gebhart/patrepeval huggingface dataset:
Size Dependence of the Plasmonic Near-Field Measured via Single-Nanoparticle Photoimaging (2013)

Plasmonic nanostructures are being exploited for optical and photovoltaic applications, particularly where field enhancement of optical processes is desirable. Extensive work has focused on the optimization of plasmonic near-fields by geometric tuning and interparticle coupling, but the size tunability of near-fields has received less attention. We used single-nanoparticle photochemical imaging to characterize the near-field intensity around a plasmonic nanoparticle as a function of size. The measured near-field intensity increases with nanoparticle size, reaching a maximum at a size of 50 nm, followed by a decrease at larger sizes. An electrodynamic model explains both the measured size dependence and the optimum size for field enhancement. Whereas intrinsic damping is size-independent, the smallest nanoparticles exhibit weak fields due to surface damping of electrons. On the other end, larger nanoparticles show low field enhancement due to strong radiative scattering. The measured volcano trend, however, most closely mirrors the size dependence of electromagnetic retardation. Above 50 nm size, retardation causes damping, but below a size of 50 nm, it surprisingly reduces nonradiative dissipation, a previously unknown effect. The size dependence of plasmonic field intensity described here can guide design of plasmonic nanostructures for applications in spectroscopy, photovoltaics, photocatalysis, and lithography.
In vivo mri of the left coronary artery branching patterns in mice and the myocardial area-at-risk during coronary ligation: towards improved understanding of an important model (2010)

Introduction Ligation of the left coronary artery (LCA) is frequently used to study ischemia in mice. However, the branching pattern of the LCA in mice and the impact of this has not been characterized. MRI of LCA branching patterns was thus performed in mice in vivo and correlated with fluorescence reflectance imaging (FRI) of the percent myocardial area at risk (AAR) during coronary ligation.
Oil Palm Biomass As Potential Substitution Raw Materials For Commercial Biomass Briquettes Production (2008)

Palm oil industry generates vast amount of palm biomass. Converting palm biomass into a uniform and solid fuel through briquetting process appears to be an attractive solution in upgrading its properties and add value. In this study, raw materials including empty fruit bunch (EFB), in powder and fibre forms, palm kernel expeller (PKE) and sawdust were densified into briquettes at high temperature and pressure using screw extrusion technology. The briquettes were analysed to determine its physical and chemical properties, mechanical strength and burning characteristics. It was found that briquettes made either from 100% pulverized EFB or mixed with sawdust exhibited good burning properties. EFB fibre and PKE, due to their physical properties, were recommended to be blended with sawdust in producing quality briquettes. In overall, converting palm biomass into briquettes has increased its energy content and reduced moisture content about minimum of 5% and 38% respectively compared to its raw materials. The properties of palm biomass briquettes obtained from the study were compared to the commercial sawdust briquettes properties and to the minimum requirements of DIN 51731. The details of the study were highlighted in this paper. Palm biomass briquettes can become an important renewable energy fuel source in the future.
High-field conductivity measurements and search for threshold in PET films (2002)

In the paper results of measurements of DC charging current performed at different values of electrical field and temperature on PET films are presented. The aim is to investigate the threshold of space charges trapping, detected on the basis of the appearance of a maximum in the charging current vs. time characteristics. The values of threshold (function of temperature) thus derived are compared with the results of accelerated life tests performed, under DC voltage and temperature, on the same films until the occurrence of electrical breakdown. It is shown that a relationship exists between the threshold of charge trapping, detected by charging current measurements, and that of electrical breakdown, deriving from multi-stress life tests.
A Computational Model for Sex-Specific Genetic Architecture of Complex Traits in Humans: Implications for Mapping Pain Sensitivity (2008)

Understanding differences in the genetic architecture of complex traits between the two sexes has significant implications for evolutionary studies and clinical diagnosis. However, our knowledge about sex-specific genetic architecture is limited largely because of a lack of analytical models that can detect and quantify the effects of sex on the complexity of quantitative genetic variation. Here, we derived a statistical model for mapping DNA sequence variants that contribute to sex-specific differences in allele frequencies, linkage disequilibria, and additive and dominance genetic effects due to haplotype diversity. This model allows a genome-wide search for functional haplotypes and the estimation and test of haplotype by sex interactions and sex-specific heritability. The model, validated by simulation studies, was used to detect sex-specific functional haplotypes that encode a pain sensitivity trait in humans. The model could have important implications for mapping complex trait genes and studying the detailed genetic architecture of sex-specific differences.
Direct Growth of a-Plane GaN on r-Plane Sapphire Substrate by Metalorganic Vapor Phase Epitaxy (2007)

We have investigated the direct growth of nonpolar a-plane GaN layers on an r-plane sapphire substrate by metalorganic vapor-phase epitaxy (MOVPE). A high-density nucleation of GaN islands was obtained on the r-plane sapphire substrate at the initial stage of the high-temperature growth without a buffer layer, which resulted in a two-dimensional (2D) growth mode. We studied the effects of V/III ratio growth conditions on the surface morphology and growth features of an a-plane GaN layer. The results showed that a high density of pits with an inverse-pyramidal shape were formed at a high V/III ratio, whereas a relatively low density of pits were formed at a low V/III ratio due to the increase in the rate of lateral growth along the c-axis direction. We successfully grew a-plane GaN layers with a flat and pit-free surface using the "two-step growth method". The method consisted of growing a first layer at a high V/III ratio and growing a second layer at a low V/III ratio. We found that the first layer plays an important role in GaN layer growth. The formation of a void-free GaN layer with sidewall facets in the first step leads to a flat and pit-free layer grown at a high rate of lateral growth along the c-axis direction in the second step.
Analysis of the Spur Characteristics of Edge-Combining DLL-Based Frequency Multipliers (2009)

A complete analysis of the spur characteristics of edge-combining delay-locked loop (DLL)-based frequency multipliers is presented in this brief. The novelty of this analysis is the fact that it can be used to estimate the effect of both the in-lock error and the delay-stage mismatch on the spurious level of the frequency multiplier with low computational complexity. In addition, a way to reduce the mismatch between the delay cells in the delay line is discussed via an analytic model and verified by the implementation of a delay cell in a 65-nm CMOS process.
CDK 4/6 Inhibition Overcomes Acquired and Inherent Resistance to PI3Kα Inhibition in Pre-Clinical Models of Head and Neck Squamous Cell Carcinoma (2020)

Activating alterations in <i>PIK3CA</i>, the gene coding for the catalytic subunit of phosphoinositide-3-kinase (PI3K), are prevalent in head and neck squamous cell carcinoma (HNSCC) and thought to be one of the main drivers of these tumors. However, early clinical trials on PI3K inhibitors (PI3Ki) have been disappointing due to the limited durability of the activity of these drugs. To investigate the resistance mechanisms to PI3Ki and attempt to overcome them, we conducted a molecular-based study using both HNSCC cell lines and patient-derived xenografts (PDXs). We sought to simulate and dissect the molecular pathways that come into play in PIK3CA-altered HNSCC treated with isoform-specific PI3Ki (BYL719, GDC0032). In vitro assays of cell viability and protein expression indicate that activation of the mTOR and cyclin D1 pathways is associated with resistance to PI3Ki. Specifically, in BYL719-resistant cells, BYL719 treatment did not induce pS6 and pRB inhibition as detected in BYL719-sensitive cells. By combining PI3Ki with either mammalian target of rapamycin complex 1 (mTORC1) or cyclin D1 kinase (CDK) 4/6 specific inhibitors (RAD001 and abemaciclib, respectively), we were able to overcome the acquired resistance. Furthermore, we found that PI3Ki and CDK 4/6 inhibitors have a synergistic anti-tumor effect when combined in human papillomavirus (HPV)-negative/PIK3CA-WT tumors. These findings provide a rationale for combining PI3Ki and CDK 4/6 inhibitors to enhance anti-tumor efficacy in HNSCC patients.
A threshold concentration of anti-merozoite antibodies is required for protection from clinical episodes of malaria (2013)

Antibodies to selected Plasmodium falciparum merozoite antigens are often reported to be associated with protection from malaria in one epidemiological cohort, but not in another. Here, we sought to understand this paradox by exploring the hypothesis that a threshold concentration of antibodies is necessary for protection. We analyzed data from two independent cohorts along the Kenyan coast, one in which antibodies to AMA1, MSP-2 and MSP-3 were associated with protection from malaria (Chonyi) and another in which this association was not observed (Junju). We used a malaria reference reagent to standardize antibody measurements across both cohorts, and applied statistical methods to derive the threshold concentration of antibodies against each antigen that best correlated with a reduced risk of malaria (the protective threshold), in the Chonyi cohort. We then tested whether antibodies in Junju reached the protective threshold concentrations observed in the Chonyi cohort. Except for children under 3 years, the age-matched proportions of children achieving protective threshold concentrations of antibodies against AMA1 and MSP-2 were significantly lower in Junju compared to Chonyi (Fishers exact test, P<0.01). For MSP-3, this difference was significant only among 4-5 year olds. We conclude that although antibodies are commonly detected in malaria endemic populations, they may be present in concentrations that are insufficient for protection. Our results have implications for the analysis and interpretation of similar data from immuno-epidemiological studies.
Sex determines the presentation and outcomes in MPN and is related to sex-specific differences in the mutational burden (2020)

The factors underlying the variable presentation and clinical course of myeloproliferative neoplasms (MPNs) remain unclear. The aim of this study was to evaluate the independent effect of sex on MPN presentation and outcomes. A total of 815 patients with essential thrombocytosis, polycythemia vera, or primary myelofibrosis were evaluated between 2005 and 2019, and the association of sex with presenting phenotype, JAK2 V617F burden, progression, and survival was examined. Men presented more often with primary myelofibrosis vs essential thrombocytosis (relative risk, 3.2; P < .001) and polycythemia vera (relative risk, 2.1; P < .001), had higher rates of transformation to secondary myelofibrosis (hazard ratio [HR], 1.55; P = .013) and acute myeloid leukemia (HR, 3.67; P < .001), and worse survival (HR, 1.63; P = .001) independent of age, phenotype at diagnosis, and MPN-specific mutation. Men had higher JAK2 V617F allele burdens in their CD34+ cells (P = .001), acquired more somatic mutations (P = .012) apart from the MPN-specific mutations, and had an increased frequency of 1 (odds ratio, 2.35; P = .017) and 2 (odds ratio, 20.20; P = .011) high-risk mutations independent of age, phenotype, and driver mutation. Male sex is an independent predictor of poor outcomes in MPNs. This seems to be due to an increased risk of non-MPN-specific somatic mutations, particularly high-risk mutations, rather than MPN-specific mutation allele frequency. Conversely, disease progression in female subjects is more dependent on JAK2 mutation allele burden than on acquisition of other somatic mutations. Sex should be considered in prognostic models and when evaluating therapeutic strategies in MPNs.
Understanding the Role of DISC1 in Psychiatric Disease and during Normal Development (2009)

The biology of schizophrenia is complex with multiple hypotheses (dopamine, glutamate, neurodevelopmental) well supported to underlie the disease. Pathways centered on the risk factor "disrupted in schizophrenia 1" (DISC1) may be able to explain and unite these disparate hypotheses and will be the topic of this mini-symposium preview. Nearly a decade after its original identification at the center of a translocation breakpoint in a large Scottish family that was associated with major psychiatric disease, we are starting to obtain credible insights into its function and role in disease etiology. This preview will highlight a number of exciting areas of current DISC1 research that are revealing roles for DISC1 during normal brain development and also in the disease state. Together these different threads will provide a timely and exciting overview of the DISC1 field and its potential in furthering our understanding of psychiatric diseases and in developing new therapies.
Continuous synthesis of pyridocarbazoles and initial photophysical and bioprobe characterization (2013)

Pyridocarbazoles when ligated to transition metals yield high affinity kinase inhibitors. While batch photocyclizations enable the synthesis of these heterocycles, the non-oxidative Mallory reaction only provides modest yields and difficult to purify mixtures. We demonstrate here that a flow-based Mallory cyclization provides superior results and enables observation of a clear isobestic point. The flow method allowed us to rapidly synthesize ten pyridocarbazoles and for the first time to document their interesting photophysical attributes. Preliminary characterization reveals that these molecules might be a new class of fluorescent bioprobe.
Transcriptional regulation and metabolism (2005)

Understanding organisms from a systems perspective is essential for predicting cellular behaviour as well as designing gene-metabolic circuits for novel functions. The structure, dynamics and interactions of cellular networks are all vital components of systems biology. To facilitate investigation of these aspects, we have developed an integrative technique called network component analysis, which utilizes mRNA expression and transcriptional network connectivity to determine network component dynamics, functions and interactions. This approach has been applied to elucidate transcription factor dynamics in Saccharomyces cerevisiae cell-cycle regulation, detect cross-talks in Escherichia coli two-component signalling pathways, and characterize E. coli carbon source transition. An ultimate test of system-wide understanding is the ability to design and construct novel gene-metabolic circuits. To this end, artificial feedback regulation, cell-cell communication and oscillatory circuits have been constructed, which demonstrate the design principles of gene-metabolic regulation in the cell.
Computed Tomography of Hepatic Cavernous Hemangioma (1987)

Fifty hepatic hemangiomas in 38 patients were evaluated by CT using sequential scanning following bolus injection. Lesions were assessed for the following CT features: (a) low density lesion on unenhanced scan; (b) early peripheral contrast enhancement; (c) progressive opacification from the periphery to the center; (d) a delay of at least 3 min before total opacification; and (e) eventual isodense appearance with or without unopacified cleft. The criteria for diagnosis of hepatic hemangioma were (d) and (e) plus at least two of the remaining three features. Forty-eight lesions were identified by CT; 38 displayed all five features, five lesions were missing one feature, and five lesions did not meet the criteria for diagnosis. Larger lesions required a significantly longer period to opacify (p less than 0.05). The positive predictive value of CT in the diagnosis of hemangioma was 100%.
ChemInform Abstract: CONTROL OF METAL‐CATALYZED REACTIONS. 3. CONTROL OF THE NICKEL‐CATALYZED MIXED OLIGOMERIZATION OF BUTADIENE WITH SCHIFF BASES BY COCATALYSTS (1977)

Abstract Mischoligomerisierungsprodukte wie (I)‐(III) entstehen mit Ausbeuten von 65 bis 42% aus 2:1‐Gemischen des Butadiens und der entsprechenden Schiffschen Basen in Gegenwart von Ni(O)‐Triphenylphosphan (l : 1) bei 40°C. Produkte vom Typ (III) bilden sich, wenn der N‐Substituent in (Je‐Stellung zum Nkeinen Wasserstoff enthält und wenn das C‐Atom der Schiffschen Base ein H‐Atom trägt.
Proceedings of the 1992 IEEE/ACM international conference on Computer-aided design (1992)

Antibodies against oxidized low-density lipoproteins (anti-oxLDL antibodies) are involved in the development of atherosclerosis in animal models, but their role in humans is not clear. The aim of this study was to explore the relationship between the presence of anti-oxLDL antibodies and the presence of anti-beta2glycoprotein I (beta2gpI) antibodies, anticardiolipin antibodies and lupus anticoagulant. We also analyzed the relationship between the appearance of anti-oxLDL antibodies and clinical signs of antiphospholipid syndrome. This study included three groups of patients: 27 patients with primary antiphospholipid syndrome, 20 with secondary antiphospholipid syndrome associated with systemic lupus erythematosus and 13 patients with systemic lupus erythematosus. Levels of anti-oxLDL, anticardiolipin and anti-beta2gpI antibodies were detected by ELISA. The presence of lupus anticoagulant was detected by coagulation tests. We found that the presence of anti-oxLDL antibodies was associated with a history of arterial thromboses in patients with secondary antiphospholipid syndrome (chi2 = 8.89, p < 0.01) and in patients with primary antiphospholipid syndrome (chi2 = 4.64, p < 0.05). Also, the appearance of anti-oxLDL antibodies was associated with the presence of anti-beta2gpI antibodies (chi2 = 4.25, p < 0.05), which was not dependent on diagnosis. These preliminary observations have to be confirmed in a larger study.
Microarray data on gene modulation by HIV-1 in immune cells: 2000–2006 (2006)

Here, we review 34 HIV microarray studies in human immune cells over the period of 2000-March 2006 with emphasis on analytical approaches used and conceptual advances on HIV modulation of target cells (CD4 T cell, macrophage) and nontargets such as NK cell, B cell, and dendritic cell subsets. Results to date address advances on gene modulation associated with immune dysregulation, susceptibility to apoptosis, virus replication, and viral persistence following in vitro or in vivo infection/exposure to HIV-1 virus or HIV-1 accessory proteins. In addition to gene modulation associated with known functional correlates of HIV infection and replication (e.g., T cell apoptosis), microarray data have yielded novel, potential mechanisms of HIV-mediated pathogenesis such as modulation of cholesterol biosynthetic genes in CD4 T cells (relevant to virus replication and infectivity) and modulation of proteasomes and histone deacetylases in chronically infected cell lines (relevant to virus latency). Intrinsic challenges in summarizing gene modulation studies remain in development of sound approaches for comparing data obtained using different platforms and analytical tools, deriving unifying concepts to distil the large volumes of data collected, and the necessity to impose a focus for validation on a small fraction of genes. Notwithstanding these challenges, the field overall continues to demonstrate progress in expanding the pool of target genes validated to date in in vitro and in vivo datasets and understanding the functional correlates of gene modulation to HIV-1 pathogenesis in vivo.
Thermal Stress Reduces Serum Luteinizing Hormone and Bioassayable Hypothalamic Content of Luteinizing Hormone-Releasing Hormone in Hens1 (1989)

Studies were conducted to evaluate the effects of acute (24 h) thermal stress on anterior pituitary function in hens. Circulating levels of luteinizing hormone (LH) were measured and the ability of the pituitary to respond to luteinizing hormone-releasing hormone (LHRH) challenge was determined. Moreover, bioassayable hypothalamic LHRH content was assessed by using dispersed anterior pituitary cells. In two separate experiments, circulating levels of LH were reduced in hens exposed to acute thermal stress (35 degrees C). Injection of LHRH did not result in significant differences in release of LH between normothermic and hyperthermic hens. However, the hypothalamic content of bioassayable hypothalamic releasing activity from hyperthermic hens were significantly reduced compared with normothermic hens. Taken together, these data suggest that the reproductive decline in the acutely heat-stressed hen is mediated by reduced LH releasing ability of the hypothalamus.
Supplementary data from A Novel Compound ARN-3236 Inhibits Salt-Inducible Kinase 2 and Sensitizes Ovarian Cancer Cell Lines and Xenografts to Paclitaxel (2023)

&lt;p&gt;Supplementary Figure 1 related to Figure 2. (A) In vitro kinetic curve of SIK2 kinase activity in the presence of ARN-3236. The reaction mixture contained SIK2 recombinant protein (15 nM), ATP (10 μM), and substrate peptide (TORC2 aa162-179) (1 μM). (B-J) Indicated cells were treated same as in Figure 1B, Cell viability was tested Supplementary Figure 2 related to Figure 3. (A-H) Different cell lines were plated at density of 8000/well in 96-well plate, then sequentially treated with ARN-3236 (IC30 of each cell line) or DMSO for 24 hr and with increasing concentration of paclitaxel for another 72 hr. Cell viability was measured with an SRB assay. Supplementary Figure 3 related to Figure 4. (A) A2780 cells were transfected with the indicated siRNA or treated with DMSO or ARN-3236 (1 μM). The average nuclear centrosome distance and the percentage of cells with NCU was calculated and plotted. (B, C) OVCAR8 and A2780 cells were treated as in Figure 4B. Bar plots represent the mean {plus minus} s.d. of the percentage of cells at different stage of mitosis (left plot) and the mean prometaphase/metaphase ratio {plus minus} s.d (right plot). Supplementary Figure 4 related to Figure 5. (A) OC316 and OVCAR8 ovarian cancer cells were treated as in Figure 5A, fixed, stained with PI, and subjected to cell cycle analysis. (B) OC316 and OVCAR8 ovarian cancer cells were treated as in Figure 5B, the representative percentage of apoptotic cells is shown. Supplementary Figure 5 related to Figure 6. (A) The expression of 272 proteins was measured using a reverse phase protein array after treatment of SKOv3 ovarian cancer cells with 2 μM of ARN-3236 for 48 hrs. The log2 (fold change) of each protein were plotted. (B) OC316, A2780 and OVCAR8 ovarian cancer cell lines were treated with ARN-3236 for 48 hrs, cell lysates were collected and analyzed by western blot for AKT-pS473, AKT-pT308, AKT and survivn, GAPDH was used as a loading control. (C) Western analysis of phosphorylation of AKT and survivin was performed using three vehicle and ARN-3236 treated tumor cell lysates.&lt;/p&gt;
Molecular Pathobiology of Uveal Melanoma (2005)

International Ophthalmology Clinics: Winter 2006 - Volume 46 - Issue 1 - p 167-180 doi: 10.1097/01.iio.0000195855.31324.db