gebhart/patrepeval huggingface dataset:
The effects of cancer therapies on physical fitness before oesophagogastric cancer surgery: a prospective, blinded, multi-centre, observational, cohort study (2021)

Chemo/chemoradiotherapy prior to oesophagogastric cancer surgery reduced physical fitness. Lower baseline fitness was associated with reduced overall survival at one-year. Careful consideration of fitness prior to chemo/chemoradiotherapy and surgery is urgently needed.
190 A PROCEDURE TO OBTAIN FIBROBLASTS FROM WILD ANIMALS (2004)

The number of wild animals threatened or at risk of extinction constantly increases and, as a result, biodiversity decreases. Therefore, it is necessary to set in motion proceedings to preserve the genetic variability and to overcome factors leading to this situation. Banks of cryopreserved cells, such as skin fibroblasts, from wild animals could be used both for genetic studies and as a cell source for technologies able to reproduce individuals. In this study we report that a single basic protocol provides a method for obtaining, culturing, and cryopreserving skin fibroblasts from a wide range of wild animals. Skin biopsies were taken in Cantabria (Spain) from live, anesthetized brown bear (Ursus arctos, n = 4), and in Asturias (Spain) from carcasses of accidentally killed individuals from the following species: grey wolf (Canis lupus, n = 1), red fox (Vulpes vulpes, n = 1), eurasian badger (Meles meles, n = 1), ermine (Mustela erminea, n = 1), fallow deer (Dama dama, n = 7), pyrenean chamois (Rupicapra pyrenaica, n = 1), western roe deer (Capreolus capreolus, n = 1), wild boar (Sus scrofa, n = 1), striped dolphin (Stenella coeruleoalba, n = 1) and one avian species, capercaillie (Tetrao urogallus, n = 1). Once obtained and transported to the laboratory, all samples were processed identically. Tissue samples were manually cut into small pieces and enzymatically digested with 0.05% trypsin-EDTA (Sigma-Aldrich, Madrid, Spain) for 30 min, and then with collagenase (300 units/mL) (Sigma) for 14 h at 38°C. Disaggregated cells were centrifuged at 1600 rpm for 10 min and the pellet was diluted with D-MEM (Sigma) containing 10% FBS. Cells were counted and a minimum of 3 × 105 cells were placed in a 25 cm2 flask for culture under 5% CO2 in air and high humidity at 37°C (red fox, badger, ermine, western roe deer) or 38°C (brown bear, grey wolf, fallow deer, pyrenean chamois, wild boar, striped dolphin, capercaillie). Confluent fibroblast monolayers were obtained after 5–7 days in culture except for the striped dolphin whose sample was contaminated. Two to three passages were performed using 75 cm2 flasks before freezing fibroblasts in D-MEM containing 10% DMSO (Sigma) and 10% FBS. Total cell yield from a confluent flask was 5–11 × 106 cells, depending on the animal species. Fibroblasts recovered from all thawed samples grew to confluence, and karyotypes were performed at this step. It was possible to obtain, culture, freeze, and thaw skin fibroblasts successfully from all the above-mentioned land species. Although more research is needed, preliminary data suggest that the above-described procedure can be applied to mammals and birds, thus helping to preserve genetic material of wild animals. Grant Support: Consejería de Medio Ambiente, Ordenación del Territorios e Infraestructuras, Asturias, SPAIN. The authors acknowledge CEPESMA, Luarca, Asturias, SPAIN.
Optimizing Epitope Conformational Ensembles Using α-Synuclein Cyclic Peptide “Glycindel” Scaffolds: A Customized Immunogen Method for Generating Oligomer-Selective Antibodies for Parkinson’s Disease (2022)

Effectively presenting epitopes on immunogens, in order to raise conformationally selective antibodies through active immunization, is a central problem in treating protein misfolding diseases, particularly neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease. We seek to selectively target conformations enriched in toxic, oligomeric propagating species while sparing the healthy forms of the protein that are often more abundant. To this end, we computationally modeled scaffolded epitopes in cyclic peptides by inserting/deleting a variable number of flanking glycines ("glycindels") to best mimic a misfolding-specific conformation of an epitope of α-synuclein enriched in the oligomer ensemble, as characterized by a region most readily disordered and solvent-exposed in a stressed, partially denatured protofibril. We screen and rank the cyclic peptide scaffolds of α-synuclein <i>in silico</i> based on their ensemble overlap properties with the fibril, oligomer-model and isolated monomer ensembles. We present experimental data of seeded aggregation that support nucleation rates consistent with computationally predicted cyclic peptide conformational similarity. We also introduce a method for screening against structured off-pathway targets in the human proteome by selecting scaffolds with minimal conformational similarity between their epitope and the same solvent-exposed primary sequence in structured human proteins. Different cyclic peptide scaffolds with variable numbers of glycines are predicted computationally to have markedly different conformational ensembles. Ensemble comparison and overlap were quantified by the Jensen-Shannon divergence and a new measure introduced here, the embedding depth, which determines the extent to which a given ensemble is subsumed by another ensemble and which may be a more useful measure in developing immunogens that confer conformational selectivity to an antibody.
Automatic solder joint inspection (1988)

The task of automating the visual inspection of pin-in-hole solder joints is addressed. Two approaches are explored: statistical pattern recognition and expert systems. An objective dimensionality-reduction method is used to enhance the performance of traditional statistical pattern recognition approaches by decorrelating feature data, generating feature weights, and reducing run-time computations. The expert system uses features in a manner more analogous to the visual clues that a human inspector would rely on for classification. Rules using these cues are developed, and a voting scheme is implemented to accumulate classification evidence incrementally. Both methods compared favorably with human inspector performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heat Transfer Enhancement Using Synthetic Jets for Cooling in Low Form Factor Electronics in Presence of Mean Flow (2007)

This paper reports the results of our experimental studies on interaction of synthetic jets with a bulk flow over a heated surface in a low profile channel as well as its impact on overall heat transfer enhancement. Particle image velocimetry (PIV) studies were conducted to study the impact of jet frequency, mean flow velocity and synthetic jet orientation on the flow and heat transfer characteristics. The results showed an increase in jet velocity and hence heat transfer with an increase in frequency. Reduction in mean flow velocity facilitated entrainment of the synthetic jet and also led to its delayed dispersion. The thermal results were consistent with the flow patterns observed and heat transfer enhancements as high as 30% were observed. However, regions of attenuated heat transfer were also seen in cross-flow which needs careful consideration during thermal design.
Shielding Electronic Devices from Monoenergetic 100-MeV Protons (2010)

This paper investigates the interaction of monoenergetic, 100-MeV protons with aluminum, enriched B4C, and C29H28O8 polymer and their effectiveness for shielding silicon-based electronics. Although not representative of an actual space radiation energy spectrum, the 100-MeV protons are suitable to investigate important modes of interaction with potential shielding materials, including the production and attenuation of secondary particles. The calculated shielding effectiveness of these materials is compared with that of the lunar regolith. The components of the total energy deposition in a 1-cm-diam sphere of silicon, representing an electronic device, are calculated as functions of the type and thickness of the shield material. The major contributors to the displacement energy deposition in the silicon sphere are by far the incident protons and the secondary protons and neutrons generated in the spallation reactions of incident protons with the nuclei of the elements in the shield materials. The primary and secondary protons are also the major contributors to the ionizing energy deposition, which is several orders of magnitude higher than the displacement energy deposition; other secondary particles contribute minimally (<5%). While the regolith is an effective shielding material, the C29H28O8 polymer is best for protecting electronics from incident high-energy protons.
Sequential Quadratic Programming Algorithm for Real-Time Mixed-Integer Nonlinear MPC (2021)

Nonlinear model predictive control (NMPC) has grown mature and algorithmic techniques exist, e.g., based on sequential quadratic programming (SQP) methods, to handle relatively complex constrained control systems. In addition, model predictive control for hybrid dynamical systems, including both continuous and discrete decision variables, can be implemented efficiently based on state of the art mixed-integer quadratic programming (MIQP) algorithms. This paper proposes a novel mixed-integer SQP (MISQP) optimization algorithm as a heuristic search technique to find feasible, but possibly suboptimal, solutions for real-time implementations of mixed-integer NMPC (MINMPC). Two variants of the MISQP algorithm are described and motivated. Based on a preliminary software implementation, the real-time MISQP performance is illustrated for closed-loop MINMPC simulations on a nontrivial vehicle control case study, featuring worst-case computation times below 30 milliseconds.
Dual Coordination Modes of Ethylene-Linked NP2 Ligands in Cobalt(II) and Nickel(II) Iodides (2011)

Here we report the syntheses and crystal structures of a series of cobalt(II) and nickel(II) complexes derived from (R)NP2 ligands (where R = OMe(Bz), H(Bz), Br(Bz), Ph) bearing ethylene linkers between a single N and two P donors. The Co(II) complexes generally adopt a tetrahedral configuration of general formula [(NP2)Co(I)(2)], wherein the two phosphorus donors are bound to the metal center but the central N-donor remains unbound. We have found one case of structural isomerism within a single crystal structure. The Co(II) complex derived from (Bz)NP2 displays dual coordination modes: one in the tetrahedral complex [((Bz)NP2)Co(I)(2)]; and the other in a square pyramidal variant, [((Bz)NP2)Co(I)(2)]. In contrast, the Ni(II) complexes adopt a square planar geometry in which the P(Et)N(Et)P donors in the ligand backbone are coordinated to the metal center, resulting in cationic species of formula [((R)NP2)Ni(I)](+) with iodide as counterion. All Ni(II) complexes exhibit sharp (1)H and (31)P spectra in the diamagnetic region. The Co(II) complexes are high-spin (S = 3/2) in the solid state as determined by SQUID measurements from 4 to 300 K. Solution electron paramagnetic resonance (EPR) experiments reveal a high-spin/low-spin Co(II) equilibrium that is dependent on solvent and ligand substituent.
Resistance to the c-Met inhibitor KRC-108 induces the epithelial transition of gastric cancer cells (2015)

Investigation of the mechanisms of resistance to targeted therapies is essential as resistance acquired during treatment may lead to relapse or refractoriness to the therapy. Our previous study identified the small molecule KRC-108 as a result of efforts to find an anticancer agent with c-Met-inhibitory activity. In the present study, the changes accompanying resistance to KRC-108 were investigated in the gastric cancer cell line MKN-45 and its KRC-108-resistant clones by western blot and immunofluorescence analyses. Increased expression of the c-Met protein was observed in KRC-108-resistant cells compared with that of the parental cells, and the phosphorylation of c-Met also increased in cell lines resistant to KRC-108. Resistance to the c-Met inhibitor was associated with cell morphological changes: MKN-45 parental cells, which had a round and poorly differentiated morphology, were altered to exhibit an epithelial cell-like phenotype in KRC-108-resistant clones. Consistent with the transition to an epithelial morphology, the expression of E-cadherin was increased in resistant cells. Using immunoprecipitation, an interaction between E-cadherin and the c-Met protein was observed in the KRC-108-resistant cells. Immunohistochemical analysis of human gastric carcinoma tissues revealed the co-expression of E-cadherin and c-Met. These results suggest that the epithelial transition in KRC-108-resistant cells is mediated by recruiting E-cadherin to c-Met protein. Thus, the present study identified a mechanism used by cancer cells to confer resistance to anticancer agents.
Characterization of the carotid and adjacent anatomy using non-contrast CT for biomechanical model development. (2007)

The path of the carotid artery and its branches through the neck is characterized through an analysis of non-contrast computed tomography (CT) scans. The distance from the vessel wall of the carotid arteries to the skin and vertebral bodies are recorded from the level of the 2nd cervical vertebrae (C2) to the 6th cervical vertebrae (C6). A total of seven individuals were included in the study. The common carotid artery exhibited the closest average distance to the skin (23.5 +/- 6.9 mm) whereas the internal carotid artery exhibited the closest average distance to the vertebral body (7.36 +/- 3.8 mm, measured to the transverse process). This study provides morphological validation data towards the development of a regional-level finite element model of the neck and may also be used for the design of biomechanical experiments for the study of carotid artery injury.
Default Router and Prefix Advertisement Options for DHCPv6 (2009)

In some IPv6 deployments, there is a requirement to communicate a list
of default routers and advertised prefixes to a host through DHCP.
This document defines DHCP options to carry that information.
Real-time data acquisition and maximum-likelihood estimation for gamma cameras (2005)

We have developed modular gamma-ray cameras for biomedical imaging that acquire data with a raw list-mode acquisition architecture. All observations associated with a gamma-ray event, such as photomultiplier (PMT) signals and time, are assembled into an event packet and added to an ordered list of event entries that comprise the acquired data. In this work we present the design of the data-acquisition system, and discuss algorithms for a specialized computing engine to reside in the data path between the front and back ends of each camera and carry out maximum-likelihood position and energy estimations in real time while data was being acquired..
Ultra-Low Leakage Silicon-on-Insulator Technology for 65 nm Node and Beyond (2007)

We report 65 nm ground-rule, partially depleted, low-power silicon-on-insulator (LPSOI) CMOS devices with total leakage current / <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Off</sub> down to 10 pA / mum at supply voltage V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> = 1.2 V. NFET / PFET drive current I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DSAT</sub> = 550/250 muA /mum at /off = 100 pA/mum and gate length L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> ~ 55 nm are achieved with a single tensile liner film. Innovative junction engineering techniques such as low-damage junction pre- amorphization implants (PAI), source-side high-damage PAI, high-energy halo, and drain-side tilted source/drain (S/D) implants are evaluated for their effectiveness in minimizing SOI floating body effect for low leakage design. Our result suggests that there is no fundamental limit for low leakage application of SOI.
Downlink resource allocation and packet scheduling in multi-numerology wireless systems (2018)

5G New Radio (NR) is moving towards flexibility and adaptability and is expected to provide optimized support for diverse 5G use case categories. With the introduction of flexible waveforms and numerologies in 5G, there is a need for new scheduling and resource allocation techniques. Using different non-orthogonal numerologies in the network complicates the resource allocation process since it introduces numerology multi-plexing. In this paper, we propose a channel quality and Quality of Service (QoS) aware resource allocation scheme for multi-numerology 5G networks. We implement a frequency domain packet scheduler which allocates packets to Resource Blocks to achieve higher spectral efficiency, maintain fairness, and satisfying the QoS requirements of users with different non-orthogonal numerologies. The results show that our algorithm achieves high throughput in different traffic mixes with different numerology QoS requirements over varying number of users.
Pi–Pi Stacking (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
Atom Transfer Radical Polymerization with Different Halides (F, Cl, Br, and I): Is the Process “Living” in the Presence of Fluorinated Initiators? (2016)

Atom transfer radical polymerization (ATRP) is often used for grafting from fluorinated polymers. Nevertheless, the possibility to initiate an ATRP from a C–F functionality and the activity of the catalysts in the presence of fluoride anions are essentially unexplored. Therefore, we investigated the thermodynamics and kinetics of C–F bond activation by ATRP catalysts and compared it with other halide systems. The ATRP equilibrium constant was estimated to be small for the reaction between [CuITPMA]+ and benzyl fluoride (TPMA = tris(2-pyridylmethyl)amine). However, [CuITPMA]+ could react with the more active initiator diethyl fluoromalonate (DEFM). With DEFM as initiator and CuIBr/TPMA as catalyst, ATRP of methyl acrylate and styrene displayed initiation efficiencies of 73% and 95%, respectively. ATRP deactivation by [F–CuIITPMA]+ was slow and followed by even slower activation of newly formed C–F bonds, leading to limited conversion. Comparison with other halides indicates that Br- and Cl-based ATRP systems are more efficient that I- and F-based systems.
Use of transmission electron microscopy to identify nanocrystals of challenging protein targets (2014)

The current practice for identifying crystal hits for X-ray crystallography relies on optical microscopy techniques that are limited to detecting crystals no smaller than 5 μm. Because of these limitations, nanometer-sized protein crystals cannot be distinguished from common amorphous precipitates, and therefore go unnoticed during screening. These crystals would be ideal candidates for further optimization or for femtosecond X-ray protein nanocrystallography. The latter technique offers the possibility to solve high-resolution structures using submicron crystals. Transmission electron microscopy (TEM) was used to visualize nanocrystals (NCs) found in crystallization drops that would classically not be considered as "hits." We found that protein NCs were readily detected in all samples tested, including multiprotein complexes and membrane proteins. NC quality was evaluated by TEM visualization of lattices, and diffraction quality was validated by experiments in an X-ray free electron laser.
Longitudinal Assessment of Ellipsoid Zone Integrity, Subretinal Hyperreflective Material, and Subretinal Pigment Epithelium Disease in Neovascular Age-Related Macular Degeneration (2021)

EZ integrity, SHRM, and sub-RPE disease features in eyes with nAMD showed improvement as early as week 4 of anti-VEGF treatment. EZ integrity measures and SHRM volume were predictors of visual acuity over the first year of treatment.
A modified Voigt method for calculation of the elastic constants of ensembles selected by diffraction methods (1999)

Abstract The Voigt assumption describes a polycrystalline material under load as having an isotropic strain tensor in all grains. Consequently the corresponding stiffness tensor is isotropic according to Voigt. Extension of the Voigt limit to the calculation of elastic compliances used with diffraction stress determination techniques by Möller and Martin yielded values that are independent of the reflection used for the measurement. Since the data obtained by diffraction originated solely from the domains that satisfy Bragg's law, one can modify the Voigt assumption by requiring that the strain tensors of the diffracting grains be equal to an average strain 〈∊ij〉hkl for the particular reflection, where this average is different from the macroscopic average strain of the aggregate. In this paper this calculation is discussed. It is shown that this modification of the Voigt assumption yields compliances that are dependent on the crystallographic orientation of the diffracting crystallites. The isotropic nature of previously calculated Voigt constants is reproduced as a special case of this more general tensor. The modified Voigt diffraction elastic constants for (h00) and (hhh) reflections are also equivalent to those derived using the traditional Reuss treatment due to Neumann's principle of symmetry.
Illumination Insensitive Model-Based 3D Object Tracking and Texture Refinement (2006)

A common approach to model-based tracking is to use a model of the object to predict what will be observed, and then to compare that with real observations. For methods that make use of the object's photometric properties (appearance) in their measurements, illumination inconsistencies between the modeled and actual scene can cause tracking problems. In this paper we address one case: model-based tracking of Lambertian objects under directional light sources. We present an iterative optimization method that uses a Kalman filter to simultaneously refine estimates of the object motion, the illumination, and the model texture. We model the illumination variance between the real and predicted observation using the intensity ratios of corresponding surface points, which we then use to make model-based image predictions consistent with the real lighting. To demonstrate the effectiveness of our method we present experimental results using both synthetic (controlled) and real image sequences.