gebhart/patrepeval huggingface dataset:
Abstract P5-10-17: Radiotherapy-induced miR expression influences the formation of local recurrence in breast cancer (2012)

Abstract In early breast cancer (EBC) patients, local disease relapse occurs at the site of the original primary tumor in 90% of cases and the addition of external beam radiotherapy (EBRT) after surgery is necessary to reduce recurrence rate. This observation suggested that surgery itself could represent a perturbing factor, possibly by altering the local microenvironment by inducing a wound healing response. Recent evidences indicate that, in selected EBC patients, 5 weeks of EBRT can be successfully replaced by a single dose of Targeted Intraoperative Radiotherapy (TARGIT). Interestingly, TARGIT acts not only affecting tumor cell survival itself, but is also able to alter the tumor microenvironment, by modifying cytokines secretion and activation of several intracellular pathways in breast cancer cells. In order to understand the significance of these modifications in breast tumor microenvironment after exposure to TARGIT we set up a mouse model of TARGIT treatment. Our results highlighted that the act of surgery alone strongly stimulates breast cancer cell growth and the addition of local irradiation completely reverses the surgery-induced breast cancer cell growth. Moreover, we evaluated the impact of TARGIT by analyzing microRNA (miR) expression both in our mouse model and in human specimens. To this aim, we collected paired specimens of peri-tumoral mammary tissues from 30 early breast cancer (EBC) patients, before and after treatment with TARGIT. Microarray approach followed by qRT-PCR validation revealed the presence of specific TARGIT-regulated miRs. Among the others, miR-223 was the most highly and significantly modified. In silico analyses indicated that epidermal growth factor (EGF) is a potential candidate of mR-223 regulation. In vitro experiments, using both normal and tumor derived cell lines validated the bioinformatic prediction, demonstrating that the 3′ UTR of EGF is a target of miR-223 and this binding results in the control of EGF production by the cells. Importantly, miR-223 overexpression was able to impair, at least in part, the wound-induced growth of normal and tumor derived breast-cancer cells, eventually influencing breast cancer cell proliferation and survival. Our results suggest that the effects of radiotherapy in the wounded tissue go far beyond the mere killing of residual tumor cells and is able to balance the negative effects of the wound healing process, both in human and mouse breast tissue. TARGIT-induced microenvironment modifications, in particular miR-223 up-regulation, significantly impair breast cancer response to surgery-induced inflammation eventually resulting in recurrence control. Our experimental findings strongly support the notion that the timely application of radiotherapy to the tumor bed, immediately after tumor removal, is critical to counteract the effects of surgery and wound healing process on residual breast cancer cells and normal peri-tumoral breast tissue. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-10-17.
Design of test modules for the analysis of MCM interconnects (1996)

Summary form only given. A thin-film Multichip Module (MCM-D) switching unit, specifically designed for performance analysis of interconnection substrates, is described. A test approach is presented for the characterisation of a given device technology as a function of geometrical, physical and electrical quantities-in this particular case, a MCM-D technology and a 0.7 /spl mu/m CMOS technology.
Sandia Optical Characterization Alignment and Flux Mapping Tools (Powerpoint Presentation). (2012)

Abstract not provided.
Duplex Structure of a Minimal Nucleic Acid (2008)

The crystal structure of an 8-mer (S)-GNA duplex is presented. As a tool for phasing, the anomalous diffraction of two copper(II) ions within two artificial metallo-base pairs was employed. The duplex structure confirms a canonical Watson-Crick base pairing scheme of GNA with antiparallel strands. The duplex secondary structure is distinct from canonical A- and B-form nucleic acids and can be described as a right-handed helical ribbon wrapped around the helix axis, resulting in a large hollow core. Most intriguingly, neighboring base pairs slide strongly against each other, resulting in extensive interstrand base-base hydrophobic interactions along with unusual hydrophobic intrastrand interactions of nucleobases with their backbone. These results reveal how a minimal nucleic acid backbone can support highly stable Watson-Crick-like duplex formation.
CXCR4 Is a Regulator Of Disease Involvement Of Extramedullary Myeloma Confirmed By a Novel Mouse Model For Extramedullary Disease (2013)

Abstract Background Extramedullary disease (EMD) in patients with multiple myeloma occurs mostly in advanced disease or relapse. EMD seems to have a different pathogenesis from medullary myeloma and is often characterized by a more aggressive clinical course. To date molecular mechanisms of development of EMD have not been fully understood. Methods: Human MM cell lines, IM-9 and MM1S were serially selected in immune-deficient mice. IM-9 and MM1S cells were inoculated intravenously and harvested from the tumors developed in the bone marrow (BM) and liver (site of extramedullary disease), aiming to establish BM-prone and liver-prone clones. Tumor progression was periodically checked by bioluminescence (BLI) and in vivo live confocal imaging. After three rounds of in vivo selections, the cells of both BM- and liver-prone were characterized by gene and protein expression and cellular functional assays. Results: We obtained three liver-prone sub-clones in both IM-9 and MM1S after serial in vivo selections. These cells had equal proliferation rates in vitro compared to the original or BM-prone cells, but exhibited more aggressive phenotype in vivo. Liver-prone clones had significantly higher migration ability than BM-prone clones (11.6% vs 6.1% migration, respectively p=0.018). Gene and protein expression analysis revealed that each liver-prone clone had a higher expression of sets of chemokine receptors specifically CXCR4. Using thein vivo metastatic model CXCR4-over expressing myeloma cells exhibited higher metastatic property to the extramedullary organs whereas CXCR4-knockdown cells has less tumor metastasis to the liver. Discussion: We established EMD-prone human multiple myeloma cell lines that reproducibly developed liverinvolvement consistent with human extramedullary disease. These cells exhibited higher migratory ability and increased expression of several chemokine receptors, specifically CXCR4. We validated the effect of CXCR4 on developing extramedullary myeloma using our established in vivo mode. Further studies to determine the role of CXCR4 for therapeutic targeting of extramedullary disease in MM are ongoing. Disclosures: Ghobrial: Sanofi: Research Funding; Noxxon: Research Funding; BMS: Advisory board, Advisory board Other, Research Funding; Onyx: Advisoryboard Other.
Experimental Evaluation of a 2-DoF Haptic Shared Control System Based on Pilot Intent Estimation (2018)

This paper presents the experimental evaluation of a novel haptic shared control system. The proposed system was designed to help human operators to perform a maneuver that is not known in advance. A Pilot Intent Estimator (PIE) was implemented to estimate the unknown trajectory that a human pilot intends to follow. Then, a haptic feedback was designed to mimic the behavior of a skilled pilot that tracks the estimated trajectory. A human-in-the-loop experiment was performed to evaluate the developed shared control system in a 2 Degrees-of- Freedom (DoF) control task. Results showed the effectiveness of the PIE to estimate the correct pilot intended path. Furthermore, the developed haptic system helped participants to achieve better performance to follow the estimated trajectory, compared to manual control.
Detection of Research Trends using Dynamic Topic Modeling (2022)

Discovering trends in research areas is helpful for researchers in finding the recent advances in a field or area of research. In addition, policy makers in universities can utilize this information in decision making. Different factors have direct influence on the growth and evolution of research topics. These include the funding, community interest and national needs. In this paper, we propose an unsupervised Dynamic Topic Modeling approach to discover and analyze the most trending research topics in a set of research areas using a collection of publications from the corresponding research areas. Furthermore, we study the correlation between emerging research trends and the different influencing factors.
Emerging role of PKA/eNOS pathway in therapeutic angiogenesis for ischaemic tissue diseases (2012)

Although an abundant amount of research has been devoted to the study of angiogenesis, its precise mechanisms are incompletely understood. Numerous clinical trials focused on therapeutic angiogenesis for the treatment of tissue ischaemia have not been as successful as those of preclinical studies. Thus, additional studies are needed to better understand critical molecular mechanisms regulating ischaemic neovascularization to identify novel therapeutic agents. Nitric oxide (NO) plays a central role in ischaemic neovascularization through the generation of cyclic guanosine monophosphate (cGMP) and the activation of several other signalling responses. Accumulated evidence suggests that endothelial protein kinase A/endothelial NO synthase (PKA/eNOS) signalling may play an important role in ischaemic disorders by promoting neovascularization. This review highlights recent advances in the role of the PKA/eNOS and NO-cGMP-kinase cascade pathway in ischaemic neovascularization. We also discuss molecular relationships of PKA/eNOS with other angiogenic pathways and explore the possibility of activation of the NO/nitrite endocrine system as potential therapeutic targets for ischaemic angiogenesis.
Morphology of the Lesser Tuberosity and Intertubercular Groove in Patients With Arthroscopically Confirmed Subscapularis and Biceps Tendon Pathology (2016)

Level III, case-control study.
Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features (2015)

A class V (glycoside hydrolase family 18) chitinase from the cycad Cycas revoluta (CrChiA) is a plant chitinase that has been reported to possess efficient transglycosylation (TG) activity. We solved the crystal structure of CrChiA, and compared it with those of class V chitinases from Nicotiana tabacum (NtChiV) and Arabidopsis thaliana (AtChiC), which do not efficiently catalyze the TG reaction. All three chitinases had a similar (α/β)8 barrel fold with an (α + β) insertion domain. In the acceptor binding site (+1, +2 and +3) of CrChiA, the Trp168 side chain was found to stack face-to-face with the +3 sugar. However, this interaction was not found in the identical regions of NtChiV and AtChiC. In the DxDxE motif, which is essential for catalysis, the carboxyl group of the middle Asp (Asp117) was always oriented toward the catalytic acid Glu119 in CrChiA, whereas the corresponding Asp in NtChiV and AtChiC was oriented toward the first Asp. These structural features of CrChiA appear to be responsible for the efficient TG activity. When binding of the inhibitor allosamidin was evaluated using isothermal titration calorimetry, the changes in binding free energy of the three chitinases were found to be similar to each other, i.e. between -9.5 and -9.8 kcal mol(-1) . However, solvation and conformational entropy changes in CrChiA were markedly different from those in NtChiV and AtChiC, but similar to those of chitinase A from Serratia marcescens (SmChiA), which also exhibits significant TG activity. These results provide insight into the molecular mechanism underlying the TG reaction and the molecular evolution from bacterial chitinases to plant class V chitinases.
Current density and continuity in discretized models (2010)

Discrete approaches have long been used in numerical modelling of physical systems in both research and teaching. Discrete versions of the Schrödinger equation employing either one or several basis functions per mesh point are often used by senior undergraduates and beginning graduate students in computational physics projects. In studying discrete models, students can encounter conceptual difficulties with the representation of the current and its divergence because different finite-difference expressions, all of which reduce to the current density in the continuous limit, measure different physical quantities. Understanding these different discrete currents is essential and requires a careful analysis of the current operator, the divergence of the current and the continuity equation. Here we develop point forms of the current and its divergence valid for an arbitrary mesh and basis. We show that in discrete models currents exist only along lines joining atomic sites (or mesh points). Using these results, we derive a discrete analogue of the divergence theorem and demonstrate probability conservation in a purely localized-basis approach.
A Kinetic Monte Carlo Study of Mesoscopic Perovskite Solar Cell Performance Behavior (2019)

Perovskite solar cells have received considerable attention in recent years due to their low processing cost and high energy conversion efficiency. However, the mechanisms of perovskite solar cell performance are not fully understood. Models based on probabilistic and statistical approaches can be used to simulate, optimize, and predict perovskite solar cell photovoltaic performance, and they can also guide experimental processing and fabrication conditions to achieve higher photovoltaic efficiency. This work developed a 3D model based on the kinetic Monte Carlo (KMC) approach to simulate 3D morphology of perovskite-based solar cells and predict their photovoltaic performance. The model incorporated the physical behavior of perovskite cells with respect to their charge generation, transport, and recombination characteristics. KMC simulation results showed that perovskite films with the pin holes-free and a homogenous perovskite capping layer of 400 nm thickness produced a maximum photovoltaic efficiency of 20.85%, resulting in minimal charge transport time (τt) and maximum charge carrier recombination lifetime (τr). Photovoltaic performance from the fabricated device has been used to validate this simulation model. This model provides significant conceptual advances in identifying current performance constraints and guiding novel device designs that enhance overall perovskite photovoltaic performance.
Anatomical rectangular tunnels identified with the arthroscopic landmarks result in excellent outcomes in ACL reconstruction with a BTB graft (2018)

Case series, Level IV.
Electron beam induced current measurements of minority carrier diffusion length in gallium nitride (1996)

Minority carrier diffusion length in epitaxial GaN layers was measured as a function of majority carrier concentration and temperature. The diffusion length of holes in n-type GaN is found to decrease from 3.4 to 1.2 μm in the doping range of 5×1015–2×1018 cm−3. The experimental results can be fitted by assuming the Einstein relation and by the experimental dependence of hole mobilities on carrier concentration. The low injection carrier lifetime of ∼15 ns, used in the fit, is largely independent of the doping level. The diffusion length, measured for ∼5×1015 and 2×1018 cm−3 dopant concentrations, shows an increase with increasing temperature, characterized by an activation energy Ea of ∼90 meV, independent of the impurity concentration.
Accurate smartphone camera simulation using 3D scenes (2022)

We assess the accuracy of a smartphone camera simulation. The simulation is an end-to-end analysis that begins with a physical description of a high dynamic range 3D scene and includes a specification of the optics and the image sensor. The simulation is compared to measurements of a physical version of the scene. The image system simulation accurately matched measurements of optical blur, depth of field, spectral quantum efficiency, scene inter-reflections, and sensor noise. The results support the use of image systems simulation methods for soft prototyping cameras and for producing synthetic data in machine learning applications.
Modeling Hypnotic Use in Insomniacs (2019)

Purpose: Chronic insomnia is a heterogeneous disorder that includes subsets in which patients\nexhibit sleep misperception where there is a mismatch between subjective total sleep time\n(sTST) and objective total sleep time (oTST) and may mis-attribute subjective sleep gains to\nhypnotics instead of their sleep homeostat. Coupled with evidence night-to-night variability is\npresent in many adults with insomnia, approach to management may be more complicated than gestalt patterns suggest. There is a need to determine the role of sleep homeostasis and night-tonight variability as well as to identify those who are taking hypnotics and suffering the detrimental side effects of those agents. To that end, we developed a model aimed at capturing key features of chronic insomnia and the extent to which misattribution of hypnotic effects may play a role in the evolution of over-use longitudinally.\nMethods: We used MATLAB to design a predictive model to simulate oTST, sTST, and hypnotic use longitudinally with data from each night being incorporated into the subsequent night. Weights were assigned to variables to create clinically relevant sleep phenotypes (SPs),\nwhich were then compared using two-tailed t-Tests after conducting 100 runs of 180 day simulations as well as 50 runs of 7 day simulations for each phenotype.\nResults: We analyzed six SPs that differed in the presence or absence of: anxiety, tendency towards habit formation, and sleep homeostat. In 180-day simulations, all phenotypes differed in oTST (p&lt;0.05), while sTST and misattribution events were not consistently phenotypedependent. In SPs with tendency towards hypnotic addiction, we observed an average increase of 34% in hypnotic use as compared to SPs without tendency towards addiction. 7-day simulations, to mimic the shorter durations typical of clinical research, did not consistently differentiate between phenotypes for oTST, sTST, or misattribution events. However, there was an average 29% increase in hypnotic use in SPs with potential towards addiction when compared to those without potential.\nConclusions: The constructed sleep model can simulate and capture night-to-night variability for clinically relevant sleep phenotypes, including addictive personalities. Misattribution events do not appear to occur frequently enough to substantively explain medication overuse. Simulations involving shorter time frames did not capture patterns evident in longer simulations. Although we observed statistically significant differences in sleep time between \nphenotypes, the absolute magnitudes were small and thus may not be clinically significant. Nevertheless, because real\nworld experiments lasting multiple months are not currently feasible, modeling allows a testing ground for hypothesis explorations.
Processing of Compton events in the PETALO readout system (2019)

PETALO (Positron Emission TOF Apparatus based on Liquid xenOn) exploits the unique characteristics of liquid xenon as a scintillator for use in a PET detector. Here initial simulation studies are detailed which highlight the potential of such a detector and outline the steps taken in the reconstruction of 511 keV gamma rays and in the full PET image reconstruction. In particular, a neural network-based approach is conceived in order to tag gamma rays that are poorly reconstructed due to Compton scattering. It is found that though a significant fraction of events undergo Compton scattering, not all of these events will necessarily be poorly reconstructed. Further study is necessary to determine whether or not an online implementation of the neural network-based event tagging will provide sufficient recovery of the image quality.
Stereospecific and quantitative photodimerisation of terminal olefins in the solid state (2010)

Reaction of 4-vinylpyridine with AgClO3 yields a crystalline solid that supports a stereospecific and quantitative [2+2] photodimerisation of two terminal olefins. Structural dynamics of the −CHCH2 group, nature of the counterion, and extended packing influence the photoreactivity.
An integrated multi-study analysis of intra-subject variability in cerebrospinal fluid amyloid-β concentrations collected by lumbar puncture and indwelling lumbar catheter (2015)

Based on our findings, we recommend minimizing the frequency of CSF draws in studies measuring Aβ levels and keeping the frequency standardized between experimental groups. The Aβ diurnal pattern was noted in all sponsors' studies and was not an artifact of study design. Averaging Aβ concentrations at each time point is recommended to minimize the effect of individual variability. Indwelling lumbar catheters are an invaluable research tool for following changes in CSF Aβ over 24-48 hours, but factors affecting Aβ concentration such as linear rise and diurnal variation need to be accounted for in planning study designs.
Nonlinear procedures for seismic evaluation of buildings (1999)

New static and dynamic displacement-based procedures have been developed by the Federal Emergency Management Agency (FEMA) for the seismic evaluation and design of buildings. The static procedures calculate displacements in yielding buildings as the product of an elastic spectral displacement and coefficients Ci. Mean elastic and mean inelastic displacements are assumed to be equal for elastic periods, T0, greater than the characteristic site period, Tg. The data presented in this paper and elsewhere support this assumption for values of the strength ratio greater than or equal to 0·20. For T0 ≤ Tg, mean inelastic displacements can substantially exceed mean elastic displacements for all values of the strength ratio; FEMA 273 accounts for this observation by the coefficient C1. However, the FEMA 273 cap on C1 (= 1·5) is not sufficiently conservative and should be increased to 3·0 for the analysis and design of modern construction. The effects of stiffness degradation, strength deterioration and pinching are represented in FEMA 273 by the coefficient C2. The values assigned to C2 appear to be most reasonable. Nonlinear dynamic analysis is being widely used to estimate maximum deformations and displacements in buildings. The values calculated for the maximum deformations and displacements will be dependent upon the means used to characterize structural damping in the building frame. Although structural damping is routinely implemented through a damping constant (or matrix), such an implementation will overestimate the effects of structural damping in a yielding building and underestimate maximum deformations and displacements. Structural damping should be characterized by the target damping ratio (typically 5% of critical) at the point of maximum displacement. Copyright © 1999 John Wiley & Sons, Ltd.