gebhart/patrepeval huggingface dataset:
Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL fromPseudomonas aeruginosa (2006)

Pathogenic gram-negative bacteria can modify the lipid A portion of their lipopolysaccharide in response to environmental stimuli. 3-O-deacylation of lipid A by the outer membrane enzyme PagL modulates signaling through Toll-like receptor 4, leading to a reduced host immune response. We found that PagL is widely disseminated among gram-negative bacteria. Only four residues are conserved: a Ser, His, Phe, and Asn residue. Here, we describe the crystal structure of PagL from Pseudomonas aeruginosa to 2.0-A resolution. It consists of an eight-stranded beta-barrel with the axis tilted by approximately 30 degrees with respect to the lipid bilayer. The structure reveals that PagL contains an active site with a Ser-His-Glu catalytic triad and an oxyanion hole that comprises the conserved Asn. The importance of active site residues was confirmed in mutagenesis studies. Although PagL is most likely active as a monomer, its active site architecture shows high resemblance to that of the dimeric 12-stranded outer membrane phospholipase A. Modeling of the substrate lipid X onto the active site reveals that the 3-O-acyl chain is accommodated in a hydrophobic groove perpendicular to the membrane plane. In addition, an aspartate makes a hydrogen bond with the hydroxyl group of the 3-O-acyl chain, probably providing specificity of PagL toward lipid A.
Supplemental Figure 3 from Expression of CD14, IL10, and Tolerogenic Signature in Dendritic Cells Inversely Correlate with Clinical and Immunologic Response to TARP Vaccination in Prostate Cancer Patients (2023)

&lt;p&gt;Interactive 3D plot showing the correlation of module 2 expression with CD14, IL-10, MDC and MCP-1.Each dot represents one DC sample. X, y and z coordinates represent concentration levels of IL-10, MDC, and MCP-1, respectively, size of dots is proportional with % of CD14+ cells, color represents module 2 expression level (red-yellow-white gradient, with red being the lowest expression level and white the highest)&lt;/p&gt;
Myokine/Cardiokine Follistatin-like Protein 1 Promotes Oxidative MyHC Expression and Mitochondrial Function in Myogenic Cells (2017)

Follistatin-like Protein 1 (FSTL1) is a glycoprotein secreted by cardiac and skeletal muscle tissues under stressful conditions. An elevated level of plasma FSTL1 has been observed after a single bout of exercise suggesting its potential myokine-like role involved in the crosstalk between muscle and other organs. PURPOSE: To investigate autocrine effects of FSTL1 on myotube differentiation, myosin heavy chain expression and mitochondrial respiration in various myogenic cells. METHODS: Primary myoblasts were isolated from canine gastrocnemius muscle. Myotube differentiation was induced by a low serum condition for 4 days. Immunostainings were performed using MF20 antibody (rod-like tail region of myosin) and DAPI (nuclei); and fusion index was determined by calculating the ratio between total number of nuclei and number of nuclei within myotubes formed. RT-PCR assays were performed using primer sets precisely designed to amplify each fiber type-associated myosin heavy chain isoforms. Oxygen consumption of intact cells were measured using a Clark-type oxygen sensor; and mitochondrial respiration was measured using Seahorse XF96 analyzer. RESULTS: During canine myotube formation, FSTL1 treatment (300 ng/ml, 4 days) significantly enhanced myogenic potential determined by fusion index (~2-fold increase). There was a significant increase in MyHC7 expression (~1.5 fold) in myotubes treated with FSTL1 during differentiation compared to non-treated myotubes. Acute FSTL1 treatment (up to 500 ng/ml) had no significant effect on mitochondrial respiration in canine myoblasts. Acute FSTL1 treatments (250 ng/ml) significantly increased mitochondrial respiration in L6 myotubes (~1.5 fold) and human rhabdomyosarcoma cells. Chronic FSTL1 treatments (250 ng/ml, 64 hours) significantly increased oxygen consumption in intact canine myoblasts and myotubes. CONCLUSION: Our preliminary data suggest that FSTL1 enhances differentiation potential and increases oxidative metabolism in myogenic cells suggesting that FSTL1 may be an important cellular mediator of the beneficial effects of exercise in the context of skeletal muscle adaptation. Supported by NIH Grant RO1 HL133248.
Conformational Control of Energy Transfer: A Mechanism for Biocompatible Nanocrystal‐Based Sensors (2012)

Live-Reporter: Die Kombination eines pH-modulierten Oligonucleotid-Konformationsschalters mit fluoreszierenden Nanokristallen ergibt einen empfindlichen pH-Nanosensor (siehe Schema). Analyt-abhängige Konformationsänderungen steuern den Abstand zwischen dem Nanokristall-Energiedonor (grün) und einem FRET-Akzeptor (rot); so erhält man einen Reporter für pH-Werte in individuellen Endosomen lebender Zellen. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Abstract 3679: Preliminary results from a patient group, excluded from the National Lung Cancer Screening Trial, who are at high risk for lung cancer- heavy smokers with HIV (2011)

Abstract Purpose: Within the HIV population, the incidence of lung cancer is estimated to be 2-4 times that of the general population. Of the non AIDS associated malignancies, lung cancer is the leading cause of death among HIV patients who develop malignancy because of its advanced stage of presentation. The National Lung Cancer Screening Trial recently reported a 20% reduction in mortality for patients undergoing low dose computed tomography (CT) screening, but individuals with HIV diagnosis were excluded. To report the results of an observational pilot study of lung cancer CT screening in a cohort of HIV heavy smokers. Materials and Methods: A prospective cohort study was performed with 185 asymptomatic individuals with confirmed HIV diagnosis who had smoked 20 pack-years or more. All participants had baseline (prevalence) chest CT scanning and 107 patients (58.2%) also received at least one subsequent annual (incidence) examination of the chest and upper abdomen. All patients underwent hand held spirometry testing, cytologic analysis of sputa, and detailed health status questioning. Results: Of the 185 individuals, there were 31.4% females, 68.6% males, 90.3% African-Americans, 8.7% Caucasian, and 1.1% Hispanic. The median age at enrolment was 48 years, and the median number of smoking pack-years was 34. Non-calcified nodules were detected in 4 participants (2.1%) by low-dose prevalent CT compared to no nodules on incident CT scans. Only one patient with malignancy was detected (0.54%) on prevalent scanning and none on incident scanning. Stage of malignancy was advanced. No biopsies were undertaken for benign disease. CT evidence of COPD and coronary artery disease were present in 24% and 27% of patients, respectively. Additional CT findings of clinical importance were noted in the chest in 132 (71.7%) patients and extrathoracically in 30 (16.3%) of patients, respectively. Conclusion: The prevalence results of this pilot study are in line with other observational studies of greater sample size for HIV indeterminate patients. Although the sample size is small, it suggests no elevated incidence of lung cancer in HIV heavy smokers. Although the rate of incident scanning is low, CT screening of HIV patients is feasible. This justifies accruing a larger sample of HIV patients perhaps from an already well defined, large, prospective cohort of HIV heavy smokers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3679. doi:10.1158/1538-7445.AM2011-3679
Three-dimensional source reconstruction with a scanned pinhole camera (1998)

We present a simple reconstruction algorithm for three-dimensional (3D) incoherent source distributions imaged by a laterally scanned pinhole camera. We consider digital sampling of multiple pinhole images for 3D reconstruction and implement an experimental demonstration with lateral resolution of 2x10(-3) rad and longitudinal resolution of approximately 0.14z(2) m , where z is the object-to-pinhole distance in meters.
Non-reversible Photoinduced Phase Transition in the RbMnFe Prussian Blue Analogue Studied by Streaming Crystallography (2022)

International audience
Hyperfine correlation spectroscopy with pulsed EPR (1994)

In dieser Arbeit sollten verschiedene Methoden der Elektronenspinecho-Enveloppenmodulation auf dem vorhandenen Puls-ESR-Spektrometer implementiert und auf den photoangeregten Triplettzustand von C60 angewendet werden. Für die Verwendung von ESEEM-Techniken wurde die Meßplatzsteuerung des Puls-ESR-Spektrometers unter besonderer Berücksichtung zweidimensionaler Verfahren von Grund auf programmiert. Am Quadratsäure-Einkristall wurden die ein- und zweidimensionalen Methoden der Hyperfeinkorrelationsspektroskopie demonstriert. Die spektrale Analyse der Daten im Zeitbereich erfolgte mit der nichtiterativen, linearen Fitmethode der Linearen Prädiktion (LPSVD), die erst seit 1985 in der Magnetischen Resonanz bekannt ist. Dazu wurde ein C-Programm erstellt und die Leistungsfähigkeit an simulierten Daten gezeigt. Die 5-Pulssequenz zur Verbesserung der Modulationstiefe wurde erstmalig zweidimensional durchgeführt. Damit konnte ein neues, zweidimensionales Korrelationsexperiment experimentell verifiziert werden. Davon angeregt, wurde eine neue 6-Puls-HYSCORE-Sequenz vorgeschlagen. Ein- und zweidimensionale ESEEM-Messungen am Triplettzustand von C60 ergaben eine eindeutige Hyperfeinlinie im Abstand von 1.8 MHz zur freien 13C-Frequenz mit einer Breite von ca. 400 kHz. Eine zweite Linie im Abstand von -3.3 MHz wurde ebenfalls beobachtet. Weiterhin wurden Messungen in Abhängigkeit vom Magnetfeld und der Temperatur durchgeführt. Eine Modellrechnung für die 3-Puls-Enveloppenmodulation von C60 hat eine ausgezeichnete Übereinstimmung mit den experimentellen Spektren ergeben. Dies war nur durch die grundlegende Annahme möglich, daß die Spindichteverteilung auf dem C60 äquatorial bezüglich der D5d-Symmetrieachse konzentriert ist und zu den Polen hin abfällt.
Spatially Organized Differentiation of Mesenchymal Stem Cells within Biphasic Microparticle‐Incorporated High Cell Density Osteochondral Tissues (2015)

Giving rise to both bone and cartilage during development, bone marrow-derived mesenchymal stem cells (hMSC) have the unique capacity to generate the complex tissues of the osteochondral interface. Utilizing a scaffold-free hMSC system, biphasic osteochondral constructs are incorporated with two types of growth factor-releasing microparticles to enable spatially organized differentiation. Gelatin microspheres (GM) releasing transforming growth factor-β1 (TGF-β1) combined with hMSC form the chondrogenic phase. The osteogenic phase contains hMSC only, mineral-coated hydroxyapatite microparticles (MCM), or MCM loaded with bone morphogenetic protein-2 (BMP-2), cultured in medium with or without BMP-2. After 4 weeks, TGF-β1 release from GM within the cartilage phase promotes formation of a glycosaminoglycan- and type II collagen-rich matrix, and has a local inhibitory effect on osteogenesis. In the osteogenic phase, type X collagen and osteopontin are produced in all conditions. However, calcification occurs on the outer edges of the chondrogenic phase in some constructs cultured in media containing BMP-2, and alkaline phosphatase levels are elevated, indicating that BMP-2 releasing MCM provides better control over region-specific differentiation. The production of complex, stem cell-derived osteochondral tissues via incorporated microparticles could enable earlier implantation, potentially improving outcomes in the treatment of osteochondral defects.
Fundamental Characteristics of Cyanide‐Related Multielement Molecular Ion‐Implanted Epitaxial Si Wafers for High‐Performance CMOS Image Sensors (2019)

To improve the performance of CMOS image sensors, the authors currently develop a cyanide-related multielement molecular (CH4N) ion-implanted epitaxial Si wafer. The CH4N ion-implanted epitaxial Si wafer has two kinds of defects; C agglomeration defects and stacking faults. These defects contribute to high metal gettering capability and retention capability for H, C, and N. More details can be found in article number 1900172 by Akihiro Suzuki, Kazunari Kurita, and co-workers.
MR Assessment of Myocardial Perfusion, Viability, and Function after Intramyocardial Transfer of VM202, a New Plasmid Human Hepatocyte Growth Factor in Ischemic Swine Myocardium (2008)

Intramyocardial transfer of VM202 improved myocardial perfusion, viability, and LV function.
Fabrication of High Aspect Ratio Millimeter-Tall Free-Standing Carbon Nanotube-Based Microelectrode Arrays (2018)

Microelectrode arrays of carbon nanotube (CNT)/carbon composite posts with high aspect ratio and millimeter-length were fabricated using carbon-nanotube-templated microfabrication with a sacrificial "hedge". The high aspect ratio, mechanical robustness, and electrical conductivity of these electrodes make them a potential candidate for next-generation neural interfacing. Electrochemical measurements were also demonstrated using an individual CNT post microelectrode with a diameter of 25 μm and a length of 1 mm to perform cyclic voltammetry on both methyl viologen and dopamine in a phosphate-buffered saline solution. In addition to detection of the characteristic peaks, the CNT post microelectrodes show a fast electrochemical response, which may be enabling for in vivo and/or in vitro measurements. The CNT post electrode fabrication process was also integrated with other microfabrication techniques, resulting in individually addressable electrodes.
Temperature estimation using ultrasonic spatial compound imaging (2004)

The feasibility of temperature estimation during high-intensity focused ultrasound therapy using pulse-echo diagnostic ultrasound data has been demonstrated. This method is based upon the measurement of thermally-induced modifications in backscattered RF echoes due to thermal expansion and local changes in the speed Of Sound. It has been shown that strong ripple artifacts due to the thermo-acoustic lens effect severely corrupt the temperature estimates behind the heated region. We propose here a new imaging technique that improves the temperature estimation behind the heated region and reduces the variance of the temperature estimates in the entire image. We replaced the conventional beamforming on transmit with multiple steered plane wave insonifications using several subapertures. A two-dimensional temperature map is estimated from axial displacement maps between consecutive RF images of identically steered plane wave insonifications. Temperature estimation is then improved by averaging the two-dimensional maps from the multiple steered plane wave insonifications. Experiments were conducted in a tissue-mimicking gelatin-based phantom and in fresh bovine liver.
Compact UHF bandpass filter with the subwavelength metamaterial ZORs and transmission zeros for enhanced channel selectivity (2011)

In this paper, a microstrip bandpass filter for a UHF 900 MHz Band is remarkably miniaturized and its performance is enhanced using the metamaterial(MTM) Zeroth Order Resonator(ZOR) characteristics. Firstly, we propose each of the resonators for a bandpass filter is implemented by a one-cell ZOR, and the coupling between neighboring different ZORs is controlled to meet the primary goal on the bandpass filtering in the form of a sequential coupling mechanism. Secondly, this MTM ZOR filter is suggested to have transmission zeros due to source-load coupling to improve the isolation from the other wireless communication bands. It is revealed that the first and second proposed filters are less than 1/6 of the conventional filters in terms of size, and they present the smaller insertion loss and return loss in the passband and the higher isolation in the stopband due to the transmission zeros, which checked by the simulation and measurement. Besides, the MTM properties are verified with the dispersion diagram and the no-phase variation electric field distribution over the ZOR by the 3D EM simulation.
Active Braking Control System Design: The D<inline-formula><tex-math>$^{\bf 2}$</tex-math> </inline-formula>-IBC Approach (2015)

In modern road vehicles, active braking control systems are crucial elements to ensure safety and lateral stability. Unfortunately, the wheel slip dynamics is highly nonlinear, and the online estimation of the road-tire conditions is still a challenging open-research problem. These facts make it difficult to devise a braking control system that is reliable in any possible situation without being too conservative. In this paper, we propose the data-driven inversion-based control approach to overcome the above issues. The method relies on a 2-DOF architecture, with a linear controller and a nonlinear controller in parallel, both designed using only experimental data. The effectiveness of the proposed approach against state-of-the-art braking control is shown by means of an extensive simulation campaign. A validation test on a commercial full-fledged multibody simulator for two-wheeled vehicles is also provided.
Generation Trouble: Reflections on Gay Male Identity, Generational Consciousness, and Social Belonging (1969)

I s There a Gay Generation Gap?" muses Out magazine in a headline on the cover of its October 200 I issue. What at first appears as a genuine question, however, turns out to be merely rhetorical.
Foxo3a is essential for maintenance of the hematopoietic stem cell pool (2009)

Hematopoietic stem cells (HSCs) are maintained in an undifferentiated quiescent state within a bone marrow niche. Here we show that Foxo3a, a forkhead transcription factor that acts downstream of the PTEN/PI3K/Akt pathway, is critical for HSC self-renewal. We generated gene-targeted Foxo3a−/− mice and showed that, although the proliferation and differentiation of Foxo3a−/− hematopoietic progenitors were normal, the number of colony-forming cells present in long-term cocultures of Foxo3a−/− bone marrow cells and stromal cells was reduced. The ability of Foxo3a−/− HSCs to support long-term reconstitution of hematopoiesis in a competitive transplantation assay was also impaired. Foxo3a−/− HSCs also showed increased phosphorylation of p38MAPK, an elevation of ROS, defective maintenance of quiescence, and heightened sensitivity to cell-cycle-specific myelotoxic injury. Finally, HSC frequencies were significantly decreased in aged Foxo3a−/− mice compared to the littermate controls. Our results demonstrate that Foxo3a plays a pivotal role in maintaining the HSC pool.
E‐cadherin is a robust prognostic biomarker in colorectal cancer and low expression is associated with sensitivity to inhibitors of topoisomerase, aurora, and HSP90 in preclinical models (2021)

Cell-cell and cell-matrix adhesion proteins that have been implicated in colorectal epithelial integrity and epithelial-to-mesenchymal transition could be robust prognostic and potential predictive biomarkers for standard and novel therapies. We analyzed in situ protein expression of E-cadherin (ECAD), integrin β4 (ITGB4), zonula occludens 1 (ZO-1), and cytokeratins in a single-hospital series of Norwegian patients with colorectal cancer (CRC) stages I-IV (n = 922) using multiplex fluorescence-based immunohistochemistry (mfIHC) on tissue microarrays. Pharmacoproteomic associations were explored in 35 CRC cell lines annotated with drug sensitivity data on > 400 approved and investigational drugs. ECAD, ITGB4, and ZO-1 were positively associated with survival, while cytokeratins were negatively associated with survival. Only ECAD showed independent prognostic value in multivariable Cox models. Clinical and molecular associations for ECAD were technically validated on a different mfIHC platform, and the prognostic value was validated in another Norwegian series (n = 798). In preclinical models, low and high ECAD expression differentially associated with sensitivity to topoisomerase, aurora, and HSP90 inhibitors, and EGFR inhibitors. E-cadherin protein expression is a robust prognostic biomarker with potential clinical utility in CRC.
Transobturator Bypass Utilizing Fluoroscopic Guidance (2016)

Live fluoroscopy is a versatile technique and in conjunction with our described surgical technique of lower extremity bypass should help increase the technical success rates of this procedure.
Worldwide Field Applications of a Polymeric Gel System for Conformance Applications (2007)

Summary Water production becomes a major problem as hydrocarbon-producing fields mature. Higher levels of water production result in increased levels of corrosion and scale, increased load on fluid-handling facilities, increased environmental concerns, and eventually well shut-in (with associated workover costs). Consequently, producing zones are often abandoned in an attempt to avoid water contact, even when the intervals still retain large volumes of recoverable hydrocarbons. Many polymer systems have been applied over the years to control undesired water production from hydrocarbon wells, with varying degrees of success. For approximately eight years, a polymer gel system based on an acrylamide/t-butyl acrylate copolymer (PAtBA) crosslinked with polyethyleneimine (PEI) has been used successfully for various water shutoff applications. This article describes results from a sampling of over 200 jobs performed throughout the world, including the average results from more than 90 jobs performed in one geographic location alone. In addition to "standard" matrix treatments, results will be shown for other types of treatment, including a design to plug annular communication and a combination of sealant and temporary gel in an openhole horizontal completion. In addition, laboratory data pertaining to work aimed at increasing the temperature limit of the system will be presented. The upper placement temperature of the system originally was ~260°F. Data presented in this article indicates the development of a retarder system that allows the upper placement temperature to be raised to at least 350°F.
Mn-implanted GeC: An Amorphous Ferromagnetic Material (2009)

both samples. The Curie temperature of the flrst samples is about 150 K, while that of the second sample is about 170 K. The in-plane saturated magnetic moment for the flrst sample is about 2:2£10 i5 emu/cm 2 and that for the second sample is about 3:0 £ 10 i5 emu/cm 2 . These results show clear enhancement of magnetic properties of the Mn-implanted GeC thin fllm over the identically implanted Ge layer due to the presence of a small amount of carbon. Further, high-resolution transmission electron microscopy showed that Mn implanted region is amorphous, without any precipitates. It is believed that it is this amorphous phase that is responsible for ferromagnetism.
Isolation and purification of recombinant outer surface protein C (rOspC) of Borrelia burgdorferi Sensu Lato (2005)

The aim of this work was isolation and purification of the major immunodominant protein, Outer surface protein C (OspC) of three members of the species group Borrelia burgdorferi, the causative agent of Lyme disease. Our aim was to obtain this protein in a quantity and purity sufficient for immunization of experimental animals. For optimalization of protein purification's yield we used immobilized metal ion affinity chromatography (IMAC) under different conditions. The greatest efficiency was achieved by using of HiTrap Chelating Column under native conditions.