gebhart/patrepeval huggingface dataset:
The HLA Dictionary 2004: a summary of HLA‐A, ‐B, ‐C, ‐DRB1/3/4/5 and ‐DQB1 alleles and their association with serologically defined HLA‐A, ‐B, ‐C, ‐DR and ‐DQ antigens (2005)

This report presents serologic equivalents of human leucocyte antigen (HLA)-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5 and -DQB1 alleles. The dictionary is an update of the one published in 2001. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for factors of the HLA System, the International Cell Exchange, the National Marrow Donor Program, recent publications and individual laboratories. This latest update of the dictionary is enhanced by the inclusion of results from studies performed during the 13th International Histocompatibility Workshop and from neural network analyses. A summary of the data as recommended serologic equivalents is presented as expert assigned types. The tables include remarks for alleles, which are or may be expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities. The equivalents provided will be useful in guiding searches for unrelated hematopoietic stem cell donors in which patients and/or potential donors are typed by either serology or DNA-based methods. The serological DNA equivalent dictionary will also aid in typing and matching procedures for organ transplant programs whose waiting lists of potential donors and recipients comprise of mixtures of serologic and DNA-based typings. The tables with HLA equivalents and a questionnaire for submission of serologic reaction patterns for poorly identified allelic products will be made available through the WMDA web page: www.worldmarrow.org. and in the near future also in a searchable form on the IMGT/HLA database.
Effect of 1.5% Topical Diclofenac on Clinical Neuropathic Pain (2015)

The findings indicate that 1.5% TD may serve as an effective treatment option for patients with neuropathic pain from postherpetic neuralgia and complex regional pain syndrome.
Establishment of PCR based methods for detection of ctDNA in blood (2013)

Cell-free DNA appears in the circulation when cells undergo apoptosis and necrosis. This is a natural process and small amounts of cell-free DNA can be found in the blood of healthy individuals. When tumors are present, a variable part of the cell-free DNA will derive from tumor. Monitoring ctDNA is attractive in solid cancers because a blood sample is less invasive than a biopsy and it might represent all lesions including metastasis. “Liquid biopsies” also give the opportunity for serial monitoring during therapy and follow up when tumor biopsies are difficult to achieve. Little is still known about the stability of ctDNA in vitro, so one of the subprojects in this thesis was to elucidate this. Cell-free DNA is extracted from plasma and ctDNA is often a minor fraction of the total plasma DNA. Our results showed that blood can be left for 24 hours in room temperature without significantly affecting the total plasma-DNA concentration. It was however not clear if ctDNA showed a slight decrease due to delayed processing or whether it was due to assay variation. More data needs to be collected. ERBB2 is amplified in 15-20 % of breast cancers and targeted therapy is available against its protein (HER2). Studies have shown that HER2-status might change during disease progression, so detection of the amplification in plasma would be desirable. Other methods like quantitative PCR (qPCR) and digital PCR (dPCR) have been used to detect the amplification, but these rely on the use of an unamplified reference gene. Breast cancers are heterogeneous and show a variety of genetic alterations. A common unamplified gene can therefore be hard to find. One of our subprojects detected ERBB2 amplification by targeted massively parallel sequencing (MPS). ERBB2 is a monoallelic event, and SNP ratios could be used to detect amplification. No reference gene was needed as the unamplified allele was the reference. The method achieved the same limit of detection as dPCR, 1.2 fold. Breast cancer also has few recurrent mutations. Massively parallel sequencing (MPS) has given the opportunity to detect the broad range of mutations that can be seen in breast tumors and to use these mutations as tumor markers for detection of ctDNA. The last subproject screened 17 genes frequently mutated in breast cancer with targeted MPS and detected somatic mutations in 94 % of the patients (49/52). 48 % of the patients had two mutations that could be tracked in serial blood samples taken during therapy. Both of the cases presented in this thesis showed evidence of subclonality. In one case, the KRAS mutation emerged during therapy. This might be due to acquisition of the mutation during treatment or that it belonged to minor subclone that was not detected at presentation. This emphasizes the importance of detecting all subclones at disease presentation and not only tracking the dominant clone in the primary tumor. Monitoring ctDNA is an important means to detect therapy response and early relapse and might be a step towards more personalized medicine.
Molecular Markers for the Scab Resistance (Vf) Region in Apple (1998)

Bulked segregant analysis was used to identify RAPD markers that display tight linkage to the V f gene in apple ( Malus sp.) that confers resistance to five races of apple scab [ Venturia inaequalis (Cke.) Wint.]. We identified several new RAPD markers linked to V f . The most tightly linked marker in the test population, S5 2500 , was cloned and sequenced. A linkage map of the V f region was developed using these markers, RAPD markers previously described by other laboratories, and the isozyme locus Pgm-1. An assay was developed for V f by multiplexing the two markers closely flanking the V f locus. This assay has a theoretical `escape' value (discarding a resistant plant) of 3% and an error rate (selection of a susceptible plant) of 0.02%.
Induction of Homologous Recombination in Mammalian Chromosomes by Using the I-SceI System of Saccharomyces cerevisiae (1995)

The mitochondrial intron-encoded endonuclease I-SceI of Saccharomyces cerevisiae has an 18-bp recognition sequence and, therefore, has a very low probability of cutting DNA, even within large genomes. We demonstrate that double-strand breaks can be initiated by the I-SceI endonuclease at a predetermined location in the mouse genome and that the breaks can be repaired with a donor molecule homologous regions flanking the breaks. This induced homologous recombination is approximately 2 orders of magnitude more frequent than spontaneous homologous recombination and at least 10 times more frequent than random integration near an active promoter. As a consequence of induced homologous recombination, a heterologous novel sequence can be inserted at the site of the break. This recombination can occur at a variety of chromosomal targets in differentiated and multipotential cells. These results demonstrate homologous recombination involving chromosomal DNA by the double-strand break repair mechanism in mammals and show the usefulness of very rare cutter endonucleases, such as I-SceI, for designing genome rearrangements.
An Overview of the Contribution of Sulfur-Containing Compounds to the Aroma in Heated Foods (2002)

Many of the most potent odorants found in foods contain sulfur. The exceptionally low odor threshold values of many of these compounds mean that only trace quantities are necessary to make a significant contribution to flavor. Heterocyclic sulfur compounds, including thiophenes, thiophenones, dithiolanes, trithiolanes, trithianes, thiazoles, and thienothiophenes, are typical products of thermal reactions in food. Non-heterocyclic sulfur compounds, such as thiols, sulfides and disulfides are also important to the aroma of heated foods. The main source of sulfur in the reactions that lead to these compounds is the amino acid, cysteine. Cysteine degradation, in the Maillard reaction or through hydrolysis, produces hydrogen sulfide, which is a vital reactant for the production of sulfur-containing aroma compounds. Other important sulfur-containing precursors are methionine and thiamin.
The 1998 HTK system for transcription of conversational telephone speech (1999)

This paper describes the 1998 HTK large vocabulary speech recognition system for conversational telephone speech as used in the NIST 1998 Hub5E evaluation. Front-end and language modelling experiments conducted using various training and test sets from both the Switchboard and Callhome English corpora are presented. Our complete system includes reduced bandwidth analysis, side-based cepstral feature normalisation, vocal tract length normalisation (VTLN), triphone and quinphone hidden Markov models (HMMs) built using speaker adaptive training (SAT), maximum likelihood linear regression (MLLR) speaker adaptation and a confidence score based system combination. A detailed description of the complete system together with experimental results for each stage of our multi-pass decoding scheme is presented. The word error rate obtained is almost 20% better than our 1997 system on the development set.
Regulatory regions of ColE1 that are involved in determination of plasmid copy number. (1983)

The copy number of plasmid ColE1 has been known to increase when the Hae II-C segment downstream from the replication origin is deleted. The presence of the 306-base-pair (bp) Hpa II region in the segment is sufficient for reduction of the copy number. Plasmids harboring the region express a trans-acting function that is responsible for the copy number reduction and synthesize a unique protein. A protein specified by the region is purified to near homogeneity and identified as the 63-amino-acid protein encoded by the Hpa II segment. The region, which includes segments 19-25 bp and 53-311 bp downstream from the start site of the primer RNA, is involved in determination of sensitivity to the inhibitory function. In vivo transcription of the galK gene, which is directed by the primer promoter in a segment inserted in front of the structural gene, is inhibited by a plasmid carrying the Hpa II region. The inhibition is strong when the promoter segment contains up to 135 bp downstream from the primer RNA start site, whereas it is weak when only the region up to 52 bp downstream is present.
Imaging Tri-Fusion Multimodality Reporter Gene Expression in Living Subjects (2004)

Imaging reporter gene expression in living subjects with various imaging modalities is a rapidly accelerating area of research. Applications of these technologies to cancer research, gene therapy, and transgenic models are rapidly expanding. We report construction and testing of several triple fusion reporter genes compatible with bioluminescence, fluorescence and positron emission tomography (PET) imaging. A triple fusion reporter vector harboring a bioluminescence synthetic Renilla luciferase (hrl) reporter gene, a reporter gene encoding the monomeric red fluorescence protein (mrfp1), and a mutant herpes simplex virus type 1 sr39 thymidine kinase [HSV1-truncated sr39tk (ttk); a PET reporter gene] was found to preserve the most activity for each protein component and was therefore investigated in detail. After validating the activities of all three proteins encoded by the fusion gene in cell culture, we imaged living mice bearing 293T cells transiently expressing the hrl-mrfp-ttk vector by microPET and using a highly sensitive cooled charge-coupled device camera compatible with both bioluminescence and fluorescence imaging. A lentiviral vector carrying the triple fusion reporter gene was constructed and used to isolate stable expressers by fluorescence-activated cell sorting. These stable 293T cells were further used to show good correlation (R(2) approximately 0.74-0.85) of signal from each component by imaging tumor xenografts in living mice with all three modalities. Furthermore, metastases of a human melanoma cell line (A375M) stably expressing the triple fusion were imaged by microPET and optical technologies over a 40-50-day time period in living mice. Imaging of reporter gene expression from single cells to living animals with the help of a single tri-fusion reporter gene will have the potential to accelerate translational cancer research.
Slide-Based Laser Scanning Cytometry (1997)

Because it is microscope based and measures cells on a slide, not in a flow chamber; records the position of each cell on the slide; and has higher resolution, LSCM provides a number of benefits that may make it more suitable than FCM for pathology laboratories.
Soluble form of P-selectin in patients with acute myocardial infarction. (1994)

Plasma concentrations of the soluble form of P-selectin were markedly higher in patients with AMI, suggesting the activation of platelets, or endothelial cells, or both. Thus, quantitative measurements of plasma P-selectin concentrations may help to assess the pathophysiology of inflammatory reactions in patients with AMI.
Creating various styles of animations using example-based filtering (2004)

A number of nonphotorealistic rendering methods for producing artistic style images have been developed. Recently, a method called "Image Analogies" was proposed. This method is based on the idea of example-based filtering that uses a pair of images (an original image and a filtered image) as training data and creates an image which has a style that resembles the filtered image of the training data. This method has great flexibility since the users can create various styles of images by simply changing the training data. We extend "Image Analogies" to create various styles of animations. The coherence between frames is considered by computing the pixel flows between the frames. From experimental results, the proposed method can create nice animation sequences.
Thermolysis of oxime O-allyl ethers: A new method for pyridine synthesis. (1983)

Thermolysis of cycloalkanone oxime O-allyl ethers in air gave the corresponding cycloal-kenopyridines, providing a new method for the synthesis of cycloalkenopyridine derivatives.
Controlling Eutrophication along the Freshwater–Marine Continuum: Dual Nutrient (N and P) Reductions are Essential (2009)

Expanding human activities along the freshwater to marine continuum of coastal watersheds increasingly impact nutrient inputs, nutrient limitation of primary production, and efforts to reduce nutrient over-enrichment and eutrophication. Historically, phosphorus (P) has been the priority nutrient controlling upstream freshwater productivity, whereas nitrogen (N) limitation has characterized coastal waters. However, changing anthropogenic activities have caused imbalances in N and P loading, making it difficult to control eutrophication by reducing only one nutrient. Furthermore, upstream nutrient reduction controls can impact downstream nutrient limitation characteristics. Recently, it was suggested that only reducing P will effectively control eutrophication in both freshwater and coastal ecosystems. However, controls on production and nutrient cycling in estuarine and coastal systems are physically and chemically distinct from those in freshwater counterparts, and upstream nutrient management actions (exclusive P controls) have exacerbated N-limited downstream eutrophication. Controls on both nutrients are needed for long-term management of eutrophication along the continuum.
The 145-kDa protein induced to associate with Shc by multiple cytokines is an inositol tetraphosphate and phosphatidylinositol 3,4,5-triphosphate 5-phosphatase. (1996)

A 145-kDa tyrosine-phosphorylated protein that becomes associated with Shc in response to multiple cytokines has been purified from the murine hemopoietic cell line B6SUtA1. Amino acid sequence data were used to clone the cDNA encoding this protein from a B6SUtA1 library. The predicted amino acid sequence encodes a unique protein containing an N-terminal src homology 2 domain, two consensus sequences that are targets for phosphotyrosine binding domains, a proline-rich region, and two motifs highly conserved among inositol polyphosphate 5-phosphatases. Cell lysates immunoprecipitated with antiserum to this protein exhibited both phosphatidylinositol 3,4,5-trisphosphate and inositol 1,3,4,5-tetrakisphosphate polyphosphate 5-phosphatase activity. This novel signal transduction intermediate may serve to modulate both Ras and inositol signaling pathways. Based on its properties, we suggest the 145-kDa protein be called SHIP for SH2-containing inositol phosphatase.
Progesterone receptor action: translating studies in breast cancer models to clinical insights. (2008)

Progesterone receptors (PR) are useful prognostic indicators of breast cancers likely to respond to anti-estrogen receptor (ER) therapies. However, the role of progesterone, therapeutic progestins, or unliganded or liganded PRin breast cancer development or progression remains controversial. PR are ligand-activated transcription factors that act in concert with intracellular signaling pathways as "sensors" of multiple growth factor inputs to hormonally regulated tissues, such as the breast. The recently defined induction of rapid signaling events upon progestin-binding to PR-B provides a means to ensure that receptors and coregulators are appropriately phosphorylated as part of optimal transcription complexes. PR-activated kinase cascades may provide additional avenues for progestin-regulated gene expression independent of PR nuclear action. Herein, we present an overview ofprogesterone/PR and signaling cross-talk in breast cancer models and discuss the potential significance ofprogestin/PR action in breast cancer biology using examples from both in vitro and in vivo models, as well as limited clinical data. Kinases are emerging as key mediators of PR action. Cross-talk between PR and membrane-initiated signaling events suggests a mechanism for coordinated regulation ofgene subsets by mitogenic stimuli in hormonally responsive normal tissues. Dysregulation of this cross-talk mechanism may contribute to breast cancer biology; further studies are needed to address the potential for targeting PR in addition to ER and selected protein kinases as part of more effective breast cancer therapies.
Vascular Remodeling in Hypertension (2001)

Remodeling of large and small arteries contributes to the development and complications of hypertension. The focus of this review is some of the mechanisms involved in the remodeling of small arteries in hypertension. In hypertension, changes in small artery structure are basically of 2 kinds: (1) inward eutrophic remodeling, in which outer and lumen diameters are decreased, media/lumen ratio is increased, and cross-sectional area of the media is unaltered; and (2) hypertrophic remodeling, in which the media thickens to encroach on the lumen, resulting in increased media cross-sectional area and media/lumen ratio. Growth, apoptosis, inflammation, and fibrosis contribute to vascular remodeling in hypertension. Apoptosis is gene-regulated cell death, with minimal membrane disruption and inflammation, that counters cell proliferation and fine-tunes developmental growth. Apoptosis has been reported in hypertension to be both increased and decreased in different tissues, including blood vessels. Inflammation, which may be low grade, probably plays an important role in triggering fibrosis in cardiovascular disease and hypertension. Vascular fibrosis entails accumulation of collagen, fibronectin, and other extracellular matrix components in the vessel wall and is an important aspect of extracellular matrix remodeling in hypertension. Associated with this, there may be increases in cell-matrix attachment sites (integrins) and changes in their topographical localization that may modulate arterial structure. Imbalance in matrix metalloproteinase/tissue inhibitors of metalloproteinases may contribute to alteration in collagen turnover and extracellular matrix remodeling. Chronic vasoconstriction may lead to embedding of the contracted vessel structure in a remodeled extracellular matrix, contributing to the inward remodeling of the blood vessel as smooth muscle cells are rearranged around a smaller lumen. The resulting remodeling of small arteries may initially be adaptive, but eventually it becomes maladaptive and compromises organ function, contributing to cardiovascular complications of hypertension.
The effect of estradiol on Candida albicans growth. (1997)

The size of colonies growing on Sabouraud's dextrose agar (SDA) supplemented with 1 microM beta estradiol (1,3,5[10]-estratiene-3,17B-diol) was compared to those growing without the estrogen supplement. Data (video pixel counts) were obtained by video capture and image analysis and revealed that yeast strains were not uniformly stimulated by estradiol. One estrogen-responsive strain was evaluated in a chemically defined medium to evaluate growth in the presence of 17-alpha and 17-beta isomers of estradiol. The beta isomer promoted more rapid growth of the test organism and resulted in greater biomass production than the alpha isomer. Understanding of the role of mammalian hormones as growth promoting signals may provide information on this organism's shift from saprophytic to commensal to pathogenic status in vivo. Strain variation in response to estrogen may provide an explanation for differences in virulence.
The production of chemotactic cytokines in an allogeneic response. The role of intercellular adhesion molecule-1 and lymphocyte function-associated antigen-3. (1993)

The in vitro mixed lymphocyte reaction (MLR) is regarded as a model of responsiveness to allogeneic major histocompatibility complex antigens and has historically been used to elucidate the pathway of T lymphocyte proliferation. In addition, the MLR response may reflect activation pathways relevant in acute allograft rejection. In the present study, we have applied the MLR to examine the role of adhesion molecules intercellular adhesion molecule-1 and lymphocyte function-associated antigen-3 in the induction of tumor necrosis factor-alpha (TNF-alpha) as well as chemotactic cytokines, interleukin-8 (IL-8), monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-1 alpha (MIP-1 alpha). Monoclonal antibodies to the adhesion molecules (5 micrograms/ml) were added to one-way human MLR cultures and supernatants collected at various time points. The monoclonal antibodies to the adhesion molecules significantly suppressed the proliferative response by 50 to 80%. Cytokine production, TNF-alpha (3.2 +/- 0.5 ng/ml), MIP-1 alpha (12.9 +/- 3.3 ng/ml), MCP-1 (18.8 +/- 3.4 ng/ml), and IL-8 (57 +/- 18 ng/ml) peaked on day 5 of the assay. The addition of anti-intercellular adhesion molecule-1 to the cultures suppressed TNF-alpha, MIP-1 alpha, MCP-1, and IL-8 production by 68% (1.05 +/- 0.29 ng/ml), 85% (2.0 +/- 1.2 ng/ml), 63% (6.8 +/- 2.9 ng/ml), and 47% (30.3 +/- 3.7 ng/ml), respectively. Likewise, the addition of anti-lymphocyte function-associated antigen-3 monoclonal antibody suppressed the cytokines by 78% (0.71 +/- 0.34 ng/ml), 66% (4.5 +/- 2.2 ng/ml), 52% (8.8 +/- 2.2 ng/ml), and 73% (15.7 +/- 4.4 ng/ml), respectively. Immunohistochemical staining indicated that monocytes were the primary source of the chemokines IL-8, MCP-1, and MIP-1 alpha. The addition of exogenous recombinant TNF-alpha (5 ng/ml) or recombinant IL-2 (5 units/ml) to the anti-intercellular adhesion molecule-1-treated cultures allowed the recovery of the proliferative response as well as restoration of IL-2, TNF-alpha, and IL-8, but not MCP-1 or MIP-1 alpha, indicating that both soluble and adhesion molecule signals are required for the production of the C-C family of chemokines in allogeneic responses. Thus, the events resulting in cellular proliferation and chemokine production were dependent on adhesion molecule interactions.