gebhart/patrepeval huggingface dataset:
A novel flow cytometric method for quantifying phagocytosis of apoptotic cells (1997)

Many eukaryotic cell types are capable of specific recognition and phagocytosis of apoptotic cells, and there is increasing interest in the mechanisms involved in this process. To facilitate analysis of these mechanisms, we designed a novel fluorescence-based method to quantify phagocytosis in vitro using endothelial cell engulfment of apoptotic cells as a model. The B-cell line WEHI-231 was labeled with the fluorophore 5-(&-6)-carboxytetramethyl-rhodamine-succinimidyl-ester (TAMRA) and then induced to undergo apoptosis by crosslinking cell surface immunoglobulin. An endothelial cell line was subsequently allowed to ingest these TAMRA-labeled apoptotic lymphocytes. After 24 h, nonbound lymphocytes were removed and the mono-layers were dissociated. Any nonphagocytosed lymphocytes that remained tightly bound to the endothelial cells were then indirectly immunofluorescein labeled for the pan leukocyte-specific marker CD45. Flow cytometric analysis of the cells distinguished three endothellal cell populations: 1) endothelial cells with surface bound lymphocytes (TAMRA+ CD45+); 2) endothelial cells containing phagocytosed apoptotic lymphocytes (TAMRA+ CD45-); and 3) endothelial cells that were not associated with lymphocytes. The identification of these populations was verified by confocal microscopy of sorted cells. The method described herein will facilitate detailed studies on phagocytic recognition of apoptotic cells and should have broad applications to other phagocytic cell systems.
Study on Inhibitors of Methionine Synthase VIII: Synthesis of 2,5-Diamino-4-oxo-6- (3-butenyl) pyrimidine (2003)

Cobalamin-dependent methionine synthase plays a crucial role in folate metabolism and such would appear to be an excellent target for rational antifolate drug design. However, to date, no anticancer agents directed at this enzyme are available, but the enzyme is efficiently and specifically inhibited by N2O and this has proven invaluable for evaluating the biochemical consequence of enzyme inhibition and for mechanistic studies. [1,2] 2,5-Diamino-4-oxo-6-(3-butenyl) pyrimidine, a key intermediate in synthetic inhibitors of methionine synthase, was first synthesized using γbutenyl-β-ketoester and guanidine carbonate (Scheme 1). [3]……
An Efficient Synthesis of (Fluoromethyl)pyridylamines for Labeling with Fluorine-18 (1999)

We have described a two-step method for the preparation of (fluoromethyl)pyridyl-substituted amines. The sequence involves fluoride ion displacement of methanesulfonates (mesylates) of 6-chloro-α-hydroxy-2- and -3-picolines, followed by arylation of the amine by chloropicoline. We have called this sequence fluorination−N-arylation. 1-Phenylpiperazine has been used as a model amine. Two key precursors for this sequence are the mesylates of 6-chloro-α-hydroxy-2- and -3-picolines. The former was synthesized in four steps from 6-chloro-2-picoline in 78% yield and the latter in three steps from 6-chloronicotinic acid in 53% yield. This fluorination−N-arylation sequence is sufficiently rapid and efficient for the preparation of a variety of aryl-substituted amine compounds labeled with the short half-life (t1/2 = 110 min) positron-emitting radionuclide fluorine-18.
Synthesis and Characterization of pH- and Temperature-Sensitive Poly(methacrylic acid)/Poly(N-isopropylacrylamide) Interpenetrating Polymeric Networks (1999)

Hydrogels of an interpenetrating polymeric network (IPN) composed of the temperature-sensitive poly(N-isopropylacrylamide) (PNIPAAm) and the pH-sensitive poly(methacrylic acid) (PMAA) were prepared by a sequential UV polymerization method. The IPN hydrogels were characterized for their temperature- and pH-responsive behavior by equilibrium swelling studies, oscillatory swelling studies, and differential scanning calorimetry. The permeability of these IPNs has been investigated under various pH and temperature conditions. The results showed that these hydrogels exhibited a combined pH- and temperature-sensitivity at a temperature range of 31−32 °C and a pH value of approximately 5.5. Permeation study results indicate a significant size exclusion behavior while model drugs with different sizes permeate through the IPN membranes. The permeability of the IPN membrane can be significantly affected by varying the pH and temperature conditions.
NMDA antagonists inhibit the development of ethanol dependence in rats. (2002)

The influence of non-competitive NMDA receptor antagonist, 1-amino-3,5-dimethyl-adamantane (memantine), and glycineB site antagonist, 7-chloro-4-hydroxy-3-(3-phenoxy)phenyl-2(1H)-quinolone (L-701,324), on the development of ethanol dependence was investigated in Wistar rats. The development of ethanol dependence was induced by intragastric administration of 20% w/v ethanol, three times a day at increasing doses. The results were quantified using withdrawal audiogenic seizures, 12 h after the last ethanol administration. Memantine (3.75 or 7.5 mg/kg) and L-701,324 (2.5 or 5 mg/kg), given before ethanol administration, prevented the development of ethanol dependence. Our results support the data that NMDA receptors are involved in the development of ethanol dependence.
Phosphite Synthesis of Oligodeoxyribonucleotides (1988)

Data in the literature published between 1983 and 1986 on the synthesis of oligodeoxyribonucleotides from nucleoside derivatives of phosphorous acid are reviewed. Attention is mainly focused on the techniques employed for preparing initial monomers for condensation. The individual stages in the solid-phase phosphite method are presented, and the potential of various approaches for achieving this type of synthesis is discussed. In addition, studies on the synthesis of oligonucleotides with the aid of monoesters of phosphorous acid (phosphonate synthesis) are assessed. The bibliography includes 101 references.
Sodium Triacetoxyborohydride (2007)

[56553-60-7] C6H10BNaO6 (MW 211.96) InChI = 1S/C6H10BO6.Na/c1-4(8)11-7(12-5(2)9)13-6(3)10;/h7H,1-3H3;/q-1;+1 InChIKey = HHYFEYBWNZJVFQ-UHFFFAOYSA-N (the prototype of a class of NaBH(OCOR)3 reagents that are selective reducing agents for a number of functional groups1 and heterocycles;1 alkylation of amines;1-4 hydroboration1) Physical Data: mp 116–120 °C (dec); the related NaBH3OAc has not been fully characterized. Solubility: NaBH(OAc)3 and related acyloxyborohydrides are rapidly destroyed by H2O and protic solvents; H2 is liberated. Cosolvents that have been employed are benzene, toluene, THF, dioxane, CH2Cl2, ClCH2CH2Cl. Form Supplied in: NaBH(OAc)3 and the related Tetramethylammonium Triacetoxyborohydride are commercially available as colorless powders. Preparative Method: NaBH(OAc)3 and NaBH3OAc can be easily prepared in situ from the appropriate amount of acetic acid and NaBH4. Analysis of Reagent Purity: NaBH(OAc)3 has been characterized by elemental analysis, IR, and 1H, 13C, and 11B NMR. Handling, Storage, and Precautions: because H2 is liberated during the preparation of these reagents, all handling and storage of acyloxyborohydrides should take place under an inert atmosphere.
Modulation of the murine immune response to human IgG by complexing with monoclonal antibodies. I. Antibody responses to determinants on the constant region of light chains and gamma chains. (1987)

Complexing a human IgG lambda paraprotein with a monoclonal antibody (McAb) to a lambda-chain determinant markedly depressed the anti-lambda response of immunized mice. No anti-lambda was found in the serum after two or four injections of the complex, whereas high titres of anti-lambda chain antibody were found in the sera of mice immunized with the IgG paraprotein complexed with any single anti-gamma chain McAb or with a pool of anti-gamma chain McAbs. Responses to the highly immunogenic Fc gamma portion of the molecule were not suppressed by complexing with a single anti-gamma chain McAb and were only slightly suppressed after complexing with a pool of anti-gamma chain McAbs. Some anti-Fc gamma antibody was produced by all animals receiving a single injection of the immunogen complexed to any McAb, but free immunogen did not generate a primary response. Complexing the IgG with an anti-Fc gamma McAb enhanced the response to to the poorly immunogenic C gamma 1 domain but no anti-C-gamma 1 was produced by mice receiving the IgG complexed with an anti-C-gamma 1 McAb. In immunizations with 'free' (Bence-Jones) lambda chain, all the antibody produced was directed against 'free'-specific determinants. Complexing the Bence-Jones protein with McAbs to 'free' or 'general' determinants on the lambda chain did not enhance or suppress the response. It is concluded that the response to weakly or moderately immunogenic, but not to strongly immunogenic, regions of the molecule may be suppressed by complexing the immunogen with a McAb of appropriate specificity. Possible reasons for this result are discussed.
Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor (2015)

Circular RNAs (circRNAs) are widespread circles of non-coding RNAs with largely unknown function. Because stimulation of mammary cells with the epidermal growth factor (EGF) leads to dynamic changes in the abundance of coding and non-coding RNA molecules, and culminates in the acquisition of a robust migratory phenotype, this cellular model might disclose functions of circRNAs. Here we show that circRNAs of EGF-stimulated mammary cells are stably expressed, while mRNAs and microRNAs change within minutes. In general, the circRNAs we detected are relatively long-lived and weakly expressed. Interestingly, they are almost ubiquitously co-expressed with the corresponding linear transcripts, and the respective, shared promoter regions are more active compared to genes producing linear isoforms with no detectable circRNAs. These findings imply that altered abundance of circRNAs, unlike changes in the levels of other RNAs, might not play critical roles in signaling cascades and downstream transcriptional networks that rapidly commit cells to specific outcomes.
cuDNN: Efficient Primitives for Deep Learning (2014)

We present a library of efficient implementations of deep learning primitives. Deep learning workloads are computationally intensive, and optimizing their kernels is difficult and time-consuming. As parallel architectures evolve, kernels must be reoptimized, which makes maintaining codebases difficult over time. Similar issues have long been addressed in the HPC community by libraries such as the Basic Linear Algebra Subroutines (BLAS). However, there is no analogous library for deep learning. Without such a library, researchers implementing deep learning workloads on parallel processors must create and optimize their own implementations of the main computational kernels, and this work must be repeated as new parallel processors emerge. To address this problem, we have created a library similar in intent to BLAS, with optimized routines for deep learning workloads. Our implementation contains routines for GPUs, although similarly to the BLAS library, these routines could be implemented for other platforms. The library is easy to integrate into existing frameworks, and provides optimized performance and memory usage. For example, integrating cuDNN into Caffe, a popular framework for convolutional networks, improves performance by 36% on a standard model while also reducing memory consumption.
Polyvinyl alcohol : developments (1992)

Partial table of contents: Manufacture of Polyvinyl Acetate for Polyvinyl Alcohol (F. Marten & C. Zvanut). Hydrolysis of Polyvinyl Acetate to Polyvinyl Alcohol (C. Zvanut & F. Marten). Modification of Polyvinyl Alcohol by Copolymerization (T. Okaya). Ethylene-Vinyl Alcohol Copolymers (T. Okaya & K. Ikari). Spectroscopic Properties of Polyvinyl Alcohol (A. Dunn). Use of Polyvinyl Alcohol in Paper Manufacture (G. Miller). Applications of Polyvinyl Alcohol in Adhesives (C. Finch). Applications of Polyvinyl Alcohol as a Binder (C. Finch). Appendices. Indexes.
Determination of the transcriptional regulatory region of a vaccinia virus late gene (1987)

A putative promoter region, extending from 218 base pairs (bp) before (-218) to 10 bp after (+10) the RNA start site of a vaccinia virus gene encoding an Mr-28,000 precursor of a core polypeptide that is expressed only after the onset of DNA replication was linked to DNA coding for the procaryotic enzyme chloramphenicol acetyltransferase (CAT). When this chimeric gene was inserted into the genome of vaccinia virus, the infectious recombinant expressed CAT in a regulated fashion. A series of deletions starting upstream of the promoter region and extending toward the RNA start site were made. The effects of these mutations on CAT expression were examined in cells infected with recombinant viruses and confirmed in a helper virus-dependent transient assay system. A gradual reduction in CAT expression occurred as the deletions extended from -61 to -18. Mutants that retained 18 bp before and 10 bp after the RNA start site still expressed CAT as a late gene product, although at a submaximal level. A further 5'-to-3' deletion of 10 bp reduced CAT expression to background levels. To demonstrate that the effect on expression was not simply due to the bringing of upstream inhibitory sequences closer to the RNA start site, a point mutation substituting a G for the A at -12 was made. The sharp decrease in CAT expression indicated the importance of a run of eight A residues located between -15 and -7. Evidence that these mutations affected the level but not the site of transcriptional initiation was demonstrated by analysis of the 5' ends of the mRNAs from infected cells. The short DNA sequence required for accurate and temporally regulated transcription suggests that the same or overlapping signals are used for both aspects of this process.
Frequency and Phenotype of Human Immunodeficiency Virus Envelope-Specific B Cells from Patients with Broadly Cross-Neutralizing Antibodies (2008)

Induction of broadly cross-reactive neutralizing antibodies (NAb) is an important goal for a prophylactic human immunodeficiency virus type 1 (HIV-1) vaccine. Some HIV-infected patients make a NAb response that reacts with diverse strains of HIV-1, but most candidate vaccines have induced NAb only against a subset of highly sensitive isolates. To better understand the nature of broad NAb responses that arise during natural infection, we screened patients for sera able to neutralize diverse HIV strains and explored the frequency and phenotype of their peripheral Envelope-specific B cells. We screened 113 HIV-infected patients of various clinical statuses for the prevalence of broad NAb. Sera able to neutralize at least four of five viral isolates were found in over one-third of progressors and slow progressors, but much less frequently in aviremic long-term nonprogressors. Most Env-specific antibody-secreting B cells were CD27(hi) CD38(hi) plasmablasts, and the total plasmablast frequency was higher in HIV-infected patients than in uninfected donors. We found that 0.0031% of B cells and 0.047% of plasmablasts secreted Env-specific immunoglobulin G (IgG) in an enzyme-linked immunospot (ELISPOT) assay. We developed a novel staining protocol to label HIV-specific B cells with Env gp140 protein. A total of 0.09% of B cells were found to be Env-specific by this method, a frequency far higher than that indicated by ELISPOT assay. gp140-labeled B cells were predominantly CD27(+) and surface IgG(+). These data describe the breadth and titer of serum NAb and the frequency and phenotype of HIV-specific B cells in a cohort of patients with broad cross-neutralizing antibody responses that are potential goals for vaccines for HIV.
Interactive Image Segmentation via Adaptive Weighted Distances (PREPRINT) (2006)

An interactive algorithm for soft segmentation of natural images is presented in this paper. The user first roughly scribbles different regions of interest, and from them the whole image is automatically segmented. This soft segmentation is obtained via fast, linear complexity, computation of weighted distances to the user-provided scribbles. The adaptive weights are obtained from a series of Gabor filters, and are automatically computed according to the ability of each single filter to discriminate between the selected regions of interest. We present the underlying framework and examples showing the capability of the algorithm to segment diverse images.
Interferon-dependent IL-10 production by Tregs limits tumor Th17 inflammation (2013)

The capacity of IL-10 and Tregs in the inflammatory tumor microenvironment to impair anticancer Th1 immunity makes them attractive targets for cancer immunotherapy. IL-10 and Tregs also suppress Th17 activity, which is associated with poor prognosis in several cancers. However, previous studies have overlooked their potential contribution to the regulation of pathogenic cancer-associated inflammation. In this study, we investigated the origin and function of IL-10–producing cells in the tumor microenvironment using transplantable tumor models in mice. The majority of tumor-associated IL-10 was produced by an activated Treg population. IL-10 production by Tregs was required to restrain Th17-type inflammation. Accumulation of activated IL-10+ Tregs in the tumor required type I IFN signaling but not inflammatory signaling pathways that depend on TLR adapter protein MyD88 or IL-12 family cytokines. IL-10 production limited Th17 cell numbers in both spleen and tumor. However, type I IFN was required to limit Th17 cells specifically in the tumor microenvironment, reflecting selective control of tumor-associated Tregs by type I IFN. Thus, the interplay of type I IFN, Tregs, and IL-10 is required to negatively regulate Th17 inflammation in the tumor microenvironment. Therapeutic interference of this network could therefore have the undesirable consequence of promoting Th17 inflammation and cancer growth.
Fabrication of nanodevices using sub-25 nm imprint lithography (2002)

The key obstacle that prevents many nanostructures and nanodevices from becoming economically viable is the lack of a high-throughput and low-cost nanolithography method. Recently, a high-throughput and low-cost nanolithography method, imprint lithography, has been proposed and demonstrated. Here, we report new progress in imprint lithography and the first fabrication of nanodevices (such as MSM photodetectors and Si quantum wire transistors) using imprint lithography. In imprint lithography a mold with nanoscale features is first pressed into a resist film cast on a substrate to create a thickness contrast pattern in the resist. After removing the mold, an anisotropic etching process is used to transfer the pattern through the entire resist thickness by removing the remaining resist in the compressed areas.
Study confirms that protease inhibitor cocktail can delay HIV disease progression and death. (1997)

A study funded by the National Institute of Allergy and Infectious Diseases (NIAID) has shown that combination protease inhibitor therapy plus two nucleoside analogues is significantly more effective than using two nucleoside analogs alone in reducing the occurrence of AIDS-defining illnesses and death. Since preliminary results of ACTG 320 provided such strong evidence, the board recommended early termination of enrollment and study closure.
Effects of clenbuterol on insulin resistance in conscious obese Zucker rats (2001)

The present study was conducted to determine the effect of chronic administration of the long-acting beta(2)-adrenergic agonist clenbuterol on rats that are genetically prone to insulin resistance and impaired glucose tolerance. Obese Zucker rats (fa/fa) were given 1 mg/kg of clenbuterol by oral intubation daily for 5 wk. Controls received an equivalent volume of water according to the same schedule. At the end of the treatment, rats were catheterized for euglycemic-hyperinsulinemic (15 mU insulin. kg(-1). min(-1)) clamping. Clenbuterol did not change body weight compared with the control group but caused a redistribution of body weight: leg muscle weights increased, and abdominal fat weight decreased. The glucose infusion rate needed to maintain euglycemia and the rate of glucose disappearance were greater in the clenbuterol-treated rats. Furthermore, plasma insulin levels were decreased, and the rate of glucose uptake into hindlimb muscles and abdominal fat was increased in the clenbuterol-treated rats. This increased rate of glucose uptake was accompanied by a parallel increase in the rate of glycogen synthesis. The increase in muscle glucose uptake could not be ascribed to an increase in the glucose transport protein GLUT-4 in clenbuterol-treated rats. We conclude that chronic clenbuterol treatment reduces the insulin resistance of the obese Zucker rat by increasing insulin-stimulated muscle and adipose tissue glucose uptake. The improvements noted may be related to the repartitioning of body weight between tissues.
High Prevalence of Autoantibodies Against Carbonic Anhydrase II and Lactoferrin in Type 1 Diabetes: Concept of Autoimmune Exocrinopathy and Endocrinopathy of the Pancreas (2003)

The high prevalence of both ACA and ALF strongly suggests the involvement of autoimmunity against the exocrine pancreas as well as the endocrine pancreas in some type 1 diabetic patients. We propose that these conditions be referred to as autoimmune exocrinopathy and endocrinopathy of the pancreas.
Picosecond pulses on superconducting striplines (1978)

The attenuation and phase velocity of a superconducting thin-film stripline are calculated at high frequencies using the theory of Mattis and Bardeen. These results are used to study the propagation of picosecond pulses which have frequency components approaching the superconducting energy-gap frequency.
Label-Free Single-Molecule Thermoscopy Using a Laser-Heated Nanopore (2017)

When light is used to excite electronic transitions in a material, nonradiative energy during relaxation is often released in the form of heat. In this work, we show that photoexcitation of a silicon nitride nanopore using a focused visible laser results in efficient localized photothermal heating, which reduces the nearby electrolyte viscosity and increases the ionic conductance. In addition, a strong localized thermal gradient in the pore vicinity is produced, evidenced by finite-element simulations and experimental observation of both ion and DNA thermophoresis. After correcting for thermophoresis, the nanopore current can be used as a nanoscale thermometer, enabling rapid force thermoscopy. We utilize this to probe thermal melting transitions in synthetic and native biomolecules that are heated at the nanopore. Our results on single molecules are validated by correspondence to bulk measurements, which paves the way to various biophysical experiments that require rapid temperature and force control on individual molecules.