gebhart/patrepeval huggingface dataset:
Least-squares model-based halftoning (1992)

A least-squares model-based approach to digital halftoning is proposed. It exploits both a printer model and a model for visual perception. It attempts to produce an 'optimal' halftoned reproduction, by minimizing the squared error between the response of the cascade of the printer and visual models to the binary image and the response of the visual model to the original gray-scale image. Conventional methods, such as clustered ordered dither, use the properties of the eye only implicitly, and resist printer distortions at the expense of spatial and gray-scale resolution. In previous work we showed that our printer model can be used to modify error diffusion to account for printer distortions. The modified error diffusion algorithm has better spatial and gray-scale resolution than conventional techniques, but produces some well known artifacts and asymmetries because it does not make use of an explicit eye model. Least-squares model-based halftoning uses explicit eye models and relies on printer models that predict distortions and exploit them to increase, rather than decrease, both spatial and gray-scale resolution. We have shown that the one-dimensional least-squares problem, in which each row or column of the image is halftoned independently, can be implemented with the Viterbi's algorithm. Unfortunately, no closed form solution can be found in two dimensions. The two-dimensional least squares solution is obtained by iterative techniques. Experiments show that least-squares model-based halftoning produces more gray levels and better spatial resolution than conventional techniques. We also show that the least- squares approach eliminates the problems associated with error diffusion. Model-based halftoning can be especially useful in transmission of high quality documents using high fidelity gray-scale image encoders. As we have shown, in such cases halftoning can be performed at the receiver, just before printing. Apart from coding efficiency, this approach permits the halftoner to be tuned to the individual printer, whose characteristics may vary considerably from those of other printers, for example, write-black vs. write-white laser printers.
Effects of Chemically Modified Messenger RNA on Protein Expression (2016)

Chemically modified nucleotides play significant roles in the effectiveness of mRNA translation. Here, we describe the synthesis of two sets of chemically modified mRNAs [encoding firefly Luciferase (FLuc) and enhanced green fluorescent protein (eGFP), respectively], evaluation of protein expression, and correlation analysis of expression level under various conditions. The results indicate that chemical modifications of mRNAs are able to significantly improve protein expression, which is dependent on cell types and coding sequences. Moreover, eGFP mRNAs with N1-methylpseudouridine (me(1)ψ), 5-methoxyuridine (5moU), and pseudouridine (ψ) modifications ranked top three in cell lines tested. Interestingly, 5moU-modified eGFP mRNA was more stable than other eGFP mRNAs. Consequently, me(1)ψ, 5moU, and ψ are promising nucleotides for chemical modification of mRNAs.
The calcium current activated by T cell receptor and store depletion in human lymphocytes is absent in a primary immunodeficiency. (1994)

Stimulation of antigen receptors of lymphocytes triggers a transitory release of Ca2+ from internal stores and the opening of a transmembrane Ca2+ conductive pathway. The latter underlies the sustained increase of intracellular free calcium concentration, and it seems to be a key event in the Ca(2+)-dependent biochemical cascade leading to T cell proliferation. Alternatively, pharmacological depletion of internal stores by itself activates Ca2+ influx. This has led to the hypothesis that antigen-triggered Ca2+ influx is secondary to Ca2+ release from internal stores. However, the precise relationship between antigen and Ca2+ release-activated Ca2+ currents remains unclear, particularly since neither of them has been electrophysiologically recorded in normal lymphocytes. Using the whole-cell and the perforated configurations of the patch clamp technique on peripheral blood lymphocytes, we found that a low amplitude Ca(2+)-selective current was triggered when intracellular stores were depleted by stimuli such as the intracellular perfusion of inositol triphosphate or thapsigargin and the extracellular perfusion of ionomycin. A similar current was elicited by the cross-linking of the T cell receptor-CD3 complex. This current displayed an inward rectification below 0 mV and was completely blocked by the divalent cation Cd2+. It was very selective for Ca2+ over Na+ and insensitive to changes in chloride concentration. The physiological relevance of this conductance was investigated with the analysis of abnormal Ca2+ signaling in lymphocytes from a patient suffering from a primary immunodeficiency associated with a defective T cell proliferation. Using fura-2 video imaging, an absence of Ca2+ influx was established in the patient's lymphocytes, whereas the Ca2+ release from internal stores was normal. This was the case whether cells were stimulated physiologically through their antigen receptors or with store depleting pharmacological agents. Most importantly, no Ca(2+)-selective current was elicited in these cells. Our data strongly suggest that the Ca2+ release-activated current underlies the sustained Ca2+ influx during antigenic stimulation and that it plays a key role in the immune function.
Natural killer cells attack tumor cells expressing high levels of sialyl Lewis x oligosaccharides (2002)

Epithelial carcinoma and leukemia cells express sialyl Lewis x oligosaccharides as tumor-associated carbohydrate antigens. To determine the role of sialyl Lewis x oligosaccharides in tumor dissemination, human melanoma MeWo cells, which do not express sialyl Lewis x, were transfected with alpha1,3-fucosyltransferase III (FTIII), and cell lines expressing different amounts of sialyl Lewis x were isolated. When these cells were injected into the tail vein of nude mice, cells expressing moderate amounts of sialyl Lewis x (MeWo-FTIII.M) produced a significantly greater number of lung tumor foci than did parental MeWo cells. In contrast, cells expressing large amounts of sialyl Lewis x (MeWo-FTIII.H) produced few lung tumor foci in nude mice but were highly tumorigenic in beige mice, which have defective natural killer (NK) cells. In vitro assays demonstrated that MeWo-FTIII.H cells are much more sensitive to NK cell-mediated cytotoxicity than are MeWo-FTIII.M cells or parental MeWo cells and the susceptibility of MeWo-FTIII.H cells to NK cell-mediated cytolysis can be inhibited by preincubating MeWo-FTIII.H cells with anti-sialyl Lewis x antibody. Moreover, we discovered that NK cell-mediated cytolysis of MeWo-FTIII.H cells can be inhibited by the addition of an antibody against the NK cell receptor CD94 or sialyl Lewis x oligosaccharides. These results, combined with structural analysis of MeWo-FTIII.H cell carbohydrates, indicate that moderate amounts of sialyl Lewis x lead to tumor metastasis, whereas expression of high levels of sialyl Lewis x leads to an NK cell attack on tumor cells, demonstrating that expression of different amounts of sialyl Lewis x results in entirely different biological consequences.
Effect of High-Dose Ibuprofen in Patients with Cystic Fibrosis (1995)

In patients with cystic fibrosis and mild lung disease, high-dose ibuprofen, taken consistently for four years, significantly slows the progression of the lung disease without serious adverse effects.
Mixed sugar fermentation by Pichia stipitis, Sacharomyces cerevisiaea, and an isolated xylose-fermenting Kluyveromyces marxianus and their cocultures. (2007)

A yeast strain with higher rates and yields in the fermentation of glucose, mannose and galactose in semiaerobic conditions than Pichia stipitis and Sacharomyces cerevisiaeand ethanol tolerance than P. stipitis, was isolated from sugarcane baggase from Iranian resources. This strain that can ferment xylose with lower rates and yields than P. stipitisis characterized as Kluyveromyces marxianus. The ability of K. marxianus to ferment mixed sugars comprised of 30 g/l glucose, 30 g/l xylose, 12 g/l mannose and 8 g/l galactose (total sugar 80 g/l), as a model of many hydrolysates, were compared to P. stipitis and S. cerevisiae and then a coculture of P. stipitis and S. cerevisiae was compared with a coculture of P. stipitis and K. marxianus. In mixed sugars fermentation with individual yeasts P. stipitis shows the highest yield (0.40 gg-1) and maximum ethanol (30.23 gl-1), but K. marxianus shows the highest Qpmax (1.09 gl-1h-1) and substrate utilization efficiency (E,>99%). P. stipiti and K. marxianuscoculture shows the best results with high yield (0.42 gg-1) and maximum ethanol (31.87 gl-1), Qpmax (1.09 gl-1h-1) and substrate utilization efficiency (E,>99%). Because of the higher rates and yields of K. marxianus to ferment hexoses than P. stipitis and its higher ethanol tolerance, K. marxianus helps the P. stipitis to reach the concentration higher than 30 g/l ethanol concentration.

	 

	Key words: Ethanol, Pichia stipitis, Kluyveromyces marxianus, xylose.
Polymer conjugates as therapeutics: future trends, challenges and opportunities (2008)

Polymer therapeutics is a rapidly emerging field with exponentially growing opportunities to achieve medical treatments with highly enhanced therapeutic value.
Review of cold fusion (1991)

Experimental results on Cold Fusion are reviewed. Most experiments find no effect and the upper limits are appreciably lower than the positive effects claimed in some experiments. It is concluded that: (a) there is no excess heat production and (b) the balance of evidence is strongly against fusion products. A curious Regionalization of Results is observed where only negative results are found in some parts of the world and only positive results in other parts. Further, the ratio of positive to negative results varies with time. Previous studies of palladium indicate that fusion should not occur inside the metal. Cold Fusion is best explained as an example of Pathological Science.
Detection of Bifidobacterium species by enzymatic methods* (1990)

The properties of Bifidobacterium strains of human origin were examined by three enzymic tests and the amounts of acetic and lactic acids produced were also quantified. It was evident that two strains of the American Type Culture Collection (ATCC) did not belong to the genus. Moreover, at least one strain of Bifidobacterium added to some milk preparations did not show distinctive characteristics of the genus. It was also shown that most of bifidobacteria studied produced alpha-galactosidase (EC 3.2.1.22) and alpha-glucosidase (EC 3.2.1.20). The presence of alpha-galactosidase could afford a rapid differentiation of bifidobacteria used in some dairy products since this enzyme was not detected in Lactobacillus strains studied.
Enantioselective Incorporation of Azobenzenes into Oligodeoxyribonucleotide for Effective Photoregulation of Duplex Formation (2001)

A drop in melting point of 21.5°C is induced by the UV-photolytic trans→cis isomerization of the duplex formed between an oligonucleotide bearing two D-threoninol-tethered azobenzene moieties in the side chain and its complementary counterpart. On irradiation with visible light, the dissociated single-stranded oligonucleotides regenerate the duplex.
Mucosal DNA Vaccine Immunization Against Measles with a Highly Attenuated Shigella flexneri Vector (1999)

An intranasal vaccine vector would elicit protective immunity at the respiratory mucosa, the portal of entry and the primary site for replication for measles virus (MV) and other respiratory viruses. In a murine model of pulmonary Shigella, we demonstrate here that a candidate-attenuated Shigella vaccine vector is safely tolerated in IFN-gamma deficient mice at an inoculum that is 1 million-fold higher than the inoculum of the wild-type parent strain that would be lethal for greater than 90% of these mice. Also, following intranasal inoculation, the Deltaasd Shigella harboring a DNA MV vaccine plasmid induces a vigorous MV-specific Th1-type (both CD8+ CTL and IFN-gamma) and, to a lesser degree, Th2-type responses among splenocytes in addition to low levels of IgG and IgA in the serum. Priming for MV-specific CTL responses was possible in mice that had prior infection with a wild-type Shigella of the same serotype. Remarkably, mice immunized by the intranasal route with attenuated Shigella harboring the DNA MV vaccine plasmid had a level of MV-specific CTL activity among splenocytes that was comparable with levels observed in mice immunized by the i.p. route with attenuated Salmonella typhi harboring the same DNA vaccine plasmid, despite the fact that Shigella remained localized to the lungs, yet Salmonella disseminated to the spleen following inoculation. Thus, Deltaasd Shigella represents a very useful vector for delivery of DNA vaccines to mucosal lymphoid tissues.
Inhibition of leukocyte adherence by anti-CD18 monoclonal antibody attenuates reperfusion injury in the rabbit ear. (1990)

Tissue injury resulting from ischemia and reperfusion forms the basis of several important disorders including myocardial infarction, stroke, and circulatory shock. To examine the role of neutrophils in this process and to determine the extent to which injury is a consequence of reperfusion, we utilized the monoclonal antibody 60.3, directed to CD18, the human leukocyte adherence glycoprotein, to block intravascular neutrophil aggregation and neutrophil adherence to endothelium in a rabbit model of tissue ischemia and reperfusion. Antibody treatment either before ischemia or after ischemia, but prior to reperfusion, resulted in the same degree of significant protection against endothelial, microvascular, and tissue injury. We conclude that neutrophils and increased neutrophil adhesiveness are important in the development of microvascular and tissue injury after ischemia and reperfusion and that under these circumstances, injury is primarily a consequence of reperfusion.
Reliable and Efficient Procedures for the Conjugation of Biomolecules through Huisgen Azide–Alkyne Cycloadditions (2011)

The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) has been established as a powerful coupling technology for the conjugation of proteins, nucleic acids, and polysaccharides. Nevertheless, several shortcomings related to the presence of Cu, mainly oxidative degradation by reactive oxygen species and sample contamination by Cu, have been pointed out. This Minireview discusses key aspects found in the development of the efficient and benign functionalization of biomacromolecules through CuAAC, as well as the Cu-free strain-promoted azide-alkyne cycloaddition (SPAAC).
Nitric Oxide in Plant Physiology (2009)

Nitric Oxide: Chemistry, Biosynthesis and Physiological Role (Hayat, Hasan, Mori, Fariduddin and Ahmad) Electron Paramagnetic Resonance (EPR) as a Tool to Study Nitric Oxide Generation in Plants (Puntarulo, Jasid, Boveris and Simontacchi) Calcium, NO, and cGMP Signaling in Plant Cell Polarity (Prado, Feijo and Porterfield) Nitric Oxide and Abiotic Stress in Higher Plants (Corpas, Palma, Leterrier, del Rio and Barroso) Polyamines and Cytokinin: Is Nitric Oxide Biosynthesis the Key to Overlapping Functions? (Wimalasekera and Scherer) Role of Nitric Oxide in Programmed Cell Death (Zottini, Costa, De Michele and Lo Schiavo) Nitrate Reductase-Deficient Plants: A Model to Study Nitric Oxide Production and Signaling in Plant Defense Response to Pathogen Attack (Salgado, Caixeta de Oliveira and Braga) Effective Plant Protection Weapons Against Pathogens Require NO bullets (Modolo) The Role of Nitric Oxide as a Bioactive Signalling Molecule in Plants under Abiotic Stress (Hao and Zhang) Interplay Between Nitric Oxide and Other Signals Involved in Plant Resistance to Pathogens (Floryszak-Wieczorek and Arasimowicz-Jelonek) Nitric Oxide Signaling by Plant-Associated Bacteria (Cohen, Lamattina and Yamasaki) Nitric Oxide Synthase (NOS)-Like Protein in Pea (Pisum sativum L.) (Wong, Huang, Davis, Sukno and Tan) Post-Translational Modifications of Proteins by Nitric Oxide: a New Tool of Metabolome Regulation (Abat and Deswal)
Structure-Function Relationships of the G Domain, a Canonical Switch Motif (2011)

GTP-binding (G) proteins constitute a class of P-loop (phosphate-binding loop) proteins that work as molecular switches between the GDP-bound OFF and the GTP-bound ON state. The common principle is the 160-180-residue G domain with an α,β topology that is responsible for nucleotide-dependent conformational changes and drives many biological functions. Although the G domain uses a universally conserved switching mechanism, its structure, function, and GTPase reaction are modified for many different pathways and processes.
Apoprotein A-I mimetic peptides and their potential anti-atherogenic mechanisms of action (2009)

Recent observations of mimetic peptides have pointed to promising therapies for patients with cardiovascular disease. The peptides appear to be well tolerated and effective in promoting the anti-inflammatory properties of HDL.
Invited reviewnative chemical ligation applied to the synthesis and bioengineering of circular peptides and proteins (2010)

Native chemical ligation methodology developed in the laboratory of Stephen Kent is a versatile approach to the linkage of peptide fragments using a native peptide bond. It is readily adaptable to the task of joining the N- and C-termini of peptides to produce cyclic molecules and we have used it for the cyclization of a range of disulfide-rich peptides. Specifically, it has been valuable for the synthesis of cyclotides, naturally occurring peptides characterized by a head-to-tail cyclized backbone and a knotted arrangement of three conserved disulfide bonds. Cyclotides have a diverse range of biological activities, including anti-HIV, antimicrobial, and insecticidal activities. They are ultrastable owing to their cyclic cystine knot motif, and native chemical ligation methodology has been invaluable in the synthesis of a range of native and modified cyclotides to explore their structure-activity relationships and applications in drug design. Similar studies have also been applied to a smaller cyclic peptide produced in sunflower seeds, sunflower trypsin inhibitor-1, which also shows promise as a template in drug design applications. We have also found native chemical ligation to be a valuable methodology for the cyclization of conotoxins, small disulfide-rich peptides from the venoms of marine cone snails. Conotoxins target a range of ions channels and receptors and are exciting leads in drug design applications. The synthetic cyclization of conotoxins with peptide linkers stabilizes them and improves their biopharmaceutical properties. In summary, this article illustrates the use of native chemical ligation technology in the cyclization of cyclotides, sunflower trypsin inhibitor-1, and conotoxins in our laboratory.
On-line detection of proteins in gel electrophoresis by ultraviolet absorption and by native fluorescence utilizing a charge-coupled device imaging system (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn-line detection of proteins in gel electrophoresis by ultraviolet absorption and by native fluorescence utilizing a charge-coupled device imaging systemLance B. Koutny and Edward S. YeungCite this: Anal. Chem. 1993, 65, 2, 183–187Publication Date (Print):January 15, 1993Publication History Published online1 May 2002Published inissue 15 January 1993https://pubs.acs.org/doi/10.1021/ac00050a017https://doi.org/10.1021/ac00050a017research-articleACS PublicationsRequest reuse permissionsArticle Views138Altmetric-Citations12LEARN 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
Quantitative dielectrophoretic tracking for characterization and separation of persistent subpopulations of Cryptosporidium parvum (2013)

Microbial persistence to antibiotics is attributed to subpopulations with phenotypic variations that cause a spread of susceptibility levels, leading to the recurrence of infections and stability of biofilms. Herein, persistent oocyst subpopulations identified by animal infectivity and excystation assays during the disinfection of Cryptosporidium parvum, a water-borne pathogen capable of causing enteric infections at ultra-low doses, are separated and characterized by quantitative dielectrophoretic tracking over a wide frequency range (10 kHz-10 MHz). To enable the simultaneous and facile dielectrophoretic tracking of individual oocysts, insulator constrictions in a microfluidic channel are utilized to spatially modulate the localized field over the extent needed for defining oocyst trajectories and for obtaining high-resolution displacement versus time measurements under both, positive and negative dielectrophoresis. In this manner, by obviating the need for averaging dielectrophoretic data over a large collection region, the force response is more sensitive to differences in electrophysiology from sub-population fractions. Hence, the electrophysiology of sensitive and persistent oocysts after heat and silver nanoparticle treatments can be quantified by correlating the force response at low frequencies (<100 kHz) to the integrity of the oocyst wall and at high frequencies (0.4-1 MHz) to the sporozoites in the oocyst. This label-free method can characterize heterogeneous microbial samples with subpopulations of phenotypically different alterations, for quantifying the intensity of alteration and fraction with a particular alteration type.
ORIGINAL ARTICLE: Serial Estimation of Th1:Th2 Cytokines Profile in Women Undergoing In‐Vitro Fertilization‐Embryo Transfer (2008)

Women with a history of unexplained recurrent failed IVF treatment have a Th1 bias and this polarization is more enhanced following hormonal manipulations during IVF treatment. Comparing pre-treatment ratios of IFN-gamma:IL-4 and TNF-alpha:IL-4 to ratios obtained at oocyte retrieval may be clinically useful. Women with recurrent failed IVF have increasing ratios.
New methodology for ultra-fast detection and reduction of non-visual defects at the 90nm node and below using comprehensive e-test structure infrastructure and in-line DualBeamTM FIB (2006)

This paper describes a methodology to quickly capture, characterize, prioritize, localize, and perform in-line FA on killer defects. The system, which includes comprehensive short-flow test wafers, fast inline e-test, a powerful data analysis system, and advanced in-line dual beam inspection, was demonstrated in a leading-edge 300mm fab at the 90nm technology node to detect and resolve both systematic and random defect mechanisms greater than 10times faster than traditional methods. This article describes several examples of detecting and resolving non-visual (subsurface) as well as visual defects for both back-end and front-end issues