gebhart/patrepeval huggingface dataset:
Photoemission and electronic structure studies of YBa sub 2 Cu sub 3 O sub x (1991)

High-resolution angle-resolved photoelectron spectroscopy measurements are reported for YBa{sub 2}Cu{sub 3}O{sub x} when the oxygen stoichiometry x is varied between 6.9 (92 K superconductor) and 6.2 (insulator). Fermi surfaces obtained from energy distribution curve measurements on a grid scanning the entire first Brillouin zone are reported for the x = 6.9 samples. Bands along the {Gamma}-S symmetry line were measured for samples with reduced oxygen stoichiometry. For superconducting samples, these bands are essentially independent of x. As the material becomes insulating (x < 6.4), a dramatic falloff of spectral weight near E{sub F} is observed. Resonant spectral features also disappear. Efforts to observe a superconducting gap are reported. 27 refs., 8 figs.
Shaly sand rock physics analysis and seismic inversion implication (2014)

The analysis of well data from the Enfield field of the Exmouth Sub-basin, WA, indicates that both cementation and pore-filling clay appear to have a stiffening effect on the reservoir sands. The elastic contrast between brine sand and the overlying shale is often small and the large amplitudes observed from seismic data are associated with hydrocarbon content. More detailed rock physics and depth trend analysis of elastic and petrophysical properties, however, indicate significant spatial variability in the cap rock shales across the field with different sand shale mixtures, causing changes in the elastic response of the rock. Areas where shales are softer produce weak seismic amplitude contrasts even with high hydrocarbon saturation; the amplitude response being similar to areas with stiffer shales and brine-filled sands. The variations in reservoir quality are, therefore, masked by the distribution of the brine, oil and gas, as well as the variations in the cap rock. The Enfield rock physics analysis provides an example of reducing amplitude ambiguity over lithology-fluid variation and improves the chance of successful interpretation of the results of seismic inversion.
Assessing transcription factor motif drift from noisy decoy sequences. (2005)

Genome scale identification of transcription factor binding sites (TFBS) is fundamental to understanding the complexities of mRNA expression at both the cell and organismal levels. While high-throughput experimental methods provide associations between transcription factors and the genes they regulate under a specified experimental condition, computational methods are still required to pinpoint the exact location of binding. Moreover, since the binding site is an intrinsic property of the promoter region, computational methods are in principle more general than condition dependent experimental methods. Computational identification of TFBSs is complicated in at least two different ways. First, transcription factors bind a heterogeneous distribution of sites and therefore have a distribution of affinities. Second, the set of sequences for which a common site is to be determined do not all have a site for the TF of interest. In this paper, we evaluate the robustness of TFBS identification with respect to both effects. We show addition of upstream regions that do not have the TFBS destroy the specificity of the predicted binding site. We also propose a method to calculate the distance between position weight matrices that can be used to measure "drift'' from the canonical binding site. The results presented here could be useful in developing future transcription factor binding site identification algorithms.
Radon Concentration in Chandigarh, India using LR-115 detector (2020)

Abstract Radon monitoring has become a global phenomenon due to its health hazards. Mostly LR-115 detectors are being used to obtain the concentration levels of radon/thoron and their daughters. Studies have reported of the total exposure of radon to human being indor radon accounts for more than 50%. So study of radon in different region gains significance. In this paper we have studied the indoor radon concentration in various localities of Chandigarh a union territory and capital town of Punjab, India. We also compared the result with all India radon concentration level and WHO/UNSCEAR effective dose limit.
Influence of HLA Supertypes on Susceptibility and Resistance to Human Immunodeficiency Virus Type 1 Infection (2000)

Certain human leukocyte antigens, by presenting conserved immunogenic epitopes for T cell recognition, may, in part, account for the observed differences in human immunodeficiency virus type 1 (HIV-1) susceptibility. To determine whether HLA polymorphism influences HIV-1 susceptibility, a longitudinal cohort of highly HIV-1-exposed female sex workers based in Nairobi, Kenya, was prospectively analyzed. Decreased HIV-1 infection risk was strongly associated with possession of a cluster of closely related HLA alleles (A2/6802 supertype; incidence rate ratio [IRR], 0.45; 95% confidence interval [CI], 0.27-0.72; P=.0003). The alleles in this supertype are known in some cases to present the same peptide epitopes for T cell recognition. In addition, resistance to HIV-1 infection was independently associated with HLA DRB1*01 (IRR, 0.22; 95% CI, 0.06-0.60; P=.0003), which suggests that anti-HIV-1 class II restricted CD4 effector mechanisms may play an important role in protecting against viral challenge. These data provide further evidence that resistance to HIV-1 infection in this cohort of sex workers is immunologically mediated.
Synthesis and Mechanistic Interrogation of Ginkgo biloba Chemical Space en route to (–)-Bilobalide (2020)

Here we interrogate the structurally dense (1.63 mcbits/Å3) GABAA receptor antagonist bilobalide, intermediates en route to its synthesis and related mechanistic questions. 13C isotope labeling identified an unexpected bromine migration en route to an α-selective, catalytic asymmetric Reformatsky reaction, ruling out an asymmetric allylation pathway. Experiment and computation converge on the driving forces behind two surprising observations. First, an oxetane acetal is shown to persist in concentrated mineral acid (1.5 M DCl in THF-d8/D2O), and its longevity is correlated to destabilizing steric clashes between substituents. Second, a regioselective oxidation of des-hydroxybilobalide is found to rely on lactone acidification through lone-pair delocalization, which leads to extremely rapid intermolecular enolate equilibration. In addition, we describe multiple pitfalls, puzzles and unexpected reactions that ultimately uncovered a concise total synthesis. These problems arose from the high information density of bilobalide that distinguishes it from other scaffolds and may characterize natural product (NP) space more generally. Therefore, we also include a Python script to quickly (ca. 132,000 molecules/ minute) calculate information content (Böttcher scores), which may be helpful to identify important features of NP space.
Modulators of Sensitivity and Resistance to Inhibition of PI3K Identified in a Pharmacogenomic Screen of the NCI-60 Human Tumor Cell Line Collection (2012)

The phosphoinositide 3-kinase (PI3K) signaling pathway is significantly altered in a wide variety of human cancers, driving cancer cell growth and survival. Consequently, a large number of PI3K inhibitors are now in clinical development. To begin to improve the selection of patients for treatment with PI3K inhibitors and to identify de novo determinants of patient response, we sought to identify and characterize candidate genomic and phosphoproteomic biomarkers predictive of response to the selective PI3K inhibitor, GDC-0941, using the NCI-60 human tumor cell line collection. In this study, sixty diverse tumor cell lines were exposed to GDC-0941 and classified by GI(50) value as sensitive or resistant. The most sensitive and resistant cell lines were analyzed for their baseline levels of gene expression and phosphorylation of key signaling nodes. Phosphorylation or activation status of both the PI3K-Akt signaling axis and PARP were correlated with in vitro response to GDC-0941. A gene expression signature associated with in vitro sensitivity to GDC-0941 was also identified. Furthermore, in vitro siRNA-mediated silencing of two genes in this signature, OGT and DDN, validated their role in modulating sensitivity to GDC-0941 in numerous cell lines and begins to provide biological insights into their role as chemosensitizers. These candidate biomarkers will offer useful tools to begin a more thorough understanding of determinants of patient response to PI3K inhibitors and merit exploration in human cancer patients treated with PI3K inhibitors.
A facile synthesis of novel unsymmetrical bis-spiro[indole-pyrazolinyl-thiazolidine]-2,4'-diones (2008)

An elegant synthesis of some novel unsymmetrical bis-indol-2,3-diones (4a-d) has been achieved via 1-(6-bromohexyl)-1H-indol-2,3-diones (3a,b). These compounds have been further used for the synthesis of novel bis-spiroindoles (7a-d) via hitherto unknown bis Schiff's bases (6a-d).
A hybrid finite-difference and integral-equation method for modeling and inversion of marine controlled-source electromagnetic data (2016)

ABSTRACT One of the major problems in the modeling and inversion of marine controlled-source electromagnetic (CSEM) data is related to the need for accurate representation of very complex geoelectrical models typical for marine environment. At the same time, the corresponding forward-modeling algorithms should be powerful and fast enough to be suitable for repeated use in hundreds of iterations of the inversion and for multiple transmitter/receiver positions. To this end, we have developed a novel 3D modeling and inversion approach, which combines the advantages of the finite-difference (FD) and integral-equation (IE) methods. In the framework of this approach, we have solved Maxwell’s equations for anomalous electric fields using the FD approximation on a staggered grid. Once the unknown electric fields in the computation domain of the FD method are computed, the electric and magnetic fields at the receivers are calculated using the IE method with the corresponding Green’s tensor for the background conductivity model. This approach makes it possible to compute the fields at the receivers accurately without the need of very fine FD discretization in the vicinity of the receivers and sources and without the need for numerical differentiation and interpolation. We have also developed an algorithm for 3D inversion based on the hybrid FD-IE method. In the case of the marine CSEM problem with multiple transmitters and receivers, the forward modeling and the Fréchet derivative calculations are very time consuming and require using large memory to store the intermediate results. To overcome those problems, we have applied the moving sensitivity domain approach to our inversion. A case study for the 3D inversion of towed streamer EM data collected by PGS over the Troll field in the North Sea demonstrated the effectiveness of the developed hybrid method.
Interrelationships in the Regulation of TSH and Prolactin Secretion in Man: Effects of L-Dopa, TRH and Thyroid Hormone in Various Combinations* (1974)

The interrelationships in the regulation of thyroid-stimulating hormone (TSH) and prolactin (PRL) secretion in man were studied by following their response to drugs and hormones known to affect the serum concentration of either TSH or PRL. Administration of a single 0.5 oral dose of l-dopa to 12 patients with primary hypothyroidism produced a consistent suppression of the elevated TSH level in all patients. In contrast, l-dopa given to patient with known primary hypothyroidism, in whom thyroid hormone replacement therapy was discontinued for 3–4 weeks, produced suppression of TSH in only 2 out of patients, and there was no correlation between the basal TSH level and the responsiveness to l-dopa. The TSH response to l-dopa in a group of 13 euthyroid patients could not be interpreted due changes in TSH within the limits of the assay sensitivity. The TSH but not the PRL response to synthetic thyrotropin releasing hormone (TRH) was blunted early in the course of thyroid hormone replacement. After 2½ to 5 months, however, both TSH and PRL responses to TRH were virtually abolished. Administration of l-dopa 1 and 2 hr but not 3 hr prior to TRH abolished or diminished the PRL rise in response to TRH in patients with hypothyroidism of long duration. The TSH response to TRS, however, was unaltered by l-dopa given 1, 2, or 3 hr prior to TRH. The time course of both stimulatory and inhibitory responses of TSH paralleled those of PRL. These results suggest that TSH and PRL secretion in man is controlled by an interrelated pathway. If a common regulatory mechanism is involved, the pituitary thyrotrophs and lactotrophs have shown differential sensitivity to the common stimulatory and inhibitory substances.
Electronic effects on conformational preferences: A-values for aryloxy groups (1992)

A. J. Kirby and N. H. Williams, J. Chem. Soc., Chem. Commun., 1992, 1285 DOI: 10.1039/C39920001285
An Alternative Approach to Atopic Dermatitis: Part I—Case‐Series Presentation (2004)

Atopic dermatitis (AD) is a complex disease of obscure pathogenesis. A substantial portion of AD patients treated with conventional therapy become intractable after several cycles of recurrence. Over the last 20 years we have developed an alternative approach to treat many of these patients by diet and Kampo herbal medicine. However, as our approach is highly individualized and the Kampo formulae sometimes complicated, it is not easy to provide evidence to establish usefulness of this approach. In this Review, to demonstrate the effectiveness of the method of individualized Kampo therapy, results are presented for a series of patients who had failed with conventional therapy but were treated afterwards in our institution. Based on these data, we contend that there exist a definite subgroup of AD patients in whom conventional therapy fails, but the 'Diet and Kampo' approach succeeds, to heal. Therefore, this approach should be considered seriously as a second-line treatment for AD patients. In the Discussion, we review the evidential status of the current conventional strategies for AD treatment in general, and then specifically discuss the possibility of integrating Kampo regimens into it, taking our case-series presented here as evidential basis. We emphasize that Kampo therapy for AD is more 'art' than technology, for which expertise is an essential pre-requisite.
α-hemolysin is required for the activation of the autophagic pathway in Staphylococcus aureus infected cells (2010)

Staphylococcus aureus is a pathogen that causes serious infectious diseases eventually leading to septic and toxic shock. Classically S. aureus has been considered an extracellular pathogen, but cumulative evidence indicates that it invades cells and replicates intracellularly leading to staphylococcal persistence and chronic disease. It has been previously shown that this pathogen localizes to LC3-labeled compartments and subverts the autophagy pathway. One of the key features of S. aureus infection is the production of a series of virulence factors, including secreted enzymes and toxins. In the present report we present evidence that the pore-forming toxin alpha-hemolysin (Hla) is a S. aureus secreted factor which participates in the activation of the autophagic pathway. In addition, our results indicate that although the toxin elicits an autophagic response this pathway is dysfunctional as indicated by the accumulation of the LC3-II form in cell lysates obtained from intoxicated cells. In addition, not only the purified Hla toxin but also the toxin-secreting pathogen prevented the maturation of autophagosomes. Interestingly, in cells infected with the wild-type strain of S. aureus the bacteria-containing compartments which recruited LC3 onto the limiting membrane did not accumulate the acidotropic probe LysoTracker. In contrast, those phagosomes containing the Hla(-) mutant (unable to produce the toxin) localized in an acidic compartment unlabeled by LC3. These results suggest that the LC3 protein is recruited only to those damaged vacuoles (i.e., perforated by the toxin), perhaps as an attempt to protect the cells. Furthermore, we have demonstrated that the toxin-dependent activation of autophagy (although it is regulated by calcium and requires Atg5) is independent of both PI3Kinase activity and Beclin 1 suggesting the involvement of a non-canonical autophagy pathway.
Airway geometry by analysis of acoustic pulse response measurements (1977)

Serial distribution of airway properties determines in part the response of the lung to high frequency oscillations. We measured the response of excised dog lungs and lobes between 156 and 10,000 Hz and determined the area-distance function of the acoustically equivalent structure having rigid walls, regular branching, and negligible internal losses. The utility of this techique was tested by determining the effects of air trapping, removal of pleura from a dried lung, central airway smooth muscle tone. A strong correlation was found between relative changes in equivalent acoustic area and relative area changes measured radiographically in individual airways at corresponding distances. We conclude that despite departures of the properties of the real lung from the characteristics of the acoustically equivalent structure, changes in the area-distance function computed by this technique provide reasonable estimates of the magnitude and serial distribution of actual changes in airway cross-sectional area.
The neuropeptide PACAP alleviates T. gondii infection-induced neuroinflammation and neuronal impairment (2022)

Together, our findings unravel the beneficial effects of exogenous PACAP treatment upon infection-induced neuroinflammation, highlighting the potential implication of neuropeptides to promote neuronal survival and minimize synaptic prejudice.
Nutritional Effects of Cyclodextrins on Liver and Serum Lipids and Cecal Organic Acids in Rats. (2001)

The effect of dietary cyclodextrins on liver and serum lipids and cecal organic acid production was investigated. Male Wistar rats were fed a basal diet and a diet containing 5% of alpha-, beta-, or gamma-cyclodextrin. The body weight gain in rats fed the alpha-cyclodextrin diet was not significantly different from rats fed the other three kinds of diets. The feeding of dietary alpha-cyclodextrin increased total lipid and phospholipids in the liver. Beta-cyclodextrin significantly lowered serum total cholesterol and phospholipid levels compared with the basal diet et al. A decrease in serum triacylglycerol levels was also observed in beta-cyclodextrin-fed rats. Dietary alpha-cyclodextrin significantly increased the weight of cecal tissues and contents, and an approximate fourfold increase in acetate, propionate, and total organic acids was noted, indicating the fermentibility of beta-cyclodextrin compared with the basal diet. It seems likely that the suppression of serum cholesterol levels by alpha- and beta-cyclodextrins might be due to the increasing acetate and propionate productions in the cecum. cecal organic acid, cyclodextrin, serum cholesterol, rats
Automated sample cell cleaner (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAutomated sample cell cleanerD. E. Bautz and J. D. IngleCite this: Anal. Chem. 1987, 59, 20, 2534–2535Publication Date (Print):October 15, 1987Publication History Published online1 May 2002Published inissue 15 October 1987https://pubs.acs.org/doi/10.1021/ac00147a020https://doi.org/10.1021/ac00147a020research-articleACS PublicationsRequest reuse permissionsArticle Views25Altmetric-Citations4LEARN 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
Design, Synthesis, and Biological Evaluation of the First Selective Nonpeptide AT2 Receptor Agonist (2004)

The first druglike selective angiotensin II AT(2) receptor agonist (21) with a K(i) value of 0.4 nM for the AT(2) receptor and a K(i) > 10 microM for the AT(1) receptor is reported. Compound 21, with a bioavailability of 20-30% after oral administration and a half-life estimated to 4 h in rat, induces outgrowth of neurite cells, stimulates p42/p44(mapk), enhances in vivo duodenal alkaline secretion in Sprague-Dawley rats, and lowers the mean arterial blood pressure in anesthetized, spontaneously hypertensive rats. Thus, the peptidomimetic 21 exerts a similar biological response as the endogenous peptide angiotensin II after selective activation of the AT(2) receptor. Compound 21, derived from the prototype nonselective AT(1)/AT(2) receptor agonist L-162,313 will serve as a valuable research tool, enabling studies of the function of the AT(2) receptor in more detail.
Biodegradable core crosslinked star polymer nanoparticles as19F MRI contrast agents for selective imaging (2013)

With the aim of developing stimuli-responsive imaging agents, we report here the synthesis of core crosslinked star (CCS) polymers and their evaluation as pH-sensitive 19F magnetic resonance imaging (19F MRI) contrast agents. Block copolymers consisting of poly(ethylene glycol)methyl ether methacrylate (PPEGMA) as the first block and a copolymer of 2-(dimethylamino)ethyl methacrylate (DMAEMA) and 2,2,2-trifluoroethyl methacrylate (TFEMA) as the second block were synthesised using RAFT polymerisation. The polymerisation kinetics were studied in detail. The block copolymers were then used as arm precursors for the arm-first synthesis of CCS polymers through RAFT dispersion polymerisation. The synthetic conditions were investigated and optimised. CCS polymers with a degradable core were also synthesised and evaluated as 19F MRI contrast agents. The degradation of the core was confirmed by treatment with various reducing agents. The particle size, 19F NMR signal and relaxation times as well as 19F MRI imaging performance of the CCS polymers were studied at a range of value of solution pH. Significant enhancement of the image intensity was observed when the pH was decreased from 8 to 5, indicating that the CCS nanoparticles could be used as 19F MRI contrast agents for the detection of the acidic environment within tumour tissue.
<title>Automatic neighbor discovery protocol for optical networks</title> (2001)

ANDP (Automatic Neighbor Discovery Protocol) provides an automatic discovery and monitoring of the channel connections between two neighboring OXCs. Based on each channel's status and attributes, OXC can automatically discover its local topology and resource information. ANDP can also be used to detect the failed channels, which do not carry any service traffic. ANDP performs its function by the hardware interrupts from the physical layer, such as DOS. A test access module that is capable of cross-connecting any type of optical signals is necessary for ANDP.