gebhart/patrepeval huggingface dataset:
Human mesenchymal stem cells elevate CD4+CD25+CD127low/- regulatory T cells of asthmatic patients via heme oxygenase-1. (2013)

Up-regulation of CD4+CD25+CD127low/- regulatory T cells (Tregs) is a new target in the treatment of asthma. Human bone marrow mesenchymal stem cells can up-regulate CD4+CD25+CD127low/- regulatory T cells in vitro, meanwhile, heme oxygenase-1 (HO-1) plays an important role in the development and maintenance of CD4+CD25+ regulatory T cells. However the mechanism has not yet been adequately understood. Hence, we wondered what effect of Heme Oxygenase-1 made on regulation of CD4+CD25+CD127low/- regulatory T cells mediated by mesenchymal stem cells. Peripheral blood mononuclear cells isolated from asthmatic patients and healthy controls were co-cultured with human bone marrow mesenchymal stem cells which were pretreated with Hemin (the revulsive of Heme Oxygenase-1), Protoporphyrin Ⅸ zinc (the inhibitor of Heme Oxygenase-1) and saline. The expression of Heme Oxygenase-1 in MSCs was enhanced by Hemin and inhibited by Protoporphyrin zinc in vitro. Overexpression of Heme Oxygenase-1 elevated the proportion of CD4+CD25+CD127low/- regulatory T cells in CD4+ T cells, meanwhile, inhibition of Heme Oxygenase-1 decreased the proportion of CD4+CD25+CD127low/- regulatory T cells in CD4+ T cells as compared with mesenchymal stem cells alone. Taken together, these data demonstrated that Heme Oxygenase-1 contributed to the up-regulation of CD4+CD25+CD127low/- regulatory T cells mediated by mesenchymal stem cells in asthma.
Polychromatic see-through near-eye display design with two waveguides and a large field-of-view (2016)

We propose a new kind of waveguide near eye display (WGNED) with new in-coupling and propagation subsystems to vertically enlarge the field-of-view (FOV). Two waveguides are stacked up with a 0.1 mm air gap so that light can propagate inside the two waveguides independently. The light from a micro-display is coupled into the first waveguide by the in-coupling subsystem. Light propagates inside the first waveguide until reaching a cylindrical mirror at its edge. In the area near the mirror, the two waveguides are combined together. Then, the light is reflected by a cylindrical mirror and coupled to the second waveguide. The out-coupling from the second waveguide is realized either by a holographic optical element or cascaded micro mirrors. A cylindrical mirror allows most of the light coming out to reach the viewer’s eye. A two-lens subsystem with freeform surfaces is used as an in-coupling element to correct the aberrations. An advantage of our design is that the chief ray of each object field converges to the eye with an enlarged FOV in the vertical direction. The system has been simulated in mixed sequential and non-sequential mode in Zemax®. It can achieve a 20&deg;&times;55&deg; total FOV which is, to our knowledge, larger than the published WGNED designs.
Orthogonal ligation strategies for peptide and protein (1999)

This review focuses on the concept, criteria, and methods of an orthogonal amide ligating strategy suitable for syntheses of peptides, peptide mimetics, and proteins. Utilizing unprotected peptides or proteins derived from chemical or biosynthetic sources, this ligation strategy has been shown to be general and exceptionally mild. Its orthogonality in ligating two unprotected segments with free N-terminal (NT)-amines at a specific NT-amine is achieved through a chemoselective capture step and then an intramolecular acyl transfer reaction. Both coupling reagents for enthalpic activation and protection schemes therefore become unnecessary. More than a dozen orthogonal ligation methods based on either imine or thioester captures have been developed to afford native and unusual amino acids at ligation sites of linear, branched, or cyclic peptides. Because unprotected peptides and proteins of different sizes and forms can be obtained from either chemical or recombinant sources, orthogonal ligation removes the size limitation imposed on the chemical synthesis of a protein with a native or non-native structure. Furthermore, by using building blocks from biosynthetic sources, orthogonal ligation provides a unifying operational concept for both total and semisynthesis of peptides and proteins.
RanBPM is an L1‐interacting protein that regulates L1‐mediated mitogen‐activated protein kinase activation (2005)

A yeast two-hybrid screen using the last 28 amino acids of the cytoplasmic domain of the neural cell adhesion molecule L1 identified RanBPM as an L1-interacting protein. RanBPM associates with L1 in vivo and the N-terminal region of RanBPM (N-RanBPM), containing the SPRY domain, is sufficient for the interaction with L1 in a glutathione S-transferase pull-down assay. L1 antibody patching dramatically changes the subcellular localization of N-RanBPM in transfected COS cells. Overexpression of N-RanBPM in COS cells reduces L1-triggered extracellular signal-regulated kinase 1/2 activation by 50% and overexpression of N-RanBPM in primary neurons inhibits L1-mediated neurite outgrowth and branching. These data suggest that RanBPM is an adaptor protein that links L1 to the extracellular signal-regulated kinase/MAPK pathway.
C–H functionalization logic in total synthesis (2011)

In this critical review, the strategic and economic benefits of C-H functionalization logic will be analyzed through the critical lens of total synthesis. In order to illustrate the dramatically simplifying effects this type of logic can potentially have on synthetic planning, we take the reader through a series of case studies in which it has already been successfully applied. In the first section, a chronological look at key historical syntheses will be examined, leading into modern day examples. In the second section, our own experience with applying and executing synthesis with a C-H functionalization "mindset" will be discussed (114 references).
Context-based adaptive binary arithmetic coding in the H.264/AVC video compression standard (2003)

Context-based adaptive binary arithmetic coding (CABAC) as a normative part of the new ITU-T/ISO/IEC standard H.264/AVC for video compression is presented. By combining an adaptive binary arithmetic coding technique with context modeling, a high degree of adaptation and redundancy reduction is achieved. The CABAC framework also includes a novel low-complexity method for binary arithmetic coding and probability estimation that is well suited for efficient hardware and software implementations. CABAC significantly outperforms the baseline entropy coding method of H.264/AVC for the typical area of envisaged target applications. For a set of test sequences representing typical material used in broadcast applications and for a range of acceptable video quality of about 30 to 38 dB, average bit-rate savings of 9%-14% are achieved.
New technology opportunities in cellular radio (1993)

A major opportunity now faces the cellular radio industry; that is the possibility to address the mass consumer market, providing mobile communications for everyone at an affordable price. The author shows how new technology, particularly in the area of radio and base-station systems will be an enabling factor in addressing the new market by reducing costs and by facilitating the development of higher capacity networks.
Integrating a Comprehensive Modal Emissions Model into ATMIS Transportation Modeling Frameworks (2001)

Intelligent Transportation Systems (ITS) have generated considerable enthusiasm in the transportation community as a potential means to improve roadway safety, reduce congestion, enhance the mobility of people and goods, and reduce energy consumption and vehicle emissions. In order to estimate these potential benefits, new and improved analytical techniques and simulation models are being developed for ITS. In terms of environmental effects, the University of California, Riverside, College of Engineering-Center for Environmental Research and Technology (CE-CERT) has developed a comprehensive modal emissions and energy consumption (CME/EC) model that can be directly used for ITS evaluation. In this project, an examination was performed on the key interface issues between the detailed CME/EC model and other ITS simulation models and analytical techniques developed within the California PATH program. Methodologies for integrating various ITS transportation models/data sets with the CME/EC model were established. These integration issues are not trivial; many ITS simulation models and analytical techniques inherently have different levels of aggregation and detail (e.g., both in time and across various vehicle fleets). Much of the work performed focused on integrating the CME/EC model with PARAMICS. PARAMICS is used throughout CALTRANS and the PATH program for various ITS studies. After successfully completing this integration, two case studies were carried out using this PARAMICS/CME-EC tool. The first case study examined the emissions impact of HOT lanes along the SR-91 corridor in Southern California. The other case study examined the emissions impact associated redesignating uphill lanes on I-60 near Riverside, California. By completing these case studies, the integrated transportation/emissions model was thoroughly debugged. These case studies can serve as examples as how to apply this new tool for creating microscale emission inventories. In this report, background material is first provided on the Comprehensive Modal Emissions/Energy Consumption (CME/EC) model and ITS traffic simulation modeling efforts in the California PATH program. This is followed by a description of the integration methodology between CME/EC and PARAMICS. In the last part of the report, two separate case studies are described, where analyses with the integrated models were carried out.
MCM Proteins in DNA Replication (1999)

The MCM proteins are essential replication initiation factors originally identified as proteins required for minichromosome maintenance in Saccharomyces cerevisiae. The best known among them are a family of six structurally related proteins, MCM2-7, which are evolutionally conserved in all eukaryotes. The MCM2-7 proteins form a hexameric complex. This complex is a key component of the prereplication complex that assembles at replication origins during early G1 phase. New evidence suggests that the MCM2-7 proteins may be involved not only in the initiation but also in the elongation of DNA replication. Orchestration of the functional interactions between the MCM2-7 proteins and other components of the prereplication complex by cell cycle-dependent protein kinases results in initiation of DNA synthesis once every cell cycle.
poc1 : An Arabidopsis mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of PIF3 , a gene encoding a phytochrome-interacting bHLH protein (1999)

The phytochrome family of informational photoreceptors has a central role in regulating light-responsive gene expression, but the mechanism of intracellular signal transduction has remained elusive. In a genetic screen for T DNA-tagged Arabidopsis mutants affected in early signaling intermediates, we identified poc1 (photocurrent 1), which exhibits enhanced responsiveness to red light. This phenotype is absent in a phyB (phytochrome B) null mutant background, indicating that the poc1 mutation enhances phyB signal transduction. The T DNA insertion in poc1 was found to be located in the promoter region of PIF3, a gene encoding a basic helix-loop-helix protein. The mutant phenotype seems to result from insertion-induced overexpression of this gene in red-light-grown seedlings, consistent with PIF3 functioning as a positively acting signaling intermediate. These findings, combined with data from a separate yeast two-hybrid screen that identified PIF3 as a phytochrome-interacting factor necessary for normal signaling, provide evidence that phytochrome signal transduction may include a direct pathway to photoresponsive nuclear genes via physical interaction of the photoreceptor molecules with the potential transcriptional regulator PIF3.
A Saliency Model Predicts Fixations in Web Interfaces (2010)

User interfaces are visually rich and complex. Consequently, it is difficult for designers to predict which locations will be attended to first within a display. Designers currently depend on eye tracking data to determine fixated locations, which are naturally associated with the allocation of attention. A computational saliency model can make predictions about where individuals are likely to fixate. Thus, we propose that the saliency model may facilitate successful interface development during the iterative design process by providing information about an interface’s stimulus-driven properties. To test its predictive power, the saliency model was used to render 50 web page screenshots; eye tracking data were gathered from participants on the same images. We found that the saliency model predicted fixated locations within web page interfaces. Thus, using computational models to determine regions high in visual saliency during web page development may be a cost effective alternative to eye tracking.
Do gastrointestinal symptoms accompanying sore throat predict streptococcal pharyngitis? An UPRNet study. Upper Peninsula Research Network. (1998)

Nausea and vomiting are somewhat more common in streptococcal than in nonstreptococcal pharyngitis, but appear to have limited usefulness as clinical predictors of streptococcal pharyngitis.
Sequences in the human cytomegalovirus 2.7-kilobase RNA promoter which mediate its regulation as an early gene (1989)

We have studied the regulation of expression of a major human cytomegalovirus (HCMV) early transcription unit located within the long repeat of the strain AD169 genome. This region specified a 2.7-kilobase RNA which underwent its largest increase in abundance between 8 and 14 h postinfection. To study the regulation of this gene, its promoter was cloned 5' of the gene for chloramphenicol acetyltransferase (CAT) for use in transient expression assays. A construct containing 651 base pairs of upstream sequence and 54 base pairs of leader sequence was transfected into human fibroblast cells, followed by HCMV infection. Analysis of the steady-state levels of RNA expressed from this hybrid gene indicated that it accumulated with the same kinetics as the authentic viral transcript early in the infection. Cotransfection of human fibroblasts with the 2.7-kilobase RNA promoter-CAT construct and plasmids containing different HCMV immediate-early (IE) genes showed that the region of the HCMV genome encoding the transcription units corresponding to IE1 and 2 and the 5' end of IE3 is capable of stimulating promoter activity but not to the same extent as HCMV infection. To define important cis-acting regulatory elements in the promoter, a series of 5' deletion mutants was constructed. Transient expression analysis showed a stepwise reduction in inducible CAT activity, suggesting the presence of multiple regulatory sites. To further characterize the nature of these sites, we used gel mobility shift assays to study DNA-protein interactions occurring within this promoter sequence. With nuclear extracts prepared from HeLa cells as well as from infected and uninfected human foreskin fibroblasts, we found specific binding of a cellular factor to a region of the promoter important in HCMV inducible activity. This region contains a palindromic octamer with homology to the binding site of the cellular factor USF/MLTF.
Interleukin-1β and Interleukin-6 in Arthritis Animal Models: Roles in the Early Phase of Transition from Acute to Chronic Inflammation and Relevance for Human Rheumatoid Arthritis (2010)

Tumor necrosis factor-α (TNF-α) is the major target of the therapeutic approach in rheumatoid arthritis. A key issue in the approach to chronic arthritis is the understanding of the crucial molecules driving the transition from the acute phase to the chronic irreversible phase of the disease. In this review we analyzed five experimental arthritis animal models (antigen-induced arthritis, adjuvant-induced arthritis, streptococcal cell wall arthritis, collagen-induced arthritis and SKG) considered as possible scenarios to facilitate interpretation of the biology of human rheumatoid arthritis. The SKG model is strictly dependent on interleukin (IL)-6. In the other models, IL-1β and IL-6, more than TNF-α, appear to be relevant in driving the transition, which suggests that these should be the targets of an early intervention to stop the course toward the chronic form of the disease.
Significance of Suppressor Macrophages for Immunosurveillance of Tumor-Bearing Mice<xref ref-type="fn" rid="FN2">2</xref> (1987)

The in vivo significance of suppressor macrophages for antitumor immunity was investigated in a syngeneic tumor system. The presence of suppressor macrophages in the spleens of X5563 C3H/HeN tumor-bearing mice (TBM) was directly shown in vitro. Thus the addition of splenic macrophages of TBM suppressed the in vitro secondary induction of both tumor-specific cytotoxic T-cells and effector cells of the delayed-type hypersensitivity reaction. Splenic macrophages of TBM exerted suppression on tumor-specific T-cell-mediated cytotoxicity in the effector phase as well. Prostaglandin production was found to be one of the major mechanisms involved in macrophage-induced suppression. In vivo treatment of TBM with carrageenan and/or indomethacin retarded tumor growth and in parallel augmented cell-mediated cytotoxicity against X5563 cells, probably by affecting suppressor macrophages in vivo. The suppressive effect of splenic macrophages from TBM was clearly demonstrated in a tumor-neutralization test indicating that suppressor macrophages were able to exert their function in vivo as well as in vitro. All these results suggested that suppressor macrophages had in vivo significance for the suppression of the immunosurveillance of the hosts.
Offensive Tastes and Odors Occurring after Chlorine Addition in Water Treatment Processes (1988)

To identify and eliminate the causes of tastes and odors in drinking water,we have developed a new robot-assisted methodology for absolute threshold flavor determination called “up and down”. A study undertaken at an important biological treatment plant in the suburb of Paris (France) over a period of one year, allowed us to compare results from physico-chemical analyses with those of up and down threshold (UDT) values.This work also demonstrated the very important influence of chlorination on water quality.Furthermore, a number of physico-chemical parameters like POX-TOX and THM were shown to be unsuitable for the prediction of UDT values, but chromatographic finger printing after CLSA extraction and ECD detection showed a possible relationship with UDT.In addition, processes involving dechlorination, stripping and ozonation have been developed to remove chlorine-like odors from treated water supplies.
Distribution of transforming growth factor‐β isoforms in the mammalian retina (1995)

The distribution of transforming growth factor-beta (TGF-beta) was examined in the posterior segment of the monkey, human, and feline eye using antisera to TGF-beta 1, TGF-beta 2, or TGF-beta 3. A number of different antibodies, tissue processing methods, immunolocalization techniques, and microscopic imaging systems were used in an attempt to gain a more comprehensive picture of TGF-beta isoform distribution in the retina and retinal pigmented epithelium (RPE). The results are generally consistent in identifying one or more of the three TGF-beta isoforms in the cytoplasm of a small, overlapping subset of cells. RPE cells, photoreceptors, Mueller cells, ganglion cells, hyalocytes, and cells associated with choroidal and retinal vessels are all represented in this immunoreactive population. No evidence of extracellular labeling was noted. The intracellular distribution of the three isoforms is distinctly different in photoreceptors. Anti-TGF-beta 1 precursor and anti-TGF-beta 2 immunoreactivity is confined primarily to rod outer segments, whereas anti-TGF-beta 3 immunoreactivities are restricted to mitochondria within inner segments. In the RPE, clusters of anti-TGF-beta 2 positive cytoplasmic granules are located near the cells' lateral borders, whereas anti-TGF-beta 3 labeling is concentrated apically. These results provide baseline information from which new hypotheses regarding the function(s) of TGF-beta isoforms in the retina can be formulated.
A Cyclic Peptide Inhibitor of HIF-1 Heterodimerization That Inhibits Hypoxia Signaling in Cancer Cells (2013)

Hypoxia inducible factor-1 (HIF-1) is a heterodimeric transcription factor that acts as the master regulator of cellular response to reduced oxygen levels, thus playing a key role in the adaptation, survival, and progression of tumors. Here we report cyclo-CLLFVY, identified from a library of 3.2 million cyclic hexapeptides using a genetically encoded high-throughput screening platform, as an inhibitor of the HIF-1α/HIF-1β protein-protein interaction in vitro and in cells. The identified compound inhibits HIF-1 dimerization and transcription activity by binding to the PAS-B domain of HIF-1α, reducing HIF-1-mediated hypoxia response signaling in a variety of cell lines, without affecting the function of the closely related HIF-2 isoform. The reported cyclic peptide demonstrates the utility of our high-throughput screening platform for the identification of protein-protein interaction inhibitors, and forms the starting point for the development of HIF-1 targeted cancer therapeutics.
Use of recombinant antigens of Borrelia burgdorferi in serologic tests for diagnosis of lyme borreliosis (1996)

Recombinant antigens of outer surface proteins (Osps) OspA, OspB, OspC, OspE, and OspF of Borrelia burgdorferi sensu stricto and of p41-G, an antigenic region of flagellin of this spirochete, were tested with human sera in class-specific and polyvalent enzyme-linked immunosorbent assays (ELISAs). In analyses for immunoglobulin M (IgM) antibodies, 18 (85.7%) of 21 serum samples from persons who had been diagnosed as having Lyme borreliosis on the basis of the presence of erythema migrans reacted positively in ELISAs with one or more Osp antigens or the p41-G antigen. Eleven serum samples contained antibodies to OspC antigen, and of these, six also reacted to the p41-G antigen and to one or more of the other recombinant antigens. The remaining five serum samples reacted solely to OspC (n = 4) or to OspC plus OspA and OspE without reactivity to p41-G (n = 1). In analyses for IgG antibodies, seropositivity was comparable to that of IgM analyses and was marked by predominant reactivity to p41-G, OspC, and OspF. Similarly, all 21 serum samples were positive in polyvalent and class-specific ELISAs with whole-cell B. burgdorferi. Minor cross-reactivity was noted when sera from persons who had syphilis, periodontitis or other oral infections, or rheumatoid arthritis were tested with OspC, OspE, OspF, and p41-G. With relatively high degrees of specificity, ELISAs with recombinant antigens, particularly OspC and p41-G, can help to confirm B. burgdorferi infections.