gebhart/patrepeval huggingface dataset:
Imaging approaches to optimize molecular therapies (2016)

Imaging, including its use for innovative tissue sampling, is slowly being recognized as playing a pivotal role in drug development, clinical trial design, and more effective delivery and monitoring of molecular therapies. The challenge is that, while a considerable number of new imaging technologies and new targeted tracers have been developed for cancer imaging in recent years, the technologies are neither evenly distributed nor evenly implemented. Furthermore, many imaging innovations are not validated and are not ready for widespread use in drug development or in clinical trial designs. Inconsistent and often erroneous use of terminology related to quantitative imaging biomarkers has also played a role in slowing their development and implementation. We examine opportunities for, and challenges of, the use of imaging biomarkers to facilitate development of molecular therapies and to accelerate progress in clinical trial design. In the future, in vivo molecular imaging, image-guided tissue sampling for mutational analyses ("high-content biopsies"), and noninvasive in vitro tests ("liquid biopsies") will likely be used in various combinations to provide the best possible monitoring and individualized treatment plans for cancer patients.
System Identification Based on Tensor Decompositions: A Trilinear Approach (2019)

The theory of nonlinear systems can currently be encountered in many important fields, while the nonlinear behavior of electronic systems and devices has been studied for a long time. However, a global approach for dealing with nonlinear systems does not exist and the methods to address this problem differ depending on the application and on the types of nonlinearities. An interesting category of nonlinear systems is one that can be regarded as an ensemble of (approximately) linear systems. Some popular examples in this context are nonlinear electronic devices (such as acoustic echo cancellers, which are used in applications for two-party or multi-party voice communications, e.g., videoconferencing), which can be modeled as a cascade of linear and nonlinear systems, similar to the Hammerstein model. Multiple-input/single-output (MISO) systems can also be regarded as separable multilinear systems and be treated using the appropriate methods. The high dimension of the parameter space in such problems can be addressed with methods based on tensor decompositions and modelling. In recent work, we focused on a particular type of multilinear structure—namely the bilinear form (i.e., two-dimensional decompositions)—in the framework of identifying spatiotemporal models. In this paper, we extend the work to the decomposition of more complex systems and we propose an iterative Wiener filter tailored for the identification of trilinear forms (where third-order tensors are involved), which can then be further extended to higher order multilinear structures. In addition, we derive the least-mean-square (LMS) and normalized LMS (NLMS) algorithms tailored for such trilinear forms. Simulations performed in the context of system identification (based on the MISO system approach) indicate the good performance of the proposed solution, as compared to conventional approaches.
A prioritisation model predictive control for multi-actuated vehicle stability with experimental verification (2022)

This paper proposes a novel prioritisation model predictive control for improving the handling and stability of all-wheel-drive vehicles configured with an electric motor and an open differential per axle with differential braking capability. The configuration of the powertrain provides a significant handling improvement by optimising front/rear torque distribution. The controller gives a high priority to front/rear torque distribution and, if needed, activates the differential braking. A coupled force prediction model of the vehicle handling dynamics is developed to capture the interaction of longitudinal and lateral tyre forces. Since differential braking causes speed drop, energy waste, and noise, two control actuations are prioritised: (1) front/rear torque shifting, (2) differential braking. Appropriate stability constraints are defined for the vehicle yaw rate and sideslip, dividing the sideslip-yaw rate phase plane into three regions – stable, marginal, unstable – based on which three control objectives are defined. Then, the priorities of the control actuations and the control objectives are combined, and a model predictive control structure is developed for this multi-objective multi-actuation control problem. The predictive controller prioritises the objectives and actuations through the prediction horizon. The performance of the proposed controller is thoroughly evaluated through numerical and full vehicle experimental studies.
Survivin in esophageal cancer: An accurate prognostic marker for squamous cell carcinoma but not adenocarcinoma (2006)

We quantified the expression of survivin, both as mRNA in real-time PCR and protein in immunohistochemistry, in tumor samples of 112 patients with esophageal cancer (56 squamous cell carcinomas and 56 adenocarcinomas). Overall survival of squamous cell carcinoma patients with high survivin mRNA levels was significantly less than that of patients with low survivin mRNA levels (p = 0.0033). Distribution pattern of survivin (nuclear vs. cytoplasmic or mixed) was not correlated to survival, while the extent of immunostaining was significantly correlated to survivin mRNA values (p = 0.016) and had prognostic relevance in univariate analysis (p = 0.0012). Cox's proportional-hazard regression model showed that tumor survivin expression in esophageal squamous cell carcinoma was the most important prognostic factor, independent of tumor stage and other histopathological factors, both as mRNA relative value (p = 0.0259) and protein immunostaining (p = 0.0147). In esophageal adenocarcinoma, survivin expression and pattern of distribution had no prognostic relevance. Thus, quantifying survivin expression provides a prognostic marker only for esophageal squamous tumors.
Single-frame characterization and nonlinear conversion of ultrafast vortex pulses carrying spatiotemporal orbital angular momentum (2023)

Spatiotemporal orbital angular momentum (ST-OAM) of light is an emergent, spatiotemporally sculptured light. Such spatiotemporal optical vortices carry transverse OAM and exhibit novel properties. However, the lack of a simple and straightforward characterization method substantially slows its progress and potential adaptions for future applications. Here we demonstrated a simple, stationary, single-frame method to quantitatively characterize ST-OAM pulses. Our new method can measure the presence of ST-OAM, space-time topological charge numbers, OAM helicity, pulse dispersion, and beam divergence. We also investigated the nonlinear properties of ST-OAM pulses, uncovering the conservation of space-time topological charges in a second-harmonic generation process.
Net renal tubular reabsorption of zinc in healthy man and impaired handling in sickle cell anemia (1989)

Zinc deficiency is a significant clinical finding in sickle cell anemia (SCA) and abnormalities of zinc handling such as hyperzincuria are present. The cause of increased urinary zinc excretion in SCA is not clear. To define the renal handling of zinc in SCA and in healthy subjects, we measured zinc (total and ultrafilterable plasma zinc, urine zinc) and creatinine clearance in eight healthy and seven SCA subjects. Ultrafilterable zinc in plasma was assessed by equilibration of plasma with 65Zn followed by filtration through Amicon Cetriflo CF25 cones. While the mean filtered load of zinc was not significantly different between the two groups, the mean zinc excretion rate was approximately three-fold higher in patients (1.73 +/- 0.96 vs. 0.63 +/- 0.39 micrograms/min, P less than .05). In controls, zinc excreted was significantly less than zinc filtered (P less than .005), the fractional excretion of zinc averaging 0.49 +/- 0.31, indicating net reabsorption. This was not the case for the SCA patients. We conclude that there is impaired renal tubular handling of zinc in SCA.
High-Efficiency Input and Output Harmonically Engineered Power Amplifiers (2017)

This paper presents an in-depth, systematic study of the impact of input and output harmonics in the design of high-efficiency power amplifiers (PAs). The study evaluates the performance of harmonically tuned amplifiers, tackling concurrently both input and output harmonics. The proposed theory starts with deriving an altered input voltage waveform under the impact of input nonlinearity. Intrinsic drain voltage and drain current components are formulated as a function of the conduction angle α considering both source and load terminations. Output power and drain efficiency are then computed as a function of input nonlinearity, α, and output loading conditions. The derived formulations allow to investigate the design sensitivity to input nonlinearity and its impact on fundamental design space. The impact of source harmonics is evaluated using harmonic source pull under different output loading conditions. Thereafter, PA design and implementation has been carried out using NXP 1.95 mm die to confirm the distinctive behavior of class GF and GF-1 amplifiers with respect to the input harmonic terminations. For practical validation, four different design cases with different second harmonic source impedances are investigated. At 2.6 GHz, drain efficiencies ranging between 76% and 83% were exhibited depending on the source and load harmonic tuning for each design case. Measurement results confirm the theoretical findings reported in this paper.
Scalable, cost-efficient synthesis and properties optimization of magnetoelectric cobalt ferrite/barium titanate composites (2021)

Cobalt ferrite (CoFe2O4)/barium titanate (BaTiO3) particulate composites exhibiting high magnetoelectric coefficients were synthesized from low-cost commercial precursors using mechanical ball milling followed by high-temperature annealing. CoFe2O4 (20 nm–50 nm) and either cubic or tetragonal BaTiO3 nanoparticle powders were used for the synthesis. It was found that utilizing a 50 nm cubic BaTiO3 powder as a precursor results in a composite with a magnetoelectric coupling coefficient value as high as 4.3 mV/Oe cm, which is comparable to those of chemically synthesized core–shell CoFe2O4–BaTiO3 nanoparticles. The microstructure of these composites is dramatically different from the composite synthesized using 200 nm tetragonal BaTiO3 powder. CoFe2O4 grains in the composite prepared using cubic BaTiO3 powder are larger (by at least an order of magnitude) and significantly better electrically insulated from each other by the surrounding BaTiO3 matrix, which results in a high electrical resistivity material. It is hypothesized that mechanical coupling between larger CoFe2O4 grains well embedded in a BaTiO3 matrix in combination with high electrical resistivity of the material enhances the observed magnetoelectric effect.
P1320ASSESSMENT OF ARTERIOVENOUS FISTULA DYSFUNCTION WITH ACCESS STENOSIS IN HEMODIALYSIS PATIENTS USING SMART-PHONE VIDEOS (2020)

Abstract Background and Aims Vascular access dysfunction is one of the leading causes of morbidity and a major contributor to healthcare costs in hemodialysis (HD) patients. Inexpensive, non-invasive tools for routine assessment of vascular access function are needed. Hemodynamically relevant stenoses in arteriovenous fistulas (AVF) lead to a reduction in access flow rate (Qa) and changes in blood flow patterns in the AVF that may be picked up by palpation and auscultation. We hypothesized that these changes in blood flow patterns can not only be felt and heard but also seen, i.e., that they may be detectable in video recordings done with commercially available smartphones after digital motion augmentation. Methods We studied HD patients with AVF dysfunction requiring balloon angioplasty and/or stenting. One-minute video recordings of the skin above the AVF and Qa measurements were conducted before and after the endovascular intervention. Videos were recorded with an iPhone 6S (Apple Inc., Cupertino, CA, USA). Qa was measured by HVT100 endovascular flowmeter (Transonic Systems Inc., Ithaca, NY, USA). Significant access stenosis was defined as a &amp;gt;50% reduction of luminal diameter. Degree of stenosis was assessed by angiography. Frame-to-frame pixel changes in video images were amplified using “Eulerian Video Magnification” (Massachusetts Institute of Technology, MA, USA; http://people.csail.mit.edu/mrub/evm/#code). The time-domain data were then transformed into the frequency-domain signals. Fifty random 10-second segments were sampled per one-minute video, and the frequency with the lowest magnitude (Fmin) was determined in each sample (example shown in Fig. 1). The average Fmin was then assessed for its association with the degree of AVF stenosis. Results Ninety subjects were studied (Table 1). AVF interventions were successful in all patients. Post-intervention Qa (1638 ± 714 ml/min) was on average 1.23-fold higher than pre-intervention Qa (1373 ± 684 ml/min; P&amp;lt;0.01, paired t-test). Subjects were grouped by degree of stenosis, and the number of subjects in each category is shown in Fig. 1B. Higher degrees of stenosis were associated with greater increases in Qa from before to after the intervention (P&amp;lt;0.01, one-way ANOVA; Fig. 1C). Interestingly, the degree of AVF stenosis was also positively related with the change in Fmin from before to after the intervention (P=0.08, one-way ANOVA; Fig. 1D). Conclusion Simple smartphone video recordings of AVF appear to contain frequency-domain information that correlates with hemodynamic changes caused by AVF stenoses. While the Fmin metric employed in our analysis is not ideal, these results should encourage the quest for other parameters that exhibit higher correlations with vascular access dysfunction. If successful, this would allow commercially-available smartphones to be used as ubiquitous tools for quick, non-invasive, ambulatory surveillance of AVF function, thereby allowing timely referrals and avoidance of emergency interventions.
Mechanisms of Polycrystalline Growth of SiGe in Thermal CVD Processes using Si2H6 and GeF4 (2008)

The mechanism of SiGe film growth from Si2H6 and GeF4 was examined by ab initio B3LYP/6-31G** calculations using three cluster surface models. Energies of reaction and activation were calculated, and the process of SiGe film growth was analyzed. It was found that the reaction of GeF4 with Si2H6 formed GeF2 by much lower activation energy than decomposition of GeF4. In addition, GeF2 made activation energy of surface reactions lower than using only Si2H6.
Implementation and evaluation of an efficient secure computation system using 'R' for healthcare statistics (2014)

We propose a secure statistical analysis system using 'R' for medical data that effectively integrates secret-sharing-based secure computation and original computation.
ChemInform Abstract: The First Evidence for Reductive Coupling of Transition‐Metal Substituted Halogermanes. (1990)

Abstract The formation of the Ge‐Ge bond in (II) is confirmed by a single‐crystal X‐ray diffraction study (space group P2 1 /n, Z=4).
High shear in situ exfoliation of 2D gallium oxide sheets from centrifugally derived thin films of liquid gallium (2021)

A diversity of two-dimensional nanomaterials has recently emerged with recent attention turning to the post-transition metal elements, in particular material derived from liquid metals and eutectic melts below 330 °C where processing is more flexible and in the temperature regime suitable for industry. This has been explored for liquid gallium using an angled vortex fluidic device (VFD) to fabricate ultrathin gallium oxide (Ga<sub>2</sub>O<sub>3</sub>) sheets under continuous flow conditions. We have established the nanosheets to form highly insulating material and have electrocatalytic activity for hydrogen evolution, with a Tafel slope of 39 mV dec<sup>-1</sup> revealing promoting effects of the surface oxidation (passivation layer).
AirPose: Multi-View Fusion Network for Aerial 3D Human Pose and Shape Estimation (2022)

In this letter, we present a novel markerless 3D human motion capture (MoCap) system for unstructured, outdoor environments that uses a team of autonomous unmanned aerial vehicles (UAVs) with on-board RGB cameras and computation. Existing methods are limited by calibrated cameras and off-line processing. Thus, we present the first method (AirPose) to estimate human pose and shape using images captured by multiple extrinsically <b>uncalibrated</b> flying cameras. AirPose itself calibrates the cameras <i>relative to the person</i> instead of relying on any pre-calibration. It uses distributed neural networks running on each UAV that communicate <i>viewpoint-independent</i> information with each other about the person (i.e., their 3D shape and articulated pose). The person&#x2019;s shape and pose are parameterized using the SMPL-X body model, resulting in a compact representation, that minimizes communication between the UAVs. The network is trained using synthetic images of realistic virtual environments, and fine-tuned on a small set of real images. We also introduce an optimization-based post-processing method (AirPose<inline-formula><tex-math notation="LaTeX">$^{+}$</tex-math></inline-formula>) for offline applications that require higher MoCap quality. We make our method&#x2019;s code and data available for research at <uri>https://github.com/robot-perception-group/AirPose</uri>. A video describing the approach and results is available at <uri>https://youtu.be/xLYe1TNHsfs</uri>.
Thin film confinement effects on the thermal properties of model photoresist polymers (2001)

The demand to print increasingly smaller microelectronic device features means that the thickness of the polymer films used in the lithographic processes must decrease. The thickness of these films is rapidly approaching the unperturbed dimensions of the polymer, length scales at which confinement deviations and dewetting are a significant concern. We combine specular x-ray reflectivity (SXR) and incoherent neutron scattering (INS) to probe the thermal stability and dynamical effects of thin film confinement in poly(hydroxy styrene) (PHS), a polymer used in a majority of the 248 nm deep UV photoresists. PHS forms stable thin films (down to 5 nm) that do not dewet over a wide temperature range on Si surfaces ranging from hydrophilic to hydrophobic. The surface energy has a profound influence on the magnitude of the thin film expansion coefficient, especially above the glass transition, in films as thick as 100 nm. Confinement also appears to suppress the mean-square atomic displacements and the level of anharmonicity in the dynamics, primarily above the bulk glass transition.
Stimuli-responsive engineered living materials (2020)

Stimuli-responsive materials are able to undergo controllable changes in materials properties in response to external cues. Increasing efforts have been directed towards building materials that mimic the responsive nature of biological systems. Nevertheless, limitations remain surrounding the way these synthetic materials interact and respond to their environment. In particular, it is difficult to synthesize synthetic materials that respond with specificity to poorly differentiated (bio)chemical and weak physical stimuli. The emerging area of engineered living materials (ELMs) includes composites that combine living cells and synthetic materials. ELMs have yielded promising advances in the creation of stimuli-responsive materials that respond with diverse outputs in response to a broad array of biochemical and physical stimuli. This review describes advances made in the genetic engineering of the living component and the processing-property relationships of stimuli-responsive ELMs. Finally, the implementation of stimuli-responsive ELMs as environmental sensors, biomedical sensors, drug delivery vehicles, and soft robots is discussed.
Studies on the glial cell-line derived neurotrophic factor (GDNF) co-receptor α1 (2002)

Glial cell line-derived neurotrophic factor (GDNF) is known to promote the survival and differentiation of many neuron populations. The receptor complex for GDNF was discovered to consist of the transmembrane RET receptor tyrosine kinase and a ligand-binding component, the GDNF co-receptor 1 (1). Binding studies (1,2) suggest that GDNF serves mainly to dimerize the coreceptor, GFR1, and interacts weakly, if at all, with RET in ternary complex. The GDNF signaling is beginning to be understood, but many questions remain open. Therefore, structural studies on the GFR1 were initiated to address these questions at the molecular level. The crystal structure of GDNF has already been solved (3). GFR1 has a signal peptide for secretion at the amino terminus, a glycosylphosphatidylinositol (GPI) -anchor signal at the Cterminus and three potential N-glycosylation sites (1). Conserved cysteine patterning (4) suggests a putative domain structure with three homologous cysteine-rich domains, each about 100 residues long, bound together with hinge regions.
Structural insight into antibody-mediated antagonism of the Glucagon-like peptide-1 Receptor (2016)

The Glucagon-like peptide-1 receptor (GLP-1R) is a member of the class B G protein-coupled receptor (GPCR) family and a well-established target for the treatment of type 2 diabetes. The N-terminal extracellular domain (ECD) of GLP-1R is important for GLP-1 binding and the crystal structure of the GLP-1/ECD complex was reported previously. The first structure of a class B GPCR transmembrane (TM) domain was solved recently, but the full length receptor structure is still not well understood. Here we describe the molecular details of antibody-mediated antagonism of the GLP-1R using both in vitro pharmacology and x-ray crystallography. We showed that the antibody Fab fragment (Fab 3F52) blocked the GLP-1 binding site of the ECD directly and thereby acts as a competitive antagonist of native GLP-1. Interestingly, Fab 3F52 also blocked a short peptide agonist believed to engage primarily the transmembrane and extracellular loop region of GLP-1R, whereas functionality of an allosteric small-molecule agonist was not inhibited. This study has implications for the structural understanding of the GLP-1R and related class B GPCRs, which is important for the development of new and improved therapeutics targeting these receptors.
Conceptions of Trust (2011)

This chapter introduces the fundamental concepts of trust, with emphasis on their applicability to the e-services platform. This sets the tone for this book and creates a platform from which the topics can be explored more deeply in the other chapters. This chapter presents a description of e-services and trust environments, provides the prevailing perspectives on trust, and introduces a unifying definition that can be used for e-services. Furthermore, the indicators that influence a trust decision when e-service invocation is desired, is specified, and the current trust models are highlighted. These models may be leveraged when designing the architecture for an e-service solution. In addition to being a resource during e-service system design, this chapter focuses on making the reader cognizant of the broader technical and management-related issues surrounding trust in e-services, and providing a common platform for discussion.Request access from your librarian to read this chapter's full text.
Demonstration of a Quantum Key Distribution Trusted Node on an Electric Utility Fiber Network (2019)

We present a trusted node quantum key distribution system deployed at an electric utility. We show the QKD distance limitation can be extended using trusted nodes with realistic utility fiber infrastructure, demonstrating the possibility of quantum technologies in providing information security to electric grid devices.