gebhart/patrepeval huggingface dataset:
Synthesis of textured complex backgrounds (1998)

The statistical characterization of realistic, complex backgrounds where targets may be embedded is essential in the optimization of methods for target acquisition. A modeling framework for complex backgrounds that yields perceptually realistic images may provide a path towards such essential characterizations. To this end, we developed a framework for the synthesis of statistical textured backgrounds. The results of the syntheses of three rock-like structures and that of grass indicate some of the capabilities of the framework. We further extended the methods to synthesize biological tissue samples which present two forms of background complexity: a slowly, spatially varying mean-background and a residual texture image. The extended framework allows synthesis of each component independently. A mathematical phantom for modeling inhomogeneous backgrounds is then proposed. First and second order statistics of various textures are then presented and a measure of distance between two images is proposed. Finally we discuss how such a framework may lead to effective statistical descriptions of such complex backgrounds for target acquisition. (C) 1998 Society of Photo-Optical Instrumentation Engineers.
Analysis of dominant-negative mutations of the Caenorhabditis elegans let-60 ras gene. (1991)

The let-60 gene of Caenorhabditis elegans controls the choice between vulval and hypodermal differentiation in response to an inductive signal from the gonad. let-60 encodes a ras protein that acts downstream of the let-23 receptor tyrosine kinase in a signal transduction pathway. Dominant-negative mutations of let-60 [let-60(dn)] cause a reduction of the gene activity in let-60(dn)/+ heterozygotes and a vulva-less mutant phenotype. We have found that nine let-60(dn) mutations cause replacements of conserved residues. Four are in two novel positions; others are in positions known previously to cause dominant-negative mutations in mammalian cells. The locations of these lesions suggest that they disrupt the ability of the ras protein to bind guanine nucleotides. Four let-60(dn) mutant genes were introduced into wild-type animals in the form of extrachromosomal arrays and were found to generate three dominant phenotypes--lethality, vulva-less, or multivulva--depending on gene dose and alleles. The dominant lethality caused by high-dose transgenic let-60(dn) genes suggests a toxic effect of these mutant genes in early development. The dominant-negative effects of these mutations in heterozygotes are likely to be caused by competition between let-60(dn) and let-60(+) protein for a positive regulator. All let-60(dn) mutations interfere with let-60(+) activity, but some alleles have partial constitutive activity, suggesting that the ability to interact with the activator is separable from the ability to exert a physiological effect (stimulation of vulval differentiation). These dn mutations might be useful for interfering with ras-mediated signal transduction pathways in other multicellular organisms.
Kindlin-3 deficiency leads to impaired erythropoiesis and erythrocyte cytoskeleton (2023)

Kindlin-3 (K3) is critical for the activation of integrin adhesion receptors in hematopoietic cells. In humans and mice, K3 deficiency is associated with impaired immunity and bone development, bleeding, and aberrant erythrocyte shape. To delineate how K3 deficiency (K3KO) contributes to anemia and misshaped erythrocytes, mice deficient in erythroid (K3KO∖EpoR-cre) or myeloid cell K3 (K3KO∖Lyz2cre), knockin mice expressing mutant K3 (Q597W598 to AA) with reduced integrin-activation function (K3KI), and control wild-type (WT) K3 mice were studied. Both K3-deficient strains and K3KI mice showed anemia at baseline, reduced response to erythropoietin stimulation, and compromised recovery after phenylhydrazine (PHZ)-induced hemolytic anemia as compared with K3WT. Erythroid K3KO and K3 (Q597W598 to AA) showed arrested erythroid differentiation at proerythroblast stage, whereas macrophage K3KO showed decreased erythroblast numbers at all developmental stages of terminal erythroid differentiation because of reduced erythroblastic island (EBI) formation attributable to decreased expression and activation of erythroblast integrin α4β1 and macrophage αVβ3. Peripheral blood smears of K3KO∖EpoR-cre mice, but not of the other mouse strains, showed numerous aberrant tear drop-shaped erythrocytes. K3 deficiency in these erythrocytes led to disorganized actin cytoskeleton, reduced deformability, and increased osmotic fragility. Mechanistically, K3 directly interacted with F-actin through an actin-binding site K3-LK48. Taken together, these findings document that erythroid and macrophage K3 are critical contributors to erythropoiesis in an integrin-dependent manner, whereas F-actin binding to K3 maintains the membrane cytoskeletal integrity and erythrocyte biconcave shape. The dual function of K3 in erythrocytes and in EBIs establish an important functional role for K3 in normal erythroid function.
Insulin-Induced GLUT4 Translocation Involves Protein Kinase C-λ-Mediated Functional Coupling between Rab4 and the Motor Protein Kinesin (2003)

Insulin stimulates glucose transport by promoting translocation of GLUT4 proteins from the perinuclear compartment to the cell surface. It has been previously suggested that the microtubule-associated motor protein kinesin, which transports cargo toward the plus end of microtubules, plays a role in translocating GLUT4 vesicles to the cell surface. In this study, we investigated the role of Rab4, a small GTPase-binding protein, and the motor protein KIF3 (kinesin II in mice) in insulin-induced GLUT4 exocytosis in 3T3-L1 adipocytes. Photoaffinity labeling of Rab4 with [gamma-(32)P]GTP-azidoanilide showed that insulin stimulated Rab4 GTP loading and that this insulin effect was inhibited by pretreatment with the phosphatidylinositol 3-kinase (PI3-kinase) inhibitor LY294002 or expression of dominant-negative protein kinase C-lambda (PKC-lambda). Consistent with previous reports, expression of dominant-negative Rab4 (N121I) decreased insulin-induced GLUT4 translocation by 45%. Microinjection of an anti-KIF3 antibody into 3T3-L1 adipocytes decreased insulin-induced GLUT4 exocytosis by 65% but had no effect on endocytosis. Coimmunoprecipitation experiments showed that Rab4, but not Rab5, physically associated with KIF3, and this was confirmed by showing in vitro association using glutathione S-transferase-Rab4. A microtubule capture assay demonstrated that insulin stimulation increased the activity for the binding of KIF3 to microtubules and that this activation was inhibited by pretreatment with the PI3-kinase inhibitor LY294002 or expression of dominant-negative PKC-lambda. Taken together, these data indicate that (i) insulin signaling stimulates Rab4 activity, the association of Rab4 with kinesin, and the interaction of KIF3 with microtubules and (ii) this process is mediated by insulin-induced PI3-kinase-dependent PKC-lambda activation and participates in GLUT4 exocytosis in 3T3-L1 adipocytes.
A Flexible Shallow Approach to Text Generation (1998)

In order to support the efficient development of NL generation systems, two orthogonal methods are currently pursued with emphasis: (1) reusable, general, and linguistically motivated surface realization components, and (2) simple, task-oriented template-based techniques. In this paper we argue that, from an application-oriented perspective, the benefits of both are still limited. In order to improve this situation, we suggest and evaluate shallow generation methods associated with increased flexibility. We advise a close connection between domain-motivated and linguistic ontologies that supports the quick adaptation to new tasks and domains, rather than the reuse of general resources. Our method is especially designed for generating reports with limited linguistic variations.
Transfection Protocol for Antisense Oligonucleotides Affects Uniformity of Transfection in Cell Culture and Efficiency of mRNA Target Reduction (2005)

In an effort to optimize the transfection of cell lines with antisense oligonucleotides, we examined cellular accumulation of a labeled oligonucleotide by flow cytometry. We were surprised to observe that a routinely used transfection protocol, a fixed lipid/oligonucleotide ratio, resulted in variable transfection efficiency depending on the concentration of oligonucleotide used. A significant population of cells, especially at lower doses of oligonucleotide and cationic lipid, were untransfected. We investigated lipid/oligonucleotide ratios, different lipid preparations, and different cell types and found that these variables did not alter the percentage of cells transfected at these lower doses of oligonucleotide. However, when lipid-oligonucleotide complexes were formed at the high dose and then diluted into a solution of lipid or a complex of lipid and unlabeled, negative control oligonucleotide, a constant percentage of cells was transfected. Under these conditions, mRNA target reduction dose-response curves were also shifted to lower doses. We hypothesize that poor transfection observed at a low concentration of lipid-oligonucleotide complex when diluted in medium is due to loss of active complexes, either by adsorption to the substrate or by changes in physical characteristics of complexes. By maintaining a constant lipid concentration, more consistent transfection was achieved.
Transient ion ejection during nanocomposite thermite reactions (2009)

We observe an intense ion pulse from nanocomposite thermite reactions, which we temporally probe using a recently developed temperature jump/time of flight mass spectrometer. These ion pulses are observed to be much shorter in duration than the overall thermite reaction time. Ion ejection appears in stages as positive ions are ejected prior to nanocomposite thermite ignition, and ignition of the thermite mixtures leads to a second ionization step which is primarily dominated by negative species. The positive species are identified from mass spectrometric measurements and the results show that the positive ion species are comprised of Na ions with minor species of Al and K ions. This observation can be explained by a diffusion based ion-current mechanism, in which strong Al ion diffusion flux formed through the oxide shell, and the surface Na and K ions from salt contaminations are ejected by the strong electrostatic repulsion. The fact that the negative ionization step occurs during the ignition event suggests a strong relation between the nanocomposite thermite reaction and the negative ionization process.
XmAb5574: In vitro and in vivo efficacy of an Fc-engineered anti-CD19 monoclonal antibody against lymphoma and leukemia and its effect on B cells in non-human primates (2008)

3078 Background: CD19 is a pan-B cell surface receptor expressed from early stages of pre-B cell development through terminal differentiation into plasma cells. It is an attractive target for cancers of lymphoid origin since it is expressed on the vast majority of Non- Hodgkin Lymphoma (NHL) and leukemia cells. The majority of NHL patients relapse after the current treatment regimen of chemotherapy combined with rituximab (CHOP-R), thus salvage regimens with non-cross resistant antibody therapies are warranted. We present the characterization of a novel humanized Fc-engineered anti-CD19 antibody (XmAb5574). Methods: We applied XmAb technology to a chimeric CD19 antibody to humanize it, increase its affinity for Fc gamma receptors, improve its effector function, and thus significantly increase its antitumor potency. This approach yielded a pre-clinical candidate (XmAb5574) that was tested in a series of in vitro cytotoxicity assays and in mouse xenograft models of NHL. We also tested the depletion of B cells in peripheral blood, lymph nodes, bone marrow and spleen of cynomolgus monkeys. Results: XmAb5574 is a novel anti-CD19 antibody that is highly cytotoxic against a panel of lymphoma and leukemia cell lines. This antibody does not appreciably internalize, and in vitro it mediates ADCC (EC50 ∼ 1 - 0.03 ng/ml) and phagocytosis (EC50 ∼ 3 - 0.1 ng/ml) superior to that of rituximab and alemtuzumab. XmAb5574-mediated ADCC is also significantly increased relative to rituximab in patient-derived ALL, CLL and MCL cells. XmAb5574 exhibits in vitro apoptotic activity that is significantly more potent than that of rituximab. Xenograft mouse models, Ramos and Raji sc and iv, show that XmAb5574 has robust protection in both protocols. Finally, we observed sustained depletion of peripheral and lymphoid B cells in cynomolgus monkeys dosed with XmAb5574. Conclusions: The main features of XmAb5574 are: i) improved in vitro cytotoxicity in tumor cells, ii) robust antitumor activity in mouse xenograft models, and iii) B cell depletion in cynomolgus monkeys. Thus XmAb5574, our anti-CD19 Fc variant antibody engineered for increased effector function, is a promising next-generation immunotherapeutic for leukemias and lymphomas. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Xencor Xencor
Recent Advancements and Applications of Logging and Surface Magnetic Resonance for Groundwater Investigations (2018)

Enhancing groundwater investigations, nuclear magnetic resonance (NMR) geophysics allows direct measurement of hydrogen in pore fluids and characterization of groundwater flow and storage parameters, including porosity, pore size, and permeability. In the field, NMR can be applied both downhole, with logging NMR tools, and non-invasively with surface NMR methods. We present recent technical advancements in logging and surface NMR, all of which are aimed to improve measurement flexibility, efficiency, and accuracy. These advancements include hardware development as well as adaptation of survey methodologies. We present applications of current logging and surface NMR technology from a range of international sites as part of practical groundwater investigations. Applications considered include characterization of the vadose zone, determination of aquifer hydrogeologic properties, detection of hydrocarbon contaminants, and imaging of thaw water in artic environments.
Recent Advances in Hydrophone-Only Receiver Deghosting (2018)

Summary Many hydrophone-only receiver deghosting approaches assume a stationary free surface profile, or that the data may be represented by linear events within a small spatial aperture. In this paper we propose methods to address these limitations. Firstly, we describe a data-driven methodology to estimate a time-variant free surface profile which may be used in combination with a modified receiver deghosting formulation. Secondly, we propose the use of a tilted hyperboloidal model of the data, which better represents travel-time moveout at short offsets in shallow water regions. Both methods are illustrated on real datasets and demonstrate more effective deghosting than conventional approaches.
Neglected Food Bubbles: The Espresso Coffee Foam (2011)

Coffee beverage known as espresso, must be topped by a velvety thick, reddish-brown foam called crema, to be considered properly prepared and to be appreciated by connoisseurs. In spite of the relevant role played by crema as a quality marker, espresso coffee foam has not yet been the subject of detailed investigations. Only recently, some aspects of the Physics and Chemistry behind the espresso coffee foam have attracted the attention of scientists. In addition to sharing several characteristics with other food foams like beer foam, for instance, the espresso coffee foam may contain solid particles (minute coffee cell-wall fragments), it is subjected to a remarkable temperature gradient and its continuous phase is an oil in water emulsion rendering it a very complex system to be studied. Moreover, in the typical regular espresso coffee cup volume (serving) of 25–30 mL, crema represents at least 10% of the total volume, and this is a limitation in obtaining experimental data by conventional instruments. The present work is aimed at reviewing the literature on espresso coffee foam. The traditional espresso brewing method will be briefly described with emphasis on the steps particularly relevant to foam formation and stabilization. In addition to present up-dated experimental data on surface properties at solid/beverage and air/beverage interface, recent advances on the espresso foam formation mechanism, as well as on foam stability, will be critically examined. The key role played by carbon dioxide generated by roasting and the effects of low and high-molecular-weight coffee compounds in promoting/inhibiting the espresso coffee foam will be discussed and emphasized.
The emergence of cross channel scripting (2010)

research-article Share on The emergence of cross channel scripting Authors: Hristo Bojinov Stanford University, Stanford, CA Stanford University, Stanford, CAView Profile , Elie Bursztein Stanford University, Stanford, CA Stanford University, Stanford, CAView Profile , Dan Boneh Stanford University, Stanford, CA Stanford University, Stanford, CAView Profile Authors Info & Claims Communications of the ACMVolume 53Issue 8August 2010pp 105–113https://doi.org/10.1145/1787234.1787257Published:01 August 2010Publication History 5citation5,177DownloadsMetricsTotal Citations5Total Downloads5,177Last 12 Months2,110Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Zero-Crossing-Time-Difference Model for Stability Analysis of VCO-Based OTAs (2019)

This paper presents the Zero-Crossing-Time-Difference Model (ZCTDM) for a Voltage-Controlled-Oscillator based Operational Transconductance Amplifier (VCO-OTA). The small-signal, linear, discrete-time model provides output current impulses at equidistant time intervals, with their magnitude proportional to the time difference between the zero-crossings of the two VCOs in the VCO-OTA. Compared to the continuous-time phase-domain model (CT-PDM) and the impulse invariant transform model (IITM), ZCTDM accounts for both the high-frequency signal generated at the output near the VCO oscillation frequency and the high-frequency input response. ZCTDM thus captures the complete loop response for a VCO-OTA in a feedback configuration, as long as the output-voltage discharge rate is less than the system update rate, which is the case in most applications. The application of the model is demonstrated with two design examples. The frequency response of the system modeled with ZCTDM is within 0.5dBRMS of the response simulated with an extensive behavioral-model, whereas the results derived using CT-PDM and IITM deviate significantly both qualitatively and quantitatively.
Development of the 2003 CU-HTK conversational telephone speech transcription system (2004)

The paper describes the development of the 2003 CU-HTK large vocabulary speech recognition system for conversational telephone speech (CTS). The system was designed based on a multipass, multibranch structure where the output of all branches is combined using system combination. A number of advanced modelling techniques, such as speaker adaptive training, heteroscedastic linear discriminant analysis, minimum phone error estimation and specially constructed single pronunciation dictionaries, were employed. The effectiveness of each of these techniques and their potential contribution to the result of system combination was evaluated in the framework of a state-of-the-art LVCSR system with sophisticated adaptation. The final 2003 CU-HTK CTS system constructed from some of these models is described and its performance on the DARPA/NIST 2003 rich transcription (RT-03) evaluation test set is discussed.
Aerodynamic factors affecting rebreathing in infants (2019)

The rebreathing of expire air, with high carbon dioxide and low oxygen concentrations, has long been implicated in unexplained Sudden Infant Death Syndrome (SIDS) when infants are placed to sleep in a prone (facedown) position. This study elucidates the effect of the aerodynamic parameters Reynolds number, Strouhal number, and Froude number on the percentage of expired air that is reinspired (rebreathed). A nasal module was designed that served as a simplified geometric representation of infant nostrils and placed above a hard, flat surface. Quantitative and flow visualization experiments were performed to measure rebreathing, using water as the working medium, under conditions of dynamic similarity. Different anatomic (e.g., tidal volume, nostril diameter), physiological (e.g., breathing frequency), and environmental (e.g., temperature, distance from the surface) factors were considered. Increases in Strouhal number (simultaneously faster and shallower breathing) always produced higher rebreathed percentages, because rolled-up vortices in the vicinity of the nostrils had less time to move away by self-induction. Positively and negatively buoyant flows resulted in significant rebreathing. In the latter case, consistent with a warm environment and a high percentage of rebreathed CO<sub>2</sub>, denser gas pooled in the vicinity of the nostrils. Reynolds numbers below 200 also dramatically increased rebreathing because the expired gas pooled much closer to the nostrils. These results clearly elucidated how the prone position dramatically increases rebreathing by a number of different mechanisms. Furthermore, the results offer plausible explanations of why a high-temperature environment and low birthweight are SIDS risk factors. NEW & NOTEWORTHY A fundamentally new aerodynamics-based approach to the study of rebreathing of expired air in infants is presented. Rebreathing is implicated in unexplained Sudden Infant Death Syndrome (SIDS) when infants sleep in a prone position. This is the first time that aerodynamic parameters are systematically varied and their effects on rebreathing quantified. The study provides us with a deeper understanding of the effects of breathing frequency, tidal volume (birthweight) and environmental conditions.
Ovonic Threshold‐Switching GexSey Chalcogenide Materials: Stoichiometry, Trap Nature, and Material Relaxation from First Principles (2020)

Density functional theory simulations are used to identify the structural factors that define the material properties of ovonic threshold switches (OTS). They show that the nature of mobility‐gap trap states in amorphous Ge‐rich Ge 50 Se 50 is related to GeGe bonds, whereas in Se‐rich Ge 30 Se 70 the Ge valence‐alternating‐pairs and Se lone‐pairs dominate. To obtain a faithful description of the electronic structure and delocalization of states, it is required to combine hybrid exchange–correlation functionals with large unit‐cell models. The extent of localization of electronic states depends on the applied external electric field. Hence, OTS materials undergo structural changes during electrical cycling of the device, with a decrease in the population of less exothermic GeGe bonds in favor of more exothermic GeSe. This reduces the amount of charge traps, which translates into coordination changes, an increase in mobility‐gap, and subsequently changes in the selector‐device electrical parameters. The threshold voltage drift process can be explained by natural evolution of the nonpreferred GeGe bonds (or “chains”/clusters thereof) in Ge‐rich Ge x Se 1– x . The effect of extrinsic doping is shown for Si and N, which introduce strong covalent bonds into the system, increase both mobility‐gap and crystallization temperature, and decrease the leakage current.