gebhart/patrepeval huggingface dataset:
Pathophysiological consequences of atherosclerosis extend into the coronary microcirculation. Restoration of endothelium-dependent responses by L-arginine. (1992)

The goals of this study were 1) to quantitate the effects of atherosclerosis on physiological and pharmacological endothelium-dependent vasoactive responses in coronary arterioles downstream from arterial lesions and 2) to determine if administration of L-arginine, the precursor for endothelium-derived was induced in pigs, and vasomotor responses of isolated, cannulated coronary arterioles (30-70 microns in diameter) were assessed by measuring diameter changes in vitro. To assess pharmacological alterations of endothelium-dependent responses, dose-response curves were constructed to ADP, serotonin, and histamine. To assess physiological alterations in endothelial function, different flow rates were established across the vessel. Arteriolar diameters were measured in vessels from normal and atherosclerotic pigs under control conditions, after administration of L-arginine, and after endothelial denudation. In arterioles from normal pigs, administration of serotonin, histamine, or ADP produced dose-dependent vasodilation, which was abolished by endothelial denudation. In arterioles from atherosclerotic pigs, administration of histamine, serotonin, and ADP produced dilation at only the highest doses (10(-6)-10(-7) M), and the extent of dilation was only 20-30% of that observed in arterioles from normal pigs. Initiation of flow also produced vasodilation in arterioles from normal pigs that was completely abolished after endothelial denudation. In arterioles from atherosclerotic pigs, flow-induced responses were absent. These abnormal physiological and pharmacological responses (i.e., blunted vasodilation to pharmacological stimulation and to flow) were restored after administration of L-arginine for 40 minutes. The vascular responses after administration of L-arginine were not different from those observed under control conditions in arterioles from normal pigs. In addition, L-arginine did not restore vasodilation to the endothelium-dependent agonists in denuded segments. From these data in arterioles downstream from atherosclerotic lesions, we conclude that 1) the ED50 and maximal responses of endothelium-dependent vasodilation to ADP, histamine, and serotonin are attenuated; 2) the physiological response to flow, that is, flow-mediated endothelium-dependent vasodilation, is absent; and 3) the abnormality in arteriolar responsiveness during large vessel disease involves an impairment of the synthesis and/or release of endothelium-derived relaxing factor.
AT2, A New Time Scale Algorithm: AT1 Plus Frequency Variance (1991)

The existing AT1 algorithm produces a time scale with a fractional frequency variation smaller than that of any clock in the ensemble. We are developing a modification to AT1 that includes the additional desirable features: automatic frequency-step detection, the option to run in an optimal post-processing mode and to run with minimal supervision in non-technical environments. These properties are facilitated by the inclusion of a Kalman-filter estimate of the frequency variance of each clock in the scale. Results are reported from both simulated and real clock data to demonstrate automatic frequency-step detection.
New coatings for high temperature materials protection (1984)

The development, characterization, and performance evaluation of two new thin (≲20 μm) ceramic coatings for high temperature materials protection is reviewed. These coatings were silica produced by two vapor deposition procedures and ceria formed by sol–gel technology. The current position regarding the use of these coatings in the UK nuclear industry is described.
Hinge Atlas: relating protein sequence to sites of structural flexibility (2007)

We found various correlations between hinges and sequence features. Some of these are expected; for instance, we found that hinges tend to occur on the surface and in coils and turns and to be enriched with small and hydrophilic residues. Others are less obvious and intuitive. In particular, we found that hinges tend to coincide with active sites, but unlike the latter they are not at all conserved in evolution. We evaluate the potential for hinge prediction based on sequence. Motions play an important role in catalysis and protein-ligand interactions. Hinge bending motions comprise the largest class of known motions. Therefore it is important to relate the hinge location to sequence features such as residue type, physicochemical class, secondary structure, solvent exposure, evolutionary conservation, and proximity to active sites. To do this, we first generated the Hinge Atlas, a set of protein motions with the hinge locations manually annotated, and then studied the coincidence of these features with the hinge location. We found that all of the features have bearing on the hinge location. Most interestingly, we found that hinges tend to occur at or near active sites and yet unlike the latter are not conserved. Less surprisingly, we found that hinge residues tend to be small, not hydrophobic or aliphatic, and occur in turns and random coils on the surface. A functional sequence based hinge predictor was made which uses some of the data generated in this study. The Hinge Atlas is made available to the community for further flexibility studies.
Intersubtype recombinant HIV-1 Sequences. (1997)

Retroviruses are highly recombinogenic, but recombination can only occur between genomes packaged within the same virion. Until about 1994, it was generally thought that individuals do not become infected with multiple distinct HIV-1 strains, and so the possibility that recombination between divergent viruses could contribute to the evolution of HIV-1 was not widely considered. However, not long after the recognition that the considerable global diversity of the major (M) group of HIV-1 could be described in terms of discrete sequence subtypes, it was also realized that a significant fraction of HIV-1 strains are in fact intersubtype recombinants [1,2]. Analyses of viruses characterized over the last few years have confirmed that substantial numbers of HIV-1 isolates have mosaic genomes [3–16]. The finding of such hybrid viruses has a number of implications both for attempts at viral characterization (phylogenetic analyses, and tracking of the epidemic), and for concerns about the future genetic diversity of HIV-1 and its impact on vaccine development.
Search algorithm for pattern match analysis of nuleic add sequences (1983)

A new type of search algorithm to find biological information inherited in nucleic acid sequences was developed. The algorithm is of pattern match type and is based on the fact that genetic information often is a function of a predictable statistical occurrence of the four bases within parts of the sequence. The search algorithm compares the known statistical pattern of bases in e.g. a promoter, with an unknown sequence and calculates the statistical significance of the match at all positions in the unknown sequence. The program was tested on 54 published prokaryotic promoters. 44 or 49 could be found with 1 or 4 false answers, respectively. The program was also used on plasmid pBR322. All promoters functioning in an in vitro transcription system were found (tet, anti-tet, p4, bla and ori) except the so called p5 promoter. A search for donor and acceptor sites was performed in a human HLA genomic sequence that contains six introns. Five of the possible six donor and acceptor sites were found.
Effects of Src Homology Domain 2 (SH2)-Containing Inositol Phosphatase (SHIP), SH2-Containing Phosphotyrosine Phosphatase (SHP)-1, and SHP-2 SH2 Decoy Proteins on FcγRIIB1-Effector Interactions and Inhibitory Functions (2000)

Coaggregation of Fc gamma RIIB1 with B cell Ag receptors (BCR) leads to inhibition of BCR-mediated signaling via recruitment of Src homology domain 2 (SH2)-containing phosphatases. In vitro peptide binding experiments using phosphotyrosine-containing sequences derived from the immunoreceptor tyrosine-based inhibitory motif (ITIM) known to mediate Fc gamma RIIB1 effects suggest that the receptor uses SH2-containing inositol phosphatase (SHIP) and SH2-containing phosphotyrosine phosphatase (SHP)-1, as well as SHP-2 as effectors. In contrast, coimmunoprecipitation studies of receptor-effector associations suggest that the predominant Fc gamma RIIB1 effector protein is SHIP. However, biologically significant interactions may be lost in such studies if reactants' dissociation rates (Kd) are high. Thus, it is unclear to what extent these assays reflect the relative recruitment of SHIP, SHP-1, and SHP-2 to the receptor in vivo. As an alternative approach to this question, we have studied the effects of ectopically expressed SHIP, SHP-1, or SHP-2 SH2-containing decoy proteins on Fc gamma RIIB1 signaling. Results demonstrate the SHIP is the predominant intracellular ligand for the phosphorylated Fc gamma RIIB1 ITIM, although the SHP-2 decoy exhibits some ability to bind Fc gamma RIIB1 and block Fc receptor function. The SHIP SH2, while not affecting Fc gamma RIIB1 tyrosyl phosphorylation, blocks receptor-mediated recruitment of SHIP, SHIP phosphorylation, recruitment of p52 Shc, phosphatidylinositol 3,4,5-trisphosphate hydrolysis, inhibition of mitogen-activated protein kinase activation, and, albeit more modestly, Fc gamma RIIB1 inhibition of Ca2+ mobilization. Taken together, results implicate ITIM interactions with SHIP as a major mechanism of Fc gamma RIIB1-mediated inhibitory signaling.
SIFT-based Segmentation of Multiple Instances of Low-Textured Objects (2013)

This paper proposes a simple yet effective approach for segmenting multiple instances of the same object for a pick-and-place application. The considered objects present several challenges, such as low texture, semi-transparent container, moving parts, and severe occlusions. Real-time constraints must be met, calling for a good trade-off between accuracy and efficiency. For all these reasons, the proposed approach is based on SIFT features and a suitable modification of the 2NN matching procedure to increase the number of available matches. Moreover, in order to reduce false segmentations, ad-hoc algorithms based on overlap detection and color similarity are used.
Scalable Light-Printing of Substrate-Engraved Free-Form Metasurfaces (2019)

A key challenge for metasurface research is locally controlling at will the nanoscale geometric features on meter-scale apertures. Such a technology is expected to enable large aperture meta-optics and revolutionize fields such as long-range imaging, lasers, laser detection and ranging (LADAR), and optical communications. Furthermore, these applications are often more sensitive to light-induced and environmental degradation, which constrains the possible materials and fabrication process. Here, we present a relatively simple and scalable method to fabricate a substrate-engraved metasurface with locally printed index determined by induced illumination, which, therefore, addresses both the challenges of scalability and durability. In this process, a thin metal film is deposited onto a substrate and transformed into a mask via local laser-induced dewetting into nanoparticles. The substrate is then dry-etched through this mask, and selective mask removal finally reveals the metasurface. We show that masking by the local nanoparticle distribution, and, therefore, the local index, is dependent on the local light-induced dewetting temperature. We demonstrate printing of a free-form pattern engraved into a fused silica glass substrate using a laser raster scan. Large-scale spatially controlled engraving of metasurfaces has implications on other technological fields beyond optics, such as surface fluidics, acoustics, and thermomechanics.
The United States Attorneys General and International Law. By David R. Deener. (The Hague: Martinus Nijhoff. 1957. Pp. xi, 416. 26.50 guilders.) (1958)

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Communication lower bounds for statistical estimation problems via a distributed data processing inequality (2016)

We study the tradeoff between the statistical error and communication cost of distributed statistical estimation problems in high dimensions. In the distributed sparse Gaussian mean estimation problem, each of the m machines receives n data points from a d-dimensional Gaussian distribution with unknown mean θ which is promised to be k-sparse. The machines communicate by message passing and aim to estimate the mean θ. We provide a tight (up to logarithmic factors) tradeoff between the estimation error and the number of bits communicated between the machines. This directly leads to a lower bound for the distributed sparse linear regression problem: to achieve the statistical minimax error, the total communication is at least Ω(min{n,d}m), where n is the number of observations that each machine receives and d is the ambient dimension. These lower results improve upon Shamir (NIPS'14) and Steinhardt-Duchi (COLT'15) by allowing multi-round iterative communication model. We also give the first optimal simultaneous protocol in the dense case for mean estimation. As our main technique, we prove a distributed data processing inequality, as a generalization of usual data processing inequalities, which might be of independent interest and useful for other problems.
Climate Change: The Business Case for Early Action (2006)

The members of the Australian Business Roundtable on Climate Change explain to CEDA why they are campaigning for more aggressive action to reduce global carbon dioxide emissions. The paper is an edited version of discussions at Climate Change - The Business Case For Early Action, a forum at CEDA in Melbourne on 19 July 2006.
Making MLSD decisions by thresholding the matched filter output (2000)

This paper presents an iterative detector that, by thresholding the output of the matched filter, gives maximum-likelihood sequence detector (MLSD) decisions on binary, antipodally modulated symbols that have been corrupted by intersymbol interference and additive Gaussian noise. The detector will make decisions on some, but often not all, of the symbols in a transmitted sequence, and those decisions will be the same decisions as the MLSD would have made. The number of symbols that are detected is stochastic, varying from sequence to sequence. The basis of the detector is a bound on a crossterm of the quadratic form in the log-likelihood function for the transmitted sequence. The detector is simple in structure, consisting of a matched filter and two variable threshold values for each symbol.
Simulating the open-loop transfer function as a means for understanding acoustic feedback in hearing aids (1989)

Suppressing unstable acoustic feedback in hearing aids will first require knowledge of the open-loop transfer functions of such systems. Reported herein is a mathematical technique for simulating the open-loop transfer function of an in situ eyeglass-type hearing aid. In particular, a computer program was developed that characterized the hearing aid as a serial connection of two-port blocks, each representing one individual component of a hearing aid. Included, for example, were two-port blocks representing the microphone, amplifier, receiver, sound tubes leading to the eardrum (including the ear canal itself), earmold vent, and external pathway from the vent outlet back to the microphone. The computer program was validated by replicating laboratory data derived from an experiment involving a nonstandard manikin fitted with a nonstandard artificial ear. Next, the open-loop transfer function of an eyeglass-type hearing aid in situ on the manikin was simulated via the computer program. Unfortunately, those computer-generated data were not replicated in the laboratory due to the difficulty encountered in actually measuring the open-loop transfer function. Nevertheless, investigators were able to utilize those data to predict, within +/- 25 Hz, the "squeal" frequency of unstable acoustic feedback.
Deracemization of Quaternary Stereocenters by Pd‐Catalyzed Enantioconvergent Decarboxylative Allylation of Racemic β‐Ketoesters (2005)

Stereochemische Alchemie! Aus racemischen Allyl-β-ketoestern lassen sich regiokontrolliert Enolate erzeugen, wobei derselbe Katalysator sowohl den Abbau (C-C-Bindungsbruch) als auch den selektiven Aufbau eines Stereozentrums (C-C-Verknüpfung) vermittelt. Auf diese Art wurden mehrere quartäre Kohlenstoffstereozentren in einer einzigen Kaskadenreaktion gebildet (siehe Schema). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z502018_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
P-SELECTIN MEDIATES REPERFUSION INJURY IN THE WARM ISCHEMIC MOUSE LIVER (1998)

35 Ischemia-reperfusion injury in liver transplantation is an important cause of subsequent graft dysfunction. Leukocyte adhesion to the hepatic vasculature is a key factor in this type of injury. Vascular adhesion molecules, such as P-selectin, are required for the early interaction between leukocytes and the endothelium. However, the role of P-selectin in liver injury remains elusive. Aims: To determine whether P-selectin mediates neutrophil adhesion and related injuries following varying periods of hepatic ischemia and reperfusion. Methods: Paired experiments with mutant (P-selectin -/-) and wild-type mice (C57BL/6) were performed. Animals were subjected to 30, 60, 90 and 120 min of partial hepatic ischemia and reperfused for 15 min, 6 hr and 24 hr. Serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were measured as markers of reperfusion injury. Cell adhesion was assessed as a function of velocity using intravital fluorescence video-microscopy and in vivo labelling of neutrophils with Acridine Orange (250µm). A new model of total hepatic ischemia in the mouse was developed to evaluate animal survival. Results: In most ischemia groups AST and ALT levels were significantly lower in the P-selectin -/- at 6 and 24 hr after reperfusion. For instance, in livers subjected to 90 min of ischemia AST levels in mutant mice were 3600±200 U/L compared to 11300±2000 U/L in wild-type mice (Students t-test, p<0.05). Neutrophil velocity was evaluated in livers subjected to 60 min of partial hepatic ischemia and was significantly greater in P-selectin -/-, 5100µm/sec compared to 4400µm/sec in wild-type mice (Students t-test, p<0.05). Animal survival was significantly better in P-selectin -/- (100%) compared to wild-type mice (28.6%) in livers subjected to 75 min of ischemia. Conclusions: P-selectin mediates neutrophil adhesion to the liver microvasculature and may significantly influence graft function following graft reperfusion in liver transplantation. Acknowledgement: This work was supported by Roche Pharmaceuticals Inc.
19‐5L: <i>Late‐News Paper</i> : Perceptually Optimized Dual‐layer Light Field 3D Display Using a Moiré‐aware Compressive Factorization (2016)

In this paper we propose a rotation angle‐based perceptual optimization framework for dual‐layer light field 3D displays. The whole framework flow can be divided into two phases; first, the moiré pattern is simulated based on the rotation angle and a moiré cost for visual perception is calculated and second, the moiré cost is further incorporated into the final optimization of the proposed compressive factorization for the light field 3D display. In this way, a moiré‐aware compressive factorization with rotation optimization is proposed to generate the final display content for our prototype. Experiments demonstrate that the proposed method provides a promising perceptual optimization in both moiré mitigation and definition enhancement for the visual perception of compressive light field displays.
Research on Thermal Dosage for High Intensity Focused Ultrasound in Bovine Liver Based on the Magnetic Resonance Thermometry (2009)

Discussing the relationships between the simulated threshold thermal dose of coagulation and coagulation on the histological slides based on the magnetic resonance (MR) thermometry. The MR imaging guided HIFU system was used, the parameters of therapeutic transducer were: frequency-1 MHz, diameter-150 mm, focal length-150 mm. Sonications were delivered in fresh bovine liver tissue in vitro at a fixed depth of 20 mm and at varying powers. Temperature-sensitive MR images obtained during the sonications were used to estimate the temperature and the thermal dosage of each voxel in the target region was calculated. The thermal dosage of each voxel can be compared with the reference threshold thermal dosage, so as to calculate the boundary and area of the coagulated tissue. After the exposure, the tissue was dissected along the maximal section of the coagulation necrosis, and the area of the biological focal region was measured. The results from this study showed that the occurrence of tissue damage correlated well with the equivalent thermal dose calculation based on the T-mapping of MRI, and they share the same variation tendency.
Biological limiting factors in Ocean Thermal Energy Conversion (1977)

Ocean thermal energy conversion (OTEC) is one of several solar energy options being considered by the U.S. Energy Research and Development Administration (ERDA). The OTEC concept utilizes the thermal difference between warm surface and cool, deep water in tropical oceans to operate a heat engine to produce either electricity or energy-intensive chemicals. Several OTEC system designs, both open and closed cycle, have been suggested. It is estimated that by the year 2020, 4 to 6% of the anticipated energy needs of the United States could be supplied by OTEC. However, primary biological films that reduce heat transfer at heat exchange surfaces are a major limiting factor to successful development of OTEC technology. Battelle, Pacific Northwest Laboratories (PNL) is managing an ERDA program aimed to define, prevent, and/or alleviate, potential biofouling problems associated with OTEC systems. Extensive research concerning open ocean biofouling and its control will be necessary. The OTEC concept, its history and potential advantages are discussed; various overall system designs are reviewed; and the biological limitations on OTEC development are dicussed. 33 references.