gebhart/patrepeval huggingface dataset:
Functional Analysis of HIV-1 Vpr: Identification of Determinants Essential for Subcellular Localization (1995)

Vpr is a conserved HIV-1 auxiliary protein that localizes to the nuclear region of cells. Vpr is also present in virions, and it is directed into the assembling virus when coexpressed with Gag. Each of these two localization activities may be important for Vpr function, and we recently identified regions of Vpr that are critical for virion incorporation. In this study we analyzed the Vpr domains involved in subcellular localization. Immunofluorescence staining of transfected cells showed that wild-type Vpr localized exclusively to the nuclear region. Mutations in the N-terminal domain that were designed to disrupt a predicted alpha-helical structure resulted in aberrant localization, while conservative substitutions showed a wild-type pattern. A region in the central portion of the protein also has the potential for helical structure, and mutagenesis of two conserved amino acids in this domain (A59, H71) impaired localization, while substitution of a third (Q65) did not. In contrast, neither the conserved Gly and Cys at positions 75-76 nor the C-terminal basic residues (R87, K95) were necessary for nuclear localization. In addition, two-residue insertions within and between the two putative helices disrupted localization but insertion in the C-terminal region did not. Thus, Vpr's subcellular localization function depends on the two putative helical domains but is independent of the conserved Gly-Cys motif and of specific C-terminal basic residues.
Effect of Niacin on Lipid and Lipoprotein Levels and Glycemic Control in Patients With Diabetes and Peripheral Arterial Disease (2000)

Our study suggests that lipid-modifying dosages of niacin can be safely used in patients with diabetes and that niacin therapy may be considered as an alternative to statin drugs or fibrates for patients with diabetes in whom these agents are not tolerated or fail to sufficiently correct hypertriglyceridemia or low HDL-C levels. JAMA. 2000;284:1263-1270
Glycine-alanine dipeptide repeat protein contributes to toxicity in a zebrafish model of C9orf72 associated neurodegeneration (2017)

These novel transgenic C9orf72 associated repeat zebrafish models demonstrate poly-GA toxicity in zebrafish. Reduction of poly-GA protein rescues toxicity validating this therapeutic approach to treat C9orf72 repeat expansion carriers. These novel animal models provide a valuable tool for drug discovery to reduce DPR associated toxicity in ALS/FTLD patients with C9orf72 repeat expansions.
Two plane camera calibration: a unified model (2002)

A unified model for camera calibration is presented. The model does not assume any explicit form of imaging process and can perform linear back projection while considering all lens distortions. This model is well suited to stereo reconstruction. It has been shown that the original two-plane model, the linear and nonlinear pin hole model, can all be realized as special cases of this model. With the two-plane model, optimal orientation of the two reference planes can be found intuitively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New technological developments in integral field spectroscopy (2008)

Integral Field Spectroscopy (IFS) provides a spectrum simultaneously for each spatial sample of an extended two-dimensional field. Basically, the IFS is located in a telescope focal plane and is composed by an Integral Field Unit (IFU or image slicer) and a spectrograph. The IFU acts as a coupler between the telescope and the spectrograph by reformatting optically a rectangular field into a quasi-continuous pseudo-slit located at the entrance focal plane of the spectrograph. The Integral Field Units (IFUs) are presently limited either by their cost/risk (when manufactured with classical glass polishing techniques) or by their performances (when constituted by metallic components). Recent innovative methods, developed conjointly by LAM (Laboratoire d'Astrophysique de Marseille, France) and WinLight Optics (Marseille, France), allow reaching high performances (accurate roughness, sharp edges, surface form, etc.) with standard glass manufactured components while saving costs and time by an order of magnitude compared with classical techniques. Last developments (in term of design and manufacturing) and applications are presented in details in this article.
Tuftsin Binds Neuropilin-1 through a Sequence Similar to That Encoded by Exon 8 of Vascular Endothelial Growth Factor (2005)

Tuftsin, Thr-Lys-Pro-Arg (TKPR), is an immunostimulatory peptide with reported nervous system effects as well. We unexpectedly found that tuftsin and a higher affinity antagonist, TKPPR, bind selectively to neuropilin-1 and block vascular endothelial growth factor (VEGF) binding to that receptor. Dimeric and tetrameric forms of TKPPR had greatly increased affinity for neuropilin-1 based on competition binding experiments. On endothelial cells tetrameric TKPPR inhibited the VEGF(165)-induced autophosphorylation of vascular endothelial growth factor receptor-2 (VEGFR-2) even though it did not directly inhibit VEGF binding to VEGFR-2. Homology between exon 8 of VEGF and TKPPR suggests that the sequence coded for by exon 8 may stabilize VEGF binding to neuropilin-1 to facilitate signaling through VEGFR-2. Given the overlap between processes involving neuropilin-1 and tuftsin, we propose that at least some of the previously reported effects of tuftsin are mediated through neuropilin-1.
0.4 W CW diffraction limited beam Al free 0.98 µmwavelength three core ARROW-type diode lasers (1996)

Diffraction limited beam operation to 0.4 W CW output power has been achieved from 20 µm aperture, 0.98 µm emitting three core antiresonant reflecting optical waveguide (ARROW)-type InGaAs/InGaAsP/InGaP diode lasers. The central lobe energy content is 73% to 0.2 W and 60% at 0.4 W.
Influence of a glycine or proline substitution on the functional properties of a 14-amino-acid analog of Escherichia coli heat-stable enterotoxin (1989)

Analogs of Escherichia coli heat-stable enterotoxin (ST) differing in chain length or the presence of turn-forming residues were assessed for binding to receptors, activation of particulate guanylate cyclase, and stimulation of secretion in suckling mice. These analogs included the native 18-amino-acid peptide (ST), the 14-amino-acid carboxy terminus of this native peptide with a proline at position 12 (ST[5-18]proline), and the 14-amino-acid carboxy terminus in which the proline at position 12 was substituted with glycine (ST[5-18]glycine). Each analog bound to the receptor in a dose-dependent fashion, completely displacing [125I]ST in competitive binding assays. However, their potencies differed significantly: ST demonstrated the highest affinity (inhibition constant [Ki], 10(-9) M), followed by ST[5-18]proline (Ki, 10(-7) M) and ST[5-18]glycine (Ki, 10(-6) M). Similarly, these peptides maximally activated particulate guanylate cyclase and stimulated intestinal secretion in suckling mice. Their rank order of potency in these assays was similar to that described for receptor binding: ST greater than ST[5-18]proline greater than ST[5-18]glycine. These data demonstrate that the full peptide structure is not absolutely required for pharmacological, biochemical, or biological activity. However, the four amino-terminal residues contribute significantly to the potency of these peptides. In addition, the turn imposed by the proline residue at position 12 is not absolutely required for receptor occupancy or activation of the biochemical cascade that results in intestinal secretion. However, it significantly increases the potency of the toxin. These data illustrate the importance of primary and secondary structures to the biochemical, pharmacological, and physiological activities of the ST produced by E. coli.
Particle sizing using laser interferometry (1977)

The theory and conditions are summarized under which single spherical particles in the size range of a few micrometers and larger may be sized using the observed fringe visibility in a cross-beam laser velocimeter. Scalar diffraction theory and experimental data are presented to show how the size information in the forward- scattered light is dependent on the collection optics geometry, including the size and shape of source beam stops, which have been neglected in previous analyses. Experimental data are also presented to show that backscattered light may not be usable for this method of sizing in the range of sizes examined.
Clock hierarchies: an abstraction for grouping and controlling media streams (1996)

Synchronization plays an important role in multimedia systems at various levels of abstraction. We propose a set of powerful abstractions for controlling and synchronizing continuous media streams in distributed environments. The proposed abstractions are based on a very general computation model, that allows media streams to be processed (i.e. produced, consumed or transformed) by arbitrarily structured networks of linked components. Further, compound components can be composed of existing ones to provide higher levels of abstractions. The clock abstraction is provided to control individual media streams, i.e., streams can be started, paused or scaled by issuing the appropriate clock operations. Clock hierarchies are used hierarchically group related streams, where each clock in the hierarchy identities and controls a certain group, or subgroup of streams. Control and synchronization requirements can be expressed in a uniform manner by associating group members with control or synchronisation attributes. An important property of the concept of clock hierarchy is that it can be combined in a natural way with component nesting.
Self-similarity through high-variability: statistical analysis of Ethernet LAN traffic at the source level (1997)

A number of empirical studies of traffic measurements from a variety of working packet networks have demonstrated that actual network traffic is self-similar or long-range dependent in nature-in sharp contrast to commonly made traffic modeling assumptions. We provide a plausible physical explanation for the occurrence of self-similarity in local-area network (LAN) traffic. Our explanation is based on convergence results for processes that exhibit high variability and is supported by detailed statistical analyzes of real-time traffic measurements from Ethernet LANs at the level of individual sources. This paper is an extended version of Willinger et al. (1995). We develop here the mathematical results concerning the superposition of strictly alternating ON/OFF sources. Our key mathematical result states that the superposition of many ON/OFF sources (also known as packet-trains) with strictly alternating ON- and OFF-periods and whose ON-periods or OFF-periods exhibit the Noah effect produces aggregate network traffic that exhibits the Joseph effect. There is, moreover, a simple relation between the parameters describing the intensities of the Noah effect (high variability) and the Joseph effect (self-similarity). An extensive statistical analysis of high time-resolution Ethernet LAN traffic traces confirms that the data at the level of individual sources or source-destination pairs are consistent with the Noah effect. We also discuss implications of this simple physical explanation for the presence of self-similar traffic patterns in modern high-speed network traffic.
Accumulation of native and methylated low density lipoproteins by healing rabbit arterial wall. (1987)

To determine whether healing arterial wall accumulation of low density lipoproteins (LDL) is mediated by the high affinity LDL receptor, normocholesterolemic rabbits were injected with 125I-LDL, 99mTc-LDL, or the reductively methylated analogs of these compounds (125I-MeLDL, 99mTc-MeLDL), 1 month after balloon catheter deendothelialization of the abdominal aorta. If the mechanism of accumulation requires interaction with the LDL receptor, reductively methylated lipoproteins which do not bind to the receptor should not accumulate in healing arterial wall. Twenty-four hours after injection of labelled lipoproteins, each animal was injected with Evans blue dye, in order to distinguish reendothelialized from deendothelialized aorta. One hour after dye injection, the aorta was fixed, removed, divided into abdominal (ballooned) and thoracic (unballooned) regions and counted. For all lipoprotein preparations, there were three to four times as many counts in the abdominal as in the thoracic aorta. En face autoradiographs were made of the aortas that had been exposed to 125I-labelled lipoproteins. In the autoradiographs, the areas of the lowest activity corresponded to the centers of healing endothelial islands. The most intense radioactivity for both lipoproteins occurred in the region of the leading edge of the endothelial islands where active endothelial regeneration was in progress. The overall distribution of native and MeLDL accumulation was the same. The results suggest that low density lipoproteins are accumulated in areas of active endothelial regeneration by a mechanism that does not involve the high affinity LDL receptor.
The Poplar MYB Transcription Factors, PtrMYB3 and PtrMYB20, are Involved in the Regulation of Secondary Wall Biosynthesis (2010)

Dicot wood is mainly composed of cellulose, xylan and lignin, and its formation requires the coordinated regulation of their biosynthesis. In this report, we demonstrate that the poplar wood-associated MYB transcriptional activators, PtrMYB3 and PtrMYB20, activate the biosynthetic pathways of cellulose, xylan and lignin when overexpressed in Arabidopsis and they are also able to activate the promoter activities of poplar wood biosynthetic genes. We also show that PtrMYB3 and PtrMYB20 are functional orthologs of Arabidopsis MYB46 and MYB83, and their expression is directly activated by poplar PtrWND2, suggesting their involvement in the regulation of wood formation in poplar.
The role of Escherichia coli UvrB in nucleotide excision repair. (1990)

The role of UvrB in determining the nucleotide dependence of Escherichia coli excision repair has been investigated. The mutation of lysine 45 in the ATPase motif of UvrB to alanine leads to an acute defect in ATP hydrolysis and failure to support incision of UV-damaged DNA. This ATP hydrolysis activity is not required for interaction of UvrB with UvrA in solution, or for formation of a damage-independent nucleoprotein complex in the presence of UvrA and nucleotide. This UvrB mutant fails, however, to support damage-specific nucleoprotein complex formation, and does not participate in a UvrA-UvrB-dependent helicase-like activity. We conclude from these results that mutation at lysine 45 in the ATPase motif of UvrB specifically inhibits a key step in nucleotide excision repair involving the UvrB ATPase-dependent translocation of nucleoprotein complexes from undamaged to damaged DNA sites.
RICK, a Novel Protein Kinase Containing a Caspase Recruitment Domain, Interacts with CLARP and Regulates CD95-mediated Apoptosis (1998)

Signaling through the CD95/Fas/APO-1 death receptor plays a critical role in the homeostasis of the immune system. RICK, a novel protein kinase that regulates CD95-mediated apoptosis was identified and characterized. RICK is composed of an N-terminal serine-threonine kinase catalytic domain and a C-terminal region containing a caspase-recruitment domain. RICK physically interacts with CLARP, a caspase-like molecule known to bind to Fas-associated protein with death domain (FADD) and caspase-8. Expression of RICK promoted the activation of caspase-8 and potentiated apoptosis induced by Fas ligand, FADD, CLARP, and caspase-8. Deletion mutant analysis revealed that both the kinase domain and caspase-recruitment domain were required for RICK to promote apoptosis. Significantly, expression of a RICK mutant in which the lysine of the putative ATP-binding site at position 38 was replaced by a methionine functioned as an inhibitor of CD95-mediated apoptosis. Thus, RICK represents a novel kinase that may regulate apoptosis induced by the CD95/Fas receptor pathway.
Gist: A Mobile Robotics Application of Context-Based Vision in Outdoor Environment (2006)

We present context-based scene recognition for mobile robotics applications. Our classifier is able to differentiate outdoor scenes without temporal filtering relatively well from a variety of locations at a college campus using a set of features that together capture the "gist" of the scene. We compare the classification accuracy of a set of scenes from 1551 frames filmed outdoors along a path and dividing them to four and twelve different legs while obtaining a classifi- cation rate of 67.96 percent and 48.61 percent, respectively. We also tested the scalability of the features by comparing the classification results from the previous scenes with four legs with a longer path with eleven legs while obtaining a classification rate of 55.08 percent. In the end, some ideas are put forth to improve the theoretical strength of the gist features.
CCL17-expressing dendritic cells drive atherosclerosis by restraining regulatory T cell homeostasis in mice (2011)

Immune mechanisms are known to control the pathogenesis of atherosclerosis. However, the exact role of DCs, which are essential for priming of immune responses, remains elusive. We have shown here that the DC-derived chemokine CCL17 is present in advanced human and mouse atherosclerosis and that CCL17+ DCs accumulate in atherosclerotic lesions. In atherosclerosis-prone mice, Ccl17 deficiency entailed a reduction of atherosclerosis, which was dependent on Tregs. Expression of CCL17 by DCs limited the expansion of Tregs by restricting their maintenance and precipitated atherosclerosis in a mechanism conferred by T cells. Conversely, a blocking antibody specific for CCL17 expanded Tregs and reduced atheroprogression. Our data identify DC-derived CCL17 as a central regulator of Treg homeostasis, implicate DCs and their effector functions in atherogenesis, and suggest that CCL17 might be a target for vascular therapy.
M+Group A Streptococci Are Phagocytized and Killed in Whole Blood by C5a-Activated Polymorphonuclear Leukocytes (2002)

Historically, resistance to phagocytosis has been determined by incubating group A streptococci in human blood and comparing the numbers of CFU before and after incubation. Utilizing a flow cytometry-based technique, we have investigated the phagocytosis of M(+) group A streptococci by polymorphonuclear leukocytes (PMNs) in heparinized human peripheral whole blood. Intracellular labeling of streptococci with a nontoxic fluorescent dye allowed us to quantify the association and phagocytosis of M(+) streptococci by PMNs in whole blood in the presence or absence of C5a, a physiologically important chemotactic activator of PMNs. We found that wild-type strains of group A streptococci that are resistant to phagocytosis (determined by the classical Lancefield method) readily associate with C5a-activated whole-blood PMNs. In the absence of opsonizing M-type-specific antibodies, the M(+) streptococci associated with PMNs are phagocytized and killed. In addition, blockade of the beta(2) integrin, CD11b/CD18, with anti-human CD11b monoclonal antibody inhibited association between M(+) streptococci and C5a-activated PMNs. These findings establish a new relationship between M(+) streptococci and PMNs, in which C5a-activated PMNs have the capacity to kill M(+) streptococci in whole blood through a receptor-mediated phagocytic mechanism.
Scalable arrays of chemical vapor sensors based on DNA-decorated graphene (2013)

Arrays of chemical vapor sensors based on graphene field effect transistors functionalized with single-stranded DNA have been demonstrated. Standard photolithographic processing was adapted for use on large-area graphene by including a metal protection layer, which protected the graphene from contamination and enabled fabrication of high quality field-effect transistors (GFETs). Processed graphene devices had hole mobilities of 1,640 ± 250 cm2·V−1·s−1 and Dirac voltages of 15 ± 10 V under ambient conditions. Atomic force microscopy was used to verify that the graphene surface remained uncontaminated and therefore suitable for controlled chemical functionalization. Single-stranded DNA was chosen as the functionalization layer due to its affinity to a wide range of target molecules and π-π stacking interaction with graphene, which led to minimal degradation of device characteristics. The resulting sensor arrays showed analyte- and DNA sequence-dependent responses down to parts-per-billion concentrations. DNA/GFET sensors were able to differentiate among chemically similar analytes, including a series of carboxylic acids, and structural isomers of carboxylic acids and pinene. Evidence for the important role of electrostatic chemical gating was provided by the observation of understandable differences in the sensor response to two compounds that differed only by the replacement of a (deprotonating) hydroxyl group by a neutral methyl group. Finally, target analytes were detected without loss of sensitivity in a large background of a chemically similar, volatile compound. These results motivate further development of the DNA/graphene sensor family for use in an electronic olfaction system.
The p55 tumour necrosis factor receptor TNFR1 contains a trans-Golgi network localization signal in the C-terminal region of its cytoplasmic tail (2002)

It has been reported in some human cells that, in addition to a plasma membrane localization, members of the tumour necrosis factor receptor superfamily may be localized to the Golgi complex. We have shown by immunofluorescence and immunoelectron microscopy that the p55 tumour necrosis factor receptor, TNFR1, is principally localized to the trans-Golgi network in the human breast carcinoma cell line, MCF7. Chimaeras consisting of the extracellular and transmembrane domains of CD8 together with the cytoplasmic tail of TNFR1 were targeted to the trans-Golgi network in stably transfected rat fibroblastic cells. Deletions in the cytoplasmic tails of these chimaeras demonstrated the requirement for the C-terminal sequence of 23 amino acids for this targeting. The 23 amino acid sequence is mostly outside the death domain and contains both an acid patch and a dileucine motif. Interaction of this sequence with membrane traffic adaptor proteins may play an important role in controlling the responses of cells to tumour necrosis factor, since binding of signalling adaptor proteins has only been demonstrated for plasma membrane, and not Golgi-localized, TNFR1.