gebhart/patrepeval huggingface dataset:
Abscisic Acid Stimulated Osmotic Adjustment and Its Involvement in Adaptation of Tobacco Cells to NaCl (1987)

Osmotic adjustment of cultured tobacco (Nicotiana tabacum L. var Wisconsin 38) cells was stimulated by 10 micromolar (+/-) abscisic acid (ABA) during adaptation to water deficit imposed by various solutes including NaCl, KCl, K(2)SO(4), Na(2)SO(4), sucrose, mannitol, or glucose. The maximum difference in cell osmotic potential (Psipi) caused by ABA treatment during adaptation to 171 millimolar NaCl was about 6 to 7 bar. The cell Psipi differences elicited by ABA were not due to growth inhibition since ABA stimulated growth of cells in the presence of 171 millimolar NaCl. ABA caused a cell Psipi difference of about 1 to 2 bar in medium without added NaCl. Intracellular concentrations of Na(+), K(+), Cl(-), free amino acids, or organic acids could not account for the Psipi differences induced by ABA in NaCl treated cells. However, since growth of NaCl treated cells is more rapid in the presence of ABA than in its absence, greater accumulation of Na(+), K(+), and Cl(-) was necessary for ion pool maintenance. Higher intracellular sucrose and reducing sugar concentrations could account for the majority of the greater osmotic adjustment of ABA treated cells. More rapid accumulation of proline associated with ABA treatment was highly correlated with the effects of ABA on cell Psipi. These and other data indicate that the role of ABA in accelerating salt adaptation is not mediated by simply stimulating osmotic adjustment.
Ligand-induced association of surface immunoglobulin with the detergent-insoluble cytoskeletal matrix of the B lymphocyte. (1982)

Ligand binding is believed to induce surface immunoglobulin (Ig) to form a physical association with the underlying cell cytoskeleton. We investigated this interaction by use of nonionic detergents, which are known to dissolve membrane proteins but preserve a detergent-insoluble cytoskeletal residue. In the absence of ligand treatment, surface Ig in the B cell plasma membrane was fully dissolved by nonionic detergent; however, interaction with a ligand converted the receptor to a novel, detergent-insoluble state. The conversion of surface Ig to a detergent-insoluble form required receptor cross-linking but occurred independently of capping. Several types of experiments demonstrated that this form of Ig was not due to the size insolubility of immune complexes and involved a stable, noncovalent association of the receptor with the detergent-insoluble, cytoskeletal residue. Incubation of ligand-bound cells at 37 degrees C promoted the degradation of surface Ig and the appearance of new, lower m.w. species, including a major soluble protein (50,000 daltons) that was antigenically related to surface Ig. These events corresponded to receptor endocytosis by several criteria (time course, temperature sensitivity, and energy dependence). Taken together, these results were consistent with the ligand-induced transmembrane attachment of receptors to the underlying cytoskeletal matrix followed by receptor internalization and catabolism.
Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: Uracil–Water Complexes and Uracil Dimers (2015)

Hydrogen-bonding interactions lead to significant changes in the infrared (IR) spectrum, like frequency shifts of the order of magnitude of hundreds of cm(-1) and increases of IR intensity for bands related to vibrational modes of functional groups directly involved in the hydrogen-bonded bridges. We are actively developing a comprehensive and robust computational protocol aimed at the quantitative reproduction of the spectra of bio-organic and hybrid organic/inorganic molecular systems with a proper account of the variety of intra- and intermolecular interactions. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended our computational protocol toward hybrid models, with the harmonic part computed at the B2PLYP level, in conjunction with the maug-cc-pVTZ basis set, or by a cost-effective ONIOM B2PLYP:B3LYP focused model, where only part of the molecular system forming the hydrogen bonds is treated at the B2PLYP level of theory. In this work experimental frequencies available for a set of four uracil-water complexes have been considered as references for the computational methodologies applied to the simulation of hydrogen-bonding effects on the infrared spectrum, obtaining average uncertainties of about 22 cm(-1) for B3LYP-D3/N07D and improved description within 10 cm(-1) by hybrid B2PLYP/B3LYP-D3 approaches. The same computational schemes have been next applied to simulate fully anharmonic IR spectra of six different hydrogen-bonded uracil dimers, providing reliable support for future experimental investigations on hydrogen-bonded systems.
Analysis of semiconductor laser optical amplifiers (1985)

A new analytical model for semiconductor laser amplifiers is presented. It has the virtue of avoiding excessive numerical computation and yet retaining sufficient accuracy for most cases of interest. The essentially new feature is the use of an appropriate mean photon density obtained by averaging the axial field distribution along the cavity length. Calculated results are presented for gain, saturation power and tuning characteristics, and their sensitivity to current density, facet reflectivities, and the spontaneous emission coefficient is explored.
3D Spectroscopic Instrumentation (2009)

In this Chapter we review the challenges of, and opportunities for, 3D spectroscopy, and how these have lead to new and different approaches to sampling astronomical information. We describe and categorize existing instruments on 4m and 10m telescopes. Our primary focus is on grating-dispersed spectrographs. We discuss how to optimize dispersive elements, such as VPH gratings, to achieve adequate spectral resolution, high throughput, and efficient data packing to maximize spatial sampling for 3D spectroscopy. We review and compare the various coupling methods that make these spectrographs ``3D,'' including fibers, lenslets, slicers, and filtered multi-slits. We also describe Fabry-Perot and spatial-heterodyne interferometers, pointing out their advantages as field-widened systems relative to conventional, grating-dispersed spectrographs. We explore the parameter space all these instruments sample, highlighting regimes open for exploitation. Present instruments provide a foil for future development. We give an overview of plans for such future instruments on today's large telescopes, in space, and in the coming era of extremely large telescopes. Currently-planned instruments open new domains, but also leave significant areas of parameter space vacant, beckoning further development.
Lower blood glucose, hyperglucagonemia, and pancreatic α cell hyperplasia in glucagon receptor knockout mice (2003)

Glucagon, the counter-regulatory hormone to insulin, is secreted from pancreatic alpha cells in response to low blood glucose. To examine the role of glucagon in glucose homeostasis, mice were generated with a null mutation of the glucagon receptor (Gcgr(-/-)). These mice display lower blood glucose levels throughout the day and improved glucose tolerance but similar insulin levels compared with control animals. Gcgr(-/-) mice displayed supraphysiological glucagon levels associated with postnatal enlargement of the pancreas and hyperplasia of islets due predominantly to alpha cell, and to a lesser extent, delta cell proliferation. In addition, increased proglucagon expression and processing resulted in increased pancreatic glucogen-like peptide 1 (GLP-1) (1-37) and GLP-1 amide (1-36 amide) content and a 3- to 10-fold increase in circulating GLP-1 amide. Gcgr(-/-) mice also displayed reduced adiposity and leptin levels but normal body weight, food intake, and energy expenditure. These data indicate that glucagon is essential for maintenance of normal glycemia and postnatal regulation of islet and alpha and delta cell numbers. Furthermore, the lean phenotype of Gcgr(-/-) mice suggests glucagon action may be involved in the regulation of whole body composition.
Fetal Aneuploidy Detection by Cell-Free DNA Sequencing for Multiple Pregnancies and Quality Issues with Vanishing Twins (2014)

Non-invasive prenatal testing (NIPT) by random massively parallel sequencing of maternal plasma DNA for multiple pregnancies is a promising new option for prenatal care since conventional non-invasive screening for fetal trisomies 21, 18 and 13 has limitations and invasive diagnostic methods bear a higher risk for procedure related fetal losses in the case of multiple gestations compared to singletons. In this study, in a retrospective blinded analysis of stored twin samples, all 16 samples have been determined correctly, with four trisomy 21 positive and 12 trisomy negative samples. In the prospective part of the study, 40 blood samples from women with multiple pregnancies have been analyzed (two triplets and 38 twins), with two correctly identified trisomy 21 cases, confirmed by karyotyping. The remaining 38 samples, including the two triplet pregnancies, had trisomy negative results. However, NIPT is also prone to quality issues in case of multiple gestations: the minimum total amount of cell-free fetal DNA must be higher to reach a comparable sensitivity and vanishing twins may cause results that do not represent the genetics of the living sibling, as described in two case reports.
Multicore bundle adjustment (2011)

We present the design and implementation of new inexact Newton type Bundle Adjustment algorithms that exploit hardware parallelism for efficiently solving large scale 3D scene reconstruction problems. We explore the use of multicore CPU as well as multicore GPUs for this purpose. We show that overcoming the severe memory and bandwidth limitations of current generation GPUs not only leads to more space efficient algorithms, but also to surprising savings in runtime. Our CPU based system is up to ten times and our GPU based system is up to thirty times faster than the current state of the art methods, while maintaining comparable convergence behavior. The code and additional results are available at http://grail.cs.washington.edu/projects/mcba.
Loss of amplified c-myc genes in the spontaneously differentiated HL-60 cells. (1994)

Amplification of the c-myc gene in the human promyelocytic leukemia cell line HL-60 is considered to be one of the major causes of its malignant phenotype. It is also well known since the establishment of the cell line that a culture of HL-60 cells contains a small but fixed percentage of spontaneously differentiated cells. We show that the spontaneous differentiation could be a result of extensive losses of amplified c-myc genes by the findings: (a) the spontaneously differentiated HL-60 cells express Mac-1 (CR3, CD11b/CD18) antigen, irreversibly stop the uptake of [3H]thymidine, and die by apoptosis; (b) these cells, when isolated, and when the copy number of c-myc genes is precisely quantitated, show extensive losses of c-myc genes; and (c) low concentrations of hydroxyurea increase the percentage of spontaneously differentiated cells in which the number of c-myc genes is further decreased. A simple theoretical consideration suggests that an active elimination process(es) must be operating besides the stochastic losses of the extrachromosomally amplified c-myc genes by unequal partition at mitosis.
Enrichment and expansion of cells using antibody‐coated micropallet arrays (2009)

Positive selection, sorting, and collection of single cells from within a heterogeneous population are required for many biological studies. We recently demonstrated a miniaturized cell array for this purpose; however, on-chip pre-enrichment and isolation of specific target cells would provide significant value for cell isolation. In the current work, mixed cell samples of fewer than 30,000 cells were used for panning by means of on-array antibody-capture to pre-enrich the target population. The cell surface receptors Fc(epsilon)R(1), c-Kit, and ErbB2 were used for positive selection of RBL, RBL, and SK-BR-3 cells, respectively, from the mixed population. The capture efficiency, selectivity, and enrichment for the target cells were calculated and compared with fibronectin-coated controls. As expected, the capture efficiency depended on the frequency of the target cell in the mixed population over the range of 0.3-33%. For a frequency of 5% target cells, the capture efficiency was 39%-53% for the three conditions, while the selectivity varied between 78% and 98% with 16-20-fold enrichment. Furthermore, single-cell cloning studies demonstrated a high cloning efficiency of target cells selectively isolated from the array. Antibody-based pre-enrichment in combination with micropallet-based cell selection will be a valuable tool for isolation and expansion of rare cells from small heterogeneous populations.
Characterization of an Akt Kinase Inhibitor with Potent Pharmacodynamic and Antitumor Activity (2008)

Akt kinases 1, 2, and 3 are important regulators of cell survival and have been shown to be constitutively active in a variety of human tumors. GSK690693 is a novel ATP-competitive, low-nanomolar pan-Akt kinase inhibitor. It is selective for the Akt isoforms versus the majority of kinases in other families; however, it does inhibit additional members of the AGC kinase family. It causes dose-dependent reductions in the phosphorylation state of multiple proteins downstream of Akt, including GSK3 beta, PRAS40, and Forkhead. GSK690693 inhibited proliferation and induced apoptosis in a subset of tumor cells with potency consistent with intracellular inhibition of Akt kinase activity. In immune-compromised mice implanted with human BT474 breast carcinoma xenografts, a single i.p. administration of GSK690693 inhibited GSK3 beta phosphorylation in a dose- and time-dependent manner. After a single dose of GSK690693, >3 micromol/L drug concentration in BT474 tumor xenografts correlated with a sustained decrease in GSK3 beta phosphorylation. Consistent with the role of Akt in insulin signaling, treatment with GSK690693 resulted in acute and transient increases in blood glucose level. Daily administration of GSK690693 produced significant antitumor activity in mice bearing established human SKOV-3 ovarian, LNCaP prostate, and BT474 and HCC-1954 breast carcinoma xenografts. Immunohistochemical analysis of tumor xenografts after repeat dosing with GSK690693 showed reductions in phosphorylated Akt substrates in vivo. These results support further evaluation of GSK690693 as an anticancer agent.
Escherichia coli Unsaturated Fatty Acid Synthesis (2009)

Although the unsaturated fatty acid (UFA) synthetic pathway of Escherichia coli is the prototype of such pathways, several unresolved issues have accumulated over the years. The key players are the fabA and fabB genes. Earlier studies of fabA transcription showed that the gene was transcribed from two promoters, with one being positively regulated by the FadR protein. The other weaker promoter (which could not be mapped with the technology then available) was considered constitutive because its function was independent of FadR. However, the FabR negative regulator was recently shown to represses fabA transcription. We report that the weak promoter overlaps the FadR-dependent promoter and is regulated by FabR. This promoter is strictly conserved in all E. coli and Salmonella enterica genomes sequenced to date and is thought to provide insurance against inappropriate regulation of fabA transcription by exogenous saturated fatty acids. Also, the fabAup promoter, a mutant promoter previously isolated by selection for increased FabA activity, was shown to be a promoter created de novo by a four-base deletion within the gene located immediately upstream of fabA. Demonstration of the key UFA synthetic reaction catalyzed by FabB has been elusive, although it was known to catalyze an elongation reaction. Strains lacking FabB are UFA auxotrophs indicating that the enzyme catalyzes an essential step in UFA synthesis. Using thioesterases specific for hydrolysis of short chain acyl-ACPs, the intermediates of the UFA synthetic pathway have been followed in vivo for the first time. These experiments showed that a fabB mutant strain accumulated less cis-5-dodecenoic acid than the parental wild-type strain. These data indicate that the key reaction in UFA synthesis catalyzed by FabB is elongation of the cis-3-decenoyl-ACP produced by FabA.
Dendritic Cells Enhance Growth and Differentiation of CD40-activated B Lymphocytes (1997)

After antigen capture, dendritic cells (DC) migrate into T cell-rich areas of secondary lymphoid organs, where they induce T cell activation, that subsequently drives B cell activation. Here, we investigate whether DC, generated in vitro, can directly modulate B cell responses, using CD40L-transfected L cells as surrogate activated T cells. DC, through the production of soluble mediators, stimulated by 3- to 6-fold the proliferation and subsequent recovery of B cells. Furthermore, after CD40 ligation, DC enhanced by 30-300-fold the secretion of IgG and IgA by sIgD- B cells (essentially memory B cells). In the presence of DC, naive sIgD+ B cells produced, in response to interleukin-2, large amounts of IgM. Thus, in addition to activating naive T cells in the extrafollicular areas of secondary lymphoid organs, DC may directly modulate B cell growth and differentiation.
NMR Analysis of Type III Antifreeze Protein Intramolecular Dimer (2001)

The structure of a new antifreeze protein (AFP) variant, RD3, from antarctic eel pout (Rhigophila dearborni) with enhanced activity has been determined for the first time by nuclear magnetic resonance spectroscopy. RD3 comprises a unique translational topology of two homologous type III AFP globular domains, each containing one flat, ice binding plane. The ice binding plane of the N domain is located approximately 3.5 A "behind" that of the C domain. The two ice binding planes are located laterally with an angle of 32 +/- 12 degrees between the planes. These results suggest that the C domain plane of RD3 binds first to the ice [1010] prism plane in the <0001> direction, which induces successive ice binding of the N domain in the <0101> direction. This manner of ice binding caused by the unique structural topology of RD3 is thought to be crucial for the significant enhancement of antifreeze activity, especially at low AFP concentrations.
High-Oleic and High-Stearic Cottonseed Oils: Nutritionally Improved Cooking Oils Developed Using Gene Silencing (2002)

Gene technology and plant breeding are combining to provide powerful means for modifying the composition of oilseeds to improve their nutritional value and provide the functional properties required for various food oil applications. Major alterations in the proportions of individual fatty acids have been achieved in a range of oilseeds using conventional selection, induced mutation and, more recently, post-transcriptional gene silencing (PTGS). In particular, a number of high-oleic oils have been developed in order to provide high-stability cooking oils. These oils provide the opportunity to replace the current widespread use of saturated fats and hydrogenated oils that contribute significantly to increased risk of cardiovascular disease due to the effect of saturated and trans-fatty acids on elevating LDL cholesterol in the bloodstream. Similarly, oils with increased stearic acid content are being developed to enable the production of solid fats without the need for hydrogenation. We have recently applied hpRNA-mediated PTGS in cotton to down-regulate key fatty acid desaturase genes and develop nutritionally-improved high-oleic (HO) and high-stearic (HS) cottonseed oils (CSOs). Silencing of the ghFAD2-1 delta12-desaturase gene raised oleic acid content from 13% to 78% and silencing of the ghSAD-1 delta9-desaturase gene substantially increased stearic acid from the normal level of 2% to as high as 40%. Additionally, palmitic acid was significantly lowered from 26% to 15% in both HO and HS lines. Intercrossing the HS and HO lines resulted in a wide range of unique intermediate combinations of palmitic, stearic, oleic and linoleic contents. The oxidative stability, flavor characteristics and physical properties of these novel CSOs are currently being evaluated by food technologists.
Elastomeric microwire-based optical gas flowmeter with stretching-enabled tunability in measurement range (2011)

We report the utilization of transparent poly(dimethylsiloxane) (PDMS) microwires as the transducer for optical gas flowmetry. The elasticity of the PDMS microwire was exploited not only to miniaturize and simplify the flowmeter but also to widen and tune the measurement range through mechanical stretching. Using a 9 mm long microwire, we achieved 2.8~9.8 dB/SLM sensitivity. A 500 μm stretching of the microwire also shifted the measurement range from 1 to 4 SLM. The experimental results agreed well with predictions based on the fluid dynamic/optical model.
Organic thermal reaction. VIII. Isolation of a potential intermediate leading to 9-phenylbicyclo[4.2.1]nona-2,4,7-triene in the thermal decomposition of .alpha.-phenyl-.alpha.-tropylacetaldehyde tosylhydrazone (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganic thermal reaction. VIII. Isolation of a potential intermediate leading to 9-phenylbicyclo[4.2.1]nona-2,4,7-triene in the thermal decomposition of .alpha.-phenyl-.alpha.-tropylacetaldehyde tosylhydrazoneHaruki Tsuruta, Katsuhiko Kurabayashi, and Toshio MukaiCite this: J. Am. Chem. Soc. 1968, 90, 25, 7167–7168Publication Date (Print):December 1, 1968Publication History Published online1 May 2002Published inissue 1 December 1968https://pubs.acs.org/doi/10.1021/ja01027a072https://doi.org/10.1021/ja01027a072research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Unmasking Representative Structures of TMP‐Active Hauser and Turbo‐Hauser Bases (2008)

The molecular engines that drive enhanced magnesiations are unveiled through structural elucidation of a 2,2,6,6-tetramethylpiperidide (TMP) Hauser base and its turbo model (see structure; Mg green, Li violet, C purple, O red, N blue, Cl yellow).