gebhart/patrepeval huggingface dataset:
Polymeric Chains of SUMO-2 and SUMO-3 Are Conjugated to Protein Substrates by SAE1/SAE2 and Ubc9 (2001)

Conjugation of the small ubiquitin-like modifier SUMO-1/SMT3C/Sentrin-1 to proteins in vitro is dependent on a heterodimeric E1 (SAE1/SAE2) and an E2 (Ubc9). Although SUMO-2/SMT3A/Sentrin-3 and SUMO-3/SMT3B/Sentrin-2 share 50% sequence identity with SUMO-1, they are functionally distinct. Inspection of the SUMO-2 and SUMO-3 sequences indicates that they both contain the sequence psiKXE, which represents the consensus SUMO modification site. As a consequence SAE1/SAE2 and Ubc9 catalyze the formation of polymeric chains of SUMO-2 and SUMO-3 on protein substrates in vitro, and SUMO-2 chains are detected in vivo. The ability to form polymeric chains is not shared by SUMO-1, and although all SUMO species use the same conjugation machinery, modification by SUMO-1 and SUMO-2/-3 may have distinct functional consequences.
Intrinsic Disorder and Autonomous Domain Function in the Multifunctional Nuclear Protein, MeCP2 (2007)

To probe the tertiary structure and domain organization of native methyl CpG-binding protein 2 (MeCP2), the recombinant human e2 isoform was purified to homogeneity and characterized by analytical ultracentrifugation, CD, and protease digestion. The location of intrinsic disorder in the MeCP2 sequence was predicted using the FoldIndex algorithm. MeCP2 was found to be monomeric in low and high salt and over a nearly 1000-fold concentration range. CD indicated that the MeCP2 monomer was nearly 60% unstructured under conditions where it could preferentially recognize CpG dinucleotides and condense chromatin. Protease digestion experiments demonstrate that MeCP2 is composed of at least six structurally distinct domains, two of which correspond to the well characterized methyl DNA binding domain and transcriptional repression domain. These domains collectively are organized into a tertiary structure with coil-like hydrodynamic properties, reflecting the extensive disorder in the MeCP2 sequence. When expressed as individual fragments, the methyl DNA binding domain and transcriptional repression domain both could function as nonspecific DNA binding domains. The unusual structural features of MeCP2 provide a basis for understanding MeCP2 multifunctionality in vitro and in vivo. These studies also establish an experimental paradigm for characterizing the tertiary structures of other highly disordered proteins.
Measles Virus Infects Human Dendritic Cells and Blocks Their Allostimulatory Properties for CD4+ T Cells (1997)

Measles causes a profound immune suppression which is responsible for the high morbidity and mortality induced by secondary infections. Dendritic cells (DC) are professional antigen-presenting cells required for initiation of primary immune responses. To determine whether infection of DC by measles virus (MV) may play a role in virus-induced suppression of cell-mediated immunity, we examined the ability of CD1a+ DC derived from cord blood CD34+ progenitors and Langerhans cells isolated from human epidermis to support MV replication. Here we show that both cultured CD1a+ DC and epidermal Langerhans cells can be infected in vitro by both vaccine and wild type strains of MV. DC infection with MV resulted within 24-48 h in cell-cell fusion, cell surface expression of hemagglutinin, and virus budding associated with production of infectious virus. MV infection of DC completely abrogated the ability of the cells to stimulate the proliferation of naive allogeneic CD4+ T cell as early as day 2 of mixed leukocyte reaction (MLR) (i.e., on day 4 of DC infection). Mannose receptor-mediated endocytosis and viability studies indicated that the loss of DC stimulatory function could not be attributed to the death or apoptosis of DC. This total loss of DC stimulatory function required viral replication in the DC since ultraviolet (UV)-inactivated MV or UV-treated supernatant from MV-infected DC did not alter the allostimulatory capacity of DC. As few as 10 MV- infected DC could block the stimulatory function of 10(4) uninfected DC. More importantly, MV-infected DC, in which production of infectious virus was blocked by UV treatment or paraformaldehyde fixation, actively suppressed allogeneic MLR upon transfer to uninfected DC-T-cultures. Thus, the mechanisms which contribute to the loss of the allostimulatory function of DC include both virus release and active suppression mediated by MV-infected DC, independent of virus production. These data suggest that carriage of MV by DC may facilitate virus spreading to secondary lymphoid organs and that MV replication in DC may play a central role in the general immune suppression observed during measles.
Structural specificity for biological activity of trichostatin a, a specific inhibitor of mammalian cell cycle with potent differentiation-inducing activity in friend leukemia cells. (1990)

Biological activities of four chemically synthesized trichostatin-related compounds, (R)-trichostatin A, (S)-trichostatin A, (R)-trichostatic acid, and (S)-trichostatic acid, were investigated. Assays of differentiation-inducing activity in Friend leukemia cells and G2-arresting activity in the cell cycle of normal rat fibroblast cells were used as monitoring systems for comparing the bioactivities of these compounds. The results clearly showed that both of the enantiomers of trichostatic acid had no activity in both the assay systems. In the case of (S)-trichostatin A, the antipode of naturally occurring trichostatin A, 50% effective concentrations were determined to be 50-70-fold higher than those of (R)-trichostatin A. The relationship between this ratio and the value of enantiomeric excess strongly suggests that (S)-trichostatin A is also biologically inactive. These results indicate that the absolute configuration and the presence of the hydroxamate group of trichostatin A are essential for its biological activity.
Enhanced ADP-glucose pyrophosphorylase activity in wheat endosperm increases seed yield (2002)

Yield in cereals is a function of seed number and weight; both parameters are largely controlled by seed sink strength. The allosteric enzyme ADP-glucose pyrophosphorylase (AGP) plays a key role in regulating starch biosynthesis in cereal seeds and is likely the most important determinant of seed sink strength. Plant AGPs are heterotetrameric, consisting of two large and two small subunits. We transformed wheat (Triticum aestivum L.) with a modified form of the maize (Zea mays L.) Shrunken2 gene (Sh2r6hs), which encodes an altered AGP large subunit. The altered large subunit gives rise to a maize AGP heterotetramer with decreased sensitivity to its negative allosteric effector, orthophosphate, and more stable interactions between large and small subunits. The Sh2r6hs transgene was still functional after five generations in wheat. Developing seeds from Sh2r6hs transgenic wheat exhibited increased AGP activity in the presence of a range of orthophosphate concentrations in vitro. Transgenic Sh2r6hs wheat lines produced on average 38% more seed weight per plant. Total plant biomass was increased by 31% in Sh2r6hs plants. Results indicate increased availability and utilization of resources in response to enhanced seed sink strength, increasing seed yield, and total plant biomass.
Resuspension and Redistribution of Plutonium in Soils (1975)

Formulae are derived which parameterize dust and plutonium fluxes in terms of micrometeorological and soil erodibility parameters. Interim, simple models utilizing the time-dependent resuspension factor and mass-loading approaches are derived which may be used to predict the average concentration of resuspended plutonium. Intensive measurements of the resuspension of plutonium at the USAEC's Nevada Test Site are summarized in terms of a resuspension rate through the use of Healy's model of transport and diffusion. Values of the resuspension rate varied from 2.7 × 10−12 to 4.8 × 10−10 sec−1. The relationship between the resuspension rate and the historical resuspension factor is developed. The various models and formulations used are shown to be internally consistent for this experimental site.
A new subtype of human immunodeficiency virus type 1 (MVP-5180) from Cameroon (1994)

A new subtype (MVP-5180) of human immunodeficiency virus type 1 (HIV-1) was isolated from a Cameroonian AIDS patient. MVP-5180 was grown in several human T-cell lines and the monocytic U937 line. MVP-5180 DNA could not be amplified by nested primer PCR with conventional env primers and could be only very faintly amplified with gag and pol primers. Most German, Ivoirian, and Malawian anti-HIV-1 sera reacted faintly or moderately with Env proteins in an MVP-5180 immunoblot, whereas some Cameroonian sera reacted strongly. Of HIV-1-infected Cameroonians, 8% were identified by serological methods as infected with MVP-5180; 7% were positive when MVP-5180-specific PCR env primers were used. DNA sequence analysis of MVP-5180 showed that its genetic organization was that of HIV-1, with 65% similarity to HIV-1 and 56% similarity to HIV-2 consensus sequences. The env gene of MVP-5180 had similarities to HIV-1 and HIV-2 of 53 and of 49%, respectively. V3 loop analysis identified a crown of Gly-Pro-Met-Arg by using cloned DNA and Gly-Pro-Leu-Arg by using PCR-amplified DNA, neither of which configuration has been described for other HIV strains. In an analysis of relationships, MVP-5180 occupied a position distant to all other HIV-1 strains, including the chimpanzee simian immunodeficiency virus type 1 SIVcpz and the Uganda virus U455, and closer to the HIV-1/HIV-2 divergence node. MVP-5180, together with another Cameroonian isolate, ANT-70, constitutes a group subtype O of the most divergent HIV-1 isolates yet identified. Characterization of MVP-5180 is important for understanding the natural history of the primate immunodeficiency viruses and for the development of vaccines and diagnostics.
A rapid method of dietary fibre estimation in wheat products (1985)

Abstract The dietary fibre contents of row and cooked wheat products are highly correlated with their total pentose contents. A colorimetric method for rapid estimation of pentosans in while flour has been adapted for use with products of a wide range of dietary fibre contents, by introducing a prehysrolysis with 0.5m sulphuric acid for 0.5h.
Über den Nickelkomplex C18H22Ni und den daraus gewonnenen Kohlenwasserstoff C13H18 (1964)

Abstract Der früher beschriebene Ni‐Komplex besitzt nicht die Konstitution II sondern ist ein Gemisch der Verbindungen Va und Vb. Ebenso ist der daraus mit Säuren gewonnene Kohlenwasserstoff C 13 H 18 kein Tetramethyl‐ dihydroinden (III), sondern ein Tetramethyl‐spiro [4.4]nonatrien (XI). Dieses entsteht auch durch Umlagerung des Cyclobutenderivates VII.
Mapping the minimal contiguous gene segment that encodes functionally active Shiga-like toxin II (1991)

Shiga-like toxin type II (SLT-II) is one of two antigenically distinct cytotoxins produced by enterohemorrhagic Escherichia coli that are believed to play a central role in the pathogenesis of enterohemorrhagic E. coli-induced disease. SLT-II is a bipartite toxin with an enzymatically active A subunit that inhibits protein synthesis and an oligomeric B subunit that binds to the glycolipid globotriaosylceramide on eukaryotic cells. In this study, functional boundaries of the slt-II operon were mapped. Mutant proteins lacking the last four amino acids from the carboxy terminus of the 70-amino-acid mature SLT-II B polypeptide had no cytotoxic activity. However, when only two amino acids were removed from the carboxy terminus of the B subunit, the cytotoxic activity of the holotoxin was not altered drastically. Furthermore, a 21-amino-acid extension to the carboxy terminus of the SLT-II B polypeptide was tolerated with a minimum reduction in cytotoxic activity of the holotoxin. Deletion of the region coding for amino acids 3 through 18 of the 296-amino-acid mature SLT-II A polypeptide resulted in complete ablation of the cytotoxic activity of the holotoxin as well as abolition of the enzymatic activity of the A subunit. Thus, it appears that both 5'- and 3'-terminal coding sequences are essential for function of the slt-II operon.
Synthetic peptide assays to detect human immunodeficiency virus types 1 and 2 in seropositive individuals. (1990)

Detection of antibodies to human immunodeficiency virus type 1 by enzyme-linked immunosorbent assay is the standard method to screen blood products. With the description of human immunodeficiency virus type 2 as a second retrovirus involved in the pathogenesis of acquired immunodeficiency syndrome, additional laboratory testing is required to screen blood products. However, owing to the serological cross-reactivity of human immunodeficiency virus types 1 and 2 at the molecular level, it is impossible to distinguish human immunodeficiency virus type 2-infected blood with enzyme-linked immunosorbent assays formatted with human immunodeficiency virus type 1 viral lysates. Synthetic peptides from the conserved envelope region of the human immunodeficiency virus transmembrane protein offer a new approach to develop site-specific diagnostic assays that will identify and discriminate between human immunodeficiency virus types 1 and 2.
Very low bit-rate video coding using wavelet-based techniques (1999)

In this paper, we propose a very low bit-rate video coding scheme based on a discrete wavelet transform (DWT), block-matching motion estimation (BME), and overlapped block motion compensation (OBMC). Our approach reveals that the coding process works more efficiently if the quantized wavelet coefficients are preprocessed by a mechanism exploiting the redundancies in the wavelet subband structure. Thus, we introduce a new framework of preceding techniques based on the concepts of partitioning, aggregation, and conditional coding (PACC). Our experimental results show that our PACC coder outperforms the VM (Version 5.1) of MPEG4 both for the coding of intraframes (1-2 dB PSNR) and residual frames (up to 1.5 dB PSNR) of typical MPEG4 test sequences. The subjective quality of reconstructed video is, in general, superior to that obtained from the VM implementation. In addition, when restricted to the intraframe mode, the proposed coding algorithm produces results which are among the best reported for still image compression.
Jitter Control and Dynamic Resource Management for Multimedia Communication Over Broadband Network (1998)

iv 1 Introduction 1 1.1 Multimedia Network Architecture . . . . . . . . . . . . . . . . . . . . . . 2 2 Jitter Control Over Broadband Networks 5 2.1 Characteristics of Jitter Link . . . . . . . . . . . . . . . . . . . . . . . . . 6 3 Initial Delay Regulator (IDR) 9 3.1 Input and Output Jitter . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 3.2 Characteristics of the Initial Delay Regulator (IDR) . . . . . . . . . . . . 10 3.3 Relation Between IDR Queue Size and Output Jitter . . . . . . . . . . . 12 3.4 Multiple Node Jitter-Buffer Relation . . . . . . . . . . . . . . . . . . . . 13 3.5 Scaling of IDR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 4 Dynamic Buffer Allocation 17 4.1 Buffer Allocation Policy for Hard QoS Requirements . . . . . . . . . . . 18 4.2 Fair Buffer Allocation Policy with Soft QoS Requirements . . . . . . . . 20 5 Simulation and Evaluation 25 5.1 IDR Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2...
Upregulation of Tissue Factor by Activated Stat3 Contributes to Malignant Pleural Effusion Generation via Enhancing Tumor Metastasis and Vascular Permeability in Lung Adenocarcinoma (2013)

Malignant pleural effusion (MPE) is a poor prognostic sign for patients with lung cancer. Tissue factor (TF) is a coagulation factor that participates in angiogenesis and vascular permeability and is abundant in MPE. We previously demonstrated that autocrine IL-6-activated Stat3 contributes to tumor metastasis and upregulation of VEGF, resulting in the generation of MPE in lung adenocarcinoma. In this study, we found IL-6-triggered Stat3 activation also induces TF expression. By using pharmacologic inhibitors, it was shown that JAK2 kinase, but not Src kinase, contributed to autocrine IL-6-induced TF expression. Inhibition of Stat3 activation by dominant negative Stat3 (S3D) in lung adenocarcinoma suppressed TF-induced coagulation, anchorage-independent growth in vitro, and tumor growth in vivo. Consistently, knockdown of TF expression by siRNA resulted in a reduction of anchorage-independent growth of lung adenocarcinoma cells. Inhibition of TF expression also decreased the adhesion ability of cancer cells in normal lung tissues. In the nude mouse model, both lung metastasis and MPE generation were decreased when PC14PE6/AS2-siTF cells (TF expression was silenced) were intravenously injected. PC14PE6/AS2-siTF cells also produced less malignant ascites through inhibition of vascular permeability. In summary, we showed that TF expression plays a pivotal role in the pathogenesis of MPE generation via regulating of tumor metastasis and vascular permeability in lung adenocarcinoma bearing activated Stat3.
Interleukin-1 enhances survival of lethally irradiated mice treated with allogeneic bone marrow cells (1989)

Interleukin-1 (IL-1) enhanced the capacity of allogeneic bone marrow (BM) cells to promote survival of mice given doses of radiation (1,200 to 1,350 cGy) that are significantly higher than those generally used for BM ablation (850 to 950 cGy). Three to five times greater numbers of lethally irradiated (1,200 to 1,350 cGy) C57B1/6 (H-2b) mice given 10(7) T-cell-depleted Balb/c (H-2d) BM cells survived over 6 weeks if also treated with a single intraperitoneal (IP) dose of 10 micrograms IL-1 20 hours before or from 1 to 3 hours after radiation. The spleens of these mice were reconstituted predominantly, but not exclusively, with donor cells (54% to 91%). Histologic examination of the epidermal and gastrointestinal tissues of mice surviving more than 6 weeks did not reveal any evidence of graft-versus-host (GVH) disease; however, since 10% to 43% of the mice died between days 30 and 46, the possibility of a GVH syndrome in these mice cannot be excluded. The spleen cells from irradiated mice given BM transplants and IL-1, which consisted of greater than or equal to 85% donor cells, were able to generate specific T-cell cytotoxic killing of unrelated allogeneic donor cells but were unreactive to target cells bearing either host or donor major histocompatibility complex (MHC) class I antigens. Thus, long-term mixed chimeric survivors were tolerant to recipient and donor alloantigens but exhibited immunologic competence. These results show that IL-1 promotes survival of lethally irradiated mice and that allogeneic hematopoietic cells in such animals develop tolerance to host MHC antigens. Although there are many unanswered questions, these data suggest that IL-1 may prove clinically useful in promoting BM engraftment.
The importance of PHB-synthase substrate specificity in polyhydroxyalkanoate synthesis byAlcaligenes eutrophus (1989)

Alcaligenes eutrophus can accumulate poly-3-hydroxybutyrate (PHB) or polyhydroxyalkanoate (PHA) containing only 3-hydroxybutyrate (HB) and 3-hydroxyvalerate (HV) units. Granule-associated PHB-synthase was active with d(−)-3-hydroxybutyryl-CoA and d(−)-3-hydroxyvaleryl-CoA of the range of d(−)- and l(+)-3-hydroxyacyl-CoA substrates tested (C4–C10). In carbon-limited cultures, PHB-synthase was predominantly soluble, becoming granule-associated on transition to nitrogen limitation. Granule-associated PHB-synthase increased in activity at least up to pH 10.0 and Km values of 0.68 mM and 1.63 mM were determined for the C4 and C5 substrates, respectively, at pH 8.5. The soluble PHB-synthase, which was unstable, showed equal activity in the range pH 8.0–10.0, had a Km value for d(−)-3-hydroxybutyryl-CoA of 0.72 mM and an Mr of 160,000. PHB does not measurably turn over under steady-state polymer-accumulating conditions.
Elevated Serum Interferon-γ-Inducible Chemokine-10/CXC Chemokine Ligand-10 in Autoimmune Primary Adrenal Insufficiency andin VitroExpression in Human Adrenal Cells Primary Cultures after Stimulation with Proinflammatory Cytokines (2005)

Chemokines are a large family of cytokines involved in the pathogenesis of inflammatory and autoimmune diseases. Among CXC chemokines, CXC chemokine ligand 10 (CXCL10) has been identified to play an important role in several endocrinological autoimmune diseases, such as Hashimoto's thyroiditis, Graves' disease, and type 1 diabetes mellitus. Although the mechanisms leading to glandular autoimmune process may be at least in part shared by different endocrine organs, the role of CXCL10 in autoimmune adrenal insufficiency is unknown. The aim of this study was to evaluate the role of CXCL10 in Addison's disease (AD). Serum CXCL10 levels were assayed in 64 patients with clinically evident autoimmune AD, 20 patients with autoimmune subclinical AD, nine patients with nonautoimmune AD, and 48 healthy volunteers. Clinically evident and subclinical AD, but not nonautoimmune AD patients, showed a significant increase in serum CXCL10 levels compared with healthy subjects: 119.9 pg/ml (range, 39.8-427.6) and 124.0 pg/ml (range, 37.0-384.7) vs. 75.6 pg/ml (range, 22.4-164.0; P < 0.001 for both groups). Comparable serum CXCL10 levels were found between patients with an isolated form of AD and patients with other autoimmune conditions associated with AD, suggesting a specific influence of the adrenal autoimmune process in determining elevated CXCL10 concentrations in such patients. No relationship was found between serum CXCL10 levels and anti-21-hydroxylase or adrenal cortex autoantibody titers or between CXCL10 levels and duration of disease. The role of CXCL10 in the adrenal gland was also evaluated in vitro in human zona fasciculata cells (hZFC). CXCL10, although not basally detected in cultured hZFC, was strongly induced by interferon-gamma and synergistically increased by TNF-alpha addition. Hydrocortisone or ACTH alone had no effect on CXCL10 secretion in hZFC, but they both significantly inhibited cytokine-induced CXCL10 secretion. Taken together, these data suggest a potential role of hZFC, through the production of CXCL10, in regulating the recruitment of specific subsets of activated lymphocytes in autoimmune AD.
New Angiotensin Converting Enzyme Inhibitors: Their Role in the Management of Hypertension (1990)

The introduction of orally active angiotensin converting enzyme (ACE) inhibitors has revolutionized the treatment of hypertensive disorders and provided an effective alternative for the management of congestive heart failure (CHF). By interfering with the formation of angiotensin II, the active agent of the renin system, ACE inhibitors block the system's vasoconstrictive and sodium-retaining effects, with a consequent reduction in systemic blood pressure. The net effect is improved blood flow and reduced cardiac work. Thus, ACE inhibitors are likely to improve cardiac work capacity and quality of life. Their mechanism of action differs markedly from that of traditional antihypertensive agents which lower blood pressure while reducing cardiac output and blood flow. Since the primary action of ACE inhibitors is to block the renin system, a dramatic response to monotherapy suggests a large renin factor while the lack of a response suggests a low-renin state more amenable to treatment with a diuretic or calcium antagonist. Because of their many attributes, ACE inhibitors are increasingly used as first-line therapy for the treatment of hypertension or CHF. The prototype orally active ACE inhibitor, captopril, is a sulfhydryl compound with a good safety profile at the recommended dosages but reported toxicity at higher dosages. Second-generation ACE inhibitors (eg, enalapril and quinapril) are more potent sulfhydryl-free esters with a greater affinity for the converting enzyme. These newer agents are pro-drugs requiring ester hydrolysis to form the active free acid compound.(ABSTRACT TRUNCATED AT 250 WORDS)