gebhart/patrepeval huggingface dataset:
Single nucleotide resolution of sterol regulatory region in promoter for 3-hydroxy-3-methylglutaryl coenzyme A reductase (1991)

Sterol-dependent regulation of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase promoter was previously localized to a 42-base pair region containing an octamer sequence, referred to as the sterol regulatory element (SRE-1). A similar motif is found in the region of DNA that is required for sterol-dependent regulation of the HMG-CoA synthase and low density lipoprotein receptor genes. Single nucleotide substitution analyses of the low density lipoprotein receptor and HMG-CoA synthase promoters confirmed that the SRE-1 is an important sterol regulatory motif. In the current studies, a series of single nucleotide mutations were introduced into the HMG-CoA reductase regulatory region and transfected into Chinese hamster ovary cells. RNA produced by each mutant promoter was then measured in the presence or absence of sterols. Thirty-seven independent mutations were analyzed, and two separate domains were identified as being critical. One essential region was spread over 10 bases and contained half of the SRE-1; however, the other half of the SRE-1 was not important for sterol regulation. The second essential region spanned four contiguous bases. These two critical elements are separated from each other by three nonessential bases. The results are interpreted to suggest that regulation of HMG-CoA reductase gene transcription by sterols requires additional or possibly separate factors from those required for sterol regulation of the low density lipoprotein receptor and HMG-CoA synthase promoters.
Percutaneous spinal fusion using bone morphogenetic protein-2 gene therapy (1999)

Results of this study clearly demonstrated that it is possible to produce in vivo endochondral bone formation by using direct adenoviral construct injection into the paraspinal musculature, which suggests that gene therapy may be useful for spinal fusion in the future.
Synthesis of 7-Alkoxyquinolines, Coumarins, and Resorufins (2000)

Abstract Synthesis of the title compounds by treatment of the sodium salts of 7-quinolinol, 7-hydroxycoumarin, and resorufin with alkyl halides is described.
Optical fiber gyroscopes: Sagnac or Fizeau effect? (1979)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Walter R. Leeb, Gerhard Schiffner, and Eduard Scheiterer, "Optical fiber gyroscopes: Sagnac or Fizeau effect?," Appl. Opt. 18, 1293-1295 (1979) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
An Analysis of the Antibody Response against West Nile Virus E Protein Purified by SDS-PAGE Indicates that This Protein Does Not Contain Sequential Epitopes for Efficient Induction of Neutralizing Antibodies (1989)

The large envelope (E) protein of flaviruses is the viral surface protein that contains neutralizing epitopes. We have analysed the E protein of the West Nile (WN) flavivirus for neutralizing epitopes generated from linear segments of the protein; if effective, these might allow the synthesis of peptides suitable for vaccination. For this study we used the E protein and defined fragments thereof as antigens in rabbits. The sera thus obtained, containing antibodies to E protein as shown by Western blot analyses, were tested for neutralizing activity by the plaque reduction neutralization test. If the E protein used as antigen was reduced (the native E protein contains six disulphide bridges) and denatured the resulting antibodies did not consistently demonstrate neutralizing activity. These results show that the E protein of WN virus does not contain a linear segment that is able to induce neutralizing antibodies efficiently. Studies using denatured E protein fragments containing subsets of the intact disulphide bridges showed that the local covalent primary structure of the protein involved in each of the six bridges was also insufficient for inducing the synthesis of neutralizing antibodies. The complete E protein, with all six disulphide bridges intact, purified by preparative SDS-PAGE under the conditions used in our experiments could, however, induce the synthesis of neutralizing antibodies in rabbits. These data indicate that at least one complex epitope which is able to induce neutralizing antibodies is not completely denatured or can be reformed to some extent if the complete E protein has been subjected to SDS-PAGE without prior destruction of the disulphide bridges.
Structural Studies of Immunoglobulins (1973)

In 1946, when I was starting work as research student under the supervision of Dr F. Sanger, the second edition of Karl Lansteiner's book” The Specificity of Serological Reactions’[I] reached England. In it was summarized the considerable body of information available on the range of antibody specificity and much of it was Landsteiner's own work or by others using his basic technique of preparing antibodies against haptenes and testing their ability to inhibit the precipitation of the antisera and t he conjugated protein. Also described in this book was the work in Uppsala of Tiselius and Pederson in collaboration with Heidelberger and Kabat in which they showed that all rabbit antibodies were in the y globulin fraction of serum proteins and that they had a molecular weight of 150.000. This combination of an apparently infinite range of antibody-combining specificity associated with what appeared to be a nearly homogeneous group of proteins astonished me and indeed still does.
CD44+/CD24-breast cancer cells exhibit enhanced invasive properties: an early step necessary for metastasis (2006)

Breast cancer cells with CD44+/CD24- subpopulation express higher levels of proinvasive genes and have highly invasive properties. However, this phenotype is not sufficient to predict capacity for pulmonary metastasis.
Circular RNAs throw genetics for a loop (2013)

RNA ‘sponges’ mop up sequences that curb gene expression.
Supporting real-time applications in an Integrated Services Packet Network (1992)

This paper considers the support of real-time applications in an Integrated Services Packet Network (ISPN). We first review the characteristics of real-time applications. We observe that, contrary to the popular view that real-time applications necessarily require a fixed delay bound, some real-time applications are more flexible and can adapt to current network conditions. We then propose an ISPN architecture that supports two distinct kinds of real-time service: guaranteed service, which is the traditional form of real-time service discussed in most of the literature and involves pre-computed worst-case delay bounds, and predicted service which uses the measure performance of the network in computing delay bounds. We then propose a packet scheduling mechanism that can support both of these real-time services as well as accommodate datagram traffic. We also discuss two other aspects of an overall ISPN architecture: the service interface and the admission control criteria.
Functional properties of leptin receptor isoforms: internalization and degradation of leptin and ligand-induced receptor downregulation. (1999)

Long (ObRb) and short (ObRa) leptin receptor isoforms are thought to play essential roles in mediating leptin signaling and the transport and degradation of leptin, respectively. Although the capacity of these cloned receptor species to mediate signal transduction has been reported, there is no information on the ability of individual receptor species to mediate leptin internalization and degradation or to undergo ligand-induced downregulation. We therefore studied these parameters in Chinese hamster ovary (CHO) cells stably expressing either ObRa or ObRb isoforms of the leptin receptor. We determined that both ObRa and ObRb mediated internalization of 125I-labeled leptin by a temperature- and coated pit-dependent mechanism. Both ObRa and ObRb also mediated degradation of 125I-leptin by a lysosomal mechanism, and this was more efficiently mediated by ObRa in these cells. Neither leptin internalization nor degradation by ObRa was affected by mutation of the conserved Box 1 motif. By studying deletion mutants of ObRa, we found that efficient internalization was dependent on a motif located between amino acids 8 and 29 of the intracellular domain of ObRa. Exposure of cells expressing ObRa or ObRb to unlabeled leptin for 90 min at 37 degrees C produced downregulation of available surface receptors, and this effect was of greater magnitude in cells expressing ObRb. Whereas CHO cells expressing the growth hormone receptor showed marked downregulation of ligand binding after exposure to dexamethasone (DEX) or phorbol myristic acid (PMA), PMA had no effect on expression of ObRa or ObRb, and DEX reduced binding to cells expressing ObRb by 15%. Thus, the two leptin receptor isoforms, ObRa and ObRb, mediate leptin internalization by a coated pit-dependent mechanism, leptin degradation by a lysosomal pathway, and ligand-induced receptor downregulation. The differential capacity of the two receptor isoforms may relate to the different roles of the receptor isoforms in the biology of leptin.
Human apolipoprotein C-II: complete nucleic acid sequence of preapolipoprotein C-II. (1984)

Apolipoprotein (apo) C-II is a cofactor for lipoprotein lipase, the enzyme that catalyzes the hydrolysis of triglycerides on plasma triglyceride-rich lipoproteins. The complete coding sequence of apoC-II mRNA has been determined from an apoC-II clone isolated from a human liver cDNA library. A 17-base-long synthetic oligonucleotide based on amino acid residues 5-10 of apoC-II was utilized as a hybridization probe to select recombinant plasmids containing the apoC-II sequence. Two thousand four hundred clones were screened and one apoC-II cDNA clone containing 500 bases was identified. DNA sequence analysis of this clone revealed a 101 amino acid C-II apolipoprotein containing a 22 amino acid signal peptide attached to the amino terminus of the 79 amino acid residue plasma apoC-II. The amino acid sequence of apoC-II determined by nucleic acid analysis is in agreement with the recently determined sequence of plasma apoC-II isolated from normal subjects. The determination of the complete cDNA sequence of apoC-II and the availability of a cDNA probe of apoC-II will facilitate our analysis of the biosynthesis and processing as well as the genomic organization of apoC-II in normal subjects and patients with dyslipoproteinemias characterized by hypertriglyceridemia.
The PredictProtein server (2004)

PredictProtein (http://www.predictprotein.org) is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments; PredictProtein returns multiple sequence alignments, PROSITE sequence motifs, low-complexity regions (SEG), nuclear localization signals, regions lacking regular structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization and functional annotations. Upon request fold recognition by prediction-based threading, CHOP domain assignments, predictions of transmembrane strands and inter-residue contacts are also available. For all services, users can submit their query either by electronic mail or interactively via the World Wide Web.
Sensory effects of capsaicin congeners I. Relationship between chemical structure and pain-producing potency of pungent agents. (1975)

A quantitative method for measuring the efficiency of pungent agents of capsaicin-type by the pain reaction elicited on the eye of rats is described. About 50 derivatives -- most of them amides or esters of homovanillic acid -- were tested by this method and the share of different chemical groups of the molecule in the pungent action was analyzed. It turned out that the presence of an acylamide linkage or alkyl chain is not essential for pungency, since acylamide linkage can be replaced by an esteric group and the alkyl chain by cycloalkyl rings. The importance of OH group on the aromatic ring is confirmed. On the basis of the findings a hypothetical pharmacological receptor for capsaicin on pain sensory nerve endings is presented.
Recent developments of Cu-Cu non-thermo compression bonding for wafer-to-wafer 3D stacking (2010)

This paper will focus on recent results of Cu-Cu non-thermo compression bonding for wafer-to-wafer 3D stacking. We report on bonding quality, wafer-to-wafer alignment accuracy and electrical connectivity. Specific pre-bonding surface conditioning is necessary to insure high bonding quality of patterned Cu wafers. A particular concern is related to the planarization (e.g. CMP) of Cu-SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> hybrid surfaces: copper dishing and erosion need to be minimized in order to obtain high bonding quality. The bonding quality is assessed by the evaluation of bonding strength, interfacial defects, wafer-to-wafer misalignment and electrical contact resistance at the Cu-Cu interface. The bonding strength evolution with post-bond annealing is reported and discussed for the case of patterned surfaces. Scanning Acoustic Microscopy (SAM) imaging of bonding interface is performed to monitor bonded defects. Process conditions have been optimized to minimize the post bond annealing (thermal budget) at temperatures below 400°C.
Isolation of receptor–ligand pairs by capture of long-lived multivalent interaction complexes (2002)

We have combined phage display and array screening for the rapid isolation of pairs of interacting polypeptides. Our strategy, named SAC (selection by avidity capture), is based on the avidity effect, the formation of highly stable complexes formed by multivalent interactions; in our case, between a receptor (multivalently displayed on phage) and a ligand (coexpressed as a multimeric fusion protein). Capture of the long-lived interaction complex allows the isolation of phage bearing cognate interaction pairs, as we demonstrate for a range of interactions, including Ab-antigen pairs and the rapamycin-dependent interaction of FKBP-12 and FRAP. Cognate phage are enriched by SAC up to 1000-fold and interacting pairs can be identified by array screening. Application of SAC to Ab-antigen interactions as a model system yielded over 140 specific Abs to a single antigen and 92 Abs to three different fetal human brain antigens in a single round of SAC each. Our results suggest that SAC should prove useful for the identification and study of receptor-ligand interactions in particular among extracellular proteins, as well as for the rapid generation of specific Abs to multiple antigens.
Gene therapy for detached retina by adeno-associated virus vector expressing glial cell line-derived neurotrophic factor. (2002)

GDNF is a potential factor that can protect photoreceptors from degeneration. In addition to preserving the OS and ONL structures, GDNF may exert its protective action by preventing the apoptosis of photoreceptors after RD. GDNF gene therapy may be a valuable adjuvant to current treatments in certain complicated forms of RD.
Involvement of tissue kallikrein but not plasma kallikrein in the development of symptoms mediated by endogenous kinins in acute pancreatitis in rats (2002)

In order to investigate the mechanism of kinin release leading to vascular symptoms in acute interstitial-oedematous pancreatitis, the novel, selective inhibitors of tissue kallikrein, (2S,2'R)-2-(2'-amino-3'-(4'-chlorophenyl)propanoylamino)-N-(3-guanidinopropyl)-3-(1-naphthyl)propanoamide (FE999024, CH-2856), and of plasma kallikrein, (2'S,2"R)-4-(2'-(2"(carboxymethylamino)-3"-cyclohexyl-propanoylamino)-3'-phenyl-propanoylamino)piperidine-1-carboxamidin (FE999026, CH-4215), were used in experimental caerulein-induced pancreatitis in rats. Oedema formation and plasma protein extravasation during the 2 h infusion of caerulein were inhibited in a dose-dependent manner by i.p. pretreatment with FE999024 (7-60 micromol kg(-1)) while FE999026 had no effect at the same doses. Haemoconcentration and hypovolaemia associated with the pancreatic oedema formation during pancreatitis were significantly attenuated by FE999024 at a dose of 20 micro mol kg(-1). The reduction in circulating plasma volume was not affected by FE999026. Accumulation of amylase and lipase in the pancreas was dose-dependently reduced by FE999024 while enzyme activities in the blood serum were increased by FE999024 at 60 micromol kg(-1) indicating improved enzyme removal from the tissue. Enzyme activities in the tissue and in the blood remained unaffected by FE999026. FE999024 (20 micromol kg(-1)) largely inhibited increased tissue kallikrein-like activity in the pancreas during acute pancreatitis and also strongly attenuated influx of plasma kallikrein into the tissue. FE999026 (20 micromol kg(-1)) significantly inhibited plasma kallikrein-like activity in the pancreas but had no effect on tissue kallikrein-like activity. In conclusion, vascular kinin-mediated symptoms observed during oedematous pancreatitis in the rat are caused by the action of tissue kallikrein in the pancreas whereas an involvement of plasma kallikrein seems to be unlikely.
In vitro and in vivo models for the study of brain tumour invasion. (1998)

Since it is difficult to study the dynamic biological aspects of brain tumour invasion using histological sections of surgical biopsy and autopsy tissues, various laboratory systems have been devised. Animal models are less than ideal as chemically-induced brain tumours suffer from the fact that they have a low incidence and a long latency, while transplanted tumours grow predominantly by expansion, due to high proliferative activity, and not by diffuse local invasion as in human brain tumours. Various in vitro assays have, therefore, been established for both migration and invasion. These include the simple scratch technique in a confluent cell monolayer, the use of cloning rings and the "Transwell" modified Boyden chamber technique. More complex, three-dimensional culture model systems have also been developed, using chick heart, optic nerve or reaggregated fetal brain as "targets" for the invasion of neoplastic glia. Each method has yielded important information on the mechanisms which underlie brain tumour invasion. Moreover, individual microenvironmental factors may be modulated in these laboratory systems to determine their influence on the migration/invasion process.
Transport Layer Security (TLS) Authorization Extensions (2010)

This document specifies authorization extensions to the Transport
Layer Security (TLS) Handshake Protocol. Extensions carried in the
client and server hello messages to confirm that both parties support
the desired authorization data types. Then, if supported by both the
client and the server, authorization information is exchanged in the
supplemental data handshake message.
Applicability of recently established reference values for serum insulin-like growth factor 1: A comparison of two assays--an (automated) chemiluminescence immunoassay and an enzyme-linked immunosorbent assay. (2005)

Analysis and interpretation of insulin-like growth factor 1 in serum (IGF-1) is a principal diagnostic and follow-up tool in growth hormone-related disorders and is becoming of interest for many other disorders. Only for the automated chemiluminescence immunoassay Nichols Advantage have age- and sex-specific reference values based on a large population and valid for different laboratories been established. The aim of the present study was to compare two different assays (the automated chemiluminescence immunoassay and the enzyme-linked immunosorbent assay DSL-10-2800) in order to prove applicability of recently published reference values. The study included 95 serum samples from 88 patients, adults as well as children, with different or no endocrine disorders, and acromegalic as well as growth hormone-deficient patients. IGF-1 measurements were performed with both methods. The results have shown a very high correlation between the IGF-1 values obtained with the two assays (r=0.971, p<0.0001). In conclusion, the reference values established for the chemiluminescence assay are applicable also for the enzyme-linked immunosorbent assay.
The IL-2 Receptor Complex: Its Structure, Function, and Target Genes (1993)

Proliferation of T lymphocytes is triggered by the interaction of IL-2 with its specific receptor following T lymphocyte activation. The receptor for IL-2 consists of at least three distinct subunits, the alpha chain (IL-2R alpha), the beta chain (IL-2R beta), and the gamma chain (IL-2R gamma). Although the role of IL-2R gamma in IL-2 signalling remains unclear, IL-2R beta is the subunit critical for receptor-mediated signalling. Because IL-2R beta lacks any apparent catalytic motifs, IL-2R beta may be physically or functionally coupled to other signalling molecules. Structure-function studies of IL-2R beta have revealed that at least two distinct cytoplasmic regions of IL-2R beta are involved in IL-2-induced cellular signalling. The "serine-rich" region of IL-2R beta was identified as a region critical for IL-2-induced mitotic signalling from experiments in which IL-2R beta mutant cDNAs lacking a particular cytoplasmic region or regions were expressed in an IL-3-dependent mouse pro-B cell line (BAF-B03). Meanwhile, another cytoplasmic region of IL-2R beta, the "acidic" region, is responsible for its physical association with an src-family protein tyrosine kinase (PTK), p56lck and is critical for activating the p56lck PTK following IL-2 stimulation. It is now evident that IL-2R beta is linked to at least two intracellular signalling pathways that mediate nuclear proto-oncogene induction. One pathway is linked to tyrosine phosphorylation events, mediated by a src-family protein tyrosine kinase (PTK), and that pathway leads to the induction of the c-fos, c-jun, and other genes of this family. Another pathway leads to c-myc gene induction by an as yet unknown mechanism. We discuss the complex signalling machinery that links the cell surface receptor to the nuclear events.
Deep filter banks for texture recognition and segmentation (2015)

Research in texture recognition often concentrates on the problem of material recognition in uncluttered conditions, an assumption rarely met by applications. In this work we conduct a first study of material and describable texture attributes recognition in clutter, using a new dataset derived from the OpenSurface texture repository. Motivated by the challenge posed by this problem, we propose a new texture descriptor, FV-CNN, obtained by Fisher Vector pooling of a Convolutional Neural Network (CNN) filter bank. FV-CNN substantially improves the state-of-the-art in texture, material and scene recognition. Our approach achieves 79.8% accuracy on Flickr material dataset and 81% accuracy on MIT indoor scenes, providing absolute gains of more than 10% over existing approaches. FV-CNN easily transfers across domains without requiring feature adaptation as for methods that build on the fully-connected layers of CNNs. Furthermore, FV-CNN can seamlessly incorporate multi-scale information and describe regions of arbitrary shapes and sizes. Our approach is particularly suited at localizing “stuff” categories and obtains state-of-the-art results on MSRC segmentation dataset, as well as promising results on recognizing materials and surface attributes in clutter on the OpenSurfaces dataset.