gebhart/patrepeval huggingface dataset:
Purification and characterization of acid trehalase from the yeast suc2 mutant. (1988)

Acid trehalase was purified from the yeast suc2 deletion mutant. After hydrophobic interaction chromatography, the enzyme could be purified to a single band or peak by a further step of either polyacrylamide gel electrophoresis, gel filtration, or isoelectric focusing. An apparent molecular mass of 218,000 Da was calculated from gel filtration. Polyacrylamide gel electrophoresis of the purified enzyme in the presence of sodium dodecyl sulfate suggested a molecular mass of 216,000 Da. Endoglycosidase H digestion of the purified enzyme resulted after sodium dodecyl sulfate gel electrophoresis in one distinct band at 41,000 Da, representing the mannose-free protein moiety of acid trehalase. The carbohydrate content of the enzyme was 86%. Amino acid analysis indicated 354 residues/molecule of enzyme including 9 cysteine moieties and only 1 methionine. The isoelectric point of the enzyme was estimated by gel electrofocusing to be approximately 4.7. The catalytic activity showed a maximum at pH 4.5. The activity of the enzyme was not inhibited by 10 mM each of HgCl2, EDTA, iodoacetic acid, phenanthrolinium chloride or phenylmethylsulfonyl fluoride. There was no activation by divalent metal ions. The acid trehalase exhibited an apparent Km for trehalose of 4.7 +/- 0.1 mM and a Vmax of 99 mumol of trehalose min-1 X mg-1 at 37 degrees C and pH 4.5. The acid trehalase is located in the vacuoles. The rabbit antiserum raised against acid trehalase exhibited strong cross-reaction with purified invertase. These cross-reactions were removed by affinity chromatography using invertase coupled to CNBr-activated Sepharose 4B. Precipitation of acid trehalase activity was observed with the purified antiserum.
Combinations of Microphase Separation and Terminal Multiple Hydrogen Bonding in Novel Macromolecules (2002)

The synthesis and characterization of terminal multiple hydrogen-bonded (MHB) polymers, such as poly(styrene) (PS), poly(isoprene) (PI), and microphase separated PS-b-PI block copolymers, possessing controlled molecular weights and narrow molecular distributions are described. Hydroxyl-terminated polymeric precursors were prepared using living anionic polymerization and subsequent quantitative termination with ethylene oxide. MHB polymers were synthesized in a controlled fashion via end-group modification of these well-defined macromolecular alcohols with excess isophorone diisocyanate and subsequent derivatization of the isocyanate-terminated polymeric intermediate with methyl isocytosine. The glass transition temperatures of the terminal MHB polymers were reproducibly higher than both nonfunctionalized and hydroxyl-terminated polymers at nearly equivalent number average molecular weights. Thin-layer chromatography analysis indicated that the interaction of terminal MHB polymers with silica was stronger as compared to both nonfunctionalized and hydroxyl-terminated polymers. Rheological characterization indicated that the melt viscosity at constant shear rate for various MHB polymers was more than 100 times higher than those for nonfunctionalized and hydroxyl-terminated polymers. Interestingly, the melt viscosity of MHB polymers was higher than those of nonfunctionalized polymers with twice the number average molecular weight. In addition, DSC and rheological characterization also suggested that terminal MHB polymers formed aggregates and not simple dimers in the melt state, and the aggregates were observed to completely dissociate at 80 degrees C.
Systemic and local silver accumulation after total hip replacement using silver-impregnated bone cement. (1994)

In a patient, at revisional Christiansen total hip arthroplasty, silver-impregnated bone cement was used as prophylaxis against deep infection. Five years later the patient developed serious neurological deficits, and the prosthesis was loose. The loose Christiansen prosthesis and the silver-impregnated bone cement were removed and a Charnley prosthesis inserted. Intra-operatively the concentration of silver in fluid drawn from the hip joint was assessed to be about 1000 times the normal serum reference value, and tissue samples from the acetabulum were densely impregnated with silver. During the following 2 years the serum concentration of silver decreased from more than 60 times to 20 times the normal; simultaneously the patient partially recovered from her grave muscle paralysis.
Contouring by electronic speckle pattern interferometry employing dual beam illumination (1990)

In this paper we extend and study the method for generating contours of diffuse objects employing a dual beam illumination coupled with electronic speckle pattern interferometry. The sensitivity and the orientation of the contour planes are analyzed. A novel method for tilting the planes of contours and experimental results incorporating phase shifting and fringe analysis are also presented. The theoretical and the experimental results show good agreement.
Mutations Conferring Resistance to a Potent Hepatitis C Virus Serine Protease Inhibitor In Vitro (2004)

BILN 2061 is a novel, specific hepatitis C virus (HCV) NS3 serine protease inhibitor discovered by Boehringer Ingelheim that has shown potent activity against HCV replicons in tissue culture and is currently under clinical investigation for the treatment of HCV infection. The poor fidelity of the HCV RNA-dependent RNA polymerase will likely lead to the development of drug-resistant viruses in treated patients. The development of resistance to BILN 2061 was studied by the in vitro passage of HCV genotype 1b replicon cells in the presence of a fixed concentration of the drug. Three weeks posttreatment, four colonies were expanded for genotypic and phenotypic characterization. The 50% inhibitory concentrations of BILN 2061 for these colonies were 72- to 1,228-fold higher than that for the wild-type replicon. Sequencing of the individual colonies identified several mutations in the NS3 serine protease gene. Molecular clones containing the single amino acid substitution A156T, R155Q, or D168V resulted in 357-fold, 24-fold, and 144-fold reductions in susceptibility to BILN 2061, respectively, compared to the level of susceptibility shown by the wild-type replicon. Modeling studies indicate that all three of these residues are located in close proximity to the inhibitor binding site. These findings, in addition to the three-dimensional structure analysis of the NS3/NS4A serine protease inhibitor complex, provide a strategic guide for the development of next-generation inhibitors of HCV NS3/NS4A serine protease.
Survival in squamous cell carcinoma of the oral cavity (2007)

In patients with stage IVA OSCC (AJCC, 1997), the survival rates for pT4 N0 are better than those for NO pT4 N0 and similar to those of patients with pstage III.
Costimulation via OX40L Expressed by B Cells Is Sufficient to Determine the Extent of Primary CD4 Cell Expansion and Th2 Cytokine Secretion In Vivo (2003)

The development of effector and memory CD4 cell populations depends upon both T cell receptor (TCR) engagement of peptide/major histocompatibility complex (MHC) class II complexes and ligation of costimulatory molecules with counter receptors on antigen-presenting cells (APCs). We showed previously that sustained interactions with APCs could be crucial for optimal expansion of CD4 cells and for development of effectors that secrete cytokines associated with Th2 cells. Using an adoptive transfer model with TCR transgenic CD4 cells, we now show that responses of CD4 cells primed in B cell-deficient mice become aborted, but are fully restored upon the transfer of activated B cells. Although B cells have the capacity to secrete multiple cytokines that could affect CD4 priming, including IL-4, we were unable to distinguish a role for cytokines that are secreted by B cells. However, B cell costimulation via the OX40L/OX40 pathway that has been implicated in CD4 cell expansion, survival, and Th2 development was required. Th2 but not Th1 responses were impaired in OX40L-deficient recipients and normal responses were restored with OX40L sufficient B cells. The results suggest that without engagement of OX40L on B cells, CD4 cell responses to many protein Ag would be dominated by Th1 cytokines. These data have important implications for strategies to achieve optimal priming of CD4 subsets.
Analysis of asymmetric deterministic bitshift errors in a hard disk file (1990)

An extensive statistical analysis of soft errors occurring in an IBM 3380 K hard-disk file has been made. About 90% of the errors was bitshift-induced involving a single bit. There was a high degree of early/late asymmetry. It is shown that decreasing system signal-to-noise ratio (S/N) increases the error rate, but reduces the early/late asymmetry. The repeatability of errors suggests that most errors happen at or near a media-direct site. Self-consistent write-process modeling, taking into account media defects, indicates bitshift and amplitude degradation commensurate with the experimental results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Tumor-Promoting Effect of Wounding: A Possible Role for TGF-β-lnduced Stromal Alterations (1994)

From clinical, chemical carcinogenesis and transgenic animal studies, it is evident that wounding has a tumor-promoting effect. We discuss the role of TGF-beta (with special emphasis on TGF-beta 1) in this process and suggest that stromal alterations during wound healing, induced by TGF-beta, can be an important determinant of tumor growth. A tumor and a wound both require similar stromal microenvironments. Thus, a chemically initiated or an oncogene-expressing cell could be complemented to grow into a tumor if it finds itself in a hospitable wound-healing stroma.
Polyol Synthesis of Silver Nanoparticles:  Use of Chloride and Oxygen to Promote the Formation of Single-Crystal, Truncated Cubes and Tetrahedrons (2004)

Single-crystal cubes and tetrahedrons of silver with truncated corners/edges have been prepared for the first time in high yields by reducing silver nitrate with ethylene glycol heated to 148 °C in the presence of poly(vinyl pyrrolidone) and a trace amount of sodium chloride. These nanoparticles were relatively monodisperse in size and shape, and their dimensions could be readily controlled in the range of 20 to 80 nm by varying the reaction time and other experimental parameters. We propose that the defects inherent in twinned nuclei of silver led to their selective etching and dissolution by chloride and oxygen (from air), leaving only the single crystalline ones to grow into nanoscale cubes and tetrahedrons.
Crystal Structures of Saccharomyces cerevisiae N-Myristoyltransferase with Bound Myristoyl-CoA and Inhibitors Reveal the Functional Roles of the N-terminal Region (2007)

Protein N-myristoylation catalyzed by myristoyl-CoA:protein N-myristoyltransferase (NMT) plays an important role in a variety of critical cellular processes and thus is an attractive target for development of antifungal drugs. We report here three crystal structures of Saccharomyces cerevisiae NMT: in binary complex with myristoyl-CoA (MYA) alone and in two ternary complexes involving MYA and two different non-peptidic inhibitors. In all three structures, the majority of the N-terminal region, absent in all previously reported structures, forms a well defined motif that is located in the vicinity of the peptide substrate-binding site and is involved in the binding of MYA. The Ab loop, which might be involved in substrate recognition, adopts an open conformation, whereas a loop of the N-terminal region (residues 22-24) that covers the top of the substrate-binding site is in the position occupied by the Ab loop when in the closed conformation. Structural comparisons with other NMTs, together with mutagenesis data, suggest that the N-terminal region of NMT plays an important role in the binding of both MYA and peptide substrate, but not in subsequent steps of the catalytic mechanism. The two inhibitors occupy the peptide substrate-binding site and interact with the protein through primarily hydrophobic contacts. Analyses of the inhibitorenzyme interactions provide valuable information for further improvement of antifungal inhibitors targeting NMT.
Antioxidant Action of Glutathione and the Ascorbic Acid/Glutathione Pair in a Model White Wine (2011)

Glutathione was assessed individually, and in combination with ascorbic acid, for its ability to act as an antioxidant with respect to color development in an oxidizing model white wine system. Glutathione was utilized at concentrations normally found in wine (30 mg/L), as well as at concentrations 20-fold higher (860 mg/L), the latter to afford ascorbic acid (500 mg/L) to glutathione ratios of 1:1. The model wine systems were stored at 45 °C without sulfur dioxide and at saturated oxygen levels, thereby in conditions highly conducive to oxidation. Under these conditions the results demonstrated the higher concentration of glutathione could initially provide protection against oxidative coloration, but eventually induced color formation. In the period during which glutathione offered a protective effect, the production of xanthylium cation pigment precursors and o-quinone-derived phenolic compounds was limited. When glutathione induced coloration, polymeric pigments were formed, but these were different from those found in model wine solutions without glutathione. In the presence of ascorbic acid, high concentrations of glutathione were able to delay the decay in ascorbic acid and inhibit the reaction of ascorbic acid degradation products with the wine flavanol compound (+)-catechin. However, on depletion, the glutathione again induced the production of a range of different polymeric pigments. These results highlight new mechanisms through which glutathione can offer both protection and spoilage during the oxidative coloration of a model wine.
Maps: a compiler-managed memory system for raw machines (1999)

This paper describes Maps, a compiler managed memory system for Raw architectures. Traditional processors for sequential programs maintain the abstraction of a unified memory by using a single centralized memory system. This implementation leads to the infamous Von Neumann bottleneck, with machine performance limited by the large memory latency and limited memory bandwidth. A Raw architecture addresses this problem by taking advantage of the rapidly increasing transistor budget to move much of its memory on chip. To remove the bottleneck and complexity associated with centralized memory, Raw distributes the memory with its processing elements. Unified memory semantics are implemented jointly by the hardware and the compiler. The hardware provides a clean compiler interface to its two inter-tile interconnects: a fast, statically schedulable network and a traditional dynamic network. Maps then uses these communication mechanisms to orchestrate the memory accesses for low latency and parallelism while enforcing proper dependence. It optimizes for speed in two ways: by finding accesses that can be scheduled on the static interconnect through static promotion, and by minimizing dependence sequentialization for the remaining accesses. Static promotion is performed using equivalence class unification and modulo unrolling; memory dependences are enforced through explicit synchronization and software serial ordering. We have implemented Maps based on the SUIF infrastructure. This paper demonstrates that the exclusive use of static promotion yields roughly 20-fold speedup on 32 tiles for our regular applications and about 5-fold speedup on 16 or more tiles for our irregular applications. The paper also shows that selective use of dynamic accesses can be a useful complement to the mostly static memory system.
Diffusing-wave-spectroscopy measurements of viscoelasticity of complex fluids (1997)

We present a new use of dynamic light scattering that permits the determination of the viscoelastic behavior of a complex fluid. By describing the motion of a scattering particle in a viscoelastic medium in terms of a generalized Langevin equation with a memory function, we relate the time evolution of its mean-square displacement to the frequency-dependent storage and loss moduli of the medium. The utility of this technique is illustrated through the application of diffusing-wave spectroscopy to probe the viscoelastic behavior of two complex fluids. The properties of a concentrated suspension of colloidal particles interacting as hard spheres are shown to be strongly influenced by the incipient colloidal glass transition, which leads to an extended range of frequencies over which they behave like an elastic solid. Similar elasticity is observed in a compressed emulsion, resulting in this case from the additional interfacial energy of the deformed droplets. In both cases diffusing-wave spectroscopy is used to measure the frequency dependence of the storage and loss moduli, and these results are compared with those from mechanical measurements. Besides providing a purely optical method for measuring mechanical properties, this technique provides new insight into the origin of the viscoelastic behavior.
Nature of Hydrogen Bonds and S···S Interactions in the l-Cystine Crystal (2016)

The intermolecular interactions that govern the stability of the l-cystine crystal were studied. This task is accomplished by using density-functional theory (DFT) with the generalized-gradient approximation (GGA) and including many-body dispersion (MBD) interactions. The strengths of the different interactions within the molecular crystal were obtained by a decomposition of the total interaction energy in two-, three-, and four-body contributions. It was determined that most of the hydrogen bonds formed within the crystal are strong (13, 15, and 19 kcal/mol) and the van der Waals nature of the S···S interaction is fully confirmed. Also, the presence of strong repulsive three-body contributions is determined. The results obtained support the idea of designing crystal growth inhibitors for this system in such a way that, when inserted in the crystal, they maintain the disulfide bridge environment but its capacity of generate hydrogen-bond networks is removed.
α,α-Dimethylcholine: Esters and Carbamates1 (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTα,α-Dimethylcholine: Esters and Carbamates1William B. WheatleyCite this: J. Am. Chem. Soc. 1954, 76, 10, 2832–2835Publication Date (Print):May 1, 1954Publication History Published online1 May 2002Published inissue 1 May 1954https://pubs.acs.org/doi/10.1021/ja01639a068https://doi.org/10.1021/ja01639a068research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations3LEARN 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
Accuracy of stone‐casts produced from selected addition‐type silicone impressions (1983)

The present study has shown that there is no correlation between the free curing contraction of three selected addition-type silicone impression materials and the effective contraction determined as the accuracy of stone dies produced in dental impressions of these materials. Depending on specific rheologic properties, the free curing contraction of an impression material can be partly compensated for by flow.
Improved noncontact optical sensor for detection of glucose concentration and indication of dehydration level (2014)

The ability to extract different bio-medical parameters from one single wristwatch device can be very applicable. The wearable device that is presented in this paper is based on two optical approaches. The first is the extraction and separation of remote vibration sources and the second is the rotation of linearly polarized light by certain materials exposed to magnetic fields. The technique is based on tracking of temporal changes of reflected secondary speckles produced in the wrist when being illuminated by a laser beam. Change in skin's temporal vibration profile together with change in the magnetic medium that is generated by time varied glucose concentration caused these temporal changes. In this paper we present experimental tests which are the first step towards an in vivo noncontact device for detection of glucose concentration in blood. The paper also shows very preliminary results for qualitative capability for indication of dehydration.
Silencing or Stimulation? siRNA Delivery and the Immune System (2011)

Since its inception more than a decade ago, the field of short interfering RNA (siRNA) therapeutics has demonstrated potential in the treatment of a wide variety of diseases. The power behind RNA interference (RNAi) therapy lies in its ability to specifically silence target genes of interest. As more biological data have become available, it has become evident that, in addition to mediating RNAi, siRNA molecules have the potential to potently induce the innate immune system. One of the significant challenges facing the field today is the differentiation between therapeutic effects caused by target-specific, RNAi-mediated gene silencing and those caused by nonspecific stimulation of the innate immune system. Unless appropriate experimental measures are taken to control for RNA-induced immunostimulation, genetic manipulation can be confused with immune activation. This review attempts to provide an accessible background in siRNA-relevant immunology and to highlight the ways in which siRNA can be engineered to avoid or provoke an innate immune response.
Discovery of Diaminopyrimidine Carboxamide HPK1 Inhibitors as Preclinical Immunotherapy Tool Compounds (2021)

Hematopoietic progenitor kinase 1 (HPK1), a serine/threonine kinase, is a negative immune regulator of T cell receptor (TCR) and B cell signaling that is primarily expressed in hematopoietic cells. Accordingly, it has been reported that HPK1 loss-of-function in HPK1 kinase-dead syngeneic mouse models shows enhanced T cell signaling and cytokine production as well as tumor growth inhibition <i>in vivo</i>, supporting its value as an immunotherapeutic target. Herein, we present the structurally enabled discovery of novel, potent, and selective diaminopyrimidine carboxamide HPK1 inhibitors. The key discovery of a carboxamide moiety was essential for enhanced enzyme inhibitory potency and kinome selectivity as well as sustained elevation of cellular IL-2 production across a titration range in human peripheral blood mononuclear cells. The elucidation of structure-activity relationships using various pendant amino ring systems allowed for the identification of several small molecule type-I inhibitors with promising <i>in vitro</i> profiles.