gebhart/patrepeval huggingface dataset:
Motion-based video retargeting with optimized crop-and-warp (2010)

We introduce a video retargeting method that achieves high-quality resizing to arbitrary aspect ratios for complex videos containing diverse camera and dynamic motions. Previous content-aware retargeting methods mostly concentrated on spatial considerations, attempting to preserve the shape of salient objects in each frame by removing or distorting homogeneous background content. However, sacrificeable space is fundamentally limited in video, since object motion makes foreground and background regions correlated, causing waving and squeezing artifacts. We solve the retargeting problem by explicitly employing motion information and by distributing distortion in both spatial and temporal dimensions. We combine novel cropping and warping operators, where the cropping removes temporally-recurring contents and the warping utilizes available homogeneous regions to mask deformations while preserving motion. Variational optimization allows to find the best balance between the two operations, enabling retargeting of challenging videos with complex motions, numerous prominent objects and arbitrary depth variability. Our method compares favorably with state-of-the-art retargeting systems, as demonstrated in the examples and widely supported by the conducted user study.
The HiBall Tracker (1999)

Our HiBall Tracking System generates over 2000 head-pose estimates per second with less than one millisecond of latency, and less than 0.5 millimeters and 0.02 degrees of position and orientation noise, everywhere in a 4.5 by 8.5 meter room. The system is remarkably responsive and robust, enabling VR applications and experiments that previously would have been difficult or even impossible.
Global Hairpin Folding of Tau in Solution (2006)

The microtubule-associated protein tau stabilizes microtubules in its physiological role, whereas it forms insoluble aggregates (paired helical filaments) in Alzheimer's disease. Soluble tau is considered a natively unfolded protein whose residual folding and intramolecular interactions are largely undetermined. In this study, we have applied fluorescence resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) to examine the proximity and flexibility of tau domains and the global folding. FRET pairs spanning the tau molecule were created by inserting tryptophans (donor) and cysteines (labeled with IAEDANS as an acceptor) by site-directed mutagenesis. The observed FRET distances were significantly different from those expected for a random coil. Notably, the C-terminal end of tau folds over into the vicinity of the microtubule-binding repeat domain, the N-terminus remains outside the FRET distance of the repeat domain, yet both ends of the molecule approach one another. The interactions between the domains were obliterated by denaturation in GdnHCl. Paramagnetic spin-labels attached in various domains of tau were analyzed by EPR and exhibited a high mobility throughout. The data indicate that tau retains some global folding even in its "natively unfolded" state, combined with the high flexibility of the chain.
The Assembly of Diverse Immune Receptors Is Focused on a Polar Membrane-Embedded Interaction Site (2006)

The majority of receptors responsible for activation of distinct cell types within the immune system assemble with dimeric signaling modules through interaction of a basic transmembrane residue with a pair of acidic residues of the signaling dimer. Because assembly of other membrane proteins requires specific interactions along extended stretches of transmembrane helices, we examined how transmembrane sequences flanking the polar interaction site contribute to assembly for three receptors that associate with different signaling modules-the natural killer cell receptors KIR and NKG2D and the Fc receptor for IgA, FcalphaRI. The KIR and NKG2D receptors assembled with the DAP12 and DAP10 dimers, respectively, even when the entire KIR or NKG2D transmembrane domains were replaced by polyleucine sequences with a properly positioned basic residue. In contrast, a high degree of specificity for the basic side chain could be observed because the KIR-DAP12 and FcalphaRI-Fcgamma interactions favored lysine or arginine, respectively. Steric hindrance among incompatible extra-membranous domains and competition for signaling modules also contributed to specificity of assembly. These results demonstrate that these interactions are focused on the polar site created by three ionizable transmembrane residues, and explain how the DAP12 and Fcgamma signaling modules can assemble with large, non-overlapping sets of receptors that have highly divergent transmembrane sequences.
Method of locating ultrasound-powered nerve stimulators (2012)

We have previously shown a small simple ultrasound-powered nerve stimulator. The piezoelectric implant receives power from an external driving ultrasound transducer. Focusing the ultrasound beam improves power transfer efficiency, but the implant location must be known to aim the focus. We show that currents driven by the stimulator might be detectable on the skin. By scanning the ultrasound focus and measuring the electrical response, we form an image of the implant location. This could give a feedback signal for aiming the beam, and allow multichannel addressing of several stimulators with no added circuitry in the implant.
Effect of oxytetracycline-medicated feed on antibiotic resistance of gram-negative bacteria in catfish ponds (1995)

The effect of oxytetracycline-medicated feeds on antibiotic resistance in gram-negative bacteria from fish intestines and water in catfish ponds was investigated. In experiments in the fall and spring, using ponds with no previous history of antibiotic usage, percentages of tetracycline-resistant bacteria in catfish intestines obtained from medicated ponds increased significantly after 10 days of treatment. In the fall, resistance of the intestinal and aquatic bacteria returned to pretreatment levels within 21 days after treatment. In the spring, resistance declined after treatment but remained higher than pretreatment levels for at least 21 days in intestinal bacteria and for 5 months in aquatic bacteria. Plesiomonas shigelloides, Aeromonas hydrophila, and Citrobacter freundii were isolated frequently in both spring and fall; Escherichia coli, Klebsiella pneumoniae, Edwardsiella tarda, and Enterobacter spp. were isolated primarily in the spring. Oxytetracycline treatment did not affect the distribution of bacterial species in the fall but may have accelerated a shift toward greater prevalence of members of the family Enterobacteriaceae in the spring. Multiple antibiotic resistance did not appear to be elicited by oxytetracycline treatment.
Maintenance of Pluripotency in Human Embryonic Stem Cells Is STAT3 Independent (2004)

The preservation of "stemness" in mouse embryonic stem (mES) cells is maintained through a signal transduction pathway that requires the gp130 receptor, the interleukin-6 (IL-6) family of cytokines, and the Janus Kinase-signal transducer and activator (JAK/STAT) pathway. The factors and signaling pathways that regulate "stemness" in human embryonic stem (hES) cells remain to be elucidated. Here we report that STAT3 activation is not sufficient to block hES cell differentiation when the cells are grown on mouse feeder cells or when they are treated with conditioned media from feeder cells. Human ES cells differentiate in the presence of members of the IL-6 family of cytokines including leukemia inhibitory factor (LIF) and IL-6 or in the presence of the designer cytokine hyper-IL-6, which is a complex of soluble interleukin-6 receptor (IL-6R) and IL-6 with greatly enhanced bioactivity. Human ES cells express LIF, IL-6, and gp130 receptors, as well as the downstream signaling molecules. Stimulation of human and mouse ES cells with gp130 cytokines resulted in a robust phosphorylation of downstream ERK1, ERK2, and Akt kinases, as well as the STAT3 transcription factor. Loss of the pluripotency markers Nanog, Oct-4, and TRA-1-60 was observed in hES cells during gp130-dependent signaling, indicating that signaling through this pathway is insufficient to prevent the onset of differentiation. These data underscore a fundamental difference in requirements of murine versus hES cells. Furthermore, the data demonstrate the existence of an as-yet-unidentified factor in the conditioned media of mouse feeder layer cells that acts to maintain hES cell renewal in a STAT3-independent manner.
Carrier ampholyte‐free free‐flow isoelectric focusing for separation of protein (2019)

Free-flow isoelectric focusing (FFIEF) has the merits of mild separation conditions, high recovery and resolution, but suffers from the issues of ampholytes interference and high cost due to expensive carrier ampholytes. In this paper, a home-made carrier ampholyte-free FFIEF system was constructed via orientated migration of H<sup>+</sup> and OH<sup>-</sup> provided by electrode solutions. When applying an electric field, a linear pH gradient from pH 4 to 9 (R<sup>2</sup> = 0.994) was automatically formed by the electromigration of protons and hydroxyl ions in the separation chamber. The carrier ampholyte-free FFIEF system not only avoids interference of ampholyte to detection but also guarantees high separation resolution by establishing stable pH gradient. The separation selectivity was conveniently adjusted by controlling operating voltage and optimizing the composition, concentration and flow rate of the carrier buffer. The constructed system was applied to separation of proteins in egg white, followed by MADLI-TOF-MS identification. Three major proteins, ovomucoid, ovalbumin and ovotransferrin, were successfully separated according to their pI values with 15 mmol/L Tris-acetic acid (pH = 6.5) as carrier buffer at a flow rate of 12.9 mL/min.
Dynamics of cellular entry and drug delivery by dendritic polymers into human lung epithelial carcinoma cells (2004)

Dendrimers and hyperbranched polymers are emerging as potentially ideal drug delivery vehicles because they provide a significant amount of tailorability and a large density of functional groups. This study explores the dynamics of cellular entry of dendrimers and hyperbranched polymers alone, and in the complexed form with ibuprofen, into A549 human lung epithelial carcinoma cells using UV/Vis spectroscopy, flow cytometry and fluorescence microscopy. Both dendrimers and hyperbranched polymers appear to enter these cells rapidly. The polyamidoamine (PAMAM) dendrimers, with NH2 and OH end functionalities appear to enter cells (in approx. 1 h) faster than the hyperbranched polyol (OH functionality) (in approx. 2 h). Cellular entry of PAMAM-NH2 was detected as early as 5 min. All branched polymers and their ibuprofen complexes entered A549 lung epithelial cells rapidly when compared to the pure drug. The drug payload was about 50% by weight in the complexes formed by PAMAM-NH2 dendrimers and was about 30% in the encapsulated form for Polyol-OH and PAMAM-OH. The complexation and encapsulation of ibuprofen with the polymers appear to facilitate rapid cellular entry of ibuprofen. The anti-inflammatory effect of the polymer-complexed drug was demonstrated by more rapid suppression of COX-2 mRNA levels than that achieved by the pure drug. This suggests that these dendritic polymers can act as efficient drug carriers, delivering high 'payloads' of drug even with complexation and encapsulation.
Fengycin - A novel antifungal lipopeptide antibiotic produced by Bacillus subtilis F-29-3. (1986)

Fengycin is an antifungal lipopeptide complex produced by Bacillus subtilis strain F-29-3. It inhibits filamentous fungi but is ineffective against yeast and bacteria. The inhibition is antagonized by sterols, phospholipids and oleic acid, whereas two other unsaturated fatty acids increase the antifungal effect. Fengycin consists of two main components differing by one amino acid exchange. Fengycin A is composed of 1 D-Ala, 1 L-Ile, 1 L-Pro, 1 D-allo-Thr, 3 L-Glx, 1 D-Tyr, 1 L-Tyr, 1 D-Orn, whereas in fengycin B the D-Ala is replaced by D-Val. The lipid moiety of both analogs is more variable, as fatty acids have been identified as anteiso-pentadecanoic acid (ai-C15), iso-hexadecanoic acid (i-C16), n-hexadecanoic acid (n-C16), and there is evidence for further saturated and unsaturated residues up to C18.
Improvement of the cantilever beam technique for stress measurement during the physical vapor deposition process (1998)

An improvement of an optical method for in situ measurement of the intrinsic stress in thin films is described. The method presented is based on the well-known beam bending technique using the deflection of a laser beam that reflects itself on a sample. The first new development lies in the evaluation of the bending plate equation. The second uses image processing to determine the deformation of the sample. The method has been applied to pure chromium films on glass substrates to validate the stress measurements. The reproducibility of stress measurement is of about 8%. Results show the great adaptability of the technique to any kind of stress evolution during the physical vapor deposition process and give additional information about the evolution of stress versus film thickness, in comparison with ex situ techniques. Finally, a correlation between stress measurement and microstructure has been carried out.
1,2,3-Triazole and its derivatives. Development of methods for the formation of the triazole ring (2005)

Data on the synthetic routes to substituted 1,2,3-triazoles, including those containing functional groups, based on cyclisation of various nitrogen compounds published during the last 15 years are described. Examples of using new triazole derivatives in agrochemistry, medicine and engineering are given.
Purification and Properties of Leucine Aminopeptidase II from Aspergillus oryzae (1973)

Aminopeptidase II from Aspergillus oryzae 460 was purified from the rivanol precipitable fraction. The purified enzyme was homogeneous in polyacrylamide gel disc electrophoresis. Its optimum pH is at pH 8.0 for L-leucyl-glycyl-glycine and L-leucyl-β-naphthylamide. The enzyme was inhibited by metal chelating agents and S-S dissociating agents, but not inhibited by SH reagents. The molecular weight of the enzyme was estimated to be about 61, 000 by gel filtration. The enzyme was most active toward oligopeptides of amino terminal leucine, indicating that it was a kind of leucine aminopeptidase. Thus, the enzyme was proposed to be called leucine aminopeptidase II of Asp. oryzae 460.
Amelioration of Retroviral Vector Silencing in Locus Control Region β-Globin-Transgenic Mice and Transduced F9 Embryonic Cells (1999)

Retroviral vectors are transcriptionally silenced in hematopoietic stem cells, and this phenomenon must be overcome for effective gene therapy of blood diseases. The murine stem cell virus (MSCV) vector completely silences beta-globin reporter genes regulated by locus control region (LCR) elements 5'HS2 to 5'HS4 in seven of eight transgenic mice. Here, we show that no single known MSCV silencer element is sufficient for complete LCR beta-globin transgene silencing. However, partial silencing of high-copy transgenes is conveyed by the MSCV direct repeat and promoter elements. The CpG methylation pattern of silenced and expressed MSCV promoter transgenes is virtually identical, demonstrating that silencing does not absolutely correlate with methylation status. Combined mutations in all four MSCV silencer elements leads to expression of beta-globin in 6 of 10 transgenic mice. The same mutations incorporated into the HSC1 retrovirus vector direct neo gene expression in 71% of transduced F9 embryonic carcinoma cells. These studies demonstrate that combined mutation of four retroviral silencer elements relieves complete silencing in most transgenic mice and transduced F9 cells and suggests that novel silencer elements remain. Enhanced expression of the HSC1 vector in primitive stem cells is well suited for blood gene therapy applications.
Isolating fetal cells in the maternal circulation (1995)

Fetal cells exist in maternal blood and can be utilized for prenatal genetic diagnosis. The use of polymerase chain reaction (PCR) technology on maternal blood has enabled the detection of fetal sex, Mendelian disorders (e.g. beta-globin mutations), HLA polymorphisms and fetal Rhesus (D) blood type. Enrichment for erythroblasts and trophoblasts by various density gradient and flow sorting techniques followed by fluorescence in-situ hybridization (FISH) with chromosome-specific DNA probes has allowed detection of trisomy 21, trisomy 18, Klinefelter syndrome (47,XXY) and 47,XYY. The fetal cell type that has generated the most success is the nucleated erythrocyte; however, trophoblasts, lymphocytes and granulocytes are also considered to be present in maternal blood. Fetal cells circulate in maternal blood during the first and second trimesters, with frequency increasing as gestation advances. Emphasis is thus now directed toward determining the most practical and efficacious manner for this technique to be applied to prenatal genetic diagnosis. A large scale collaboration of clinical evaluations is underway in the USA, upon completion of which assessment can be made of whether this technology can serve as an alternative to conventional invasive and non-invasive methods of prenatal cytogenetic diagnosis.
Natural Product-like Combinatorial Libraries Based on Privileged Structures. 1. General Principles and Solid-Phase Synthesis of Benzopyrans (2000)

Herein we report a novel strategy for the design and construction of natural and natural product-like libraries based on the principle of privileged structures, a term originally introduced to describe structural motifs capable of interacting with a variety of unrelated molecular targets. The identification of such privileged structures in natural products is discussed, and subsequently the 2,2-dimethylbenzopyran moiety is selected as an inaugural template for the construction of natural product-like libraries via this strategy. Initially, a novel solid-phase synthesis of the benzopyran motif is developed employing a unique cycloloading strategy that relies on the use of a new, polystyrene-based selenenyl bromide resin. Once the loading, elaboration, and cleavage of these benzopyrans was established, this new solid-phase method was then thoroughly validated through the construction of six focused combinatorial libraries designed around natural and designed molecules of recent biological interest.
Functional analysis of upstream regulating regions from the Yarrowia lipolytica XPR2 promoter (1999)

The XPR2 gene from Yarrowia lipolytica encodes an inducible alkaline extracellular protease. Its complex regulation involves pH, carbon, nitrogen and peptones. Two previously identified upstream activating sequence (UAS) regions were analysed in a reporter system, outside the XPR2 context. Fragments from the UAS regions were inserted upstream of a minimal LEU2 promoter directing the expression of a reporter gene. The activity of the hybrid promoters was assessed following integration into the Y. lipolytica genome. This study confirmed the presence of two UASs composed of several interacting elements. Within the distal UAS (UAS1), a TUF/RAP1 binding site exhibited a UAS activity, which was enhanced by the presence of two adjacent repeats, overlapping sites similar to the CAR1 upstream repressing sequence from Saccharomyces cerevisiae. Within the proximal UAS (UAS2), the UAS activity required the interaction of both an ABF1-like binding site and a decameric repeat, containing Aspergillus nidulans PacC site consensus sequences. This decameric repeat was able to mediate repression due to carbon and/or nitrogen sources as well as pH-dependent activation. A study in the context of trans-regulatory mutations in the Y. lipolytica RIM101 gene showed that the PacC-like sites, potential binding sites for YlRim101p, were implicated in the derepression of UAS2-driven expression at neutral-alkaline pH. The in vivo response of the PacC-like decamers to external pH was dependent on the status of the pH-regulated activator YlRim101p, which is homologous to the A. nidulans PacC regulator. The carbon/nitrogen regulation imposed on the decamers was shown to be independent of YlRim101p and to override its effects.
Amino Acid Metabolism in Mammalian Cell Cultures (1959)

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Biosynthesis of 2-Nor-6-deoxyerythronolide B by Rationally Designed Domain Substitution (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTBiosynthesis of 2-Nor-6-deoxyerythronolide B by Rationally Designed Domain SubstitutionLu Liu, Arinthip Thamchaipenet, Hong Fu, Mary Betlach, and Gary AshleyView Author Information KOSAN Biosciences, Incorporated 1450 Rollins Road Burlingame, California 94010 Cite this: J. Am. Chem. Soc. 1997, 119, 43, 10553–10554Publication Date (Web):October 29, 1997Publication History Received21 July 1997Published online29 October 1997Published inissue 1 October 1997https://doi.org/10.1021/ja972451yCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views340Altmetric-Citations46LEARN 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 InReddit Read OnlinePDF (62 KB) Get e-AlertscloseSUBJECTS:Bacteria,Biosynthesis,Genetics,Metabolism,Peptides and proteins Get e-Alerts
Rapid protein fold determination using unassigned NMR data (2003)

Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs), intensities of NOESY crosspeaks [nuclear Overhauser effects (NOEs)], and residual dipolar couplings (RDCs), but use of these data are limited by the time and effort needed to assign individual resonances to specific atoms. Here, we develop a method for generating low-resolution protein structures by using unassigned NMR data that relies on the de novo protein structure prediction algorithm, rosetta [Simons, K. T., Kooperberg, C., Huang, E. & Baker, D. (1997) J. Mol. Biol. 268, 209-225] and a Monte Carlo procedure that searches for the assignment of resonances to atoms that produces the best fit of the experimental NMR data to a candidate 3D structure. A large ensemble of models is generated from sequence information alone by using rosetta, an optimal assignment is identified for each model, and the models are then ranked based on their fit with the NMR data assuming the identified assignments. The method was tested on nine protein sequences between 56 and 140 amino acids and published CS, NOE, and RDC data. The procedure yielded models with rms deviations between 3 and 6 A, and, in four of the nine cases, the partial assignments obtained by the method could be used to refine the structures to high resolution (0.6-1.8 A) by repeated cycles of structure generation guided by the partial assignments, followed by reassignment using the newly generated models.