gebhart/patrepeval huggingface dataset:
Configuring an electrostatic membrane mirror by least-squares fitting with analytically derived influence functions (1986)

Electrostatic membrane mirrors are potentially useful as aberration generators. To realize this capability, it is necessary to know the influence functions (each giving mirror response to a single electrode) and then to use a fitting procedure to determine the optimal voltage settings for reproducing a desired surface shape. We show that an approximate analytical solution of Poisson’s equation exists that can generate the influence functions for a circular electrostatic mirror. We also show, by demonstration, that it is computationally feasible to calculate these influence functions and to use them with a fitting procedure to fit the surface of a 109-electrode mirror to a desired shape. Our methods allow one to test the theoretical performance of the 109-electrode mirror; we find that good fits are obtainable for Zernike polynomials of up to degree 6.
Soft bioelectronics using nanomaterials (2016)

Recently, soft bioelectronics has attracted significant attention because of its potential applications in biointegrated healthcare devices and minimally invasive surgical tools. Mechanical mismatch between conventional electronic/optoelectronic devices and soft human tissues/organs, however, causes many challenges in materials and device designs of bio-integrated devices. Intrinsically soft hybrid materials comprising twodimensional nanomaterials are utilized to solve these issues. In this paper, we describe soft bioelectronic devices based on graphene synthesized by a chemical vapor deposition process. These devices have unique advantages over rigid electronics, particularly in biomedical applications. The functionalized graphene is hybridized with other nanomaterials and fabricated into high-performance sensors and actuators toward wearable and minimally invasive healthcare devices. Integrated bioelectronic systems constructed using these devices solve pending issues in clinical medicine while providing new opportunities in personalized healthcare.
An analysis of expressed sequence tags of developing castor endosperm using a full-length cDNA library (2007)

Our results suggest that transcriptional regulation of FAD2 and FAH12 genes maybe one of the mechanisms that contribute to a high level of ricinoleate accumulation in castor endosperm. The full-length cDNA library will be used to search for additional genes that affect ricinoleate accumulation in seed oils. Our EST sequences will also be useful to annotate the castor genome, which whole sequence is being generated by shotgun sequencing at the Institute for Genome Research (TIGR).
On the Uptake of Carbon Dioxide and Bicarbonate by Roots, and Its Influence on Growth. (1957)

From the viewpoint of the efficient use of light in photosynthesis, algae possess the advantage (over higher plants) that the medium in which they grow can be readily enriched with bicarbonate, and growth correspondingly increased. For higher plants, un- fortunately, it would hardly be possible to enrich the atmosphere appreciably with CO2. However, it oc- curred to one of us that it might be practical to en- rich the soil or the nutrient solution (17). One or two unsuccesful attempts at this have been made in the past, but without any-systematic study of the factors involved.4 Recent claims of increased yields following carbonate fertilization, by Kursanov and co- workers in Russia (see below) make a study of this problem more urgent. Such a practice would depend critically on whether roots can absorb CO2 or bicarbonate to an appreciable extent. The present work was therefore undertaken to determine the amount of CO or bicarbonate which could be absorbed by the roots of intact plants, and to study the effect of CO2, applied in the root medium, on the growth of the root system and of the whole plant. Both monoco- tyledons and dictyledons have been included in the experiments.
The MADS-Box Family of Transcription Factors (1995)

The MADS-box family of transcription factors has been defined on the basis of primary sequence similarity amongst numerous proteins from a diverse range of eukaryotic organisms including yeasts, plants, insects, amphibians and mammals. The MADS-box is a conserved motif found within the DNA-binding domains of these proteins and the name refers to four of the originally identified members: MCM1, AG, DEFA and SRF. Several proteins within this family have significant biological roles. For example, the human serum-response factor (SRF) is involved in co-ordinating transcription of the protooncogene c-fos, whilst MCM1 is central to the transcriptional control of cell-type specific genes and the pheromone response in the yeast Saccharomyces cerevisiae. The RSRF/MEF2 proteins comprise a sub-family of this class of transcription factors which are key components in muscle-specific gene regulation. Moreover, in plants, MADS-box proteins such as AG, DEFA and GLO play fundamental roles during flower development. The MADS-box is a contiguous conserved sequence of 56 amino acids, of which 9 are identical in all family members described so far. Several members have been shown to form dimers and consequently two functional regions within the MADS-box have been defined. The N-terminal half is the major determinant of DNA-binding specificity whilst the C-terminal half is necessary for dimerisation. This organisation allows the potential formation of numerous proteins, with subtly different DNA-binding specificities, from a limited number of genes by heterodimerisation between different MADS-box proteins. The majority of MADS-box proteins bind similar sites based on the consensus sequence CC(A/T)6GG although each protein apparently possesses a distinct binding specificity. Moreover, several MADS-box proteins specifically recruit other transcription factors into multi-component regulatory complexes. Such interactions with other proteins appears to be a common theme within this family and play a pivotal role in the regulation of target genes.
Multidimensional access methods (1998)

Search operations in databases require special support at the physical level. This is true for conventional databases as well as spatial databases, where typical search operations include the point query (find all objects that contain a given search point) and the region query (find all objects that overlap a given search region). More than ten years of spatial database research have resulted in a great variety of multidimensional access methods to support such operations. We give an overview of that work. After a brief survey of spatial data management in general, we first present the class of point access methods , which are used to search sets of points in two or more dimensions. The second part of the paper is devoted to spatial access methods to handle extended objects, such as rectangles or polyhedra. We conclude with a discussion of theoretical and experimental results concerning the relative performance of various approaches.
A new poly(ortho ester)-based drug delivery system as an adjunct treatment in filtering surgery. (2001)

In this rabbit model of trabeculectomy, the formulation based on POE and containing a precise amount of 5-FU reduced IOP and prolonged bleb persistence in a way similar to the conventional method of a 5-FU tamponade, while significantly reducing 5-FU toxicity.
Application of Bayesian Modeling of Autologous Antibody Responses against Ovarian Tumor-Associated Antigens to Cancer Detection (2006)

Biomarkers for early detection of epithelial ovarian cancer (EOC) are urgently needed. Patients can generate antibodies to tumor-associated antigens (TAAs). We tested multiplex detection of antibodies to candidate ovarian TAAs and statistical modeling for discrimination of sera of EOC patients and controls. Binding of serum antibody of women with EOC or healthy controls to candidate TAA-coated microspheres was assayed in parallel. A Bayesian model/variable selection approach using Markov Chain Monte Carlo computations was applied to these data, and serum CA125 values, to determine the best predictive model. The selected model was subjected to area under the receiver-operator curve (AUC) analysis. The best model generated an AUC of 0.86 [95% confidence interval (95% CI), 0.78-0.90] for discrimination between sera of EOC patients and healthy patients using antibody specific to p53, NY-CO-8, and HOXB7. Inclusion of CA125 in the model provided an AUC of 0.89 (95% CI, 0.84-0.92) compared with an AUC of 0.83 (95% CI, 0.81-0.85) using CA125 alone. However, using TAA responses alone, the model discriminated between independent sera of women with nonmalignant gynecologic conditions and those with advanced-stage or early-stage EOC with AUCs of 0.71 (95% CI, 0.67-0.76) and 0.70 (95% CI, 0.48-0.75), respectively. Serum antibody to p53 and HOXB7 is positively associated with EOC, whereas NY-CO-8-specific antibody shows negative association. Bayesian modeling of these TAA-specific serum antibody responses exhibits similar discrimination of patients with early-stage and advanced-stage EOC from women with nonmalignant gynecologic conditions and may be complementary to CA125.
Enantioselective Total Synthesis of Gracilins B and C Using Catalytic Asymmetric Diels-Alder Methodology. [Erratum to document cited in CA123:340457] (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective Total Synthesis of Gracilins B and C Using Catalytic Asymmetric Diels-Alder Methodology. [Erratum to document cited in CA123:340457]E. J. Corey and Michael A. LetavicCite this: J. Am. Chem. Soc. 1995, 117, 48, 12017Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ja00153a033https://doi.org/10.1021/ja00153a033research-articleACS PublicationsRequest reuse permissionsArticle Views361Altmetric-Citations-LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Helios Deficiency Has Minimal Impact on T Cell Development and function (2009)

Abstract Helios is a member of the Ikaros family of zinc finger transcription factors. It is expressed mainly in T cells, where it associates with Ikaros-containing complexes and has been proposed to act as a rate-limiting factor for Ikaros function. Overexpression of wild-type or dominant-negative Helios isoforms profoundly alters αβ T cell differentiation and activation, and endogenous Helios is expressed at strikingly high levels in regulatory T cells. Helios has also been implicated as a tumor suppressor in human T cell acute lymphoblastic leukemias. These studies suggest a central role for Helios in T cell development and homeostasis, but whether this protein is physiologically required in T cells is unclear. We report herein that inactivation of the Helios gene by homologous recombination does not impair the differentiation and effector cell function of αβ and γδ T cells, NKT cells, and regulatory T cells. These results suggest that Helios is not essential for T cells, and that its function can be compensated for by other members of the Ikaros family.
Effect of Strain on Deformation Microstructure and Subsequent Annealing Behavior of IF Steel Heavily Deformed by ARB Process (2004)

Ultra low-carbon interstitial free (IF) steel having ferrite (b.c.c.) single phase was deformed to various equivalent strains ranging from 0.8 to 5.6 by the accumulative roll bonding (ARB) process at 500°C. The microstructure and crystallographic feature of the deformed specimens were characterized mainly by FE-SEM/EBSD analysis. Grain subdivision during the plastic deformation up to very high strain was clarified quantitatively. After heavy deformation above 4.0 of strain, the specimens showed the lamellar boundary structure uniformly, in which the mean spacing of the lamellar boundaries was about 200nm and more than 80% of the boundaries were high-angle ones. Annealing behavior of the ARB processed IF steel strongly depended on the strain. The specimens deformed to medium strains exhibited discontinuous recrystallization characterized by nucleation and growth, while the specimens deformed above strain of 4.0 showed continuous recrystallization. The recrystallization behaviors are discussed on the basis of the microstructural and crystallographic parameters quantitatively measured in the as-deformed samples.
Fibrogenic cell reversion underlies fibrosis regression in liver (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Rolipram, a specific type IV phosphodiesterase inhibitor, is a potent inhibitor of HIV-1 replication (1995)

Rolipram is a potent inhibitor HIV-1 replication and therefore deserves further investigation as a potential therapeutic agent in the treatment of HIV-1-infected patients.
Collagen fibril formation in vitro. A quasielastic light-scattering study of early stages. (1980)

Purified rat tail tendon collagen used in our in vitro assembly studies has been characterized by quasielastic light scattering. At 4 degrees C and neutral pH it behaves as a single monomeric species with a translational diffusion coefficient, D20,w, at infinite dilution of 0.78 X 10(-7) cm2/s. This value is consistent with a somewhat flexible rod (300 X 1.2 nm( having 0.5 to 1.0 g of associated water/g of protein. When the temperature of a neutral solution of this collagen (0.1 mg/ml) is raised to 26 degrees C to initiate assembly, D20,w decreases in 10 min or less to 0.15 X 10(-7) cm2/s (Step 1) and remains constant for about 50 min (Step 2). The material present during Step 2 behaves as if it were a single high molecular weight species. These results together with earlier turbidity studies are consistent with an assembly mechanism whereby during Step 1 monomer is rapidly converted to aggregates > 1500 nm long and < 8 mm in diameter. The minimal number of collagen molecules in these aggregates is between 5 and 100, and they could be polydisperse with monomer still present. Linear growth continues during Step 2 until a critical length is reached. The constant value of D20,w may be explained by its insensitivity to length at these high asymmetries. Step 3, during which the turbidity increases and D20,w cannot be measured, consists of lateral association of the product of Step 2 to form native fibrils.
RNA polymerase III (1993)

Recent studies on RNA polymerase III (pol III) gene transcription have provided a new awareness of the molecular complexity of this process. Fortunately, while the number of transcription components has been increasing, fundamental similarities have emerged regarding the function of eukaryotic promoter elements and the factors that bind them to form preinitiation complexes. Among these, the ability of transcription factor IIIB (TFIIIB) and pol III to transcribe the Saccharomyces cerevisiae U6 gene suggests that the concept of a minimal pol II promoter comprising a TATA box and an initiator region has a parallel in the pol III system. Furthermore, for each of the three classes of eukaryotic RNA polymerase, the assembly of transcription preinitiation complexes and, to some extent, the nature of these complexes appears to be more similar than was previously anticipated. This work highlights the novel functions and transcriptional properties of newly identified pol III genes, discusses the diversity of pol III promoter structures and presents the notion that the exclusive use of extragenic promoters by some pol III genes (so-called type-3 genes) may have evolved since the divergence of yeast and higher eukaryotes. Additionally, recent progress is reviewed on the identification and cloning of subunits for TFIIIC and TFIIIB. Particular emphasis is given to two components of TFIIIB, the TATA-binding protein and a protein with TFIIB homology (PCF4), since the properties of these molecules suggest a model whereby the polymerase specificity of transcription complexes is determined.
Expression of interleukin-8 receptors on tumor cells and vascular endothelial cells in human breast cancer tissue. (1998)

Our results demonstrate that tumor and VEC express the IL-8 receptors and likely play a role in regulating tumor and VEC activation which controls proliferation, angiogenesis and metastasis in HBC.
Profiling alternatively spliced mRNA isoforms for prostate cancer classification (2006)

These results demonstrate that profiling of splice isoforms is able to provide unique and important information which cannot be detected by conventional microarrays.
Amino acids encoded downstream of gag are not required by Rous sarcoma virus protease during gag-mediated assembly (1991)

Rous sarcoma virus (RSV) and its relatives are unique in that they appear to encode their viral protease in the gag reading frame. As a result, this 124-amino-acid sequence is found at the carboxy terminus of each Gag precursor molecule and, upon ribosome frameshifting, embedded within each Gag-Pol molecule. However, rigorous proof has never been obtained for the activity of this 124-amino-acid Gag domain during virion assembly in vivo. If the active protease actually included amino acids encoded downstream in the pol reading frame, then the sequence organization would be more in line with those of other retroviruses. To examine this issue, mutations that disrupt the addition of amino acids by ribosome frameshifting were analyzed for their effects on particle assembly and Gag processing in a mammalian expression system (J. W. Wills, R. C. Craven, and J. A. Achacoso, J. Virol. 63:4331-4343, 1989). A 2-base substitution which created a nonsense mutation in the pol reading frame and was predicted to disrupt the hairpin structure of the ribosome frameshift signal had no effect on particle assembly or Gag processing, definitively showing that downstream amino acids are unnecessary. Mutations that fused the gag and pol reading frames to place 85 amino acids at the carboxy terminus of Gag hindered particle assembly and totally abolished the activity of the protease. A smaller fusion protein containing only the seven-amino-acid spacer peptide that links Gag and reverse transcriptase allowed particle formation but slowed processing. The reduced rate of processing exhibited by this mutant also revealed a previously unnoticed series of late maturation steps associated with the RSV capsid (CA) protein. Another mutant containing two substituted amino acids plus one additional amino acid at the carboxy terminus of protease nearly abolished processing. Together, these results demonstrate the importance of the carboxy terminus for proteolytic activity and suggest that this end must be unrestrained for optimal activity. If this hypothesis is correct, then the RSV protease may be encoded at the end of gag simply to ensure the production of a free carboxy terminus by translational termination.
Anchored Design of Protein-Protein Interfaces (2011)

This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.
Predictors of Behavioral Disturbance in Alzheimer's Disease (1991)

The relationship of behavioral disturbances in Alzheimer's disease to disease severity, age at onset, and the presence of extrapyramidal signs was investigated in three studies. Five categories of behavior disturbance were ascertained through structured interview with the patient's primary caregiver: apathy, agitation, psychotic symptoms, disinhibition, and irritability. In Study 1, measures of disease severity accounted for 42% of the variance in the Apathy scale but less than 20% of the variance in the remaining scales. In Study 2, the presence of extrapyramidal signs was associated with increased Apathy and moderated the association between disease severity and the Psychotic Symptoms and Irritability scales. In Study 3, age at onset was associated with the Agitation scale and moderated the association between disease severity and the Apathy, Psychotic Symptoms, and Irritability scales. The findings are discussed in terms of the clinical heterogeneity within Alzheimer's disease, the possible biological bases of these behavioral disturbances, and the psychometric issues pertinent to their measurement.
Dividing neuron precursors express neuron‐specific tubulin (1995)

Neuronal differentiation involves specific molecular and morphological changes in precursors and results in mature, postmitotic neurons. The expression of neuron-specific beta tubulin, as detected by the monoclonal antibody TuJ1, begins during the period of neurogenesis. Indeed, TuJ1 expression precedes that of the 160 kD neurofilament protein in both the central and peripheral nervous systems. In the embryonic rat spinal cord, bipolar cells and some mitotic cells in the ventricular zone were TuJ1 immunoreactive (IR). Sensory ganglia also contained cells with TuJ1-IR mitotic spindles in situ. In embryonic rat sensory and sympathetic ganglion cell cultures pulsed with the thymidine analog bromodeoxyuridine (BrdU), TuJ1 label was detected in the spindle of mitotic cells and in the midbody of cells joined at cytokinesis, indicating that neuron-specific tubulin expression was initiated during or before the final mitosis of neuronal progenitors. Dorsal root ganglion cultures included TuJ1-IR cells with several shapes that may reflect morphological transitions, from flattened stellate neural crest-like cells to differentiated bipolar neurons. Indeed, the presence of flattened TuJ1-IR cells was correlated with neurogenesis. Some sympathetic neuron precursors possessed long TuJ1-IR neurites, as well as TuJ1-IR spindle microtubules and BrdU-labeled chromosomes, indicating that these precursors can possess long processes during metaphase. These results support the hypothesis that neuron-specific tubulin expression represents an early molecular event in neuronal differentiation exhibited by a wide range of neuronal precursors. The cessation of proliferation can occur at different points during neuronal differentiation, as TuJ1-IR was detected in cells undergoing mitosis. Future studies directed toward understanding the molecules that initiate neuron-specific tubulin expression may lead to the factors that control the initial phases of neuronal differentiation.