gebhart/patrepeval huggingface dataset:
Fourier Ptychographic Imaging (2016)

This book demonstrates the concept of Fourier ptychography, a new imaging technique that bypasses the resolution limit of the employed optics. In particular, it transforms the general challenge of high-throughput, high-resolution imaging from one that is coupled to the physical limitations of the optics to one that is solvable through computation. Demonstrated in a tutorial form and providing many MATLAB® simulation examples for the reader, it also discusses the experimental implementation and recent developments of Fourier ptychography. This book will be of interest to researchers and engineers learning simulation techniques for Fourier optics and the Fourier ptychography concept.
The connection between splicing and cancer (2006)

Alternative splicing is a crucial mechanism for generating protein diversity. Different splice variants of a given protein can display different and even antagonistic biological functions. Therefore, appropriate control of their synthesis is required to assure the complex orchestration of cellular processes within multicellular organisms. Mutations in cis-acting splicing elements or changes in the activity of constitutive or alternative splicing could have a profound regulatory proteins that compromise the accuracy of either impact on human pathogenesis, in particular in tumor development and progression. Mutations in splicing elements, for example, have been found in genes such as LKB1, KIT, CDH17, KLF6 and BRCA1, and changes in trans-acting regulators can affect the expression of genes such as Ron, RAC1 and CD44.
Development of Azeliragon, an Oral Small Molecule Antagonist of the Receptor for Advanced Glycation Endproducts, for the Potential Slowing of Loss of Cognition in Mild Alzheimer's Disease (2018)

Increasing evidence supports the role of the Receptor for Advanced Glycation Endproducts (RAGE) in the pathology of Alzheimer's disease. Azeliragon (TTP488) is an orally bioavailable small molecule inhibitor of RAGE in Phase 3 development as a potential treatment to slow disease progression in patients mild AD. Preclinical studies in animal models of AD (tgAPPSwedish/London) have shown azeliragon to decrease Aβ plaque deposition; reduce total Aβ brain concentration while increasing plasma Aβ levels; decreases sAPPβ while increasing sAPPα; reduce levels of inflammatory cytokines; and slow cognitive decline and improve cerebral blood flow. In the Phase 2b study, 18-months treatment in patients with mild-to-moderate AD indicated a baseline to endpoint change in ADAS-cog of 3.1 points in favor of drug. A greater magnitude of effect was evident in the sub-group of patients with mild AD (MMSE 21-26) with a baseline to endpoint change of 4 points on the ADAS-cog in favor of azeliragon and a 1 point change in CDR-sb in favor of drug. Azeliragon 5 mg/day delayed time to cognitive deterioration (7-point change in ADAS-cog from baseline, logrank p=0.0149). Based on promising results from the Phase 2b study, a Phase 3 registration program (STEADFAST) is being conducted under a Special Protocol Assessment from FDA. The ongoing Phase 3 program, if successful may demonstrate azeliragon can slow cognitive decline in mild AD patients.
Semantic Human Matting (2018)

Human matting, high quality extraction of humans from natural images, is crucial for a wide variety of applications. Since the matting problem is severely under-constrained, most previous methods require user interactions to take user designated trimaps or scribbles as constraints. This user-in-the-loop nature makes them difficult to be applied to large scale data or time-sensitive scenarios. In this paper, instead of using explicit user input constraints, we employ implicit semantic constraints learned from data and propose an automatic human matting algorithm Semantic Human Matting(SHM). SHM is the first algorithm that learns to jointly fit both semantic information and high quality details with deep networks. In practice, simultaneously learning both coarse semantics and fine details is challenging. We propose a novel fusion strategy which naturally gives a probabilistic estimation of the alpha matte. We also construct a very large dataset with high quality annotations consisting of 35,513 unique foregrounds to facilitate the learning and evaluation of human matting. Extensive experiments on this dataset and plenty of real images show that SHM achieves comparable results with state-of-the-art interactive matting methods.
The Effect of Pyruvate Decarboxylase Gene Knockout inSaccharomyces cerevisiaeonL-Lactic Acid Production (2006)

A plant- and crop-based renewable plastic, poly-lactic acid (PLA), is receiving attention as a new material for a sustainable society in place of petroleum-based plastics. We constructed a metabolically engineered Saccharomyces cerevisiae that has both pyruvate decarboxylase genes (PDC1 and PDC5) disrupted in the genetic background to express two copies of the bovine L-lactate dehydrogenase (LDH) gene. With this recombinant, the yield of lactate was 82.3 g/liter, up to 81.5% of the glucose being transformed into lactic acid on neutralizing cultivation, although pdc1 pdc5 double disruption led to ineffective decreases in cell growth and fermentation speed. This strain showed lactate productivity improvement as much as 1.5 times higher than the previous strain. This production yield is the highest value for a lactic acid-producing yeast yet reported.
Sequential testing algorithms for multiple fault diagnosis (2000)

We consider the problem of constructing optimal and near-optimal test sequences for multiple fault diagnosis. The computational complexity of solving the optimal multiple-fault isolation problem is super exponential, that is, it is much more difficult than the single-fault isolation problem, which, by itself, is NP-hard. By employing concepts from information theory and AND/OR graph search and by exploiting the single fault testing strategies of Pattipati et al. (1990), we present several test sequencing algorithms for the multiple fault isolation problem. These algorithms provide a trade-off between the degree of suboptimality and computational complexity. Furthermore, we present novel diagnostic strategies that generate a diagnostic directed graph, instead of a traditional diagnostic tree, for multiple fault diagnosis. Using this approach, the storage complexity of the overall diagnostic strategy reduces substantially. The algorithms developed herein have been successfully applied to several real-world systems.
Beta3 -Adrenoceptor Agonists as Anti-diabetic and Anti-obesity Drugs in Humans (2001)

In the early 1980s, an "atypical" beta-adrenergic receptor was discovered and subsequently called the beta (3)-adrenoceptor (beta(3)-AR). Agonists of the beta(3)-AR were observed to simultaneously increase lipolysis, fat oxidation, energy expenditure and insulin action leading to the belief that this receptor might serve as an attractive target for the treatment of diabetes and obesity. In vivo studies lent credence to this postulate with the finding that stimulation of this receptor by selective agonists lead to glycemic improvements and weight loss in rodent models of diabetes and obesity. This lead to intensive research efforts directed at developing beta(3)-AR selective agonists for the treatment of type 2 diabetes and obesity in humans. Unfortunately, endeavour been largely unsuccessful to date. Major obstacles have included the pharmacological differences between the rodent and human beta(3)-AR, the lack of selectivity of previous compounds for the beta(3)-AR over beta(1)-/beta(2)-ARs, and unsatisfactory oral bioavailability and pharmacokinetic properties. Cloning of the human beta(3)-AR has allowed for the development of novel compounds targeted specifically at the human receptor. Encouraging data has emerged from clinical studies wherein CL-316,243, a highly selective, albeit rodent specific beta(3)-AR agonist was observed to increase lipolysis, fat oxidation and insulin action in humans. More recently, beta(3)-AR agonists directed at the human receptor are showing promising results in their ability to increase energy expenditure in humans following a single dose. However, they do nor appear to be able to sustain their effects when administered chronically. Further clinical testing will be necessary, using compounds with improved oral bioavailability and potency, to help assess the physiology of the beta(3)-AR in humans and its attractiveness as a potential therapeutic for the treatment of type 2 diabetes and obesity.
Fiber optic immunochemical sensor for continuous, reversible measurement of phenytoin. (1988)

This fiber optic sensor, based on a homogeneous fluorescence energy-transfer immunoassay, operates in a continuous, reversible manner to quantify the anticonvulsant drug phenytoin. B-Phycoerythrin-phenytoin and Texas Red-labeled antibody to phenytoin were sealed inside a short length of cellulose dialysis tubing, which was cemented to the distal end of an optical fiber. When the sensor was alternately placed into solutions with various concentrations of free phenytoin, the drug crossed the dialysis membrane and displaced a fraction of the B-phycoerythrin-phenytoin from the antibody. The resulting change in fluorescence signal was measured with a fiber optic fluorometer. A typical competitive-binding calibration curve was seen between 5 and 500 mumol of phenytoin per liter. Equilibrium response time ranged from 5 to 30 min for different sensors. Replicate equilibrium measurements with one sensor, alternated eight times between two solutions of phenytoin, gave a CV of 2.1% (n = 16) at 0 mumol/L and 2.4% (n = 13) at 100 mumol/L. A reversible immunochemical sensor can be made that has a response time suitable for continuous concentration measurements.
Therapeutic antibodies, vaccines and antibodyomes (2010)

The potential for antibodies to act as "magic bullets" for treatment of human disease was recognized a century ago, but its full realization has began to occur only during the last decade. A key to their current success is the ability to make libraries of antibodies/B cells, isolate a single species, and engineer it to be safe, efficacious and of high quality. Despite this progress, major challenges to the effective prevention, diagnosis and treatment of a vast majority of diseases remain. Limited success in the development of effective vaccines against diseases such as AIDS and cancer reflects our incomplete understanding of how antibodies are generated and function. Only a miniscule number of antibodies are characterized out of the universe of antibodies generated by the immune system. Knowledge of antibodyomes-the complete sets of antibodies-could help solve these and other challenges.
Cystamine and cysteamine increase brain levels of BDNF in Huntington disease via HSJ1b and transglutaminase (2006)

There is no treatment for the neurodegenerative disorder Huntington disease (HD). Cystamine is a candidate drug; however, the mechanisms by which it operates remain unclear. We show here that cystamine increases levels of the heat shock DnaJ-containing protein 1b (HSJ1b) that are low in HD patients. HSJ1b inhibits polyQ-huntingtin-induced death of striatal neurons and neuronal dysfunction in Caenorhabditis elegans. This neuroprotective effect involves stimulation of the secretory pathway through formation of clathrin-coated vesicles containing brain-derived neurotrophic factor (BDNF). Cystamine increases BDNF secretion from the Golgi region that is blocked by reducing HSJ1b levels or by overexpressing transglutaminase. We demonstrate that cysteamine, the FDA-approved reduced form of cystamine, is neuroprotective in HD mice by increasing BDNF levels in brain. Finally, cysteamine increases serum levels of BDNF in mouse and primate models of HD. Therefore, cysteamine is a potential treatment for HD, and serum BDNF levels can be used as a biomarker for drug efficacy.
Extended adaptive RBF equaliser for overcoming co-channelinterference (1998)

The authors investigate the problem of nonlinear adaptive equalisation in the presence of intersymbol interference, additive white Gaussian noise and co-channel interference. An extended radial basis function (RBF) network is proposed, in which regression weights are used in the output layer and the hidden unit is defined to have the Gaussian formula with the Mahalanobis distance. It is shown by simulation that the proposed structure gives reduced computational complexity without performance degradation, compared to that of the conventional RBF equaliser.
Mild and Selective Deuteration and Isomerization of Alkenes by a Bifunctional Catalyst and Deuterium Oxide (2009)

H/D exchange is achieved at allylic positions of alkenes using D(2)O in acetone and alkene isomerization catalyst 1, which features a bifunctional imidazolylphosphine. The basic nitrogen of the latter is thought to deprotonate an alkene substrate coordinated to the CpRu center; at this stage the protonated nitrogen could undergo H/D exchange with deuterium oxide. An exceptional degree of deuteration is achieved at positions accessible to isomerization, with a high degree of control. Using biphasic settings one can literally wash out reactive protons on the substrate without using organic solvents.
Regulatory Role of PBAN in Sex Pheromone Biosynthesis of Heliothine Moths (2011)

Both males and females of heliothine moths utilize sex-pheromones during the mating process. Females produce and release a sex pheromone for the long-range attraction of males for mating. Production of sex pheromone in females is controlled by the peptide hormone (pheromone biosynthesis activating neuropeptide, PBAN). This review will highlight what is known about the role PBAN plays in controlling pheromone production in female moths. Male moths produce compounds associated with a hairpencil structure associated with the aedaegus that are used as short-range aphrodisiacs during the mating process. We will discuss the role that PBAN plays in regulating male production of hairpencil pheromones.
In vitro corrosion, cytotoxicity and hemocompatibility of bulk nanocrystalline pure iron (2010)

Bulk nanocrystalline pure iron rods were fabricated by the equal channel angular pressure (ECAP) technique up to eight passes. The microstructure and grain size distribution, natural immersion and electrochemical corrosion in simulated body fluid, cellular responses and hemocompatibility were investigated in this study. The results indicate that nanocrystalline pure iron after severe plastic deformation (SPD) would sustain durable span duration and exhibit much stronger corrosion resistance than that of the microcrystalline pure iron. The interaction of different cell lines reveals that the nanocrystalline pure iron stimulates better proliferation of fibroblast cells and preferable promotion of endothelialization, while inhibits effectively the viability of vascular smooth muscle cells (VSMCs). The burst of red cells and adhesion of the platelets were also substantially suppressed on contact with the nanocrystalline pure iron in blood circulation. A clear size-dependent behavior from the grain nature deduced by the gradual refinement microstructures was given and well-behaved in vitro biocompatibility of nanocrystalline pure iron was concluded.
Environmental and Heritable Factors in the Causation of Cancer — Analyses of Cohorts of Twins from Sweden, Denmark, and Finland (2000)

Inherited genetic factors make a minor contribution to susceptibility to most types of neoplasms. This finding indicates that the environment has the principal role in causing sporadic cancer. The relatively large effect of heritability in cancer at a few sites suggests major gaps in our knowledge of the genetics of cancer.
Lab-on-a-Disc for Simultaneous Determination of Nutrients in Water (2013)

In this study, we describe a novel platform based on centrifugal microfluidics for simultaneous determination of nitrite, nitrate and nitrite, ammonium, orthophosphate, and silicate in water samples. All processes from sample metering to detection were integrated and automatically conducted on a rotating disc-shaped device. Fluid transfer was controlled by laser irradiation on the ferrowax-based microvalves. Liquid samples and reagents were pumped by centrifugal force in the rotating disc, and their positions and movements were controlled through a programmable light from a laser diode. This novel water analysis platform required only 500 μL of sample (100 μL for each nutrient) and 10-30 μL of reagents for colorimetric detection. In addition, the fully automated parallel processes and efficient mixing in the rotating disc allowed for a significant reduction in total analysis time (∼7 min 40 s) and increased accuracy. Validation with a seawater certified reference material indicated that the platform accurately measured nutrient concentrations in water samples. In addition, we showed that the nutrients in the seawater collected from Chunsu Bay in Korea measured by the proposed lab-on-a-disc and by a commercialized autoanalyzer are comparable.
The effects of testosterone treatment on body composition and metabolism in middle-aged obese men. (1992)

Twenty-three middle-aged abdominally obese men were treated for eight months with testosterone or with placebo. Testosterone treatment was followed by a decrease of visceral fat mass, measured by computerized tomography, without a change in body mass, subcutaneous fat mass or lean body mass. Insulin resistance, measured by the euglycemic/hyperinsulinemic glucose clamp method, improved and blood glucose, diastolic blood pressure and serum cholesterol decreased with testosterone treatment. A small increase in prostate volume was noted, but serum prostate specific antigen concentrations were unchanged and no adverse functional side-effects were found. Insulin sensitivity improved more in men with relatively low testosterone values at the outset. The mechanisms involved in these changes might act either via effects on visceral fat accumulation, followed by metabolic improvements, and/or via direct effects on muscle insulin sensitivity, as suggested by results of other recent studies. It is concluded that testosterone treatment of middle-aged abdominally obese men gives beneficial effects on well-being and the cardiovascular and diabetes risk profile, results similar to those observed after hormonal replacement therapy in postmenopausal women.
Renal protection in chronic kidney disease: hypoxia-inducible factor activation vs. angiotensin II blockade (2010)

The 5/6(th) nephrectomy or ablation/infarction (A/I) preparation has been used as a classic model of chronic kidney disease (CKD). We observed increased kidney oxygen consumption (Q(O2)) and altered renal hemodynamics in the A/I kidney that were normalized after combined angiotensin II (ANG II) blockade. Studies suggest hypoxia inducible factor as a protective influence in A/I. We induced hypoxia-inducible factor (HIF) and HIF target proteins by two different methods, cobalt chloride (CoCl(2)) and dimethyloxalyglycine (DMOG), for the first week after creation of A/I and compared the metabolic and renal hemodynamic outcomes to combined ANG II blockade. We also examined the HIF target proteins expressed by using Western blots and real-time PCR. Treatment with DMOG, CoCl(2), and ANG II blockade normalized kidney oxygen consumption factored by Na reabsorption and increased both renal blood flow and glomerular filtration rate. At 1 wk, CoCl(2) and DMOG increased kidney expression of HIF by Western blot. In the untreated A/I kidney, VEGF, heme oxygenase-1, and GLUT1 were all modestly increased. Both ANG II blockade and CoCl(2) therapy increased VEGF and GLUT1 but the cobalt markedly so. ANG II blockade decreased heme oxygenase-1 expression while CoCl(2) increased it. By real-time PCR, erythropoietin and GLUT1 were only increased by CoCl(2) therapy. Cell proliferation was modestly increased by ANG II blockade but markedly after cobalt therapy. Metabolic and hemodynamic abnormalities were corrected equally by ANG II blockade and HIF therapies. However, the molecular patterns differed significantly between ANG II blockade and cobalt therapy. HIF induction may prove to be protective in this model of CKD.
Effects of thyrotoxicosis and selective hepatic autonomic denervation on hepatic glucose metabolism in rats (2008)

Thyrotoxicosis is known to induce a broad range of changes in carbohydrate metabolism. Recent studies have identified the sympathetic and parasympathetic nervous system as major regulators of hepatic glucose metabolism. The present study aimed to investigate the pathogenesis of altered endogenous glucose production (EGP) in rats with mild thyrotoxicosis. Rats were treated with methimazole in drinking water and l-thyroxine (T(4)) from osmotic minipumps to either reinstate euthyroidism or induce thyrotoxicosis. Euthyroid and thyrotoxic rats underwent either a sham operation, a selective hepatic sympathetic denervation (Sx), or a parasympathetic denervation (Px). After 10 days of T(4) administration, all animals were submitted to a hyperinsulinemic euglycemic clamp combined with stable isotope dilution to measure EGP. Plasma triiodothyronine (T(3)) showed a fourfold increase in thyrotoxic compared with euthyroid animals. EGP was increased by 45% in thyrotoxic compared with euthyroid rats and correlated significantly with plasma T(3). In thyrotoxic rats, hepatic PEPCK mRNA expression was increased 3.5-fold. Relative suppression of EGP during hyperinsulinemia was 34% less in thyrotoxic than in euthyroid rats, indicating hepatic insulin resistance. During thyrotoxicosis, Sx attenuated the increase in EGP, whereas Px resulted in increased plasma insulin with unaltered EGP compared with intact animals, compatible with a further decrease in hepatic insulin sensitivity. We conclude that chronic, mild thyrotoxicosis in rats increases EGP, whereas it decreases hepatic insulin sensitivity. Sympathetic hepatic innervation contributes only to a limited extent to increased EGP during thyrotoxicosis, whereas parasympathetic hepatic innervation may function to restrain EGP in this condition.
Genetic variants of human serum albumin in Italy: point mutants and a carboxyl-terminal variant. (1994)

Of the > 50 different genetic variants of human serum albumin (alloalbumins) that have been characterized by amino acid or DNA sequence analysis, almost half have been identified in Italy through a long-term electrophoretic survey of serum. Previously we have reported structural studies of 11 Italian alloalbumins with point mutations, 2 different carboxyl-terminal variants, and 1 case of analbuminemia in an Italian family. This article describes confirmation by DNA sequencing of mutations previously inferred from protein sequencing of 4 of the above alloalbumins; it also reports the mutations identified by protein and DNA sequence analysis of 4 other Italian alloalbumins not previously recorded: albumin Larino, His3-->Tyr; Tradate-2 (protein sequencing only), Lys225-->Gln; Caserta, Lys276-->Asn; and Bazzano, a carboxyl-terminal variant. The first 3 have point mutations that produce a single amino acid substitution, but a nucleotide deletion causes a frameshift and an altered and truncated carboxyl-terminal sequence in albumin Bazzano. In these 4 instances the expression of the alloalbumin is variable, ranging from 10% to 70% of the total albumiN, in contrast to the usual 50% each for the normal and mutant albumin. The distribution of point mutations in the albumin gene is nonrandom; most of the 47 reported point substitutions involve charged amino acid residues on the surface of the molecule that are not concerned with ligand-binding sites.