gebhart/patrepeval huggingface dataset:
Cellular and molecular basis of wound healing in diabetes (2007)

Diabetic foot ulcers (DFUs), a leading cause of amputations, affect 15% of people with diabetes. A series of multiple mechanisms, including decreased cell and growth factor response, lead to diminished peripheral blood flow and decreased local angiogenesis, all of which can contribute to lack of healing in persons with DFUs. In this issue of the JCI, Gallagher and colleagues demonstrate that in diabetic mice, hyperoxia enhances the mobilization of circulating endothelial progenitor cells (EPCs) from the bone marrow to the peripheral circulation (see the related article beginning on page 1249). Local injection of the chemokine stromal cell-derived factor-1 then recruits these EPCs to the cutaneous wound site, resulting in accelerated wound healing. Thus, Gallagher et al. have identified novel potential targets for therapeutic intervention in diabetic wound healing.
Strategies for Hepatic Gene Correction (2002)

Gene augmentation has been the paradigm in the majority of gene therapy protocols but in recent years the potential of repairing the mutated gene in situ by targeted gene correction has become a reality. In fact, targeted gene repair has many advantages over conventional replacement strategies, notably the possibility to treat dominant as well as recessive disorders, and the small molecular size of the pharmacologically active agent. Chimeric RNA/DNA oligonucleotides, small fragment homologous replacement, as well as triplex-forming and single-stranded oligonucleotides are all examples of the growing armamentarium for gene repair, and are the subject of this review. In addition, we have also included a discussion of the reawakened Sleeping Beauty (SB) transposon system as a novel non-viral gene replacement strategy.
Role of Large Arteries in Regulation of Cerebral Blood Flow in Dogs (1978)

Previous studies have demonstrated a significant pressure gradient from carotid artery to pial or middle cerebral arteries. This pressure gradient suggests that large cerebral arteries contribute to cerebral resistance. We have tested the hypothesis that large cerebral arteries contribute to regulation of cerebral blood flow during changes in blood gases and arterial pressure. Microspheres were used to measure brain blood flow in anesthetized dogs. Resistance of large cerebral arteries was estimated by determining the pressure gradient between common carotid and wedged vertebral artery catheters. Systemic hypercapnia and hypoxia dilated large cerebral arteries, and hypocapnia constricted large cerebral arteries. Resistance of large arteries was 0.6+/-0.1 (mean +/- SE) mm Hg per ml/min per 100 g during normocapnia. During hypercapnia and hypoxia, large artery resistance decreased significantly to 0.2 +/- 0.03 and 0.3 +/- 0.05, respectively. During hypocapnia large artery resistance increased significantly to 1.0 +/- 0.1. In other experiments, we found that large cerebral arteries participate in auto-regulatory responses to hemorrhagic hypotension. When arterial pressure was reduced from 110 to 58 mm Hg, autoregulation maintained cerebral blood flow constant, and resistance of large cerebral arteries decreased significantly from 1.0 +/- 0.2 to 0.6 +/- 0.1 mm Hg per ml/min per 100 g. In absolute terms, we calculated that 20-45% of the change in total cerebral resistance during these interventions was accounted for by changes in large artery resistance. These studies indicate that large cerebral arteries, as well as arterioles, participate actively in regulation of cerebral blood flow during changes in arterial blood gases and during autoregulatory responses to hemorrhagic hypotension.
Differences in the role of the cytoplasmic domain of human parainfluenza virus fusion proteins (1995)

We have investigated the roles of the cytoplasmic domains of the human parainfluenza virus type 2 (PI2) and type 3 (PI3) fusion (F) proteins in protein transport and cell fusion activity. By using the vaccinia virus-T7 transient expression system, a series of F protein cytoplasmic tail truncation mutants was studied with respect to intracellular and surface expression and the ability to induce cell fusion when coexpressed with the corresponding hemagglutinin-neuraminidase (HN) proteins. All of the cytoplasmic tail truncation mutants of PI2F were expressed at high levels intracellularly or on cell surfaces as measured by immunoprecipitation and cell surface biotinylation assays. In addition, when coexpressed with PI2HN, these truncation mutants of PI2F were all found to be essentially unimpaired in the ability to induce cell fusion as measured by a quantitative cell fusion assay. In contrast, surface expression and cell fusion activity were found to be eliminated by a mutant of PI3F in which the entire cytoplasmic tail was deleted, and the mutant protein appeared to be unable to assemble into a high-molecular-weight oligomeric structure. To further investigate whether there is a specific sequence requirement in the cytoplasmic tail of PI3F, a chimeric protein consisting of the PI3F extracellular and transmembrane domains and the PI2F cytoplasmic tail was constructed. This chimeric protein was detected on the surface, and it was capable of inducing cell fusion when expressed together with PI3HN, although the fusogenic activity was reduced compared with that of wild-type PI3F. These results demonstrate that although PI2 and PI3 viruses belong to the same parainfluenza virus genus, these viruses show marked differences with respect to functional requirements for the cytoplasmic tail of the F glycoprotein.
Retention of Subunits of the Oligosaccharyltransferase Complex in the Endoplasmic Reticulum (2000)

Membrane proteins of the endoplasmic reticulum (ER) may be localized to this organelle by mechanisms that involve retention, retrieval, or a combination of both. For luminal ER proteins, which contain a KDEL domain, and for type I transmembrane proteins carrying a dilysine motif, specific retrieval mechanisms have been identified. However, most ER membrane proteins do not contain easily identifiable retrieval motifs. ER localization information has been found in cytoplasmic, transmembrane, or luminal domains. In this study, we have identified ER localization domains within the three type I transmembrane proteins, ribophorin I (RI), ribophorin II (RII), and OST48. Together with DAD1, these membrane proteins form an oligomeric complex that has oligosaccharyltransferase (OST) activity. We have previously shown that ER retention information is independently contained within the transmembrane and the cytoplasmic domain of RII, and in the case of RI, a truncated form consisting of the luminal domain was retained in the ER. To determine whether other domains of RI carry additional retention information, we have generated chimeras by exchanging individual domains of the Tac antigen with the corresponding ones of RI. We demonstrate here that only the luminal domain of RI contains ER retention information. We also show that the dilysine motif in OST48 functions as an ER localization motif because OST48 in which the two lysine residues are replaced by serine (OST48ss) is no longer retained in the ER and is found instead also at the plasma membrane. OST48ss is, however, retained in the ER when coexpressed with RI, RII, or chimeras, which by themselves do not exit from the ER, indicating that they may form partial oligomeric complexes by interacting with the luminal domain of OST48. In the case of the Tac chimera containing only the luminal domain of RII, which by itself exits from the ER and is rapidly degraded, it is retained in the ER and becomes stabilized when coexpressed with OST48.
Subquarter-micron lithography with dual-trench-type alternating PSM (1996)

Lithographic characteristics of dual-trench type alternating phase-shifting mask (PSM), whose shifters are made of perpendicular trenches with different depth alternately, are evaluated numerically and experimentally. The structure of dual-trench type PSM could reduce the difference of adjacent peak intensities created by topography on the mask. Exposure characteristics of the mask varied with depth of deep and shallow trenches, and depth of both trenches should be controlled so as to have the optimum value. Mainly, the difference in depth of deep and shallow trenches caused varying "effective phase" and depth of shallow trench caused varying "effective transmission". The depth of focus using the mask was sensitive to the effective phase difference controlled by adjusting etched depth difference between both trenches, and insensitive to depth of shallow portion. From analysis of mask process margin, respecting acceptable error of depth of both trenches, it was found that the effective transmission error caused reduction of acceptable depth error.
A continuous assay for DNA cleavage: The application of “break lights” to enediynes, iron-dependent agents, and nucleases (2000)

Although extensive effort has been applied toward understanding the mechanism by which enediynes cleave DNA, a continuous assay for this phenomenon is still lacking. In fact, with the exception of assays for DNase, continuous assays for most DNA cleavage events are unavailable. This article describes the application of "molecular break lights" (a single-stranded oligonucleotide that adopts a stem-and-loop structure and carries a 5'-fluorescent moiety, a 3'-nonfluorescent quenching moiety, and an appropriate cleavage site within the stem) to develop the first continuous assay for cleavage of DNA by enediynes. Furthermore, the generality of this approach is demonstrated by using the described assay to directly compare the DNA cleavage by naturally occurring enediynes [calicheamicin and esperamicin), non-enediyne small molecule agents (bleomycin, methidiumpropyl-EDTA-Fe(II), and EDTA-Fe(II]), as well as the restriction endonuclease BamHI. Given the simplicity, speed, and sensitivity of this approach, the described methodology could easily be extended to a high throughput format and become a new method of choice in modern drug discovery to screen for novel protein-based or small molecule-derived DNA cleavage agents.
TolC – the bacterial exit duct for proteins and drugs (2003)

The TolC structure has unveiled a common mechanism for the movement of molecules, large and small, from the bacterial cell cytosol, across two membranes and the intervening periplasm, into the environment. Trimeric TolC is a remarkable cell exit duct that differs radically from other membrane proteins, comprising a 100-A long alpha-barrel that projects across the periplasmic space, anchored by a 40-A long beta-barrel spanning the outer membrane. The periplasmic entrance of TolC is closed until recruitment by substrate-specific translocases in the inner membrane triggers its transition to the open state, achieved by an iris-like 'untwisting' of the tunnel alpha-helices. TolC-dependent machineries present ubiquitous exit routes for virulence proteins and antibacterial drugs, and their conserved structure, specifically the electronegative TolC entrance constriction, may present a target for inhibitors of multidrug-resistant pathogens.
An epitope in hepatitis C virus core region recognized by cytotoxic T cells in mice and humans (1994)

Several cytotoxic T-lymphocyte (CTL) epitopes have been defined in hepatitis C virus (HCV) proteins. CTL may play an important role in the control of infection by HCV. Here, we identify a highly conserved antigenic site in the HCV core recognized by both murine and human CTL. Spleen cells from mice immunized with a recombinant vaccinia virus expressing the HCV core gene were restimulated in vitro with 11 peptides from the core protein. CTL from H-2d mice responded to a single 16-residue synthetic peptide (HCV 129-144). This conserved epitope was presented by a murine class I major histocompatibility molecule (H-2Dd) to conventional CD4- CD8+ CTL mapped by using transfectants expressing Dd, Ld, or Kd, but was not seen by CTL restricted by H-2b. The murine epitope was mapped to the decapeptide LMGYIPLVGA. The same 16-residue peptide was recognized by CTL from two HCV-seropositive patients but not by CTL from any seronegative donors. CTL from two HLA-A2-positive patients with acute and chronic hepatitides C recognized a 9-residue fragment (DLMGYIPLV) of the peptide presented by HLA-A2 and containing an HLA-A2-binding motif, extending only 1 residue beyond the murine epitope. Therefore, this conserved peptide, seen with murine CTL and human CTL with a very prevalent HLA class I molecule, may be a valuable component of an HCV vaccine against a broad range of HCV isolates. This study demonstrates that the screening for CTL epitopes in mice prior to human study may be useful.
Novel routing schemes for IC layout part I (1991)

Article Free Access Share on Novel routing schemes for IC layout part I: Two-layer channel routing Author: Deborah C. Wang Department of Electrical Engineering and Computer Science, Electronics Research Laboratory, University of California, Berkeley, CA Department of Electrical Engineering and Computer Science, Electronics Research Laboratory, University of California, Berkeley, CAView Profile Authors Info & Claims DAC '91: Proceedings of the 28th ACM/IEEE Design Automation ConferenceJune 1991 Pages 49–53https://doi.org/10.1145/127601.127626Published:01 June 1991Publication History 20citation1,019DownloadsMetricsTotal Citations20Total Downloads1,019Last 12 Months24Last 6 weeks8 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Growth hormone‐albumin conjugates Reduced renal toxicity and altered plasma clearance (1988)

The effective therapeutic use of many small peptides such as growth hormone has been limited by their small molecular masses and rapid clearance by the kidneys. Moreover, various degrees of nephrotoxicity have been reported for small proteins which are readily filtered at the level of the glomerulus. We have attempted to circumvent this drawback by conjugating growth hormone (somatotropin) to serum albumin in an effort to alter the peptide's pharmacokinetics while retaining its biological activity.
Is there a best hyperspectral detection algorithm? (2009)

A large number of hyperspectral detection algorithms have been developed and used over the last two decades. Some algorithms are based on highly sophisticated mathematical models and methods; others are derived using intuition and simple geometrical concepts. The purpose of this paper is threefold. First, we discuss the key issues involved in the design and evaluation of detection algorithms for hyperspectral imaging data. Second, we present a critical review of existing detection algorithms for practical hyperspectral imaging applications. Finally, we argue that the "apparent" superiority of sophisticated algorithms with simulated data or in laboratory conditions, does not necessarily translate to superiority in real-world applications.
Synthesis of cis- and trans-4-mercapto-L-proline derivatives (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of cis- and trans-4-mercapto-L-proline derivativesAnthony J. Verbiscar and Bernhard WitkopCite this: J. Org. Chem. 1970, 35, 6, 1924–1927Publication Date (Print):June 1, 1970Publication History Published online1 May 2002Published inissue 1 June 1970https://pubs.acs.org/doi/10.1021/jo00831a045https://doi.org/10.1021/jo00831a045research-articleACS PublicationsRequest reuse permissionsArticle Views287Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Processing of Natural Sounds in Human Auditory Cortex: Tonotopy, Spectral Tuning, and Relation to Voice Sensitivity (2012)

Auditory cortical processing of complex meaningful sounds entails the transformation of sensory (tonotopic) representations of incoming acoustic waveforms into higher-level sound representations (e.g., their category). However, the precise neural mechanisms enabling such transformations remain largely unknown. In the present study, we use functional magnetic resonance imaging (fMRI) and natural sounds stimulation to examine these two levels of sound representation (and their relation) in the human auditory cortex. In a first experiment, we derive cortical maps of frequency preference (tonotopy) and selectivity (tuning width) by mathematical modeling of fMRI responses to natural sounds. The tuning width maps highlight a region of narrow tuning that follows the main axis of Heschl's gyrus and is flanked by regions of broader tuning. The narrowly tuned portion on Heschl's gyrus contains two mirror-symmetric frequency gradients, presumably defining two distinct primary auditory areas. In addition, our analysis indicates that spectral preference and selectivity (and their topographical organization) extend well beyond the primary regions and also cover higher-order and category-selective auditory regions. In particular, regions with preferential responses to human voice and speech occupy the low-frequency portions of the tonotopic map. We confirm this observation in a second experiment, where we find that speech/voice selective regions exhibit a response bias toward the low frequencies characteristic of human voice and speech, even when responding to simple tones. We propose that this frequency bias reflects the selective amplification of relevant and category-characteristic spectral bands, a useful processing step for transforming a sensory (tonotopic) sound image into higher level neural representations.
Correlation of Increased Vascular Endothelial Growth Factor With Neovascularization and Permeability in Ischemic Central Vein Occlusion (2002)

The close temporal correlation between aqueous VEGF levels and the course of neovascularization and permeability in human ischemic central retinal vein occlusion indicates that increased aqueous VEGF level may predict the need for treatment, and that anti-VEGF therapy at an early stage of ischemic central retinal vein occlusion may be therapeutically beneficial.
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium (2009)

A comparison of a series of 027 isolates showed that some of these genes appeared to have been gained by 027 strains over the past two decades. This study provides genetic markers for the identification of 027 strains and offers a unique opportunity to explain the recent emergence of a hypervirulent bacterium.
TGF-β1, TGF-β2, and TGF-β3 Exhibit Distinct Patterns of Expression During Cranial Suture Formation and Obliteration In Vivo and In Vitro (1997)

Cranial sutures function as bone growth centers while themselves remaining unossified. Rat frontonasal sutures become obliterated by neonatal day 21 (N21), while coronal sutures do not fuse over the life of the animal. Coronal sutures induced to undergo osseous obliteration in vitro after removal of the dura mater were found to require soluble, heparin-binding factors present in dura mater to resist osseous obliteration. Transforming growth factor beta 1 (TGF-beta 1), beta 2, and beta 3, heparin-binding factors known to regulate bone cell proliferation and differentiation, were considered likely candidates. The presence and distribution of these factors in calvarial tissues both in vivo and in vitro were established by immunohistochemical analysis, while reverse transcription followed by polymerase chain reaction (RT/PCR) was employed to determine the presence of transcripts for these factors in mRNA isolated from microdissected dura mater. Results indicated that the presence of TGF-beta 1 and TGF-beta 2 were associated with developing coronal and frontonasal sutures, and that the continued presence of these factors was associated with osseous obliteration of the frontonasal suture. However, increased TGF-beta 3 immunoreactivity was associated with the coronal suture remaining unossified. RT/PCR demonstrated the presence of transcripts for TGF-beta 1, beta 2, and beta 3 in dural tissues isolated from rat calvaria. These data support the notion of a role for TGF-beta s in regulating cranial suture morphogenesis and establish the in vitro model as a valid system for examining mechanisms by which growth factors regulate both suture morphogenesis and bone growth at the suture site.
Differential requirements for co-stimulatory signals from B7 family members by resting versus recently activated memory T cells towards soluble recall antigens (1996)

The interaction between CD28 on T cells with CD80 (B7-1) and CD86 (B7-2) on APCs is considered to be of critical importance for primary T cell activation both in vivo and in vitro. The relative importance of this co-stimulatory signal in memory T cell activation is, however, less clear, and was therefore studied by in vitro experiments on T cell responses to soluble recall antigens using peripheral blood mononuclear cells or T cell clones. Our data demonstrate that B7-2 represents the major co-stimulatory signal for the activation of resting peripheral blood memory T cells with recall antigens, as evidenced by the effects of anti-B7-1 and anti-B7-2 on T cell proliferation as well as on IL-2 and INF-gamma production. Since CTLA-4-lg and anti-CD28 Fab fragments had similar inhibitory effects to the combination of anti-B7-1 plus anti B7-2, the involvement of a third co-stimulatory CD28/CTLA-4 ligand is unlikely. Despite the strong effects of B7-blocking agents, a variable fraction of the memory T cells was resistant to inhibition. Moreover, T cell clones or in vitro preactivated T cells could efficiently be restimulated by soluble atigens on autologous APCs in the absence of B7-1 or B7-2 co-stimulation. These data show that most memory T cells that are freshly isolated from the blood are still dependent on CD28 triggering for their activation. However, recently activated T cells can apparently bypass the requirement for B7 and use other co-stimulatory signals for reactivation, a finding with important implications for the development of immunosuppressive strategies.