gebhart/patrepeval huggingface dataset:
SUN-662 Praliciguat, a Clinical-Stage Soluble Guanylate Cyclase Stimulator, Improves Lipid Handling and Insulin Sensitivity in Diet-Induced Obese Mice (2020)

Abstract Praliciguat (PRL) is a soluble guanylate cyclase (sGC) stimulator which in animal models distributes broadly to tissues and elicits hemodynamic, anti-inflammatory, anti-fibrotic, and metabolic effects. Here, we assessed metabolic effects of PRL in a mouse diet-induced obesity model. Six-week-old male C57BL/6N mice were maintained on a low-fat diet (LFD, lean mice) or placed on a 60% high-fat diet (HFD, obese mice). At age 14 weeks, one group of obese mice was maintained on HFD (obese controls) and one group of obese mice was switched to HFD formulated with PRL to achieve a Cmax similar to a 6-mg/kg oral dose (PRL-treated mice). After 38 days of treatment, an oral lipid tolerance test (LTT) was conducted. In a 2nd study under the same dosing paradigm, overnight fasted blood and organs were collected on day 28. As reported previously (1), compared to obese controls, PRL-treated mice had lower fasting insulin (-28%), HOMA-IR (-26%) and triglycerides (-16%) as well as lower plasma triglycerides AUC after LTT (-34%). Gene expression and phosphorylated proteins associated with insulin pathways were measured in liver, skeletal muscle and white adipose tissue. PRL treatment normalized expression of genes involved in lipid handling (liver Pnpla3, Slc27a1, Lpl; muscle Lipe; white adipose tissue Fdft1, Ppara). Expression of proinflammatory genes (liver Tnf; muscle Ccl2; white adipose tissue Akt1, Icam1) was lower in PRL-treated mice than in obese controls. Liver insulin signaling was assessed by determining pAKT (T308) and pAKT (S473), markers of PI3K pathway activity and pERK, a marker of MAPK pathway activity. Compared to lean mice, pAKT (T308) and pERK were lower in obese controls, whereas pAKT (S473) was similar; PRL-treated mice had higher pAKT (T308) and pAKT (S473) compared to obese controls while pERK was unchanged. In skeletal muscle and white adipose tissue, levels of pVASP, a key mediator of the sGC pathway, were higher in PRL-treated mice than in obese controls. In summary, PRL improved insulin sensitivity and lipids in diet-induced obese mice by affecting mechanisms of lipid handling, inflammation, and insulin signaling in key tissues associated with metabolism. 1. Author information excluded, 1924-P: Praliciguat, a Clinical-Stage sGC Stimulator, Improves Insulin Sensitivity, Lipid Tolerance, and Energy Utilization in a Mouse Diet-Induced Obesity Model Housed at Thermoneutrality. Diabetes, 2019. 68(Supplement 1): p. 1924-P.
Properties of Cr:LiSrAlF_6 crystals for laser operation (1994)

We have performed several physical and optical measurements on the Cr:LiSAF (LiSrAlF(6)) laser material that are relevant to its laser performance, including thermal and mechanical properties, water durabilities, and Auger upconversion constants. The expansion coefficient, Young's modulus, fracture toughness, thermal conductivity, and heat capacity are all used to determine an overall thermomechanical figure of merit for the crystal. An investigation of the water durability suggests that the cooling solution should be maintained at pH = 7 to ameliorate problems associated with water dissolution. The Auger constant was found to become much more significant at higher Cr doping, in which excited-state migration leads to a substantial increase in the upconversion rate. We propose a design for a 50-W Cr:LiSAF laser system that is based on a detailed knowledge of all the relevant material parameters.
Photorefractive gain enhancement in InP:Fe using band-edge resonance and temperature stabilization (1990)

We report photorefractive two beam coupling gain coefficients as high as Γ=19 cm−1 and net gains of Γ-α=14 cm−1 in InP:Fe at around 970 nm. This enhancement was achieved by combining band-edge resonant nonlinearities with a second resonant enhancement derived from the bipolar transport in this material. Measurements of gain as a function of pump intensity, applied field, grating spacing, wavelength, and temperature are presented. No moving gratings were required.
Spectral Graph Forge: A Framework for Generating Synthetic Graphs With a Target Modularity (2019)

Community structure is an important property that captures inhomogeneities common in large networks, and modularity is one of the most widely used metrics for such community structure. In this paper, we introduce a principled methodology, the Spectral Graph Forge, for generating random graphs that preserves community structure from a real network of interest, in terms of modularity. Our approach leverages the fact that the spectral structure of matrix representations of a graph encodes global information about community structure. The Spectral Graph Forge uses a low-rank approximation of the modularity matrix to generate synthetic graphs that match a target modularity within user-selectable degree of accuracy, while allowing other aspects of structure to vary. We show that the Spectral Graph Forge outperforms state-of-the-art techniques in terms of accuracy in targeting the modularity and randomness of the realizations, while also preserving other local structural properties and node attributes. We discuss extensions of the Spectral Graph Forge to target other properties beyond modularity, and its applications to anonymization.
Tomlinson-Harashima Precoding for Fiber-Optic Communication Systems (2013)

The performance of Tomlinson-Harashima precoding (THP) is investigated for a 12.5 GBaud 16QAM transmission. THP is shown to reduce significantly the computational load compared with linear equalization and to eliminate the error propagation phenomenon associated with decision-feedback equalization.
Shifts in the Fecal Microbiota Associated with Adenomatous Polyps (2017)

Background: Adenomatous polyps are the most common precursor to colorectal cancer, the second leading cause of cancer-related death in the United States. We sought to learn more about early events of carcinogenesis by investigating shifts in the gut microbiota of patients with adenomas. Methods: We analyzed 16S rRNA gene sequences from the fecal microbiota of patients with adenomas (n = 233) and without (n = 547). Results: Multiple taxa were significantly more abundant in patients with adenomas, including Bilophila, Desulfovibrio, proinflammatory bacteria in the genus Mogibacterium, and multiple Bacteroidetes species. Patients without adenomas had greater abundances of Veillonella, Firmicutes (Order Clostridia), and Actinobacteria (family Bifidobacteriales). Our findings were consistent with previously reported shifts in the gut microbiota of colorectal cancer patients. Importantly, the altered adenoma profile is predicted to increase primary and secondary bile acid production, as well as starch, sucrose, lipid, and phenylpropanoid metabolism. Conclusions: These data hint that increased sugar, protein, and lipid metabolism along with increased bile acid production could promote a colonic environment that supports the growth of bile-tolerant microbes such as Bilophilia and Desulfovibrio. In turn, these microbes may produce genotoxic or inflammatory metabolites such as H2S and secondary bile acids, which could play a role in catalyzing adenoma development and eventually colorectal cancer. Impact: This study suggests a plausible biological mechanism to explain the links between shifts in the microbiota and colorectal cancer. This represents a first step toward resolving the complex interactions that shape the adenoma–carcinoma sequence of colorectal cancer and may facilitate personalized therapeutics focused on the microbiota. Cancer Epidemiol Biomarkers Prev; 26(1); 85–94. ©2016 AACR.
Cyclic sulphones. Part X. Kinetic evidence for the aromatic character of anions derived from benzo- and dibenzothiopyran SS-dioxide systems (1971)

Kinetic acidities of benzo- and dibenzothiopyran SS-dioxides of some methyl derivatives, and of the corresponding open-chain analogues have been determined in [2H5]pyridine–heavy water; it is found that the two pairs of isomers show similar kinetic acidities and that their deuterium exchange rates exceed those of the open-chain analogues by a factor of 103–105. Other stabilising features being common in the two series, the greater stability of the cyclic anions must be associated with their cyclic unsaturated nature: to account for the magnitude of the effect, it is suggested that the conjugative stabilisation developing in the anions is aromatic in character.
The Kinetics of the Oxidative Polymerization of 2, 6-Dimethylphenol with Copper-Amine Complex (1971)

銅(II)-アミン錯体による2,6-キシレノールの酸化重合が,定常状態を保ちながらMichaelis-Nienten型の機構で進行することを見出し,反応の動力学的解析を行なった。Lineweaver-Burkプロットは直線に乗り,この取扱いの妥当性を支持した。動力学的定数の比較から酸素は中間錯体に作用して反応を促進する。用いたアミン配位子種により瓦(Michaelis定数Kmの逆数)は変化するが,速度定数k2は一定であった。K1は単量体錯形成定数K1'と電子移動速度定数ke,の積に比例する値である。単量体濃度が比較的低い領域で見かけの重合速度がアミン配位子種により異なるのはK1の大小に起因し,keの大きいピリジンや立体障害が少なくK1'が大きいと考えられるジエチルアミン,ピペリジンは配位子として有利である。配位子比[ピリジン]/[Cu]が大きくなるに従い,すなわちC-0カップリング分率が増加するにつれてK1が増加することを見出し,カップリング選択の機構をK1と関連させ考察した。
Genomic cytosine methylation level: a molecular marker of stress in the species Gammarus fossarum? (2018)

Genotoxic evaluation has been developing for a couple decade among ecotoxicological assessment approaches in the aquatic field. It offers some prospect for understanding delayed effects on the offspring and the population dynamics (provided genetic mutations affect gametic genome). However, the modification of the DNA sequence by genetic mutation (as a result of primary DNA damage) is not the only impact of toxic substances on the genome. For example, epigenetic effects, defined as hereditary effects on the DNA function, may add up to mediated effects by genetics way. Among these marks, DNA methylation is very studied by scientists. As such, it is important to examine epigenetic changes in the context of population level perspective. This provides a complementary approach to effects on the primary structure of the genome for taking into account the time interval between the exposure to environmental contaminants and their effects. This issue is a real challenge in ecotoxicology. Moreover, the epigenetic allows improving the understanding of changes of life history traits (reproduction, growth and development). These parameters are suitable for assessing the toxicity and are known to be regulated by epigenetic. Finally, epigenic could also help better understand the variability of effects related to experimental conditions between the studies. Therefore, epigenetic marks have an innovative nature for the evaluation of environmental risks. In this regard, we have investigated the measurement of genomic DNA methylation level as a possible stress biomarker in the ecologically relevant species Gammarus fossarum. First, the basal level was explored by studying the difference of overall DNA methylation between male, female and juvenile. Then, we evaluated the effects of natural factors on genomic DNA methylation level as starvation and exposed to different temperatures (8, 12 and 18°C) for 7 days and 1 month. To know the variability of DNA methylation in populations of Gammarus fossarum, three French populations from the same genetic strain, were studied. Lastly, the epigenetic biomarker response to a chemical stress was evaluated in a field experience. We encaged gammarids stemming from a reference unpolluted station in sited impacted by various human activities.
Direct measurements of the terminal laser level lifetime in neodymium-doped crystals and glasses (1995)

We have measured the terminal level lifetime (τ11/2) for the 1-μm neodymium transition in several laser media, using a novel pump (2.41-μm) and probe (1.06-μm) technique. This method allows us to populate the 4I13/2 level directly and subsequently to monitor the terminal level 4I11/2 population as a function of time by observing the change in integrated fluoresence of the 0.88-μm emission for each time delay between the pump and the probe pulses. We developed a computer model to analyze the data and determined the upper and lower limits for the τ11/2 lifetime. The results for some of the materials investigated are 115–225 ps for Nd:Y3Al5O12, 250–450 ps for Nd:LG-750 (phosphate glass), 535–740 ps for Nd:LG-660 (silicate glass), 896–1900 ps for Nd:YAlO3, and 10.5–20 ns for Nd:YLiF4. In addition, we found the lifetimes to be independent of the neodymium doping concentration for the phosphate and silicate glass samples investigated.
Dynamics and Control of a Helicopter Carrying a Payload Using a Cable-Suspended Robot (2005)

This paper presents a study of the dynamics and control of a helicopter carrying a payload through a cable-suspended robot. The helicopter can perform gross motion, while the cable suspended robot underneath the helicopter can modulate a platform in position and orientation. Due to the under-actuated nature of the helicopter, the operation of this dual system consisting of the helicopter and the cable robot is challenging. We propose here a two time scale control method, which makes it possible to control the helicopter and the cable robot independently. In addition, this method provides an effective estimation on the bound of the motion of the helicopter. Therefore, even in the case where the helicopter motion is unknown, the cable robot can be stabilized by implementing a robust controller. Simulation results of the dual system show that the proposed control approach is effective for such a helicopter-robot system.
Dissection of RNA-primed DNA synthesis catalyzed by gene 4 protein and DNA polymerase of bacteriophage T7. Coupling of RNA primer and DNA synthesis. (1986)

Gene 4 protein and DNA polymerase of bacteriophage T7 catalyze RNA-primed DNA synthesis on single-stranded DNA templates. T7 DNA polymerase exhibits an affinity for both gene 4 protein and single-stranded DNA, and gene 4 protein binds stably to single-stranded DNA in the presence of dTTP (Nakai, H. and Richardson, C. C. (1986) J. Biol. Chem. 261, 15208-15216). Gene 4 protein-T7 DNA polymerase-template complexes may be formed in both the presence and absence of nucleoside 5'-triphosphates. The protein-template complexes may be isolated free of unbound proteins and nucleotides by gel filtration and will catalyze RNA-primed DNA synthesis in the presence of ATP, CTP, and the four deoxynucleoside 5'-triphosphates. RNA-primed DNA synthesis may be dissected into separate reactions for primer synthesis and DNA synthesis. Upon incubation of gene 4 protein with single-stranded DNA, ATP, and CTP, a primer-template complex is formed; it is likely that gene 4 protein mediates stable binding of the oligonucleotide to the template. The complex, purified free of unbound proteins and nucleotides, supports DNA synthesis upon addition of DNA polymerase and deoxynucleoside 5'-triphosphates. Association of primers with the template is increased by the presence of dTTP or DNA polymerase during primer synthesis. DNA synthesis supported by primer-template complexes initiates predominantly at gene 4 recognition sequences, indicating that primers are bound to the template at these sites.
Experimental study of the atmospheric neutrino backgrounds forp→e+π0searches in water Cherenkov detectors (2008)

The atmospheric neutrino background for proton decay via $p\ensuremath{\rightarrow}{e}^{+}{\ensuremath{\pi}}^{0}$ in ring imaging water Cherenkov detectors is studied with an artificial accelerator neutrino beam for the first time. In total, $3.14\ifmmode\times\else\texttimes\fi{}{10}^{5}$ neutrino events corresponding to about 10 megaton-years of atmospheric neutrino interactions were collected by a 1000 ton water Cherenkov detector (KT). The KT charged-current single ${\ensuremath{\pi}}^{0}$ production data are well reproduced by simulation programs of neutrino and secondary hadronic interactions used in the Super-Kamiokande (SK) proton decay search. The obtained $p\ensuremath{\rightarrow}{e}^{+}{\ensuremath{\pi}}^{0}$ background rate by the KT data for SK from the atmospheric neutrinos whose energies are below 3 GeV is ${1.63}_{\ensuremath{-}0.33}^{+0.42}(\mathrm{stat}{)}_{\ensuremath{-}0.51}^{+0.45}(\mathrm{syst})(\mathrm{megaton}\mathrm{\text{\ensuremath{-}}}\mathrm{year}{)}^{\ensuremath{-}1}$. This result is also relevant to possible future, megaton-scale water Cherenkov detectors.
Photorefractive Properties of Undoped and Doped Single Crystal SBN:60 (1986)

We present the results of our theoretical and experimental studies of the photorefrac-tive effect in single crystal SBN:60, SBN:Ce, and SBN:Fe. Specifically, the two-beam coupling coefficients, response times and absorption coefficients of these materials are given.
On the origin of frequency power-law for tissue mechanics in elastography (2020)

The imaginary part of the complex shear modulus in tissue is not negligible. In liver the phase angle (ranging between 0 and 1) is about 0.2 while in kidney it is about 0.3. The presence of dispersion can have its origin either in a constitutive loss—i.e., absorption of energy—or in scattering of the wave and hence represents an apparent loss. Since dispersion in tissue follows over a wide range a frequency power-law, fractional order derivative models such as the springpot model are well suited to fit the data in the clinically accessible range of 30–200Hz. They, however, do not provide a fundamental understanding of whether loss is due to friction and hence conversion to heat, or due to material heterogeneities and thus scattering. Models such as ODA are able to relate the observable frequency power-law to the spatial distribution of scatterers. If loss in low-frequency elastography were solely due to scattering, this would render the method extremely powerful in characterizing for instance blood vessel architecture in oncology. To distinguish whether the measured prominant loss in porcine tissue (phase angle ∼0.4) is originating from absorption or scattering, we use MR-Spectroscopy to measure absolute temperature via the resonance-frequency-shift between water and methylene, at precisions better than 0.1 °C. Temperature should increase theoretically by about 1/2 °C at an amplitude of 10 μm, 500 Hz, and an exposure of 1000 s, which is not observed. This points towards scattering as the main mechanism for wave attenuation.
Late‐onset allograft rejection, cytomegalovirus infection, and renal allograft loss: Is anti‐CMV prophylaxis required following late‐onset allograft rejection? (2021)

Renal transplant recipients remain at risk of delayed-onset cytomegalovirus (CMV) infection occurring beyond a complete course of prophylaxis. In this retrospective cohort, all 278 patients who received renal allografts from deceased donors from 2014 to 2016 were followed until September 1, 2019. We determined the effect of early-vs late-onset acute rejection (EAR vs LAR [ie, occurring beyond 12 months after transplantation]) on CMV infection and subsequently long-term allograft outcome. Median (IQR) duration of follow-up was 1186.0 (904.7-1531.2) days. Seventy patients including 49 patients with EAR and 21 with LAR received augmented immunosuppression. In the same interval, 40 patients developed CMV infection (36 patients beyond 90 days after transplantation [90%]). In logistic regression analysis, D+/R- CMV serostatus (OR: 5.5, 95% CI: 2.5-12.2) and LAR (OR: 7.9, 95% CI: 2.8-22.2) significantly increased the risk of CMV infection. In Cox proportional hazard model, delayed-onset CMV infection (HR: 2.51, 95% CI: 1.08-5.86) and LAR (HR: 5.46, 95% CI: 2.26-13.14) significantly increased the risk of allograft loss. Patients with LAR are at risk of late-onset CMV infection. Post-LAR, targeted prophylaxis may reduce the risk of CMV infection and subsequently allograft loss. Further studies are required to demonstrate the effect of targeted prophylaxis following LAR.
Abstract 10706: The Interplay Between Leukocyte Integrin Mac-1 And Estrogen Receptors Protects Against Atherosclerosis (2019)

Atherosclerosis is a chronic inflammatory disease of the arterial wall, characterized by accumulation of lipid-loaded macrophages and fibrous material in developing lesions. Integrin αMβ2 (Mac-1) i...
An Aptameric Microfluidic System for Specific Purification, Enrichment, and Mass Spectrometric Detection of Biomolecules (2009)

We present an innovative microfluidic system that accomplishes specific capture, enrichment, and isocratic elution of biomolecular analytes with coupling to label-free mass spectrometric detection. Analytes in a liquid phase are specifically captured and enriched via their affinity binding to aptamers, which are immobilized on microbeads packed inside a microchamber. Exploiting thermally induced reversible disruption of aptamer-analyte binding via on-chip temperature control with an integrated heater and temperature sensor, the captured analytes are released into the liquid phase and then isocratically eluted and transferred via a microfluidic flow gate for detection by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The utility of the device is demonstrated using adenosine monophosphate (AMP) as a model analyte. Experimental results indicate that the device is capable of purifying and enriching the analyte from a sample mixed with nonspecific analytes and contaminated with salts. In addition, thermally induced analyte release is performed at modest temperatures (45degC), and mass spectra obtained from MALDI-MS demonstrate successful detection of AMP at concentrations as low as 10 nM following enrichment by consecutive infusion of a diluted sample.
Supplementary Legends from Heparin-Binding EGF-Like Growth Factor Is a Promising Target for Ovarian Cancer Therapy (2023)

Supplementary Legends from Heparin-Binding EGF-Like Growth Factor Is a Promising Target for Ovarian Cancer Therapy
Podocyte injury-driven intracapillary plasminogen activator inhibitor type 1 accelerates podocyte loss via uPAR-mediated β1-integrin endocytosis (2015)

Podocyte-endothelial cell cross-talk is paramount for maintaining the filtration barrier. The present study investigated the endothelial response to podocyte injury and its subsequent role in glomerulosclerosis using the podocyte-specific injury model of NEP25/LMB2 mice. NEP25/LMB2 mice showed proteinuria and local podocyte loss accompanied by thrombotic microangiopathy on day 8. Mice showed an increase of glomerular plasminogen activator inhibitor type 1 (PAI-1) mRNA and aberrant endothelial PAI-1 protein already on day 1, before thrombosis and proteinuria. A PAI-1-specific inhibitor reduced proteinuria and thrombosis and preserved podocyte numbers in NEP25/LMB2 mice by stabilization of β1-integrin translocation. Heparin loading significantly reduced thrombotic formation, whereas proteinuria and podocyte numbers were unchanged. Immortalized podocytes treated with PAI-1 and the urokinase plasminogen activator (uPA) complex caused significant cell detachment, whereas podocytes treated with PAI-1 or uPA alone or with the PAI-1/uPA complex pretreated with an anti-uPA receptor (uPAR) antibody failed to cause detachment. Confocal microscopy and cell surface biotinylation experiments showed that internalized β1-integrin was found together with uPAR in endocytotic vesicles. The administration of PAI-1 inhibitor or uPAR-blocking antibody protected cultured podocytes from cell detachment. In conclusion, PAI-1/uPA complex-mediated uPAR-dependent podocyte β1-integrin endocytosis represents a novel mechanism of glomerular injury leading to progressive podocytopenia. This aberrant cross-talk between podocytes and endothelial cells represents a feedforward injury response driving podocyte loss and progressive glomerulosclerosis.