gebhart/patrepeval huggingface dataset:
Signal-regulatory protein α (SIRPα) but not SIRPβ is involved in T-cell activation, binds to CD47 with high affinity, and is expressed on immature CD34+CD38−hematopoietic cells (2001)

Signal-regulatory proteins (SIRPs) represent a new family of inhibitory/activating receptor pairs. They consist of 3 highly homologous immunoglobulin (Ig)-like domains in their extracellular regions, but differ in their cytoplasmic regions by the presence (SIRPalpha) or absence (SIRPbeta) of immunoreceptor tyrosine-based inhibitory motifs (ITIMs). To analyze the differential expression on hematopoietic cells, function and ligand binding capacity of SIRPalpha and SIRPbeta molecules, soluble fusion proteins consisting of the extracellular domains of SIRPalpha1, SIRPalpha2, and SIRPbeta1, as well as SIRPalpha/beta-specific and SIRPbeta-specific monoclonal antibodies (MoAbs) were generated. In contrast to SIRPalpha1 and SIRPalpha2, no adhesion of SIRPbeta1 to CD47 could be detected by cell attachment assays and flow cytometry. Using deletion constructs of SIRPalpha1, the epitope responsible for SIRPalpha1 binding to CD47 could be confined to the N-terminal Ig-like loop. Flow cytometry analysis with SIRPalpha/beta- and SIRPbeta-specific MoAbs revealed that SIRPalpha but not SIRPbeta is expressed on CD34(+)CD38(-) hematopoietic cells. In addition, a strong SIRPalpha expression was also observed on primary myeloid dendritic cells (DCs) from peripheral blood as well as on in vitro generated DCs. Analysis of the T-cell stimulatory capacity of in vitro generated DCs in the presence of soluble SIRPalpha1 fusion proteins as well as SIRPalpha/beta-specific and CD47-specific MoAbs revealed a significant reduction of T-cell proliferation in mixed lymphocyte reaction and inhibition of induction of primary T-cell responses under these conditions. In contrast, soluble SIRPalpha or SIRPbeta-specific antibodies had no effect. The data suggest that the interaction of SIRPalpha with CD47 plays an important role during T-cell activation and induction of antigen-specific cytotoxic T-lymphocyte responses by DCs.
Overexpression of c-Maf Contributes to T-Cell Lymphoma in Both Mice and Human (2006)

c-Maf translocation or overexpression has been observed in human multiple myeloma. Although c-maf might function as an oncogene in multiple myeloma, a role for this gene in other cancers has not been shown. In this study, we have found that mice transgenic for c-Maf whose expression was direct to the T-cell compartment developed T-cell lymphoma. Moreover, we showed that cyclin D2, integrin beta(7), and ARK5 were up-regulated in c-Maf transgenic lymphoma cells. Furthermore, 60% of human T-cell lymphomas (11 of 18 cases), classified as angioimmunoblastic T-cell lymphoma, were found to express c-Maf. These results suggest that c-Maf might cause a type of T-cell lymphoma in both mice and humans and that ARK5, in addition to cyclin D2 and integrin beta(7), might be downstream target genes of c-Maf leading to malignant transformation.
The McbR repressor modulated by the effector substanceS‐adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism ofCorynebacterium glutamicumATCC 13032 (2005)

In a recent proteomics study we have shown that the mcbR gene of Corynebacterium glutamicum ATCC 13032 most probably encodes a transcriptional repressor of the TetR type, which regulates the expression of at least six genes involved in the synthesis of sulphur-containing amino acids. By means of DNA microarray hybridizations we detected 86 genes with enhanced transcription in an mcbR mutant when compared with the wild-type strain. Bioinformatic analysis identified the inverted repeat 5'-TAGAC-N6-GTCTA-3' as a consensus sequence within the upstream region of 22 genes and operons, suggesting that the transcription of at least 45 genes is directly controlled by the McbR repressor. These 45 genes encode a variety of functions in (S-adenosyl)methionine and cysteine biosynthesis, in sulphate reduction, in uptake and utilization of sulphur-containing compounds and in transcriptional regulation. The function of the inverted repeat motif as potential McbR binding site in front of the genes hom, cysI, cysK, metK and mcbR was verified experimentally by competitive electrophoretic mobility shift analysis. A systematic search for the potential effector substance modulating the function of McbR revealed that only S-adenosylhomocysteine prevented the binding of McbR to its target sequence. These results indicate that the transcriptional repressor McbR directly regulates a set of genes comprising all aspects of transport and metabolism of the macroelement sulphur in C. glutamicum. As the activity of McbR is modulated by S-adenosylhomocysteine, a major product of transmethylation reactions, the results point also to a novel regulatory mechanism in bacteria to control the biosynthesis of S-adenosylmethionine.
Proliferation of unilocular fat cells in the primary culture (1987)

Mature white fat cells (unilocular fat cells) have generally been considered to be in terminal differentiation and, hence, to have no proliferative ability. A new method, referred to as "ceiling culture," has been devised in our laboratory to culture unilocular fat cells in vitro. Under such culture conditions, the fat cells continue to exhibit specific functions of lipid metabolism and proliferate extensively. Intracytoplasmic lipid droplets did not inhibit division of the cells. There were two modes of proliferation of unilocular fat cells: "loculus-dividing" cell division, in which the single loculus of fat in the dividing cell was broken down into multiple droplets and distributed evenly between the daughter cells, and "loculus-preserving" cell division, in which the loculus in the dividing cell was minimally broken down and inherited with its shape preserved by one of the daughter cells with the other getting only a small number of fine lipid droplets. Such findings suggest that unilocular fat cells in mature fat tissue in vivo are probably capable of proliferation in such modes under some conditions.
Bringing resources to innovation (2002)

A ten-year study follows the venture capital business from relative obscurity to boom to retrenchment
Colorectal Carcinoma Metastases in Liver: Laser-induced Interstitial Thermotherapy—Local Tumor Control Rate and Survival Data (2004)

MR imaging-guided LITT yields high local tumor control and survival rates in well-selected patients with limited liver metastases of colorectal carcinoma.
Nucleotide sequence analysis of the V regions of two IgM cold agglutinins. Evidence that the VH4-21 gene segment is responsible for the major cross-reactive idiotype (1991)

Cold agglutinins are human autoantibodies, usually of the IgM class, which agglutinate RBC at low temperature. The major subset recognizes the I/i carbohydrate Ag, and many of these antibodies bear cross-reacting idiotypic determinants. An anti-idiotypic mAb that is specific for one of the idiotopes largely confined to cold agglutinins has been used to identify and monitor tumor cells that secrete these molecules in two patients. The tumor cells were immortalized with EBV and the idiotope-positive lines used to investigate the utilization of the VH and VL genes by these antibodies. Nucleotide sequence analysis of the two cold agglutinins (FS-1 and FS-2) revealed the utilization of a single common gene segment, VH4-21. Serologic analysis documented that only human antibodies utilizing the VH4-21 gene segment were reactive in the idiotope assay, other VHIV antibodies as well as a panel of antibodies derived from other VH families being negative. The DH, JH, VK, and JK gene segments of FS-1 and FS-2 were structurally distinct. These data suggest that the structural basis for the cross-reactive idiotope as well as cold agglutinin activity is the VH4-21 gene segment. A nucleotide change in H chain CDR1 of both cold agglutinins results in the substitution of an aspartic acid residue for glycine at position 31, suggesting that this amino acid might be critical to recognition of the red cell Ag.
Query processing in the ObjectStore database system (1992)

ObjectStore is an object-oriented database system supporting persistence orthogonal to type, transaction management, and associative queries. Collections are provided as objects. The data model is non-1NF, as objects may have embedded collections. Queries are integrated with the host language in the form of query operators whose operands are a collection and a predicate. The predicate may itself contain a (nested) query operating on an embedded collection. Indexes on paths may be added and removed dynamically. Collections, being treated as objects, may be referred to indirectly, e.g., through a by-reference argument. For this reason and others, multiple execution strategies are generated, and a final selection is made just prior to query execution. Nested queries can result in interleaved execution and strategy selection.
Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures (2020)

Abstract Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 19 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients and may be a positive indicator of disease outcome. Clonal expansion of the B cell memory response is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 777 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralising antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand and predict positive patient responses.
T-Cell Receptor-Like Antibodies: Targeting the Intracellular Proteome Therapeutic Potential and Clinical Applications (2013)

Major histocompatibility complex (MHC) class I molecules are key in the immune response against malignant cells by shaping the T-cell repertoire and presenting peptides from endogenous antigens to CD8+ cytotoxic T cells. Because of their unique specificity, MHC-peptide complexes are a desirable target for novel immunotherapeutic approaches. These complexes can be targeted by recombinant T-cell receptors (TCRs). However, most TCRs produced thus far have affinities which are too low for target detection under normal assay conditions, and limited stability (due to their generation in a single-chain version). Developing high-affinity soluble antibody molecules endowed with a TCR-like specificity toward tumor epitopes, termed TCR-like antibodies, addresses the low affinity of TCRs. These TCR-like antibodies are being developed as a new immunotherapeutic class for targeting tumor cells and mediating their specific killing. In addition, these antibodies are valuable research reagents enabling the study of human class I peptide-MHC ligand-presentation and TCR–peptide–MHC interactions.
Personal photo enhancement using example images (2010)

We describe a framework for improving the quality of personal photos by using a person's favorite photographs as examples. We observe that the majority of a person's photographs include the faces of a photographer's family and friends and often the errors in these photographs are the most disconcerting. We focus on correcting these types of images and use common faces across images to automatically perform both global and face-specific corrections. Our system achieves this by using face detection to align faces between “good” and “bad” photos such that properties of the good examples can be used to correct a bad photo. These “personal” photos provide strong guidance for a number of operations and, as a result, enable a number of high-quality image processing operations. We illustrate the power and generality of our approach by presenting a novel deblurring algorithm, and we show corrections that perform sharpening, superresolution, in-painting of over- and underexposured regions, and white-balancing.
New and faster filters for multiple approximate string matching (2001)

Abstract We present three new algorithms for on‐line multiple string matching allowing errors. These are extensions of previous algorithms that search for a single pattern. The average running time achieved is in all cases linear in the text size for moderate error level, pattern length, and number of patterns. They adapt (with higher costs) to the other cases. However, the algorithms differ in speed and thresholds of usefulness. We theoretically analyze when each algorithm should be used, and show their performance experimentally. The only previous solution for this problem allows only one error. Our algorithms are the first to allow more errors, and are faster than previous work for a moderate number of patterns (e.g. less than 50–100 on English text, depending on the pattern length). © 2002 John Wiley &amp; Sons, Inc. Random Struct. Alg., 20, 23–49, 2002
E6*, the 50 Amino Acid Product of the Most Abundant Spliced Transcript of the E6 Oncoprotein in High-Risk Human Papillomavirus, Is a Promiscuous Folder and Binder (2011)

High-risk human papillomavirus E6 participates in tumorigenic progression, mainly by its ability to promote p53 degradation. HPV transcripts show a complex splicing pattern, where E6* is the most abundant transcript in high-risk HPV types, comprising the first 50 amino acids of E6. No structural or biochemical information of this polypeptide, which contains half of the first zinc binding motif of E6, is available, due to the difficulty to acquire a compact monomeric fold in such a small polypeptide. We show that HPV16-E6* can fold into either α-helix or β-sheet large oligomers at pH 7.5 and 5.0, respectively, in the absence of zinc. The β-sheet oligomers are highly stable and unaffected by the presence of zinc, while the α-helix oligomers tend to rapidly form aggregates, prevented by the presence of the metal. Two E6* molecules bind per atom of zinc, suggesting a tetrahedral, high-affinity arrangement (K(D) < 10(-12) M), which results in a zinc-mediated E6* dimer with significant secondary structure. Endogenous E6 oligomers were previously found in the cytosol of high-risk HPV transformed cell lines, and we propose that the oligomerization determinant resides within E6*. E6* effects were reported to counteract those of E6 in cells, and the ratio between these two species modulates p53 degradation and other apoptosis-dependent signaling cascades. A residue of an evolved splicing event related to regulation of oncogene expression in HPV or a splicing event resulting from the selection of a small deleterious viral polypeptide, the abundant existence of E6* with a "chameleon" nature correlates with target plasticity, and its fate is linked to a balance between protein levels, zinc availability, redox potential, and oligomerization. In addition, the results presented here have strong implications for zinc binding sites in nascent polypeptides. This evolved promiscuous folder speaks of effect rather than function of a viral product that, when highly increased, can directly or indirectly affect various cellular processes leading to cell deregulation and tumorigenesis.
The Junctional Adhesion Molecule JAML Is a Costimulatory Receptor for Epithelial γδ T Cell Activation (2010)

Gammadelta T cells present in epithelial tissues provide a crucial first line of defense against environmental insults, including infection, trauma, and malignancy, yet the molecular events surrounding their activation remain poorly defined. Here we identify an epithelial gammadelta T cell-specific costimulatory molecule, junctional adhesion molecule-like protein (JAML). Binding of JAML to its ligand Coxsackie and adenovirus receptor (CAR) provides costimulation leading to cellular proliferation and cytokine and growth factor production. Inhibition of JAML costimulation leads to diminished gammadelta T cell activation and delayed wound closure akin to that seen in the absence of gammadelta T cells. Our results identify JAML as a crucial component of epithelial gammadelta T cell biology and have broader implications for CAR and JAML in tissue homeostasis and repair.
Altered States of Consciousness Induced by Exogenous Audio Signals (2022)

Rhythm deeply permeates the environment and is perceived by nearly all sensory modalities. There is a developing trend in cognitive science to look to neural rhythms at varying scales as the source of subjective experience. This approach, which looks to the oscillatory correlates of consciousness—electromagnetic field oscillations generated by the brain—as a quantifiable measure of consciousness, provides a novel avenue for bridging the subjective-objective divide. Oscillatory rhythms in the brain can originate endogenously or exogenously and can have varying impacts on subjective experience. Some exogenous rhythms, including audio rhythms, can have surprisingly strong impacts, sufficient to label these induced states “altered states of consciousness.” This piece examines the role of external auditory rhythms (speech, binaural beats, and music) in influencing conscious states of affected individuals at individual and interpersonal scales. This new methodology expands the scope by which cognitive science can be practically applied in studying the subjective experience.
Prognostic significance of peritumoral lymphatic and blood vessel invasion in node-negative carcinoma of the breast. (1990)

The prognostic significance of intramammary lymphatic and blood vessel invasion was evaluated in a retrospective series of 221 patients with node-negative carcinoma of the breast treated with modified radical mastectomy. To facilitate identification of lymphatic and blood vessel invasion, the tumors were studied with an immunohistochemical technique using antibodies to endothelial markers. Peritumoral lymphatic and blood vessel invasion (PLBI) (encompassing both lymphatic and blood vessel invasion) was an adverse prognostic indicator independent of menopausal status, tumor size, and other histologic variables. Recurrence of disease and death resulting from carcinoma were significantly higher for patients with PLBI-present (+) tumors compared with patients with PLBI-absent (-) tumors (P less than .0001). The risk of recurrence for patients with PLBI+ tumors was 4.7 times that for their PLBI- counterparts. The presence of intratumoral lymphatic and blood vessel invasion (ILBI) is less important because few examples were found without concomitant PLBI. When PLBI was separated into lymphatic invasion and blood vessel invasion individually, the prognostic significance was retained in both groups. The immunohistochemical approach reduced both false-negative and false-positive observations and identified about 40% of PLBI that would have been missed by routine histologic examination alone. The presence of PLBI appears to be a potentially useful discriminant in predicting the outcome of patients with node-negative carcinoma of the breast.
Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates (2003)

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.
Implementing a RosettaNet Business-to-Business Integration Platform Using J2EE and Web Services (2006)

E-business frameworks provide standards and specifications for integrating enterprise applications of business partners with less effort. We report experiences from developing a prototype implementing the messaging part of the RosettaNet e-business framework using commonly available open source tools. The requirements, design and implementation of the prototype are presented. The tools turned out to be suitable for the task, but some problems exist that e.g. limit the maximum message size. In addition, interoperability problems between different implementations of RosettaNet messaging arose due to RosettaNet using low expressive power message specification languages, thus leaving room for interpretation regarding message validation.
Directed acyclic graph kernels for structural RNA analysis (2008)

Stem kernels can be utilized as a reliable similarity measure of structural RNAs, and can be used in various kernel-based applications.
MEDIA FROM RHABDOMYOSARCOMA AND NEUROBLASTOMA CELL CULTURES STIMULATE IN VITRO AGGREGATION AND FIBRILLIZATION OF AMYLOID BETA-PROTEIN (1996)

In vitro aggregation and fibrillization of synthetic amyloid beta-protein Aβ 1–40 was assessed in the conditioned media from rhabdomyosarcoma (CRL 1598, HTB 82, HTB 153, CCL 136), adenocarcinoma (CCL 218), neuroblastoma (SY5Y), and COS cells cultured in the absence and presence of 10% heat-inactivated fetal bovine serum (FBS). The aggregation and formation of cross β-pleated sheet structures in Aβ was quantitated by Thioflavin T (ThT) fluorescence spectroscopy, while the morphology of Aβ fibrils was examined in negative staining in the electronmicroscope (EM). In cultures supplemented with 10% FBS, the conditioned media from CRL 1598, HTB 82, CCL 218, and SY5Y cell cultures stimulated Aβ aggregation in a time-dependent manner as compared to that of control (serum-containing medium that had not been exposed to cells). The order of stimulation was SY5Y > CRL 1598 ≥ HTB 82 > CCL 218, and the stimulation was higher in 2 week cultures than in 1 week cultures. Similar studies using media from HTB 153, CCL 136 and COS cell cultures showed no effect on Aβ 1–40 aggregation. In serum-free cell cultures, only media from SY5Y and CRL 1598 could promote significant aggregation of Aβ 1–40. Negative staining in EM revealed Aβ fibril formation only with conditioned media from SY5Y and CRL 1598 cultured under serum free conditions; no Aβ fibrils were noticed in media from cell cultures supplemented with 10% FBS. We propose that both the SY5Y neuroblastoma cell line and the CRL 1598 rhabdomyosarcoma cell line may serve as experimental models for in vitro studies of extracellular aggregation and fibrillization of Aβ-protein in cell cultures, while rhabdomyosarcoma HTB 82 and adenocarcinoma CCL 218 may be models for study of Aβ aggregation only.