gebhart/patrepeval huggingface dataset:
Suppression of the zero-order term in off-axis digital holography through nonlinear filtering (2009)

We present experimental validation of a new reconstruction method for off-axis digital holographic microscopy (DHM). This method effectively suppresses the object autocorrelation, namely, the zero-order term, from holographic data, thereby improving the reconstruction bandwidth of complex wavefronts. The algorithm is based on nonlinear filtering and can be applied to standard DHM setups with realistic recording conditions. We study the robustness of the technique under different experimental configurations, and quantitatively demonstrate its enhancement capabilities on phase signals.
Endogenous ligands of the aryl hydrocarbon receptor regulate lung dendritic cell function (2015)

The aryl hydrocarbon receptor (AhR) is a transcription factor that has been extensively studied as a regulator of toxicant metabolism. However, recent evidence indicates that the AhR also plays an important role in immunity. We hypothesized that the AhR is a novel, immune regulator of T helper type 2 (Th2) -mediated allergic airway disease. Here, we report that AhR-deficient mice develop increased allergic responses to the model allergen ovalbumin (OVA), which are driven in part by increased dendritic cell (DC) functional activation. AhR knockout (AhR(-/-) ) mice sensitized and challenged with OVA develop an increased inflammatory response in the lung compared with wild-type controls, with greater numbers of inflammatory eosinophils and neutrophils, greater T-cell proliferation, greater production of Th2 cytokines, and higher levels of OVA-specific IgE and IgG1. Lung DCs from AhR(-/-) mice stimulated antigen-specific proliferation and Th2 cytokine production by naive T cells in vitro. Additionally, AhR(-/-) DCs produced higher levels of tumour necrosis factor-α and interleukin-6, which promote Th2 differentiation, and expressed higher cell surface levels of stimulatory MHC Class II and CD86 molecules. Overall, loss of the AhR was associated with enhanced T-cell activation by pulmonary DCs and heightened pro-inflammatory allergic responses. This suggests that endogenous AhR ligands are involved in the normal regulation of Th2-mediated immunity in the lung via a DC-dependent mechanism. Therefore, the AhR may represent an important target for therapeutic intervention in allergic airways inflammation.
Block copolymer composition drives function of self‐assembled nanoparticles for delivery of small‐molecule cargo (2019)

Nanoparticles are useful for the delivery of small molecule therapeutics, increasing their solubility, <i>in vivo</i> residence time, and stability. Here, we used organocatalytic ring opening polymerization to produce amphiphilic block copolymers for the formation of nanoparticle drug carriers with enhanced stability, cargo encapsulation, and sustained delivery. These polymers comprised blocks of poly(ethylene glycol) (PEG), poly(valerolactone) (PVL), and poly(lactide) (PLA). Four particle chemistries were examined: (a) PEG-PLA, (b) PEG-PVL, (c) a physical mixture of PEG-PLA and PEG-PVL, and (d) PEG-PVL-PLA tri-block copolymers. Nanoparticle stability was assessed at room temperature (20 °C; pH = 7), physiological temperature (37 °C; pH = 7), in acidic media (37 °C; pH = 2), and with a digestive enzyme (lipase; 37 °C; pH = 7.4). PVL-based nanoparticles demonstrated the highest level of stability at room temperature, 37 °C and acidic conditions, but were rapidly degraded by lipase. Moreover, PVL-based nanoparticles demonstrated good cargo encapsulation, but rapid release. In contrast, PLA-based nanoparticles demonstrated poor stability and encapsulation, but sustained release. The PEG-PVL-PLA nanoparticles exhibited the best combination of stability, encapsulation, and release properties. Our results demonstrate the ability to tune nanoparticle properties by modifying the polymeric architecture and composition. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1322-1332.
Lassa virus-like particles displaying all major immunological determinants as a vaccine candidate for Lassa hemorrhagic fever (2010)

These results established that modular LASV VLP can be generated displaying high levels of immunogenic viral proteins, and that small laboratory scale mammalian expression systems are capable of producing multi-milligram quantities of pseudoparticles. These VLP are structurally and morphologically similar to native LASV virions, but lack replicative functions, and thus can be safely generated in low biosafety level settings. LASV VLP were immunogenic in mice in the absence of adjuvants, with mature IgG responses developing within a few weeks after the first immunization. These studies highlight the relevance of a VLP platform for designing an optimal vaccine candidate against Lassa hemorrhagic fever, and warrant further investigation in lethal challenge animal models to establish their protective potential.
Inter-photoreceptor distance calibrated by axial length in adaptive optics fundus camera (2006)

We measured the inter-photoreceptor distance (IPD) using an adaptive optics fundus camera. The magnification of the images was calibrated by the eye’s axial length. The IPD was correlated with the axial length and the average IPD in the moderate and high myopia group was significantly larger than that in the normal and low myopia group.
GSK3 makes a comeback (2001)

Conference Abstract| June 01 2001 GSK3 makes a comeback R. Biondi; R. Biondi 1MRC Protein Phosphorylation Unit & Division of Signal Transduction Therapy, University of Dundee, Dundee, DD1 5EH, Scotland, UK Search for other works by this author on: This Site PubMed Google Scholar S. Frame; S. Frame 1MRC Protein Phosphorylation Unit & Division of Signal Transduction Therapy, University of Dundee, Dundee, DD1 5EH, Scotland, UK Search for other works by this author on: This Site PubMed Google Scholar G. Thomas; G. Thomas 1MRC Protein Phosphorylation Unit & Division of Signal Transduction Therapy, University of Dundee, Dundee, DD1 5EH, Scotland, UK Search for other works by this author on: This Site PubMed Google Scholar P. Cohen P. Cohen 1MRC Protein Phosphorylation Unit & Division of Signal Transduction Therapy, University of Dundee, Dundee, DD1 5EH, Scotland, UK Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (2001) 29 (3): A59. https://doi.org/10.1042/bst029a059b Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation R. Biondi, S. Frame, G. Thomas, P. Cohen; GSK3 makes a comeback. Biochem Soc Trans 1 June 2001; 29 (3): A59. doi: https://doi.org/10.1042/bst029a059b Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2001 Biochemical Society2001 Article PDF first page preview Close Modal You do not currently have access to this content.
The Prognostic Value of Midregional Proatrial Natriuretic Peptide in Patients with Hemorrhagic Stroke (2014)

Increased levels of MR-proANP are independently associated with poor functional outcome and increased mortality after 180 days in patients with hemorrhagic stroke. Endovascular temperature control had no significant influence on MR-proANP levels.
Lower Hounsfield Units on Computed Tomography are Associated with Cage Subsidence After Lateral Lumbar Interbody Fusion (2020)

Xi, Zhuo MD, PhD; Mummaneni, Praveen V MD; Wang, Minghao MD, PhD; Ruan, Hui B MD; Burch, Shane; Deviren, Vedat; Clark, Aaron J MD, PhD; Berven, Sigurd; Chou, Dean MD Author Information
Sex hormones have pervasive effects on thymic epithelial cells (2015)

The goal of our study was to evaluate at the systems-level, the effect of sex hormones on thymic epithelial cells (TECs). To this end, we sequenced the transcriptome of cortical and medullary TECs (cTECs and mTECs) from three groups of 6 month-old mice: males, females and males castrated at four weeks of age. In parallel, we analyzed variations in the size of TEC subsets in those three groups between 1 and 12 months of age. We report that sex hormones have pervasive effects on the transcriptome of TECs. These effects were exquisitely TEC-subset specific. Sexual dimorphism was particularly conspicuous in cTECs. Male cTECs displayed low proliferation rates that correlated with low expression of Foxn1 and its main targets. Furthermore, male cTECs expressed relatively low levels of genes instrumental in thymocyte expansion (e.g., Dll4) and positive selection (Psmb11 and Ctsl). Nevertheless, cTECs were more abundant in males than females. Accumulation of cTECs in males correlated with differential expression of genes regulating cell survival in cTECs and cell differentiation in mTECs. The sexual dimorphism of TECs highlighted here may be mechanistically linked to the well-recognized sex differences in susceptibility to infections and autoimmune diseases.
β-Gallium oxide power electronics (2022)

Gallium Oxide has undergone rapid technological maturation over the last decade, pushing it to the forefront of ultra-wide band gap semiconductor technologies. Maximizing the potential for a new semiconductor system requires a concerted effort by the community to address technical barriers which limit performance. Due to the favorable intrinsic material properties of gallium oxide, namely, critical field strength, widely tunable conductivity, mobility, and melt-based bulk growth, the major targeted application space is power electronics where high performance is expected at low cost. This Roadmap presents the current state-of-the-art and future challenges in 15 different topics identified by a large number of people active within the gallium oxide research community. Addressing these challenges will enhance the state-of-the-art device performance and allow us to design efficient, high-power, commercially scalable microelectronic systems using the newest semiconductor platform.
The Synthesis and Characterization of Compounds of the Type Hg{1-C6H4-2-C(H)NC6H5-nRn}2 (2002)

The organomercurial compounds Hg[1-C(6)H(4)-2-C(H)=NC(6)H(5-n)R(n)](2) (R = 4-NMe(2), 6a; 4-Me, 6b; 4-I, 6c; 4-NO(2), 6d; 2-(i)Pr, 6e; 2-Me, 6f; 2,6-(i)Pr(2), 6g; 2,6-Me(2), 6h) have been prepared in good overall yield from 2-bromobenzaldehyde. All of the compounds have been characterized by elemental analysis, (1)H NMR, (13)C[(1)H] NMR, and infrared spectroscopy. In addition, compounds 6a [C(30)H(30)HgN(4), triclinic, P, a = 6.20000(10) A, b = 9.2315(2) A, c = 10.9069(3) A, alpha = 85.8510(10) degrees, beta = 89.3570(10) degrees, gamma = 87.206(2) degrees, Z = 1], 6b [C(28)H(24)HgN(2), monoclinic, P2(1)/c, a = 12.8260(5) A, b = 14.0675(4) A, c = 6.1032(2) A, beta = 90.0990(10) degrees, Z = 2], 6g [C(38)H(44)HgN(2), triclinic, P, a = 8.2626(2) A, b = 9.8317(2) A, c = 11.8873(3) A, alpha = 103.6650(10) degrees, beta = 109.3350(10) degrees, gamma = 104.627(2) degrees, Z = 1], and 6h [C(30)H(28)HgN(2), monoclinic, P2(1)/c, a = 12.5307(2) A, b = 10.9852(2) A, c = 18.2112(2) A, beta = 104.0190(10) degrees, gamma = 87.206(2) degrees, Z = 4] have been characterized by low-temperature single-crystal X-ray diffraction studies, and two different molecular geometries about the central mercury atom have been observed; intramolecular contacts suggest a van der Waals radius for Hg of 2.1-2.2 A.
Effects of breast density and compression on normal breast tissue hemodynamics through breast tomosynthesis guided near-infrared spectral tomography (2016)

Optically derived tissue properties across a range of breast densities and the effects of breast compression on estimates of hemoglobin, oxygen metabolism, and water and lipid concentrations were obtained from a coregistered imaging system that integrates near-infrared spectral tomography (NIRST) with digital breast tomosynthesis (DBT). Image data were analyzed from 27 women who underwent four IRB approved NIRST/DBT exams that included fully and mildly compressed breast acquisitions in two projections—craniocaudal (CC) and mediolateral-oblique (MLO)—and generated four data sets per patient (full and moderate compression in CC and MLO views). Breast density was correlated with HbT (r=0.64, p=0.001), water (r=0.62, p=0.003), and lipid concentrations (r=?0.74, p<0.001), but not oxygen saturation. CC and MLO views were correlated for individual subjects and demonstrated no statistically significant differences in grouped analysis. Comparison of compressed and uncompressed imaging demonstrated a significant decrease in oxygen saturation under compression (58% versus 50%, p=0.04). Mammographic breast density categorization was correlated with measured optically derived properties.
Phylogeny of the phylum nematoda based on small subunit ribosomal DNA sequences (2003)

On the basis of full-length SSU rDNA sequences (e¨ 1700 bp), the phylogeny of the phylum Nematoda was reconstructed. The majority of nematode sequences were collected at the Laboratory of Nematology (Wageningen University). Sequences obtained from GenBank were added to these. In order to obtain a SSU rDNA sequence, we isolated DNA from a single individual nematode, which had been identified and photographed beforehand. The SSU rDNA was PCR amplified, cloned into vectors and sequenced. A number of nematode species were sequenced multiple times to assess intraspecific variation and sequence errors. For these species a consensus sequence was constructed. This resulted in an alignment, which included the SSU sequences of 355 nematode species. Ten members of the phyla Arthropoda, Priapulida, Tardigrada, Nematomorpha and Kinorhyncha represented the outgroup. The alignment was constructed with the ClustalW algorithm and checked manually. Two regions of the SSU (99 and 76 bp), which were difficult to align, were omitted from the analysis. Trees were constructed using Neighbour-Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference of phylogeny. All methods showed consensus in that they revealed five major clades. Our results suggest that the classic division of the nematodes into the Adenophorea and Secernentea is invalid: the Adenophorea are paraphyletic with respect to the Secernentea. This is in correspondence with earlier molecular phylogenetic analyses.
Multimodal wide-field two-photon excitation imaging: characterization of the technique for in vivo applications (2011)

We report fast, non-scanning, wide-field two-photon fluorescence excitation with spectral and lifetime detection for in vivo biomedical applications. We determined the optical characteristics of the technique, developed a Gaussian flat-field correction method to reduce artifacts resulting from non-uniform excitation such that contrast is enhanced, and showed that it can be used for ex vivo and in vivo cellular-level imaging. Two applications were demonstrated: (i) ex vivo measurements of beta-amyloid plaques in retinas of transgenic mice, and (ii) in vivo imaging of sulfonated gallium(III) corroles injected into tumors. We demonstrate that wide-field two photon fluorescence excitation with flat-field correction provides more penetration depth as well as better contrast and axial resolution than the corresponding one-photon wide field excitation for the same dye. Importantly, when this technique is used together with spectral and fluorescence lifetime detection modules, it offers improved discrimination between fluorescence from molecules of interest and autofluorescence, with higher sensitivity and specificity for in vivo applications.
Techniques for Visualizing the Coronary Sinus and Coronary Venous Anatomy (2008)

This chapter contains sections titled: Introduction Magnetic resonance imaging Real-time 3D echocardiography Cardiac computed tomography Rotational coronary venous angiography Intracardiac echocardiography Conclusions References
Intestinal Stromal Tumors in a Simian Immunodeficiency Virus-infected, Simian Retrovirus-2 Negative Rhesus Macaque (Macaca mulatta) (2005)

Multifocal submucosal stromal tumors were diagnosed in a 5.5-year-old rhesus macaque (Macaca mulatta) experimentally infected with simian immunodeficiency virus, strain SIVsmE660, and CD4+ T cell depleted. The animal was negative for simian retroviruses, SRV-1, -2, and -5. Polymerase chain reaction analysis of DNA from tumor and spleen tissue revealed abundant, preferential presence of retroperitoneal fibromatosis herpesvirus, the macaque homologue of the Kaposi sarcoma-associated herpesvirus (human herpesvirus-8), in the tumors. This was corroborated by demonstration of viral latent nuclear antigen-1 in the nuclei of a majority of the spindeloid tumor cells. Low levels of an additional macaque herpesvirus, rhesus rhadinovirus, were also detected in the spleen and tumor tissues. The spindeloid cells labeled positively for vimentin and CD117 but were negative for CD31, CD68, desmin, and smooth muscle cell actin. Collectively, these findings suggest a relation to but not absolute identity with simian mesenchymoproliferative disorders (MPD) or typical gastrointestinal stromal tumors (GISTs).
3D MRI of impaired hyperpolarized 129Xe uptake in a rat model of pulmonary fibrosis (2014)

A variety of pulmonary pathologies, in particular interstitial lung diseases, are characterized by thickening of the pulmonary blood-gas barrier, and this thickening results in reduced gas exchange. Such diffusive impairment is challenging to quantify spatially, because the distributions of the metabolically relevant gases (CO2 and O2) cannot be detected directly within the lungs. Hyperpolarized (HP) (129)Xe is a promising surrogate for these metabolic gases, because MR spectroscopy and imaging allow gaseous alveolar (129)Xe to be detected separately from (129)Xe dissolved in the red blood cells (RBCs) and the adjacent tissues, which comprise blood plasma and lung interstitium. Because (129)Xe reaches the RBCs by diffusing across the same barrier tissues (blood plasma and interstitium) as O2, barrier thickening will delay (129)Xe transit and, thus, reduce RBC-specific (129)Xe MR signal. Here we have exploited these properties to generate 3D, MR images of (129)Xe uptake by the RBCs in two groups of rats. In the experimental group, unilateral fibrotic injury was generated prior to imaging by instilling bleomycin into one lung. In the control group, a unilateral sham instillation of saline was performed. Uptake of (129)Xe by the RBCs, quantified as the fraction of RBC signal relative to total dissolved (129)Xe signal, was significantly reduced (P = 0.03) in the injured lungs of bleomycin-treated animals. In contrast, no significant difference (P = 0.56) was observed between the saline-treated and untreated lungs of control animals. Together, these results indicate that 3D MRI of HP (129)Xe dissolved in the pulmonary tissues can provide useful biomarkers of impaired diffusive gas exchange resulting from fibrotic thickening.
Regulation of IRAK2 gene and innate immune response to tumor cells (2005)

6035 It was recently suggested that gastric cancer could originate from bone marrow-derived cells (Houghton et al., 2004). Another group demonstrated that diminished expression of Interleukin 1 Receptor-Associated Kinase 1 (IRAK1), a key protein facilitating immune response, is common in peripheral blood mononuclear cells of patients with gastric cancer (Siedlar et al., 2004). Therefore, down-regulation of IRAK1 antagonists can be beneficial for treatment of gastric cancer. Here we investigated transcriptional regulation of IRAK2 gene, which counteracts the effects of IRAK1 on the Interleukin 1 Receptor signaling pathway (Ruckdeschel et al., 2002). Analysis of the IRAK2 promoter region reveals putative binding sites for several transcriptional factors, including ZIP (EGR1 and SP1), CTCF and AP-2beta. Deletion of the ZIP or AP-2 sites did not significantly affect IRAK2 promoter activity in mononuclear cells, in Jurkat T cells, in lung and kidney cells. In contrast, we found that CTCF plays a major role in IRAK2 transcription. An electrophoretic mobility shift assay of the DNA fragments containing the IRAK2 CpG island, revealed a single high affinity-binding site for the transcriptional regulator and a chromatin insulator protein, CTCF. We also identified CTCF binding site within the mouse Irak2 promoter. The presence of the CTCF protein in human IRAK2 promoter was confirmed by chromatin immunoprecipitation assay. Specific residues, which interacted with the CTCF protein, were identified by methylation interference assay. In all analyzed cell lines, including cells of lung, renal, monocytic and T-cell origin; the IRAK2 luciferase reporter construct, containing an intact CTCF binding site, showed strong promoter activity. However, IRAK2 promoter activity was dramatically decreased for the constructs with a mutated CTCF binding site. Funded in part by NO1-CO-12400 and NO1-CO-56000.
Reduction of risk of pneumonia associated with use of angiotensin I converting enzyme inhibitors in elderly inpatients (1999)

Pneumonia is a major direct cause of death in the elderly. Although aspiration based on a reduced cough reflex is one of the causes of pneumonia in the elderly, there are few studies of angiotensin-I converting enzyme inhibitors (ACE inhibitors), which are antihypertensive drugs that induce cough, as a factor influencing the incidence of pneumonia in institutionalized elderly subjects. To assess the effect of ACE inhibitors and dihydropiridine calcium-channel blockers on the incidence of pneumonia, we conducted a hospital-based case-control study. Cases were 55 pneumonia patients aged 65 years during a 1-year period. The controls were elderly subjects, frequency matched to the cases by age and gender (n = 220). Data were collected on known risk factors and on medication for hypertension, consisting of ACE inhibitors, calcium-channel blockers, and nonantihypertensive medication. The significance of differences in risk factors was analyzed using univariate and multivariate comparisons of cases and controls. After adjustment for potential confounding factors, the relative risk estimates for pneumonia were 0.38 (95% confidence interval [CI], 0.15–0.97) and 1.84 (95% CI, 0.89–3.78) for ACE inhibitors and calcium-channel blockers, respectively, relative to nonantihypertensive medication. The preventive effect of ACE inhibitors on pneumonia was apparent in long-acting ACE inhibitor users (0.24; 95% CI, 0.07–0.88). We conclude that ACE inhibitor use is an independent factor reducing risk of pneumonia among elderly inpatients. Am J Hypertens 1999;12:778–783 © 1999 American Journal of Hypertension, Ltd.
Successful Hemostatic Management of Dieulafoy's Ulcer in Two Patients with Hemophilia A with Inhibitor (1995)

Dieulafoy's ulcer, a special category, is one of the serious gastric lesions with a high mortality rate even in individuals without bleeding tendency. We present two cases of hemophilia A with high-responder inhibitor associated with Dieulafoy's ulcer in which treatment with a combination of endoscopic hemostatic procedure and inhibitor by-passing therapy was effective.Both patients were very pale and in acute distress on admission. Endoscopic examination of the stomach under an infusion of FEIBA® revealed hemorrhage from an exposed artery and a diagnosis of Dieulafoy's ulcer was established. Absolute ethanol and hypertonic saline containing 0.005% epinephrine were injected into the exposed vessel and its surroundings. These procedures were performed easily and safely and local hemastasis was obtained.This is the first reported cases of successful management of Dieulafoy's ulcer in patients with hemophilia A with inhibitor using a combination of local hemostasis with an endoscope and FEIBA® infusion.
Supplementary Table 1 from Yes-Associated Protein 1 Is Activated and Functions as an Oncogene in Meningiomas (2023)

&lt;p&gt;XLS file - 13K, Summary of nuclear YAP1 immunohistochemistry in human meningiomas&lt;/p&gt;