gebhart/patrepeval huggingface dataset:
Compound prism design principles, II: triplet and Janssen prisms (2011)

Continuing the work of the first paper in this series [Appl. Opt. 50, 4998-5011 (2011)], we extend our design methods to compound prisms composed of three independent elements. The increased degrees of freedom of these asymmetric prisms allow designers to achieve greatly improved dispersion linearity. They also, however, require a more careful tailoring of the merit function to achieve design targets, and so we present several new operands for manipulating the compound prisms' design algorithm. We show that with asymmetric triplet prisms, one can linearize the angular dispersion such that the spectral sampling rate varies by no more than 4% across the entire visible spectral range. Doing this, however, requires large prisms and causes beam compression. By adding a beam compression penalty to the merit function, we show that one can compromise between dispersion linearity and beam compression in order to produce practical systems. For prisms that do not deviate the beam, we show that Janssen prisms provide a form that maintains the degrees of freedom of the triplet and that are capable of up to 32° of dispersion across the visible spectral range. Finally, in order to showcase some of the design flexibility of three-element prisms, we also show how to design for higher-order spectral dispersion to create a two-dimensional spectrum.
Advanced glycation end products and RAGE: a common thread in aging, diabetes, neurodegeneration, and inflammation (2005)

The products of nonenzymatic glycation and oxidation of proteins and lipids, the advanced glycation end products (AGEs), accumulate in a wide variety of environments. AGEs may be generated rapidly or over long times stimulated by a range of distinct triggering mechanisms, thereby accounting for their roles in multiple settings and disease states. A critical property of AGEs is their ability to activate receptor for advanced glycation end products (RAGE), a signal transduction receptor of the immunoglobulin superfamily. It is our hypothesis that due to such interaction, AGEs impart a potent impact in tissues, stimulating processes linked to inflammation and its consequences. We hypothesize that AGEs cause perturbation in a diverse group of diseases, such as diabetes, inflammation, neurodegeneration, and aging. Thus, we propose that targeting this pathway may represent a logical step in the prevention/treatment of the sequelae of these disorders.
Characterization of a Class of Peptide Boronates with Neutral P1 Side Chains as Highly Selective Inhibitors of Thrombin (1995)

Z-D-Phe-Pro-boroMpg-OPin (9a)1,2 has been shown previously to be a highly specific inhibitor of thrombin in spite of lacking an arginine-like guanidino group at the P1 site. A range of compounds have been synthesized based upon this lead compound, varying the neutral side chain at the P1 site. Of the 20 examples based upon the structures at P2 and P3 of Z-D-X-Pro (X being Phe or beta,beta-diphenylalanine), all were found to be effective inhibitors of thrombin (Ki's between 10 and 100 nM). Furthermore all exhibited a high specificity toward thrombin having values for a Ki(trypsin)/Ki(thrombin) ratio of between 10- and 100-fold. High ratio values were found for a number of the compounds tested against a range of serine proteinases (plasmin, factor Xa, kallikrein, urokinase, protein Ca, chymotrypsin, elastase, and cathepsin G). As far as potency toward thrombin, compounds containing the methoxypropyl group at P1 were favored over those with a methoxy grouping on a shorter alkyl chain (8) or without the methoxy group (1-5). The compounds display potent anticoagulant activity with values for 18 in thrombin time of 0.63 microM and in activated partial thromboplastin time of 2.0 microM. 11B NMR has been used to confirm interaction of the boron atom with the active site. From the high specificity shown with all the compounds we propose that the compounds, constitute a new class of thrombin inhibitors.
Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. (1989)

We developed mobility shift analysis of single-stranded DNAs on neutral polyacrylamide gel electrophoresis to detect DNA polymorphisms. This method follows digestion of genomic DNA with restriction endonucleases, denaturation in alkaline solution, and electrophoresis on a neutral polyacrylamide gel. After transfer to a nylon membrane, the mobility shift due to a nucleotide substitution of a single-stranded DNA fragment could be detected by hybridization with a nick-translated DNA fragment or more clearly with RNA copies synthesized on each strand of the DNA fragment as probes. As the mobility shift caused by nucleotide substitutions might be due to a conformational change of single-stranded DNAs, we designate the features of single-stranded DNAs as single-strand conformation polymorphisms (SSCPs). Like restriction fragment length polymorphisms (RFLPs), SSCPs were found to be allelic variants of true Mendelian traits, and therefore they should be useful genetic markers. Moreover, SSCP analysis has the advantage over RFLP analysis that it can detect DNA polymorphisms and point mutations at a variety of positions in DNA fragments. Since DNA polymorphisms have been estimated to occur every few hundred nucleotides in the human genome, SSCPs may provide many genetic markers.
Coupled Mutagenesis Screens and Genetic Mapping in Zebrafish (2003)

Forward genetic analysis is one of the principal advantages of the zebrafish model system. However, managing zebrafish mutant lines derived from mutagenesis screens and mapping the corresponding mutations and integrating them into the larger collection of mutations remain arduous tasks. To simplify and focus these endeavors, we developed an approach that facilitates the rapid mapping of new zebrafish mutations as they are generated through mutagenesis screens. We selected a minimal panel of 149 simple sequence length polymorphism markers for a first-pass genome scan in crosses involving C32 and SJD inbred lines. We also conducted a small chemical mutagenesis screen that identified several new mutations affecting zebrafish embryonic melanocyte development. Using our first-pass marker panel in bulked-segregant analysis, we were able to identify the genetic map positions of these mutations as they were isolated in our screen. Rapid mapping of the mutations facilitated stock management, helped direct allelism tests, and should accelerate identification of the affected genes. These results demonstrate the efficacy of coupling mutagenesis screens with genetic mapping.
Lack of In Vivo Function of CD31 in Vascular Thrombosis (2001)

A murine model of endothelial cell injury-based vascular thrombosis was used to test the role of platelet-endothelial cell adhesion molecule-1 (PECAM-1, CD31) in blood cell aggregate formation and vessel occlusion in vivo. Photochemically-induced thrombus formation was analyzed in detail using intravital fluorescence microscopy of individual microvessels in cremaster muscle preparations of CD31-deficient and wildtype mice. In venules, epi-illumination induced rapid thrombus formation with first platelet deposition after 0.56 +/- 0.11 min and complete vessel occlusion within 5.05 +/- 0.45 min. In arterioles, thrombus formation was markedly delayed with first platelet deposition after 3.03 +/- 0.47 min and complete vessel occlusion within 10.04 +/- 1.26 min. Kinetics of thrombus formation in both venules (first platelet deposition: 0.52 +/- 0.1 min; vessel occlusion: 5.03 +/- 0.52 min) and arterioles (first platelet deposition: 3.06 +/- 0.68 min; vessel occlusion: 10.02 +/- 1.38 min) of CD31-deficient mice was found almost identical compared with that in wildtype animals. Tail bleeding time was 233 +/- 24 s in wildtype and 243 +/- 32 s in CD31-deficient mice. Moreover, CD31-deficient and wildtype mice revealed comparable interaction of leukocytes to endothelium. This study shows for the first time in vivo that CD31 is not critically involved in blood cell thrombus formation upon endothelial cell injury.
Nitro-oleic acid protects the mouse kidney from ischemia and reperfusion injury (2008)

Nitroalkene derivatives of linoleic acid (nitrolinoleic acid; LNO2) and nitro-oleic acid (OA-NO2) are endogenous lipid products with potent anti-inflammatory properties. The present study was undertaken to evaluate the therapeutic potential of OA-NO2 in a mouse model of renal ischemia-reperfusion (I/R) injury. B6129SF2/J mice were subjected to bilateral renal ischemia for 30 min, followed by 24 h of reperfusion. Fifty minutes after ischemia, mice received intraperitoneal (ip) injections of OA-NO2 (500 microg/kg; I/R OA-NO2), vehicle for OA-NO2 (i.e., 0.8 ml/kg ethanol; I/R veh), or oleic acid (500 microg/kg; I/R OA) every 6 h during the 24-h recovery period. A sham-operated group was not subjected to ischemia and received 0.8 ml/kg ethanol ip every 6 h during the 24-h recovery period (sham veh). While plasma urea and creatinine were elevated (P<0.05) in I/R veh vs. sham veh mice, the severity was less (P<0.05) in I/R OA-NO2 animals. Indices of histological damage, polymorphonucleocyte infiltration, together with expression of intracellular adhesion molecule-1, interleukin-1beta, and tumor necrosis factor-alpha, p47(phox), and gp91(phox) were greater in I/R veh vs. sham veh mice, but were attenuated (P<0.05) in I/R OA-NO2 animals. Because indices of renal dysfunction were similar between I/R veh and I/R OA mice (P>0.05), but less (P<0.05) in I/R OA-NO2 animals compared with both groups, protection from bilateral renal ischemia is afforded by the nitrated but not free form of oleic acid. Together, delayed administration of nitrated fatty acid OA-NO2 attenuates renal I/R injury in the mouse likely via inhibition of the inflammatory response.
Inhibition of interleukin 1 activity by a factor in submandibular glands of rats. (1986)

With the sequential use of ammonium sulfate precipitation, gel filtration and chromatofocusing, we have partially purified from extracts of the submandibular glands of rats a factor (referred to as submandibular gland's immunosuppressive factor or SMG-ISF) capable of inhibiting the in vitro proliferation of mitogen- and antigen-stimulated murine lymphocytes. The semi-purified suppressor fractions had an isoelectric point of 4.4 to 4.5 and consisted of at least three molecular species. These active fractions suppressed the mitogenic effects of Concanavalin A phytohemagglutinin, and lipopolysaccharide. In vitro immune reactions such as the mixed lymphocyte culture MLC reaction and the production of cytotoxic T lymphocytes (CTL) across major histocompatibility barriers in mice were also suppressed. These in vitro immunosuppressive effects required the addition of the suppressor fractions early after the initiation of the cultures and were reversed if the factor was removed from the cultures at least 48 to 72 hr before the completion of the assays. The active fractions did not affect the proliferation of CTLL 2 cells induced by interleukin 2 (IL 2), but inhibited the mitogenic and co-stimulatory effects of IL 1 on mouse thymocytes, and in this effect showed a dose-response relation suggestive of a competitive mechanism. These characteristics of SMG-ISF indicate a specific inhibition of the activity of IL 1.
Heart Failure in Elderly African-Americans. (1997)

Heart failure has emerged as one of the most important cardiovascular diseases in the elderly and has a major functional, economic, and social impact in older individuals. Racial differences in the morbidity and mortality, as well as in rates of hospitalization, have been reported in national surveys and epidemiologic studies. Because of the higher prevalence of hypertension and left ventricular hypertrophy in African-Americans compared to whites, these risk factors may be the principle determinants of the hemodynamic and clinical features of heart failure in African-Americans. The contribution of coronary disease with left ventricular remodeling secondary to myocardial ischemia or infarction varies among African-American populations, depending on the prevalence and impact of traditional risk factors for coronary heart disease. Atherosclerosis may play a greater role in the pathogenesis of heart failure in African-Americans as the impact of urbanization and the adoption of unhealthy lifestyles results in increased prevalence of risk factors for coronary artery disease. The hemodynamic and functional features of ventricular dysfunction in African-Americans with heart failure may range from asymptomatic diastolic dysfunction to typical systolic dysfunction. The differentiation of diastolic from systolic dysfunction, and hypertensive from ischemic cardiomyopathy, may be difficult in African-Americans and usually requires utilization of noninvasive cardiac diagnostic techniques. In addition to the type of ventricular dysfunction and the role of neurohormonal activation, consideration of age-related differences, ventricular structure and function, and variations in drug metabolism and pharmacokinetics are important.
MelanoGANs: High Resolution Skin Lesion Synthesis with GANs (2018)

Generative Adversarial Networks (GANs) have been successfully used to synthesize realistically looking images of faces, scenery and even medical images. Unfortunately, they usually require large training datasets, which are often scarce in the medical field, and to the best of our knowledge GANs have been only applied for medical image synthesis at fairly low resolution. However, many state-of-the-art machine learning models operate on high resolution data as such data carries indispensable, valuable information. In this work, we try to generate realistically looking high resolution images of skin lesions with GANs, using only a small training dataset of 2000 samples. The nature of the data allows us to do a direct comparison between the image statistics of the generated samples and the real dataset. We both quantitatively and qualitatively compare state-of-the-art GAN architectures such as DCGAN and LAPGAN against a modification of the latter for the task of image generation at a resolution of 256x256px. Our investigation shows that we can approximate the real data distribution with all of the models, but we notice major differences when visually rating sample realism, diversity and artifacts. In a set of use-case experiments on skin lesion classification, we further show that we can successfully tackle the problem of heavy class imbalance with the help of synthesized high resolution melanoma samples.
Education with and without the state (1995)

Since today’s prosperous nations were once “developing ” countries, it is useful to compare their historical circumstance with those of current developing countries. The characteristics of education in 19th century Britain (then a developing country) turn out to be remarkably similar to
Mechanochemical Synthesis and Anode Properties of SnO‐Based Amorphous Materials (1999)

Amorphous materials in the system , with or without the addition of , were synthesized by mechanical milling treatment of starting oxides in a dry atmosphere at room temperature. These materials, obtained as fine powders, worked as an anode for a lithium‐ion secondary battery using a conventional liquid electrolyte. The first discharge capacities of the anode of materials obtained by mechanical milling were more than at a constant current of . The capacity for added materials was comparable or slightly larger than that for the materials without the addition of . Charge‐discharge curves obtained using these materials were similar to those for the glassy powders in the system prepared by a melt quenching procedure. SnO‐based amorphous materials obtained by mechanochemical synthesis are promising candidates as high‐capacity anode materials for lithium‐ion secondary batteries. © 1999 The Electrochemical Society. All rights reserved.
Following Nature's Lead: Generating Compounds for Stabilizing Biomolecules (2012)

We describe here a unique approach to identifying small molecules that are useful in stabilizing biomolecules in the dry and liquid states. Using biostability screens aided by in silico docking experiments and synthetic chemistry, libraries of biostability molecules are analyzed for their ability to protect important biological materials. In the case of DNA stabilization in the dry state, interactions of suitable candidate biostability compounds with DNA are studied in initial screens to identify their ability to form glasses at elevated temperatures. The most promising compounds are then tested for their capacity to preserve DNA during long-term storage. The results have led to a commercial product for storage of DNA that is being adopted for many commercial and experimental applications. Further studies have shown that small molecules for preservation of RNA, proteins, and tissue samples can be developed by following the same progression of screens.
New Pressure Swing Adsorption Cycle Schedules for Producing High-Purity Oxygen Using Carbon Molecular Sieve (2016)

Two 3-bed 5-step and two 4-bed 7-step continuous feed pressure swing adsorption (PSA) cycle schedules were systematically devised and studied via simulation for producing high-purity O2 (≥99.5 vol %) at high recovery using a carbon molecular sieve (CMS). Two binary (O2:Ar) and two ternary (O2:Ar:N2) feed mixtures were investigated to mimic the product produced from a typical O2 PSA system. In addition to feed composition, the effects of light end (LE) versus heavy end (HE) equalization (Eq), two sequential Eq steps versus Eq followed by forced cocurrent depressurization (CoD)/light end pressurization (LEP) steps, feed flow rate (i.e., feed throughput θ), cycle time (tc), Eq step valve coefficient (Cv), and countercurrent depressurization (CnD) step Cv on the process performance were studied in terms of O2 purity (Pur, vol %), O2 recovery (Rec, %), and θ (LSTP, h/kg). In descending order, the best performance from each cycle was Pur = 99.5, Rec = 93.3, and θ = 455.7 for a 4-bed 7-step PSA cycle with LE Eq and forced CoD/LEP (III); Pur = 99.6, Rec = 85.7, and θ = 471.4 for a 4-bed 7-step cycle with two LE Eqs (II); Pur = 99.5, Rec = 77.4, and θ = 1089.5 for a 3-bed 5-step cycle with LE Eq (Ia); and Pur = 99.5, Rec = 68.7, and θ = 628.6 for a 3-bed 5-step cycle with HE Eq (Ib). The two Cv values exhibited only marginally unfavorable effects on Pur at smaller values. All four cycles were very sensitive to both tc and θ, with Pur decreasing and Rec increasing with decreasing θ, and Rec decreasing and Pur exhibiting a maximum with increasing tc. For cycle III, the Pur exhibited a maximum with a change in the CoD end pressure, with more negative effects on Pur at longer tc. Changing the levels of Ar or N2 in the feed at fixed O2 content had essentially no effect on Pur or Rec, while decreasing the level of O2 in the feed had an almost proportionally negative effect on Pur and no effect on Rec. When N2 was replaced with Ar in the feed, an unexpected equilibrium effect counteracted an expected kinetic effect, producing a counterintuitive negative result on Pur.
Purification and Characterization of a High-Molecular-Weight Insecticidal Protein Complex Produced by the Entomopathogenic Bacterium Photorhabdus luminescens (1998)

Photorhabdus luminescens is a gram-negative enteric bacterium that is found in association with entomopathogenic nematodes of the family Heterorhabditidae. The nematodes infect a variety of soil-dwelling insects. Upon entering an insect host, the nematode releases P. luminescens cells from its intestinal tract, and the bacteria quickly establish a lethal septicemia. When grown in peptone broth, in the absence of the nematodes, the bacteria produce a protein toxin complex that is lethal when fed to, or injected into the hemolymph of, Manduca sexta larvae and several other insect species. The toxin purified as a protein complex which has an estimated molecular weight of 1,000,000 and contains no protease, phospholipase, or hemolytic activity and only a trace of lipase activity. The purified toxin possesses insecticidal activity whether injected or given orally. Analyses of the denatured complex by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed it to be composed of several protein subunits ranging in size from 30 to 200 kDa. The complex was further separated by native gel electrophoresis into three components, two of which retained insecticidal activity. The purified native toxin complex was found to be active in nanogram concentrations against insects representing four orders of the class Insecta.
In vivostudy of human skin using pulsed terahertz radiation (2004)

Studies in terahertz (THz) imaging have revealed a significant difference between skin cancer (basal cell carcinoma) and healthy tissue. Since water has strong absorptions at THz frequencies and tumours tend to have different water content from normal tissue, a likely contrast mechanism is variation in water content. Thus, we have previously devised a finite difference time-domain (FDTD) model which is able to closely simulate the interaction of THz radiation with water. In this work we investigate the interaction of THz radiation with normal human skin on the forearm and palm of the hand in vivo. We conduct the first ever systematic in vivo study of the response of THz radiation to normal skin. We take in vivo reflection measurements of normal skin on the forearm and palm of the hand of 20 volunteers. We compare individual examples of THz responses with the mean response for the areas of skin under investigation. Using the in vivo data, we demonstrate that the FDTD model can be applied to biological tissue. In particular, we successfully simulate the interaction of THz radiation with the volar forearm. Understanding the interaction of THz radiation with normal skin will form a step towards developing improved imaging algorithms for diagnostic detection of skin cancer and other tissue disorders using THz radiation.
Relation Between Surface Roughness and Specular Reflectance at Normal Incidence (1961)

Expressions relating the roughness of a plane surface to its specular reflectance at normal incidence are presented and are verified experimentally. The expressions are valid for the case when the root mean square surface roughness is small compared to the wavelength of light. If light of a sufficiently long wavelength is used, the decrease in measured specular reflectance due to surface roughness is a function only of the root mean square height of the surface irregularities. Long-wavelength specular reflectance measurements thus provide a simple and sensitive method for accurate measurement of surface finish. This method is particularly useful for surface finishes too fine to be measured accurately by conventional tracing instruments. Surface roughness must also be considered in precise optical measurements. For example, a non-negligible systematic error in specular reflectance measurements will be made even if the root mean square surface roughness is less than 0.01 wavelength. The roughness of even optically polished surfaces may thus be important for measurements in the visible and ultraviolet regions of the spectrum.
Fileprints: identifying file types by n-gram analysis (2005)

We propose a method to analyze files to categorize their type using efficient 1-gram analysis of their binary contents. Our aim is to be able to accurately identify the true type of an arbitrary file using statistical analysis of their binary contents without parsing. Consequently, we may determine the type of a file if its name does not announce its true type. The method represents each file type by a compact representation we call a fileprint, effectively a simple means of representing all members of the same file type by a set of statistical 1-gram models. The method is designed to be highly efficient so that files can be inspected with little or no buffering, and on a network appliance operating in high bandwidth environment or when streaming the file from or to disk.