gebhart/patrepeval huggingface dataset:
The UV visual world of fishes: a review (1999)

Ultraviolet‐A radiation (320–400 nm) is scattered rapidly in water. Despite this fact, UV is present in biologically useful amounts to at least 100 m deep in clear aquatic environments. Discovery of UV visual pigments with peak absorption at around 360 nm in teleost cone photoreceptors indicates that many teleost fishes may be adapted for vision in the UV range. Considering the characteristic absorption curve for visual pigments, about 18% of the downwelling light that illuminates objects at 30‐m depth would be available to UV‐sensitive cones. Strong scattering of UV radiation should produce unique imaging conditions as a very bright UV background in the horizontal view and a marked veiling effect that, with distance, obscures an image. Many teleosts have three, or even four, classes of cone cells mediating colour vision in their retina and one can be sensitive to UV. These UV‐sensitive cones contain a visual pigment based on a unique opsin which is highly conserved between fish species. Several powerful methods exist for demonstration of UV vision, but all are rather demanding in terms of technique and equipment. Demonstration that the eye lacks UV‐blocking compounds that are present in many fish eyes is a simpler method that can indicate the possibility of UV vision. The only experimental evidence for the use of UV vision by fishes is connected to planktivory: detection of UV‐opaque objects at close range against a bright UV background is enhanced by the physical properties of UV light. Once present, perhaps for the function of detecting food, UV vision may well be co‐opted through natural selection for other functions. Recent discovery that UV vision is critically important for mate choice in some birds and lizards is a strong object lesson for fish ecologists and behaviourists. Other possible functions amount to far more than merely adding a fourth dimension to the visible spectrum. Since UV is scattered so effectively in water, it may be useful for social signalling at short range and reduce the possibility of detection by other, illegitimate, receivers. Since humans are blind to UV light, we may be significantly in error, in many cases, in our attempts to understand and evaluate visual aspects of fish behaviour. A survey of the reflectance properties of skin pigments in fishes reveals a rich array of pigments with reflectance peaks in the UV. For example, the same yellow to our eyes may comprise two perceptually different colours to fish, yellow and UV‐yellow. It is clearly necessary for us to anticipate that many fishes may have some form of UV vision.
Successful Human Islet Isolation Utilizing Recombinant Collagenase (2003)

The enzymatic dissociation of acinar tissue by collagenase is a substantial step in the isolation of pancreatic islets. Although essential collagenase components have been purified, the variability in the activity of different batches limits long-term reproducibility of isolation success. The utilization of purified recombinant proteases would solve this problem. In the present study, pancreases from multiorgan donors were dissociated by means of digestion-filtration using either Liberase HI (n = 51) or a recombinant collagenase blend (n = 25). No significant differences were found regarding islet yield before and after purification, the percent of exocrine-attached islets, and final purity. However, the ratio between islet equivalents and islet numbers indicated a lesser fragmentation in islets isolated with recombinant collagenase (P < 0.01). In contrast, viability was slightly higher in islets isolated with Liberase (92.3 +/- 0.8 vs. 85.6 +/- 2.9%; P < 0.05). Insulin release during static glucose incubation was not different between experimental groups. Islet transplantation into diabetic nude mice resulted in sustained normoglycemia in either group until the graft was removed. These results demonstrated that viable human islets can be isolated using recombinant collagenase. Final optimization of this enzyme blend would offer continuous reproducibility of isolation success.
Complement C5 Mediates Experimental Tubulointerstitial Fibrosis (2007)

Renal fibrosis is the final common pathway of most progressive renal diseases. C5 was recently identified as a risk factor for liver fibrosis. This study investigated the role of C5 in the development of renal tubulointerstitial fibrosis by (1) induction of renal fibrosis in wild-type and C5(-/-) mice by unilateral ureteral ligation (UUO) and (2) investigation of the effects of a C5a receptor antagonist (C5aRA) in UUO. In C5(-/-) mice, when compared with wild-type controls, markers of renal fibrosis (Sirius Red, type I collagen, fibronectin, alpha-smooth muscle actin, vimentin, and infiltrating macrophages) were significantly reduced on day 5 of UUO. On day 10, fibronectin mRNA and protein expression were still reduced in the C5(-/-) mice. Cortical mRNA of all PDGF isoforms and of TGF-beta(1) (i.e., central mediators of renal disease) were significantly reduced in C5(-/-) mice when compared with controls. Renal tubular cell expression of the C5aR was sparse in normal cortex but markedly upregulated after UUO. Treatment of wild-type UUO mice with C5aRA also led to a significant reduction of cortical Sirius Red staining, fibronectin protein expression, and PDGF-B mRNA expression on day 5. Neither genetic C5 deficiency nor C5aRA treatment caused any histologic changes in the nonobstructed kidneys. In cultured murine cortical tubular cells, C5a stimulated production of TGF-beta(1), and this was inhibited by C5aRA. Using a combined genetic and pharmacologic approach, C5, in particular C5a, is identified as a novel profibrotic factor in renal disease and as a potential new therapeutic target.
Photon shot noise dephasing in the strong-dispersive limit of circuit QED (2012)

We study the photon shot noise dephasing of a superconducting transmon qubit in the strong-dispersive limit, due to the coupling of the qubit to its readout cavity. As each random arrival or departure of a photon is expected to completely dephase the qubit, we can control the rate at which the qubit experiences dephasing events by varying in situ the cavity mode population and decay rate. This allows us to verify a pure dephasing mechanism that matches theoretical predictions, and in fact explains the increased dephasing seen in recent transmon experiments as a function of cryostat temperature. We observe large increases in coherence times as the cavity is decoupled from the environment, and after implementing filtering find that the intrinsic coherence of small Josephson junctions when corrected with a single Hahn echo is greater than several hundred microseconds. Similar filtering and thermalization may be important for other qubit designs in order to prevent photon shot noise from becoming the dominant source of dephasing.
Orientation Dependence of Charge-Transfer Processes on TiO[sub 2] (Anatase) Single Crystals (2000)

Electrochemical measurements in aqueous and aprotic media have been carried out on anatase single crystals with exposed (101) and (001) surfaces, respectively. Water reduction and photo‐oxidation take place at more negative potentials for the (001) surface than for the (101) surface. This can be rationalized in terms of a more negative flatband potential (by ca. 0.06 V) for the (001) face, which is due to dissociative chemisorption of water molecules on this surface. Lithium insertion is favored on the (001) surface, as evidenced by a higher standard rate constant for charge transfer and a higher chemical diffusion coefficient for insertion for the propagation along the c axis. This can be explained by a more open structure of the anatase lattice in this direction. © 2000 The Electrochemical Society. All rights reserved.
Detection of Life-Threatening Arrhythmias Using Feature Selection and Support Vector Machines (2013)

Early detection of ventricular fibrillation (VF) and rapid ventricular tachycardia (VT) is crucial for the success of the defibrillation therapy. A wide variety of detection algorithms have been proposed based on temporal, spectral, or complexity parameters extracted from the ECG. However, these algorithms are mostly constructed by considering each parameter individually. In this study, we present a novel life-threatening arrhythmias detection algorithm that combines a number of previously proposed ECG parameters by using support vector machines classifiers. A total of 13 parameters were computed accounting for temporal (morphological), spectral, and complexity features of the ECG signal. A filter-type feature selection (FS) procedure was proposed to analyze the relevance of the computed parameters and how they affect the detection performance. The proposed methodology was evaluated in two different binary detection scenarios: shockable (FV plus VT) versus nonshockable arrhythmias, and VF versus nonVF rhythms, using the information contained in the medical imaging technology database, the Creighton University ventricular tachycardia database, and the ventricular arrhythmia database. sensitivity (SE) and specificity (SP) analysis on the out of sample test data showed values of SE=95%, SP=99%, and SE=92% , SP=97% in the case of shockable and VF scenarios, respectively. Our algorithm was benchmarked against individual detection schemes, significantly improving their performance. Our results demonstrate that the combination of ECG parameters using statistical learning algorithms improves the efficiency for the detection of life-threatening arrhythmias.
miRCancer: a microRNA–cancer association database constructed by text mining on literature (2013)

miRCancer is freely available on the web at http://mircancer.ecu.edu/
Effects of Catalyst Model and High Adsorbate Coverages in ab Initio Studies of Alkane Hydrogenolysis (2018)

Bare, low-index periodic surface models are typically used to examine metal-catalyzed reactions in density functional theory (DFT) studies, and these most closely resemble low-pressure surface science reactions and catalyzed reactions that occur on large terraces that prevail on large (>5 nm) supported nanoparticles. Many catalytic reactions, however, occur near conditions at which catalytic surfaces are saturated by one or more adsorbed intermediates, leading to strong coadsorbate interactions and surface reconstruction leading to increased curvature. Alkane hydrogenolysis is such a reaction and has been extensively studied using DFT—often on bare metal surfaces—with the assumption that omitted coadsorbed hydrogen atoms (H*) do not significantly alter the relative activation barriers and with ad hoc assumptions about the site requirements for relevant reactions. Here, we use ethane hydrogenolysis on H*-covered Ir catalysts (using a periodic surface model and a nanoparticle model) as a probe reaction to examine coadsorbate interactions and to demonstrate the rigorous determination of site requirements. The kinetically relevant transition state [*CH–CH*]⧧ is larger than the 0–3 coadsorbed H* atoms it replaces, such that the reaction has a positive activation area (a concept analogous to activation volume in homogeneous reactions) and thus repels coadsorbed H* atoms when fewer than four H* vacancies are created. This induced strain cannot be relieved on the periodic surface models, resulting in large effective free energy barriers and predictions that four vacant sites are required (γ = 4). These barriers and site requirements lead to turnover rates that are 4 orders of magnitude lower than measured rates and incorrect H2-pressure dependencies. Furthermore, varying the unit cell size of the Ir(111) surface dramatically alters the calculated reaction energetics, indicating that relevant transition states destabilize one another over long distances through the H* adlayer. Curved H*-covered Ir hemispherical particle models (119 atoms), however, stabilize transition states at a lower number of vacant sites (γ = 2) through lateral relaxation of the adlayer, resulting in correct predictions of H2-pressure dependencies and quantitative agreement between calculated and measured rates.
The role of tissue factor in the production of thrombin (1993)

Tissue factor is now widely accepted to be the major physiological initiator of blood coagulation. The importance of this protein to normal haemostasis may be inferred from the clinical effects of factor VII deficiency and by the fact that congenital tissue factor deficiency has not been described. Tissue factor is a single polypeptide with an established amino acid sequence that may be divided into cytoplasmic, extracellular and transmembrane regions. There are no close structural similarities with other proteins although tissue factor may be a member of the cytokine receptor family. This paper reviews current knowledge of the role of tissue factor in the production of thrombin with particular reference to its expression, location, control and relevance to haemostasis.
Pharmaceutical Crystallization (2011)

Crystallization is crucial in the pharmaceutical industry as a separation process for intermediates and as the final step in the manufacture of active pharmaceutical ingredients (APIs). In this perspective article to celebrate 10 years of Crystal Growth & Design, we focus on three areas related to crystallization in the pharmaceutical industry: (1) advances in our understanding of the fundamentals of nucleation, (2) production and scale-up of novel solid forms, and (3) continuous processing. While the areas discussed are not new, they are areas, in our opinion, of significant current interest to the community engaged in crystallization in the pharmaceutical industry.
Efficient oxidative folding of conotoxins and the radiation of venomous cone snails (2003)

The 500 different species of venomous cone snails (genus Conus) use small, highly structured peptides (conotoxins) for interacting with prey, predators, and competitors. These peptides are produced by translating mRNA from many genes belonging to only a few gene superfamilies. Each translation product is processed to yield a great diversity of different mature toxin peptides (approximately 50,000-100,000), most of which are 12-30 aa in length with two to three disulfide crosslinks. In vitro, forming the biologically relevant disulfide configuration is often problematic, suggesting that in vivo mechanisms for efficiently folding the diversity of conotoxins have been evolved by the cone snails. We demonstrate here that the correct folding of a Conus peptide is facilitated by a posttranslationally modified amino acid, gamma-carboxyglutamate. In addition, we show that multiple isoforms of protein disulfide isomerase are major soluble proteins in Conus venom duct extracts. The results provide evidence for the type of adaptations required before cone snails could systematically explore the specialized biochemical world of "microproteins" that other organisms have not been able to systematically access. Almost certainly, additional specialized adaptations for efficient microprotein folding are required.
Dye-Ligand Affinity Chromatography: The Interaction of Cibacron Blue F3GA® with Proteins and Enzyme (1984)

The dye Cibacron Blue F3GA has a high affinity for many proteins and enzymes. It has therefore been attached to various solid supports such as Sephadex, Sepharose, polyacrylamide, and the like. In the immobilized form the dye has rapidly been exploited as an affinity chromatographic medium to separate and purify a variety of proteins including dehydrogenases, kinases, serum albumin, interferons, several plasma proteins, and a host of other proteins. Such a diversity shown by the blue dye in binding several unrelated classes of proteins has generated considerable work in terms of studies of the chromophore itself and also the immobilized ligand. As a prelude to realizing the full potential of the immobilized Cibacron Blue F3GA, an understanding of the basic interactions of the dye with its surroundings must be gained. It has been recognized that the dye is capable of hydrophobic and/or electrostatic interactions at the instance of the ambient conditions. The study of interactions of the dye with salts, solvents, and other small molecules indicates the nature of the interactions of the dye with different kinds of groups at the interacting sites of proteins. The review will cover such interactions of the dye with the proteins, the interactions of the proteins with the immobilized ligand, and the media used to elute the bound protein in several cases, and thus consolidate the available information on such studies into a cogent and comprehensive explanation.
Temporal and spatial changes in fecundity of eastern oysters, Crassostrea virginica (Gmelin, 1791) in the James River, Virginia (1992)

A~u1t Crass~strea virgi.nic~ ~Gmelin) were examined during the reproductive season of 1986 to determine temporal and spatial vanation m fecundity among md!Vldual female oysters from four reefs in the James River, Virginia. Sex ratio and oyster abu.ndance were. ~so determined to :acilitate ~s~imation of total reproductive output of oyster assemblages. Fecundity was highly vanable, both w1thm and among locations. Vanation was attributed to differences in oyster size, asynchrony and variation in time since pri~r spawning, prevalence of parasites (especially Haplosporidium nelsoni (MSX) and Perkinsus marinus) and differing salinity regimes.
Establishment and characterization of three transplantable EBV‐containing nasopharyngeal carcinomas (1988)

Three transplantable nasopharyngeal carcinoma (NPC) tumors, designated C15, C17 and C18, have been obtained and characterized. C15, derived from a primary NPC tumor, has been propagated in nude mice for 30 passages. C17 and C18, derived from metastatic NPC tissue, have been passaged 10 times. Desmosomes, present in every case, provided confirmation of the epithelial origin of all 3 tumors. The Epstein-Barr virus (EBV) genome is contained in C15, C18 and C17 tumor cells with 30, 12 and 3 copies, respectively. The Epstein-Barr virus nuclear antigen (EBNA) was stained by the classical anti-complement immunofluorescence (ACIF) technique. Fluorescence intensity was strong in C15, moderate in C18, and hardly detectable in C17 cells. No expression of the EA and VCA antigens was detected. Flow cytometry analysis performed on monocellular suspensions showed the absence of detectable CR2 molecules (the EBV receptor on B lymphocytes) in all 3 tumors, and the constitutive expression of HLA class-II antigens in C15 and C17 cells. IL-1 activity was demonstrated in the supernatant of C15 and C17 cells cultivated in vitro for 3 days. These data confirm that the constitutive synthesis of MHC class-II molecules and the release of IL-1-like activities are frequent features of NPC cells. These characteristics could be of importance in relation with the T-cell infiltrate found in NPC primary tumors.
50-GHz optically injection-locked 1.55-/spl mu/m VCSELs (2005)

High-speed directly modulated diode lasers are important for optical communications and optical interconnects. In this work, we demonstrate greatly enhanced resonance frequency for vertical-cavity surface-emitting lasers, from 7 to 50 GHz, under ultrahigh injection-locking conditions. In addition, a 20-dB gain is achieved for small signal modulation below resonance frequency.
Idiopathic Pulmonary Fibrosis: CT and Risk of Death (2014)

CT fibrosis score can replace diffusion capacity of carbon monoxide test results in a modified GAP gender, age, and physiology model (the CT- GAP gender, age, and physiology model) with comparable performance. This may be a useful alternative model in situations where CT scoring is more reliable and available than diffusion capacity of carbon monoxide.
MN/CA IX/G250 as a potential target for immunotherapy of renal cell carcinomas (1999)

The monoclonal antibody G250 (mAbG250) raised against a human renal cell carcinoma (RCC) has been shown to react with a large number of RCCs. Recently, G250 antigen was isolated and found to be homologous to the MN/CA9 gene originally identified in HeLa cells. To determine whether G250 antigen (MN/CA IX/G250) could be a potential therapeutic target and a tumour marker, a total of 147 cases of RCC were investigated immunohistochemically as well as by reverse transcriptase polymerase chain reaction (RT-PCR) analysis. In addition, total RNAs extracted from patients' peripheral blood samples were analysed for MN/CA9/G250 mRNA signals. Immunohistochemistry demonstrated strong expression in 128/147 (87.1%) of RCCs, in contrast to the lack of expression observed in normal tissues. RT-PCR analyses of frozen specimens resulted in the clear detection of MN/CA9/G250 mRNA signals in 137/147 (93.2%), and despite subtle differences the results were almost identical to those for immunohistochemistry. Although high-grade and -stage tumours exhibited significantly lower expression than low-grade and -stage tumours, a large proportion of tumours expressed MN/G250 protein as well as mRNA. RT-PCR analysis of patients' blood samples revealed the presence of circulating MN/CA9/G250 expressing cells. These findings suggest that this antigen may be a potential therapeutic target as well as diagnostic marker for RCCs.
In VitroAntimalarial Activity of Different Inhibitors of the Plasmodial Isoprenoid Synthesis Pathway (2015)

Previous studies have shown that fosmidomycin, risedronate, and nerolidol exert antimalarial activity in vitro. We included squalestatin, an inhibitor of the isoprenoid metabolism in Erwinia uredovora, and found that combinations of compounds which act on different targets of the plasmodial isoprenoid pathway possess important supra-additivity effects.
Study of resolution and super resolution in electromagnetic imaging for half-space problems (2004)

It has been observed that super resolution is possible in the electromagnetic imaging. In the first part of the paper, the possible resolution of image is investigated in the inversion of far-field data using the diffraction tomographic (DT) algorithm, where two cases are considered when the object is in a homogeneous space and in an air-earth half space. The study shows that the resolution of image for inversion of far-field data has been limited theoretically to 0.3536-0.5 wavelength using the DT algorithm in homogeneous-space problems, and it is even worse in half-space problems. If the transmitters and receivers are located in the near-field regime, however, the image resolution is less than 0.25 wavelength, which is the super-resolution phenomenon. In the second part of the paper, the physical reason for the super-resolution phenomenon is investigated using different electromagnetic inverse scattering methods. The study has demonstrated that the information of evanescent waves in the measurement data and its involvement in inversion algorithms is the main reason for the super resolution. Four inversion algorithms are considered for half-space problems: the DT algorithm, the spatial-domain Born approximation (BA), the Born iterative method (BIM), and the distorted BIM (DBIM). The first two belong to linear inverse scattering, while the last two belong to nonlinear inverse scattering. Further analysis shows that DBIM provides a better super resolution than BIM, and BIM provides a better super resolution than BA. Numerical simulations validate the above conclusions.