gebhart/patrepeval huggingface dataset:
Phosphorylation or Glutamic Acid Substitution at Protein Kinase C Sites on Cardiac Troponin I Differentially Depress Myofilament Tension and Shortening Velocity (2003)

There is evidence that multi-site phosphorylation of cardiac troponin I (cTnI) by protein kinase C is important in both long- and short-term regulation of cardiac function. To determine the specific functional effects of these phosphorylation sites (Ser-43, Ser-45, and Thr-144), we measured tension and sliding speed of thin filaments in reconstituted preparations in which endogenous cTnI was replaced with cTnI phosphorylated by protein kinase C-epsilon or mutated to cTnI-S43E/S45E/T144E, cTnI-S43E/S45E, or cTnI-T144E. We used detergent-skinned mouse cardiac fiber bundles to measure changes in Ca(2+)-dependence of force. Compared with controls, fibers reconstituted with phosphorylated cTnI, cTnI-S43E/S45E/T144E, or cTnI-S43E/S45E were desensitized to Ca(2+), and maximum tension was as much as 27% lower, whereas fibers reconstituted with cTnI-T144E showed no change. In the in vitro motility assay actin filaments regulated by troponin complexes containing phosphorylated cTnI or cTnI-S43E/S45E/T144E showed both a decrease in Ca(2+) sensitivity and maximum sliding speed compared with controls, whereas filaments regulated by cTnI-S43E/S45E showed only decreased maximum sliding speed and filaments regulated by cTnI-T144E demonstrated only desensitization to Ca(2+). Our results demonstrate novel site specificity of effects of PKC phosphorylation on cTnI function and emphasize the complexity of modulation of the actin-myosin interaction by specific changes in the thin filament.
Disseminating the Genome: Joining, Resolving, and Separating Sister Chromatids During Mitosis and Meiosis (2001)

The separation of sister chromatids at the metaphase to anaphase transition is one of the most dramatic of all cellular events and is a crucial aspect of all sexual and asexual reproduction. The molecular basis for this process has until recently remained obscure. New research has identified proteins that hold sisters together while they are aligned on the metaphase plate. It has also shed insight into the mechanisms that dissolve sister chromatid cohesion during both mitosis and meiosis. These findings promise to provide insights into defects in chromosome segregation that occur in cancer cells and into the pathological pathways by which aneuploidy arises during meiosis.
A study of smoothing methods for language models applied to information retrieval (2004)

Language modeling approaches to information retrieval are attractive and promising because they connect the problem of retrieval with that of language model estimation, which has been studied extensively in other application areas such as speech recognition. The basic idea of these approaches is to estimate a language model for each document, and to then rank documents by the likelihood of the query according to the estimated language model. A central issue in language model estimation is smoothing , the problem of adjusting the maximum likelihood estimator to compensate for data sparseness. In this article, we study the problem of language model smoothing and its influence on retrieval performance. We examine the sensitivity of retrieval performance to the smoothing parameters and compare several popular smoothing methods on different test collections. Experimental results show that not only is the retrieval performance generally sensitive to the smoothing parameters, but also the sensitivity pattern is affected by the query type, with performance being more sensitive to smoothing for verbose queries than for keyword queries. Verbose queries also generally require more aggressive smoothing to achieve optimal performance. This suggests that smoothing plays two different role---to make the estimated document language model more accurate and to "explain" the noninformative words in the query. In order to decouple these two distinct roles of smoothing, we propose a two-stage smoothing strategy, which yields better sensitivity patterns and facilitates the setting of smoothing parameters automatically. We further propose methods for estimating the smoothing parameters automatically. Evaluation on five different databases and four types of queries indicates that the two-stage smoothing method with the proposed parameter estimation methods consistently gives retrieval performance that is close to---or better than---the best results achieved using a single smoothing method and exhaustive parameter search on the test data.
Effects of Dairy Fats within Different Foods on Plasma Lipids (2008)

This review considers within the epidemiology of dairy fats and cardiovascular risk including the effects of 1. Fats within different dairy foods, 2. Specific dairy fatty acids including ruminant trans fats (TFA), conjugated linoleic acid (CLA), myristic acid and 3. The influence of metabolic syndrome.
Agrobacterium tumefaciens-mediated transformation as a tool for insertional mutagenesis in the symbiotic ectomycorrhizal fungusHebeloma cylindrosporum (2003)

We transformed haploid mycelium of Hebeloma cylindrosporum via Agrobacterium tumefaciens and optimised the procedure to develop a new tool for insertional mutagenesis in this fungus. Southern blot analysis of 83 randomly selected transformants showed that they all contained plasmid inserts. Each of them showed a unique hybridisation pattern, suggesting that integration was random in the fungal genome. Sixty percent of transformants obtained in the presence of bacteria pre-treated with acetosyringone integrated a single transferred DNA copy. Thermal asymmetric interlaced polymerase chain reaction allowed us to recover the left border and the right border junctions in 85% and 15% of transformants analysed, respectively. Results show that A. tumefaciens-mediated transformation may be a powerful tool for insertional mutagenesis in H. cylindrosporum.
Phenylbutyrate therapy for maple syrup urine disease (2010)

Therapy with sodium phenylacetate/benzoate or sodium phenylbutyrate in urea cycle disorder patients has been associated with a selective reduction in branched-chain amino acids (BCAA) in spite of adequate dietary protein intake. Based on this clinical observation, we investigated the potential of phenylbutyrate treatment to lower BCAA and their corresponding α-keto acids (BCKA) in patients with classic and variant late-onset forms of maple syrup urine disease (MSUD). We also performed in vitro and in vivo experiments to elucidate the mechanism for this effect. We found that BCAA and BCKA are both significantly reduced following phenylbutyrate therapy in control subjects and in patients with late-onset, intermediate MSUD. In vitro treatment with phenylbutyrate of control fibroblasts and lymphoblasts resulted in an increase in the residual enzyme activity, while treatment of MSUD cells resulted in the variable response which did not simply predict the biochemical response in the patients. In vivo phenylbutyrate increases the proportion of active hepatic enzyme and unphosphorylated form over the inactive phosphorylated form of the E1α subunit of the branched-chain α-keto acid dehydrogenase complex (BCKDC). Using recombinant enzymes, we show that phenylbutyrate prevents phosphorylation of E1α by inhibition of the BCKDC kinase to activate BCKDC overall activity, providing a molecular explanation for the effect of phenylbutyrate in a subset of MSUD patients. Phenylbutyrate treatment may be a valuable treatment for reducing the plasma levels of neurotoxic BCAA and their corresponding BCKA in a subset of MSUD patients and studies of its long-term efficacy are indicated.
Unprecedented Catalytic Asymmetric Reduction of N−H Imines (2004)

[Reaction: see text] Addition of lithium bis(trimethylsilyl)amide to perfluorinated ketones 1a-j affords (E)-N-TMS-ketimines 2a-j that are reduced in situ to afford racemic perfluoromethylated amine hydrochloride salts 3a-j in 54-97% yields. Solvolysis of the N-Si bond in MeOH leads to formation of bench-stable, isolable N-H imine Z/E isomer mixtures along with a methanol adduct. Enantioselective reduction of these three-component mixtures provides the first catalytic asymmetric synthesis of trifluoromethylated amines in 72-95% yields and 75-98% ee.
A catalytic 13-mer ribozyme (1989)

A 13-mer oligoribonucleotide can act as a ribozyme for the specific self-cleavage of a 41-mer oligoribonucleotide substrate in the presence of Mg2+. The two sequences involved correspond to the self-cleavage hammerhead structure of the virusoid of lucerne transient streak virus. The Michaelis-menten kinetic parameters for the reaction were; Km 1.3 microM, Vmax 0.012 microM min-1, kcat 0.5 min-1. The 13-mer RNA is the smallest ribozyme so far reported. A DNA analogue of the 13-mer can not substitute for the RNA in the reaction.
ULTRAVIOLET AND γ‐RAY‐INDUCED REACTIONS OF NUCLEIC ACID CONSTITUENTS. REACTIONS OF PURINES WITH AMINES (1974)

Abstract— Photochemical and γ‐ray‐induced reactions of purines with amines are described. These lead to the appropriate 8‐substituted purines. The photoproducts were obtained in yields of up to 100% by the use of a variety of photosensitizers, including peroxides. A free radical mechanism is proposed for these reactions. Such reactions may be relevant to the problem of the nature of DNA‐protein cross‐links induced by ultraviolet radiation.
Atelocollagen‐mediated systemic administration of myostatin‐targeting siRNA improves muscular atrophy in caveolin‐3‐deficient mice (2011)

Small interfering RNA (siRNA)-mediated silencing of gene expression is rapidly becoming a powerful tool for molecular therapy. However, the rapid degradation of siRNAs and their limited duration of activity require efficient delivery methods. Atelocollagen (ATCOL)-mediated administration of siRNAs is a promising approach to disease treatment, including muscular atrophy. Herein, we report that ATCOL-mediated systemic administration of a myostatin-targeting siRNA into a caveolin-3-deficient mouse model of limb-girdle muscular dystrophy 1C (LGMD1C) induced a marked increase in muscle mass and a significant recovery of contractile force. These results provide evidence that ATCOL-mediated systemic administration of siRNAs may be a powerful therapeutic tool for disease treatment, including muscular atrophy.
Panobinostat in lymphoid and myeloid malignancies (2013)

The results of Phase II trials prove that oral panobinostat is deliverable with dosing regimens of three times per week, either weekly or biweekly. The major hematologic side-effect of myelosuppression, in particular thrombocytopenia, is transient and manageable, as are the non-hematologic side-effects. Encouraging responses are observed in HL, CTCL, myelofibrosis and WM. The safety and efficacy results from studies of combination therapy with azacitidine in acute myeloid leukemia and myelodysplastic syndromes suggest that this agent may find a place in the management of a range of hematologic cancers.
Intra prediction with spatial gradient (2008)

Spatial intra prediction has been added recently to the latest video coding standard H.264/AVC. In the intra prediction of H.264/AVC, there are 9, 9 and 4 prediction modes for 4×4, 8×8 and 16×16 blocks, respectively. Prediction signals are generated by using one or several reference pixels. The value of a reference pixel is copied as the prediction value. In some prediction modes, we calculate a weighted mean by averaging several pixels. The same prediction value is copied to several of the pixels lying in the prediction direction. However, if original image has patterns like gradations, the residual energy could increase which would result in low coding efficiency. In this paper, we propose a new intra prediction that generates prediction signals with a spatial gradient to deal with this problem. Simulation results show that it improves the picture quality and reduce the bit-rate by about 0.14 dB and 1.0 % on average for CIF sequences, respectively. It is also confirmed that our method is effective at high bit-rates.
Carbon nanotube FET process variability and noise model for radiofrequency investigations (2012)

This work focuses on process variability and noise in carbon nanotube field-effect transistors (CNFET) to obtain a compact model usable for radiofrequency (RF) design and simulations. CNFET figures of merit (FoM) are determined and compared to International Technology Roadmap for Semiconductors (ITRS) requirements on conventional analog silicon-based devices. The developed model is also used to investigate on the impact of manufacturing process variability on the CNFET's RF-performance and noise behavior.
[Study on microspheres for embolization of the hepatic artery]. (1988)

In this paper microspheres for embolization of hepatic artery have been prepared from gelatin and polyvinyl alcohol by emulsion polymerization, and systematic studies on the pharmaceutical aspects of microspheres, including the manuiacturing procedures, microsphere size and size distribution, drug incorporation, determination of the drug in the microspheres, their dissolution in vitro and the stability during sterilization by gamma radiation were conducted, By orthogonal designs on several factors affecting size and size distribution, optimal procedures in preparing microspheres with special size have been established. Using methotrexate and 5-fluorouracil as the model drugs, the release characteristics of gelatin microspheres were investigated. By complex chemical cross-linking the release of drug from microspheres could be delayed.
The pathologic examination showed that microspheres infused via a percutaneously introduced catheter into the hepatic artery could occlude muscular arterioles before hepatic blood sinuses. Angiography which was performed before and immediately after each embolization illustrated that the branches of hepatic artery disappeared to a variable extent. γ-Ray scanning also illustrated the special localization of ~(99m)Tc labelling microspheres in liver.
Higher plants contain homologs of the bacterial celA genes encoding the catalytic subunit of cellulose synthase. (1996)

In spite of much effort, no one has succeeded in isolating and characterizing the enzyme(s) responsible for synthesis of cellulose, the major cell wall polymer of plants. We have characterized two cotton (Gossypium hirsutum) cDNA clones and identified one rice (Oryza sativa) cDNA that are homologs of the bacterial celA genes that encode the catalytic subunit of cellulose synthase. Three regions in the deduced amino acid sequences of the plant celA gene products are conserved with respect to the proteins encoded by bacterial celA genes. Within these conserved regions, there are four highly conserved subdomains previously suggested to be critical for catalysis and/or binding of the substrate UDP-glucose (UDP-Glc). An overexpressed DNA segment of the cotton celA1 gene encodes a polypeptide fragment that spans these domains and binds UDP-Glc, while a similar fragment having one of these domains deleted does not. The plant celA genes show little homology at the N- and C-terminal regions and also contain two internal insertions of sequence, one conserved and one hypervariable, that are not found in the bacterial gene sequences. Cotton celA1 and celA2 genes are expressed at high levels during active secondary wall cellulose synthesis in developing cotton fibers. Genomic Southern blot analyses in cotton demonstrate that celA forms a small gene family.
Resistance to Apoptosis Conferred by Cdk Inhibitors During Myocyte Differentiation (1996)

Proliferating murine C2C12 myoblasts can undergo either terminal differentiation or programmed cell death under conditions of mitogen deprivation. Unlike myoblasts, differentiated myotubes were resistant to apoptosis. During myogenesis the appearance of the apoptosis-resistant phenotype was correlated with the induction of the cyclin-dependent kinase (Cdk) inhibitor p21(CIP1) but not with the appearance of myogenin, a marker expressed earlier in differentiation. Forced expression of the Cdk inhibitors p21(CIP1) or p16(INK4A) blocked apoptosis during myocyte differentiation. These data indicate that induction of Cdk inhibitors may serve to protect differentiating myocytes from programmed cell death as well as play a role in establishing the postmitotic state.
Mixed Electronic-Oxide Ionic Conductivity and Oxygen Permeating Property in Ni Doped LaGaO3 Perovskite Oxide (1999)

Abstract It was found that LaGaO3 perovskite oxide doped with Ni for Ga site exhibits a high mixed electronic-oxide ionic conduction. Oxygen permeation rate was increased with increasing Ni content and it attained to a maximum value of 2.15 cm3/min cm2 at 1273 K when 25 mol% Ni was doped.
Exogenous growth factors induce the production of ganglion cells at the retinal margin (2002)

Neural progenitors at the retinal margin of the post-hatch chicken normally produce amacrine and bipolar cells, but not photoreceptor or ganglion cells. The purpose of this study was to test whether exogenous growth factors influence the types of cells produced by progenitors at the retinal margin. We injected insulin, FGF2 or a combination of insulin and FGF2 into the vitreous chamber of post-hatch chickens. To assay for growth factor-induced changes at the retinal margin, we used in situ hybridization and immunocytochemistry on cryosections. One day after the final injection, we found that insulin alone stimulated the addition of cells to the retinal margin, but this was not further increased when FGF2 was applied with insulin. Insulin alone increased the number of cells in the progenitor zone that expressed neurofilament, and this was further increased when FGF2 was applied with insulin. These neurofilament-expressing cells in the progenitor zone included differentiating neurons that expressed Islet1 or Hu. Four days after the final dose of growth factor, we found that the production of ganglion cells was induced by co-injection of insulin and FGF2, but not by either insulin or FGF2 alone. We conclude that the types of cells produced by progenitors at the retinal margin can be altered by exogenous growth factors and that normally the microenvironment imposes limitations on the types of neurons produced.
Online CIEF‐ESI‐MS in glycerol–water media with a view to hydrophobic protein applications (2009)

A new online coupling of CIEF with ESI-MS has been developed in glycerol-water media. This improved protocol provides: (i) the electric continuity during the whole analysis by a discontinuous filling of the capillary with 60:40 (cm/cm) catholyte/proteins-ampholyte mixture; (ii) the use of an anticonvective medium, i.e. 30:70 glycerol/water, v/v, compatible with MS detection and as an aid to hydrophobic protein solubilization and (iii) the use of unmodified bare fused-silica capillaries, as the glycerol/water medium strongly reduces EOF. Focusing was performed in positive polarity and cathodic mobilization was achieved by both voltage and pressure application. The setup was optimized with respect to analysis time, sensitivity and precision on pI determination. The optimized anolyte and catholyte were composed of 50 mM formic acid/1 mM glutamic acid (pH 2.35) and 100 mM NH(3)/1 mM lysine (pH 10.6), respectively. The effects of ampholyte concentration, focusing time and ESI parameters were presented for model proteins and discussed. This new integrated protocol should be an easy and effective additional tool in the field of proteome analysis, providing a means for the characterization of a large number of hydrophilic and hydrophobic proteins.
Binding of a SART3 tumor-rejection antigen to a pre-mRNA splicing factor RNPS1: A possible regulation of splicing by a complex formation (2001)

We recently reported the identification of a human SART3 gene that encodes a tumor-rejection antigen recognized by cytotoxic T lymphocytes (CTLs). The squamous-cell carcinoma antigen recognized by T cells-3 (SART3) is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. To determine its biologic function, we employed a 2-hybrid screening in yeast for proteins interacting with SART3, and this method yielded a pre-mRNA splicing factor (RNA-binding protein prevalent during the S phase or RNA-binding protein with a serine-rich domain [RNPS1]) that activated both constitutive and alternative splicing of pre-mRNA in vitro. Interaction of SART3 with RNPS1 through the physical association of N-terminal domains of RNPS1 was confirmed by both in vitro pull-down assay and immunoprecipitation assay. Cotransfection of the 2 genes changed the distribution pattern of SART3 from diffuse nucleoplasmic spreading to nuclear speckled regions in which the RNPS1 was colocalized, suggesting a complex formation of the 2 proteins. In cooperation with RNPS1, SART3 stimulated the proximal alternative 3' splicing of a calcitonin-dihydrofolate reductase chimeric minigene pre-mRNA. These results suggest that SART3 is involved in the regulation of mRNA splicing probably via its complex formation with RNPS1.
Abnormal in vivo metabolism of apolipoprotein E4 in humans. (1986)

Apolipoprotein E (apoE) is important in modulating the catabolism of remnants of triglyceride-rich lipoprotein particles. It is a polymorphic protein with the three common alleles coding for apoE2, apoE3, and apoE4. ApoE3 is considered the normal isoform, while apoE4 is associated both with hypercholesterolemia and type V hyperlipoproteinemia. We quantitated the kinetics of metabolism of apoE4 in 19 normolipidemic apoE3 homozygotes and 1 normolipidemic apoE4 homozygote, and compared this with the metabolism of apoE3 in 12 normolipidemic apoE3 homozygotes. In the apoE3 homozygous subjects, apoE4 was catabolized twice as fast as apoE3, with a mean plasma residence time of 0.37 +/- 0.01 d (+/- SEM) and 0.73 +/- 0.05 (P less than 0.001), respectively. When plasma was fractionated into the lipoprotein subclasses, the greatest amount of labeled apoE4 was present on very low density lipoproteins, while the largest fraction of labeled apoE3 was associated with high density lipoproteins. The plasma apoE concentration was decreased in an apoE4 homozygote compared with the apoE3 homozygotes (3.11 mg/dl vs. 4.83 +/- 0.35 mg/dl). The reduced apoE4 concentration was entirely due to a decreased apoE4 residence time in the apoE4 homozygote (0.36 d vs. 0.73 +/- 0.05 d for apoE3 in apoE3 homozygotes). These results indicate that apoE4 is kinetically different than apoE3, and suggest that the presence of apoE4 in hypercholesterolemic and type V hyperlipoproteinemic individuals may play an important pathophysiological role in the development of these dyslipoproteinemias.