gebhart/patrepeval huggingface dataset:
A finite element model for 3D shape reconstruction and nonrigid motion tracking (2002)

The authors present a physics-based approach for recovering the 3-D shape and tracking the motion of nonrigid objects using a 3-D elastically deformable balloon model. The balloon model is based on a thin-plate under tension spline which deforms to fit visual data according to internal forces stemming from the elastic properties of the surface and external forces which are produced from the data. The finite element method is used to represent the model as a continuous surface. A natural finite element is used whose nodal variables comprise the position of the surface plus its first and second partial derivatives, reflecting each of the partial derivatives that occur in the spline's strain energy functional. Hence, the model directly estimates all the information needed to measure the differential geometric properties of the fitted surface. The balloon model was applied to the reconstruction of 3-D objects with irregular shape features. Its effectiveness is demonstrated in extracting the left ventricular surface and tracking its nonrigid motion in dynamic computerized tomography volume images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Determination of natural frequencies and mode shapes of a wind turbine rotor blade using Timoshenko beam elements (2019)

Abstract. When simulating a wind turbine, the lowest eigenmodes of the rotor blades are usually used to describe their elastic deformation in the frame of a multi-body system. In this paper, a finite element beam model for the rotor blades is proposed which is based on the transfer matrix method. Both static and kinetic field matrices for the 3-D Timoshenko beam element are derived by the numerical integration of the differential equations of motion using a Runge–Kutta fourth-order procedure. In the general case, the beam reference axis is at an arbitrary location in the cross section. The inertia term in the motion differential equation is expressed using appropriate shape functions for the Timoshenko beam. The kinetic field matrix is built by numerical integration applied on the approximated inertia term. The beam element stiffness and mass matrices are calculated by simple matrix operations from both field matrices. The system stiffness and mass matrices of the rotor blade model are assembled in the usual finite element manner in a global coordinate system accounting for the structural twist angle and possible pre-bending. The program developed for the above-mentioned calculations and the final solution of the eigenvalue problem is accomplished using MuPAD, a symbolic math toolbox in MATLAB®. The natural frequencies calculated using generic rotor blade data are compared with the results proposed from the FAST and ADAMS software.
Selective One-Step Synthesis of Dimethoxymethane via Methanol or Dimethyl Ether Oxidation on H<sub>3+<i>n</i></sub>V<i><sub>n</sub></i>Mo<sub>12-<i>n</i></sub>PO<sub>40</sub> Keggin Structures (2003)

The one-step selective synthesis of dimethoxymethane (DMM; CH3OCH2OCH3) was achieved by oxidation of dimethyl ether (DME) or methanol (CH3OH) with O2 at low temperatures (453-513 K) on unsupported and SiO2-supported heteropolyacids with Keggin structures [H3+nPVnMo12-nO40 (n) 0-4)]. These materials provide redox and Brönsted acid sites required for bifunctional DMM synthesis pathways. Supported structures at submonolayer coverages (0.1-0.28 Keggin units per nm2) are much more accessible than bulk structures and remove diffusional constraints. Their higher dispersions lead to marked improvements in DMM synthesis rates and selectivities and to lower COx yields using either CH3OH or DME reactants. The presence of H2O during DME oxidation increases DMM synthesis rates because of a consequent increase in the rate of DME hydrolysis reactions, which form CH3OH molecules required as intermediates in the DMM synthesis reaction sequence. Pure CH3OH reactants form DMM at much higher rates than DME reactants. The replacement of some Mo atoms in H3PMo12O40 structures with V increases DMM synthesis rates and selectivities while inhibiting the formation of COx. In fact, COx was not detected on H3+nPVnMo12-nO40 (n) 2, 4; 0.1 KU/ nm2) even at high CH3OH conversions (50%). CH3OH converts to DMM via primary CH3OH reactions to form formaldehyde (HCHO) and subsequent secondary reactions of HCHO with CH3OH in steps requiring both redox and acid sites; CH3OH also reacts to form DME on acid sites. These pathways are consistent with
The choice between two distinct T cell determinants within a 23-amino acid region of lysozyme depends on their structural context. (1986)

The specificity of C57BL/6 T cells reactive to peptide aa 74-96 of hen egg-white lysozyme (HEL) was analyzed by using a panel of synthetic peptides of varying lengths from this region. It was found that peptide 74-96-reactive T cells induced by native HEL (aa 1-129) or its denatured fragment L2 (aa 13-105) recognized two distinct but overlapping determinants contained within aa 74-90 or aa 81-96, respectively. Peptide 74-96 itself induced both peptide 74-90-and peptide 81-96-specific T cells. Thus, a choice was made between these two potential T cell determinants on peptide 74-96, depending on which immunogen was used. Interestingly, the ability of both peptide determinants aa 74-90 and aa 81-96 to stimulate peptide 74-96-reactive T cells was partly dependent on the presence of residues within the overlap region (aa 81-90), suggesting that this region may play an important role in Iab-restricted T cell activation. This was further supported by the poor immunogenicity of shorter peptides 74-86 or 85-96, lacking residues from the overlap region in B6 mice. These two short peptides were nevertheless capable of eliciting T cell responses in B10.A mice, suggesting that the importance of this overlap region in obtaining a response to peptide 74-96 is related to the MHC haplotype.
Magnetite nanoparticles for cancer diagnosis, treatment, and treatment monitoring: recent advances (2015)

The development of nanoparticles (NPs) for use in all facets of oncological disease detection and therapy has shown great progress over the past two decades. NPs have been tailored for use as contrast enhancement agents for imaging, drug delivery vehicles, and most recently as a therapeutic component in initiating tumor cell death in magnetic and photonic ablation therapies. Of the many possible core constituents of NPs, such as gold, silver, carbon nanotubes, fullerenes, manganese oxide, lipids, micelles, etc., iron oxide (or magnetite) based NPs have been extensively investigated due to their excellent superparamagnetic, biocompatible, and biodegradable properties. This review addresses recent applications of magnetite NPs in diagnosis, treatment, and treatment monitoring of cancer. Finally, some views will be discussed concerning the toxicity and clinical translation of iron oxide NPs and the future outlook of NP development to facilitate multiple therapies in a single formulation for cancer theranostics.
Utilization of Heterologous Siderophores Enhances Levels of Iron Available to <i>Pseudomonas putida</i> in the Rhizosphere (1999)

Pseudomonas spp. have the capacity to utilize siderophores produced by diverse species of bacteria and fungi, and the present study was initiated to determine if siderophores produced by rhizosphere microorganisms enhance the levels of iron available to a strain of Pseudomonas putida in this natural habitat. We used a previously described transcriptional fusion (pvd-inaZ) between an iron-regulated promoter (pvd) and the ice nucleation reporter gene (inaZ) to detect alterations in iron availability to P. putida. Ice nucleation activity (INA) expressed from the pvd-inaZ fusion by P. putida N1R or N1R Pvd(-), a derivative deficient in the production of a pyoverdine siderophore, was inversely related to the concentration of ferric citrate in a culture medium. In culture, INA expressed by N1R Pvd(-) (pvd-inaZ) was reduced in the presence of the ferric complex of pseudobactin-358, a pyoverdine siderophore produced by P. putida WCS358 that can be utilized as a source of iron by N1R Pvd(-). In the rhizosphere of cucumbers grown in sterilized soil, N1R Pvd(-) (pvd-inaZ) expressed INA, indicating that iron availability was sufficiently low in that habitat to allow transcription of the iron-regulated pvd promoter. Coinoculation with WCS358 or N1R significantly decreased INA expressed by N1R Pvd(-) (pvd-inaZ) in the rhizosphere, whereas coinoculation with a pyoverdine-deficient mutant of WCS358 did not reduce INA expressed by N1R Pvd(-) (pvd-inaZ). These results indicate that iron availability to N1R Pvd(-) (pvd-inaZ) in the rhizosphere was enhanced by the presence of another strain of P. putida that produces a pyoverdine that N1R Pvd(-) (pvd-inaZ) was able to utilize as a source of iron. In culture, strain N1R Pvd(-) also utilized ferric complexes of the siderophores enterobactin and aerobactin as sources of iron. In the rhizosphere of cucumbers grown in sterilized soil, INA expressed by N1R Pvd(-) (pvd-inaZ) was reduced in the presence of strains of Enterobacter cloacae that produced enterobactin, aerobactin, or both siderophores, but INA expressed by N1R Pvd(-) (pvd-inaZ) was not altered in the presence of a mutant of E. cloacae deficient in both enterobactin and aerobactin production. Therefore, the iron status of P. putida was altered by siderophores produced by an unrelated bacterium coinhabiting the rhizosphere. Finally, we demonstrated that INA expressed by N1R containing pvd-inaZ in the rhizosphere differed between plants grown in sterilized versus nonsterilized field soil. The results of this study demonstrate that (i) P. putida expresses genes for pyoverdine production and uptake in the rhizosphere, but the level of gene expression is influenced by other bacteria that coexist with P. putida in this habitat, and (ii) diverse groups of microorganisms can alter the availability of chemical resources in microbial habitats on root surfaces.
The Role of 5-HT Dysregulation in Inflammatory Bowel Disease. (2013)

Thegut is the largest producer of serotonin—that is, 5-hydroxytryptamine (5-HT)—in the body. About 95% of the body’s 5-HT is located in the gut, and entero-chromaffin(EC) cells are its main source. 5-HT is an important enteric signaling molecule that influencesgut physiology. 5-HT plays a vital role in intestinal secretion, sensation, and peristalsis. Recent research suggests that 5-HT can act as a proinflammatorymolecule and can modulate immune cell function in the gut.
<title>CORDIC algorithms in four dimensions</title> (1990)

CORDIC algorithms offer an attractive alternative to multiply-and-add based algorithms for the implementation of two-dimensional rotations preserving either norm: (x2 + 2) or (x2 _ y2)/2 Indeed these norms whose computation is a significant part of the evaluation of the two-dimensional rotations are computed much more easily by the CORDIC algorithms. However the part played by norm computations in the evaluation of rotations becomes quickly small as the dimension of the space increases. Thus in spaces of dimension 5 or more there is no practical alternative to multiply-and-add based algorithms. In the intermediate region dimensions 3 and 4 extensions of the CORDIC algorithms are an interesting option. The four-dimensional extensions are particularly elegant and are the main object of this paper.
Bacterial Small RNA-based Negative Regulation: Hfq and Its Accomplices (2013)

A large group of bacterial small regulatory RNAs (sRNAs) use the Hfq chaperone to mediate pairing with and regulation of mRNAs. Recent findings help to clarify how Hfq acts and highlight the role of the endonuclease RNase E and its associated proteins (the degradosome) in negative regulation by these sRNAs. sRNAs frequently uncouple transcription and translation by blocking ribosome access to the mRNA, allowing other proteins access to the mRNA. As more examples of sRNA-mediated regulation are studied, more variations on how Hfq, RNase E, and other proteins collaborate to bring about sRNA-based regulation are being found.
Atacicept, a homodimeric fusion protein for the potential treatment of diseases triggered by plasma cells. (2008)

Atacicept (TACI:Fc5) is a homodimeric fusion protein obtained through recombinant DNA technology being developed by Merck Serono SA, under license from ZymoGenetics Inc, for the potential treatment of B-cell diseases. Atacicept is undergoing phase II/III clinical trials for systemic lupus erythematosus, lupus nephritis, rheumatoid arthritis, multiple sclerosis, as well as for several B-cell malignancies.
Colorization of H&E stained tissue using Deep Learning (2018)

Histopathology is a critical tool in the diagnosis and stratification of cancer. Digital Pathology involves the scanning of stained and fixed tissue samples to produce highresolution images that can be used for computer-aided diagnosis and research. A common challenge in digital pathology related to the quality and characteristics of staining, which can vary widely from center to center and also within the same institution depending on the age of the stain and other human factors. In this paper we examine the use of deep learning models for colorizing H&E stained tissue images and compare the results with traditional image processing/statistical approaches that have been developed for standardizing or normalizing histopathology images. We adapt existing deep learning models that have been developed for colorizing natural images and compare the results with models developed specifically for digital pathology. Our results show that deep learning approaches can standardize the colorization of H&E images. The performance as measured by the chi-square statistic shows that the deep learning approach can be nearly as good as current state-of-the art normalization methods.
Distinct roles for extracellular-signal-regulated protein kinase (ERK) mitogen-activated protein kinases and phosphatidylinositol 3-kinase in the regulation of Mcl-1 synthesis (2001)

Alterations in the expression of various Bcl-2 family members may act as one means by which a cell's survival may be regulated. The mechanism by which cytokines regulate expression of Bcl-2 family members was examined in the haemopoietic cell line TF-1. Cytokine-induced Mcl-1 protein expression was shown to be controlled through a pathway dependent upon phosphatidylinositol 3-kinase (PI 3-kinase). The cytokine-induced increase in mRNA transcription was not dependent upon PI 3-kinase, thus dissociating the immediate-early transcription factors responsible for Mcl-1 transcription from the PI 3-kinase signalling pathway. In contrast, Mcl-1 mRNA levels were dependent upon MEK [mitogen-activated protein kinase (MAPK)/extracellular-signal-regulated protein kinase kinase] activation, suggesting a role for the Ras/MEK/MAPK pathway in Mcl-1 transcription. Activation of PI 3-kinase was shown to be necessary to stimulate Mcl-1 protein translation. This was not due to any effect on prolonging the half-life of the protein. Finally, the lipid second messenger ceramide was shown to cause a reduction in Mcl-1 protein translation, probably via its ability to inhibit protein kinase B activation, providing further clues regarding the death-inducing effect of this lipid.
Efficient Arrival Management Utilizing ATC and Aircraft Automation (2000)

In this paper we present an airspace capacity research project at NASA’s Ames and Langley Research Centers within the Terminal Area Productivity program, TAP. We describe an application area that deals with arrival traffic management and control in a 2010 time frame. We investigate utilizing and integrating air traffic control and aircraft automation. We address potential benefits and limitations and initial observations gathered from several controllers and pilots in the loop simulations.
Use of Electrical Power in Control of Wax and Hydrates (1997)

Abstract Electrical heating of subsea flowlines represents an effective method to prevent wax and hydrate formations, especially at long transportation distances and in deep waters with a low seabed temperature. Such systems are available to be used in conjunction with bundles, pipe-in-pipe and wet thermal insulation systems, enabling an environmental friendly fluid temperature control without use of chemicals and flaring for pipeline depressurizing. Enhanced production availability is achieved as no time is lost by unnecessary de-pressurizing, pigging, heating medium circulation or removal of hydrate and wax blockages. Introduction The seabed temperature at 100 m water depth and lower may range from 7 °C to -1.5° C, causing a rapid cooling of hot well streams being transported in subsea flowlines, see Fig. 1. Vulnerable crudes and multiphase compositions will at such super cooling deposit wax and asphalts, and the gas - water phase may freeze solid hydrate particles that can permanently block the pipeline. A conventional approach to secure a safe subsea transportation has been to use thermal insulated flowlines in combination with the following measures:Continuous injection of chemicals to reduce the hydrate freezing point and the rate of wax deposition.Depressurization of the flowline to enable a further reduction of the hydrate freezing-point.Use of twin parallel flowlines to achieve a more effective depressurizating of potential hydrate plugs, and to perform pig cleaning operations. Further to circulate hot waterloil in order to melt out wax and to pre-warm the flowlines after long lasting shut downs. It is obvious that these measures do have physical, economical and environmental limitations especially in deeper waters and over very long transportation distances:The pressure head in deep water pipelines may give an insufficient pressure relieve at blow downs.Blow down and pressurisation of pipelines will involve pressure drop expansions and a related Joule-Thomson supercooling of multiphase fluids, that by itself can cause severe wax deposits and hydrate plugs.Heat loss in long twin pipelines that shall be preheated in a serial configuration, will restrict adequate heating above 10-15 km length.Continuous injection of large amounts of hydrate and wax inhibitors will dissolve in the produced water that may have a restricted release to sea.Long twin flowline installations will generate high investment and operational costs. Thermal insulated and electrically heated flowlines represent an alternative prevention method for wax and hydrates that will not be restricted with the same limitations. A market review of different designs and functional principles conclude that electrical heating technology is available for flexible risers and flowlines, pipelines, pipe-in-pipe and bundle systems for all practical lengths in subsea transportation. Some of these have been in operation with a satisfactory performance over a period of more than 20 years.
Solid-state Electrochemical Stamping of Functional Metallic Nanostructures (2007)

A new approach of directly patterning metal at nano-scale with excellent dimensional resolution and flexibility is introduced for fabrication of functional nano-structures. This technique is based on the solid-state electrochemical dissolution of a metallic substrate at its contact with a pre-patterned surface of a solid electrolyte tool, and the subsequent formation of the complimentary pattern on the metal substrate as the solid electrolyte etches through the metal layer. Our results demonstrate repeatable and high-fidelity patterning of metal structures with a wide dimension range (20μm to 50nm). As this process is carried out in ambient environment and does not require wet chemicals, its potential for use as a simple and yet high-throughput metal patterning technique offers a highly competitive approach to fabricating functional structures and devices such as chemical sensors and photonic devices.
Pathogenesis of Borna Disease Virus: Granulocyte Fractions of Psychiatric Patients Harbor Infectious Virus in the Absence of Antiviral Antibodies (1999)

Borna disease virus (BDV) causes acute and persistent infections in various vertebrates. During recent years, BDV-specific serum antibodies, BDV antigen, and BDV-specific nucleic acid were found in humans suffering from psychiatric disorders. Furthermore, viral antigen was detected in human autopsy brain tissue by immunohistochemical staining. Whether BDV infection can be associated with psychiatric disorders is still a matter of debate; no direct evidence has ever been presented. In the present study we report on (i) the detection of BDV-specific nucleic acid in human granulocyte cell fraction from three different psychiatric patients and (ii) the isolation of infectious BDV from these cells obtained from a patient with multiple psychiatric disorders. In leukocyte preparations other than granulocytes, either no BDV RNA was detected or positive PCR results were obtained only if there was at least 20% contamination with granulocytes. Parts of the antigenome of the isolated virus were sequenced, demonstrating the close relationship to the prototype BDV strains (He/80 and strain V) as well as to other human virus sequences. Our data provide strong evidence that cells in the granulocyte fraction represent the major if not the sole cell type harboring BDV-specific nucleic acid in human blood and contain infectious virus. In contrast to most other reports of putative human isolates, where sequences are virtually identical to those of the established laboratory strains, this isolate shows divergence in the region previously defined as variable in BDV from naturally infected animals.
Cold crucible induction casting of semiconductor silicon for solar cell (2002)

Cold-crucible induction casting of silicon for solar cell material was performed. In the casting, molten silicon was heated and pinched electromagnetically, allowing the metal to avoid contact with the crucible wall. Hence, impurities were prevented and crucible consumption was unnecessary. The cold crucible used was an open-bottom type, having an 85 mm*85 mm cross section. The silicon material was fed continuously from the open top of the crucible, and the ingot was pulled down at a rate of 1.0 to 4.0 mm/min. Solar cell efficiencies above 13% were obtained, equal to conventional mold methods using cast silicon.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis and properties of chiral stilbene diacrylates (2003)

Two chiral and isomerizable liquid crystalline diacrylates were synthesized. The purpose of these compounds was to tune the helical twisting power of cholesteric materials containing these compounds by means of an E–Z photoisomerization of the photoactive group derived from stilbene. The photochemical behaviour of these compounds was studied with the aid of two model compounds containing the same isomerizable mesogenic group. The mesogenic group derived from 4-(4-hydroxybenzoyloxy)-4′-hydroxystilbene decomposes upon irradiation. Its isomer, derived from 4-(4-hydroxyphenoxycarbonyl)-4′-hydroxystilbene, shows a clean E–Zisomerization. The HTP of the chiral diacrylate derived from the latter mesogenic group changes from 7 to 3 μm-1 in dilute nematic solution. Colour changes in a cholesteric material containing this compound were observed. The effect was very dependent on temperature and concentration due to the strong smectic character of this diacrylate.