gebhart/patrepeval huggingface dataset:
Local complexity of amino acid interactions in a protein core (2003)

Atomic resolution structures of proteins indicate that the core is typically well packed, suggesting a densely connected network of interactions between amino acid residues. The combinatorial complexity of energetic interactions in such a network could be enormous, a problem that limits our ability to relate structure and function. Here, we report a case study of the complexity of amino acid interactions in a localized region within the core of the GFP, a particularly stable and tightly packed molecule. Mutations at three sites within the chromophore-binding pocket display an overlapping pattern of conformational change and are thermodynamically coupled, seemingly consistent with the dense network model. However, crystallographic and energetic analyses of coupling between mutations paint a different picture; pairs of mutations couple through independent "hotspots" in the region of structural overlap. The data indicate that, even in highly stable proteins, the core contains sufficient plasticity in packing to uncouple high-order energetic interactions of residues, a property that is likely general in proteins.
Transition of Ionic Liquid [bmim][PF<sub>6</sub>] from Liquid to High-Melting-Point Crystal When Confined in Multiwalled Carbon Nanotubes (2007)

In this communication, we report our finding on the transition of ionic liquid [bmim][PF6] from the liquid state to high-melting-point crystal when confined in multiwalled carbon nanotubes. This novel crystallization behavior is explained by the nanosized effect of carbon nanotubes on the structure of ionic liquid.
Thermo‐plasmonics: using metallic nanostructures as nano‐sources of heat (2012)

Abstract Recent years have seen a growing interest in using metal nanostructures to control temperature on the nanoscale. Under illumination at its plasmonic resonance, a metal nanoparticle features enhanced light absorption, turning it into an ideal nano‐source of heat, remotely controllable using light. Such a powerful and flexible photothermal scheme is the basis of thermo‐plasmonics . Here, the recent progress of this emerging and fast‐growing field is reviewed. First, the physics of heat generation in metal nanoparticles is described, under both continuous and pulsed illumination. The second part is dedicated to numerical and experimental methods that have been developed to further understand and engineer plasmonic‐assisted heating processes on the nanoscale. Finally, some of the most recent applications based on the heat generated by gold nanoparticles are surveyed, namely photothermal cancer therapy, nano‐surgery, drug delivery, photothermal imaging, protein tracking, photoacoustic imaging, nano‐chemistry and optofluidics.
Wearable and Stretchable Strain Sensors: Materials, Sensing Mechanisms, and Applications (2020)

Recent advances in the design and implementation of wearable resistive, capacitive, and optical strain sensors are summarized herein. Wearable and stretchable strain sensors have received extensive research interest due to their applications in personalized healthcare, human motion detection, human–machine interfaces, soft robotics, and beyond. The disconnection of overlapped nanomaterials, reversible opening/closing of microcracks in sensing films, and alteration of the tunneling resistance have been successfully adopted to develop high‐performance resistive‐type sensors. On the other hand, the sensing behavior of capacitive‐type and optical strain sensors is largely governed by their geometrical changes under stretching/releasing cycles. The sensor design parameters, including stretchability, sensitivity, linearity, hysteresis, and dynamic durability, are comprehensively discussed. Finally, the promising applications of wearable strain sensors are highlighted in detail. Although considerable progress has been made so far, wearable strain sensors are still in their prototype stage, and several challenges in the manufacturing of integrated and multifunctional strain sensors should be yet tackled.
Functional heterogeneity of parietal cells along the pig-gland axis (1997)

The gastric epithelium forms numerous short pits continuous with long tubular glands divisible into isthmus neck, and base regions. Parietal cells are produced in the isthmus and migrate down to the neck and base regions as they mature and age. Stimulation of parietal cells is manifested by translocation of H(+)-K(+)-adenosinetriphosphatase-rich tubulovesicles (TV) from the cytoplasm into the secretory-apical (SA) membrane. In this study we used rabbit isolated gastric glands to examine the physiological responses of parietal cells to graded levels of stimulation. Quantitative morphometry was used to evaluate parietal cell response along the longitudinal axis of the gland. Acid secretion as estimated by [14C]aminopyrine uptake was well correlated with parallel enzymatic and immunoblot assays for the redistribution of H(+)-K(+)-ATPase from TV to SA membranes. These responses also correlated well with morphological transformations of parietal cells within the isthmus and neck regions of the gastric gland; however, parietal cells in the base of the gland showed very little morphological change in response to any of the stimuli used. The poor responsiveness of basal parietal cells is in agreement with observations of intact mucosa and suggests that older parietal cells may serve some function other than acid secretion.
Low-threshold, strained-layer, GaInP/AlGaInP GRINSCH visible diode lasers (1991)

Graded-index, separate-confinement heterostructure (GRlNSCH) semiconductor diode visible lasers employing a strained-layer GaInP single quantum well were fabricated from metalorganic chemical-vapor deposition (MOCVD)-grown epitaxial material. CW threshold current densities as low as 650 A/cm/sup 2/ were measured for uncoated, 1200- mu m-long, 15- mu m-wide ridge structures operating at 30 degrees C and emitting at 655-670 nm. A maximum output under quasi-CW conditions (100 mu s pulse length, 1% duty factor) as high as 320 mW/facet was achieved before catastrophic failure. This threshold current density is believed to be the lowest reported to date for visible light diode lasers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dense 3D Object Reconstruction from a Single Depth View (2018)

In this paper, we propose a novel approach, 3D-RecGAN++, which reconstructs the complete 3D structure of a given object from a single arbitrary depth view using generative adversarial networks. Unlike existing work which typically requires multiple views of the same object or class labels to recover the full 3D geometry, the proposed 3D-RecGAN++ only takes the voxel grid representation of a depth view of the object as input, and is able to generate the complete 3D occupancy grid with a high resolution of 256<sup>3</sup> by recovering the occluded/missing regions. The key idea is to combine the generative capabilities of 3D encoder-decoder and the conditional adversarial networks framework, to infer accurate and fine-grained 3D structures of objects in high-dimensional voxel space. Extensive experiments on large synthetic datasets and real-world Kinect datasets show that the proposed 3D-RecGAN++ significantly outperforms the state of the art in single view 3D object reconstruction, and is able to reconstruct unseen types of objects.
The quest for quality tags (2007)

Many online communities use tags - community selected words or phrases - to help people find what they desire. The quality of tags varies widely, from tags that capture akey dimension of an entity to those that are profane, useless, or unintelligible. Tagging systems must often select a subset of available tags to display to users due to limited screen space. Because users often spread tags they have seen, selecting good tags not only improves an individual's view of tags, it also encourages them to create better tags in the future. We explore implicit (behavioral) and explicit (rating) mechanisms for determining tag quality. Based on 102,056 tag ratings and survey responses collected from 1,039 users over 100 days, we offer simple suggestions to designers of online communities to improve the quality of tags seen by their users.
Inter-personnel communications and network security procedures (2004)

This paper proposes an approach to creating domains in organizations based upon a level of information exchange between their employees. Network security procedures that are created for entire organization are very often too restrictive [1,2]. Using our proposed approach, the security procedures (filtering, file access, etc.) can be developed in different ways for different domains.
Laser plasma spectrochemistry (2011)

An overview of laser plasma spectrochemistry is presented to demonstrate its wide range of capabilities. Laser plasmas offer the ability to perform elemental, isotopic, molecular, quantitative and qualitative sample analysis with sub-micron spatial resolution, and each feature can be measured at standoff distances. Obviously, these attributes are not all achievable at the same time, but they can be optimized for specific applications. This manuscript gives a sampling (pun intended) of the research in our group that has demonstrated each of these capabilities. Although the technology is commonly referred to as LIBS (laser-induced breakdown spectroscopy), the authors prefer to use laser plasma spectrometry to represent the underlying science.
A Practical Approach to Achieving Recommended Blood Pressure Goals in Diabetic Patients (2001)

Approximately 11 million Americans have both hypertension and diabetes mellitus. This double diagnosis places such patients at high risk for renal damage, especially end-stage renal disease. The sixth report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure recommends a blood pressure goal of less than 130/85 mm Hg to reduce or slow the onset of renal disease and cardiovascular events in patients with hypertension and diabetes mellitus. Recent data, however, now suggest that an even lower diastolic blood pressure goal (ie, <80 mm Hg) may be necessary. Studies have shown that use of angiotensin-converting enzyme inhibitors can prevent the progression of microalbuminuria to overt proteinuria, reduce proteinuria in patients with overt diabetic nephropathy, slow the deterioration of the glomerular filtration rate, delay progression to end-stage renal disease, and lower blood pressure. Thus, all diabetic patients with blood pressure greater than 130/80 mm Hg should begin angiotensin-converting enzyme inhibitor treatment and be titrated to moderate or high doses until the blood pressure goal is achieved. However, monotherapy still may not control blood pressure to the recommended target. Studies have shown that use of multiple antihypertensive agents is necessary and successful in helping patients reach their target blood pressure, and this may offer more renoprotection than one agent used singly. A case study that applies these concepts in outpatient practice is included.
Cloning and sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme (1993)

The panB gene from Escherichia coli, encoding the first enzyme of the pantothenate biosynthesis pathway, ketopantoate hydroxymethyltransferase (KPHMT), has been isolated by functional complementation of a panB mutant strain with an E. coli genomic library. The gene is 792 bp long, encoding a protein of 264 amino acids with a predicted M(r) of 28,179. The identity of the gene product as ketopantoate hydroxymethyltransferase was confirmed by purification of the enzyme protein, which was overexpressed approximately 50-fold in the mutant harboring the gene on a high-copy-number plasmid. The N-terminal amino acid sequence of the purified protein was found to be identical to that predicted from the gene sequence, as was its mass, determined by electrospray mass spectrometry. Upstream of the panB gene is an incomplete open reading frame encoding a protein of 220 amino acids, which shares sequence similarity to fimbrial precursor proteins from other bacteria. Northern (RNA) analysis showed that the panB gene is likely to be cotranscribed with at least one other gene but that this is not the putative fimbrial protein, since no transcripts for this gene could be detected.
Interobserver study of liver histopathology using the Ishak score in patients with chronic hepatitis C virus infection (1999)

The Ishak system is associated with good interobserver reliability if a deviance of one categorical level in each variable of the system is accepted as agreement. Compared to the Knodell system it provides more detailed information but is less reliable regarding fibrosis.
An element removal and reintroduction strategy for the topology optimization of structures and compliant mechanisms (2003)

Abstract A method is developed to systematically remove and reintroduce low density elements from and into the finite element mesh on which the structural topology optimization problem is defined. The material density field which defines the topology and the local ‘stiffness’ of the structure is optimally distributed via non‐linear programming techniques. To prevent elements from having zero stiffness, an arbitrarily small lower bound on the material density is typically imposed to ensure that the global stiffness matrix does not become singular. While this approach works well for most minimum compliance problems, the presence of low density elements can cause computational problems, particularly in structures that exhibit geometric non‐linearities, e.g. in compliant mechanisms. To resolve this problem, a systematic approach for removing and reintroducing low density elements is presented, and the substantial performance improvements both in design and computational efficiency of the method over current methods are discussed. Several structures and compliant mechanisms are designed to demonstrate the method. Copyright © 2003 John Wiley & Sons, Ltd.
CMOS Detector Cells For Holographic Optical Interconnects In Microcircuits (1987)

This paper reports on the characterization of CMOS detectors for holographic optical interconnects in microcircuits. A VLSI temporal response system has been built, which has high-magnification viewing capabilities to facilitate identifying the sample area under investigation. A isolated photodiode and load circuit has been characterized to determine responsivity, response time and light spot positioning effects. The threshold of optical gate cells (OGC) incorporating the above detectors and a transistor inverter stage to couple to other circuitry has been determined. The rise time and fall time of the optical gate cells have also been determined experimentally. The results were compared with the results of SPICE simulation, and show satisfactory agreement. The time delay of optical gate cell output was thus determined to be 70 ns at 10 μW light input. Threshold power was 0.5 μW light input.
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats (2005)

harold.garner@utsouthwestern.edu.
Vasoconstriction to endogenous endothelin-1 is impaired in patients with Type II diabetes mellitus (2000)

Endothelin-1 has potent vasoconstrictor and vasopressor actions contributing to basal vascular tone and maintenance of blood pressure acting predominantly through endothelin-A receptors. Endothelin antagonists may be of value in the treatment of hypertension and heart failure. However, the role of endothelin-1 in the regulation of vascular tone and the potential benefits of endothelin antagonists in non-insulin-dependent diabetes mellitus (Type II diabetes) are less clear. Vasoconstriction to exogenous endothelin-1 is impaired in Type II diabetes. The purpose of this study was to determine whether vasoconstriction to endogenous endothelin-1 acting through the endothelin-A receptor is impaired in Type II diabetes. In ten patients with Type II diabetes and nine controls the endothelin-A receptor antagonist BQ123 was infused intra-arterially at 100 nmol/min for 60 min followed by normal saline for 30 min. Forearm blood flow was measured using venous occlusion plethysmography. Control subjects showed gradual onset of vasodilation in response to BQ123 (P < 0.001). Diabetic subjects, however, showed no significant response (P > 0.05). There was a significant difference between the diabetic and control groups (P < 0.05). Blockade of the endothelin-A receptor is associated with impaired vasodilation in Type II diabetes indicating vasoconstriction to endogenous endothelin-1 mediated by the endothelin-A receptor is impaired.
<i>In vivo</i>effects of targeting CD79b with antibodies and antibody-drug conjugates (2009)

Antibodies directed against B cells are in use for the treatment of non-Hodgkin's lymphoma and autoimmune disorders. The B-cell-restricted surface antigen CD79b, a signaling component of the B-cell receptor, has been shown as a promising antibody target in mouse efficacy models of systemic lupus erythematosus. Anti-CD79b antibody-drug conjugates (ADC), cytotoxic drugs linked through specialized chemical linkers to antibodies, are effective in mouse xenograft models of non-Hodgkin's lymphoma. We were interested in evaluating the systemic effects of anti-CD79b antibodies and ADCs in normal animals as a step toward the development of these molecules as therapeutics. As we were unable to identify any cell surface binding anti-human CD79b antibodies that were cross-reactive to other species, we developed an antibody to cynomolgus monkey (Macaca fascicularis) CD79b (anti-cyCD79b). The anti-cynomolgus antibody, anti-cyCD79b (10D10), and the maytansine (tubulin inhibitor)-conjugated ADC, anti-cyCD79b (10D10)-MCC-DM1, were administered to cynomolgus monkeys at approximately 30 mg/kg (6,000 microg DM1/m(2)) for two doses 3 weeks apart. Anti-cyCD79b and anti-cyCD79b-MCC-DM1 resulted in peripheral blood B-cell depletion of approximately 65% and approximately 94%, respectively. In addition, anti-cyCD79b-MCC-DM1 resulted in near-complete absence of splenic germinal centers, an observation supporting an effect on dividing B cells. Both molecules were well tolerated, with minimal findings for the antibody and findings for the ADC limited to the lymphoid and hematopoietic systems, liver, and peripheral nerves. These preclinical data suggest that targeting CD79b with antibodies or ADCs may provide safe and effective therapies for B-cell malignancies and autoimmune diseases.
Antithrombotic activity of a monoclonal antibody inducing the substrate form of plasminogen activator inhibitor type 1 in rat models of venous and arterial thrombosis (1998)

1. Elevated plasminogen activator inhibitor 1 (PAI-1) is a risk factor for thrombosis, and inhibitors of the interaction between PAI-1 and tissue plasminogen activator (t-PA) have antithrombotic and prothrombolytic activity in animals. We describe the antithrombotic effects in the rat of a monoclonal antibody (MA33H1) which converts PAI-1 to a non-inhibitory substrate. 2. The activity of MA33H1 against rat PAI-1 was confirmed using two-chain t-PA and a chromogenic substrate. MA33H1 was evaluated in rat venous (thromboplastin + stasis in the abdominal vena cava) and arterial (electric current applied to a carotid artery) thrombosis models. The effects on tail-transection bleeding time were studied. 3. MA33H1 at 100 ng ml(-1) inhibited both human (44.1%) and rat PAI-1 (49.7%). This effect was concentration-dependent. Its effect on human PAI-1 was not significantly inhibited by 1 microg ml(-1) fibrin or a approximately 7 fold molar excess of vitronectin (1 nM). Inhibition of rat PAI-1 was unchanged by fibrin, but vitronectin reduced inhibition from 0.5 nM. 4. In the venous thrombosis model, MA33H1 significantly reduced thrombus weights by 38 and 58.6% at 50 and 100 microg kg(-1) min(-1) i.v. respectively. This effect was inhibited by tranexamic acid. In the arterial model, MA33H1 significantly increased the delay to occlusive thrombus formation by 58 and 142% at 50 and 100 microg kg(-1) min(-1) i.v., and did not affect bleeding time at 300 microg kg(-1) min(-1) i.v. 5. Thus, a monoclonal antibody which transforms PAI-1 to a t-PA substrate prevents thrombus formation in the rat with no effect on bleeding time at a higher dose.
Efficient Syntheses of AZD4407 via Thioether Formation by Nucleophilic Attack of Organometallic Species on Sulphur (2005)

The development of two efficient strategies for the synthesis of AZD4407 is reported, both of which are considered suitable for large-scale manufacture. In the first approach, 3-bromothiophene is coupled with (2S)-2-methyltetrahydropyran-4-one using Grignard chemistry. Following hydroxyl protection and lithiation at thiophene C-2, reaction with a protected 5-mercapto-1-methyl-1,3-dihydro-indol-2-one derivative bearing a leaving group on sulphur provides AZD4407 after acid-catalysed deprotection and epimerisation. The second approach starts from 2,4-dibromothiophene, which undergoes a selective Grignard exchange reaction at C-2 followed by reaction with similar protected mercapto-oxindole derivatives. Reprotection of the oxindole ring, followed by a second Grignard exchange, and reaction with (2S)-2-methyltetrahydropyran-4-one provides AZD4407 after acid-catalysed deprotection and epimerisation.
Optimal shape design of an electrostatic comb drive in microelectromechanical systems (1998)

Polynomial driving-force comb drives are synthesized using numerical simulation. The electrode shapes are obtained using the indirect boundary element method. Variable-gap comb drives that produce combinations of linear, quadratic, and cubic driving-force profiles are synthesized. This inverse problem is solved by an optimization procedure. Sensitivity analysis is carried out by the direct differentiation approach (DDA) in order to compute design sensitivity coefficients (DSCs) of force profiles with respect to parameters that define the shapes of the fingers of a comb drive. The DSCs are then used to drive iterative optimization procedures. Designs of variable-gap comb drives with linear, quadratic, and cubic driving force profiles are presented in this paper.
An open comparative study of dispersible piroxicam versus soluble acetylsalicylic acid for the treatment of osteoarticular painful attack during sickle cell crisis (2000)

We compared the efficacy and tolerability of oral piroxicam 1 mg/kg/day with soluble aspirin given at 100 mg/kg/day taken four-hourly in 58 patients with sickle cell anaemia and severe ostcoarticular painful attacks requiring hospitalization in a randomized, paralleled study. Main investigational criteria were pain relief, limitation of movement, fever, and insomnia or agitation. Both groups were well-matched at the commencement of therapy but most patients on piroxicam showed remarkable and significant pain relief and improvement in other parameters within 24 h. Unwanted effects were absent in the piroxicam-treated group whereas those treated with aspirin experienced nausea and vomiting. There were no significant changes in liver function tests with both forms of treatment. Oral piroxicam is an effective and safe treatment in the management of the osteoarticular painful crisis in sickle cell anaemia. It might prevent the use of parenteral analgesics and hospitalization and reduce the loss of school hours in patients who are being treated for bone pain crises that characterize sickle cell anaemia.
Biochemical aspects of insulin secretion: Diabetes in the Young (1984)

info:eu-repo/semantics/published