gebhart/patrepeval huggingface dataset:
Effects of using different wavelengths in wave-front sensing and correction (1982)

Adaptive-optics systems that use a return-wave concept for compensating for atmospheric turbulence distortions on a transmitted laser beam usually assume that the phase profile of the sensed radiation equals the appropriate phase profile for the laser wavelength. Certainly geometrical optics would predict this to within a scale factor directly related to the index of refraction of the air at the different wavelengths. Diffraction manifests itself in an interference phenomenon and amplitude modulation. Shorter wavelengths are more quickly affected than the longer wavelengths. When amplitude scintillation becomes important, the geometrical-optics-predicted wave-front distortions may differ from the real diffracted beam. The problem reduces to considering the phase difference measured at two different wavelengths after propagating through the same turbulence, and this paper describes these differences.
Characterization of a New Porous Pt-Containing Metal-Organic Framework Containing Potentially Catalytically Active Sites:  Local Electronic Structure at the Metal Centers (2006)

A crystalline and thermally stable metal-organic framework (MOF) with PtII and GdIII sites incorporated in the structure has been recently reported. This material has been synthesized with the aim to develop a heterogeneous PtII counterpart to homogeneous metal-organic complexes having C−H activating properties. The first account focused on the MOF synthesis and on structural and stability characterization of the material. In the present work, a multitechnique approach has been adopted to investigate the effect of solvent removal and the reversibility of this process. Structural features have been investigated by means of powder X-ray diffraction and extended X-ray absorption fine structure spectroscopy at both Pt and Gd L3-edges. Electronic properties have been studied with diffuse reflectance surface UV−vis and X-ray absorption near-edge spectroscopies. Finally, IR spectroscopy has been used to determine the vibration properties. Thermogravimetric methods have been used to quantify the water loss. X-ray absorption spectroscopy has been used to compare the Pt environment in the periodic MOF structure, in related molecular complexes, and in the linkers. Our results demonstrate that the environment around Pt is more or less unaffected by the incorporation of the Pt centers in the molecular complexes into the 3D extended framework of the Pt−Gd MOF. The principle of using known homogeneous complexes as building blocks for the construction of single-site heterogeneous catalysts therefore seems applicable in the present case. Removal of solvent water molecules from the internal voids of the as-prepared MOF presents an opportunity to attain a porous material with accessible PtII sites. We observe that the structure undergoes a reversible loss of long-range order upon dehydration at ambient temperature. The environment of Gd is somewhat perturbed in the dehydration/hydration process, while that of Pt is almost unaffected. When a total dehydration is achieved, the original structure is only partially recovered upon rehydration.
Termination of DNA synthesis by 9-beta-D-arabinofuranosyl-2-fluoroadenine. A mechanism for cytotoxicity. (1990)

The action of 9-beta-D-arabinofuranosyl-2-fluoroadenine (F-ara-A) on DNA synthesis was evaluated both in whole cells and in vitro. 9-beta-D-Arabinofuranosyl-2-fluoroadenine was converted to its 5'-triphosphate 9-beta-D-arabinofuranosyl-2-fluoroadenine 5'-triphosphate (F-ara-ATP) in cells and then incorporated into DNA in a self-limiting manner. More than 94% of the analogue was incorporated into DNA at the 3' termini, indicating a chain termination action. In vitro DNA primer extension experiments further revealed that F-ara-ATP compared with dATP for incorporation into the A site of the extending DNA strand. The incorporation of F-ara-AMP into DNA resulted in termination of DNA strand elongation. Human DNA polymerase alpha incorporated more F-ara-AMP into DNA than polymerase epsilon (proliferating cell nuclear antigen-independent DNA polymerase delta) and was more sensitive to inhibition by F-ara-ATP. On the other hand, DNA polymerase epsilon was able to excise the incorporated F-ara-AMP from DNA in vitro. The incorporation of F-ara-AMP into DNA was linearly correlated both with inhibition of DNA synthesis and with loss of clonogenicity; thus it may be the mechanism of cytotoxicity.
The TigerSHARC DSP architecture (2000)

This highly parallel DSP architecture based on a short-vector memory system incorporates techniques found in general-purpose computing. It promises sustained performance close to its peak computational rates of 900 MFLOPS (32-bit floating-point) or 3.6 BOPS (16-bit fixed-point).
Tree ring analysis (2006)

Tree ring analysis provides useful data for dendrochnologists that can help them for better understanding of climatic and environmental changes. Yet detection and counting of rings in cross section of tree were realized manually which is time consuming and tedious work. Our research was motivated by the need of a fast and accurate method. This paper describes a semi automatic approach for tree rings detection and areas measurement based on 2D gray scale image analysis. Best results are obtained with the developed procedures. A newly algorithm well adapted for blurred and noisy image that smoothes it before detecting the boundaries with a 3/sup rd/ order recursive filter followed by edge extraction and 3D reconstruction of the tree.
Development of Postinfection Epilepsy After Theiler's Virus Infection of C57BL/6 Mice (2010)

Viral infection of the central nervous system can lead to long-term neurologic defects, including increased risk for the development of epilepsy. We describe the development of the first mouse model of viral-induced epilepsy after intracerebral infection with Theiler's murine encephalomyelitis virus. Mice were monitored with long-term video-electroencephalogram at multiple time points after infection. Most mice exhibited short-term symptomatic seizures within 3 to 7 days of infection. This was followed by a distinct latent period in which no seizures were observed. Prolonged video-electroencephalogram recordings at 2, 4, and 7 months after the initial infection revealed that a significant proportion of the mice developed profound, spontaneous epileptic seizures. Neuropathologic examination revealed hippocampal sclerosis in animals with epilepsy. Theiler's murine encephalomyelitis virus-infected C57BL/6 mice represent a novel "hit-and-run" model to investigate mechanisms underlying viral-induced short-term symptomatic seizures, epileptogenesis, and epilepsy. Importantly, this model will also be useful to investigate novel therapies for the treatment and prevention of epilepsy.
Development of sequence specific radioimmunoassay of human parathyroid hormone and its use in the diagnosis of hyperparathyroidism (1979)

Two antisera which were raised against bovine parathyroid hormone (bPTH), and which cross-reacted with the human hormone, have been characterized. The antisera which originated from rooster and guinea-pig, were found to contain several populations of antibodies directed against both N-terminal and C-terminal sequences of the hormone. However, at proper dilutions the rooster antiserum did not bind the N-terminal fragment nor could this fragment displace the [125I] bPTH (1--84 amino acid residue) from binding to the antiserum. Furthermore, preincubation experiments with excess N-terminal fragment showed only a negligible reduction in maximal binding of the iodinated intact hormone using the rooster antiserum. In contrast, the guinea-pig antiserum reacted equally well with the N-terminal fragment and the intact hormone, and preincubation with this fragment reduced the binding of the [125I]bPTH (1--84 amino acid residues) by 75%. Gel filtration of hyperparathyroid serum on Bio-Gel P-60 showed immunoreactive material which was measured with both antisera, eluting at a position similar to the intact hormone. However, in the C-terminal specific, but not in the N-terminal specific radioimmunoassay the major component eluted together with or somewhat earlier than the N-terminal bPTH fragment (1--34 amino acid residue), and this peak represented more than 90% of total immunoreactive PTH (iPTH) in serum. This major iPTH component must therefore represent fragment(s) with intact carboxy-terminal sequences. The N-terminal specific radioimmunoassay was unable to measure iPTH in about 80--90% of healthy individuals while the C-terminal specific assay detected iPTH in about 88% of these sera (equal to or above 0.1 micrograms/l). Similarly, the N-terminal specific antiserum measured consistently lower serum iPTH concentrations in patients with primary hyperparathyroidism. In thirty-four out of forty-one patients with surgically verified primary hyperparathyroidism, serum iPTH concentrations equal to or above 0.60 micrograms/l were demonstrated using the C-terminal, specific radioimmunoassay.
Colorectal cancer prevention 2000: screening recommendations of the American College of Gastroenterology (2000)

Colorectal cancer prevention 2000: screening recommendations of the American College of Gastroenterology
Compact MIMO-arrays based on polarisation-diversity (2004)

The application of MIMO (multiple input multiple output) systems in small handheld devices is difficult, since usually large antenna spacings are required to obtain uncorrelated channel coefficients. This paper shows, using dipoles, that a combination of pattern- and polarisation diversity yields uncorrelated channel coefficients that can be exploited by MIMO system. A way of modeling the impact of antennas on MIMO systems is presented here. The complex radiation pattern, polarisation, mutual coupling of the antennas and cross polarisation coupling within the transmission channel are taken into account. It is shown that a combination of polarisation and pattern diversity leads to very compact antenna arrays, that still yield uncorrelated channels.
Isolation and Characterization of the Hyperthermostable Serine Protease, Pyrolysin, and Its Gene from the Hyperthermophilic Archaeon Pyrococcus furiosus (1996)

The hyperthermostable serine protease pyrolysin from the hyperthermophilic archaeon Pyrococcus furiosus was purified from membrane fractions. Two proteolytically active fractions were obtained, designated high (HMW) and low (LMW) molecular weight pyrolysin, that showed immunological cross-reaction and identical NH2-terminal sequences in which the third residue could be glycosylated. The HMW pyrolysin showed a subunit mass of 150 kDa after acid denaturation. Incubation of HMW pyrolysin at 95 degrees C resulted in the formation of LMW pyrolysin, probably as a consequence of COOH-terminal autoproteolysis. The 4194-base pair pls gene encoding pyrolysin was isolated and characterized, and its transcription initiation site was identified. The deduced pyrolysin sequence indicated a prepro-enzyme organization, with a 1249-residue mature protein composed of an NH2-terminal catalytic domain with considerable homology to subtilisin-like serine proteases and a COOH-terminal domain that contained most of the 32 possible N-glycosylation sites. The archaeal pyrolysin showed highest homology with eucaryal tripeptidyl peptidases II on the amino acid level but a different cleavage specificity as shown by its endopeptidase activity toward caseins, casein fragments including alphaS1-casein and synthetic peptides.
Identification of 53 compounds that block Ebola virus-like particle entry via a repurposing screen of approved drugs (2014)

In light of the current outbreak of Ebola virus disease, there is an urgent need to develop effective therapeutics to treat Ebola infection, and drug repurposing screening is a potentially rapid approach for identifying such therapeutics. We developed a biosafety level 2 (BSL-2) 1536-well plate assay to screen for entry inhibitors of Ebola virus-like particles (VLPs) containing the glycoprotein (GP) and the matrix VP40 protein fused to a beta-lactamase reporter protein and applied this assay for a rapid drug repurposing screen of Food and Drug Administration (FDA)-approved drugs. We report here the identification of 53 drugs with activity of blocking Ebola VLP entry into cells. These 53 active compounds can be divided into categories including microtubule inhibitors, estrogen receptor modulators, antihistamines, antipsychotics, pump/channel antagonists, and anticancer/antibiotics. Several of these compounds, including microtubule inhibitors and estrogen receptor modulators, had previously been reported to be active in BSL-4 infectious Ebola virus replication assays and in animal model studies. Our assay represents a robust, effective and rapid high-throughput screen for the identification of lead compounds in drug development for the treatment of Ebola virus infection.
Responses of NBT-II bladder carcinoma cells to conditioned medium from normal fetal urogenital sinus. (1987)

In vitro studies were conducted to determine whether conditioned medium from rat fetal urogenital sinus explants would affect phenotypic characteristics of NBT-II urinary bladder carcinoma cells in culture. NBT-II cells were exposed to medium (30%, v/v) conditioned for 48 h by intact urogenital sinus explants derived from 18-day fetal rats. Upon exposure for 23 h the [3H]thymidine incorporation by NBT-II cells was decreased by 40.3% relative to control cultures. This effect was paralleled by a similar decrease in proliferation. NBT-II cultures decreased in cell number by 32.1 and 45.8% on days 2 and 4, respectively, after exposure to conditioned medium. Although cell proliferation was inhibited, conditioned medium acted to induce an increase in protein secretion. An increase of 18.6% was observed in the incorporation of [35S]methionine into newly synthesized, secreted proteins by NBT-II cells exposed to conditioned medium for 23 h. Morphologically the NBT-II cells exposed to conditioned medium were larger, more spread out, and exhibited a greater array of lamellipodia and filopodia, although [35S]methionine incorporation into cellular proteins was decreased by 11.1%. These results suggest that diffusable factors produced by fetal urogenital sinus explants can induce changes in proliferation, protein synthesis, protein secretion, and phenotypic morphology of NBT-II carcinoma cells in culture.
Ensemble Classification and Regression-Recent Developments, Applications and Future Directions [Review Article] (2016)

Ensemble methods use multiple models to get better performance. Ensemble methods have been used in multiple research fields such as computational intelligence, statistics and machine learning. This paper reviews traditional as well as state-of-the-art ensemble methods and thus can serve as an extensive summary for practitioners and beginners. The ensemble methods are categorized into conventional ensemble methods such as bagging, boosting and random forest, decomposition methods, negative correlation learning methods, multi-objective optimization based ensemble methods, fuzzy ensemble methods, multiple kernel learning ensemble methods and deep learning based ensemble methods. Variations, improvements and typical applications are discussed. Finally this paper gives some recommendations for future research directions.
Selective Inhibition of JAK1 and JAK2 Is Efficacious in Rodent Models of Arthritis: Preclinical Characterization of INCB028050 (2010)

Inhibiting signal transduction induced by inflammatory cytokines offers a new approach for the treatment of autoimmune diseases such as rheumatoid arthritis. Kinase inhibitors have shown promising oral disease-modifying antirheumatic drug potential with efficacy similar to anti-TNF biologics. Direct and indirect inhibition of the JAKs, with small molecule inhibitors like CP-690,550 and INCB018424 or neutralizing Abs, such as the anti-IL6 receptor Ab tocilizumab, have demonstrated rapid and sustained improvement in clinical measures of disease, consistent with their respective preclinical experiments. Therefore, it is of interest to identify optimized JAK inhibitors with unique profiles to maximize therapeutic opportunities. INCB028050 is a selective orally bioavailable JAK1/JAK2 inhibitor with nanomolar potency against JAK1 (5.9 nM) and JAK2 (5.7 nM). INCB028050 inhibits intracellular signaling of multiple proinflammatory cytokines including IL-6 and IL-23 at concentrations <50 nM. Significant efficacy, as assessed by improvements in clinical, histologic and radiographic signs of disease, was achieved in the rat adjuvant arthritis model with doses of INCB028050 providing partial and/or periodic inhibition of JAK1/JAK2 and no inhibition of JAK3. Diminution of inflammatory Th1 and Th17 associated cytokine mRNA levels was observed in the draining lymph nodes of treated rats. INCB028050 was also effective in multiple murine models of arthritis, with no evidence of suppression of humoral immunity or adverse hematologic effects. These data suggest that fractional inhibition of JAK1 and JAK2 is sufficient for significant activity in autoimmune disease models. Clinical evaluation of INCB028050 in RA is ongoing.
Characteristics of short‐chain alcohol dehydrogenases and related enzymes (1991)

Different short-chain dehydrogenases are distantly related, constituting a protein family now known from at least 20 separate enzymes characterized, but with extensive differences, especially in the C-terminal third of their sequences. Many of the first known members were prokaryotic, but recent additions include mammalian enzymes from placenta, liver and other tissues, including 15-hydroxyprostaglandin, 17 beta-hydroxysteroid and 11 beta-hydroxysteroid dehydrogenases. In addition, species variants, isozyme-like multiplicities and mutants have been reported for several of the structures. Alignments of the different enzymes reveal large homologous parts, with clustered similarities indicating regions of special functional/structural importance. Several of these derive from relationships within a common type of coenzyme-binding domain, but central-chain patterns of similarity go beyond this domain. Total residue identities between enzyme pairs are typically around 25%, but single forms deviate more or less (14-58%). Only six of the 250-odd residues are strictly conserved and seven more are conserved in all but single cases. Over one third of the conserved residues are glycine, showing the importance of conformational and spatial restrictions. Secondary structure predictions, residue distributions and hydrophilicity profiles outline a common, N-terminal coenzyme-binding domain similar to that of other dehydrogenases, and a C-terminal domain with unique segments and presumably individual functions in each case. Strictly conserved residues of possible functional interest are limited, essentially only three polar residues. Asp64, Tyr152 and Lys156 (in the numbering of Drosophila alcohol dehydrogenase), but no histidine or cysteine residue like in the completely different, classical medium-chain alcohol dehydrogenase family. Asp64 is in the suggested coenzyme-binding domain, whereas Tyr152 and Lys156 are close to the center of the protein chain, at a putative inter-domain, active-site segment. Consequently, the overall comparisons suggest the possibility of related mechanisms and domain properties for different members of the short-chain family.
Stereoscopic Visualization and 3-D Technologies in Medical Endoscopic Teleoperation (2014)

Stereoscopic 3-D visualization (S3D) provides a user with higher comprehension of remote environments in teleoperation when compared to 2-D viewing. Studies in the literature have shown how stereo vision may contribute to improving perception of some depth cues, but it is hard to find work assessing stereoscopic 3-D viewing in telenavigation tasks involving medical flexible endoscopes. Nonetheless, the increased level of depth awareness provided by stereo viewing is remarkable, which facilitates endoscope teleguide, teleexploration, and teleintervention, leading to accurate navigation and faster decision-making. This paper assesses S3D in medical endoscopic teleoperation. We evaluate the usability of a flexible stereoscopic bronchoscope. Twenty test users are asked to teleguide a virtual endoscope, which operates in a realistically simulated bronchus environment under different viewing conditions and displays. The evaluation involves seven systems (from laptops to wall screen and head-mounted display), four approaches to stereo viewing (colored Anaglyph, polarized filters, shutter glasses, and separated displays), and five types of display technologies (digital light processing, cathode ray tube, liquid crystal display, light-emitting diode (LED), and organic LED). The results show a strong improvement in users' performance when the endoscope-camera view is (depth-) enhanced by stereo viewing. Users' performance and appreciation may vary in different systems, which is also commented in this paper. This study supports system designers in making informed decisions.
High-level heterologous expression and secretion in rapidly growing nonpathogenic mycobacteria of four major Mycobacterium tuberculosis extracellular proteins considered to be leading vaccine candidates and drug targets (1997)

Mycobacterium tuberculosis, the primary etiologic agent of tuberculosis, is the world's leading cause of death from a single infectious agent, and new vaccines and drugs to combat it are urgently needed. The major extracellular proteins of M. tuberculosis, which are released into its phagosome in macrophages, its host cells in humans, are leading candidates for a vaccine and prime targets for new drugs. However, the development of these biologicals has been hampered by the unavailability of large quantities of recombinant extracellular proteins identical to their native counterparts. In this report, we describe the heterologous expression and secretion of four major M. tuberculosis extracellular proteins (the 30-, 32, 16-, and 23.5-kDa proteins--the first, second, third, and eighth most abundant, respectively) in rapidly growing, nonpathogenic mycobacterial species. Multiple attempts to obtain secretion of the proteins by using Escherichia coli- and Bacillus subtilis-based expression systems were unsuccessful, suggesting that high-level expression and secretion of these Mycobacterium-specific proteins require a mycobacterial host. All four recombinant proteins were stably expressed from the cloned genes' own promoters at yields that were 5- to 10-fold higher than those observed for the native proteins. The four proteins were purified to apparent homogeneity from culture filtrates by ammonium sulfate precipitation and ion-exchange and molecular sieve chromatography. The recombinant proteins were indistinguishable from their native counterparts by multiple criteria. First, N-terminal amino acid sequence determination demonstrated that processing of the leader peptides was highly accurate. Second, sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis revealed identical migration patterns. Third, mass spectrometry analysis confirmed that differences in mass were < or = 5 Da. A homolog of the M. tuberculosis 30-kDa protein was identified in M. smegmatis by means of DNA analyses and immunoscreening. This is the first time that secretion of recombinant M. tuberculosis extracellular proteins in their native form has been achieved. This study opens the door to mass production of correctly processed and secreted extracellular proteins of M. tuberculosis in a heterologous host and allows ready evaluation of their biologic and immunologic function.