gebhart/patrepeval huggingface dataset:
Decreased Cell Wall Digestibility in Canola Transformed with Chimeric Tyrosine Decarboxylase Genes from Opium Poppy1 (1999)

Tyrosine decarboxylase (TYDC) is a common plant enzyme involved in the biosynthesis of numerous secondary metabolites, including hydroxycinnamic acid amides. Although a definite function has not yet been determined, amides have been proposed to form a physical barrier against pathogens because they are usually found as integral cell wall components. Canola (Brassica napus) was independently transformed with chimeric genes (35S::TYDC1 and 35S::TYDC2) under the transcriptional control of the cauliflower mosaic virus 35S promoter, and encoding two TYDC isoforms from opium poppy (Papaver somniferum). All T0 plants displayed a suppressed level of wild-type TYDC activity, and transgene mRNAs were not detected. Silencing of 35S::TYDC1 was overcome in the T1 progeny of self-pollinated T0 plants, since high levels of TYDC1 mRNAs were detected, and TYDC activity increased up to 4-fold compared with wild-type levels. However, TYDC1 mRNA levels decreased in T2 plants and were not detected in the T3 progeny. TYDC activity also gradually declined in T2 and T3 plants to nearly wild-type levels. In contrast, silencing of 35S::TYDC2 was maintained through four consecutive generations. T1 plants with a 3- to 4-fold increase in wild-type TYDC activity showed a 30% decrease in cellular tyrosine pools and a 2-fold increase in cell wall-bound tyramine compared with wild-type plants. An increase in cell wall-bound aromatic compounds was also detected in these T1 plants by ultraviolet autofluorescence microscopy. The relative digestibility of cell walls measured by protoplast release efficiency was inversely related to the level of TYDC activity.
A functional role for endogenous atrial natriuretic peptide in a canine model of early left ventricular dysfunction. (1995)

Asymptomatic or early left ventricular dysfunction in humans is characterized by increases in circulating atrial natriuretic peptide (ANP) without activation of the renin-angiotensin-aldosterone system (RAAS). We previously reported a canine model of early left ventricular dysfunction (ELVD) produced by rapid ventricular pacing and characterized by an identical neurohumoral profile and maintenance of the natriuretic response to volume expansion (VE). To test the hypothesis that elevated endogenous ANP suppresses the RAAS and maintains sodium excretion in ELVD, we assessed the effects of antagonism of ANP on cardiorenal and neurohumoral function in ELVD. Chronic ANP suppression was produced by bilateral atrial appendectomies before the production of ELVD by rapid ventricular pacing (ELVD-APPX, n = 5). This group was compared with a separate group with ELVD and intact atrial appendages (ELVD-INTACT, n = 8). ELVD-APPX was characterized by lower circulating ANP (50 +/- 11 vs. 158 +/- 37 pg/ml, P < 0.05), activation of plasma renin activity (PRA) (9.4 +/- 2.4 vs. 0.6 +/- 0.4 ng/ml per h, P < 0.05) and aldosterone (36.4 +/- 12.5 vs. 2.5 +/- 0.0 ng/dl, P < 0.05) when compared to ELVD-INTACT. In comparison to the ELVD-INTACT group, sodium excretion was decreased before and during VE in the ELVD-APPX group. Acute ANP antagonism was produced by administration of the particulate guanylate cyclase coupled natriuretic peptide receptor antagonist, HS-142-1, to seven conscious dogs with ELVD and intact atrial appendages (ELVD-INTACT). HS-142-1 decreased plasma concentrations and renal generation of the ANP second messenger, cGMP, and was associated with activation of PRA and sodium retention with enhanced tubular sodium reabsorption. These data support a significant role for elevated endogenous ANP in the maintenance of sodium excretion and regulation of the RAAS in experimental ELVD.
Propranolol apparently separates the physical and compositional characteristics of muscle growth induced by clenbuterol (1987)

The effect of propranolol on clenbuterol-induced changes in muscle fibre size and protein content were studied. Propranolol did not inhibit the ability of clenbuterol to stimulate protein accretion but reduced the increase in muscle fibre size. The compositional and physical characteristics of clenbuterol-induced muscle growth thus appeared to be separated by propranolol.
Detection of Rare Allelic Variants of the Interferon-α 2 Gene in Human Genomic DNA (1995)

We have analyzed human donor DNA for the presence of sequences corresponding to allelic variants of the IFN-alpha 2 locus. Using both restriction enzyme digestion of PCR-amplified fragments and sequence analysis of these fragments, we have identified the three reported allelic variants, IFN-alpha 2a, IFN-alpha 2b, and IFN-alpha 2c, in genomic DNA derived from donors of African or Afro-Caribbean origin. This is the first report of the IFN-alpha 2a and IFN-alpha 2c alleles occurring in human donor DNA and supports the view that these are variants of the predominant IFN-alpha 2b allele rather than arising from mutations occurring in cultured cells.
IL‐15: a central regulator of celiac disease immunopathology (2014)

Interleukin-15 (IL-15) exerts many biological functions essential for the maintenance and function of multiple cell types. Although its expression is tightly regulated, IL-15 upregulation has been reported in many organ-specific autoimmune disorders. In celiac disease, an intestinal inflammatory disorder driven by gluten exposure, the upregulation of IL-15 expression in the intestinal mucosa has become a hallmark of the disease. Interestingly, because it is overexpressed both in the gut epithelium and in the lamina propria, IL-15 acts on distinct cell types and impacts distinct immune components and pathways to disrupt intestinal immune homeostasis. In this article, we review our current knowledge of the multifaceted roles of IL-15 with regard to the main immunological processes involved in the pathogenesis of celiac disease.
Histone Deacetylase Inhibitors Improve In Vitro and In Vivo Developmental Competence of Somatic Cell Nuclear Transfer Porcine Embryos (2010)

Faulty epigenetic reprogramming of somatic nuclei is likely to be a major cause of low success observed in all mammals produced through somatic cell nuclear transfer (SCNT). It has been demonstrated that the developmental competence of SCNT embryos in several species were significantly enhanced via treatment of histone deacetylase inhibitors (HDACi) such as trichostatin A (TSA) to increase histone acetylation. Here we report that 50 nM TSA for 10 h after activation increased the developmental competence of porcine SCNT embryos constructed from Landrace fetal fibroblast cells (FFCs) in vitro and in vivo, but not at higher concentrations. Therefore, we optimized the application of another novel HDACi, Scriptaid, for development of porcine SCNT embryos. We found that treatment with 500 nM Scriptaid significantly enhanced the development SCNT embryos to the blastocyst stage when outbred Landrace FFCs and ear fibroblast cells (EFCs) were used as donors compared to the untreated group. Scriptaid increased the overall cloning efficiency from 0.4% (untreated group) to 1.6% for Landrace FFCs and 0 to 3.7% for Landrace EFCs. Moreover, treatment of SCNT embryos with Scriptaid improved the histone acetylation on Histone H4 at lysine 8 (AcH4K8) in a pattern similar to that of the in vitro fertilized (IVF) embryos.
A Novel Mechanism of Action of Methyl-2-cyano-3,12 dioxoolean-1,9 diene-28-oate (CDDO-Me): Direct Permeabilization of the Inner Mitochondrial Membrane To Inhibit Electron Transport and Induce Apoptosis. (2005)

Abstract CDDO-Me is a synthetic oleanolic acid derivative that displays antitumorigenic and anti-inflammatory activities, and we have previously reported that this agent potently activates the intrinsic apoptotic pathway in leukemia cells. Here we demonstrate that mitochondrial dysfunction induced by CDDO-Me in leukemia cells is mediated by direct permeabilization of the inner mitochondrial membrane that results in the rapid depletion of mitochondrial glutathione (GSXm), loss of cardiolipin, and inhibition of mitochondrial respiration. More importantly, we demonstrate that in addition to activating the intrinsic apoptotic pathway, the mitochondrial effects of CDDO-Me may mediate its anti-inflammatory activity by modulating the generation of superoxide anion (O2−). Interestingly, CDDO-Me did not increase the generation of O2−, and in fact pretreatment of leukemia cells with CDDO-Me prevented the increase of this reactive oxygen species elicited by inhibition of complex I or III in the absence of de novo protein synthesis. CDDO-Me, but not other inhibitors of respiration, induced a time- and dose-dependent, cyclosporin A-independent permeability transition (mPT) of isolated mitochondria that was sensitive to sulfhydryl antioxidants but not to EDTA. PT induced by CDDO-Me and Ca2+ was accompanied by loss of GSXm suggesting that the increased permeability of the inner mitochondrial membrane facilitates the loss of this antioxidant. Finally, transmission electron microscopy revealed that CDDO-Me rapidly induced caspase-independent mitochondrial swelling and loss of inner membrane structure prior to the release of cytochrome c. Taken together, our results indicate that CDDO-Me is a novel antileukemic agent that induces apoptosis and inhibits mitochondrial electron transport via perturbations in inner mitochondrial membrane integrity.
Molecular interactions during pregnancy: Association between mannan binding protein deficiency and recurrent miscarriage (1995)

The distribution of mannan binding protein (MBP) in blood donor sera was determined by enzyme-linked immunosorbent assay to establish normal concentrations. Abnormally low MBP concentrations were found in 16% (21 out of 135) of female partners and 14% (15 out of 108) of male partners of couples experiencing recurrent miscarriage, compared with < 5% of obstetrically normal controls (P < 0.005). This relationship was even stronger (9.5 versus 1.0%) and more significant (P < 0.002) when only subjects presumed to be homozygous for the mutant allele responsible for MBP deficiency were considered. By immunohistochemistry, MBP could be demonstrated in first trimester placenta. We suggest that low concentrations of MBP within the feto-placental unit increase susceptibility to fetal loss, possibly via an infection-induced placental cytokine imbalance.
Expression and Self-Assembly of Grimsby Virus: Antigenic Distinction from Norwalk and Mexico Viruses (1999)

A cDNA obtained from Grimsby virus (GRV), a Norwalk-like virus, purified from a stool sample of a symptomatic adult associated with a gastroenteritis outbreak in the United Kingdom, was used to obtain the complete nucleotide sequence of the second open reading frame (ORF2). The ORF2 sequence of GRV predicts a capsid of 539 amino acids (aa) which exhibits aa identities of 96% to Lordsdale virus, 67% to Mexico virus (MXV), and 43% to Norwalk virus (NV). The GRV capsid protein was expressed in insects cells by using a recombinant baculovirus, and the resulting virus-like particles (VLPs) possessed a protein with an apparent molecular weight of 58,000. Hyperimmune antisera raised against purified GRV, MXV, and NV VLPs were tested in an indirect enzyme-linked immunosorbent assay (ELISA) against GRV, NV, and MXV VLPs, revealing that GRV is antigenically distinct from both NV and MXV. The antigenic specificity of the GRV-hyperimmune antiserum was confirmed in an antigen capture ELISA using GRV-, NV-, or MXV-containing fecal specimens. The expression of the GRV capsid protein has, for the first time, allowed the antigenic comparison of three distinct recombinant Norwalk-like viruses.
A Chemical Epitope‐Targeting Strategy for Protein Capture Agents: The Serine 474 Epitope of the Kinase Akt2 (2013)

Target and click: Peptide ligands targeted to the C-terminal motif of the kinase Akt2 were obtained by combining phosphate recognition of a dinuclear zinc(II) complex with in situ click chemistry to target this epitope. The peptide ligands (shown as XXXXX) selectively bind the C-terminal polypeptide of Akt2, and are selective for Akt2 relative to the Akt1 and Akt3 isoforms. The ligands differentially modulate Akt2 activity. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
1100 x 1100 port MEMS-based optical crossconnect with 4-dB maximum loss (2003)

We present a microelectromechanical systems-based beam steering optical crossconnect switch core with port count exceeding 1100, featuring mean fiber-to-fiber insertion loss of 2.1 dB and maximum insertion loss of 4.0 dB across all possible connections. The challenge of efficient measurement and optimization of all possible connections was met by an automated testing facility. The resulting connections feature optical loss stability of better than 0.2 dB over days, without any feedback control under normal laboratory conditions.
The p75 receptor is associated with inflammatory thermal hypersensitivity (2008)

Inflammatory pain, characterized by a decrease in the nociceptive threshold, arises through the actions of inflammatory mediators, and one of the key molecules is nerve growth factor (NGF). Here we report that the administration of neutralizing antibody to the neurotrophin receptor p75 (p75(NTR)) blocks hyperalgesia, which develops with complete Freund's adjuvant (CFA)-induced inflammation or with an intraplantar injection of NGF. Although CFA injection results in the up-regulation of calcitonin gene-related peptide (CGRP) levels in the primary sensory neurons, blocking p75(NTR) abolishes this effect. We further demonstrate that pro-NGF is the predominant ligand of p75(NTR) in vivo. Plasmin treatment, which is intended to decompose pro-NGF, ameliorates CFA-induced hyperalgesia. In addition, an intraplantar injection of pro-NGF induces hyperalgesia. These data together suggest that pro-NGF, as well as mature NGF, binding to p75(NTR) plays an important role in inflammation-induced hyperalgesia. Interference in the binding may provide a therapeutic approach for the treatment of inflammatory pain.
Transactional lock-free execution of lock-based programs (2002)

This paper is motivated by the difficulty in writing correct high-performance programs. Writing shared-memory multi-threaded programs imposes a complex trade-off between programming ease and performance, largely due to subtleties in coordinating access to shared data. To ensure correctness programmers often rely on conservative locking at the expense of performance. The resulting serialization of threads is a performance bottleneck. Locks also interact poorly with thread scheduling and faults, resulting in poor system performance.We seek to improve multithreaded programming trade-offs by providing architectural support for optimistic lock-free execution. In a lock-free execution, shared objects are never locked when accessed by various threads. We propose Transactional Lock Removal (TLR) and show how a program that uses lock-based synchronization can be executed by the hardware in a lock-free manner, even in the presence of conflicts, without programmer support or software changes. TLR uses timestamps for conflict resolution, modest hardware, and features already present in many modern computer systems.TLR's benefits include improved programmability, stability, and performance. Programmers can obtain benefits of lock-free data structures, such as non-blocking behavior and wait-freedom, while using lock-protected critical sections for writing programs.
Equilibrium and kinetic acidities of benzylic ketones. Application of the Marcus equation to the deprotonation of carbon acids (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEquilibrium and kinetic acidities of benzylic ketones. Application of the Marcus equation to the deprotonation of carbon acidsJohn W. Bunting and Dimitrios. StefanidisCite this: J. Am. Chem. Soc. 1988, 110, 12, 4008–4017Publication Date (Print):June 1, 1988Publication History Published online1 May 2002Published inissue 1 June 1988https://pubs.acs.org/doi/10.1021/ja00220a046https://doi.org/10.1021/ja00220a046research-articleACS PublicationsRequest reuse permissionsArticle Views723Altmetric-Citations27LEARN 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
Time-efficient docking of flexible ligands into active sites of proteins. (1995)

We present an algorithm for placing flexible molecules in active sites of proteins. The two major goals in the development of our docking program, called FLEXX, are the explicit exploitation of molecular flexibility of the ligand and the development of a model of the docking process that includes the physico-chemical properties of the molecules. The algorithm consists of three phases: The selection of a base fragment, the placement of the base fragment in the active site, and the incremental construction of the ligand inside the active site. Except for the selection of the base fragment, the algorithm runs without manual intervention. The algorithm is tested by reproducing 11 receptor-ligand complexes known from X-ray crystallography. In all cases, the algorithm predicts a placement of the ligand which is similar to the crystal structure (about 1.5 A RMS deviation or less) in a few minutes on a workstation, assuming that the receptor is given in the bound conformation.
Computational modeling of mechanical anisotropy in the cornea and sclera (2005)

The mathematical model described appears to provide a framework for further development, capturing the essential features of mechanical anisotropy of the cornea. The tunnel incision simulation indicated the importance of the anisotropy in this case.
General-purpose telepresence with head-worn optical see-through displays and projector-based lighting (2013)

In this paper we propose a general-purpose telepresence system design that can be adapted to a wide range of scenarios and present a framework for a proof-of-concept prototype. The prototype system allows users to see remote participants and their surroundings merged into the local environment through the use of an optical see-through head-worn display. Real-time 3D acquisition and head tracking allows the remote imagery to be seen from the correct point of view and with proper occlusion. A projector-based lighting control system permits the remote imagery to appear bright and opaque even in a lit room. Immersion can be adjusted across the VR continuum. Our approach relies only on commodity hardware; we also experiment with wider field of view custom displays.
Synthesis of 14C‐labelled 1‐methanesulphonyl‐3‐(1‐methyl‐5‐nitro‐1H‐imidazol‐2‐YL)‐2‐imidazolidinone, (Go 10213) (1983)

Abstract For pharmacokinetic and metabolism studies in animals and humans, Go 10213 was labelled with carbon‐14 at the 2‐position of the 5‐nitroimidazole ring system, in an overall yield of 22% starting with potassium[ 14 C]‐thiocyanate. The labelled compound had a specific activity of 4.65 μCi/mg or 1.34 mCi/mmol.
Neutrophil Apoptosis during the Development and Resolution of Oleic Acid-Induced Acute Lung Injury in the Rat (1998)

The oleic acid (OA) model of acute lung injury in rats is characterized by a massive and rapid influx of polymorphonuclear neutrophils (PMN) within 1 h, with a peak inflammatory response at 4 h and resolution by 72 h. We hypothesized that PMN apoptosis is involved in the resolution of OA-induced acute lung injury. To test this hypothesis, healthy adult Fischer 344 rats were given 30 microl OA in 0.1% bovine serum albumin (BSA) intravenously; controls were given BSA alone and killed at 1, 4, 24, and 72 h after OA to obtain bronchoalveolar lavage fluid (BALF) and lung tissue. Cell pellets from BALF and formalin-fixed, paraffin-embedded tissue section samples were processed for terminal deoxyribonucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) to identify apoptotic cells. Propidium iodide was used to counterstain nuclei. Percentage of nuclei undergoing apoptosis was counted under a fluorescent microscope. Control rats showed only resident alveolar macrophages (AM) in the BALF with no apoptosis. At the peak of injury, 1 h and 4 h after OA injection, we observed a massive PMN response without any evidence of apoptosis. At 24 h, when the OA injury is clinically and histologically in early resolution, we observed intense apoptosis of PMN nuclei along with evidence of apoptotic bodies in the cytoplasm of AM. Some of the AM also showed apoptotic nuclei at 72 h. Similar observations were made in the lung tissue sections. The results of the TUNEL assay were confirmed by DNA ladders and electron microscopy. We conclude that apoptosis of PMN and clearance by AM is an important mechanism in resolution of OA- induced acute lung injury.
Synthesis and structure of isolated L1/sub 0/ FePt particles (2000)

Isolated FePt particles were fabricated by taking advantage of overgrowth of Fe on Pt particles and subsequent annealing at 873 K. The annealing lead to the formation of ordered tetragonal (L1/sub 0/) FePt particles with three orthogonal variants. The average size of FePt particles could be adjusted to less than 10 nm and no significant grain coarsening occurred upon annealing due to the existence of an amorphous Al/sub 2/O/sub 3/ layer. Nano-beam electron diffraction revealed that the lattice constant ratio c/a was approximately 0.97 for the annealed FePt particles with Fe composition close to 50 at.%.