gebhart/patrepeval huggingface dataset:
A preliminary study of cushion properties of a 3D printed thermoplastic polyurethane Kelvin foam (2017)

The cells in conventional packaging foams have random size and orientation, and the energy‐absorbing behaviour of these foams is determined by the collective contribution of different sizes of cells. In contrast to the random nature of stochastic foams, 3D printing technologies allow engineers to design and produce foams having engineered cellular structures. In this study, engineered cellular structures based on the classic Kelvin 1887 model were 3D printed in 30 × 30 × 30 mm thermoplastic polyurethane cubes with a repeating size of 216 unit cells. One hundred consecutive cyclic compression tests were performed to assess the 3D printed foam's resilience and energy absorption characteristics. The stress‐strain curve of the 3D printed thermoplastic polyurethane foam indicated viscoelastic behaviour and a Mullins effect indicative of resilient rubber. A long wave buckling mode was observed during cyclic compression cycles due to the Kelvin structure. The cushion factor computed from the stress‐strain curve was close to that of a metal spring with linear elasticity. The combination of the 3D printed foam's resilience, its much lower density than rubber, and the complete geometric freedom of the engineered cellular structures offer designers the potential to create high‐performance cushion materials tailored for packaging applications.
Comparison of the effect of semen from HIV-infected and uninfected men on CD4+ T-cell infection (2016)

Semen from HIV-infected donors exhibits a significantly reduced enhancing potential on CD4 T-cell infection by R5-tropic HIV-1 when compared with semen from uninfected donors. Our data indicate that elevated seminal concentrations of RANTES in HIV-infected men can influence the ability of semen to enhance infection.
Modeling the Surface Pressure Spectrum Beneath Turbulent Boundary Layers in Pressure Gradients (2022)

A wide variety of models and methods for the prediction of the surface pressure spectrum beneath turbulent boundary layers are presented and assessed. A thorough review is made of the current state-of-the-art in empirical and analytical pressure spectrum models, and predictions of zero, adverse, favorable, and non-equilibrium pressure gradient boundary layers are examined using steady RANS prediction of a subset of a pressure gradient boundary layer benchmark flow case. The existing empirical models show either an inability to adapt to pressure gradient conditions or an over-sensitivity to model inputs, producing non-physical results under certain flow conditions. The various input options for analytical modeling are presented and assessed, and recommendations for best practices are made. New empirical models are created using a Gene Expression Programming machine learning algorithm, based on either experimental or RANS inputs. The developed models show improvement in both accuracy and robustness over existing models.
TOWARDS THE 'IN VIVO' COMPUTATIONAL MULTI-SCALE HEMODYNAMICS FROM ENDOTHELIAL CELL TO LARGE ARTERY (2003)

Abstract. A prototype, multi-scale, computational hemodynamic model is presented. Applications to aortic arch, carotid artery, renal artery and so forth, has demonstrated its feasibility in medical applications of the computation-based diagnosis and surgery; and with this novel multi-scale computational method in hemodynamics the noninvasive simulation of cardiovascular blood flow would become possible. We have recently developed a multi-scale, computational method that is able to predict blood flow and pressure in the systematic arteries at any position along the vessels, to compute local flow patterns as well as wall shear stresses at any point in any vessel or organ, and further to predict the behavior of the endothelial cells subjected to the local wall shear stress. A one-dimensional model is established on a basis of the axisymmetric Navier-Stokes equations for flow and pressure propagation in compliant and tapering vessels. The three-dimensional model is utilized for specific vessel or organ, which is an in-house solver for the full Navier-Stokes equations and is embedded into the one-dimensional network model for the systematic arteries. 1.
Effects of Aclidinium Bromide in a Cigarette Smoke–Exposed Guinea Pig Model of Chronic Obstructive Pulmonary Disease (2013)

Long-acting muscarinic antagonists are widely used to treat chronic obstructive pulmonary disease (COPD). In addition to bronchodilation, muscarinic antagonism may affect pulmonary histopathological changes. The effects of long-acting muscarinic antagonists have not been thoroughly evaluated in experimental models of COPD induced by chronic exposure to cigarette smoke (CS). We investigated the effects of aclidinium bromide on pulmonary function, airway remodeling, and lung inflammation in a CS-exposed model of COPD. A total of 36 guinea pigs were exposed to CS and 22 were sham exposed for 24 weeks. Animals were nebulized daily with vehicle, 10 μg/ml, or 30 μg/ml aclidinium, resulting in six experimental groups. Pulmonary function was assessed weekly by whole-body plethysmography, determining the enhanced pause (Penh) at baseline, after treatment, and after CS/sham exposure. Lung changes were evaluated by morphometry and immunohistochemistry. CS exposure increased Penh in all conditions. CS-exposed animals treated with aclidinium showed lower baseline Penh than untreated animals (P = 0.02). CS induced thickening of all bronchial wall layers, airspace enlargement, and inflammatory cell infiltrate in airways and septa. Treatment with aclidinium abrogated the CS-induced smooth muscle enlargement in small airways (P = 0.001), and tended to reduce airspace enlargement (P = 0.054). Aclidinium also attenuated CS-induced neutrophilia in alveolar septa (P = 0.04). We conclude that, in guinea pigs chronically exposed to CS, aclidinium has an antiremodeling effect on small airways, which is associated with improved respiratory function, and attenuates neutrophilic infiltration in alveolar septa. These results indicate that, in COPD, aclidinium may exert beneficial effects on lung structure in addition to its bronchodilator action.
“Population” Approach Improves Parameter Estimation of Kinetic Models From Dynamic PET Data (2004)

Kinetic modeling is used to indirectly measure physiological parameters from dynamic positron emission tomography (PET) data. Usually, the unknown parameters of the model are estimated, in any given region of interest (ROI), by least squares (LS). However, when the signal-to-noise ratio (SNR) of PET data is too low, LS does not allow reliable parameter estimation. To overcome this problem, we study in this paper the applicability of approaches originally developed in the pharmacokinetic/pharmacodynamic literature and referred to as "population approaches." In particular, we consider the iterative two stage (ITS) method, which, given a set of M ROIs drawn on PET images of a given individual, estimates the unknown model parameters of each ROI by exploiting the information contained in all the M ROIs. After having revised the theory behind ITS, we assess its performance versus LS by using Monte Carlo simulations which allow us to evaluate the bias of the two methods in a variety of situations. Then, we compare the performance of LS and ITS in two case studies on [18F]FDG kinetics in human skeletal muscle. Both simulated and real case studies results show that a population approach is of potential in modeling PET images since it allows to reliably estimate model parameters also in those ROIs where either a bad SNR or a poor sampling (e.g., infrequent scanning and/or short experiment duration) make the use of LS unsuccessful.
Generating 3D Molecules for Target Protein Binding (2022)

A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D molecules that bind to given proteins by placing atoms of specific types and locations to the given binding site one by one. In particular, at each step, we first employ a 3D graph neural network to obtain geometry-aware and chemically informative representations from the intermediate contextual information. Such context includes the given binding site and atoms placed in the previous steps. Second, to preserve the desirable equivariance property, we select a local reference atom according to the designed auxiliary classifiers and then construct a local spherical coordinate system. Finally, to place a new atom, we generate its atom type and relative location w.r.t. the constructed local coordinate system via a flow model. We also consider generating the variables of interest sequentially to capture the underlying dependencies among them. Experiments demonstrate that our GraphBP is effective to generate 3D molecules with binding ability to target protein binding sites. Our implementation is available at https://github.com/divelab/GraphBP.
Haphazard neural connections underlie the visual deficits of cats with strabismic or deprivation amblyopia (2005)

Identification of the neural basis of the visual deficits experienced by humans with amblyopia, particularly when associated with strabismus (strabismic amblyopia), has proved to be difficult in part because of the inability to observe directly the neural changes at various levels of the human visual pathway. Much of our knowledge has necessarily been obtained on the basis of sophisticated psychophysical studies as well as from electrophysiological explorations on the visual pathways in animal models of amblyopia. This study combines these two approaches to the problem by employing similar psychophysical probes of performance on animal models of two forms of amblyopia (deprivation and strabismic) to those employed earlier on human amblyopes (Hess & Field, 1994, Vis. Res., 34, 13397-13406). The tests explore two competing explanations for the visual deficits, namely an evenly distributed loss of neural connections (undersampling) with the amblyopic eye as opposed to disordered connections with this eye (neural disarray). Unexpectedly, the results in animal models of deprivation amblyopia were not in accord with expectations based upon an even distribution of lost connections with the amblyopic eye. However, the results were similar to those observed in a strabismic amblyopic animal and to strabismic amblyopic humans. We suggest that deprivation amblyopia may be accompanied by an uneven loss of connections that results in effective neural disarray. By contrast, amblyopia associated with strabismus might arise from neural disarray of a different origin such as an alteration of intrinsic cortical connections.
SO2 Capture Using Porous Organic Cages (2021)

Abstract We report the first experimental investigation of porous organic cages (POCs) for the demanding challenge of SO 2 capture. Three structurally related N‐containing cage molecular materials were studied. An imine‐functionalized POC (CC3) showed modest and reversible SO 2 capture, while a secondary‐amine POC (RCC3) exhibited high but irreversible SO 2 capture. A tertiary amine POC (6FT‐RCC3) demonstrated very high SO 2 capture (13.78 mmol g −1 ; 16.4 SO 2 molecules per cage) combined with excellent reversibility for at least 50 adsorption–desorption cycles. The adsorption behavior was investigated by FTIR spectroscopy, 13 C CP‐MAS NMR experiments, and computational calculations.
Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene (2001)

A method for encoding insertions and deletions (indels) has been developed and adapted to the SplitsTree program. Following phylogenetic reconstruction, the relative frequencies of indels were estimated for a large number of in vivo sequence sets corresponding to the env V1 hypervariable region of the simian immunodeficiency virus SIVmac251. The method allowed recovery of many point mutations hitherto lost due to gap stripping. Deletions were as frequent as transversions and were 4- to 8-fold more frequent than insertions, invariably duplications. The high proportion of deletions among mutation events suggests that lentivirus vectors may readily delete parts of their cargo.
Catalytic combustion of residual fuels (1981)

A noble metal catalytic reactor was tested using two grades of petroleum derived residual fuels at specified inlet air temperatures, pressures, and reference velocities. Combustion efficiencies greater than 99.5 percent were obtained. Steady state operation of the catalytic reactor required inlet air temperatures of at least 800 K. At lower inlet air temperatures, upstream burning in the premixing zone occurred which was probably caused by fuel deposition and accumulation on the premixing zone walls. Increasing the inlet air temperature prevented this occurrence. Both residual fuels contained about 0.5 percent nitrogen by weight. NO sub x emissions ranged from 50 to 110 ppm by volume at 15 percent excess O2. Conversion of fuel-bound nitrogen to NO sub x ranged from 25 to 50 percent.
Reconstructive management of the rare bilateral oral submucos fibrosis using nasolabial flap in comparison with free radial forearm flap - a randomised prospective trial (2013)

Oral sub mucous fibrosis is a rare chronic, progressive, pre malignant collagen disorder of oral mucosa in people of Asian descent characterized by trismus, blanching and stiffness of mucosa, burning sensation in mouth and hypomobility of soft palate and tongue with loss of gustatory sensation. Betel nut chewing is the most common etiological agent. Surgery remains the main stay in severe cases and aims at release of fibrotic bands and resurfacing the raw areas with different options. Reconstruction can be done by using nasolabial flap or radial free forearm flap. The purpose of this study was to compare the mouth opening after the reconstruction with either nasolabial flap or radial free forearm flap.METHODS This study was carried out on fifty (50) patients with oral sub mucous fibrosis. Twenty five (25) of these were reconstructed by nasolabial flap and twenty five (25) were reconstructed by radial free forearm flap. At different intervals of their post-operative visits, they were evaluated for the interincisal distance and the difference between the two groups was assessed.RESULTS Average increase in interincisal distance was greater in patients reconstructed with radial free forearm flap compared with patient reconstructed by nasolabial flap i.e. 18.96 mm and 15.16 mm respectively with 'P' value > 0.05.CONCLUSIONS Based on the results of this study, there was no significant difference in mouth opening after reconstruction with radial forearm free flap compared to nasolabial flap [corrected].
MiR-9 is overexpressed in spontaneous canine osteosarcoma and promotes a metastatic phenotype including invasion and migration in osteoblasts and osteosarcoma cell lines (2016)

Our findings demonstrate that miR-9 promotes a metastatic phenotype in normal canine osteoblasts and malignant OS cell lines, and that this is mediated in part by enhanced GSN expression. As such, miR-9 represents a novel target for therapeutic intervention in OS.
Genetic divergence among members of the Kokobera group of flaviviruses supports their separation into distinct species (2013)

The Kokobera virus group comprises mosquito-borne flaviviruses that cluster together phylogenetically. These viruses are unique to Australia and Papua New Guinea, and have been associated with a mild polyarticular disease in humans. Recent isolation of genetically diverse viruses within this group has prompted analysis of their genetic and phenotypic relationships. Phylogenetic analysis based on complete ORF, the envelope gene or the NS5/3′ untranslated region supported the separation of the group into distinct species: Kokobera virus (KOKV), Stratford virus, New Mapoon virus, MK7979 and TS5273. Virulence studies in 3-week-old mice also provided the first evidence that a member of the KOKV group (MK7979) was neuroinvasive after intraperitoneal inoculation. In this context, our recent detection of KOKV group-specific antibodies in horses in the field suggests that these viruses should be considered in the epidemiology of flavivirus encephalitis in Australia.
Alternative Mechanisms for Coordinating Polymerase α and MCM Helicase (2009)

Functional coordination between DNA replication helicases and DNA polymerases at replication forks, achieved through physical linkages, has been demonstrated in prokaryotes but not in eukaryotes. In Saccharomyces cerevisiae, we showed that mutations that compromise the activity of the MCM helicase enhance the physical stability of DNA polymerase alpha in the absence of their presumed linker, Mcm10. Mcm10 is an essential DNA replication protein implicated in the stable assembly of the replisome by virtue of its interaction with the MCM2-7 helicase and Polalpha. Dominant mcm2 suppressors of mcm10 mutants restore viability by restoring the stability of Polalpha without restoring the stability of Mcm10, in a Mec1-dependent manner. In this process, the single-stranded DNA accumulation observed in the mcm10 mutant is suppressed. The activities of key checkpoint regulators known to be important for replication fork stabilization contribute to the efficiency of suppression. These results suggest that Mcm10 plays two important roles as a linker of the MCM helicase and Polalpha at the elongating replication fork--first, to coordinate the activities of these two molecular motors, and second, to ensure their physical stability and the integrity of the replication fork.
See the Brain at Work — Intraoperative Laser Doppler Functional Brain Imaging (2009)

During open brain surgery we acquire perfusion images non-invasively using laser Doppler imaging. The regions of brain activity show a distinct signal in response to stimulation providing intraoperative functional brain maps of remarkably strong contrast.
Implementation of a fast distributed scattering model for Ray Tracing prediction (2013)

It is known that Diffuse Scattering (DS) modelling must be embedded into Ray Tracing propagation prediction tools to achieve realistic results. However, the extension of the common ray based approach to include DS phenomena results in an increased computational burden due to the distributed nature of DS, which supposedly requires wall-surface discretization and therefore a much higher number of elements to be considered in the visibility algorithm. In this work a fast DS model which doesn't require discretization is implemented into a Ray Tracing propagation simulator and performance is assessed in terms of CPU time and result accuracy with respect to more conventional DS models.
Z-Source-Inverter-Based Flexible Distributed Generation System Solution for Grid Power Quality Improvement (2009)

Udgivelsesdato: September
A secreted PD-L1 splice variant that covalently dimerizes and mediates immunosuppression (2018)

Targeting immune checkpoint pathways, such as programmed death ligand-1 (PD-L1, also known as CD274 or B7-H1) or its receptor programmed cell death-1 (PD-1) has shown improved survival for patients with numerous types of cancers, not limited to lung cancer, melanoma, renal cell carcinoma, and Hodgkin lymphoma. PD-L1 is a co-inhibitory molecule whose expression on the surface of tumor cells is associated with worse prognosis in many tumors. Here we describe a splice variant (secPD-L1) that does not splice into the transmembrane domain, but instead produces a secreted form of PD-L1 that has a unique 18 amino acid tail containing a cysteine that allows it to homodimerize and more effectively inhibit lymphocyte function than monomeric soluble PD-L1. We show that recombinant secPD-L1 can dimerize and inhibit T-cell proliferation and IFN-gamma production in vitro. The secPD-L1 variant is expressed by malignant cells in vitro that also express high levels of full-length PD-L1. Transcriptomic analysis of gene expression across The Cancer Genome Atlas found the strongest association of secPD-L1 with full-length PD-L1, but also with subsets of immunologic genes, such as in myeloid-derived suppressor cells. Moreover, the splice variant is also expressed in normal tissues and within normal peripheral blood cells it is preferentially expressed in activated myeloid cells. This is the first report of a form of secreted PD-L1 that homodimerizes and is functionally active. SecPD-L1 may function as a paracrine negative immune regulator within the tumor, since secPD-L1 does not require a cell-to-cell interaction to mediate its inhibitory effect.
Temporal modulation of dielectric permittivity in transparent conducting oxides: from tunable photonics to new phenomena (2022)

Ultrafast modulation of the dielectric permittivity of materials has made great strides in the past decade, resulting in practical applications such as beam-steering, and the realization of novel physical phenomena such as time refraction. Control over the dynamics of permittivity modulation adds an additional degree of freedom in tunable optics, broadening the scope of applications. In this presentation, we report our work on controlling the dynamic optical properties of transparent conducting oxides for a wide array of nonlinear optical demonstrations. We show large changes in the epsilon-near-zero points in undoped zinc oxide, with 20ps response time, and utilize the permittivity modulation to enhance the third-harmonic generation, and develop optically controlled polarization switches. With TiN-AZO Berreman-metasurfaces, we demonstrate wide tuning of the switching times varying from picosecond to nanosecond timescales. Employing the rapid permittivity modulation in aluminum-doped zinc oxide, we demonstrate time refraction in ENZ films. Our work will develop a better understanding of nonlinear optics employing ultrafast permittivity modulation at adjustable speeds, heralding the way to further novel optical phenomena such as photonic time crystals.
Supplementary Figure S2 from Therapy of Small Cell Lung Cancer (SCLC) with a Topoisomerase-I–inhibiting Antibody–Drug Conjugate (ADC) Targeting Trop-2, Sacituzumab Govitecan (2023)

&lt;p&gt;Immunohistology expression of Trop-2 vs response&lt;/p&gt;
Human-robot ensemble between robot thereminist and human percussionist using coupled oscillator model (2010)

This paper presents a novel synchronizing method for a human-robot ensemble using coupled oscillators. We define an ensemble as a synchronized performance produced through interactions between independent players. To attain better synchronized performance, the robot should predict the human's behavior to reduce the difference between the human's and robot's onset timings. Existing studies in such synchronization only adapts to onset intervals, thus, need a considerable time to synchronize. We use a coupled oscillator model to predict the human's behavior. Experimental results show that our method reduces the average of onset time errors; when we use a metronome, a tempo-varying metronome or a human drummer, errors are reduced by 38%, 10% or 14% on the average, respectively. These results mean that the prediction of human's behaviors is effective for the synchronized performance.