gebhart/patrepeval huggingface dataset:
Failure to demonstrate long-lived MHC saturation both in vitro and in vivo. Implications for therapeutic potential of MHC-blocking peptides. (1994)

Peptides that bind with high affinity to class II MHC molecules can inhibit T cell activation both in vitro and in vivo. Thus, they have been suggested as potential therapeutic agents for MHC-associated autoimmune diseases. We have constructed nonnatural peptides with high affinity for certain disease-associated MHC alleles. More specifically, a particular peptide, designated as CY-760.50, was found to have a high binding affinity for DR1, slow dissociation kinetics after binding to MHC, and prolonged stability in human serum. However, when the ability of this peptide to block peptide presentation to an influenza hemagglutinin 307-319 peptide-specific, DR1-restricted T cell clone was examined, it was found that MHC blockade could only be achieved when high concentrations of peptide were present along with Ag in the fluid phase. Thus, pretreatment of APC with MHC class II blocker, followed by removal of unbound blocker, did not result in saturation of MHC molecules, because practically immediate reacquisition of Ag-presenting capacity was observed after removal of fluid phase blocker. The pharmacokinetic behavior and the duration of blocking activity of CY-760.50 were also examined in vivo, taking advantage of the fact that the mouse MHC class II molecule I-Ab also bound CY-760.50 with high affinity. CY-760.50 administered i.v. to C57BL/6 mice was rapidly cleared from the circulation and virtually undetectable in the serum 10 min after injection. This fast clearance rate was paralleled by a similarly short duration of the MHC blockade effect. These in vivo results have implications concerning the biology of peptide-MHC interactions, and suggest that MHC blockade may not be feasible as a therapeutic approach unless effective concentrations of inhibitor can be maintained over extended periods of time in the extracellular fluids.
3D is here: Point Cloud Library (PCL) (2011)

With the advent of new, low-cost 3D sensing hardware such as the Kinect, and continued efforts in advanced point cloud processing, 3D perception gains more and more importance in robotics, as well as other fields. In this paper we present one of our most recent initiatives in the areas of point cloud perception: PCL (Point Cloud Library - http://pointclouds.org). PCL presents an advanced and extensive approach to the subject of 3D perception, and it's meant to provide support for all the common 3D building blocks that applications need. The library contains state-of-the art algorithms for: filtering, feature estimation, surface reconstruction, registration, model fitting and segmentation. PCL is supported by an international community of robotics and perception researchers. We provide a brief walkthrough of PCL including its algorithmic capabilities and implementation strategies.
Clustering of Resting State Networks (2012)

The clustering of resting state activity using different optimal numbers of clusters identified resting state networks comparable to previously obtained results. This work reinforces the observation that resting state networks are hierarchically organized.
Efficient ray tracing of subdivision surfaces using tessellation caching (2015)

A common way to ray trace subdivision surfaces is by constructing and traversing spatial hierarchies on top of tessellated input primitives. Unfortunately, tessellating surfaces requires a substantial amount of memory storage, and involves significant construction and memory I/O costs. In this paper, we propose a lazy-build caching scheme to efficiently handle these problems while also exploiting the capabilities of today's many-core architectures. To this end, we lazily tessellate patches only when necessary, and utilize adaptive subdivision to efficiently evaluate the underlying surface representation. The core idea of our approach is a shared lazy evaluation cache, which triggers and maintains the surface tessellation. We combine our caching scheme with SIMD-optimized subdivision primitive evaluation and fast hierarchy construction over the tessellated surface. This allows us to achieve high ray tracing performance in complex scenes, outperforming the state of the art while requiring only a fraction of the memory. In addition, our method stays within a fixed memory budget regardless of the tessellation level, which is essential for many applications such as movie production rendering. Beyond the results of this paper, we have integrated our method into Embree, an open source ray tracing framework, thus making interactive ray tracing of subdivision surfaces publicly available.
Apolipoprotein C-I modulates the interaction of apolipoprotein E with beta-migrating very low density lipoproteins (beta-VLDL) and inhibits binding of beta-VLDL to low density lipoprotein receptor-related protein. (1990)

The binding of native rabbit beta-very low density lipoproteins (beta-VLDL) to the low density lipoprotein receptor-related protein (LRP) requires incubation with exogenous apolipoprotein (apo) E. Inclusion of a mixture of the C apolipoproteins in the incubation inhibits this binding. In the present study, the ability of the individual C apolipoproteins (C-I, C-II, and C-III) to block binding of beta-VLDL to the LRP was examined by measuring cholesteryl ester formation in mutant fibroblasts that lack low density lipoprotein receptors or by measuring binding to the LRP using ligand blotting. In each assay, both apoC-I and apoC-II inhibited binding; apoC-I was the more effective inhibitor. Apolipoprotein C-III had no effect on binding activity, regardless of its sialylation level. Binding of human apoE to rabbit beta-VLDL in the absence or presence of human apoC-I, apoC-II, and monosialo-apoC-III was also determined, by gel filtration and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The results of these studies are consistent with a mechanism in which exogenous human apoE displaces the endogenous apoE and the beta-VLDL particle becomes enriched with apoE (by 4.2-fold in this study). At this higher apoE content, the beta-VLDL bound to the LRP. Inclusion of apoC-I, apoC-II, or apoC-III in the incubation mixture resulted in a differential displacement of apoE from the beta-VLDL; however, at the concentrations examined, only apoC-I and apoC-II were capable of displacing sufficient apoE to abolish binding to LRP.
Trends in odor intensity for human and electronic noses: Relative roles of odorant vapor pressure vs. molecularly specific odorant binding (1998)

Response data were collected for a carbon black-polymer composite electronic nose array during exposure to homologous series of alkanes and alcohols. The mean response intensity of the electronic nose detectors and the response intensity of the most strongly driven set of electronic nose detectors were essentially constant for members of a chemically homologous odorant series when the concentration of each odorant in the gas phase was maintained at a constant fraction of the odorant's vapor pressure. A similar trend is observed in human odor detection threshold values for these same homologous series of odorants. Because the thermodynamic activity of an odorant at equilibrium in a sorbent phase is equal to the partial pressure of the odorant in the gas phase divided by the vapor pressure of the odorant and because the activity coefficients are similar within these homologous series of odorants for sorption of the vapors into specific polymer films, the data imply that the trends in detector response can be understood based on the thermodynamic tendency to establish a relatively constant concentration of sorbed odorant into each of the polymeric films of the electronic nose at a constant fraction of the odorant's vapor pressure. Similarly, the data are consistent with the hypothesis that the odor detection thresholds observed in human psychophysical experiments for the odorants studied herein are driven predominantly by the similarity in odorant concentrations sorbed into the olfactory epithelium at a constant fraction of the odorant's vapor pressure.
CD40 signaling pathway: anti-CD40 monoclonal antibody induces rapid dephosphorylation and phosphorylation of tyrosine-phosphorylated proteins including protein tyrosine kinase Lyn, Fyn, and Syk and the appearance of a 28-kD tyrosine phosphorylated protein. (1994)

CD40 plays an important role in B cell activation, proliferation, and Ig class switching. The signal transduction pathway mediated by CD40 was studied using monoclonal antibody (mAb) 626.1 to CD40. Burkitt's lymphoma and Epstein-Barr virus-transformed B cell lines and tonsilar B lymphocytes were treated with the anti-CD40 mAb for various lengths of time. The early events triggered by CD40 were examined by monitoring the changes in tyrosine phosphorylation of cellular proteins with anti-phosphotyrosine mAb. Dephosphorylation of specific proteins ranging between 50-110 kD and the appearance of a 28-kD tyrosine phosphorylated protein were seen within 30 s in human B cell lines. The dephosphorylation was reversed and the 28-kD protein was dephosphorylated in cells stimulated for 1 min. In resting B cells, the appearance of the 28-kD phosphoprotein was observed in 30 s after the addition of the anti-CD40 mAb. The tyrosine phosphorylation of this protein persisted. The patterns of protein tyrosine phosphorylation differed from those induced by an anti-immunoglobulin M mAb. The changes in the state of tyrosine phosphorylation induced by the anti-CD40 mAb were obviated by mAb to CD45, a protein tyrosine phosphatase (PTP) or by the addition of sodium orthovanadate, a broad PTP inhibitor. They were also blocked by protein tyrosine kinase (PTK) inhibitors, herbimycin A and genistein, and PKC and protein serine/threonine kinase inhibitors, H7 and HA1004. In addition, the alteration in the tyrosine phosphorylation of PTKs Lyn, Fyn, and Syk was directly demonstrated. Engagement of CD40 for 30 s induced a transient decrease in tyrosine phosphorylation of these PTKs. These results indicate that the early events in CD40 signaling involve the complex interaction between PTP and protein kinases.
Expression of a Platelet-Derived Growth Factor-Like Protein in Simian Sarcoma Virus Transformed Cells (1983)

The near identity of the partial amino acid sequence of human platelet-derived growth factor (PDGF) and that predicted for p28sis, the putative transforming protein of the simian sarcoma virus (SSV), suggests expression of a growth factor activity may be central for transformation by SSV. It is now reported that SSV-transformed cells but not control cells contain a growth factor activity that is identical to PDGF in immunoassay, in mitogenic dose response, and in specific mitogenic activity. The protein immunoprecipitated by antiserum to human PDGF has an apparent molecular weight of 20,000, identical to that of p20sis, the putative intracellular degradation product of p28sis. The results support the concept that expression of a PDGF-like molecule, which appears to be the product of the viral-sis gene, is responsible for the abnormal regulation of growth is SSV-transformed cells.
Sialic acid uptake by fibroblasts (1976)

The existence of surface sialytransferases that use cytidine monophosphate (CMP)-sialic acid as substrate has been postulated in previous studies. This is based on the assumption that if whole, viable cells can catalyze the transfer of sialic acid from CMP-sialic acid to endogenous acceptors, then the transferases carrying out the reaction must be on the cell surface, provided that (1) CMP-sialic acid does not enter the cells, and (2) CMP-sialic acid does not break down outside the cells, yielding free sialic acid which then may enter the cells, in amounts large enough to explain the incorporation. We now report evidence showing that after incubation of intact NIL, BHK, and 3T3 fibroblasts with CMP-sialic acid, at least 78% of the sialic acid incorporated by these cells is the result of free sialic acid uptake. When cells growing in a monolayer were incubated with a mixture of CMP-[14C]sialic acid and [3H]CMP-sialic acid with a ratio of 3H/14C=0.60, this ratio was found to be markedly increased in whole cells. Chemical analyses of the radioactive species in the incubation medium showed that a considerable portion of the radiolabeled sugar nucleotide had broken down to cytidine, phosphoric acid, and sialic acid. Upon incubation of cells with doubly labeled sugar nucleotide in the presence of a large excess of both nonradiolabeled cytidine and sialic acid, the cells incorporated less than 6% of both isotopes. Incubation of cells with a mixture of CMP-[14C]sialic acid and [3H]sialic acid resulted in only 20-40% of the radioactivity within the cells being membrane bound, and 70-90% of this incorporation could be inhibited by the addition of 10 mM azide to the incubation medium. The possibility that a small fraction of the total incorporation of sialic acid by these cells is due to surface sialytransferases cannot be completely ruled out. The uptake of free sialic acid by these fibroblasts is concentration dependent and a portion of it is incorporated into glycoproteins and glycolipids. Considerable loss of cell integrity was observed when fibroblasts grown on plates were removed by (ethylenedinitrilo)-tetraacetic acid or trypsin and subsequently incubated in buffer, indicating that these preparations are not suitable for intact cell studies.
ANTIBODIES TO POLYNUCLEOTIDES IN HUMAN SERA: ANTIGENIC SPECIFICITY AND RELATION TO DISEASE (1971)

The specificities of anti-polynucleotide antibodies found in human sera were studied using several immunological procedures. Anti-native DNA (NDNA) antibodies and certain anti-double-stranded RNA (DSRNA) antibodies were found to react with single-stranded DNA (SDNA), and anti-NDNA antibodies were observed to react more avidly with SDNA than with NDNA in most sera tested. Antibodies to NDNA showed no preferential reactivity with NDNA or SDNA derived from mammalian tissue, bacterial, or viral sources. Precipitating antibodies reactive with individual bases, with common determinants of bases, and with common determinants of SDNA and NDNA were detected utilizing synthetic polydeoxyribonucleotides. Antibodies to DSRNA were also heterogeneous and reactive with both Poly A . Poly U and Poly I . Poly C in addition to reactivity with Poly A and SDNA. In contrast, antibodies to a ribonucleo-protein determined by hemagglutination and by precipitation showed no reaction with NDNA, SDNA, or DSRNA. Serial studies of serum specimens from patients with systemic lupus erythematosus (SLE) indicated that anti-NDNA antibodies were closely associated with disease activity. Titers of antibodies to SDNA or DSRNA were also frequently increased during these periods but in addition showed peaks during quiescent periods. Anti-NDNA antibodies were detected in most patients' sera at sometime during the course of the disease. Three patients were observed with active SLE, who did not develop anti-NDNA antibodies, even in the presence of severe renal disease. Evidence that other antigen-antibody systems may also play a role in the pathogenesis of the renal disease was particularly apparent in these patients. Anti-ribonucleoprotein antibodies were not well correlated with the peaks of antibody activity of other polynucleotide antibodies, suggesting that an independent immunogen was responsible for induction of these antibodies. The close association of certain populations of anti-polynucleotide antibodies during the course of active SLE, the presence of cross-reacting antigenic determinants of SDNA, NDNA, and DSRNA, the preferential avidity of anti-NDNA antibodies for SDNA, and the frequent increase of anti-SDNA antibodies in SLE and other diseases associated with active tissue destruction suggest that SDNA is a ubiquitous antigen that may stimulate the formation of antibodies reactive with a variety of polynucleotides.
Sequential assessment of individually cultured human embryos as an indicator of subsequent good quality blastocyst development (2003)

Early embryo assessment can be used as an indicator of subsequent good blastocyst development.
An Efficient Random Mutagenesis Technique Using an E. coli Mutator Strain (2003)

Site-directed mutagenesis has become an extremely powerful means by which the nature and function of critical amino acids within a protein can be assessed and altered. However, the ability to exploit this technique requires that detailed structural information about the protein (or related proteins) is available. For many gene products of interest, this information does not yet exist. In addition, variants that have particular qualities can be missed if one relies solely on the introduction of specific predetermined mutations.
Cathepsin B1. A lysosomal enzyme that degrades native collagen (1974)

1. Experiments were made to determine whether the purified lysosomal proteinases, cathepsins B1 and D, degrade acid-soluble collagen in solution, reconstituted collagen fibrils, insoluble collagen or gelatin. 2. At acid pH values cathepsin B1 released (14)C-labelled peptides from collagen fibrils reconstituted at neutral pH from soluble collagen. The purified enzyme required activation by cysteine and EDTA and was inhibited by 4-chloromercuribenzoate, by the chloromethyl ketones derived from tosyl-lysine and acetyltetra-alanine and by human alpha(2)-macroglobulin. 3. Cathepsin B1 degraded collagen in solution, the pH optimum being pH4.5-5.0. The initial action was cleavage of the non-helical region containing the cross-link; this was seen as a decrease in viscosity with no change in optical rotation. The enzyme also attacked the helical region of collagen by a mechanism different from that of mammalian neutral collagenase. No discrete intermediate products of a specific size were observed in segment-long-spacing crystalloids (measured as native collagen molecules aligned with N-termini together along the long axis) or as separate peaks on gel filtration chromatography. This suggests that once an alpha-chain was attacked it was rapidly degraded to low-molecular-weight peptides. 4. Cathepsin B1 degraded insoluble collagen with a pH optimum below 4; this value is lower than that found for the soluble substrate, and a possible explanation is given. 5. The lysosomal carboxyl proteinase, cathepsin D, had no action on collagen or gelatin at pH3.0. Neither cathepsin B1 nor D cleaved Pz-Pro-Leu-Gly-Pro-d-Arg. 6. Cathepsin B1 activity was shown to be essential for the degradation of collagen by lysosomal extracts. 7. Cathepsin B1 may provide an alternative route for collagen breakdown in physiological and pathological situations.
Ultra wide band wireless communications: A tutorial (2003)

Ultra wide band (UWB) radio has recently attracted increased attention due to its expected unlicensed operation, and potential to provide very high data rates at relatively short ranges. In this article we briefly describe some main candidate multiple access and modulation schemes for UWB communications, followed with their power spectral density calculation and properties. We also present some illustrative capacity results, and provide a discussion of the impact of network topology on multiple access capacity.
Chemotherapy and Targeted Therapy Combinations in Advanced Melanoma (2006)

For three decades, clinical trials with chemotherapy in melanoma have failed to show superiority of any one regimen over another. Dacarbazine remains the only "standard" agent. With response rates of <10% and median progression-free survival of 2 months or less in contemporary trials, there is a need to improve systemic therapy. Combination chemotherapy is associated with higher response rates than single-agent therapy but this has not translated into improved survival. An increasing number of potential therapeutic targets have been identified. For some, pharmacologic inhibitors are available, including sorafenib for BRAF, farnesyltransferase inhibitors for NRAS, PD-0325901 for mitogen-activated protein kinase/extracellular signal-regulated kinase kinase, rapamycin analogues for mammalian target of rapamycin, and agents that inhibit either vascular endothelial growth factor or its receptors. Several multitargeted kinase inhibitors have potency against the fibroblast growth factor receptor, c-kit, and platelet-derived growth factor receptor. Small-molecule inhibitors of c-met and Akt are in preclinical development. Another class of agents indirectly affect aberrant signaling, including inhibitors of chaperones and proteasomes. Several targeted agents seem to enhance the cytotoxicity of chemotherapy in preclinical models. The mechanism by which signaling inhibition might synergize with chemotherapy requires more study so that rational combinations move forward. Very few targeted agents have been studied rigorously in this fashion.
Gata5 is required for the development of the heart and endoderm in zebrafish (1999)

The mechanisms regulating vertebrate heart and endoderm development have recently become the focus of intense study. Here we present evidence from both loss- and gain-of-function experiments that the zinc finger transcription factor Gata5 is an essential regulator of multiple aspects of heart and endoderm development. We demonstrate that zebrafish Gata5 is encoded by the faust locus. Analysis of faust mutants indicates that early in embryogenesis Gata5 is required for the production of normal numbers of developing myocardial precursors and the expression of normal levels of several myocardial genes including nkx2.5. Later, Gata5 is necessary for the elaboration of ventricular tissue. We further demonstrate that Gata5 is required for the migration of the cardiac primordia to the embryonic midline and for endodermal morphogenesis. Significantly, overexpression of gata5 induces the ectopic expression of several myocardial genes including nkx2.5 and can produce ectopic foci of beating myocardial tissue. Together, these results implicate zebrafish Gata5 in controlling the growth, morphogenesis, and differentiation of the heart and endoderm and indicate that Gata5 regulates the expression of the early myocardial gene nkx2.5.