gebhart/patrepeval huggingface dataset:
Skinning with dual quaternions (2007)

Skinning of skeletally deformable models is extensively used for real-time animation of characters, creatures and similar objects. The standard solution, linear blend skinning, has some serious drawbacks that require artist intervention. Therefore, a number of alternatives have been proposed in recent years. All of them successfully combat some of the artifacts, but none challenge the simplicity and efficiency of linear blend skinning. As a result, linear blend skinning is still the number one choice for the majority of developers. In this paper, we present a novel GPU-friendly skinning algorithm based on dual quaternions. We show that this approach solves the artifacts of linear blend skinning at minimal additional cost. Upgrading an existing animation system (e.g., in a videogame) from linear to dual quaternion skinning is very easy and has negligible impact on run-time performance.
Structure of cholesteric gels and their electrically induced light scattering and colour changes (1992)

Abstract Networks with a helical structure containing large amounts of low mass liquid crystal molecules (gels) were produced by photopolymerization of a nematic diacrylate in the presence of low mass cholesteric mixtures. Prior to polymerization the systems selectively reflected a band of circularly polarized light. Upon polymerization, the gels obtained gave rise to two reflection peaks which were subsequently associated with polymer rich and polymer poor phases. At high network concentrations (>40 per cent w/w) one of the peaks did not appear, indicating that the behaviour of the molecules which were not chemically attached to the network was totally dominated by the network. From the gap required for the suppression of the rotation of the director, it was estimated that the molecules, which were not crosslinked, were confined in layers thinner than 85 nm. The gels were very transparent and did not give rise to excess light scattering as compared with the monomeric state. Upon application of an electric field, colour changes as well as light scattering were induced. These efffects were found to be highly dependent on the state of the polarization of the light as well as the kind of field applied. The response times were very short and they depended strongly on the structure of the network.
Transfer of cloned human class I major histocompatibility complex genes into HLA mutant human lymphoblastoid cells. (1986)

Three new kinds of recombinant DNA constructs were used to transfer cloned human class I HLA genes (A2 and B8) into unique HLA mutant lymphoblastoid cells: pHeBo(x): a class I gene, "x," in plasmid vector pHeBo, which contains a hygromycin resistance gene and Epstein-Barr virus oriP element that sustains extrachromosomal replication; pHPT(x): gene x in a vector with a hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene; pHPTe(x): gene x in a vector with the HPRT gene and oriP element. Cell surface class I antigen expression was strong in transferents made with class I-deficient lymphoblastoid cell line mutants .144 (A-null), .53 (B-null), and .184 (A-null, B-null). Transferents expressing HLA-A2 were recognized specifically by HLA-A2-specific cytotoxic T lymphocytes. When introduced on either of the vectors with the Epstein-Barr virus oriP element, the class I gene replicated extrachromosomally and was lost at rates of 0.2 to 0.3 per cell division. When introduced with vector pHPT (lacking Epstein-Barr virus oriP), the B8 gene was inserted at different chromosomal locations. Introduction of the HLA-B8 gene failed to restore antigen expression by HLA-B-null mutant .174, providing evidence that, unlike mutants exemplified by .53, .144, and .184, some HLA antigen loss mutants are deficient in a trans-acting function needed for class I antigen expression. Of more general interest, the results obtained with HLA class I genes in vectors that replicate extrachromosomally suggest ways of relating genic expression to chromatin structure and function and of attempting to clone functional human centromeres.
Inhibition of Bone Morphogenetic Protein 1 by Native and Altered Forms of α2-Macroglobulin (2006)

The four mammalian bone morphogenetic protein 1 (BMP1)-like proteinases act to proteolytically convert procollagens to the major fibrous components of the extracellular matrix. They also activate lysyl oxidase, an enzyme necessary to the covalent cross-linking that gives collagen fibrils much of their tensile strength. Thus, these four proteinases are attractive targets for interventions designed to limit the excess formation of fibrous collagenous matrix that characterizes fibrosis. Although it has previously been reported that the serum protein alpha(2)-macroglobulin is unable to inhibit the astacin-like proteinases meprin alpha and meprin beta, we herein demonstrate alpha(2)-macroglobulin to be a potent inhibitor of the similar BMP1-like proteinases. BMP1 is shown to cleave the alpha(2)-macroglobulin "bait" region, at a single specific site, which resembles the sites at which BMP1-like proteinases cleave the C-propeptides of procollagens I-III. alpha(2)-Macroglobulin is an irreversible inhibitor that is shown to bind bone morphogenetic protein 1 in a covalent complex. It is also demonstrated that genetically modified alpha(2)-macroglobulin, in which the native bait region is replaced by sequences flanking the probiglycan BMP1 cleavage site, is enhanced approximately 24-fold in its ability to inhibit BMP1, and is capable of inhibiting the biosynthetic processing of procollagen I by cells. These findings suggest possible therapeutic interventions involving ectopic expression of modified versions of alpha(2)-macroglobulin in the treatment of fibrotic conditions.
AXR1 Acts after Lateral Bud Formation to Inhibit Lateral Bud Growth in Arabidopsis (1999)

The AXR1 gene of Arabidopsis is required for many auxin responses. The highly branched shoot phenotype of mature axr1 mutant plants has been taken as genetic evidence for a role of auxin in the control of shoot branching. We compared the development of lateral shoots in wild-type Columbia and axr1-12 plants. In the wild type, the pattern of lateral shoot development depends on the developmental stage of the plant. During prolonged vegetative growth, axillary shoots arise and develop in a basal-apical sequence. After floral transition, axillary shoots arise rapidly along the primary shoot axis and grow out to form lateral inflorescences in an apical-basal sequence. For both patterns, the axr1 mutation does not affect the timing of axillary meristem formation; however, subsequent lateral shoot development proceeds more rapidly in axr1 plants. The outgrowth of lateral inflorescences from excised cauline nodes of wild-type plants is inhibited by apical auxin. axr1-12 nodes are resistant to this inhibition. These results provide evidence for common control of axillary growth in both patterns, and suggest a role for auxin during the late stages of axillary shoot development following the formation of the axillary bud and several axillary leaf primordia.
Advances in Primary Recovery: Centrifugation and Membrane Technology (2008)

Significant and continual improvements in upstream processing for biologics have resulted in challenges for downstream processing, both primary recovery and purification. Given the high cell densities achievable in both microbial and mammalian cell culture processes, primary recovery can be a significant bottleneck in both clinical and commercial manufacturing. The combination of increased product titer and low viability leads to significant relative increases in the levels of process impurities such as lipids, intracellular proteins and nucleic acid versus the product. In addition, cell culture media components such as soy and yeast hydrolysates have been widely applied to achieve the cell culture densities needed for higher titers. Many of the process impurities can be negatively charged at harvest pH and can form colloids during the cell culture and harvest processes. The wide size distribution of these particles and the potential for additional particles to be generated by shear forces within a centrifuge may result in insufficient clarification to prevent fouling of subsequent filters. The other residual process impurities can lead to precipitation and increased turbidity during processing and even interference with the performance of the capturing chromatographic step. Primary recovery also poses significant challenges owing to the necessity to execute in an expedient manner to minimize both product degradation and bioburden concerns. Both microfiltration and centrifugation coupled with depth filtration have been employed successfully as primary recovery processing steps. Advances in the design and application of membrane technology for microfiltration and dead-end filtration have contributed to significant improvements in process performance and integration, in some cases allowing for a combination of multiple unit operations in a given step. Although these advances have increased productivity and reliability, the net result is that optimization of primary recovery processes has become substantially more complicated. Ironically, the application of classical chemical engineering approaches to overcome issues in primary recovery and purification (e.g., turbidity and trace impurity removal) are just recently gaining attention. Some of these techniques (e.g., membrane cascades, pretreatment, precipitation, and the use of affinity tags) are now seen almost as disruptive technologies. This paper will review the current and potential future state of research on primary recovery, including relevant papers presented at the 234th American Chemical Society (ACS) National Meeting in Boston.
Diversity and evolution of the green fluorescent protein family (2002)

The family of proteins homologous to the green fluorescent protein (GFP) from Aequorea victoria exhibits striking diversity of features, including several different types of autocatalytically synthesized chromophores. Here we report 11 new members of the family, among which there are 3 red-emitters possessing unusual features, and discuss the similarity relationships within the family in structural, spectroscopic, and evolutionary terms. Phylogenetic analysis has shown that GFP-like proteins from representatives of subclass Zoantharia fall into at least four distinct clades, each clade containing proteins of more than one emission color. This topology suggests multiple recent events of color conversion. Combining this result with previous mutagenesis and structural data, we propose that (i) different chromophore structures are alternative products synthesized within a similar autocatalytic environment, and (ii) the phylogenetic pattern and color diversity in reef Anthozoa is a result of a balance between selection for GFP-like proteins of particular colors and mutation pressure driving the color conversions.
Babesia bovis : Continuous Cultivation in a Microaerophilous Stationary Phase Culture (1980)

The protozoan parasite Babesia bovis, a causative agent of bovine babesiosis, has been continuously cultivated in a settled layer of bovine erythrocytes. Lowered oxygen tension within the layer of host erythrocytes results in a darkening of infected cultures and provides a rapid means of evaluating parasite growth. Deprivation of carbon dioxide causes the merozoites to accumulate in the medium rather than involving new erythrocytes. When separated from the culture, these extraerythrocytic parasites retain their infectivity. Parasites produced in vitro are morphologically identical to parasites from the blood of infected cattle and are susceptible to antibabesial drugs.
COMBINATION THERAPY FOR AGE-RELATED MACULAR DEGENERATION (2009)

Vascular endothelial growth factor (VEGF) is an important mediator of angiogenesis in age-related macular degeneration (AMD) and is a validated therapeutic target. However, combination of anti-VEGF agents with complementary inhibition of other mediators of angiogenesis, such as platelet-derived growth factor and integrin alpha5beta1, may result in enhanced visual acuity. Other concomitant treatments, such as inhibitors of inflammation, may generate an even stronger barrier to the progression of AMD than that now observed in individuals receiving anti-VEGF therapies alone. Experimental studies are providing support for the general principles of combination treatment in AMD.
EGF/TGFβ1 co-stimulation of oral squamous cell carcinoma cells causes an epithelial-mesenchymal transition cell phenotype expressing laminin 332 (2010)

Epithelial-mesenchymal transition (EMT) is suggested to be crucial for the development of an invasive and metastatic carcinoma cell phenotype. Therefore, the definition of this phenotype is of great clinical interest. We recently evidenced vimentin positive cells in oral squamous cell carcinoma (OSCC) invasive front expressing laminin γ2 chain mRNA implicating an EMT origin of these cells. To further elucidate the nature of these cells, we have investigated the relation between EMT criteria and laminin-332 expression in a cell culture model of transforming growth factor beta-1 (TGFβ1)/epithelial growth factor (EGF) long time co-stimulation. We demonstrate that in contrast to TGFβ1 or EGF alone, co-stimulation induces phenotype transition in OSCC cells which fulfils the criteria of EMT in terms of vimentin up-regulation and E-cadherin down-regulation on protein level as well as cell scattering. Furthermore, cells displayed a strongly enhanced invasiveness and adhesion to type I-IV collagens. Phenotype transition is accompanied by an enhanced expression of laminin-332, especially of its γ2 chain. We further analyse the expression of extracellular matrix related genes by RT-PCR profiling. With respect to strongly enhanced proteins, data confirm the EMT phenotype of co-stimulated OSCC cells and expression of laminin-332. Furthermore, alpha catenin, collagen type 16, the integrin α7 and β1 chains, and MMP11 are suggested as candidates with potential role in EMT in OSCC. In summary we are able to show that EMT in OSCC is mediated by multiple growth factors and is accompanied by laminin γ2 chain up-regulation evidencing the existence of an intermediate Vim(+) /Ln332(+) EMT phenotype as seen in situ.
Analysis of Large Strain Hot Torsion Textures Associated With “Continuous” Dynamic Recrystallization (2008)

The development of ideal orientations within the steady-state region of hot torsion flow curves of fcc and bcc metals undergoing “continuous” dynamic recrystallization is analyzed. It is well known that in fcc metals, e.g., Al deformed at 400°C and above, the experimentally observed end texture consists of the twin-symmetric B(112¯)[11¯0]/B¯(1¯1¯2)[1¯10] component, whereby the (hkl)[uvw] indices correspond to the shear plane z and the shear direction θ, respectively. In bcc iron however, only one of the self-symmetric D1(112¯)[111] and D2(1¯1¯2)[111] components dominates (the former in the case of positive shear or clockwise rotation about the r-axis, and the latter during negative shear). The tendency toward a single end orientation imposes certain limitations on grain refinement, as this would ultimately imply the coalescence of subgrains of or close to this orientation, and therefore the disappearance of existing high angle boundaries (≥15 deg). It is believed that the preference of D1 over D2, or vice versa, could be related to phenomena other than glide-induced rotations, e.g., grain boundary migration resulting from differences in work hardening rates. In this paper, the standard Taylor model is first used to predict the texture evolution in simple shear under the full-constraint rate-sensitive scheme. This is then coupled with an approach that takes into account grain boundary migration resulting from differences in dislocation densities within grains of varying orientations. The preliminary results are in agreement with experimental findings, i.e., grains with initial orientations close to D2 grow at the expense of neighboring grains during negative shear and vice versa.
Applications of gold nanoparticles in cancer nanotechnology (2008)

It has been almost 4 decades since the "war on cancer" was declared. It is now generally believed that personalized medicine is the future for cancer patient management. Possessing unprecedented potential for early detection, accurate diagnosis, and personalized treatment of cancer, nanoparticles have been extensively studied over the last decade. In this review, we will summarize the current state-of-the-art of gold nanoparticles in biomedical applications targeting cancer. Gold nanospheres, nanorods, nanoshells, nanocages, and surface enhanced Raman scattering nanoparticles will be discussed in detail regarding their uses in in vitro assays, ex vivo and in vivo imaging, cancer therapy, and drug delivery. Multifunctionality is the key feature of nanoparticle-based agents. Targeting ligands, imaging labels, therapeutic drugs, and other functionalities can all be integrated to allow for targeted molecular imaging and molecular therapy of cancer. Big strides have been made and many proof-of-principle studies have been successfully performed. The future looks brighter than ever yet many hurdles remain to be conquered. A multifunctional platform based on gold nanoparticles, with multiple receptor targeting, multimodality imaging, and multiple therapeutic entities, holds the promise for a "magic gold bullet" against cancer.
Hybrid optoelectronics: A polymer laser pumped by a nitride light-emitting diode (2008)

We demonstrate indirect electrically pumped lasing in a hybrid polymer laser. The lasers comprise a corrugated fluorene copolymer waveguide on an InGaN light-emitting diode and were driven under nanosecond pulsed operation. We observe the onset of distributed feedback lasing at 568nm for peak drive currents above 144A. Angle-resolved photoluminescence measurements identify the lasing mechanism as band edge feedback from a photonic stopband in the TE0 waveguide mode.
Preparation and characterization of antifouling poly(vinylidene fluoride) blended membranes (2011)

Abstract Poly(vinylidene fluoride) (PVDF) membranes have been widely used in microfiltration and ultrafiltration because of their excellent chemical resistance and thermal properties. However, PVDF membranes have exhibited severe membrane fouling because of their hydrophobic properties. In this study, we investigated the antifouling properties of PVDF blended membranes. Antifouling PVDF blended membranes were prepared with a PVDF‐ g ‐poly(ethylene glycol) methyl ether methacrylate (POEM) graft copolymer. The PVDF‐ g ‐POEM graft copolymer was synthesized by the atom transfer radical polymerization (ATRP) method. The chemical structure and properties of the synthesized PVDF‐ g ‐POEM graft copolymer were determined by NMR, Fourier transform infrared spectroscopy, and gel permeation chromatography. To investigate the antifouling properties of the membranes, we prepared microfiltration membranes by using the phase‐inversion method, which uses various PVDF/PVDF‐ g ‐POEM concentrations in dope solutions. The pure water permeabilities were obtained at various pressures. The PVDF/PVDF‐ g ‐POEM blended membranes exhibited no irreversible fouling in the dead‐end filtration of foulants, including bovine serum albumin, sodium alginate, and Escherichia coli broth. However, the hydrophobic PVDF membrane exhibited severe fouling in comparison with the PVDF/PVDF‐ g ‐POEM blended membranes. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Inversionless decoding of binary BCH codes (1971)

The iterative algorithm for decoding binary BCH codes presented by Berlekamp and, in an alternative form, by Massey is modified to eliminate inversion. Because inversion in a finite field is time consuming and requires relatively complex circuitry, this new algorithm should he useful in practical applications of multiple-error-correcting binary BCH codes.
Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. (1991)

In this report, we describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., cystic fibrosis and sickle cell disease), and in others in which multiple mutations cause the disease and the sequence variation in an affected member of a given family is known (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then prepared. Each contains the amplified fragment, a primer (18-mer or longer) whose sequence is identical to the coding sequence of the normal gene immediately flanking the 5' end of the mutation site, and either an alpha-32P-labeled nucleotide corresponding to the normal coding sequence at the mutation site or an alpha-32P-labeled nucleotide corresponding to the mutant sequence. Single nucleotide primer extensions are then carried out and analyzed by denaturing polyacrylamide gel electrophoresis and autoradiography. As predicted by the Watson-Crick base-pair rule, in the wild type only the normal base, in an affected member only the mutant base, and in carriers both the normal and the mutant base are incorporated into the primer. Thus, an essential feature of the present methodology is that the base immediately 3' to the template-bound primer is one of those altered in the mutant, since in this way an extension of the primer by a single base will give an extended molecule characteristic of either the mutant or the wild type. The method is rapid and should be useful in carrier detection and prenatal diagnosis of every genetic disease with a known sequence variation.
<title>All-fiber optic coherence domain interferometric techniques</title> (2001)

Traditional white-light scanning interferometers utilize bulk optic components mounted on a mechanical scanning mechanism. Many emerging applications for these interferometers require fiber optic probes. By design, such fiber compatible instruments are expensive and are limited to slow scan rates. A new “all-fiber” design approach is presented, which reduces the cost of the design and enables higher scan rates.
F8 haplotype and inhibitor risk: results from the Hemophilia Inhibitor Genetics Study (HIGS) Combined Cohort (2012)

Ancestral background, specifically African descent, confers higher risk for development of inhibitory antibodies to factor VIII (FVIII) in haemophilia A. It has been suggested that differences in the distribution of FVIII gene (F8) haplotypes, and mismatch between endogenous F8 haplotypes and those comprising products used for treatment could contribute to risk. Data from the Hemophilia Inhibitor Genetics Study (HIGS) Combined Cohort were used to determine the association between F8 haplotype 3 (H3) vs. haplotypes 1 and 2 (H1 + H2) and inhibitor risk among individuals of genetically determined African descent. Other variables known to affect inhibitor risk including type of F8 mutation and human leucocyte antigen (HLA) were included in the analysis. A second research question regarding risk related to mismatch in endogenous F8 haplotype and recombinant FVIII products used for treatment was addressed. Haplotype 3 was associated with higher inhibitor risk among those genetically identified (N = 49) as of African ancestry, but the association did not remain significant after adjustment for F8 mutation type and the HLA variables. Among subjects of all racial ancestries enrolled in HIGS who reported early use of recombinant products (N = 223), mismatch in endogenous haplotype and the FVIII proteins constituting the products used did not confer greater risk for inhibitor development. Haplotype 3 was not an independent predictor of inhibitor risk. Furthermore, our findings did not support a higher risk of inhibitors in the presence of a haplotype mismatch between the FVIII molecule infused and that of the individual.