gebhart/patrepeval huggingface dataset:
Hands Deep in Deep Learning for Hand Pose Estimation (2015)

We introduce and evaluate several architectures for Convolutional Neural Networks to predict the 3D joint locations of a hand given a depth map. We first show that a prior on the 3D pose can be easily introduced and significantly improves the accuracy and reliability of the predictions. We also show how to use context efficiently to deal with ambiguities between fingers. These two contributions allow us to significantly outperform the state-of-the-art on several challenging benchmarks, both in terms of accuracy and computation times.
Beagle Dog Pulmonary Surfactant Lipids (1971)

The lipids from normal beagle dog lungs, pulmonary surfactant, and exfoliated lining cells were quantitated by established procedures. The surfactant and cells were obtained by endobronchial saline lavage. Phospholipids accounted for more than 70% of the surfactant and cell lipids: phosphatidyl choline was the predominant phosphatide. Phosphatidyl glycerol is present in beagle dog pulmonary surfactant (10% of phospholipid-P), exfoliated lining cells (7% of phospholipid-P) and lung tissue (3% of phospholipid-P). Cholesterol and its esters accounted for more than 60% of the neutral lipid fractions. Alkyl and alk-1-enyl glycerol ethers were quantitated in the neutral lipids and phospholipids from all samples.
Characterization of apxlVA, a new RTX determinant of Actinobacillus pleuropneumoniae (1999)

A fourth type of RTX determinant was identified in Actinobacillus pleuropneumoniae and was designated apxIVA. When expressed in Escherichia coli, recombinant ApxIVA showed a weak haemolytic activity and co-haemolytic synergy with the sphingomyelinase (beta-toxin) of Staphylococcus aureus. These activities required the presence of an additional gene, ORF1, that is located immediately upstream of apxIVA. The apxIVA gene product could not be detected in A. pleuropneumoniae cultures grown under various conditions in vitro; however, pigs experimentally infected with A. pleuropneumoniae serotypes 1, 5 and 7 started to produce antibodies that reacted with recombinant ApxIVA 14 d post-infection, indicating that apxIVA is expressed in vivo. In addition, sera from pigs naturally and experimentally infected with any of the serotypes all reacted with recombinant ApxIVA. The apxIVA gene from the serotype 1 A. pleuropneumoniae type strain Shope 4074T encodes a protein with a predicted molecular mass of 202 kDa which has typical features of RTX proteins including hydrophobic domains in the N-terminal half and 24 glycine-rich nonapeptides in the C-terminal half that bind Ca2+. The glycine-rich nonapeptides are arranged in a modular structure and there is some variability in the number of modules in the ApxIVA proteins of different serotypes of A. pleuropneumoniae. The deduced amino acid sequences of the ApxIVA proteins have significant similarity with the Neisseria meningitidis iron-regulated RTX proteins FrpA and FrpC, and to a much lesser extent with other RTX proteins. The apxIVA gene could be detected in all A. pleuropneumoniae serotypes and seems to be species-specific. Although the precise role of this new RTX determinant in pathogenesis of porcine pleuropneumonia needs to be determined, apxIVA is the first in vivo induced toxin gene that has been described in A. pleuropneumoniae.
Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response (2013)

We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography-high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique V(H) CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigen-specific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody V(H) clonotypes. Of these 34 CDRH3s, 12 account for ∼60% of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.
Package-level Implementation of Multiband Electromagnetic Band-Gap Structures (2006)

The design and implementation of package-level electromagnetic band-gap structures is demonstrated. By using spiral-based electromagnetic band-gap structures (EBG), the relative periodicity for achieving band-gap at extremely low frequency is substantially minimized in comparison to traditional EBG's. Using both full wave electromagnetic simulation and experimental characterization it is demonstrated that this type of structure can exhibit multiple band-gaps, which are individually tunable through variation of the inductance per unit area and its periodicity. Sample structures with dimensions compatible to today's packaging technology are fabricated and show stop-band behavior in frequency band of interest for commercial wireless communication systems
Regulation and Role of Nuclear Receptors during Larval Molting and Metamorphosis of Lepidoptera (1999)

The regulation of the ecdysteroid-induced cascade of transcription factors by 20-hydroxyecdysone (20E) and juvenile hormone (JH) in the epidermis of the lepidopteran Manduca sexta is summarized. Both the levels and isoforms of the ecdysone receptor (EcR) and Ultraspiracle (USP) change during the molt. The 20E induction of MHR3, an orphan receptor that appears relatively late in the cascade, is dependent on the predominant intermolt isoforms, EcR-B1 and USP-1, and on the orphan receptor E75A which appears early in the cascade. The USP-2 isoform induced by 20E pairs with EcR-B1 but this heterodimer cannot up-regulate MHR3. Thus, the specific transcription factors induced by 20E are dependent on the particular isoforms present in the heterodimeric EcR/USP complex. Juvenile hormone modulates responses of the transcription factor cascade to 20E. For E75A, the presence of JH increased both its sensitivity to 20E and the accumulation of its mRNA, indicating that high E75A may be important for maintenance of the larval state. By contrast, JH prevented the 20E induction of the Broad Complex group of transcription factors which appear as the larval epidermis becomes pupally committed and are necessary for metamorphosis in Drosophila . During the decline of ecdysteroid, the orphan receptors, GRF and βFTZ-F1, appear and may regulate transcription of dopa decarboxylase, a key enzyme in sclerotization of the new cuticle. Thus, the ecdysteroid-induced regulatory cascade is set in motion and regulated by the changing concentration and types of ecdysteroids and receptor isoforms. The presence of JH further modulates this cascade by acting selectively on the responses of specific factors and thus prevents the 20E-induced gene switching neccessary for metamorhposis.
Sputum T lymphocytes in asthma, COPD and healthy subjects have the phenotype of activated intraepithelial T cells (CD69+ CD103+) (2003)

Sputum T lymphocytes are predominantly of activated intraepithelial phenotype (CD103+ CD69+), and normal numbers of CD4+ and CD8+ T cell populations are found in the sputum of patients with asthma and COPD.
Jones matrix of polarization mode dispersion (1999)

We describe how to calculate the Jones matrix transfer function of a fiber if its principal states of polarization and its differential group delay as functions of frequency are known. Using two counterexamples related to second-order polarization mode dispersion (PMD), we also show that a previous method used for the same purpose induces overestimation of second-order PMD effects by a factor of 2. Our new method is used to solve the problem for both counterexamples.
Role for the Ran Binding Protein, Mog1p, in Saccharomyces cerevisiae SLN1-SKN7 Signal Transduction (2004)

Yeast Sln1p is an osmotic stress sensor with histidine kinase activity. Modulation of Sln1 kinase activity in response to changes in the osmotic environment regulates the activity of the osmotic response mitogen-activated protein kinase pathway and the activity of the Skn7p transcription factor, both important for adaptation to changing osmotic stress conditions. Many aspects of Sln1 function, such as how kinase activity is regulated to allow a rapid response to the continually changing osmotic environment, are not understood. To gain insight into Sln1p function, we conducted a two-hybrid screen to identify interactors. Mog1p, a protein that interacts with the yeast Ran1 homolog, Gsp1p, was identified in this screen. The interaction with Mog1p was characterized in vitro, and its importance was assessed in vivo. mog1 mutants exhibit defects in SLN1-SKN7 signal transduction and mislocalization of the Skn7p transcription factor. The requirement for Mog1p in normal localization of Skn7p to the nucleus does not fully account for the mog1-related defects in SLN1-SKN7 signal transduction, raising the possibility that Mog1p may play a role in Skn7 binding and activation of osmotic response genes.
On the shape of bottle-brush macromolecules: Systematic variation of architectural parameters (2005)

We measured the form factor of bottle-brush macromolecules under good solvent conditions with small-angle neutron scattering and static light scattering. The systems under investigation are brushes, synthesized via the grafting-from route, built from a poly(alkyl methacrylate) backbone to which poly(n-butyl acrylate) side chains are densely grafted. The aim of our work is to study how the systematic variation of structural parameters such as the side chain length and backbone length change the conformation of the polymer brushes in solution. All spectra can be consistently described by a model, considering the bottle-brush polymers as flexible rods with internal density fluctuations. Parameters discussed are (1) the contour length per main chain monomer lb, (2) the fractal dimension of the side chains Ds, as well as (3) the fractal dimension D, and (4) the Kuhn length λk of the overall brush. lb=0.253±0.008nm is found to be independent of the side chain length and equal to the value found for the bare main chain, indicating a strongly stretched conformation for the backbone due to the presence of the side chains. The fractal dimension of the side chains is determined to be Ds=1.75±0.07 which is very close to the value of 1∕0.588≈1.70 expected for a three-dimensional self-avoiding random walk (3D-SAW) under good solvent conditions. On larger length scales the overall brush appears to be a 3D-SAW itself (D=1.64±0.08) with a Kuhn-step length of λk=70±4nm. The value is independent of the side chain length and 46 times larger than the Kuhn length of the bare backbone (λk=1.8±0.2nm). The ratio of Kuhn length to brush diameter λk∕d⩾20 determines whether lyotropic behavior can be expected or not. Since longer side chains do not lead to more persistent structures, λk∕d decreases from 8 to 4 with increasing side chain length and lyotropic behavior becomes unlikely.
Experimental podophyllotoxin (bajiaolian) poisoning: III. Biochemical bases for toxic effects. (1994)

The biochemical mechanism underlying the toxicity of podophyllotoxin is investigated. Previous studies from our laboratories suggested that hepatocytes were extremely sensitive to the toxicity of podophyllotoxin and a disruption of protein synthesis was suspected. Dose-response and time-course studies on the effects of podophyllotoxin on protein. RNA, and DNA syntheses on hepatocellular cultures were made. Inhibitions of protein, RNA, and DNA syntheses were demonstrated, and a direct correlated dose-response relationship on such effects was also evident. Inhibition of protein synthesis appeared to be a direct toxic effect of podophyllotoxin and occurred independently from that of RNA. The reduction of DNA synthesis was reflected by a reduction of H3-thymidine incorporation, which is believed to be the consequence of inhibition on the mitotic activity by podophyllotoxin.
TGF-beta induced transdifferentiation of mammary epithelial cells to mesenchymal cells: involvement of type I receptors. (1994)

The secreted polypeptide transforming growth factor-beta (TGF-beta) exerts its multiple activities through type I and II cell surface receptors. In epithelial cells, activation of the TGF-beta signal transduction pathways leads to inhibition of cell proliferation and an increase in extracellular matrix production. TGF-beta is widely expressed during development and its biological activity has been implicated in epithelial-mesenchymal interactions, e.g., in branching morphogenesis of the lung, kidney, and mammary gland, and in inductive events between mammary epithelium and stroma. In the present study, we investigated the effects of TGF-beta on mouse mammary epithelial cells in vitro. TGF-beta reversibly induced an alteration in the differentiation of normal mammary epithelial NMuMG cells from epithelial to fibroblastic phenotype. The change in cell morphology correlated with (a) decreased expression of the epithelial markers E-cadherin, ZO-1, and desmoplakin I and II; (b) increased expression of mesenchymal markers, such as fibronectin; and (c) a fibroblast-like reorganization of actin fibers. This phenotypic differentiation displays the hallmarks of an epithelial to mesenchymal transdifferentiation event. Since NMuMG cells make high levels of the type I TGF-beta receptor Tsk7L, yet lack expression of the ALK-5/R4 type I receptor which has been reported to mediate TGF-beta responsiveness, we evaluated the role of the Tsk7L receptor in TGF-beta-mediated transdifferentiation. We generated NMuMG cells that stably overexpress a truncated Tsk7L type I receptor that lacks most of the cytoplasmic kinase domain, thus function as a dominant negative mutant. These transfected cells no longer underwent epithelial to mesenchymal morphological change upon exposure to TGF-beta, yet still displayed some TGF-beta-mediated responses. We conclude that TGF-beta has the ability to modulate E-cadherin expression and induce a reversible epithelial to mesenchymal transdifferentiation in epithelial cells. Unlike other transdifferentiating growth factors, such as bFGF and HGF, these changes are accompanied by growth inhibition. Our results also implicate the Tsk7L type I receptor as mediating the TGF-beta-induced epithelial to mesenchymal transition.
Dart Throwing on Surfaces (2009)

Abstract In this paper we present dart throwing algorithms to generate maximal Poisson disk point sets directly on 3D surfaces. We optimize dart throwing by efficiently excluding areas of the domain that are already covered by existing darts. In the case of triangle meshes, our algorithm shows dramatic speed improvement over comparable sampling methods. The simplicity of our basic algorithm naturally extends to the sampling of other surface types, including spheres, NURBS, subdivision surfaces, and implicits. We further extend the method to handle variable density points, and the placement of arbitrary ellipsoids without overlap. Finally, we demonstrate how to adapt our algorithm to work with geodesic instead of Euclidean distance. Applications for our method include fur modeling, the placement of mosaic tiles and polygon remeshing.
The class I major histocompatibility complex related Fc receptor shows pH-dependent stability differences correlating with immunoglobulin binding and release (1993)

Maternal immunoglobulin G (IgG) in milk is transported to the bloodstream of newborn rodents via an Fc receptor (FcRn) expressed in the gut. The receptor shows a striking structural similarity to class I major histocompatibility complex (MHC) molecules, being composed of a related heavy chain and the identical light chain (beta 2-microglobulin). FcRn binds IgG at the pH of milk in the proximal intestine (pH 6.0-6.5) and releases it at the pH of blood (pH approximately 7.5). We have compared the stability of a soluble form of FcRn in these two pH ranges and find that the heterodimer is markedly more stable at the permissive pH for IgG binding. Using the rate of beta 2m exchange as a correlate of heterodimer stability, we find that exchange is more than 10 times slower at pH 6.1 compared to pH 7.8. Thermal denaturation profiles of FcRn heterodimers at pH 8.0 indicate a two-step, sequential heavy-chain (Tm = 52 degrees C) and beta 2m (Tm = 67 degrees C) denaturation. By contrast, at pH 6.0, a single transition is observed, centered at 62 degrees C, corresponding to denaturation of both chains. The striking difference in stability does not appear to be correlated with the binding of peptide as in class I MHC molecules, because analysis of purified FcRn by acid dissociation and sequencing suggests that FcRn is not associated with cellular peptides. These results are indicative of pH-dependent conformational changes in the FcRn heterodimer, which may be related to its physiological function.
Locally Enhanced Angiogenesis Promotes Transplanted Cell Survival (2004)

A developing therapy for complete or partial loss of function in various tissues and organs involves transplanting an appropriate cell population, capable of compensating for the existing deficiencies. Clinical application of this type of strategy is currently limited by the death or dedifferentiation of the transplanted cells after delivery to the recipient. A delay in thorough vascularization of the implant area creates an environment low in oxygen and other nutrients, and likely contributes to the initial death of transplanted cells. We have addressed this problem by sustained delivery of vascular endothelial growth factor (VEGF), an initiator of angiogenesis, from a porous polymer matrix utilized simultaneously for cell delivery. As expected from previous studies, VEGF delivered from these constructs elicited an enhanced angiogenic response over a 2-week period when implanted subcutaneously in SCID mice. Hepatocytes implanted using VEGF-containing matrices demonstrated significantly greater survival after 1 week in vivo as compared with cells implanted on matrices without growth factor. The results of this study therefore indicate that enhancing vascularization in the location of transplanted cells promotes their survival. In addition, this delivery system may be used in future studies to directly promote cell survival and function by also providing growth factors specific to the transplanted cells.
High Frequency of Mutations of the PIK3CA Gene in Human Cancers (2004)

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Microwave‐Assisted Heterogeneous Gas‐Phase Catalysis (2004)

Abstract This article reviews microwave‐assisted heterogeneous gas‐phase catalysis. To date, this special means of non‐classical energy input by microwave radiation is still a fringe area of catalysis research, and alternative reaction engineering in chemistry and chemical engineering. However, microwave‐assisted heterogeneous gas‐phase catalysis is expected to gain significant popularity in academia and industry in the near future. Experimental set‐ups that have been described in literature are critically reviewed, and concepts for the design of improved experimental set‐ups are provided in this article. Historical developments, current tendencies, and a short introduction to the theory of dielectric heating are discussed.
Stroke order and stroke number free on-line Chinese character recognition using attributed relational graph matching (1996)

A structural method for on-line recognition of Chinese characters is proposed, which is stroke order and stroke number free. Both input characters and the model characters are represented with complete attributed relational graphs (ARGs). A new optimal matching measure between two ARGs is defined. Classification of an input character can be implemented by matching its ARG against every ARG of the model base. The matching procedure is formulated as a search problem of finding the minimum cost path in a state space tree, using the A* algorithm. In order to speed up the search of the A*, besides a heuristic estimate, a novel strategy that utilizes the geometric position information of stroke segments of Chinese characters to prune the tree is employed. The efficiency of our method is demonstrated by the promising experimental results.
Assembly of Subtype 1 Influenza Neuraminidase Is Driven by Both the Transmembrane and Head Domains (2012)

Neuraminidase (NA) is one of the two major influenza surface antigens and the main influenza drug target. Although NA has been well characterized and thought to function as a tetramer, the role of the transmembrane domain (TMD) in promoting proper NA assembly has not been systematically studied. Here, we demonstrate that in the absence of the TMD, NA is synthesized and transported in a predominantly inactive state. Substantial activity was rescued by progressive truncations of the stalk domain, suggesting the TMD contributes to NA maturation by tethering the stalk to the membrane. To analyze how the TMD supports NA assembly, the TMD was examined by itself. The NA TMD formed a homotetramer and efficiently trafficked to the plasma membrane, indicating the TMD and enzymatic head domain drive assembly together through matching oligomeric states. In support of this, an unrelated strong oligomeric TMD rescued almost full NA activity, whereas the weak oligomeric mutant of this TMD restored only half of wild type activity. These data illustrate that a large soluble domain can force assembly with a poorly compatible TMD; however, optimal assembly requires coordinated oligomerization between the TMD and the soluble domain.
Brønsted Acid-Catalyzed Intramolecular Hydroamination of Protected Alkenylamines. Synthesis of Pyrrolidines and Piperidines (2002)

[reaction: see text]. The cyclization of aminoalkenes bearing an electron-withdrawing group on the nitrogen atom was catalyzed by triflic or sulfuric acid in toluene. Pyrrolidines and piperidines were formed in excellent yields. N-phenylanilides also underwent cyclization to form gamma-lactams.