gebhart/patrepeval huggingface dataset:
Identification of a second Klotho interaction site in the C terminus of FGF23 (2021)

FGF23 interacts with a FGFR/KL-receptor complex to propagate cellular signaling, where its C-terminal C26 peptide is critical for engaging the co-receptor KL. We identify a distinct peptide sequence C28 residing in the FGF23 C terminus that regulates its interaction with KL. C28 can independently function as an FGF23 antagonist, and we report an optimized peptide antagonist of much enhanced potency. FGF23 can use either of the two C-terminal sites to exert biological effects, as shown by in vitro and in vivo studies. The loss of both KL-interaction sites inactivates the protein. We conclude that the C terminus of FGF23 is a bidentate ligand possessing two independent KL-interaction sites. The identification of this second KL-association site provides an additional perspective in the molecular basis of FGF23-receptor signaling and raises questions pertaining to its structural mechanism of action and the potential for biased biological signaling.
Methods for measuring insecticide susceptibility levels in bed-bugs, cone-nosed bugs, fleas and lice. (1961)

A standard kit is prepared and distributed by WHO for testing insecticide resistance in adult mosquitos, and it would seem advantageous to be able to use the filter papers impregnated with DDT and dieldrin contained in this kit for testing resistance in other insects. Experiments have been successfully conducted with a view to developing methods based on the use of these papers for testing susceptibility levels in bed-bugs, cone-nosed bugs, fleas and lice. The designs of the various test methods and the results obtained are described in this paper. The tests for bed-bugs and fleas have been adopted as provisional methods by the WHO Expert Committee on Insecticides; those for cone-nosed bugs and lice have been designated tentative methods, requiring further investigation prior to the drawing up of specifications.
Giant coronary arteriovenous fistula between left superior pulmonary vein and left atrial appendage (2013)

A 71-year-old male patient had symptomatic paroxysmal atrial fibrillation. Computed tomography detected that coronary arteriovenous fistula originated from the coronary left circumflex …
A screen for drugs that protect against the cytotoxicity of polyglutamine-expanded androgen receptor (2003)

Spinobulbar muscular atrophy is a neurodegenerative disorder caused by expansion of a CAG triplet repeat sequence encoding a polyglutamine tract in the androgen receptor. It has been shown that the mutant protein is toxic in cell culture and triggers an apoptotic cascade resulting in activation of caspase-3. We developed an assay of caspase-3 activation in cells expressing the mutant androgen receptor. This assay was used to screen 1040 drugs, most of which are approved for clinical use. Drugs that inhibit polyglutamine-dependent activation of caspase-3 were subjected to follow-up screens to identify compounds that reproducibly prevent polyglutamine-induced cytotoxicity. Four drugs satisfied these criteria. Three of these (digitoxin, nerifolin and peruvoside) are structurally and functionally related compounds of the cardiac glycoside class and known inhibitors of Na(+)K(+)-ATPase. The fourth compound, suloctidil, is a calcium channel blocker.
Metabolic and Microbial Responses to Exercise in C57 Wild-type and Adenylyl Cyclase 5 KO Mice (2018)

Please download pdf version here.
High performance of multiplex fluorescence in situ hybridization to simultaneous detection of BCL2 and BCL6 rearrangements: useful application in the characterization of DLBCLs (2021)

Chromosomal rearrangements involving BCL2, BCL6 and MYC are commonly found in the most frequent B cell lymphomas, namely follicular lymphomas (FLs) and diffuse large B-cell lymphomas (DLBCLs). Particularly, BCL2-rearrangement represents a diagnostic hallmark in FLs, whereas MYC translocation can occur simultaneously with BCL2 and/or BCL6 rearrangements, defining a specific category of DLBCLs with a poorer prognosis. In this study, we aim to validate the diagnostic performance of multiplex BCL2/BCL6 FISH approach in formalin-fixed paraffin-embedded FLs and DBCLs and cytological samples of DLBCL comparing to the classic set of single break-apart probes. We collected a series of lymphomas, including 85 DLBCLs, 45 FLs and 36 other B-cell lymphoma histotypes and 16 cytological samples of DLBCLs. MYC, BCL2 and BCL6 rearrangements were previously assessed by a classic FISH test using single break-apart probes. All samples were analysed by a multiplex FISH assay. In the FL series, 38 cases showed BCL2-R; in the DLBCLs series, MYC-R was detected in 21 out of 85 DLBCL patients, BCL2-R in 10 out of 85 and BCL6-R in 33 out of 85. In the DLBCL cytological series, MYC-R was detected in 4 out of 16, BCL2-R in 4 out of 16 and BCL6-R in 1 out of 16. Notably, in FFPE, 13 double-hit lymphomas (DHLs) and 3 triple-hit lymphomas (THLs) were detected; in the cytological series, only 3 DHL cases were observed. The dual BCL2/BCL6 FISH probe test results were fully concordant with the results obtained using classic BCL2 and BCL6 single break apart. Particularly, multiplex FISH to simultaneously detect BCL2-R and BCL6-R on a single slide could find a wide application in the characterisation of double- and triple-hit DLBCLs.
H MAS and 1H/27Al TRAPDOR NMR Studies of Oxygen−Zeolite Interactions at Low Temperatures:  Probing Bronsted Acid Site Accessibility (1999)

Sorption of oxygen in the pores of zeolite HY and 1H MAS NMR has been used to determine which Brønsted acid sites are accessible to oxygen. Large increases in the 1H spinning-sideband manifolds are observed at low temperatures for the supercage protons that can directly interact with the oxygen molecules; a much smaller increase in sideband intensity is seen for the sodalite protons. Dramatic reductions of the T1's of all the protons, of approximately 2 orders of magnitude, are observed at −150 °C, in comparison to T1 measurements made in air at room temperature, or at −150 °C for samples with adsorbed N2. The T1's of the supercage protons are, however, shorter than those measured for the sodalite protons. Both the decrease in the T1's, and the large sideband manifolds, are due to the dipolar coupling interactions with the unpaired electrons present on the O2 molecules. Second moment (M2) analysis is used to quantify the increase in the width of the 1H spinning sideband manifolds, in samples of zeolites HY and HZSM-5. Comparison between samples run in air and with fixed loading levels of oxygen allows changes in loading level with temperature to be detected and oxygen loading levels to be estimated. The contribution to M2 of the protons due to bulk magnetic susceptibility effects and from oxygen molecules that do not directly interact with the protons was estimated from the values of M2 extracted from the 29Si MAS NMR of the same samples. The contribution to M2 from the direct interaction of the protons with the oxygen molecules could then be estimated.
Structure of fosfomycin resistance protein FosA from transposon Tn2921 (2004)

The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 A. The protein crystallized without bound Mn(II) and K+, ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three-dimensional domain-swapped arrangement of the paired betaalphabetabetabeta-motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa (PA1129). The basic architecture of the active site is also maintained, despite the absence of the catalytically essential Mn(II). However, the absence of K+, which has been shown to enhance enzymatic activity, appears to contribute to conformational heterogeneity in the K(+)-binding loops.
A sensitive genetic-based detection capability for Didymosphenia geminata (2006)

It is now well recognized that the increase in global transportation over the last two decades has brought with it an increased potential for the introduction of unwanted microorganisms (aquatic or terrestrial) that may have drastic effects on human and ecosystem health and agriculture. We have developed and validated a unique genetic fingerprinting tool for D. geminata. In concert, we developed field collection and preservation techniques specific for D. geminata along with genetic-based procedures that can now reliably detect D. geminate from a complex environmental community with a high degree of sensitivity. Recent work (Phase 2) has shown that the described methods will provide detection levels from &lt;1 – 10,000 cells ml-1. We contend that the genetic based detection approaches used in this study offer great promise to meet the increasing demands to monitor the global threat from invasive micro-organisms.
T-614 Promotes Osteoblastic Cell Differentiation by Increasing Dlx5 Expression and Regulating the Activation of p38 and NF-κB (2018)

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease characterized by bone loss. Degree of inflammation has been identified as an important initiator of skeletal damage in RA. Iguratimod (T-614) is an anti-inflammatory agent which has been reported to show the inhibitory effect of bone destruction in RA. However, the role of T-614 in osteoblast differentiation is still not clear. In this study, we intended to find the effect of T-614 on the osteogenesis process. We detected osteogenesis markers and transcription factors associated with osteoblastic lineage and bone formation in the culture of mesenchymal stem cells which differentiate osteoblast. The contents and activity of alkaline phosphatase, levels of collagen type I and bone gla protein, and calcium nodule formation were increased significantly after T-614 treated. Meanwhile, the mRNAs expressions of <i>Osterix</i> and <i>Dlx5</i> were also found to be increased significantly by real-time PCR. The changes of levels of phosphorylation of p38 and NF-<i>κ</i>B were also detected by Western blot. The results showed that T-614 promotes osteoblastic differentiation by increasing the expression of <i>Osterix</i> and <i>Dlx5</i> and increasing the activation of P38. T-614 could advance the ectopic expression of NF-<i>κ</i>B to suppress inflammation, which indirectly inhibits the damage of the osteoblasts.
Author response: HIF-1α regulates IL-1β and IL-17 in sarcoidosis (2019)

Sarcoidosis, a granulomatous disease characterized by macrophage and T-cell activation, is found to be associated with increased HIF-1α transcriptional activity, and modulation of HIF-1α regulates inflammatory immune responses.
Implementation of Vendor-Independent Stochastic Inversion for Improving Quality and Efficiency of Well Placement on the Field of Novatek Company (2021)

Abstract The article describes the application of a new stochastic inversion of the deep-azimuthal resistivity data, independent from the tool vendor. The new model was performed on the data from several wells of the PAO «Novatek», that were drilled using deep-azimuthal resistivity tools of two service companies represented in the global oilfield services market. This technology allows to respond in a timely manner when the well approaches the boundaries with contrasting resistivity properties and to avoid exit to unproductive zones. Nowadays, the azimuthal resistivity data is the method with the highest penetration depth for the geosteering in real time. Stochastic inversion is a special mathematical algorithm based on the statistical Monte Carlo method to process the readings of resistivity while drilling in real time and provide a geoelectrical model for making informed decisions when placing horizontal and deviated wells. Until recently, there was no unified approach to calculate stochastic inversion, which allows to perform calculations for various tools. Deep-azimuthal resistivity logging tool vendors have developed their own approaches. This article presents a method for calculating stochastic inversion. This approach was never applied for this kind of azimuthal resistivity data. Additionally, it does not depend on the tool vendor, therefore, allows to compare the data from various tools using a single approach.
Stereo vision-based obstacle detection using dense disparity map (2011)

In this paper, we propose stereo vision-based obstacle detection method on the road using a dense disparity map. We use the dense disparity map to detect obstacles robustly in real traffic situations. Our method consists of three stages, namely road feature extraction, column detection, obstacle segmentation. First, we extract a road feature from a v- disparity map calculated from a dense disparity map. And we perform a column detection using the extracted road feature as a criterion that decides whether obstacles exist or not. Finally, we perform a segmentation using a bird's-eye view mapping to divide the merged obstacle into each obstacle accurately. We conduct experiments to verify our method in the real traffic situations.
Generation of radiation by four-wave interaction in a feedback system in the λ=10 µ range (1987)

A self-pumped mirror was implemented experimentally for CO2 laser radiation generated by a four-wave interaction with feedback in CCl4 and SF6. The lowest threshold energy of the input signal was ~8 mJ for CCl4 and ~2 mJ for SF6. The energy reflection coefficient was 5 for CCl4 and 11 for SF6. The maximum energy of the output radiation exceeded 0.2 J.
Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures (2020)

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.
Synthesis of a Piperidone Model Compound and Revision of the Structures of Jenamidines A to C. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Mechanisms of Gene Duplication and Amplification (2015)

Changes in gene copy number are among the most frequent mutational events in all genomes and were among the mutations for which a physical basis was first known. Yet mechanisms of gene duplication remain uncertain because formation rates are difficult to measure and mechanisms may vary with position in a genome. Duplications are compared here to deletions, which seem formally similar but can arise at very different rates by distinct mechanisms. Methods of assessing duplication rates and dependencies are described with several proposed formation mechanisms. Emphasis is placed on duplications formed in extensively studied experimental situations. Duplications studied in microbes are compared with those observed in metazoan cells, specifically those in genomes of cancer cells. Duplications, and especially their derived amplifications, are suggested to form by multistep processes often under positive selection for increased copy number.
An iterative and interdisciplinary categorisation process towards FAIRer digital resources for sensitive life-sciences data (2022)

For life science infrastructures, sensitive data generate an additional layer of complexity. Cross-domain categorisation and discovery of digital resources related to sensitive data presents major interoperability challenges. To support this FAIRification process, a toolbox demonstrator aiming at support for discovery of digital objects related to sensitive data (e.g., regulations, guidelines, best practice, tools) has been developed. The toolbox is based upon a categorisation system developed and harmonised across a cluster of 6 life science research infrastructures. Three different versions were built, tested by subsequent pilot studies, finally leading to a system with 7 main categories (sensitive data type, resource type, research field, data type, stage in data sharing life cycle, geographical scope, specific topics). 109 resources attached with the tags in pilot study 3 were used as the initial content for the toolbox demonstrator, a software tool allowing searching of digital objects linked to sensitive data with filtering based upon the categorisation system. Important next steps are a broad evaluation of the usability and user-friendliness of the toolbox, extension to more resources, broader adoption by different life-science communities, and a long-term vision for maintenance and sustainability.
Enhanced upconversion emission in Yb3+and Er3+codoped NaGdF4nanocrystals by introducing Li+ions (2011)

β-NaGdF(4) : Yb(3+)/Er(3+) nanoparticles (NPs) codoped with Li(+) ions were prepared for the first time via a thermal decomposition reaction of trifluoroacetates in oleylamine. The influence of site occupancy of Li(+) on the upconversion emission of β-NaGdF(4) : Yb(3+)/Er(3+) NPs was investigated in detail. The upconversion emission intensity was significantly enhanced by introducing different concentrations of Li(+) ions. In contrast to lithium-free β-NaGdF(4) : Yb(3+)/Er(3+), the green and red UC emission intensities of the NPs codoped with 7 mol% Li(+) ions were enhanced by about 47 and 23 times, respectively. The luminescence enhancement should be attributed to the distortion of the local asymmetry around Er(3+) ions. The mechanisms for the enhancement of upconversion emission were discussed. In addition, it was found in our research work that β-NaGdF(4) : Yb(3+)/Er(3+) NPs exhibited paramagnetic features at room temperature and the magnetization was slightly increased by introducing Li(+) ions.
Polarized binding of lipoprotein lipase to endothelial cells. Implications for its physiological actions. (1992)

Lipoprotein lipase (LPL) that is associated with the luminal surface of capillary endothelial cells hydrolyzes circulating lipoprotein triglyceride molecules. Because LPL is synthesized by cells on the abluminal side of endothelial cells, LPL must contact both the abluminal as well as the luminal sides of the endothelium. To determine whether LPL interacts identically with apical (luminal) and basolateral (abluminal) sides of endothelial cells, we investigated binding, transport, and cellular uptake of LPL presented to each side of bovine aortic endothelial cell monolayers grown on semipermeable filters. When LPL was included in the medium on either the apical or basolateral side of the cells, a similar amount of LPL was found in the medium on the opposite side of the cells. Heat-inactivated LPL crossed the monolayers more rapidly in both directions. When cell surface LPL was assessed, more LPL bound to the apical than the basolateral endothelial cell surface. Release of cell surface-associated LPL was assessed with the use of heparin. Less heparin was required to dissociate apical-surface LPL. When LPL (4 micrograms/ml) was in contact with the apical surface for 1 hour, 32.8 +/- 4.9 ng LPL per 24-mm filter were internalized by the cells. If the LPL was in the basolateral medium, only 6 +/- 1.8 ng LPL were found inside the cells. Heat inactivation decreased LPL binding to cell surfaces and internalization by the cells. LPL interactions with the cells were also studied morphologically by using Texas Red (TR)-labeled LPL and confocal microscopy. More TR-LPL was associated with and internalized by the apical endothelial surface. Incubation of cells with TR-LPL in the basolateral medium led to accumulation of LPL on the apical surface, suggesting that the LPL was transported across the cells. Inclusion of TR-LPL on the apical surface did not lead to appreciable accumulation of LPL on the basolateral cell surface. Therefore, endothelial cells are polarized to accumulate LPL on the apical surface. In addition, more LPL is internalized from this side of the cells. We postulate that the polarity of endothelial cells allows LPL to collect at its physiological site of action, i.e., on the luminal surface.
Parenteral Structured Triglyceride Emulsion Improves Nitrogen Balance and Is Cleared Faster from the Blood in Moderately Catabolic Patients (2001)

The parenteral structured triglyceride emulsion improves the nitrogen balance and is cleared faster from the blood, compared with the emulsion of the physical mixture of medium- and long-chain triglycerides, in moderately catabolic patients.
Omega-lognormal analysis of oscillatory movements as a function of brain stroke risk factors (2022)

The development of predictive tools has been commonly utilized as the most effective manner to prevent illnesses that strike suddenly. Within this context, investigations linking fine human motor control with brain stroke risk factors are considered to have a high potential but they are still in an early stage of research. The present paper analyses neuromuscular features of oscillatory movements based on the Omega-Lognormal model of the Kinematic Theory. On a database of oscillatory movements from 120 subjects, we demonstrate that the proposed features differ significantly between subjects with and without brain stroke risk factors. This promising result motivates the development of predictive tools based on the Omega-Lognormal model.
E.s.r. study of the homolytic ring fission of cyclobutenylmethyl radicals (1980)

Cyclobutenylmethyl radicals undergo homolytic ring fission at temperatures above 230 K to give EE pentadienyl radicals; the unrearranged and rearranged radicals have been observed by e.s.r. spectroscopy.
Segmented mirror adaptive optics system (1987)

An adaptive optics system that utilizes a segmented mirror as the active component is described and discussed. The mirror is a 10-in. diam spherical mirror composed of 13 independently controllable segments of equal area. The system linearity and control laws are discussed assuming a modal wavefront expansion. Two approaches to modal aberration expansion are briefly outlined using (1) Zernike polynomials as the basis set and (2) a modified set of Zernike polynomials. Both approaches allow calculation of the coefficient vector with a matrix–vector multiplication if a fixed sampling geometry is used. Assuming the employment of Zernike polynomials in the wavefront expansion, the feedback matrix G which governs actuator movement in the presence of measured aberration is computed. The mirror fitting errors to the Zernike polynomials are then estimated, and a finite number of polynomials are chosen which can be adequately corrected.
Transmitral Thrombectomy via Minithoracotomy in a Patient with Takotsubo Cardiomyopathy (2023)

Left ventricular thrombus is a complication of myocardial infarction, ventricular aneurysm, myocarditis, and cardiomyopathies, such as Takotsubo syndrome. We report the case of a 74-year-old woman who was diagnosed as left ventricular thrombus resulting from transient Takotsubo syndrome. The thrombus was completely removed using video-assisted thoracoscopy through right minithoracotomy. This approach is less invasive and can provide better visualization, thereby avoiding left ventriculotomy.