gebhart/patrepeval huggingface dataset:
Robust full‐motion recovery of head by dynamic templates and re‐registration techniques (2003)

Abstract This article presents a method to recover the full‐motion (3 rotations and 3 translations) of the head from an input video using a cylindrical head model. Given an initial reference template of the head image and the corresponding head pose, the head model is created and full head motion is recovered automatically. The robustness of the approach is achieved by a combination of three techniques. First, we use the iteratively reweighted least squares (IRLS) technique in conjunction with the image gradient to accommodate nonrigid motion and occlusion. Second, while tracking, the templates are dynamically updated to diminish the effects of self‐occlusion and gradual lighting changes and to maintain accurate tracking even when the face moves out of view of the camera. Third, to minimize error accumulation inherent in the use of dynamic templates, we re‐register images to a reference template whenever head pose is close to that in the template. The performance of the method, which runs in real time, was evaluated in three separate experiments using image sequences (both synthetic and real) for which ground truth head motion was known. The real sequences included pitch and yaw as large as 40° and 75°, respectively. The average recovery accuracy of the 3D rotations was about 3°. In a further test, the method was used as part of a facial expression analysis system intended for use with spontaneous facial behavior in which moderate head motion is common. Image data consisted of 1‐min of video from each of 10 subjects while engaged in a two‐person interview. The method successfully stabilized face and eye images allowing for 98% accuracy in automatic blink recognition. © 2003 Wiley Periodicals, Inc. Int J Imaging Syst Technol 13: 85–94, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ima.10048
Neurobehavioral Techniques to Assess the Effects of Chemicals on the Nervous System (1984)

Due to the massive data sets available for drug candidates, modern drug discovery has advanced to the big data era. Central to this shift is the development of artificial intelligence approaches to implementing innovative modeling based on the dynamic, ...Read More
Measurement of membrane phospholipid asymmetry in normal and sickle-cell erythrocytes by means of annexin V binding. (1994)

We investigated the use of annexin V (placental anticoagulant protein I), a calcium-dependent protein that binds tightly to phosphatidylserine-containing membranes, as a means to measure membrane phospholipid asymmetry in human erythrocytes. Iodine 125-labeled annexin V bound to erythrocytes in a specific, reversible, calcium-dependent reaction (dissociation constant = 25 +/- 4 nmol/L at 37 degrees C and 2.5 mmol/L calcium). Lysed erythrocytes contained 1.2 x 10(6) binding sites for annexin V. Treatment of erythrocytes with 1 mumol/L A23187 in the presence of 2.5 mmol/L calcium at 37 degrees C caused a gradual but marked increase in annexin V binding sites, reaching a level of approximately 300,000 sites per cell after 8 hours of incubation. We also noted a very gradual spontaneous exposure of annexin V binding sites during storage of purified erythrocytes, reaching a level of approximately 20,000 sites per cell after 30 days. Measurements could also be made directly on diluted whole blood specimens. In samples freshly drawn from 35 normal donors, a mean number of 276 sites per cell were present; this increased to 858 sites per cell after storage of specimens at 4 degrees C for 24 hours. Measurement of annexin V binding to samples from patients with sickle-cell anemia revealed a marked increase in binding (mean of 12,430 sites per cell for all samples); serial measurements in a patient hospitalized with sickle-cell crisis showed a progressive decline in annexin V binding over a period of 6 days.(ABSTRACT TRUNCATED AT 250 WORDS)
3D imaging and flow characterization of the pore space of carbonate core samples (2006)

Carbonate rocks are inherently heterogeneous having been laid down in a range of depositional environments and having undergone significant diagenesis. They are particularly difficult to characterise as the pore sizes can vary over orders of magnitudes and connectivity of pores of different scales can impact greatly on flow properties. For example, separate vuggy porosity in an underlying matrix pore system can increase the porosity, but not the permeability and lead to large residual oil saturations due to trapping in vugs. A touching vug network can have a dramatic effect on permeability and lead to higher recoveries. In this paper we image a range of carbonate core material; from model carbonate cores to core material from outcrops and reservoirs via 3D via micro-CT. Image-based calculations of porosity, MICP and permeability on 3D images of the carbonate systems are directly compared to experimental data from the same or sister core material and give good agreement. The carbonate systems studied include samples with well connected macroporous systems and other where the macroporosity is poorly&#13;\nconnected. Simulation of permeability on these systems and direct analysis of local flow properties within the system allows one to directly illustrate the important role of the connectivity of macropores on flow properties. Pore network models generated from the&#13;\nimages illustrate the varied topology obtained in different carbonate samples and show a dramatic difference when compared to clastic samples. Many carbonate samples can include a significant proportion of microporosity (pores of 2 microns or less in extent) which are not directly accessible via current micro-CT capabilities. We discuss how one can map the structure and the topology of microporous regions crucial in studies of flow, production and recovery in carbonates. A hybrid numerical scheme is developed to measure the contribution of microporosity to the overall core permeability. Overall these results show the important role of identifying the connectivity of the pore sizes in dictating the single phase flow properties. Implications to two phase relative permeability and recovery are briefly discussed.
Proteopathic tau seeding predicts tauopathy in vivo (2014)

Transcellular propagation of protein aggregates, or proteopathic seeds, may drive the progression of neurodegenerative diseases in a prion-like manner. In tauopathies such as Alzheimer's disease, this model predicts that tau seeds propagate pathology through the brain via cell-cell transfer in neural networks. The critical role of tau seeding activity is untested, however. It is unknown whether seeding anticipates and correlates with subsequent development of pathology as predicted for a causal agent. One major limitation has been the lack of a robust assay to measure proteopathic seeding activity in biological specimens. We engineered an ultrasensitive, specific, and facile FRET-based flow cytometry biosensor assay based on expression of tau or synuclein fusions to CFP and YFP, and confirmed its sensitivity and specificity to tau (∼ 300 fM) and synuclein (∼ 300 pM) fibrils. This assay readily discriminates Alzheimer's disease vs. Huntington's disease and aged control brains. We then carried out a detailed time-course study in P301S tauopathy mice, comparing seeding activity versus histological markers of tau pathology, including MC1, AT8, PG5, and Thioflavin S. We detected robust seeding activity at 1.5 mo, >1 mo before the earliest histopathological stain. Proteopathic tau seeding is thus an early and robust marker of tauopathy, suggesting a proximal role for tau seeds in neurodegeneration.
Cell proliferation in colorectal tumor progression: An immunohistochemical approach to intermediate biomarkers (1992)

Cell renewal in the large intestine mucosa is normally tied to a rigidly compartmentalized model. Immunohistochemical identification of cells in S phase through uptake of bromodeoxyuridine is the method of choice for detailed compartmental mapping of proliferation, while immunohistochemical detection of proliferation-associated antigens (Ki-67, PCNA, DNA polymerase alpha) provides information in advanced tumor cases. Mucosal hyperproliferation due to inflammation may be transient (self-limited colitis, Crohn's disease, acute radiation damage) or lasting (ulcerative colitis). Progressive shifting of the proliferation zone to the crypt surface (Stage II abnormality) is a late feature of irradiated rectal mucosa and subgroups of ulcerative colitis patients at high risk for cancer. Hyperproliferation and Stage II abnormality coexist in the mucosa of patients with colorectal neoplasia, but are mutually independent and correlated to different clinical and pathological features of the disease. These cytokinetic abnormalities are highly predictive markers of the adenoma-carcinoma sequence, but are not associated with de novo adenocarcinoma. Proliferation increases progressively in the subsequent steps of this sequence, except in early cancer.
Bridged Polysilsesquioxanes. Highly Porous Hybrid Organic-Inorganic Materials (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBridged Polysilsesquioxanes. Highly Porous Hybrid Organic-Inorganic MaterialsDouglas A. Loy and Kenneth J. SheaCite this: Chem. Rev. 1995, 95, 5, 1431–1442Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/cr00037a013https://doi.org/10.1021/cr00037a013research-articleACS PublicationsRequest reuse permissionsArticle Views4932Altmetric-Citations868LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Nucleotide excision repair 3' endonuclease XPG stimulates the activity of base excision repairenzyme thymine glycol DNA glycosylase (1999)

An ionizing radiation-induced DNA lesion, thymine glycol, is removed from DNA by a thymine glycol DNA glycosylase with an apurinic/apyrimidinic (AP) lyase activity encoded by the Escherichia coli endonuclease III ( nth ) gene and its homolog in humans. Cells from Cockayne syndrome patients with mutations in the XPG gene show approximately 2-fold reduced global repair of thymine glycol. Hence, I decided to investigate the molecular mechanism of the effect of XPG protein observed in vivo on thymine glycol removal by studying the interactions of XPG protein and human endonuclease III (HsNTH) protein in vitro and the effect of XPG protein on the activity of HsNTH protein on a substrate containing thymine glycol. The XPG protein stimulates the binding of HsNTH protein to its substrate and increases its glycosylase/AP lyase activity by a factor of approximately 2 through direct interaction between the two proteins. These results provide in vitro evidence for a second function of XPG protein in DNA repair and a mechanistic basis for its stimulatory activity on HsNTH protein.
Effects of Pyruvate Decarboxylase Overproduction on Flux Distribution at the Pyruvate Branch Point in Saccharomyces cerevisiae (1998)

A multicopy plasmid carrying the PDC1 gene (encoding pyruvate decarboxylase; Pdc) was introduced in Saccharomyces cerevisiae CEN. PK113-5D. The physiology of the resulting prototrophic strain was compared with that of the isogenic prototrophic strain CEN.PK113-7D and an empty-vector reference strain. In glucose-grown shake-flask cultures, the introduction of the PDC1 plasmid caused a threefold increase in the Pdc level. In aerobic glucose-limited chemostat cultures growing at a dilution rate of 0.10 h-1, Pdc levels in the overproducing strain were 14-fold higher than those in the reference strains. Levels of glycolytic enzymes decreased by ca. 15%, probably due to dilution by the overproduced Pdc protein. In chemostat cultures, the extent of Pdc overproduction decreased with increasing dilution rate. The high degree of overproduction of Pdc at low dilution rates did not affect the biomass yield. The dilution rate at which aerobic fermentation set in decreased from 0.30 h-1 in the reference strains to 0.23 h-1 in the Pdc-overproducing strain. In the latter strain, the specific respiration rate reached a maximum above the dilution rate at which aerobic fermentation first occurred. This result indicates that a limited respiratory capacity was not responsible for the onset of aerobic fermentation in the Pdc-overproducing strain. Rather, the results indicate that Pdc overproduction affected flux distribution at the pyruvate branch point by influencing competition for pyruvate between Pdc and the mitochondrial pyruvate dehydrogenase complex. In respiratory cultures (dilution rate, <0.23 h-1), Pdc overproduction did not affect the maximum glycolytic capacity, as determined in anaerobic glucose-pulse experiments.
Interfaces are the dominant feature of dielectrics at the nanometric level (2004)

It is argued that the behavior of dielectric particles as they shrink in size through micrometric to nanometric scales will be increasingly dominated by the properties of their interfaces with the environment. The various interatomic and intermolecular forces that determine the structure of these interfaces are reviewed with special emphasis on their electrical nature. A number of situations in which passive and dynamic dielectric properties are traceable to nanometric interfacial properties are considered. It is also demonstrated that such interfaces are nanometric electromechanical (NEM) systems which acting collectively also explain piezoelectricity in macroscopic systems. Interfaces are naturally nanometric entities and must have a major role in the future development of nanotechnology. Their ubiquitous employment in living systems is noted and comparison suggests synergistic opportunities.
Analyzing interaction orderings with model checking (2004)

Human-computer interaction (HCI) systems control an ongoing interaction between end-users and computer-based systems. For software-intensive systems, a graphic user interface (GUI) is often employed for enhanced usability. Traditional approaches to validation of GUI aspects in HCI systems involve prototyping and live-subject testing. These approaches are limited in their ability to cover the set of possible human-computer interactions that a system may allow, since patterns of interaction may be long running and have large numbers of alternatives. In this paper, we propose a static analysis that is capable of reasoning about user-interaction properties of GUI portions of HCI applications written in Java using modern GUI frameworks, such as Swing/spl trade/. Our approach consists of partitioning an HCI application into three parts: the Swing library, the GUI implementation, i.e., code that interacts directly with Swing, and the underlying application. We develop models of each of these parts that preserve behavior relevant to interaction ordering. We describe how these models are generated and how we have customized a model checking framework to efficiently analyze their combination.
Increased Levels of Galactose-Deficient Anti-Gal Immunoglobulin G in the Sera of Hepatitis C Virus-Infected Individuals with Fibrosis and Cirrhosis (2007)

Hepatitis B and C viruses are major causative agents of liver fibrosis, cirrhosis, and liver cancer. Using comparative glycoproteomics, we identified a glycoprotein that is altered both in amount and in glycosylation as a function of liver fibrosis and cirrhosis. Specifically, this altered glycoprotein is an immunoglobulin G (IgG) molecule reactive to the heterophilic alpha-Gal epitope [Galalpha-1-3Galbeta1-(3)4GlcNAc-R]. While similar changes in glycosylation have been observed in several autoimmune diseases, the specific immunoglobulins and their antigen recognition profiles were not determined. Thus, we provide the first report identifying the specific antigenic recognition profile of an immunoglobulin molecule containing altered glycosylation as a function of liver disease. This change in glycosylation allowed increased reactivity with several fucose binding lectins and permitted the development of a plate-based assay to measure this change. Increased lectin reactivity was observed in 100% of the more than 200 individuals with stage III or greater fibrosis and appeared to be correlated with the degree of fibrosis. The reason for the alteration in the glycosylation of anti-Gal IgG is currently unclear but may be related to the natural history of the disease and may be useful in the noninvasive detection of fibrosis and cirrhosis.
Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-derived Exosomal Proteins Following Epithelial-Mesenchymal Transition (2013)

Epithelial-mesenchymal transition (EMT) is a highly conserved morphogenic process defined by the loss of epithelial characteristics and the acquisition of a mesenchymal phenotype. EMT is associated with increased aggressiveness, invasiveness, and metastatic potential in carcinoma cells. To assess the contribution of extracellular vesicles following EMT, we conducted a proteomic analysis of exosomes released from Madin-Darby canine kidney (MDCK) cells, and MDCK cells transformed with oncogenic H-Ras (21D1 cells). Exosomes are 40-100 nm membranous vesicles originating from the inward budding of late endosomes and multivesicular bodies and are released from cells on fusion of multivesicular bodies with the plasma membrane. Exosomes from MDCK cells (MDCK-Exos) and 21D1 cells (21D1-Exos) were purified from cell culture media using density gradient centrifugation (OptiPrep™), and protein content identified by GeLC-MS/MS proteomic profiling. Both MDCK- and 21D1-Exos populations were morphologically similar by cryo-electron microscopy and contained stereotypical exosome marker proteins such as TSG101, Alix, and CD63. In this study we show that the expression levels of typical EMT hallmark proteins seen in whole cells correlate with those observed in MDCK- and 21D1-Exos, i.e. reduction of characteristic inhibitor of angiogenesis, thrombospondin-1, and epithelial markers E-cadherin, and EpCAM, with a concomitant up-regulation of mesenchymal makers such as vimentin. Further, we reveal that 21D1-Exos are enriched with several proteases (e.g. MMP-1, -14, -19, ADAM-10, and ADAMTS1), and integrins (e.g. ITGB1, ITGA3, and ITGA6) that have been recently implicated in regulating the tumor microenvironment to promote metastatic progression. A salient finding of this study was the unique presence of key transcriptional regulators (e.g. the master transcriptional regulator YBX1) and core splicing complex components (e.g. SF3B1, SF3B3, and SFRS1) in mesenchymal 21D1-Exos. Taken together, our findings reveal that exosomes from Ras-transformed MDCK cells are reprogrammed with factors which may be capable of inducing EMT in recipient cells.
The neurotransmitters glycine and GABA stimulate glucagon‐like peptide‐1 release from the GLUTag cell line (2005)

The incretin hormone, glucagon-like peptide-1 (GLP-1) is released from intestinal L-cells following food ingestion. Its secretion is triggered by a range of nutrients, including fats, carbohydrates and proteins. We reported previously that Na(+)-dependent glutamine uptake triggered electrical activity and GLP-1 release from the L-cell model line GLUTag. However, whereas alanine also triggered membrane depolarization and GLP-1 secretion, the response was Na+ independent. A range of alanine analogues, including d-alanine, beta-alanine, glycine and l-serine, but not d-serine, triggered similar depolarizing currents and elevation of intracellular [Ca2+], a sensitivity profile suggesting the involvement of glycine receptors. In support of this idea, glycine-induced currents and GLP-1 release were blocked by strychnine, and currents showed a 58.5 mV shift in reversal potential per 10-fold change in [Cl-], consistent with the activation of a Cl(-)-selective current. GABA, an agonist of related Cl- channels, also triggered Cl- currents and secretion, which were sensitive to picrotoxin. GABA-triggered [Ca2+]i increments were abolished by bicuculline and partially impaired by (1,2,5,6-tetrahydropyridine-4-yl)methylphosphinic acid (TPMPA), suggesting the involvement of both GABA(A) and GABA(C) receptors. Expression of GABA(A), GABA(C) and glycine receptor subunits was confirmed by RT-PCR. Glycine-triggered GLP-1 secretion was impaired by bumetanide but not bendrofluazide, suggesting that a high intracellular [Cl-] maintained by Na(+)-K(+)-2Cl- cotransporters is necessary for the depolarizing response to glycine receptor ligands. Our results suggest that GABA and glycine stimulate electrical activity and GLP-1 release from GLUTag cells by ligand-gated ion channel activation, a mechanism that might be important in responses to endogenous ligands from the enteric nervous system or dietary sources.
Depletion of Free 30S Ribosomal Subunits in Escherichia coli by Expression of RNA Containing Shine-Dalgarno-Like Sequences (2002)

We have constructed synthetic coding sequences for the expression of poly(alpha,L-glutamic acid) (PLGA) as fusion proteins with dihydrofolate reductase (DHFR) in Escherichia coli. These PLGA coding sequences use both GAA and GAG codons for glutamic acid and contain sequence elements (5'-GAGGAGG-3') that resemble the consensus Shine-Dalgarno (SD) sequence found at translation initiation sites in bacterial mRNAs. An unusual feature of DHFR-PLGA expression is that accumulation of the protein is inversely related to the level of induction of its mRNA. Cellular protein synthesis was inhibited >95% by induction of constructs for either translatable or untranslatable PLGA RNAs. Induction of PLGA RNA resulted in the depletion of free 30S ribosomal subunits and the appearance of new complexes in the polyribosome region of the gradient. Unlike normal polyribosomes, these complexes were resistant to breakdown in the presence of puromycin. The novel complexes contained 16S rRNA, 23S rRNA, and PLGA RNA. We conclude that multiple noninitiator SD-like sequences in the PLGA RNA inhibit cellular protein synthesis by sequestering 30S small ribosomal subunits and 70S ribosomes in nonfunctional complexes on the PLGA mRNA.