gebhart/patrepeval huggingface dataset:
An O(N²) Square Root Unscented Kalman Filter for Visual Simultaneous Localization and Mapping (2008)

This paper develops a square root unscented Kalman filter (SRUKF) for performing video-rate visual simultaneous localization and mapping (SLAM) using a single camera. The conventional UKF has been proposed previously for SLAM, improving the handling of nonlinearities compared with the more widely used extended Kalman filter (EKF). However, no account was taken of the comparative complexity of the algorithms: In SLAM, the UKF scales as <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) in the state length, compared to the EKF's <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), making it unsuitable for video-rate applications with other than unrealistically few scene points. Here, it is shown that the SRUKF provides the same results as the UKF to within machine accuracy and that it can be reposed with complexity <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) for state estimation in visual SLAM. This paper presents results from video-rate experiments on live imagery. Trials using synthesized data show that the consistency of the SRUKF is routinely better than that of the EKF, but that its overall cost settles at an order of magnitude greater than the EKF for large scenes.
Cell lines inducibly expressing the adeno-associated virus (AAV) rep gene: requirements for productive replication of rep-negative AAV mutants (1994)

The adeno-associated virus (AAV) rep gene codes for a family of nonstructural proteins which are required for AAV gene regulation and DNA replication. In addition, rep has been implicated in a variety of activities outside the AAV life cycle which have been difficult to study, since attempts to achieve separate and constitutive expression of rep in stable cell lines have failed so far. Here we report the generation of two cell lines which inducibly express Rep78 under the control of the glucocorticoid-responsive mouse mammary tumor virus promoter. In addition, one of the cell lines constitutively expresses relatively high levels of Rep52. Both cell lines showed similar plating efficiencies with and without induction of Rep78 expression, which rules out cytotoxic effects of Rep78. The cell lines efficiently support DNA replication of a rep-negative AAV genome and initiate the formation of AAV particles. However, despite the correct sizes and stoichiometry of the three capsid proteins, the AAV particles were noninfectious. This was found to be due to a defect in the accumulation of single-stranded AAV DNA. Transient transfection of single expression constructs for constitutive, high-level expression of individual Rep proteins (either Rep78, Rep68, Rep52, or Rep40) complemented this defect. Infectious rep-negative AAV progeny was produced at varying efficiencies depending on the rep expression construct used. These data show that functional expression of full-length Rep in recombinant cell lines is possible and that the state of Rep expression is critical for the infectivity of AAV progeny produced.
The fluxgate magnetometer (1979)

Presents a review of fluxgate magnetometry based on a survey of the literature and on the work of the author and colleagues. The theory is outlined and an evaluation of the merit of the different types of sensors is made based on the sensor geometry. The design of a second-harmonic feedback magnetometer is discussed with respect to sensor configuration, frequency response, noise, offset, temperature dependence and long-term stability. Examples of the parameters are compiled from the literature and some new results on the long-term stability are presented.
Overview of pathophysiology and treatment of human lupus nephritis (2016)

Alternate video abstract introduction (see Video, Supplemental Digital Content 1, with introduction by two of the authors - VL and KT). Abstract Video: http://links.lww.com/COR/A35.
Phenotypic heterogeneity of melanoma. Relation to the differentiation program of melanoma cells. (1987)

Phenotypic heterogeneity is a characteristic feature of tumor lesions in patients with melanoma. Variability can be observed in cell morphology, pigmentation, and antigen expression. To test whether phenotypic heterogeneity could be the result of events regulated during cell differentiation, we evaluated the expression of a panel of differentiation traits on melanoma cells. Metastatic melanoma lesions from two patients, designated FD and AP, were examined histologically and found to contain mixed populations of cells. Established melanoma cell lines derived from each of these lesions were subcloned at early passage in culture (passages 7 and 8) to create a panel of clones derived from each tumor. There was heterogeneity in the expression of differentiation-related traits in clones, corresponding to distinct phenotypes observed within the original tumors. Clones from patient FD corresponded to early to intermediate stages of melanocyte differentiation, and clones from patient AP ranged from intermediate to late stages. The influence of cholera toxin and PMA on differentiation of parental cultures and subclone was studied. Results of induction studies demonstrated a number of features of differentiation of melanoma cells: regulation of differentiation traits is coordinated as a program of traits expressed sequentially at specific stages; early traits, such as the epidermal growth factor receptor and the melanoma chondroitin sulfate proteoglycan antigen, are downregulated as melanoma cells differentiate, whereas late markers, including melanin, tyrosinase activity, and antigens expressed in mature melanosomes, are upregulated; Ia (class II major histocompatibility) antigens are characteristically expressed on melanomas corresponding to early or intermediate stages of differentiation and are regulated as part of the differentiation program; minimal changes in stage of differentiation were observed during induction of parental cultures with either cholera toxin or PMA, whereas definite shifts in differentiation could be induced in selected cloned subpopulations. We conclude that melanoma cells are not frozen at a specific stage of differentiation, but rather are capable of differentiating when exposed to appropriate signals. Diversity in the differentiation state of melanoma cells can account for much of the phenotypic heterogeneity observed in melanoma lesions.
CO2 Emulsified Fracturing Fluid for Unconventional Applications (2015)

Abstract The demand for hydraulic fracturing has increased intensely with the transformation from conventional to unconventional reservoirs. High temperatures and extreme depths often amplify the complexity of any fracturing treatment. In addition, the sought synergy between different additives of the fracturing fluid becomes more challenging. As a result, the uncertainty of fracturing performance elevates as these factors become more complicated. Viscosity, propant transport and cleanup are the main criteria for assessing the performance of a fracture fluid. In this study, a fracturing fluid with unconventional composition is evaluated in terms of these parameters for the high temperature applications (300°F). Most fracturing fluids are mainly composed of water. Since the frequency of fracturing applications is increasing, massive quantities of fresh water are daily consumed in these treatments. Sea-water is an alternative to fresh water; however, it requires accurate and cautious design to prevent incompatibility and instability. Another approach to avoid high water consumption is the use of CO2 emulsified fracturing fluid, where liquid CO2 reaches up to 70 vol%, thus, reducing the need for fresh water. Moreover, CO2 emulsified fracturing fluids offer better cleanup and artificial lift to flow backs. Series of tests has been conducted to evaluate and optimize a CO2 emulsified fracturing fluid, where liquid CO2 constituted 50-70 vol% of the emulsion. The base gel is non-crosslinked and polysaccharide-based, with environmental friendly properties. The testing was done at different temperatures ranging from 220-300°F. The emulsion of liquid CO2 and base gel generated viscosity values compared to and better than guar-based foamed and gelled fracturing fluids.
Viral and cellular cytokines in AIDS-related malignant lymphomatous effusions (2000)

Kaposi sarcoma-associated herpesvirus encodes viral IL-6 (vIL-6). To investigate the potential role of vIL-6 in the pathogenesis of human immunodeficiency virus (HIV)- related primary effusion lymphomas (PEL), a sensitive enzyme-linked immunosorbent assay was developed for vIL-6 and applied to the study of PEL. Whereas vIL-6 was detectable in 6 of 8 PEL effusions (range, 1390-66 630 pg/mL), it was not detectable in any of the control effusions. As expected, all PEL effusions contained human IL-6 (range, 957-37 494 pg/mL), and 7 of 8 contained detectable human IL-10 (range, 66-2,521,297 pg/mL). Human and vIL-6 have previously been shown to induce vascular endothelial growth factor, which in turn can increase vascular permeability. The results of the current study suggest that these cytokines play a central role in the pathogenesis and manifestations of PEL. (Blood. 2000;96:1599-1601)
Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site. (1991)

The consensus binding site for the muscle regulatory factor myogenin was determined from an unbiased set of degenerate oligonucleotides using CASTing (cyclic amplification and selection of targets). Stretches of totally random sequence flanked by polymerase chain reaction priming sequences were mixed with purified myogenin or myotube nuclear extracts, DNA-protein complexes were immunoprecipitated with an antimyogenin antibody, and the DNA was amplified by polymerase chain reaction. Specific binding was obtained after four to six cycles of CASTing. The population of selected binding sites was then cloned, and a consensus was determined from sequencing individual isolates. Starting from a pool with 14 random bases, purified myogenin yielded a consensus binding site of AACAG[T/C]TGTT, while nuclear extracts retrieved the sequence TTGCACCTGTTNNTT from a pool containing 35 random bases. The latter sequence is consistent with that predicted from combining an E12/E47 half-site (N[not T]CAC) with the purified myogenin half-site ([T/C] TGTT). The presence of paired E boxes in many of the sequences isolated following CASTing with nuclear extracts proves that myogenin can bind cooperatively with other E-box-binding factors.
The realistic versus the spherical head model in EEG dipole source analysis in the presence of noise (2005)

The performance of the three-shell spherical head model versus the performance of the realistic head model is investigated when solving the inverse problem with a single dipole, in the presence of noise. This is evaluated by inspecting the average dipole location error when applying a spherical and a realistic head model, for 1000 noisy scalp potentials, originating from the same test dipole and having the same noise level. The location errors are obtained utilizing a local linearization, which is validated with a Monte Carlo simulation. For 27 electrodes, an EEG epoch of one time sample and spatially white Gaussian noise we found that the importance of the realistic head model over the spherical head model reduces by increasing the noise level.
Investigation of Subsite Preferences in Aminopeptidase A (EC 3.4.11.7) Led to the Design of the First Highly Potent and Selective Inhibitors of This Enzyme (1999)

The study of the physiological roles of the membrane-bound zinc-aminopeptidase A (glutamyl aminopeptidase, EC 3.4.11.7) needs the design of efficient and selective inhibitors of this enzyme. An acute exploration of aminopeptidase A active site was performed by a combinatorial approach using (3-amino-2-mercapto-acyl)dipeptides able to fit its S(1), S(1)', and S(2)' subsites. This analysis confirmed that the S(1) subsite is optimally blocked by a glutamate or isosteric residues and demonstrated that the S(1)' subsite is hydrophobic whereas the S(2)' subsite recognizes preferentially negatively charged residues derived from aspartic acid. The optimization of these structural parameters led to the synthesis of nanomolar and subnanomolar inhibitors of aminopeptidase A such as H(3)N(+)CH(CH(2)CH(2)SO(3)(-))CH(SH)CO-Ile-(3-COOH)Pro that exhibits a K(i) of 0.87 nM. The best compounds were synthesized by a stereochemically controlled route. These first described highly potent inhibitors could allow studies about the role of physiological substrates of APA such as angiotensin II and cholecystokinin CCK(8) in the central nervous system.
Escherichia coli Strains Blocked in Tat-Dependent Protein Export Exhibit Pleiotropic Defects in the Cell Envelope (2001)

The Tat system is a recently discovered protein export pathway that serves to translocate folded proteins, often containing redox cofactors, across the bacterial cytoplasmic membrane. Here we report that tat strains are associated with a mutant cell septation phenotype, where chains of up to 10 cells are evident. Mutant strains are also hypersensitive to hydrophobic drugs and to lysis by lysozyme in the absence of EDTA, and they leak periplasmic enzymes, characteristics that are consistent with an outer membrane defect. Both phenotypes are similar to those displayed by strains carrying point mutations in the lpxC (envA) gene. The phenotype was not replicated by mutations affecting synthesis and/or activity of all known or predicted Tat substrates.
Miniaturized three-dimensional endoscopic imaging system based on active stereovision (2003)

A miniaturized three-dimensional endoscopic imaging system is presented. The system consists of two imaging in channels that can be used to obtain an image from an object of interest and to project as tructured light onto the imaged object to measure the surface topology. The structured light was generated with a collimated monochromatic light source and a holographic binary phase grating. The imaging and projection channels were calibrated by use of a modified pinhole camera. The surface profile was extracted by use of triangulation between the projected feature points and the two channel ofthe endoscope. The imaging system was evaluated in three-dimensional measurements of several objects with known geometries. The results show that surface profiles of the objects with different surfaces and dimensions can be obtained at high accuracy. The in vivo measurements at tissue sites of human skin and an oral cavity demonstrated the potential of the technique for clinical applications.
CAR models: next-generation CAR modifications for enhanced T-cell function (2016)

T cells genetically targeted with a chimeric antigen receptor (CAR) to B-cell malignancies have demonstrated tremendous clinical outcomes. With the proof in principle for CAR T cells as a therapy for B-cell malignancies being established, current and future research is being focused on adapting CAR technology to other cancers, as well as enhancing its efficacy and/or safety. The modular nature of the CAR, extracellular antigen-binding domain fused to a transmembrane domain and intracellular T-cell signaling domains, allows for optimization by replacement of the various components. These modifications are creating a whole new class of therapeutic CARs. In this review, we discuss the recent major advances in CAR design and how these modifications will impact its clinical application.
Pseudomonas oleovorans as a Source of Poly(β-Hydroxyalkanoates) for Potential Applications as Biodegradable Polyesters (1988)

Pseudomonas oleovorans was grown in homogeneous media containing n-alkanoic acids, from formate to decanoate, as the sole carbon sources. Formation of intracellular poly(beta-hydroxyalkanoates) was observed only for hexanoate and the higher n-alkanoic acids. The maximum isolated polymer yields were approximately 30% of the cellular dry weight with growth on either octanoate or nonanoate. In most cases, the major repeating unit in the polymer had the same chain length as the n-alkanoic acid used for growth, but units with two carbon atoms less or more than the acid used as a carbon source were also generally present in the polyesters formed. Indeed, copolymers containing as many as six different types of beta-hydroxyalkanoate units were formed. The weight average molecular weights of the poly(beta-hydroxyalkanoate) copolymers produced by P. oleovorans ranged from 90,000 to 370,000. In spite of the higher cell yields obtained with octanoate and nonanoate, the use of hexanoate and heptanoate yielded higher-molecular-weight polymers. These copolyesters represent an entirely new class of biodegradable thermoplastics.
Culture of Animal Cells (2005)

The most complete resource on the techniques, equipment,principles, and practices of animal cell culture

Since publication of the previous edition of this benchmark text, numerous groundbreaking advances have occurred in stem cell research, cloning, tissue engineering, and in vitro toxicity testing. These and other developments have been incorporated into this fully revised and expanded Fifth Edition of Culture of Animal Cells. In addition, to answer the needs of the exponential increase in newcomers to cell culture, particularly in the biopharmaceutical industry, a completely new chapter on training in cell culture technology has been introduced.

The most complete resource on the techniques, equipment, principles, and practices of animal cell culture, this text offers a complete background related to growth of animal cells in culture. Beginning with laboratory design, safety, validation and bioethics, then continuing with preparation of media, primary culture and cell lines, through to characterization and authentication, contamination, specialized techniques, and troubleshooting, the coverage includes:
* An all-new section of training exercises, separated into basic, intermediate, and advanced procedures, cross-referenced to the relevant protocols
* New coverage of stem cells, bioethics, validation, cloning, cell signaling, in vitro toxicity testing, and tissue engineering
* An expanded full-color atlas section, with images of primary culture, cell lines, subculture, differentiation, cancer cells and transformation, three-dimensional culture, contamination, and specialized equipment
* Enhanced treatment of troubleshooting, with full cross-referencing to the relevant protocols and sections of text
* Fully updated references
* The clearest, most consistent presentation of step-by-step protocols available
* Numerous diagrams, photographs, tables, and charts
* Detailed and up-to-date information on reagent preparation and sourcing of materials and equipment, including a fully updated list of suppliers and other resources with Web sites

Indispensable for clinical and biopharmaceutical researchers and scientists, students, trainees, and technicians, this landmark text presents the most accessible and comprehensive introduction available to the culture and experimental manipulation of animal cells.
Dual Receptor Recognizing Cell Penetrating Peptide for Selective Targeting, Efficient Intratumoral Diffusion and Synthesized Anti-Glioma Therapy (2015)

Cell penetrating peptides (CPPs) were widely used for drug delivery to tumor. However, the nonselective in vivo penetration greatly limited the application of CPPs-mediated drug delivery systems. And the treatment of malignant tumors is usually followed by poor prognosis and relapse due to the existence of extravascular core regions of tumor. Thus it is important to endue selective targeting and stronger intratumoral diffusion abilities to CPPs. In this study, an RGD reverse sequence dGR was conjugated to a CPP octa-arginine to form a CendR (R/KXXR/K) motif contained tandem peptide R8-dGR (RRRRRRRRdGR) which could bind to both integrin αvβ3 and neuropilin-1 receptors. The dual receptor recognizing peptide R8-dGR displayed increased cellular uptake and efficient penetration ability into glioma spheroids in vitro. The following in vivo studies indicated the active targeting and intratumoral diffusion capabilities of R8-dGR modified liposomes. When paclitaxel was loaded in the liposomes, PTX-R8-dGR-Lip induced the strongest anti-proliferation effect on both tumor cells and cancer stem cells, and inhibited the formation of vasculogenic mimicry channels in vitro. Finally, the R8-dGR liposomal drug delivery system prolonged the medium survival time of intracranial C6 bearing mice by 2.1-fold compared to the untreated group, and achieved an exhaustive anti-glioma therapy including anti-tumor cells, anti-vasculogenic mimicry and anti-brain cancer stem cells. To sum up, all the results demonstrated that R8-dGR was an ideal dual receptor recognizing CPP with selective glioma targeting and efficient intratumoral diffusion, which could be further used to equip drug delivery system for effective glioma therapy.
Synthesis and quantitative structure-activity relationships of antiallergic 2-hydroxy-N-(1H-tetrazol-5-yl)benzamides and N-(2-hydroxyphenyl)-1H-tetrazole-5-carboxamides (1986)

The synthesis and antiallergic activity of a series of 2-hydroxy-N-1H-tetrazol-5-ylbenzamides and isomeric N-(2-hydroxyphenyl)-1H-tetrazole-5-carboxamides is described. A relationship between structure and intravenous antiallergic activity in the rat passive cutaneous anaphylaxis (PCA) test has been established using a Hansch/Free-Wilson model and used to direct studies toward potent derivatives. The contribution of physicochemical properties to activity is discussed. One member of this series, N-(3-acetyl-5-fluoro-2-hydroxyphenyl)-1H-tetrazole-5-carboxamide (3f), which was selected for further evaluation, has an ID50 value of 0.16 mg/kg po and is 130 times more potent than disodium cromoglycate (DSCG) on intravenous administration.
The Guanylyltransferase Domain of Mammalian mRNA Capping Enzyme Binds to the Phosphorylated Carboxyl-terminal Domain of RNA Polymerase II (1998)

We have conducted a biochemical and genetic analysis of mouse mRNA capping enzyme (Mce1), a bifunctional 597-amino acid protein with RNA triphosphatase and RNA guanylyltransferase activities. The principal conclusions are as follows: (i) the mammalian capping enzyme consists of autonomous and nonoverlapping functional domains; (ii) the guanylyltransferase domain Mce1(211-597) is catalytically active in vitro and functional in vivo in yeast in lieu of the endogenous guanylyltransferase Ceg1; (iii) the guanylyltransferase domain per se binds to the phosphorylated RNA polymerase II carboxyl-terminal domain (CTD), whereas the triphosphatase domain, Mce1(1-210), does not bind to the CTD; and (iv) a mutation of the active site cysteine of the mouse triphosphatase elicits a strong growth-suppressive phenotype in yeast, conceivably by sequestering pre-mRNA ends in a nonproductive complex or by blocking access of the endogenous yeast triphosphatase to RNA polymerase II. These findings contribute to an emerging model of mRNA biogenesis wherein RNA processing enzymes are targeted to nascent polymerase II transcripts through contacts with the CTD. The phosphorylation-dependent interaction between guanylyltransferase and the CTD is conserved from yeast to mammals.