gebhart/patrepeval huggingface dataset:
Levels of detail (LOD) engineering of VR objects (1999)

For real-time performance, virtual reality systems often employ various performance optimization techniques. One of the most popular methods is using geometric models with different “Levels of Detail (LOD)”. In a previous paper by this author [1], we have proposed to use software engineering principles such as the concept of hierarchical and incremental modeling, and simultaneous consideration of form, function and behavior for modeling VR objects. Each refinement stage driven by such a modeling philosophy produces step-by-step form, function and behavior specifications of a VR object. We can make good use of these by-products as LOD for adaptive display and simulation by additionally specifying conditions for LOD switching. These specifications can be simulated and analyzed in advance for an estimation of performance for a given VR execution environment. Such an engineering process deals with behavior and geometry together; different geometric LOD may possess different behaviors and vice versa. A certain function or behavior might dictate an inclusion of a particular geometric feature that may not be possible to preserve, if the geometric LOD were to created in a bottom-up fashion (e.g. using the mesh simplification algorithms). We demonstrate our approach by modeling an automobile object with three levels of geometric and behavior detail in a top-down manner, simulate their instances in a small virtual town, and based on the simulation result, make predictions to the maximum allowable number of vehicles that will maintain an acceptable frame rate if executed in a faster simulation environment. We believe that our approach combines the idea of hierarchical refinement of virtual objects and the use of LOD in a very natural and intuitive manner.
ChemInform Abstract: DEGRADATION OF 1,2‐DIHYDRO‐1‐HYDROXY‐2‐(ORGANOSULFONYL)‐2,3,1‐BENZODIAZABORINES AND ‐THIENO(3,2‐D)(1,2,3)DIAZABORINES IN ALKALINE AQUEOUS SOLUTION (1985)

Abstract Die Hydrolyse der Benzodiazaborine (IV) mit heißer Natronlauge führt zu den Hydroxy‐benz‐ ‐oxaborolen‐(′V), die oxidativ zu den Hydroxy‐benzylalkoholen (VI) gespalten werden.
A Mass Spectrometric-Derived Cell Surface Protein Atlas (2015)

Cell surface proteins are major targets of biomedical research due to their utility as cellular markers and their extracellular accessibility for pharmacological intervention. However, information about the cell surface protein repertoire (the surfaceome) of individual cells is only sparsely available. Here, we applied the Cell Surface Capture (CSC) technology to 41 human and 31 mouse cell types to generate a mass-spectrometry derived Cell Surface Protein Atlas (CSPA) providing cellular surfaceome snapshots at high resolution. The CSPA is presented in form of an easy-to-navigate interactive database, a downloadable data matrix and with tools for targeted surfaceome rediscovery (http://wlab.ethz.ch/cspa). The cellular surfaceome snapshots of different cell types, including cancer cells, resulted in a combined dataset of 1492 human and 1296 mouse cell surface glycoproteins, providing experimental evidence for their cell surface expression on different cell types, including 136 G-protein coupled receptors and 75 membrane receptor tyrosine-protein kinases. Integrated analysis of the CSPA reveals that the concerted biological function of individual cell types is mainly guided by quantitative rather than qualitative surfaceome differences. The CSPA will be useful for the evaluation of drug targets, for the improved classification of cell types and for a better understanding of the surfaceome and its concerted biological functions in complex signaling microenvironments.
Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns (2017)

Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer. We analyzed the coverage spectrum of the human genome in our cfDNA samples. cfDNA exhibited no large regions with significant under-coverage, although we observed unbalanced coverage depth in cfDNA at transcription start sites and exon boundaries as a consequence of biased fragmentation due to ordered nucleosome positioning. We also analyzed the copy number variant status based on the whole-genome sequencing results and found high similarity between copy number profile constructed from tumor samples and cfDNA samples. Overall, we conclude that cfDNA comprises a good representation of the tumor genome in late stage gastric and lung cancer.
Restauración de la Tabla de San Esteban y los Apóstoles atribuida al autor gótico Joan Rexach (1990)

A strain of Plasmodium falciparum from a Montagnard refugee was shown to produce large numbers of gametocytes in culture. Attempts were made to establish this strain in Aotus monkeys via trophozoite and sporozoite inoculation. The Montagnard S-1 strain was readily adapted to A. l. griseimembra monkeys via trophozoite inoculation. Other species of Aotus failed to support the development of high density parasitemia. None of 12 attempts to transmit the infection via sporozoites from Anopheles freeborni or An. dirus mosquitoes was successful; however, developing exoerythrocytic stages were demonstrated in hepatocytes of an A. lemurinus griseimembra monkey.
MEMS accelerometer based low-cost collision impact analyzer (2016)

Accident impact analysis helps to minimize losses such as death, injuries and property damage due to vehicle collision on road. An efficient impact analyzer is capable of accumulating and processing large amount of data very quickly. Hardware and software both plays important role to collect, process and store large amount of data within a very short period of time. MEMS accelerometers are cost effective and offer better performance with high functionalities compared to conventional piezoelectric accelerometers. The purpose of this paper is to conduct in-depth analyses of low-cost impact analyzer. Hardware and software consideration to implement a low cost impact analyzer (LCIA) are discussed. To simulate the accident, the system has been dropped from a certain height. With time-stamp, the tested data was recorded into microSD card and later the data was analyzed in computer and discussed.
Laboratory Permeability and Diffusivity Measurements of Unconventional Reservoirs: Useless or Full of Information? A Montney Example from the Western Canada Sedimentary Basin (2013)

Abstract Permeability is one of the most critical parameters characterizing unconventional (shale or tight) gas and oil reservoirs for resource evaluation and exploitation. Permeability is also perhaps the most difficult parameter to be accurately characterized because it is not just a single number but a complicate property with attributes that depend on many factors (namely sampling or testing scale, pore shape and size and distribution, different transport mechanisms, different test fluids, pore pressure, effective stress, and even temperature). Laboratory permeability measurements are mainly conducted on cores or smaller samples. The size and scale of laboratory measurements are hence severely limited as compared to the meters or kilometers scale of exploration or producing fields. Even in the scale of centimeters or less, for the same core samples, laboratory measurements likely yield variable permeability spanning several orders of magnitudes, leading to seemingly useless laboratory permeability for field applications. In this study, using samples from the Montney Formation in the Western Canada Sedimentary Basin as an example, we first present contrasting laboratory permeability measurements with different methods or experimental conditions. Explanations to the seemingly contradictory permeability measurements are then provided in context of different transport modes in highly heterogeneous microporous unconventional reservoir rocks, highlighting that the contrast laboratory measurements are not useless but full of information for understanding the complex characteristics of microporous unconventional rocks. Appropriate experiments to determine the appropriate permeability and their application to field problems are also discussed, which is helpful for petroleum geologists and engineers to better understand the unique permeability system of unconventional reservoirs and hence to make optimal decisions for successful unconventional resource exploitation.
Formation and Stability of Nano-Emulsions Prepared Using the Phase Inversion Temperature Method (2001)

Formation of O/W nano-emulsions has been studied in water/C̄12Ē4/oil systems by the phase inversion temperature emulsification method. Emulsification was carried out at the corresponding HLB (hydrophilic-lipophilic balance) temperature, and then the emulsions were cooled fast to 25 °C. The influence of surfactant concentration and oil solubility on HLB temperature, nano-emulsion droplet size, and stability has also been studied. Droplet size was determined by dynamic light scattering, and nano-emulsion stability was assessed, measuring the variation of droplet size as a function of time. The results obtained showed that the breakdown process of nano-emulsions studied could be attributed to Ostwald ripening. An increase of nano-emulsion instability with the increase in surfactant concentration and oil solubility was also found.
Cholesterol Is an Important Factor Affecting the Membrane Insertion of β-Amyloid Peptide (Aβ1–40), Which May Potentially Inhibit the Fibril Formation (2002)

beta-Amyloid peptide (A beta), a normal constituent of neuronal and non-neuronal cells, has been proven to be the major component of extracellular plaque of Alzheimer's disease. Interactions between A beta and neuronal membranes have been postulated to play an important role in the neuropathology of Alzheimer's disease. Here we show that A beta is able to insert into lipid bilayer. The membrane insertion ability of A beta is critically controlled by the ratio of cholesterol to phospholipids. In a low concentration of cholesterol A beta prefers to stay in membrane surface region mainly in a beta-sheet structure. In contrast, as the ratio of cholesterol to phospholipids rises above 30 mol%, A beta can insert spontaneously into lipid bilayer by its C terminus. During membrane insertion A beta generates about 60% alpha-helix and removes almost all beta-sheet structure. Fibril formation experiments show that such membrane insertion can reduce fibril formation. Our findings reveal a possible pathway by which A beta prevents itself from aggregation and fibril formation by membrane insertion.
The Clinical Utilization of Circulating Cell Free DNA (CCFDNA) in Blood of Cancer Patients (2013)

Qualitative and quantitative testing of circulating cell free DNA (CCFDNA) can be applied for the management of malignant and benign neoplasms. Detecting circulating DNA in cancer patients may help develop a DNA profile for early stage diagnosis in malignancies. The technical issues of obtaining, using, and analyzing CCFDNA from blood will be discussed.
Targeting Antibody Responses to the Membrane Proximal External Region of the Envelope Glycoprotein of Human Immunodeficiency Virus (2012)

Although human immunodeficiency type 1 (HIV-1) infection induces strong antibody responses to the viral envelope glycoprotein (Env) only a few of these antibodies possess the capacity to neutralize a broad range of strains. The induction of such antibodies represents an important goal in the development of a preventive vaccine against the infection. Among the broadly neutralizing monoclonal antibodies discovered so far, three (2F5, Z13 and 4E10) target the short and hidden membrane proximal external region (MPER) of the gp41 transmembrane protein. Antibody responses to MPER are rarely observed in HIV-infected individuals or after immunization with Env immunogens. To initiate antibody responses to MPER in its membrane-embedded native conformation, we generated expression plasmids encoding the membrane-anchored ectodomain of gp41 with N-terminal deletions of various sizes. Following transfection of these plasmids, the MPER domains are displayed on the cell surface and incorporated into HIV virus like particles (VLP). Transfected cells displaying MPER mutants bound as efficiently to both 2F5 and 4E10 as cells transfected with a plasmid encoding full-length Env. Mice immunized with VLPs containing the MPER mutants produced MPER-specific antibodies, the levels of which could be increased by the trimerization of the displayed proteins as well as by a DNA prime-VLP boost immunization strategy. Although 2F5 competed for binding to MPER with antibodies in sera of some of the immunized mice, neutralizing activity could not be detected. Whether this is due to inefficient binding of the induced antibodies to MPER in the context of wild type Env or whether the overall MPER-specific antibody response induced by the MPER display mutants is too low to reveal neutralizing activity, remains to be determined.
Inhibition of colony-stimulating-factor-1 signalingin vivowith the orally bioavailable cFMS kinase inhibitor GW2580 (2005)

Colony-stimulating-factor-1 (CSF-1) signaling through cFMS receptor kinase is increased in several diseases. To help investigate the role of cFMS kinase in disease, we identified GW2580, an orally bioavailable inhibitor of cFMS kinase. GW2580 completely inhibited human cFMS kinase in vitro at 0.06 microM and was inactive against 26 other kinases. GW2580 at 1 microM completely inhibited CSF-1-induced growth of mouse M-NFS-60 myeloid cells and human monocytes and completely inhibited bone degradation in cultures of human osteoclasts, rat calvaria, and rat fetal long bone. In contrast, GW2580 did not affect the growth of mouse NS0 lymphoblastoid cells, human endothelial cells, human fibroblasts, or five human tumor cell lines. GW2580 also did not affect lipopolysaccharide (LPS)-induced TNF, IL-6, and prostaglandin E2 production in freshly isolated human monocytes and mouse macrophages. After oral administration, GW2580 blocked the ability of exogenous CSF-1 to increase LPS-induced IL-6 production in mice, inhibited the growth of CSF-1-dependent M-NFS-60 tumor cells in the peritoneal cavity, and diminished the accumulation of macrophages in the peritoneal cavity after thioglycolate injection. Unexpectedly, GW2580 inhibited LPS-induced TNF production in mice, in contrast to effects on monocytes and macrophages in vitro. In conclusion, GW2580's selective inhibition of monocyte growth and bone degradation is consistent with cFMS kinase inhibition. The ability of GW2580 to chronically inhibit CSF-1 signaling through cFMS kinase in normal and tumor cells in vivo makes GW2580 a useful tool in assessing the role of cFMS kinase in normal and disease processes.
A non-covalent peptide-based carrier for in vivo delivery of DNA mimics (2007)

The dramatic acceleration in identification of new nucleic-acid-based therapeutic molecules has provided new perspectives in pharmaceutical research. However, their development is limited by their poor cellular uptake and inefficient trafficking. Here we describe a short amphipathic peptide, Pep-3, that combines a tryptophan/phenylalanine domain with a lysine/arginine-rich hydrophilic motif. Pep-3 forms stable nano-size complexes with peptide-nucleic acid analogues and promotes their efficient delivery into a wide variety of cell lines, including primary and suspension lines, without any associated cytotoxicity. We demonstrate that Pep-3-mediated delivery of antisense-cyclin B1-charged-PNA blocks tumour growth in vivo upon intratumoral and intravenous injection. Moreover, we show that PEGylation of Pep-3 significantly improves complex stability in vivo and consequently the efficiency of antisense cyclin B1 administered intravenously. Given the biological characteristics of these vectors, we believe that peptide-based delivery technologies hold a true promise for therapeutic applications of DNA mimics.
Flux Measurements across Caco-2 Monolayers May Predict Transport in Human Large Intestinal Tissue (1996)

Confluent monolayers of Caco-2 cells, a human colonic carcinoma cell line, have been used extensively to predict intestinal absorption. A direct comparison of uptake characteristics, however, between cell monolayers and human tissue is missing in the literature. We have determined the flux for a series of small organic molecules, peptide and protein therapeutics, across Caco-2 monolayers and normal human colonic and rectal tissue in vitro to assess whether or not a predictive correlation of transport exists. Caco-2 cells were grown to confluency of Snapwells, and human tissue was obtained from patients undergoing surgery for localized tumors. Mucosa-serosa fluxes were measured by HPLC for small molecules and peptides, and proteins were analyzed by ELISA or RIA. Permeability coefficients were calculated from flux data and compared with previously published coefficients where possible. The permeability coefficients for the examined molecules were of a similar magnitude across Caco-2 cell monolayers and human tissues, ranging from 10(-7) to 10(-5) cm/s. A best-fit analysis of a log-log plot of transport measurements obtained in these two systems gave a good correlation (R2 = 0.991). From this limited data set it appears that uptake characteristics for human colon and rectum are similar to those of Caco-2 cell monolayers. Thus, flux measurements across Caco-2 monolayers may be predictive for permeabilities of human colon and rectum for different classes of therapeutics.
Statistical Bases of Reference Values in Laboratory Medicine (1995)

Examining the strengths and limitations of various standards of accuracy in clinical laboratory analyses, this detailed reference presents an in-depth study of important theoretical and empirical issues concerning the description, collection, and application of reference values in laboratory medicine.
Axonal loss in normal-appearing white matter in a patient with acute MS (2001)

These studies confirm axonal degeneration in the absence of myelin loss as one histopathologic correlate to abnormal MR findings in patients with MS.
<title>Significance of correlation in ultrasound signal processing</title> (2001)

The correlation between ultrasonic speckle patterns acquired with different system configurations determines the effectiveness of spatial and frequency compounding, phase aberration correction, elastography, and other applications. For some algorithms, such as compounding, decorrelation has a direct effect on performance. In others decorrelation indirectly degrades performance by reducing the accuracy of signal processing methods such as time delay estimation (TDE). This paper reviews the causes of echo decorrelation for a variety of applications. The mechanisms of decorrelation are described using k-space and simulation. We show examples of signals at different correlation levels to build intuition. The direct impact of decorrelation is described for several of the aforementioned applications. We quantify the indirect effect of decorrelation by examining TDE performance. This analysis shows that reducing correlation from 1.0 to 0.99 increases TDE errors by a factor of 3 under reasonable conditions. This paper also describes a new method of computing speckle pattern correlation directly from system point spread functions, assuming either shift- invariant or shift-variant systems. This paper concludes that echo decorrelation has a major impact on the performance of ultrasound signal processing, and that this decorrelation can be computed using simulation, k-space, or the system point spread function.
Quantification of polymerase chain reaction products by affinity-based hybrid collection (1988)

We have used oligonucleotides modified with biotin in the 5'-end as primers in the polymerase chain reaction (PCR)-amplification. This results in the synthesis of 5'-biotinylated DNA molecules, which are detected by hybridization to a labelled probe in solution. The formed hybrids are collected on an avidin-matrix by mediation of the biotin residue of the target molecules. The affinity-based hybrid collection method is quantitative and makes it possible to measure the amount of DNA produced in the PCR-amplification. At low concentrations of template the efficiency of the process is close to 100%, making it possible to detect the presence of a few molecules of target DNA in 25 cycles. With high template concentrations the efficiency of the process is low.
Profilaggrin is a major epidermal calcium-binding protein. (1993)

Profilaggrin is a major highly phosphorylated protein component of the keratohyalin granules of mammalian epidermis. It contains 10 to 12 tandemly repeated filaggrin units and is processed into the intermediate filament-associated protein filaggrin by specific dephosphorylation and proteolysis during terminal differentiation of the epidermal cells. Later, filaggrin itself is degraded to free amino acids that participate in maintenance of epidermal flexibility. The present paper describes the structural organization of the 5' region of the human profilaggrin gene as well as the amino terminus of the profilaggrin protein. The primary profilaggrin transcript consists of three exons and two introns. The first exon (exon I) is only 54 bp and is untranslated. The coding sequences are distributed between exon II (159 bp) and exon III, which contains the information for 10 to 12 filaggrin repeats (972 bp each) and the 3' noncoding sequences. A very large intron separates exons I and II. The combination of a very short exon I with an unusually long intron 1 makes the structure of the profilaggrin gene unique among the epidermally expressed genes investigated so far. Comparison of the expression patterns revealed by primer extension and RNase protection analysis of foreskin epidermal and cultured keratinocyte RNAs suggests that alternately spliced messages, which are different from profilaggrin mRNA, are transcribed from the profilaggrin gene system at earlier stages of epidermal differentiation. The amino terminus of profilaggrin exhibits a significant homology to the small calcium-binding S100-like proteins. It contains two alpha-helical regions, termed EF-hands, that bind calcium in vitro. This is the first example of functional calcium-binding domains fused to a structural protein. We suggest that in addition to its role in filament aggregation and the maintenance of epidermal flexibility, profilaggrin may play an important role in the differentiation of the epidermis by autoregulating its own processing in a calcium-dependent manner or by participating in the transduction of calcium signal in epidermal cells.