestinal lipid transporters may play a role in the uptake of lipids by the enterocytes, and how chylomicrons are formed in the enterocytes and packaged for export into the lymphatic system through exocytosis. The classification and properties of lipids is first described followed by a discussion of structured lipids and their role in human nutrition. Digestion of triacylglycerols takes place in the stomach aided by the enzyme gastric lipase. The origin and properties of lingual and gastric lipase are reviewed. Most digestion of triacylglycerols by pancreatic lipase occurs in the intestinal lumen. Similarly, digestion of cholesteryl ester and phospholipids also takes place in the intestinal lumen. This review describes in considerable detail the uptake of lipid digestion products by the enterocytes, particularly the role of recently identified lipid transporters. The intracellular trafficking and the resynthesis of complex lipids from the lipid digestion products are talked about, particularly within the context of the recently generated knockout mouse that lacks the key lipid reesterification enzymes. Finally, the mechanisms of the formation and secretion of chylomicrons is described and clinical disorders discussed.
Immunohistological Localization of the Human Endometrial Secretory Protein Pregnancy-Associated Endometrialα1-Globulin, an Insulin-Like Growth Factor-Binding Protein, During the Menstrual Cycle* (1988)

Pregnancy-associated endometrial alpha 1-globulin (alpha 1-PEG), a 29,000 mol wt insulin-like growth factor-binding protein, is the major secretory protein of the human endometrium from the latter half of the first trimester to the end of pregnancy. It is also produced and secreted by nonpregnant endometrial tissue, especially during the late secretory phase of the menstrual cycle. We studied the localization of this protein in the endometrium during different phases of the cycle using immunohistochemistry with monoclonal antibodies. Immunostaining was first observed in the midsecretory phase and was most consistently detected during the late secretory phase, during which it was principally associated with stromal cell populations. These cells were localized initially surrounding spiral arteries and subsequently also in the subluminal epithelial region of the endometrium. These results suggest that alpha 1-PEG synthesis is principally associated with the process of stromal cell differentiation. i.e. predecidualization. However, the presence of alpha 1-PEG was not directly correlated with the presence of mature predecidual cells, suggesting that its synthesis is not an inherent feature of this cell.
Sudden Death Syndrome of Soybean:Fusarium solanias Incitant and Relation ofHeterodera glycinesto Disease Severity (1989)

Two morphologically distinct forms of Fusarium solani, designated FS-A and FS-B,were isolated from soybean plants with symptoms of sudden death syndrome, a disease of unproven etiology. Form FS-A was isolated seven to 17 times more frequently from symptomatic than from asymptomatic plants, whereas FS-B was equally frequent on symptomatic and asymptomatic plants. (...)
Customising graphics applications: techniques and programming interface (2002)

This paper identifies opportunities for customising architectures for graphics applications, such as infrared simulation and geometric visualisation. We have studied methods for exploiting custom data formats and datapath widths, and for optimising graphics operations such as texture mapping and hidden-surface removal. Techniques for balancing the graphics pipeline and for run-time reconfiguration have been implemented. The customised architectures are captured in Handel-C, a C-like language supporting parallelism and flexible data size, and compiled for Xilinx 4000 and Virtex FPGAs. We have also developed an application programming interface based on the OpenGL standard for automatic speedup of graphics applications, including the Quake 2 action game.
Interleukin-17: A New Bone Acting Cytokine In Vitro (1999)

Interleukin-17 (IL-17) is a recently cloned cytokine that is exclusively produced by activated T cells, but its receptor has been found on several cells and tissues. Like other proinflammatory cytokines produced by activated T cells, IL-17 may affect osteoclastic resorption and thereby mediate bone destruction accompanying some inflammatory diseases. In the present study, we investigated whether osteogenic cells possess the receptor for IL-17 (IL-17R) and whether IL-17 affects osteoclastic resorption. We found that IL-17R mRNA is expressed both in mouse MC3T3-E1 osteoblastic cells and fetal mouse long bones, suggesting that osteogenic cells may be responsive to IL-17. In fetal mouse long bones, IL-17 had no effect on basal and IL-1beta-stimulated osteoclastic bone resorption, but when given together with tumor necrosis factor-alpha (TNF-alpha) it increased bone resorption dose dependently in serum-free conditions. In addition, IL-17 increased TNF-alpha-induced IL-1alpha, IL-1beta, and IL-6 mRNA expression in fetal mouse metatarsals and IL-1alpha and IL-6 mRNA expression in MC3T3-E1 cells. In conclusion, IL-17R mRNA was expressed by mouse osteoblastic cells and fetal mouse long bones, and IL-17 in combination with TNF-alpha, but not IL-1beta, increased osteoclastic resorption in vitro. IL-17 may therefore affect bone metabolism in pathological conditions characterized by the presence of activated T cells and TNF-alpha production such as rheumatoid arthritis and loosening of bone implants.
Both NS and L proteins are required for in vitro RNA synthesis by vesicular stomatitis virus (1975)

Vesicular stomatitis virions, Indiana serotype, were solubilized with high salt solubilizer and separated by ultracentrifugation into a supernatant fraction containing L, G, NS, and M proteins and pellet fraction containing the RNA complexed with N protein. NS protein was purified from the supernatnat fluid by sequential chromatography on phosphocellulose and diethylaminoethyl cellulose columns. The purified NS protein was assayed in a standard transcription system in combination with purified L protein and purified template (pellet fraction) prepared by renografin or CsCl banding. Results of the polymerase assays indicate that both L and NS proteins are required to reconstitute transcription activity with a highly purified template composed of only RNA and N protein. The NS protein polymerase activity is destroyed by trypsin but withstands 90 C temperatures for 10 min. Cytoplasmic NS protein can substitute for virion NS protein in the in vitro transcription assay.
Mapping of Specific and Promiscuous HLA-DR-Restricted T-Cell Epitopes on thePlasmodium falciparum27-Kilodalton Sexual Stage-Specific Antigen (1998)

We have characterized HLA-DR-restricted T-cell epitopes on the 27-kDa protein (Pfg27), a sexual stage-specific antigen, of the human malaria parasite Plasmodium falciparum in subjects with a history of malaria. Pfg27, expressed early in the sexual stages, is recognized by monoclonal antibodies capable of reducing the infectivity of gametocytes in mosquitoes. By using 16 Pfg27-specific CD4(+)-T-cell clones derived from three donors, seven different T-cell epitopes were identified. Among them, P11 (amino acids 191 to 210 of the Pfg27 sequence, IDVVDSYIIKPIPALPVTPD) was found to contain a previously described binding motif for multiple HLA-DR allotypes. Indeed, P11 was found to be promiscuous in that it could be recognized by T cells in the context of at least five different HLA-DR molecules. The cytokine profile of the clones was mixed. Seven of nine T-cell clones exhibited a Th0-like cytokine profile, producing high levels of gamma interferon (IFN-gamma) and interleukin-4 (IL-4) upon stimulation with specific peptides and mitogens. The other two clones had a Th1-like cytokine profile with high expression of IFN-gamma and no IL-4. Identification of a promiscuous epitope in Pfg27 could play a significant role in the design of a subunit vaccine for suppressing malaria transmission.
Linkage Disequilibrium of Interleukin‐1 Genetic Polymorphisms With Early‐Onset Periodontitis (1999)

Recent theoretical analyses indicate that our findings are most consistent with an interpretation of EOP as a complex, oligogenic disorder, with IL-1 genetic variation contributing an important but not exclusive influence on disease risk.