gebhart/patrepeval huggingface dataset:
Structural shape optimization of three dimensional finite element models (1987)

The thesis presents a three dimensional shape optimization program which analyzes models made up of linear isoparametric elements. The goal of the program is to achieve a near uniform model stress state and thereby to minimize material volume. The algorithm is iterative, and performs two analyses per iteration. The first analysis is a static stress analysis of the model for one or more load cases. Based on results from the static analysis, an expansion analysis is performed. Model elements are expanded or contracted based on whether they are stressed higher or lower than a reference stress. The shape changing is done by creating an expansion load vector using the differences between the calculated element stresses and the reference stress. Expansion displacements are solved for, and instead of using them to calculate stresses, the displacements are added to the nodal coordinates to reshape the structure. This process continues until a user defined convergence tolerance is met. Four programs were used for the analysis process. Models were created using a finite element modeling program called I-IDEAS or CAIEDS. The I-IDEAS output files were converted to input files for the optimizer by a conversion program. The model was optimized using the shape optimization process described above. Post- processing was done using a program written with a graphical programming language called graPHIGS. Models used to test the program were: a cylindrical pressure vessel with nonuniform thickness, a spherical pressure vessel with non-uniform thickness, a torque arm, and a draft sill casting o a railroad hopper car. Results were compared to similar studies from selected references. Both pressure vessels converged to near uniform thicknesses, which compared ell with the reference work. In a two dimensional analysis, the torque arm volume decreased 24 percent, which compared well with published results. A three dimensional analysis showed a volume reduction of l3 percent, but there were convergence problems. Finally, the draft sill casting was reduced in volume by 9 percent from a manually optimized design.
Recombinant Modified Vaccinia Virus Ankara Generating Excess Early Double-Stranded RNA Transiently Activates Protein Kinase R and Triggers Enhanced Innate Immune Responses (2014)

Efficient cellular sensing of pathogen-specific components, including double-stranded RNA (dsRNA), is an important prerequisite of an effective antiviral immune response. The prototype poxvirus vaccinia virus (VACV) and its derivative modified vaccinia virus Ankara (MVA) produce dsRNA as a by-product of viral transcription. We found that inhibition of cellular dsRNA recognition established by the virus-encoded proteins E3 and K3 can be overcome by directing viral overexpression of dsRNA early in infection without compromising replication of MVA in permissive cells. Early dsRNA induced transient activation of the cellular dsRNA sensor protein kinase R (PKR), resulting in enhanced production of interferons and cytokines in cells and mice. Enhancing the capacity of MVA to activate the innate immune system is an important approach to further improve the immunogenicity of this promising vaccine vector.
Wie kann man den Engineering-Prozess systematisch verbessern? (2013)

In diesem Beitrag werden die Ergebnisse der Arbeit des GMA-Fachausschusses 6.12 Durchgangiges Engineering von Leitsystemen der letzten 1½ Jahre vorgestellt und zur Diskussion gestellt. Die Ergebnisse beinhalten eine Systematik zur Einordnung der Arbeitsweise einer Engineering-Organisation bezogen auf ihr wirtschaftliches, organisatorisches und technisches Umfeld und mogliche Masnahmen zur Weiterentwicklung einer Engineering-Organisation.
Early prophylaxis impact for newborns at risk for HIV-1 transmission at birth: viral clearance and attenuation with neutralizing monoclonal antibodies in infant rhesus macaques (2016)

Abstract Our pre-clinical infant macaque model addresses translational implications for early intervention in mother-to-child transmission (MTCT). This model has shown that neutralizing monoclonal antibody (NmAb) therapy given 1 day after SHIVSF162P3 virus exposure intercepts the earliest stages of infection in lymphoid and mucosal tissues. Serial sacrifices revealed that within 2 weeks early viral foci in tissues were eradicated. All animals followed for up to 28 weeks were completely clear of virus infection with no viral rebound after CD8-depletion. Here, twelve 1-month-old rhesus macaques, negative for MHC class I alleles Mamu B*08, B*17 and A*01, were inoculated orally with SHIVSF162P3. Cocktails of NmAbs PGT121 and VRC07-523 were delivered subcutaneously at days 1, 4, 7, and 10 after SHIV exposure. Control groups did not receive NmAbs. Plasma, PBMC, and multiple tissues at necropsy were monitored for viral RNA and DNA. ICS was used to detect Gag and Vif T cell responses. We report that lowering NmAb dosing from 10 to 5 mg/kg given 24 h after virus exposure resulted in only one animal infected, with viremia persisting at about 1 log10 below controls. NmAb treatment at 10 mg/kg delayed for 48 h after oral SHIVSF162P3 exposure resulted in ablated virus infection in 3 of 6 macaques. CD8-depletion resulted in no evidence of virus rebound, indicating the absence of viral latency. In 2 macaques, NmAbs attenuated set-point viremia by 1 – 2 log10, compared to viremia in control animals. These results show that antibodies can have powerful and durable effects on viremia and disease in newborns, but timing and dose are critical. Moreover, post-exposure viral clearance from infected tissue marks a significant advance in pre-clinical platforms to prevent MTCT.
Data from Augmentation of the Enhanced Permeability and Retention Effect with Nitric Oxide–Generating Agents Improves the Therapeutic Effects of Nanomedicines (2023)

&lt;div&gt;Abstract&lt;p&gt;Enhanced permeability and retention (EPR) effect–based nanomedicine is a promising strategy for successful anticancer therapy. The EPR effect is based on tumor blood flow. Because advanced large tumors, as frequently seen in clinical settings, are heterogeneous, with regions of defective vasculature and blood flow, achieving the desired tumor drug delivery is difficult. Here, we utilized the EPR effect to increase drug delivery. To augment the EPR effect for improved therapeutic effects of nanomedicine, we exploited vascular mediators—the nitric oxide (NO) generators nitroglycerin (NG), hydroxyurea, and l-arginine. These compounds generate NO in tumors with relatively high selectivity. Using different nanosized drugs in our protocol significantly increased (1.5–2 times) delivery of nanomedicines to different solid tumor models, along with markedly improving (2–3-fold) the antitumor effects of these drugs. Also, in 7,12-dimethylbenz[&lt;i&gt;a&lt;/i&gt;]anthracene–induced advanced end-stage breast cancer, often seen in clinical settings, 2 mg/kg polymer-conjugated pirarubicin (P-THP) with NG (0.2 mg/mouse) showed better effects than did 5 mg/kg P-THP, and 5 mg/kg P-THP used with NG resulted in cures or stable tumors (no tumor growth) for up to 120 days. Moreover, in a murine autochthonous azoxymethane/dextran sulfate sodium-induced colon cancer model, NO donors markedly improved the therapeutic effects of P-THP even after just one injection, results that were comparable with those achieved with three weekly P-THP treatments. These findings strongly suggest the potential usefulness of NO donors as EPR effect enhancers to improve the therapeutic efficacy of nanomedicines.&lt;/p&gt;&lt;/div&gt;
Immunohistologic Responses Within Dermal Metastatic Melanoma Lesions of Patients Treated With a Synthetic Peptide Vaccine (2000)

Three patients with dermal metastatic melanoma lesions responding to a synthetic peptide vaccine (g209-2M) derived from the sequence of gp100 melanoma-associated antigen, along with either IL-2 or granulocyte-monocyte colony-stimulating factor were studied to characterize the immunologic response occurring within and around the lesions during therapy. Standard immunocytochemical techniques were used to study the T-cell response (CD3, CD4, and CD8), the B-cell response (CD20), and the expression of class II major histocompatibility complex (HLA-DR) antigens. Between 40 and 65 days after the initiation of vaccine therapy (more than 3 weeks after the second dose of vaccine), the gross tumor size decreased and the tumors from all three patients showed substantial histologic regression associated with increased numbers of tumor-infiltrating lymphocytes and melanophages. The increased lesional tumor-infiltrating lymphocytes consisted of CD3+ T cells and very few CD20+ B cells. In two of the three patients, the T-cell infiltrate occurring during the initial tumor regression consisted predominantly of CD8+ cells. The number of perivascular T cells surrounding small vessels adjacent to melanoma lesions also increased during the time of peak histologic tumor regression. Also during the course of vaccine therapy, the expression of HLA-DR by vascular endothelial cells of the small vessels adjacent to lesions increased in all three patients, and elevated endothelial expression of HLA-DR was maintained in two of the three patients. These results show that patients with metastatic melanoma, who responded to melanoma vaccine therapy, had a predominantly CD8+ T-cell infiltrate associated with a loss of tumor cells. As the tumor cells diminished, they were replaced by heavily pigmented melanophages.
Algorithms for Adapting Materialised Views in Data Warehouses (1996)

In this paper we consider the problem of materialised view adaptation in data warehouses. Materialised views are important in data warehousing where they are used to speed up query processing on large amounts of data. User requirements change over time, which may change the de#nitions of views dynamically. For such situations, the question arises whether the materialised views should be recomputed from scratch for every change in the de#nition or they should be obtained by adapting old materialised views. Changes to a view de#nition may be expensive, if the view is recomputedfrom scratch. Therefore, it is worthwhile to examine ways of performing changes to the materialised view without recomputing the entire view which has undergone a change in de#nition. We present adaptation algorithms for adapting views when the changes are made in each SELECT, FROM, and WHERE clause. The main idea of our algorithms is to augment the schemas of base relations by adding `joincount &amp;apos; attributes to the...
Clinico-pathological evidence that axonal loss underlies disability in progressive multiple sclerosis (2010)

Growing evidence suggests that axonal degeneration rather than demyelination is the pathological substrate underlying chronic, irreversible disability in multiple sclerosis. However, direct evidence linking clinical disability measured in vivo with corresponding post-mortem measures of axonal pathology is lacking. Our objective in this study was to investigate the relationship between motor disability accumulated by patients with multiple sclerosis during life and the degree of axonal loss observed in their descending motor tracts after death. Human spinal cord derived at autopsy from 45 patients with multiple sclerosis was investigated. The medical records of each patient were reviewed by a multiple sclerosis neurologist to determine the degree of motor disability reached before death. Spinal cord sections were stained immunohistochemically. The degree of demyelination and the number of surviving corticospinal tract axons were measured in each patient. Patients who had accumulated higher levels of motor disability prior to death demonstrated fewer surviving corticospinal axons. Motor disability did not correlate with degree of demyelination. This study provides for the first time, direct clinico-pathological evidence that axonal loss is the pathological substrate of established disability in multiple sclerosis.
Coupling the SAEM algorithm and the extended Kalman filter for maximum likelihood estimation in mixed-effects diffusion models (2013)

We consider some general mixed-effects diffusion models, in which the observations are made at discrete time points and include measurement errors. In these models, the observed likelihood is generally not explicit, making maximum likelihood estimation of the parameters particularly complex. We propose a specific inference methodology for these models. In particular, we combine the SAEM algorithm with the extended Kalman filter to estimate the population parameters. We also provide some tools for estimating the individual parameters, for recovering the individual underlying diffusion trajectories and for evaluating the model. The methods are evaluated on simulations and applied to a pharmacokinetics example.
Spatial relationship between the nucleotide‐binding site, Lys‐61 and Cys‐374 in actin and a conformational change induced by myosin subfragment‐1 binding (1987)

The spatial relationship between Lys-61, the nucleotide binding site and Cys-374 was studied. Lys-61 was labelled with fluorescein-5-isothiocyanate as a resonance energy acceptor, the nucleotide-binding site was labelled with the fluorescent ATP analogues epsilon ATP or formycin-A 5'-triphosphate (FTP) and Cys-374 was labelled with 5-(2-[(iodoacetyl)amino]ethyl)aminonaphthalene-1-sulfonic acid (1,5-IAEDANS) as a resonance energy donor. The distances between the nucleotide binding site and Lys-61 or between Lys-61 and Cys-374 were calculated to be 3.5 +/- 0.3 nm and 4.60 +/- 0.03 nm, respectively. (The assumption has been made in calculating these distances that the energy donor and acceptor rotate rapidly relative to the fluorescence lifetime.) On the other hand, when doubly-labelled actin with 1,5-IAEDANS at Cys-374 and FITC at Lys-61 was polymerized in the presence of a twofold molar excess of phalloidin [Miki, M. (1987) Eur. J. Biochem. 164, 229-235], the fluorescence of 1,5-IAEDANS bound to actin was quenched significantly. This could be attributed to inter-monomer energy transfer. The inter-monomer distance between FITC attached to Lys-61 in a monomer and 1,5-IAEDANS attached to Cys-374 in its nearest-neighbour monomer in an F-actin filament was calculated to be 3.34 +/- 0.06 nm, assuming that the likely change in the intra-monomer distance does not change during polymerization by more than 0.4 nm. One possible spatial relationship between Lys-61, Cys-374 and the nucleotide binding site in an F-actin filament is proposed. The effect of myosin subfragment-1 (S1) binding on the energy transfer efficiency was studied. The fluorescence intensity of AEDANS-FITC-actin decreased by 30% upon interaction with S1. The fluorescence intensity of AEDANS-FITC-actin polymer in the presence of phalloidin increased by 21% upon interaction with S1. The addition of ATP led to the fluorescence intensity returning to the initial level. Assuming that the change of fluorescence intensity can be attributed to conformational change in the actin molecule induced by S1 binding, the intra-monomer distance was reduced by 0.4 nm and the inter-monomer distance was increased by 0.2 nm.
THE EXPRESSION AND PURIFICATION OF OCTA-ARGININE APOPTIN AND ITS ABILITY TO KILL CANCER CELLS (2016)

&lt;p&gt;&lt;strong&gt;Objective: &lt;/strong&gt;In this research, &lt;em&gt;chicken anemia virus&lt;/em&gt; apoptin optimized genetically for expression in &lt;em&gt;Escherichia coli&lt;/em&gt; and also modified using (His)&lt;sub&gt;6&lt;/sub&gt; tag, (Arg)&lt;sub&gt;8&lt;/sub&gt; tag, and HlyA tag intended for purification needs, penetration enhancement, and secretion from&lt;em&gt; &lt;/em&gt;bacterial host&lt;em&gt; &lt;/em&gt;to the growth media.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods&lt;/strong&gt;&lt;strong&gt;:&lt;/strong&gt;&lt;strong&gt; &lt;/strong&gt;The modified apoptin gene was optimized using an Integrated DNA Technology (IDT). The gene (606 bp) then ordered and synthesized by Eurofins. The apoptin gene was expressed using &lt;em&gt;E. coli&lt;/em&gt; BL21 CodonPlus as host, in cultivation temperature of 37 °C, and 25 °C and purified using Ni-NTA agarose beads. The addition of (His)&lt;sub&gt; 6&lt;/sub&gt; tag enabled the apoptin to be purified in only one step by using nickel column. The expression and purification data analyzed qualitatively as well as quantitatively using SDS-PAGE. MTT assay was used to identify the antitumor effect of octa arginine-apoptin to two kinds of cancer cells, cervix HeLa cancer cell and colon Widr cancer cell. The viability of cell was analyzed when the cell incubated in the variation concentration protein for 72 h.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The constructed apoptin gene were expressed in &lt;em&gt;E. coli &lt;/em&gt;successfully. The MTT assay indicated that Octaarginin-Apoptin was able to induce apoptosis of HeLa and Widr cells lines in a dose-dependent manner. The recombinant apoptin without tagging with octa-arginine, have no ability to induce apoptosis of HeLa and Widr cells lines. &lt;strong&gt;&lt;/strong&gt;&lt;/p&gt;&lt;p class="Abstract"&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;&lt;em&gt;This octa arginine-apoptin may in the future allow the development of a therapeutic protein that is able to kill cancer cells specifically.&lt;/em&gt;&lt;/p&gt;
Comparison of Antenna Types and Orientations for Detecting Hydrocarbon Layers in Seabed Logging (2007)

In seabed logging applications, only three types of sources: VED, HED-R (in-line) and HMD-P (cross line) are sensitive in detecting the target — a thin horizontal hydrocarbon layer. The other three types of the sources: VMD, HED-P (cross line), HMD-R are not sensitive in detecting the target. DOI: 10.2529/PIERS060905055727
Grasp-specific high-frequency broadband mirror neuron activity during reach-and-grasp movements in humans (2022)

Broadly congruent mirror neurons, responding to any grasp movement, and strictly congruent mirror neurons, responding only to specific grasp movements, have been reported in single-cell studies with primates. Delineating grasp properties in humans is essential to understand the human mirror neuron system with implications for behavior and social cognition. We analyzed electrocorticography data from a natural reach-and-grasp movement observation and delayed imitation task with 3 different natural grasp types of everyday objects. We focused on the classification of grasp types from high-frequency broadband mirror activation patterns found in classic mirror system areas, including sensorimotor, supplementary motor, inferior frontal, and parietal cortices. Classification of grasp types was successful during movement observation and execution intervals but not during movement retention. Our grasp type classification from combined and single mirror electrodes provides evidence for grasp-congruent activity in the human mirror neuron system potentially arising from strictly congruent mirror neurons.
Radioimmunoassay for human myoglobin: methods and results in patients with skeletal muscle or myocardial disorders. (1978)

This paper is concerned with the diffraction of an electromagnetic wave by a unidirectionally conducting circular disk.\nFirst, the behavior of a time-harmonic electromagnetic field near the edge of an arbitrary plane unidirectionally conducting screen is determined from the condition that the energy density must be integrable over any finite domain.\nSecondly, the problem of the diffraction of an arbitrary time-harmonic electromagnetic wave by a plane unidirectionally conducting circular disk is treated for the low-frequency case, i.e., the product $ka$ of the wave number $k$ and the disk radius $a$ is small. Expansions in powers of $ka$ are derived for the far field, the scattered energy and the field on the disk. Some special results for the case of plane-wave excitation are presented.
Soft breakdown in ultrathin gate oxides: Correlation with the percolation theory of nonlinear conductors (1998)

The dielectric breakdown under constant current stressing of 4.2 nm SiO2 gate oxides is investigated. After soft breakdown, which corresponds to an anomalous increase of the stress-induced leakage current of metal–oxide–semiconductor capacitors, the current behaves like a power law of the applied gate voltage VG. After soft breakdown, charge is further injected into the SiO2 layer in order to extract the effective resistivity ρeff of the system as a function of the density of oxide traps D generated in the layer. It is found that ρeff behaves like a power law of (D−Dc) where Dc is the critical density of traps generated at soft breakdown. These results are in fair agreement with the predictions of the percolation theory of nonlinear conductor networks. Besides, the value of the critical exponent related to the resistivity is close to the one expected in two dimensions.
Biomechanical Analysis of Experimental Diffuse Axonal Injury (1995)

The purpose of this paper is to present results from methodologies used in our laboratory that are targeted toward identifying specific brain injury thresholds. Results from studying one form of brain injury, diffuse axonal injury, are presented in this report. Physical models, or surrogates, of the skull-brain complex are used to estimate the relationship between inertial loading and brain deformation. A porcine model of diffuse axonal injury, developed with information from these physical models and earlier in vitro tissue modeling studies, is used to correlate histologic and radiologic evidence of axonal injury to predicted regions of injury from the experimental and theoretical analysis. These results form the basis for developing improved diffuse brain injury tolerance levels, as well as identifying new means of diagnostic and treatment techniques for diffuse axonal injury.
Apolipoprotein D Gene Polymorphism: A New Genetic Marker for Type 2 Diabetic Subjects in Nauru and South India (1994)

Type 2 diabetes is characterized by abnormalities in both glucose and lipoprotein metabolism and genes involved in lipid metabolism are legitimate candidates for involvement in Type 2 diabetes. We have previously reported an association in Nauruans between a Taq 1 polymorphism of the apolipoprotein D gene (apo D) and Type 2 diabetes. In this study these findings were investigated further in the Nauruan population as well as two other ethnic groups. In South Indian subjects, there was a significant difference in genotype distribution of apo D genotypes between diabetic subjects (n = 110) and controls (n = 88; p = 0.004) which was similar to that previously found in the Nauruan subjects. No such association was seen in elderly Finnish subjects (diabetic n = 69; impaired glucose tolerance n = 26 and normal glucose tolerance n = 31). Linkage between the apo D polymorphism and diabetes in 12 Nauruan families was only excluded under a highly penetrant dominant model and was unlikely under other single gene models. Since the beta cell glucose transporter gene (Glut 2) is found in a similar chromosomal location to apo D, South Indian subjects (diabetic n = 95 and controls n = 56) were typed at this locus. No association between diabetes and the Glut 2 Taq I polymorphism was found in the South Indian subjects. Furthermore, there was no evidence of linkage disequilibrium between the apo D and Glut 2 genes. In conclusion, apo D might act as a modifying gene for Type 2 diabetes in some ethnic groups.