gebhart/patrepeval huggingface dataset:
Cloning, sequencing, and expression in Escherichia coli of the Clostridium tetanomorphum gene encoding .beta.-methylaspartase and characterization of the recombinant protein (1992)

The gene encoding methylaspartase (EC 4.3.1.2) from Clostridium tetranomorphum has been cloned, sequenced, and expressed in Escherichia coli. The open reading frame (ORF) codes for a polypeptide of 413 amino acid residues (M(r) 45,539) of which seven are cysteine residues. The size of the ORF indicates that methylaspartase is a homodimer rather than an (AB)2 tetramer. The deduced primary structure of the protein shows no homology to enzymes that catalyze similar reactions or, indeed, any convincing homology with any other characterized protein. The recombinant protein is identical to the enzyme isolated directly from C. tetanomorphum as determined by several criteria. The enzyme is obtained in a highly active form (approximately 70% of the activity of the natural enzyme) and migrates as a single band (M(r) 49,000) in SDS-polyacrylamide gels. The kinetic parameters for the deamination of (2S,3S)-3-methylaspartic acid by the natural and recombinant proteins are very similar, and the proteins display identical potassium ion-dependent primary deuterium isotope effects for V and V/K when (2S,3S)-3-methylaspartic acid is employed as the substrate. In accord with the activity of the natural enzyme, the recombinant protein is able to catalyze the slow formation of (2S,3R)-3-methylaspartic acid, the L-erythro-epimer of the natural substrate, from mesaconic acid and ammonia. Earlier work in which the cysteine residues in the protein were labeled with N-ethylmaleimide had indicated that there were eight cysteine residues per protein monomer. One cysteine residue was protected by substrate. Here evidence is forwarded to suggest that the residue that was protected by the substrate is not a cysteine residue but the translation product of a serine codon. Kinetic data indicate that this serine residue may be modified in the active enzyme. The implications of these findings on the mechanism of catalysis are discussed within the context of a few emerging mode of action for methylaspartate ammonia-lyase.
Photochemical Generation of Conducting Patterns in Polybutadiene Films (1996)

Certain polydiene rubbers can be doped by iodine to become electrically conducting. In particular, the conductivity of trans-1,4-polybutadiene can be increased by 8 orders of magnitude upon conjugation and self-doping by iodine at room temperature, whereas cis-1,4-polybutadiene cannot be made conducting by reaction with iodine under the same conditions. cis-1,4-Polybutadiene, however, can be converted into the trans-isomer by UV irradiation. On the basis of these previous findings, we have developed a simple and selective method for the photochemical generation of conducting patterns in a nonconducting (iodinated) cis-1,4-polybutadiene matrix. This was done by microlithographically patterned photoisomerization of cis-1,4-polybutadiene films followed by I2-induced conjugation and self-doping of the UV exposed regions. The conducting patterns thus produced have remained stable for 10 months to date. They are colored and show strong fluorescence emission, which enables visualization of the conducting polymer regions. This facile method of conducting pattern generation could make polybutadiene attractive for microelectronic applications.
The Episode File System (1992)

We describe the design of Episode®, a highly portable POSIX-compliant file system. Episode is designed to utilize the disk bandwidth efficiently, and to scale well with improvements in disk capacity and speed. It utilizes logging of meta-data to obtain good performance, and to restart quickly after a crash. Episode uses a layered architecture and a generalization of files called containers to implement filesets. A fileset is a logical file system representing a connected subtree. Filesets are the unit of administration, replication, and backup in Episode. The system works well, both as a standalone file system and as a distributed file system integrated with the OSF&amp;apos;s Distributed Computing Environment (DCE). Episode will be shipped with the DCE as the Local File System component, and is also exportable by NFS. As for performance, Episode meta-data operations are significantly faster than typical UNIX Berkeley Fast File System implementations due to Episode&amp;apos;s use of logging, while normal I/O operations run near disk capacity.
Solid Phase Microextraction Coupled to High-Performance Liquid Chromatography (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolid Phase Microextraction Coupled to High-Performance Liquid ChromatographyJian. Chen and Janusz B. PawliszynCite this: Anal. Chem. 1995, 67, 15, 2530–2533Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/ac00111a006https://doi.org/10.1021/ac00111a006research-articleACS PublicationsRequest reuse permissionsArticle Views1536Altmetric-Citations264LEARN 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
The actin‐binding protein Filamin‐A interacts with the metabotropic glutamate receptor type 7 (2002)

A yeast two-hybrid screen identified Filamin-A as a binding partner of the metabotropic glutamate receptor type 7b (mGluR7b) splice variant. In addition, Filamin-A interacted with mGluR4a, mGluR5a, mGluR5b, mGluR7a and mGluR8a. Domain mapping revealed that alternative splicing of mGluR4, mGluR7 and mGluR8 C-termini regulated the interaction. A conserved tyrosine within mGluR C-termini was identified to mediate the binding to Filamin-A. Protein interactions were verified in biochemical assays using recombinant and native proteins. Finally, co-expression of Filamin-A and mGluR7 splice variants was shown in brain regions. These findings suggest that Filamin-A may physically link metabotropic glutamate receptors to the actin cytoskeleton.
Relationship between MRI lesion activity and response to IFN-β in relapsing–remitting multiple sclerosis patients (2008)

In RRMS patients treated with IFN-beta the MRI changes occurring during the first year may have a prognostic value for identifying patients with a confirmed increase of disability after 2 years of therapy.
Local Anticandidal Immune Responses in a Rat Model of Vaginal Infection by and Protection againstCandida albicans (2000)

Humoral (antibody [Ab]) and cellular Candida-specific immune responses in the vaginas of pseudoestrus rats were investigated during three successive infections by Candida albicans. After the first, protective infection, Abs against mannan and aspartyl proteinase antigens were present in the vaginal fluid, and their titers clearly increased during the two subsequent, rapidly healing infections. In all animals, about 65 and 10% of vaginal lymphocytes (VL) were CD3(+) (T cells) and CD3(-) CD5(+) (B cells), respectively. Two-thirds of the CD3(+) T cells expressed the alpha/beta and one-third expressed the gamma/delta T-cell receptor (TCR). This proportion slightly fluctuated during the three rounds of C. albicans infection, but no significant differences between infected and noninfected rats were found. More relevant were the changes in the CD4(+)/CD8(+) T-cell ratio, particularly for cells bearing the CD25 (interleukin-2 receptor alpha) marker. In fact, a progressively increased number of both CD4(+) alpha/beta TCR and CD4(+) CD25(+) VL was observed after the second and third Candida challenges, reversing the high initial CD8(+) cell number of controls (estrogenized but uninfected rats). The CD3(-) CD5(+) cells also almost doubled from the first to the third infection. Analysis of the cytokines secreted in the vaginal fluid of Candida-infected rats showed high levels of interleukin 12 (IL-12) during the first infection, followed by progressively increasing amounts of IL-2 and gamma interferon during the subsequent infections. No IL-4 or IL-5 was ever detected. During the third infection, VL with in vitro proliferative activity in response to an immunodominant mannoprotein antigen of C. albicans were present in the vaginal tissue. No response to this antigen by mitogen-responsive blood, lymph node, and spleen cells was found. In summary, the presence of protective Ab and T helper type 1 cytokines in the vaginal fluids, the in vitro proliferation of vaginal lymphocytes in response to Candida antigenic stimulation, and the increased number of activated CD4(+) cells and some special B lymphocytes after C. albicans challenge constitute good evidence for induction of locally expressed Candida-specific Ab and cellular responses which are potentially involved in anticandidal protection at the vaginal level.
Insulin-Like Growth Factor-I Inhibits Progesterone Receptor Expression in Breast Cancer Cells via the Phosphatidylinositol 3-Kinase/Akt/Mammalian Target of Rapamycin Pathway: Progesterone Receptor as a Potential Indicator of Growth Factor Activity in Breast Cancer (2003)

Although interactions between estrogen and growth factor signaling pathways have been studied extensively, how growth factors and progesterone regulate each other is less clear. In this study, we found that IGF-I sharply lowers progesterone receptor (PR) mRNA and protein levels in breast cancer cells. Other growth factors, such as epidermal growth factor, also showed the same effect. The decrease of PR levels was associated with reduced PR activity. Unlike progestins, IGF-I does not utilize the proteasome for down-regulating PR. Instead, the IGF-I-mediated decrease in PR levels is via an inhibition of PR gene transcription. In addition, the phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway was found to be specifically involved in this IGF-I effect. Our data also suggest that the IGF-I down-regulation of PR is not mediated via a reduction of estrogen receptor (ER) levels or activity. First, IGF-I induced ligand-independent ER activity while reducing ER-dependent PR levels. Second, whereas PR and cyclin D1 are both ER up-regulated, IGF-I increased cyclin D1 levels while decreasing PR levels. Third, constitutively active PI3K or Akt induced ER activity but reduced PR levels and activity. Taken together, our data indicate that IGF-I inhibits PR expression in breast cancer cells via the PI3K/Akt/mTOR pathway. Because low or absent PR in primary breast cancer is associated with poor prognosis and response to hormone therapy, our results suggest that low PR status may serve as an indicator of activated growth factor signaling in breast tumor cells, and therefore of an aggressive tumor phenotype and resistance against hormonal therapy.
Glomerular size and the association of focal glomerulosclerosis in long-surviving human renal allografts. (1993)

This biopsy study exploits the unique opportunity offered by long-surviving human renal allografts to analyze the effects of nephronopenia-induced glomerular hypertrophy on the association of focal glomerulosclerosis. Methods include glomerular morphometry and analysis of variance. Only allografts with focal glomerulosclerosis detected after 3 yr posttransplantation (Group TxFGS > 2 yr) have a group mean glomerular diameter (203.1 microns +/- SE (mean) 10.36) significantly larger (P < 0.05) than that of allografts biopsied beyond 2 yr posttransplantation but without focal glomerulosclerosis (Group No TxFGS > 2 yr; 158.3 microns +/- SE (mean) 8.32), allografts biopsied within 2 yr of transplantation with (Group TxFGS < 2 yr; 165.3 microns +/- SE (mean) 5.35) or without (Group NoTxFGS < 2 yr; 155.8 microns +/- SE (mean) 5.53) focal glomerulosclerosis, or allograft diameters at transplantation (Group CTx; 148.3 microns +/- SE (mean) 5.66). However, the increase is approximately 37% over that at transplantation, significantly less than the increase of approximately 70% attained by congenitally nephronopenic native kidneys (P < 0.50) with focal glomerulosclerosis (Group CNP; 264.4 microns +/- SE (mean) 11.01) over their controls (Group CN; 154.8 microns +/- SE (mean) 4.46). This observation suggests that the nephronopenic allograft has a curtailed ability for glomerular hypertrophy when compared with congenitally nephronopenic native kidneys and may explain the association of focal glomerulosclerosis in long-surviving renal homografts at a significantly smaller glomerular diameter. Although smaller, this appears to be the maximal glomerular dimension attained by long-surviving nephronopenic homografts in the absence of intrinsic glomerular disease (excluding focal glomerulosclerosis). Thus, these results are in accord with and offer further support for the general hypothesis that focal glomerulosclerosis develops in maximally hypertrophied glomeruli.
A predictive parameter in patients with brain related complications after cardiac surgery? (1997)

The early serum levels of NSE after cardiopulmonary bypass, in those patients with severe neurological deficits, indicate that NSE is a suitable marker for the detection and quantification of cerebral injury after open heart surgery. Therefore, in addition NSE seems to be of predictive value for the clinical outcome and gives implications for the treatment and prognosis of patients with brain related complications in cardiac surgery.
Matrix metalloproteinases: protective roles in cancer (2011)

The original notion that matrix metalloproteinases (MMPs) act as tumour and metastasis-promoting enzymes by clearing a path for tumour cells to invade and metastasize has been challenged in the last decade. It has become clear that MMPs are involved in numerous steps of tumour progression and metastasis, and hence are now considered to be multifaceted proteases. Moreover, more recent experimental evidence indicates that some members of the MMP family behave as tumour-suppressor enzymes and should therefore be regarded as anti-targets in cancer therapy. The complexity of the pro- and anti-tumorigenic and -metastatic functions might partly explain why broad-spectrum MMP inhibitors failed in phase III clinical trials. This review will provide a focussed overview of the published data on the tumour-suppressive behaviour of MMPs.
PF-4/CXCL4 and CXCL4L1 exhibit distinct subcellular localization and a differentially regulated mechanism of secretion (2007)

PF-4/CXCL4 is a member of the CXC chemokine family, which is mainly produced by platelets and known for its pleiotropic biological functions. Recently, the proteic product of a nonallelic variant gene of CXCL4 was isolated from human platelets and named as CXCL4L1. CXCL4L1 shows only 4.3% amino acid divergence in the mature protein, but exhibits a 38% amino acid divergence in the signal peptide region. We hypothesized that this may imply a difference in the cell type in which CXCL4L1 is expressed or a difference in its mode of secretion. In different types of transfected cells, CXCL4 and CXCL4L1 exhibited a distinct subcellular localization and a differential regulation of secretion, CXCL4 being stored in secretory granules and released in response to protein kinase C activation, whereas CXCL4L1 was continuously synthesized and secreted through a constitutive pathway. A protein kinase C-regulated CXCL4 secretion was observed also in lymphocytes, a cell type expressing mainly CXCL4 mRNA, whereas smooth muscle cells, which preferentially expressed CXCL4L1, exhibited a constitutive pathway of secretion. These results demonstrate that CXCL4 and CXCL4L1 exhibit a distinct subcellular localization and are secreted in a differentially regulated manner, suggesting distinct roles in inflammatory or homeostatic processes.
Dynamic Changes of Smooth Muscle and Endothelial Markers in the Early Healing Process of Dacron Vascular Grafts in the Dog, Using RT-PCR (2000)

Previous studies of neointima formation on Dacron vascular grafts mainly focused on the late stages using immunohistochemistry staining for von Willebrand factor (vWF) and smooth muscle (SM) α-actin. However, it is impossible to use immunohistochemistry to study the early events of neointima formation, because graft samples lack sufficient cellular material. Therefore, we used reverse transcriptase-polymerase chain reaction (RT-PCR) to demonstrate dynamic changes of SM and endothelial markers during the early stages of neointima formation. Preclotted Dacron grafts were implanted in the descending thoracic aorta of 14 mongrel dogs. Specimens were retrieved at 1–4 weeks. Total RNAs were extracted from mid-portion of graft flow surfaces, and RT-PCR for vWF, SM myosin heavy chain (MHC), and SM α-actin were performed and expressed as a ratio to the ribosome s17 signal. SM MHC and vWF mRNA expression was low at 1–2 weeks but elevated at 3–4 weeks (P < 0.05). However, SM α-actin mRNA levels were expressed consistently throughout the study period. At 3–4 weeks, vWF mRNA expression was inversely correlated to thrombus formation on the graft flow surface. Increased expressions of SM MHC and vWF mRNA corresponded to the formation of neointima and an endothelial layer at the later stages. However, SM α-actin mRNA expression did not vary during the healing process. The application of RT-PCR should permit further studies of gene regulation in the early vascular graft healing process in vivo. This model can also be used to study the molecular events that are involved in SM cell differentiation.
Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes (2007)

Recent advances in far-field optical nanoscopy have enabled fluorescence imaging with a spatial resolution of 20 to 50 nanometers. Multicolor super-resolution imaging, however, remains a challenging task. Here, we introduce a family of photo-switchable fluorescent probes and demonstrate multicolor stochastic optical reconstruction microscopy (STORM). Each probe consists of a photo-switchable "reporter" fluorophore that can be cycled between fluorescent and dark states, and an "activator" that facilitates photo-activation of the reporter. Combinatorial pairing of reporters and activators allows the creation of probes with many distinct colors. Iterative, color-specific activation of sparse subsets of these probes allows their localization with nanometer accuracy, enabling the construction of a super-resolution STORM image. Using this approach, we demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nanometer resolution. This technique will facilitate direct visualization of molecular interactions at the nanometer scale.
Oxidative photoredox catalysis: mild and selective deprotection of PMB ethers mediated by visible light (2011)

Herein we report an advancement in the application of visible light photoredox catalysts in the oxidation of electron-rich arenes resulting in the selective deprotection of para-methoxybenzyl (PMB) ethers. This method is highlighted by excellent functional group tolerance, protecting group orthogonality, mild reaction conditions and avoidance of stoichiometric redox byproducts.
Cell Wall Lysin as a Component of the Bacteriophage ø6 Virion (1979)

Cell wall lytic activity was found in particles of the lipid-containing bacteriophage ø6. The activity can be extracted from the virion with Triton X-100 in the presence of salt. This treatment removes the membrane-like envelope of the virion which includes five proteins. The lysin requires detergent for in vitro activity. Virus particles formed in nonsuppressor cells by several classes of ø6 nonsense mutants contained the lysin activity; however, particles formed by a mutant (unable to make proteins P5 and P11) had very low activity; high activity was produced when particles were formed in a suppressor host. A study of the time course of the appearance of the lysin during infection showed that it appeared and increased in cells infected with wild-type virus and in suppressor cells infected with a mutant of class 511, but it did not increase in nonsuppressor cells infected with the class 511 mutant. It is concluded that protein P5 is a component of the lysin and that the role of its activity is in both early and late stages of infection. In particular, the lysin may be necessary for the passage of the infecting core of the virion through the cell wall of the bacterium, as well as in the final lysis necessary for the liberation of progeny phage. A mutant of the virus that produces a larger-than-normal protein P10 does not induce normal lysin activity in host Pseudomonas phaseolicola HB10Y, although it does in strain ERA Pseudomonas pseudoalcaligenes. This indicates that protein P5 is probably not sufficient for lysin activity, but the nature of the interaction between P5 and P10 is unknown.
Metal‐face InAlN/AlN/GaN high electron mobility transistors with regrown ohmic contacts by molecular beam epitaxy (2011)

Abstract Ohmic regrowth by molecular beam epitaxy (MBE) has been investigated for metal‐face InAlN/AlN/GaN high electron mobility transistors (HEMTs) for the first time. Using SiO 2 mask n + ‐GaN was regrown in the source/drain region while deposition on the mask was lifted off in buffered HF after regrowth. The lowest contact resistance measured was 0.40 ± 0.23 Ω mm by the transmission line method (TLM) in this initial study. The peak output current density of 1.25 A/mm at V gs = 3 V and extrinsic transconductance of 264 mS/mm at V ds = 5 V were observed in 500‐nm gate length InAlN/Al/GaN HEMTs passivated by SiN with regrowth contacts.
Human Amnion Mesenchyme Harbors Cells with Allogeneic T-Cell Suppression and Stimulation Capabilities (2007)

Cells derived from the amniotic membrane of human placenta have been receiving particular attention because of their stem cell potentiality and immunomodulatory properties, which make them an attractive candidate source for cell therapy approaches. In this study, we isolated cells from the mesenchymal region of amnion and identified two subpopulations discordant for expression of the HLA-DR, CD45, CD14, and CD86 cellular markers. We therefore refer to the unfractionated cell population derived from this region as amniotic mesenchymal tissue cells (AMTC). We studied the suppressive and stimulatory characteristics of the unfractionated, HLA-DR-positive, and HLA-DR-negative AMTC populations and demonstrated that all three fail to induce an allogeneic T-cell response. However, unfractionated AMTC, which could inhibit T-cell allogeneic proliferation responses, induced proliferation of T cells stimulated via the T-cell receptor (TcR), in a cell-cell contact setting. We have shown that this stimulatory capacity can be attributed to the HLA-DR-positive AMTC subpopulation. Indeed, even though the HLA-DR-positive AMTC fraction surprisingly failed to induce proliferation of resting allogeneic T cells, they could cause strong proliferation of anti-CD3-primed allogeneic T cells. This stimulatory effect was not observed using the HLA-DR-negative AMTC fraction. The revelation that human amniotic mesenchyme possesses cell populations with both suppressive and stimulatory properties sheds additional light on the immunomodulatory functions of this tissue and may contribute to the clarification of some ongoing controversies associated with mesenchymal stromal cells of other sources, such as the presence of HLA-DR-positive cells and the suppressive versus stimulatory properties of these cells.