gebhart/patrepeval huggingface dataset:
The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data (2004)

Virtual screening and high-throughput screening are two major components of lead discovery within the pharmaceutical industry. In this paper we describe improvements to previously published methods for similarity searching with reduced graphs, with a particular focus on ligand-based virtual screening, and describe a novel use of reduced graphs in the clustering of high-throughput screening data. Literature methods for reduced graph similarity searching encode the reduced graphs as binary fingerprints, which has a number of issues. In this paper we extend the definition of the reduced graph to include positively and negatively ionizable groups and introduce a new method for measuring the similarity of reduced graphs based on a weighted edit distance. Moving beyond simple similarity searching, we show how more flexible queries can be built using reduced graphs and describe a database system that allows iterative querying with multiple representations. Reduced graphs capture many important features of ligand-receptor interactions and, in conjunction with other whole molecule descriptors, provide an informative way to review HTS data. We describe a novel use of reduced graphs in this context, introducing a method we have termed data-driven clustering, that identifies clusters of molecules represented by a particular whole molecule descriptor and enriched in active compounds.
Polyurethane rubber as a mems material: characterization and demonstration of an all-polymer two-axis artificial hair cell flow sensor (2005)

Characterization and utilization of a two-part room temperature curing polyurethane elastomer as a MEMS material is presented. Chemical resistance, thermal degradation, elastic modulus, and adhesion are tested and compared to the performance of polydimethylsiloxane (PDMS). Polyurethane elastomer is found to exhibit excellent elastic and adhesion performance, with reduced solvent resistance when compared to PDMS. A two-axis artificial hair cell (AHC) is fabricated with carbon impregnated polyurethane force sensitive resistors (FSRs) at the base of a vertical polyurethane cantilever hair. The FSRs transduce the motion of the cilium into a change in resistance via a half-bridge. Device sensitivity is found to be 245 ppm resistance change per micron (ppm/um) of tip deflection.
Integration between a percutaneous implant and the porcine small bowel (2011)

Inflammatory bowel diseases, cancer or trauma may require removal of all or part of the intestines, leaving the patient with a need to wear external stoma appliances for collection of bowel contents. By connecting the small bowel to a percutaneous port, equipped with a sealing lid, a fully continent and leak proof stoma can be created without a need for permanently wearing stoma appliance. The prerequisites for a connection between a permanent, transabdominal implant and a visceral organ are largely unexplored. Stoma ports made of titanium were implanted in the abdominal wall of domestic pigs and a branch of distal ileum was inserted through the ports. After being followed for 1-3 weeks, the ports were removed and subjected to histological evaluation to study the influence of their shape, structure, and position on the tissue response. Particular focus was attended to the attachment of the ileal serosal surface to the implants inner structure consisting of a titanium mesh. Macroscopic examination revealed fistulas and formation of abscesses in 4 of 11 the retrieved implants. Histological examination revealed regenerated and well-vascularized collagenous tissue around the mesh structure inside the implant. The integration was complete or partial for 10 of 11 ports. Despite various degrees of inflammation and tissue ingrowth, it was demonstrated for the first time that the serosal surface of ileum was firmly attached to the internal structure of the implant. These experiments provide a basis for optimization of the implant and surgical procedure before long-term functional animal experiments.
Duration of type 2 diabetes does not appear to moderate hypoglycaemia rate with insulin degludec versus insulin glargine U100 (2021)

In the DEVOTE and SWITCH 2 trials, insulin degludec 100 units/mL (degludec) was superior to insulin glargine 100 units/mL (glargine U100) with respect to the rates of severe (DEVOTE; across trial) and overall symptomatic (SWITCH 2; during the maintenance period of the trial) hypoglycaemia in individuals with type 2 diabetes. In this post hoc analysis, data from 7635 individuals from DEVOTE and 720 individuals from SWITCH 2 were analysed by subgroups of diabetes duration at baseline (<10, ≥10-<15, ≥15-<20 and ≥20 years) using prespecified models from both trials. There was a trend towards lower rates of hypoglycaemia with degludec versus glargine U100 across all diabetes duration subgroups in both trials, with the difference being statistically significant in some subgroups in DEVOTE and SWITCH 2. Overall, however, no significant interaction was observed between diabetes duration and treatment (DEVOTE interaction, P = .496; SWITCH 2 interaction, P = .144). Therefore, in this post hoc analysis of DEVOTE and SWITCH 2, diabetes duration did not appear to affect the reduction in rates of hypoglycaemia observed with degludec compared with glargine U100.
A Panel of Alloreactive T Cell Assay That More Accurately Assesses Levels of T Cell Alloreactivity. (2014)

The presence of high numbers of alloreactive memory CD8 T cells in the peripheral blood of transplant patients is a risk factor for acute graft rejection and resistance to CTLA4-Ig immunosuppression. A panel of alloreactive T-cells (PRT) in an enzyme-linked immunosorbent spot (ELISPOT) measuring IFN-γ has shown that a high PRT (>40% reactivity to the panel) was statistically significantly higher in patients with acute cellular rejection (ACR). However, there are patients with a high PRT that do not reject and patients with a low PRT that have ACR. We recently showed that interleukin 15 (IL-15) provokes CD28- memory CD8T cells to proliferate and produce cytokines. This study tested the ability of added IL-15 to reveal the presence of alloreactive CD28- memory CD8 T cells in the PRT. CD28+ and CD28- CD8 memory RO+ T cells were isolated from healthy donor PBMCs and cultured with either a mix of six or individual allogeneic B cell lines. IFN-γ ELISPOT was used to test reactivity in the presence or absence of exogenous IL-15. A 2-5 fold enhancement of alloreactive T cells producing IFN-γ was observed by addition of IL-15 to the PRT assay and the enhancement varied with the PBMC donor when each of the individual allogeneic B cell lines was used as a stimulator in the assay. Low to absent numbers of IFN-y producing cells were observed during culture of isolated CD28- memory CD8 T cells and the allogeneic B cells but addition of IL-15 revealed the numbers of alloreactive T cells producing IFN-y. Addition of IL-15 did not increase the number of IFN-y producing cells in cultures of isolated CD28+ memory CD8 T cells and the allogeneic B cells. The current PRT underestimates the number of alloreactive T cells producing IFN-γ as CD28- memory CD8 T cells are minimally activated in the assay. Addition of IL-15 to the PRT assay reveals the presence of alloreactive CD28- memory CD8 T cells and may provide a more accurate assessment of immunological risk for transplant patients.
Comparative in vitro and in vivo studies on the effects of tricyclic antidepressants on myocardial contractility. (1975)

The effects of the similarily structured antidepressant drugs imipramine and dimetacrine and their demethylated derivatives on myocardial performance were studied in vitro on 42 right ventricular papillary muscles of cats. The hemodynamic effects of intravenous administration of 22 mg of free base imipramine and dimetacrine were investigated in 12 patients with coronary disease. The results of the in vitro studies show that imipramine greater than dimetacrine greater than desmethyl compounds have a marked dose-dependent negative inotropic effect on all parameters of myocardial contractility, i.e., afterloaded isotonic contractions (delta L), dL/dtmax, dL/dtmin,dT/dt. The hemodynamic investigations indicate that imipramine greater than dimetacrine induces a significant increase in end-diastolic left ventricular pressure. Both drugs increase mean arterial blood pressure, correlated to a peripheral vasoconstriction and corresponding to an increase on the plasma level of catecholamines. It is concluded that both effects of these antidepressant drugs (reduction of myocardial performance and an increase in the plasma level of catecholamines) must be considered a risk in patients predisposed to myocardial failure.
Colloidal Interactions and Self-Assembly Using DNA Hybridization (2005)

The specific binding of complementary DNA strands has been suggested as an ideal method for directing the controlled self-assembly of microscopic objects. We report the first direct measurements of such DNA-induced interactions between colloidal microspheres, as well as the first colloidal crystals assembled using them. The interactions measured with our optical tweezer method can be modeled in detail by well-known statistical physics and chemistry, boding well for their application to directed self-assembly. The microspheres' binding dynamics, however, have a surprising power-law scaling that can significantly slow annealing and crystallization.
Modeling of transmission spectra in photonic bandgap waveguides (2003)

Summary from only given. Photonic crystal fibers have received much attention recently as they show promise for potential device and transmission fiber applications. They have been broadly classified into two categories depending on the light-guiding mechanism in the core: (1) total internal reflection, and (2) Bragg scattering off multiple layers. The latter has generated significant interest because of the possibility of guiding light in air, hence reducing nonlinearity and loss. In this paper, we show that, in addition to Bragg scattering, the spectral characteristics of a 1D photonic bandgap (PBG) waveguide in which the core index is less than the cladding index are also determined by Fresnel reflections from the first high-index layers surrounding the core. The latter will be referred to as the Fresnel regime.
Sesquiterpenes from Baizhu Stimulate Glucose Uptake by Activating AMPK and PI3K (2016)

Baizhu, the dried rhizome of Atractylodes Macrocephala Koidz (Compositae), is one of the most important traditional Chinese herbal medicines. Baizhu is generally used to treat digestive disorders and diabetes in Asian countries. This study investigates the activity of two sesquiterpenes isolated from Baizhu, atractylenolide I (AT-I) and atractylenolide II (AT-II), for their effects on glucose uptake in mouse skeletal muscle C2C12 cells, and the corresponding mechanism. These compounds show a significant stimulatory effect on glucose uptake in C2C12 myotubes. Both AT-I and AT-II significantly increased GLUT4 but not GLUT1 protein levels, and promoted GLUT4 translocation to the plasma membrane. The increased glucose uptake induced by these compounds is associated with activation of AMP-activated protein kinase (AMPK) and PI3K/Akt pathways in these cells. Further studies have indicated that AT-I and AT-II ameliorate TNF-[Formula: see text]-induced insulin resistance in C2C12 myotubes. In summary, our findings highlight the insulin mimetic activity of Baizhu in myotubes, and provide insights into the action mechanism underlying these effects. Our findings may also prove highly relevant to the development of novel therapeutic applications for these compounds.
Analytical modeling of fire growth on fire-resistive wood-based materials with changing conditions (2006)

Our analytical model of fire growth for the ASTM E 84 tunnel, which simultaneously predicts heat release rate, flame-over area, and pyrolysis area as functions of time for constant conditions, was documented in the 2001 BCC Symposium for different treated wood materials. The model was extended to predict ignition and fire growth on exterior fire-resistive structures and ornamental vegetation for an efficient assessment of fire hazard in the wildland-urban interface. The improved model accommodates the following changing conditions: (1) transient variation of imposed heat fluxes in pyrolysis and flame-over regions, (2) non-linearity in flame-over lengths, (3) transient changes in environmental conditions, and (4) transition in flame spreading from thermally thick to thin behavior. Re-validation of the updated model with an ISO 9705 room-burn series that contained upward fire spread data is in process and will be presented at the proceedings. Cone calorimeter data for fireresistive materials such as redwood, fire-resistant-treated plywood, and single-layer stucco-coated oriented strandboard were used in the validation work. Burning characteristics of Class B brand used in the ASTM E 108 test were also determined in a specialized cone calorimeter test to help guide model development.
The Clock-Drawing Test: Time for a Change? (2008)

Clock-drawing tests are simple and rapid screening devices for dementia. It was observed that individuals <60 years of age showed similar performance with a digital prompt (" . . .make the clock read 12:45") or an analog prompt (" . . .quarter to 1"), whereas individuals >70 years of age showed improved performance with an analog prompt. The digital prompt has routinely been used to force participants to recode the prompt via conceptualization. Differential scoring across a range of ages has likely derived from the advent and increase of digital clocks with the younger segment of the population. This implies the need for as-yet undetermined alteration in the nature of prompts to force recoding as the current younger population ages.
A reconstruction filter for plausible motion blur (2012)

This paper describes a novel filter for simulating motion blur phenomena in real time by applying ideas from offline stochastic reconstruction. The filter operates as a 2D post-process on a conventional framebuffer augmented with a screen-space velocity buffer. We demonstrate results on video game scenes rendered and reconstructed in real-time on NVIDIA GeForce 480 and Xbox 360 platforms, and show that the same filter can be applied to cinematic post-processing of offline-rendered images and real photographs. The technique is fast and robust enough that we deployed it in a production game engine used at Vicarious Visions.
Relationship between nanoleakage and long-term durability of dentin bonds. (2001)

This study tested the hypothesis that long-term durability of resin bonds to dentin would directly relate to the nanoleakage of dentin bonding systems. Twenty extracted third molars were ground flat with #600 grit SIC paper under running water to expose middle dentin. One-Step or Single Bond was applied to the dentin surface according to the manufacturer's instruction. A crown was built-up with Clearfil AP-X resin composite and the specimens were stored in water for 24 hours at 37 degrees C. The bonded assemblies were cut mesio-distally perpendicular to the interface in approximately 0.7 mm thick slabs and trimmed for microtensile bond strength testing. All slabs were immersed in individual bottles containing 37 degrees C water that was changed daily. Specimens were randomly assigned to four groups (one day, three, six and nine months), and at the specified time period, the specimens to be tested were randomly divided into two subgroups for testing: 50% AgNO3 and the control. In the 50% AgNO3 subgroup, the slabs were coated with fingernail varnish except for approximately 0.5 mm around the bonded interface and immersed for one hour in 50% AgNO3, followed by exposure in a photo developing solution for 12 hours just prior to debonding. The specimens in the control subgroup were soaked in water until they were debonded. Then, all specimens were subjected to microtensile bond testing. Micrographs of the fractured surfaces of the debonded specimens in the AgNO3 subgroup were taken using light microscopy. They were then subjected to image analysis by NIH Image PC (Scion, Fredrick, MD, USA), and the area of silver penetration was quantitated. The fractured surface was further analyzed under the SEM. Bond strength data and the silver penetration areas were subjected to two and three-way ANOVA and Fisher's PLSD test at the 95% level of confidence. Regression analysis was used to test the relationship between bond strengths and the silver penetra tion area at each time period. The tensile bond strength of both materials gradually decreased over time. Specimens bonded with One-Step showed less silver nanoleakage at one day compared to three, six and nine months (p<0.05), but there were no significant differences between the nanoleakage measured at three, six and nine months. In contrast, for specimens bonded with Single Bond, there were no statistically significant differences in the silver nanoleakage among the four time periods tested (p>0.05). No correlation was observed between bond strength and nanoleakage for either bonding system. Nanoleakage occurred in both adhesive systems, and bond strengths gradually decreased over time. However, there was no correlation between bond strength and nanoleakage for either adhesive system in this study.
Hypothalamic Proopiomelanocortin Neurons Are Glucose Responsive and Express KATPChannels (2003)

Hypothalamic proopiomelanocortin (POMC) neurons are critical for controlling homeostatic functions in the mammal. We used a transgenic mouse model in which the POMC neurons were labeled with enhanced green fluorescent protein to perform visualized, whole-cell patch recordings from prepubertal female hypothalamic slices. The mouse POMC-enhanced green fluorescent protein neurons expressed the same endogenous conductances (a transient outward K(+) current and a hyperpolarization-activated, cation current) that have been described for guinea pig POMC neurons. In addition, the selective micro -opioid receptor agonist DAMGO induced an outward current (maximum of 12.8 +/- 1.2 pA), which reversed at K(+) equilibrium potential (E(K+)), in the majority (85%) of POMC neurons with an EC(50) of 102 nM. This response was blocked by the opioid receptor antagonist naloxone with an inhibition constant of 3.1 nM. In addition, the gamma-aminobutyric acid(B) receptor agonist baclofen (40 micro M) caused an outward current (21.6 +/- 4.0 pA) that reversed at E(K+) in these same neurons. The ATP-sensitive potassium channel opener diazoxide also induced an outward K(+) current (maximum of 18.7 +/- 2.2 pA) in the majority (92%) of POMC neurons with an EC(50) of 61 micro M. The response to diazoxide was blocked by the sulfonylurea tolbutamide, indicating that the POMC neurons express both Kir6.2 and sulfonylurea receptor 1 channel subunits, which was verified using single cell RT-PCR. This pharmacological and molecular profile suggested that POMC neurons might be sensitive to metabolic inhibition, and indeed, we found that their firing rate varied with changes in glucose concentrations. Therefore, it appears that POMC neurons may function as an integrator of metabolic cues and synaptic input for controlling homeostasis in the mammal.
Diagnostic and treatment preferences for developmental dysplasia of the hip: A survey of EPOS and POSNA members (2018)

Purpose The aim of this study was to elucidate developmental dysplasia of the hip (DDH) diagnosis and treatment preferences among members of the Pediatric Orthopaedic Society of North America (POSNA) and European Paediatric Orthopaedic Society (EPOS). Methods A 54-question survey on DDH diagnosis and treatment preferences was distributed to POSNA and EPOS members. Descriptive statistics were performed. Results A total of 459 responses were analyzed. Ultrasound was the preferred modality for diagnosing DDH in infants less than six months old; few surgeons preferred radiographs. In all, 57% of POSNA members had radiology technicians perform ultrasounds, only 7% of EPOS members did. The percent coverage defining a dislocated hip varied greatly, the most frequent response being &lt; 20% for POSNA and &lt; 40% for EPOS members. Pavlik harnesses were the most popular harness/brace, used by 90% of POSNA and 71% of EPOS members. POSNA members were more likely than EPOS members to use a rigid abduction brace following initial harness/brace failure. For residual acetabular dysplasia, POSNA members were twice as likely as EPOS members to institute hip abduction bracing. Most surgeons would not perform closed reduction at less than three months of age or open reduction at less than six months of age. Most EPOS ­members used traction prior to reduction; few POSNA members did. Few POSNA and EPOS members believed that reduction should be delayed until the ossific nucleus was visible. Conclusion There is great variation in the preferred methods for diagnosing and treating DDH. This survey is the largest transcontinental survey to compile diagnostic and treatment preferences for DDH. With wide variations in practice, there is room for quality improvement. Level of Evidence II
Modulation of procoagulant activity of extracellular endothelial matrix by anti-tissue factor antibody and the synthetic peptide Arg-Gly-Asp-Val. Experiments with flowing nonanticoagulated human blood (1993)

Fibrin forms on and binds to the extracellular matrix of endotoxin-stimulated endothelium when exposed to flowing non-anticoagulated blood. These processes have been investigated by employing a human ex vivo perfusion model, a synthetic peptide Arg-Gly-Asp-Val and a monoclonal anti-tissue factor antibody which inhibits tissue factor/FVIIa-induced coagulation. Procoagulant extracellular matrix on plastic cover-slips was prepared from cultures of endotoxin-stimulated human endothelium following brief exposure to 0.1 M NH4OH. Non-anticoagulated blood was drawn directly from an antecubital vein by a pump at venous (100/s) and arterial (650/s) wall shear rates over the matrix-coated cover-slips positioned in parallel-plate perfusion chambers. Deposition of fibrin and platelets on the matrix was quantified by morphometry. Preincubation of the matrix with Arg-Gly-Asp-Val inhibited fibrin deposition by 80-90% at both venous (P < 0.001) and arterial shear (P < 0.05). However, the peptide had no effect on the clotting time in a modified one-stage clotting assay where coagulation was initiated by lysed endotoxin-stimulated endothelial cells, indicating that the peptide interfered with the binding of fibrin to the matrix in the perfusion model. Preincubation of the matrix with the anti-tissue factor antibody, which blocked the coagulant activity ( > 95%, P < 0.01) in the modified coagulation assay, also inhibited fibrin deposition on the matrix by 90-95% (P < 0.01) at both shear rates. In the absence of either inhibitor, platelets adhered preferentially to the fibrin meshwork, and more so at arterial shear. Platelet thrombus formation on the fibrin coat was in particular pronounced at arterial shear. Thus, it appears that the extracellular matrix of endotoxin-stimulated endothelium initiates coagulation predominantly through tissue factor/FVIIa and that the resulting fibrin meshwork forming on the surface induces rapid platelet thrombus formation. The inhibitory effect of Arg-Gly-Asp-Val on the binding of fibrin to the matrix may indicate the presence of specific matrix fibrinogen/fibrin binding site(s) with a recognition sequence of Arg-Gly-Asp.