gebhart/patrepeval huggingface dataset:
Treatment of lupus‐prone mice with a dual inhibitor of TLR7 and TLR9 leads to reduction of autoantibody production and amelioration of disease symptoms (2007)

The presence of autoantibodies specific for nucleic acid-associated antigens is the hallmark of systemic lupus erythematosus (SLE). We have recently developed a specific inhibitor of TLR7 and TLR9, called immunoregulatory sequence (IRS) 954, and showed that it inhibits the induction of IFN-alpha by human plasmacytoid dendritic cells in response to DNA and RNA viruses and isolated immune complexes from lupus patients. In this study, we show that IRS 954 can prevent progression of disease when injected in the lupus prone (NZBxNZW)F1 mice. Following treatment, we observed a significant reduction of serum levels of nucleic acid-specific autoantibodies as well as decreased proteinuria, reduced glomerulonephritis, end-organ damage and increased survival. These data demonstrate that in addition to its ability to block IFN-alpha, IRS 954 can reduce symptoms in a lupus model and thus represents a promising therapeutic agent for the treatment of SLE.
Synthesis of 9H-Pyrrolo[1,2-a]-1,4-diazaindol-9-one (1984)

The synthesis o f 9H-pyrrolo [l,Z-a7J-1,
Photoconductive gain greater than unity in CdSe films with Schottky barriers at the contacts (1973)

Photoconductive gains greater than unity can be obtained by illuminating a homogeneous photoconductor having blocking contacts with band gap radiation. A model is presented, which conceives such a possibility. Au contacts to CdSe form a Schottky barrier at the interface. Upon illumination the photogenerated holes are trapped in the Schottky barrier, shrinking the barrier and allowing injection of electrons in the CdSe. This gives rise to the possibility of gain greater than unity. Experimental evidence supporting the model is presented. Photoconductive gains as large as 300 have been measured when these films were illuminated with a photon flux of 2×1015 photons/cm2/sec.
[Molecular characteristics of methicillin resistant Staphylococcus aureus isolated from Chinese children]. (2012)

The results indicate that MRSA isolates from Chinese children are largely associated with the ST59-MRSA-IV(t437) and ST239-MRSA-III(t037) clones. These two may belong to community-acquired MRSA and hospital-acquired ones, respectively. Different prevalent clones were detected in different diseases and different regions. Therefore, there is a need to conduct further research on clinical isolates, which can guide the choice of antibiotic treatment and the examination of MRSA prevalence.
Neuromorphic Photonic Integrated Circuits (2018)

This paper reviews some recent progress in the field of neuromorphic photonics, with a particular focus on scalability. We provide a framework for understanding the underlying models, and demonstrate a neuron-like processing device—an excitable laser—that has many favorable properties for integration with emerging photonic integrated circuit platforms. On a systems level, we compare several proposed interconnection frameworks that allow for fully tunable networks of photonic neurons.
Modeling Kinect Sensor Noise for Improved 3D Reconstruction and Tracking (2012)

We contribute an empirically derived noise model for the Kinect sensor. We systematically measure both lateral and axial noise distributions, as a function of both distance and angle of the Kinect to an observed surface. The derived noise model can be used to filter Kinect depth maps for a variety of applications. Our second contribution applies our derived noise model to the KinectFusion system to extend filtering, volumetric fusion, and pose estimation within the pipeline. Qualitative results show our method allows reconstruction of finer details and the ability to reconstruct smaller objects and thinner surfaces. Quantitative results also show our method improves pose estimation accuracy.
Influence of Frozen-Section Analysis of Sentinel Lymph Node and Lumpectomy Margin Status on Reoperation Rates in Patients Undergoing Breast-Conservation Therapy (2007)

Among patients having BCT with SLN biopsy, FS identified the positive SLN in 56% of patients with positive SLNs, allowing immediate ALND, and was false negative in 44%. Margin status remains a frequent indication for reoperation in BCT; routine FS analysis of the SLN ultimately saves only a minority of patients a second operation.
In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5 (2006)

Two types of short double-stranded RNA molecules, namely microRNAs (miRNAs) and short interfering RNAs (siRNAs), have emerged recently as important regulators of gene expression. Although these molecules show similar sizes and structural features, the mechanisms of action underlying their respective target silencing activities appear to differ: siRNAs act primarily through mRNA degradation, whereas most miRNAs appear to act primarily through translational inhibition. Our understanding of how these overlapping pathways are differentially regulated within the cell remains incomplete. In the present work, quantitative fluorescence microscopy was used to study how siRNAs are processed within human cells. We found that siRNAs are excluded from non-nucleolar areas of the nucleus in an Exportin-5 dependent process that specifically recognizes key structural features shared by these and other small RNAs such as miRNAs. We further established that the Exportin-5-based exclusion of siRNAs from the nucleus can, when Exp5 itself is inhibited, become a rate-limiting step for siRNA-induced silencing activity. Exportin 5 therefore represents a key point of intersection between the siRNA and miRNA pathways, and, as such, is of fundamental importance for the design and interpretation of RNA interference experimentation.
IL-12-induced reversal of human Th2 cells is accompanied by full restoration of IL-12 responsiveness and loss of GATA-3 expression (2001)

IL-12 is a potent inducer of IFN-gamma production and drives the development of Th1 cells. Human polarized Th2 cells do not express the signaling beta2-subunit of the IL-12R and, therefore, do not signal in response to IL-12. The question was raised as to what extent the loss of the IL-12Rbeta2 chain in Th2 cells has bearing on the stability of the human Th2 phenotype. In the present report, we show that restimulation of human fully polarized Th2 cells in the presence of IL-12 primes for a shift towards Th0/Th1 phenotypes, accompanied by suppression of GATA-3 expression and induction of T-bet expression. These reversed cells are further characterized by a marked IL-12Rbeta2 chain expression and fully restored IL-12-inducible STAT4 activation. The IL-12-induced phenotypic shift proved to be stable as a subsequent restimulation in the presence of IL-4 and in the absence of IL-12 could not undo the accomplished changes. Identical results were obtained with cells from atopic patients, both with polyclonal Th2 cell lines and allergen-specific Th2 cell clones. These findings suggest the possibility of restoring IL-12 responsiveness in established Th2 cells of atopic patients by stimulation in the presence of IL-12, and that IL-12-promoting immunotherapy can be beneficial for Th2-mediated immune disorders, targeting both naive and memory effector T cells.
Identification of the Hemogenic Endothelial Progenitor and Its Direct Precursor in Human Pluripotent Stem Cell Differentiation Cultures (2012)

Hemogenic endothelium (HE) has been recognized as a source of hematopoietic stem cells (HSCs) in the embryo. Access to human HE progenitors (HEPs) is essential for enabling the investigation of the molecular determinants of HSC specification. Here, we show that HEPs capable of generating definitive hematopoietic cells can be obtained from human pluripotent stem cells (hPSCs) and identified precisely by a VE-cadherin(+)CD73(-)CD235a/CD43(-) phenotype. This phenotype discriminates true HEPs from VE-cadherin(+)CD73(+) non-HEPs and VE-cadherin(+)CD235a(+)CD41a(-) early hematopoietic cells with endothelial and FGF2-dependent hematopoietic colony-forming potential. We found that HEPs arise at the post-primitive-streak stage of differentiation directly from VE-cadherin-negative KDR(bright)APLNR(+)PDGFRα(low/-) hematovascular mesodermal precursors (HVMPs). In contrast, hemangioblasts, which are capable of forming endothelium and primitive blood cells, originate from more immature APLNR(+)PDGFRα(+) mesoderm. The demarcation of HEPs and HVMPs provides a platform for modeling blood development from endothelium with a goal of facilitating the generation of HSCs from hPSCs.
Evidence for CGRP accumulation and activity in experimental neuromas (1995)

Calcitonin gene-related peptide (CGRP) is a potent vasodilator and widely distributed neuropeptide that may participate in the injury response of peripheral nerve. We examined evidence for the presence of CGRP immunoreactivity (IR) and its activity in experimental neuromas of Sprague-Dawley rats created by sectioning the midsciatic nerve with resection of 2-3 cm of its distal portion and branches. CGRP activity was evaluated by measuring local blood flow in neuromas using hydrogen polarography and laser-Doppler flowmetry. At all time points studied after nerve section (24 h, 48 h, 7 days, 14 days) there was a rise in local blood flow in the neuroma stumps. At 48 h the hyperemia was maximum but was reversed by topical application of human CGRP(8--37), a specific CGRP-receptor antagonist. CGRP presence was evaluated by immunohistochemistry and radioimmunoassay (RIA). At 24 and 48 h, CGRP IR was intense and distributed in a globular and diffuse pattern apparently not confined to discrete axonlike profiles. At 7 and 14 days, CGRP IR remained prominent and was associated with disorganized axonlike profiles, sometimes directed in a circumferential pattern around the outside of the neuroma. RIA confirmed rises in CGRP content at 24 and 48 h that accompanied the changes in local blood flow and altered distribution of CGRP IR. CGRP accumulates in a time-related fashion within experimental neuromas, where it induces among other possible actions prominent local vasodilatation. CGRP may be important in the regenerative milieu of injured nerves.
Ligand-Directed Acyl Imidazole Chemistry for Labeling of Membrane-Bound Proteins on Live Cells (2012)

Chemistry-based protein labeling in living cells is undoubtedly useful for understanding natural protein functions and for biological/pharmaceutical applications. Here, we report a novel approach for endogenous membrane-bound protein labeling for both in vitro and live cell conditions. A moderately reactive alkyloxyacyl imidazole (AI) assisted by ligand-binding affinity (ligand-directed AI (LDAI)) chemistry allowed us to selectively modify natural proteins, such as dihydrofolate reductase (DHFR) and folate receptor (FR), neither of which could be efficiently labeled using the recently developed ligand-directed tosylate approach. It was clear that LDAI selectively labeled a single Lys(K32) in DHFR, proximal to the ligand-binding pocket. We also demonstrate that the fluorescein-labeled (endogenous, by LDAI) FR works as a fluorescent biosensor on the live KB cell surface, which allowed us to carry out unprecedented in situ kinetic analysis of ligand binding to FR.
Cartilage proteoglycans: Structure and potential functions (1994)

Hyaline cartilage contains five well-characterized proteoglycans in its extracellular matrix, and it is likely that others exist. The largest in size and most abundant by weight is aggrecan, a proteoglycan that possesses over 100 chondroitin sulfate and keratan sulfate chains. Aggrecan is also characterized by its ability to interact with hyaluronic acid to form large proteoglycan aggregates. Both the high anionic charge on the individual aggrecan molecules endowed by the sulfated glycosaminoglycan chains and the localization within the matrix endowed by aggregate formation are essential for aggrecan function. The molecule provides cartilage with its osmotic properties, which give articular cartilage its ability to resist compressive loads. The other proteoglycans are characterized by their ability to interact with collagen. They are much smaller than aggrecan in size but may be present in similar molar amounts. Decorin, biglycan, and fibromodulin are closely related in protein structure but differ in glycosaminoglycan composition and function. Decorin and biglycan possess one and two dermatan sulfate chains, respectively, whereas fibromodulin bears several keratan sulfate chains. Decorin and fibromodulin both interact with the type II collagen fibrils in the matrix and may play a role in fibrillogenesis and interfibril interactions. Biglycan is preferentially localized in the pericellular matrix, where it may interact with type VI collagen. Finally, type IX collagen can also be considered as a proteoglycan, as its alpha 2(IX) chain may bear a glycosaminoglycan chain. It may serve as a bridge between the collagen fibrils or with the interspersed aggrecan network.
Single-chain Variable Fragment Albumin Fusions Bind the Neonatal Fc Receptor (FcRn) in a Species-dependent Manner (2013)

Albumin has a serum half-life of 3 weeks in humans. This has been utilized to extend the serum persistence of biopharmaceuticals that are fused to albumin. In light of the fact that the neonatal Fc receptor (FcRn) is a key regulator of albumin homeostasis, it is crucial to address how fusion of therapeutics to albumin impacts binding to FcRn. Here, we report on a detailed molecular investigation on how genetic fusion of a short peptide or an single-chain variable fragment (scFv) fragment to human serum albumin (HSA) influences pH-dependent binding to FcRn from mouse, rat, monkey, and human. We have found that fusion to the N- or C-terminal end of HSA only slightly reduces receptor binding, where the most noticeable effect is seen after fusion to the C-terminal end. Furthermore, in contrast to the observed strong binding to human and monkey FcRn, HSA and all HSA fusions bound very poorly to mouse and rat versions of the receptor. Thus, we demonstrate that conventional rodents are limited as preclinical models for analysis of serum half-life of HSA-based biopharmaceuticals. This finding is explained by cross-species differences mainly found within domain III (DIII) of albumin. Our data demonstrate that although fusion, particularly to the C-terminal end, may slightly reduce the affinity for FcRn, HSA is versatile as a carrier of biopharmaceuticals.
Regulation of the Procoagulant Activity within the Bronchoalveolar Compartment of Normal Human Lung (1988)

The nature of the procoagulant activity of normal bronchoalveolar fluid was examined both qualitatively and quantitatively. Unconcentrated, cell-free lavage freshly obtained from normal volunteers clotted normal plasma in a mean of 84 +/- 20 s. The procoagulant activity was initiated by Factor VII-tissue factor complexes as judged by differential activity in various plasmas genetically deficient in single clotting factors, by neutralization of the procoagulant activity with antibodies to either Factor VII or tissue factor, and by a Factor X activation assay. Preincubation of the lavage with calcium was required to demonstrate Factor VII activity in unconcentrated samples. The cell-free fluid contained about 8,500 thromboplastin units/mg protein, equivalent to a third of the thromboplastin standard and indicating high amounts of cofactor. Quantitation of Factor VII was estimated by functional analysis in coagulation and amidolytic assays with reference to dilutions of normal plasma of known Factor VII concentration. When lavage and diluted plasma were adjusted to yield equivalent amidolytic activities, the average ratio of the Factor VII-clotting activity of the alveolar fluid relative to plasma Factor VII was 19 +/- 7, suggesting the presence of Factor VIIa in lavage. In contrast to previous reports with serum or activated plasma, immunoblots of concentrated lavage revealed only single-chain Factor VII, and 125I-Factor VII added to the fluid was not converted to 125I-Factor VIIa, suggesting a unique control mechanism in the lung compartment which differs from plasma. When equivalent Factor VII amidolytic activities in diluted plasma and cell-free lavage were compared, the rates of Factor Xa formation were very similar.(ABSTRACT TRUNCATED AT 250 WORDS)
Exploring web protocols for use on cellular networks : QUIC on poor network links (2018)

New developments in web transport such as HTTP/2 and first and foremost QUIC promise fewer connections to track as well as shorter connection setup times. These protocols have proven themselves on modern reliable connections with a high bandwidth-delay-product, but how do they perform over cellular connections in rural or crowded areas where the connections are much more unreliable? A lot of new users of the web in todays mobile-first usage scenarios are located on poor connections. A testbench was designed that allowed for web browsing over limited network links in a con- trolled environment. We have compared the network load time of page loading over the protocols QUIC, HTTP/2 and HTTP/1.1 using a variety of different network conditions. We then used these measurements as a basis for suggesting which protocol to use during different conditions. The results show that newer is not always better. QUIC in general works reasonably well under all conditions, while HTTP/1.1 and HTTP/2 trade blows depending on connection conditions, with HTTP/1.1 sometimes outperforming both of the newer protocols.
LNA/DNA mixmer-based antisense oligonucleotides correct alternative splicing of the SMN2 gene and restore SMN protein expression in type 1 SMA fibroblasts (2017)

Spinal muscular atrophy (SMA) is an autosomal recessive disorder affecting motor neurons, and is currently the most frequent genetic cause of infant mortality. SMA is caused by a loss-of-function mutation in the survival motor neuron 1 (SMN1) gene. SMN2 is an SMN1 paralogue, but cannot compensate for the loss of SMN1 since exon 7 in SMN2 mRNA is excluded (spliced out) due to a single C-to-T nucleotide transition in the exon 7. One of the most promising strategies to treat SMA is antisense oligonucleotide (AON)-mediated therapy. AONs are utilized to block intronic splicing silencer number 1 (ISS-N1) on intron 7 of SMN2, which causes exon 7 inclusion of the mRNA and the recovery of the expression of functional SMN protein from the endogenous SMN2 gene. We developed novel locked nucleic acid (LNA)-based antisense oligonucleotides (LNA/DNA mixmers), which efficiently induce exon 7 inclusion in SMN2 and restore the SMN protein production in SMA patient fibroblasts. The mixmers are highly specific to the targeted sequence, and showed significantly higher efficacy than an all-LNA oligonucleotide with the equivalent sequence. These data suggest that use of LNA/DNA mixmer-based AONs may be an attractive therapeutic strategy to treat SMA.
Antigenic implications of human immunodeficiency virus type 1 envelope quaternary structure: oligomer-specific and -sensitive monoclonal antibodies. (1994)

A majority of monoclonal antibodies (mAbs) raised against soluble oligomeric human immunodeficiency virus type 1 isolate IIIB (HIV-1IIIB) envelope (env) glycoprotein reacted with conformational epitopes within the gp120 or gp41 subunits. Of 35 mAbs directed against gp41, 21 preferentially reacted with oligomeric env. A subset of these mAbs reacted only with env oligomers (oligomer-specific mAbs). In contrast, only 1 of 27 mAbs directed against the gp120 subunit reacted more strongly with env oligomers than with monomers, and none were oligomer-specific. However, 50% of anti-gp120 mAbs preferentially recognized monomeric env, suggesting that some epitopes in gp120 are partially masked or altered by intersubunit contacts in the native env oligomer. Two mAbs to oligomer-dependent epitopes in gp41 neutralized HIV-1IIIB and HIV-1SF2, and binding of these mAbs to env was blocked by preincubation with HIV-1-positive human serum. Thus, immunization with soluble, oligomeric env elicits antibodies to conserved, conformational epitopes including a newly defined class of neutralizing antibodies that bind to oligomer-specific epitopes in gp41, and may also minimize the production of antibodies that preferentially react with monomeric env protein.
Yeast ABC transporters – A tale of sex, stress, drugs and aging (2005)

Yeast ATP-binding cassette (ABC) proteins are implicated in many biological phenomena, often acting at crossroads of vital cellular processes. Their functions encompass peptide pheromone secretion, regulation of mitochondrial function, vacuolar detoxification, as well as pleiotropic drug resistance and stress adaptation. Because yeast harbors several homologues of mammalian ABC proteins with medical importance, understanding their molecular mechanisms, substrate interaction and three-dimensional structure of yeast ABC proteins might help identifying new approaches aimed at combating drug resistance or other ABC-mediated diseases. This review provides a comprehensive discussion on the functions of the ABC protein family in the yeast Saccharomyces cerevisiae.
Effect of nitric oxide and nitric oxide donors on red blood cell oxygen transport (2000)

A mechanism has been proposed in which nitric oxide (NO) may bind to cysteine beta93 and be transported by haemoglobin from the lungs to the tissues and modify vascular tone. In addition, it has been reported that treatment of sickle cell anaemia blood with 80 p.p.m. NO gas in air shifts the oxygen affinity, as measured by P50 to the left. We exposed normal and sickle cell anaemia blood to 80 p.p.m. NO in air for 1 h in vitro and found no change in P50 of either normal or sickle cell blood. In addition, we exposed normal and sickle cell blood in buffer to aqueous NO (NO gas dissolved in buffer) at varying concentrations and found that the induced left shift in P50 correlates strongly and linearly with methaemoglobin formation. We also treated normal and sickle cell blood with other nitric oxide donors, such as sodium 2-(N, N-diethylamino)-diazenolate-2-oxide (DEANO), S-nitrosocysteine (CysNO) and sodium trioxodinitrate (OXINO, or Angeli's salt). In all cases, we found a dose-dependent increase in methaemoglobin that was strongly correlated with the dose-dependent P50 reduction. Our data do not support the report that low NO concentrations can selectively increase the oxygen affinity of sickle cell blood without affecting methaemoglobin levels significantly. NO, however, may have benefit in sickle cell disease by other mechanisms.
Quantitative carbon detector (QCD) for calibration-free, high-resolution characterization of complex mixtures (2014)

Current research of complex chemical systems, including biomass pyrolysis, petroleum refining, and wastewater remediation requires analysis of large analyte mixtures (>100 compounds). Quantification of each carbon-containing analyte by existing methods (flame ionization detection) requires extensive identification and calibration. In this work, we describe an integrated microreactor system called the Quantitative Carbon Detector (QCD) for use with current gas chromatography techniques for calibration-free quantitation of analyte mixtures. Combined heating, catalytic combustion, methanation and gas co-reactant mixing within a single modular reactor fully converts all analytes to methane (>99.9%) within a thermodynamic operable regime. Residence time distribution of the QCD reveals negligible loss in chromatographic resolution consistent with fine separation of complex mixtures including cellulose pyrolysis products.