gebhart/patrepeval huggingface dataset:
Average case analysis of multichannel basis pursuit (2009)

We consider the recovery of jointly sparse multichannel signals from incomplete measurements using convex relaxation methods. Worst case analysis is not able to provide insights into why joint sparse recovery is superior to applying standard sparse reconstruction methods to each channel individually. Therefore, we analyze an average case by imposing a probability model on the measured signals. We show that under a very mild condition on the sparsity and on the dictionary characteristics, measured for example by the coherence, the probability of recovery failure decays exponentially in the number of channels. This demonstrates that most of the time, multichannel sparse recovery is indeed superior to single channel methods. 1.
The CIS/SOCS proteins: a family of cytokine-inducible regulators of signaling. (1999)

This review describes the main properties of a new family of cytokine-inducible proteins which interfere with the Jak/Stat transduction pathway and negatively regulate the duration of cytokine-induced signal activation. These proteins act not only as negative feedback regulators but also inhibit response to cytokines different from those used to induce their expression. These proteins are potentially important regulators of inflammatory and immune responses of hematopoiesis and hormone response.
In vitro biological effects of novel type I photosensitizers and their mechanism of action (2010)

Photodynamic therapy involving Type 2 photosenstizers has been conspicuously successful in the treatment of various lesions. Type 1 process, in contrast has not received much attention despite its considerable potential. We have prepared several classes of molecules containing fragile bonds that will produce reactive intermediates such as radicals and nitrenes upon photoexcitation with UV-A and visible light. In a primary screen, many of these compounds had a significant concentration and light dose dependent effect on the cell viability on U937. The chemistry of these compounds differentiated their ability to induced cytotoxic effects. To further establish these findings, we tested one compound representing each class of chemistry in three different tumor cell lines. Cells were incubated with three different concentrations (100&mu;M, 25&mu;M and 6.25&mu;M) and exposed to UV light dose of 4J/cm<sup>2</sup> and 8J/cm<sup>2</sup>. The compounds showed varying effects on viability in different cell lines. Finally we also investigated the ability to induce apoptosis as the mechanism of cell death in HCT116 cell lines using the experimental conditions mentioned. The type 1 photosensitizers induced apoptosis as early as 4 hours after exposure in HCT116 cells and the rate of apoptosis increased with time with majority of cells in late apoptotic or necrotic stage.
Application of an improved single-radial-immunodiffusion technique for the assay of haemagglutinin antigen content of whole virus and subunit influenza vaccines. (1978)

An improved single-radial-diffusion technique for the assay of influenza haemagglutinin antigen is described. The modified method enables the results of assays of antigen to be obtained more rapidly and with greater precision than previously. The use of immunoplates containing varied, preselected concentrations of antihaemagglutinin antibody allows accurate assays to be performed over a wide range of antigen concentration. In tests on "whole virus" antigen preparations it was found that the ratio between haemagglutination titre (iu/ml) and haemagglutinin antigen activity (microgram/ml) determined by single-radial-diffusion was relatively constant for antigens containing a given strain but showed variation between strains (range 16.5 to 26.8 iu/microgram HA activity). For the subunit vaccines examined this ratio showed a large degree of variation (range 1.4 to 16.6 iu/microgram HA activity) and in general was considerably lower than for whole virus antigens. It was concluded that single-radial-diffusion may be of value for assays of the haemagglutinin concentration of both "whole virus" vaccines and subunit vaccines. The data presented suggest that, in the event of antigenic drift, it may be possible to use the existing reference anti-haemagglutinin serum to assay a variant strain of influenza virus.
All screen-printed 18% homogeneous emitter solar cells using high volume manufacturing equipment (2010)

The Innovalight Cougar <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">™</sup> Platform is a portfolio of simple to implement technologies that, when combined with Innovalight Silicon Ink, enables the manufacture of a selective emitter solar cell with a non-masking single-step diffusion. Cell efficiencies of up to 19% have been achieved. Innovalight Silicon Ink is a highly engineered silicon nanoparticle colloidal dispersion, implemented for both high volume ink-jet and screen deposition, and further optimized to be produced and delivered in commercial volumes. To compare the advancement of the Innovalight Cougar Platform against a standard process, a screen-printed solar cell structure with a homogeneous 50-60Ω/sq emitter, has been developed. It uses standard production equipment and closely mirrors the process typically used by photovoltaic manufactures today. In an effort to emulate the best cells currently in production, we have advanced the reference cell through surface texture, both acidic (ISO) and random pyramids, and diffusion optimization using in-line and tube diffusion. The tube diffusion has an advantage, over in-line processing, in open-circuit voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OC</sub> ) of 9mV and fill factor of 0.9% resulting in an increase in efficiency by 0.4% absolute for the ISO texture process. Comparing tube diffused ISO to random pyramid textured substrates, a difference in V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OC</sub> of +4mV and short-circuit current (J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SC</sub> ) of +2.3mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> was found without a loss in fill factor for the random pyramid textured substrates. This results in an efficiency gain of 1.1% absolute to a 17.8% median. Additionally, we successfully demonstrated scaling the substrate size from 125mm to 156mm for this process flow without affecting the cell performance and achieving equivalent efficiency of 18%.
Infrared Reflectance of Evaporated Aluminum Films (1962)

The specular reflectance of evaporated aluminum films has been measured with high precision (±0.1%) from 0.55 to 32 μ. The measurements were made at normal incidence on fresh and aged films deposited on fuzed quartz substrates with rapid evaporation rates at pressures of about 1×10−5 Torr. The dependence of the reflectance on the evaporation conditions was also investigated, and it was found that the infrared reflectance of aluminum prepared under the usual high-vacuum conditions is reproducible and insensitive to the conditions of film preparation. Although the measured reflectance of freshly evaporated aluminum films differs by only 0.1% at 30 μ from the value calculated from the free-electron approximation assuming bulk parameters for aluminum, the variation of the measured reflectance with wavelength does not fit the theory in the infrared. It is felt that the validity of the free-electron approximation should be further tested by using films deposited in ultra-high vacuum.
Dependence of the Rate of an Interfacial Diels−Alder Reaction on the Steric Environment of the Immobilized Dienophile:  An Example of Enthalpy−Entropy Compensation (2002)

This paper describes a physical organic study of the relationship between the rate for an interfacial Diels-Alder reaction and the steric environment around the reacting molecules. The study used as a model reaction the cycloaddition of cyclopentadiene with a self-assembled monolayer (SAM) presenting benzoquinone groups surrounded by hydroxyl-terminated alkanethiolates. The accessibility of the quinone was varied by preparing monolayers from hydroquinone-terminated alkanethiols of different lengths [HS(CH(2))(n)-HQ, n = 6-14] and a hydroxyl-terminated alkanethiol [HS(CH(2))(11)-OH] of constant length. Cyclic voltammetry was used to measure the rate of the reaction by monitoring the decay of the redox-active quinone. The second-order rate constant showed a modest change as the position of quinone was varied relative to the hydroxyl groups of the monolayer. For monolayers wherein the quinone groups were extended from the interface, the rate constants oscillated near 0.20 M(-1) s(-1) with an even-odd dependence on the length of the alkanethiol. For monolayers that positioned the quinone groups below the surrounding hydroxyl groups, the rate constants decreased by approximately 8-fold. Examination of the activation parameters revealed that the quinone groups that were positioned below the interface (and in a crowded environment) reacted with an enthalpy of activation that was 4 kcal/mol greater than did the quinones that were accessible at the interface. The reaction of the buried quinone, however, proceeded with an entropy of activation that was more favorable by 13 eu, and therefore with a similar free energy of activation. The combination of SAMs for preparing model interfaces and cyclic voltammetry for measuring rates provides a new opportunity for physical organic studies of interfacial reactions.
Enrichment of Single Chirality Carbon Nanotubes (2007)

Two liquid chromatography techniques for single-walled carbon nanotube (SWNT) separation, size-exclusion chromatography (SEC), and ion-exchange chromatography (IEX) are combined to obtain small diameter semiconducting SWNTs with defined length and chirality. It is observed that these tubes elutes in the IEX separation in the order of (6,4), (9,1), (6,5), (8,3), and (7,5). The improved resolution allows clear separation of (6,5) from (9,1), two semiconducting SWNTs with identical diameter but different chirality.
[Taxol-induced apoptosis in Jurkat T cell lymphoma cell line and its molecular mechanisms]. (2000)

Taxol can specifically induce Jurkat cell apoptosis. It might provide a theoretical basis for clinical treatment and a good model for studying apoptotic gene modulation. Bax and bcl-x(s) participate in the taxol induced apoptosis of Jurkat cells.
The E. Donnall Thomas Lecture: Normal and Neoplastic Stem Cells (2008)

Dr. Irving Weissman was the honored E. Donnall Thomas lecturer at the Tandem BMT Meetings, held on February 10, 2007, at Keystone, Colorado. Dr. Weissman has been a major player, and has provided us with enormous insight into many areas of biology, dating back to his high school days in Montana. He led an enormously productive career at Stanford University where he has taught us many lessons involving our understanding of lymphocyte homing, stem cell biology, both of the hematopoietic system and other types of stem cells, and also now, about cancer stem cells. Dr. Weissman has made enormous contributions to this burgeoning field that has provided us new insights and new opportunities for treatment strategies. In addition to a very productive laboratory career, he is also currently the director of both the Stem Cell Institute, as well as the Cancer Center at Stanford University. The following text is a modified transcribed version of the presentation made by Dr. Weissman.
Development of meta-tetrahydroxyphenylchlorin-monoclonal antibody conjugates for photoimmunotherapy. (1999)

A limitation of photodynamic therapy is the lack of tumor selectivity of the photosensitizer. To overcome this problem, a protocol was developed for coupling of meta-tetrahydroxyphenylchlorin (mTHPC), one of the most promising photosensitizers, to tumor-selective monoclonal antibodies (MAbs). mTHPC was radiolabeled with 131I to facilitate the assessment of the in vitro and in vivo behavior. After the modification to 131I-mTHPC-(CH2COOH)4, thus increasing the water solubility and creating a functional moiety suitable for coupling, conjugation was performed using a labile ester. Insoluble aggregates were not formed when mTHPC-MAb conjugates with a molar ratio of up to 4 were prepared. These conjugates showed a minimal impairment of the integrity on SDS-PAGE, full stability in serum in vitro, and an optimal immunoreactivity. To test the in vivo behavior of the mTHPC-MAb conjugates, the head and neck squamous cell carcinoma-selective chimeric MAb U36 was used in head and neck squamous cell carcinoma-bearing nude mice. Biodistribution data showed that the tumor selectivity of cMAb U36-conjugated mTHPC was increased in comparison with free mTHPC, despite the fact that conjugates with a higher mTHPC:MAb ratio were more rapidly cleared from the blood. Preliminary results on the in vitro efficacy of photodynamic therapy with MAb-conjugated mTHPC showed that mTHPC coupled to the internalizing murine MAb 425 exhibited more phototoxicity than when coupled to the noninternalizing chimeric MAb U36.
Cardiovascular Regulation in Mice Lacking α 2 -Adrenergic Receptor Subtypes b and c (1996)

alpha2-Adrenergic receptors (alpha2ARs) are essential components of the neural circuitry regulating cardiovascular function. The role of specific alpha2AR subtypes (alpha2a, alpha2b, and alpha2c) was characterized with hemodynamic measurements obtained from strains of genetically engineered mice deficient in either alpha2b or alpha2c receptors. Stimulation of alpha2b receptors in vascular smooth muscle produced hypertension and counteracted the clinically beneficial hypotensive effect of stimulating alpha2a receptors in the central nervous system. There were no hemodynamic effects produced by disruption of the alpha2c subtype. These results provide evidence for the clinical efficacy of more subtype-selective alpha2AR drugs.
Correlation between in Vitro Stability and in Vivo Performance of Anti-GCN4 Intrabodies as Cytoplasmic Inhibitors (2000)

A cellular assay system for measuring the activity of cytoplasmically expressed anti-GCN4 scFv fragments directed against the Gcn4p dimerization domain was established in the budding yeast Saccharomyces cerevisiae. The inhibitory potential of different constitutively expressed anti-GCN4 scFv intrabodies was monitored by measuring the activity of beta-galactosidase expressed from a GCN4-dependent reporter gene. The in vivo performance of these scFv intrabodies in specifically decreasing reporter gene activity was related to their in vitro stability, measured by denaturant-induced equilibrium unfolding. A framework-engineered stabilized version showed significantly improved activity, while a destabilized point mutant of the anti-GCN4 wild-type showed decreased effects in vivo. These results indicate that stability engineering can result in improved performance of scFv fragments as intrabodies. Increasing the thermodynamic stability appears to be an essential factor for improving the yield of functional scFv in the reducing environment of the cytoplasm, where the conserved intradomain disulfides of antibody fragments cannot form.
Amino Acid Ingestion Strongly Enhances Insulin Secretion in Patients With Long-Term Type 2 Diabetes (2003)

The insulin secretory capacity in long-term type 2 diabetic patients is substantially underestimated, as the insulin response following carbohydrate intake can be nearly tripled by coingestion of a free amino acid/protein mixture. Future research should be performed to investigate whether such nutritional interventions can improve postprandial glucose disposal.
Crystal Structure of Yeast Acetyl-Coenzyme A Synthetase in Complex with AMP (2004)

Acetyl-coenzyme A synthetase (ACS) belongs to the family of AMP-forming enzymes that also includes acyl-CoA synthetases, firefly luciferase, and nonribosomal peptide synthetases. ACS catalyzes the two-step activation of acetate to acetyl-CoA: formation of an acetyl-AMP intermediate from acetate and ATP and the transfer of the acetyl group to CoA. In mammals, the acetyl-CoA product is used for biosynthesis of long chain fatty acids as well as energy production. We have determined the crystal structure of yeast ACS in a binary complex with AMP at 2.3 A resolution. The structure contains a large, N-terminal domain and a small, C-terminal domain. AMP is bound at the interface between the two domains. This structure represents a new conformation for the ACS enzyme, which may be competent for catalyzing the first step of the reaction. A Lys residue that is critical for this step is located in the active site. A rotation of 140 degrees in the small domain is needed for the binding of CoA and the catalysis of the second step. In contrast to the monomeric bacterial enzyme, yeast ACS is a stable trimer.
CHANGES IN CONTENTS OF CARBOHYDRATE AND FATTY ACID IN THE CELLS OF CHLORELLA PROTOTHECOIDES DURING THE PROCESSES OF DE- AND RE-GENERATION OF CHLOROPLASTS (1966)

Journal Article CHANGES IN CONTENTS OF CARBOHYDRATE AND FATTY ACID IN THE CELLS OF CHLORELLA PROTOTHECOIDES DURING THE PROCESSES OF DE- AND RE-GENERATION OF CHLOROPLASTS Get access MITSUO MATSUKA, MITSUO MATSUKA Institute of Applied Microbiology, University of Tokyo, and Tokugawa Institute for Biological ResearchTokyo Search for other works by this author on: Oxford Academic Google Scholar HAMA OTSUKA, HAMA OTSUKA Institute of Applied Microbiology, University of Tokyo, and Tokugawa Institute for Biological ResearchTokyo Search for other works by this author on: Oxford Academic Google Scholar EIJI HASE EIJI HASE Institute of Applied Microbiology, University of Tokyo, and Tokugawa Institute for Biological ResearchTokyo Search for other works by this author on: Oxford Academic Google Scholar Plant and Cell Physiology, Volume 7, Issue 4, December 1966, Pages 651–662, https://doi.org/10.1093/oxfordjournals.pcp.a079217 Published: 01 December 1966 Article history Received: 24 September 1966 Published: 01 December 1966
Contributions of mass spectrometry to structural immunology (2000)

Mass spectrometry has made important contributions to the field of immunology in the past decade. A variety of mass spectrometric-based techniques have been applied to study the structures of macromolecules that play a vital role in the immune response. These include traditional molecular mass measurements to identify post-translational modifications and structural heterogeneity, mass mapping of proteolysis products, sequencing by tandem mass spectrometry and conformational analysis. Antigen-antibody and other immune complexes have been detected by mass spectrometry, providing an avenue to study macromolecular assemblies that are important to immune function. By virtue of the ability of mass spectrometry based techniques to analyze complex biological mixtures, mass spectrometry has also been employed to identify and sequence protein epitopes important in both the humoral and cellular immune responses. This has been achieved through a combination of immunoaffinity and mass spectrometric techniques, and the coupling of high-performance chromatographs to mass spectrometers. These approaches are important for the identification of pathogens and show promise for the early diagnosis of disease associated with viral and bacterial infection and malignancy. These investigations will enable the mechanisms associated with normal and impaired immune function to be elucidated. Mass spectrometry has been utilized to characterize the structure of peptide mimics, multiple antigenic peptides and other constructs in the design of synthetic immunogens. Information derived from these studies will aid in the development of novel therapeutics and vaccines.
Teichuronic acid operon of Bacillus subtilis 168 (1999)

Sequence analysis reveals that the Bacillus subtilis 168 tuaABCDEFGH operon encodes enzymes required for the polymerization of teichuronic acid as well as for the synthesis of one of its precursors, the UDP-glucuronate. Mutants deficient in any of the tua genes, grown in batch cultures under conditions of phosphate limitation, were characterized by reduced amounts of uronate in their cell walls. The teichuronic acid operon belongs to the Pho regulon, as phosphate limitation induces its transcription. Placing the tuaABCDEFGH operon under the control of the inducible Pspac promoter allowed its constitutive expression independently of the phosphate concentration in the medium; the level of uronic acid in cell walls was dependent on the concentration of the inducer. Apparently, owing to an interdependence between teichoic and teichuronic acid incorporation into the cell wall, in examined growth conditions, the balance between the two polymers is maintained in order to insure a constant level of the wall negative charge.
Direct contact between human primitive hematopoietic progenitors and bone marrow stroma is not required for long-term in vitro hematopoiesis (1992)

Long-term bone marrow cultures support both differentiation and conservation of primitive human hematopoietic progenitors in the absence of exogenous cytokines. It is believed that hematopoiesis in such cultures requires direct contact between hematopoietic progenitors and stroma. In the present study, we demonstrate that primitive progenitors physically separated from the stromal layer by a 0.45-microns microporous membrane continue to generate differentiated progenitors for at least 8 weeks. Moreover, primitive progenitors are conserved to a greater extent under these conditions, as when cultured in direct contact with the stroma. However, excessive production of granulocyte-macrophage progenitors occurs when primitive progenitors are not allowed to interact directly with the stroma. Thus, direct contact between hematopoietic and stromal cells is not required for either differentiation or conservation of primitive hematopoietic progenitors but is essential for the regulated production of mature blood elements. These findings can now be used to define the role of diffusible factors and cell-cell or cell-extracellular matrix adhesion events in the regulation of conservation, proliferation, and differentiation of primitive human hematopoietic progenitors in vitro.
Human Liver Bioengineering Using a Whole Liver Decellularized Bioscaffold (2013)

As a result of significant progress made in the last years in developing methods of whole organ decellularization techniques, organ bioengineering may now look more feasible than ever before. In this chapter, we describe in detail the necessary steps in human liver bioengineering. These include ferret liver decellularization by detergent perfusion, human liver progenitor and endothelial cell isolation, and finally, liver bioscaffold recellularization in a perfusion bioreactor.