gebhart/patrepeval huggingface dataset:
Establishment of a human induced pluripotent stem cell neuronal model for identification of modulators of A53T α-synuclein levels and aggregation (2021)

Inhibiting formation or promoting degradation of α-synuclein aggregates are among the therapeutical approaches under investigation as disease-modifying treatment strategies for Parkinson's disease. To support these developments, several in vitro models based on seeded α-synuclein aggregation have been established in immortalized cell lines and murine primary neurons. Here, we report on a humanized model with a reproducibility and throughput that enables its use in supporting target identification and validation in pharmacological research. A human induced pluripotent stem cell (iPSC) line was genetically modified to express HA-tagged α-synuclein with the point mutation in position 53 from Alanine to Threonine (A53T) under an inducible system and differentiated into cortical neurons expressing neuronal markers and exhibiting spontaneous activity. Intracellular α-synuclein aggregation was triggered by exposure to exogenous added fibrillated recombinant wild-type human α-synuclein fibrils91 and demonstrated by several endpoints; the formation of Triton-insoluble SDS-soluble α-synuclein, biochemically in a fluorescence resonance energy transfer based aggregation assay and by immunocytochemistry of phosphorylated α-synuclein positive puncta. We demonstrate the feasibility of upscaling the iPSC neuron production for drug discovery and that the model has a suitable dynamic range allowing for both detection of increased and decreased α-synuclein aggregation. Moreover, gene modulation is feasible using siRNAs, making the model suitable for genetic screening for modulators of α-synuclein aggregation. Data on effects of USP8, USP13 and USP9X knockdown on α-synuclein expression and aggregation contradicts published data from immortalized cell lines and murine systems. This highlight the importance of including humanized neuronal models in the confirmation of biological mechanisms in specific variations of Parkinson's disease.
Conversion Rules Between X-Parameters and Linearized Two-Port Network Parameters for Large-Signal Operating Conditions (2018)

This paper presents conversion rules between X-parameters, linearized impedance parameters, linearized admittance parameters, linearized cascade parameters, linearized scattering transfer parameters, linearized hybrid parameters, and linearized inverse hybrid parameters of a two-port network under large-signal operating conditions. The rules have been developed along with a set of equations that allow obtaining the expressions of each linearized parameter from the remaining ones. The proposed approach has been evaluated, and very good agreement has been obtained between calculated parameters and simulated ones.
Perspective of Combustion Modeling for Gas Turbine Combustors (2004)

• Empirical/analytical design tools A status summary report is given on the development of comprehensive computational combustor design (CCD) tool activities of GEAE combustion group conducted for the last three years. A “no-fudge factor” pretest prediction approach is being pursued for the combustors that use rich or lean-dome swirl cups (Single Annular and Dual Annular combustors, SAC, DAC); Twin Annular Premixing Swirler, TAPS (SAC and DAC), and Dry Low Emissions’ DACRS mixers for triple annular combustor domes. The pretest prediction capability is being gauged with existing data including emissions, exit temperature quality and wall temperatures from nine different combustors selected from a group of production and technology combustors. The agreement between predictions and data is good considering this is the 1 st
On the theory of Point Weight Designs (2001)

A point-weight incidence structure is a structure of blocks and points where each point is associated with a positive integer weight. A point-weight design is a point-weight incidence structure where the sum of the weights of the points on a block is constant and there exist some condition that specifies the number of blocks that certain sets of points lie on. These structures share many similarities to classical designs. Chapter one provides an introduction to design theory and to some of the existing theory of point-weight designs. Chapter two develops a new type of point-weight design, termed a row-sum point-weight design, that has some of the matrix properties of classical designs. We examine the combinatorial aspects of these designs and show that a Fisher inequality holds and that this is dependent on certain combinatorial properties of the points of minimal weight. We define these points, and the designs containing them, to be either `awkward&amp;apos; or `difficult&amp;apos; depending on these properties. Chapter three extends the combinatorial analysis of row-sum point-weight designs. We examine structures that are simultaneously row-sum and point-sum point-weight designs, paying particular attention to the question of regularity. We also present several general construction techniques and specific examples of row-sum point-weight designs that are generated using these techniques. Chapter four concentrates on the properties of the automorphism groups of point-weight designs with particular emphasis on row-sum point-weight designs. We introduce the idea of a structure being &amp;quot;t-homogeneous with respect to its orbital partition&amp;quot; and use this to derive a formula for the number of blocks a set of points lies upon. We also discuss the properties of the orbits of subgroups of the automor...
A heuristic approach to program verification (1973)

We present various heuristic techniques for use in proving the correctness of computer programs. The techniques are designed to obtain automatically the assertions attached to the loops of the program which previously required human understanding of the program''s performance. We distinguish between two general approaches: one in which we obtain the inductive assertion by analyzing predicates which are known to be true at the entrances and exits of the loop ($underline{top-down}$ approach), and another in which we generate the inductive assertion directly from the statements of the loop ($underline{bottom-up}$ approach).
Genetic programming for image classification with unbalanced data (2009)

Image classification methods using unbalanced data can produce results with a performance bias. If the class representing important objects-of-interest is in the minority class, learning methods can produce the deceptive appearance of ¿good looking¿ results while recognition ability on the important minority class can be poor. This paper develops and compares two genetic programming (GP) methods for image classification problems with class imbalance. The first focuses on adapting the fitness function in GP to evolve classifiers with good individual class accuracy. The second uses a multi-objective approach to simultaneously evolve a set of classifiers along the trade-off surface representing minority and majority class accuracies. Evaluating our GP methods on two benchmark binary image classification problems with class imbalance, our results show that good solutions were evolved using both GP methods.
A Framework for Evaluating Intrusion Detection Architectures in Advanced Metering Infrastructures (2014)

The scale and complexity of Advanced Metering Infrastructure (AMI) networks requires careful planning for the deployment of security solutions. In particular, the large number of AMI devices and the volume and diversity of communication expected to take place on the various AMI networks make the role of intrusion detection systems (IDSes) critical. Understanding the trade-offs for a scalable and comprehensive IDS is key to investing in the right technology and deploying sensors at optimal locations. This paper reviews the benefits and costs associated with different IDS deployment options, including either centralized or distributed solution. A general cost-model framework is proposed to help utilities (AMI asset owners) make more informed decisions when selecting IDS deployment architectures and managing their security investments. We illustrate how the framework can be applied through case studies, and highlight the interesting cost/benefit trade-offs that emerge.
A highly oriented Al[111] texture developed on ultrathin metal underlayers (1995)

A highly oriented [111] texture is developed in ion beam sputtered Al films on metal underlayers of Ti, V, Cr, Co, Ni, Cu, or Y. The textured Al films show an extremely smooth surface. Deposition of highly textured Al films depends on the presence of this underlayer, the thickness of which must lie within a specific range that varies with the metal being used. We discuss here the mechanisms of texturing in terms of phenomenological surface-interface energy balance considerations. The great tolerance for high-power operations of Al films with a highly oriented [111] texture makes them particularly suitable for use as electrodes in surface acoustic wave devices.
Cochlear implantation in children with bacterial meningitic deafness: The influence of the degree of ossification and obliteration on impedance and charge of the implant (2014)

To optimize the outcome in post-meningitic deaf children, surgery is advisable at an early stage prior to the onset of cochlear ossification.
The Measurement of Refractive Indexes of Liquids in the Infrared (1951)

A method of measuring the refractive indexes of liquids in the infrared is described. A Perkin-Elmer spectrometer is adapted for this purpose without interfering with its normal operation as a routine instrument. Although use is made of a Fabry-Perot etalon, the method is not interferometric in the accepted sense. The accuracy that has been obtained is 0.002 at a wavelength of 1μ, but in principle the possible accuracy of the method may be equal to that of the best goniometer.
Novel wavefront sensor for optical space communications (2002)

Summary form only given. Compensation of atmosphere turbulences by means of adaptive optics (AO) is a well-known technique in the field of astronomy, but so far has been mostly left out of considerations with respect to space laser links (SLL). In a first step, to reduce the complexity of the traditional adaptive optics system employing the bulky Shack-Hartmann sensor, we designed and fabricated a new type of compact polymer waveguide array in-line sensor keeping nearly 100% of the received power for the data transmission after wavefront correction is achieved.
Mapping Lithofacies in a Siliciclastic and a Carbonate Reservoir Using Statistical Rock Physics (2012)

In order to characterize two highly heterogeneous reservoirs (one siliciclastic and other carbonate), this paper shows how through the integration of well-log data and 3D pre-stack seismic data, using a statistical rock physics approach, it was possible to extrapolate the lateral continuity of the target lithofacies present in studied reservoirs. The implemented methodology consists of three phases. In the first phase, seismic lithofacies were defined and Vp, Vs and density logs were used to compute elastic attribute logs. This information was used to generate cross-plots of elastic attributes colored by lithofacies to understand the relationship between seismic attributes and lithofacies. In the second phase, 3D pre-stack seismic data and well-log data was used to estimate volumes of AI and EI(20) using a post-stack inversion algorithm. In the last phase, by means of Bayesian analysis, probability maps of the target lithofacies were made with the purpose of identifying the zones with the best petrophysical properties in the reservoirs. The resulting probability maps of lithofacies characterize the heterogeneity of the reservoir and help to reduce the risk associated with the location of future development wells in the field.
Faculty Opinions recommendation of Short- and Long-term Outcomes After Lung Transplantation From Circulatory-Dead Donors: A Single-Center Experience. (2018)

BACKGROUND: Donation after cardiac death (DCD) to overcome the donor organ shortage is well accepted in the clinical setting, although long-term outcome after DCD lung transplantation (LTx) remains largely unknown.METHODS: In this retrospective study, DCD LTx recipients (n = 59) were compared with a cohort of donation after brain death (DBD) LTx recipients (n = 331) transplanted between February 2007 and September 2013; follow-up was until January 1, 2016. Short-term (duration of mechanical ventilation, intensive care unit stay, hospital stay, and highest primary graft dysfunction score within 72 hours) and long-term (chronic lung allograft dysfunction-free and overall survival) follow-up were compared over a median follow-up of 50.5 (±3.7) months for DCD and 66.8 (±1.5) months for DBD.RESULTS: There were no differences between groups with regard to patient characteristics: age (P = 0.78), underlying disease (P = 0.30) and type of type of LTx (P = 0.10), except sex where more males were transplanted with a DCD donor (62.7%) vs (48.3%, P = 0.048). There was no difference in time on mechanical ventilation (P = 0.59), intensive care unit stay (P = 0.74), highest primary graft dysfunction score (P = 0.67) and hospital stay (P = 0.99). Moreover, chronic lung allograft dysfunction-free (P = 0.86) and overall survival (P = 0.15) did not differ between the DBD and DCD groups.CONCLUSIONS: In our experience, both short- and long-term outcomes in DCD lung recipients are comparable to that of DBD lung recipients. Therefore, DCD LTx can be considered a safe strategy that significantly increased our transplant activity. PMID: 28207629
FACTORS INFLUENCING ANASTAMOTIC STRICTURE FOLLOWING GASTRIC BYPASS (2003)

s Submitted for the 68th Annual Scientific Meeting of the American College of Gastroenterology October 10-15, 2003, Baltimore, Maryland: ENDOSCOPY: PDF Only
Clinimetrics of freezing of gait (2008)

The clinical assessment of freezing of gait (FOG) provides great challenges. Patients often do not realize what FOG really is. Assessing FOG is further complicated by the episodic, unpredictable, and variable presentation, as well as the complex relationship with medication. Here, we provide some practical recommendations for a standardized clinical approach. During history taking, presence of FOG is best ascertained by asking about the characteristic feeling of "being glued to the floor." Detection of FOG is greatly facilitated by demonstrating what FOG actually looks like, not only to the patient but also to the spouse or other carer. History taking further focuses on the specific circumstances that provoke FOG and on its severity, preferably using standardized questionnaires. Physical examination should be done both during the ON and OFF state, to judge the influence of treatment. Evaluation includes a dedicated "gait trajectory" that features specific triggers to elicit FOG (gait initiation; a narrow passage; dual tasking; and rapid 360 degrees axial turns in both directions). Evaluating the response to external cues has diagnostic importance, and helps to determine possible therapeutic interventions. Because of the tight interplay between FOG and mental functions, the evaluation must include cognitive testing (mainly frontal executive functions) and judgment of mood. Neuroimaging is required for most patients in order to detect underlying pathology, in particular lesions of the frontal lobe or their connections to the basal ganglia. Various quantitative gait assessments have been proposed, but these methods have not proven value for clinical practice.
REGIMap (2013)

Coarse-Grained Reconfigurable Architectures (CGRAs) are an extremely attractive platform when both performance and power efficiency are paramount. Although the power-efficiency of CGRAs can be very high, their performance critically hinges upon the capabilities of the compiler. This is because a CGRA compiler has to perform explicit pipelining, scheduling, placement, and routing of operations. Existing CGRA compilers struggle with two main problems: 1) effectively utilizing the local register files in the PEs, and 2) high compilation times. This paper significantly improves the state-of-the-art in CGRA compilers by first creating a precise and general formulation of the problem of loop mapping on CGRAs, considering the local registers, and from the insights gained from the problem formulation, distilling an efficient and constructive heuristic solution. We show that the mapping problem, once characterized, can be reduced to the problem of finding maximal weighted clique in the product graph of the time-extended CGRA and the data dependence graph of the kernel. The heuristic we've developed results in average of 1.89 X better performance than the state-of-the-art methods when applied to several kernels from multimedia and SPEC2006 benchmarks. A unique feature of our heuristic is that it learns from failed attempts and constructively changes the schedule to achieve better mappings at lower compilation times.
Développement d'un environnement de modélisation micromagnétique : couplage macroscopique-microscopique (2004)

Dans le contexte actuel de l'augmentation de la densite d'information, la miniaturisation poussee des tetes de lecture implique des differences d'echelle de plus en plus importantes entre les divers elements du systeme. Ce projet de these est dedie a la realisation d'un outil de modelisation numerique pour decrire le comportement des composants magnetiques d'une tete de lecture MR dans le processus de lecture magnetique sur bandes multi-pistes de haute capacite. Il repose sur une technique originale de couplage d'echelles de longueur macroscopique et microscopique, nommee couplage macro-micro. Dans notre approche, les elements magnetiques macroscopiques comme les ecrans magnetiques sont decrits comme des milieux lineaires isotropes avec une permeabilite finie. Le champ de fuite genere par les transitions magnetiques du media en tenant compte des ecrans magnetiques est evalue par l'intermediaire du potentiel magnetique scalaire, solution d'une equation de Poisson. Un developpement en series de Fourier est applique a la distribution de charges magnetiques tridimensionnelle. Ainsi le probleme initial 3D est resolu par un traitement 2D. La resolution de ce probleme est faite par la methode des integrales de frontiere. L'etat magnetique stable du capteur est ensuite modelise par des calculs micromagnetiques qui repose sur l'integration temporelle de l'equation Landau-Lifsitz-Gilbert dans l'approximation des differences finies. Cette technique constitue un outil puissant dans l'optimisation du design des tetes de lecture MR multi-pistes, pour lesquelles aucun outil de modelisation existant ne permettait de rendre compte de la complexite tridimensionnelle du probleme.
An alternative methylation pathway in lignin biosynthesis in Zinnia. (1994)

S-Adenosyl-L-methionine:trans-caffeoyl-coenzyme A 3-O-methyltransferase (CCoAOMT) is implicated in disease resistant response, but whether it is involved in lignin biosynthesis is not known. We isolated a cDNA clone for CCoAOMT in differentiating tracheary elements (TEs) induced from Zinnia-isolated mesophyll cells. RNA gel blot analysis showed that the expression of the CCoAOMT gene was markedly induced during TE differentiation from the isolated mesophyll cells. Tissue print hybridization showed that the expression of the CCoAOMT gene is temporally and spatially regulated and that it is associated with lignification in xylem and in phloem fibers in Zinnia organs. Both CCoAOMT and caffeic acid O-methyltransferase (COMT) activities increased when the isolated Zinnia mesophyll cells were cultured, whereas only CCoAOMT activity was markedly enhanced during lignification in the in vitro-differentiating TEs. The induction pattern of the OMT activity using 5-hydroxyferuloyl CoA as substrate during lignification was the same as that using caffeoyl CoA. Taken together, the results indicate that CCoAOMT is associated with lignification during xylogenesis both in vitro and in the plant, whereas COMT is only involved in a stress response in vitro. We propose that CCoAOMT is involved in an alternative methylation pathway in lignin biosynthesis. In Zinnia in vitro-differentiating TEs, the CCoAOMT mediated methylation pathway is dominant.
Radiotherapy waiting times, resources and protocols for breast carcinoma: a survey of UK radiotherapy centres (2003)

Purpose: Radiation techniques employed for breast cancer must be efficient as well as effective in order to minimise waiting lists. Protocol restrictions, or the technical application of treatment, may influence planning and treatment times as radiographers follow departmental policies. A national survey of UK radiotherapy centres was undertaken to establish trends in waiting times for breast cancer irradiation; and to investigate relationships of waiting times with the deployment of equipment and personnel and technical procedures adopted. Method: A questionnaire was posted to the Head of Radiotherapy Services and a Clinical Oncologist with an interest in breast cancer in the radiotherapy centres in the UK. Survey questions investigated a number of issues, including the number of breast patients planned per week; protocols chosen; average treatment and planning times; levels of personnel and equipment; and the population served. Results: A total of 53 centres were contacted, of which 51 centres responded to some aspect of the survey (96%). Average waiting times for treatment fluctuated from 1 to 7 weeks and maximum waiting times of 11 weeks were reported. Variation in clinical practice was found, including procedure times and the number of radiographers employed per linear accelerator. A multiple regression analysis indicated that a combination of equipment levels, simulation times, and the number of breast contours taken best predicted the average waiting time for breast treatment. Conclusion: Waiting times reported were influenced by a combination of levels of equipment available and protocols adopted.
Radiotherapy is an independent prognostic marker of favorable prognosis in non‐small cell lung cancer patients after treatment with the immune checkpoint inhibitor, nivolumab (2019)

Previous RT was an independent prognostic marker of favorable prognosis after nivolumab administration and improved the response rate to nivolumab treatment. Previous RT was clinically identified to have a synergistic effect with nivolumab treatment, increasing the response rate and improving the outcome of patients with advanced NSCLC.
Can lepton flavor violating interactions explain the atmospheric neutrino problem? (2000)

We investigate whether flavor changing neutrino interactions (FCNIs) can be sufficiently large to provide a viable solution to the atmospheric neutrino problem. Effective operators induced by heavy boson exchange that allow for flavor changing neutrino scattering off quarks or electrons are related by an ${\mathrm{SU}(2)}_{L}$ rotation to operators that induce anomalous tau decays. Since ${\mathrm{SU}(2)}_{L}$ violation is small for new physics at or above the weak scale, one can use the upper bounds on lepton flavor violating tau decays or on lepton universality violation to put severe, model-independent bounds on the relevant non-standard neutrino interactions. Also Z-induced flavor changing neutral currents, due to heavy singlet neutrinos, are too small to be relevant for the atmospheric neutrino anomaly. We conclude that the FCNI solution to the atmospheric neutrino problem is ruled out.