gebhart/patrepeval huggingface dataset:
Abstract 1340: Assessing autophagic flux in cell culture models with a novel plate-based assay (2018)

Abstract The importance of autophagy in normal cell health and diseased states, including cancer, immunology and inflammation, has become quite clear. Given the growing interest in screening for autophagy modulators, we have developed a homogeneous plate-based assay to measure autophagic flux in cell culture models using NanoLuc® Binary Technology (NanoBiT™). LC3B (Atg8) protein was tagged on its N-terminus with an 11 amino acid peptide, (HiBiT), as well as an intervening “spacer” sequence. When expressed at low-to-moderate levels in mammalian cell lines, this LC3-based reporter is subject to degradation by the autophagic pathway. Changes in reporter levels following cell treatment are determined by addition of a lytic reagent containing Large BiT (LgBiT), which rapidly associates with HiBiT to produce a bright, luciferase activity in the presence of added substrate. In stable U2OS reporter cells, mTORC inhibitor treatment decreased assay signal by 25% (rapamycin) to 60% (PP242, AZD8055), consistent with compound stimulation of autophagic flux and degradation of the autophagy reporter. In contrast, treatment with autophagy inhibitors (bafilomycin A1, chloroquine) produced a 70-80% increase in assay signal, consistent with accumulation of autophagy reporter following blockade of basal autophagy. Similar results were obtained in HEK293 cells stably expressing the reporter, as well as in cells in which autophagy reporter was transiently expressed via simple, one-step transduction with BacMam viral particles. Mechanism of action of autophagy modulators was confirmed through blockade of effects by 50nM bafilomycin A1 cotreatment. Multiplex with a cell necrosis detection agent allowed for same-well determination of cytotoxic effects that might undermine analysis of a compound's discrete effects on autophagic flux. When assayed in 384-well plates with automation, U2OS and HEK293 autophagy reporter cells produced Z' values of 0.6-0.7 in response to autophagy induction (PP242), and Z' values of 0.7-0.8 by subsequent blockade of autophagy (PP242 + bafilomycin A1). Therefore, using this novel plate-based assay system for the determination of autophagic flux, it is possible to screen test agents and quantitatively assess their effects in cell culture models. Citation Format: Dan F. Lazar, Ryan W. Kessens, Amani A. Gillette, Braeden L. Butler, Christopher T. Eggers, Brock F. Binkowski, Gediminas Vidugiris, Michael R. Slater, Dongping Ma, James J. Cali. Assessing autophagic flux in cell culture models with a novel plate-based assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1340.
P3‐159: Impact of the MRI acquisition protocol on the hippocampus volume obtained by two methodologically distinct methods for fully automated volumetry: Spm12 and fsl‐first (2015)

The translation of core neuroimaging markers such as the MRI-based hippocampus volume for early diagnosis of Alzheimer's disease from research settings into daily clinical practise is a major challenge, not least because of the lack of harmonization of MRI acquisition protocols across MRI systems. This problem might be reduced by using methods for hippocampal volumetry that are rather stable with respect to variations of the acquisition protocol. The aim of this study therefore was to investigate the impact of different MRI acquisition protocols on the results of 2 methodologically distinct methods for fully-automated quantification of the hippocampus volume: SPM12 and FSL-FIRST. MPRAGE-MRI of 100 healthy ADNI subjects from 35 centres and 100 healthy subjects from 15 clinical centres (CC) in Germany were included. ADNI images had been acquired according to harmonized acquisition protocols, whereas the CCs had used their vendor-specific standard acquisition protocols. Fully automated hippocampal volumetry was performed with atlas-based volumetry (SPM12) and model-based hippocampal segmentation (FSL-FIRST). Individual hippocampal volumes (HVs) were adjusted for total intracranial volume and age. A t-test was used to compare HVs of the two cohorts, the Levene test to assess equality of variances. The two samples were well matched with respect to age (75.6±5.4 vs 74.9±5.4; p = 0.361). Mean HV did not differ between the 2 samples neither with SPM12 (ADNI 6.51±0.63 ml; CC 6.47±0.89 ml; p = 0.712) nor with FSL-FIRST (ADNI 7.47±0.90 ml, CC 7.44±1.02 ml; p = 0.807). The variance of the HV was larger in the CC sample than in the ADNI sample with SPM12 (p = 0.018, coefficient of variation: ADNI 9.7%, CC 13.8%), whereas there was no difference with FSL-FIRST (ADNI 12.0% vs CC: 13.6%; p = 0.183). SPM12 shows less variation in estimating hippocampal volumes than FSL-FIRST if harmonized acquisition protocols are deployed. Results further suggest that FSL-FIRST is more robust against variations of the acquisition protocol than SPM12.
Validation of the ‘FeMorph’ software in planning cam osteochondroplasty by incorporating labral morphology (2014)

Impingement resulting from a cam deformity may cause pain, limit the hip joint range of motion (RoM) and lead to osteoarthritis. We have previously developed FeMorph software to quantify and plan corrective surgery and predict hip RoM post surgery. This study aimed to validate the software and evaluate the influence of the acetabular labrum on hip RoM. Computed tomography data from 92 femur-pelvis pairs were analysed in conjunction with the inter/intra-observer reliability. Four cadaveric hips were dissected, and the three-dimensional (3D) shape and size of the acetabular labrum for these hips was obtained using laser scan. The influence of the acetabular labrum in the RoM and subsequent planning for corrective surgery were then evaluated in cadavers for models with and without a labrum, and used as a first step towards validation of FeMorph RoM prediction. FeMorph was successfully used to model cam deformities and plan corrective surgery. Three-dimensional alpha angles were reduced to below 50° after virtual surgery without an excessive reduction in femoral neck cross-sectional area, which could increase fracture risk. A mean increase of 8° ± 2° in permitted internal rotation was observed during impingement testing following removal of the labrum. FeMorph provides a reliable and useful method to model and plan cam deformity correction. This study indicates that the presence of the labrum is responsible for a substantial decrease in permitted internal rotation at the hip joint. This has implications for surgical planning models which often only account for bony impingement.
Cheminformatics (2012)

Open-source chemistry software and molecular databases broaden the research horizons of drug discovery.
P‐176L: Late‐News Poster : Deposition and Structuring Processes of a Newly Developed Transparent Amorphous Oxide Semiconductor for the Electron Transport and Injection Layers of AM‐OLEDs (2015)

Processes of a new transparent amorphous oxide semiconductor (TAOS) as ETL and EIL were developed. Conventional processes can be applied for the deposition and structuring of the new TAOS, which enables to fabricate inverted OLEDs. The new TAOS materials make it possible to realize thicker ETL, potentially giving impacts not only on yield, but also on higher aperture ratio and cost reduction by omitting resin banks.
Structures and a Two-Band Model for the SystemV1−xCrxO2 (1973)

The evolution with $x$ of the monoclinic-to-tetragonal transition temperature and of the room-temperature monoclinic structures of the system ${\mathrm{V}}_{1\ensuremath{-}x}{\mathrm{Cr}}_{x}{\mathrm{O}}_{2}$ have been reexamined and extended to cover the entire solid-solution range $0\ensuremath{\le}x&lt;0.20$. The space group of the room-temperature monoclinic phase changes from $\frac{P{2}_{1}}{c}$ at $x=0$ to $\frac{C2}{m}$ for $0.005\ensuremath{\le}x\ensuremath{\le}0.065$ and $\frac{P2}{m}$ for $0.07\ensuremath{\le}x&lt;0.20$. The monoclinic $\frac{P2}{m}$ structure is determined for the first time. The distortion from tetragonal symmetry is accomplished by a contraction of the V-O bonds in the tetragonal ${(110)}_{r}$ planes and an expansion in the ${(1\overline{1}0)}_{r}$ planes. The structures and the conductivity changes are interpreted in terms of two overlapping bands that change their relative stabilities with $x$. The substitutional ${\mathrm{Cr}}^{3+}$ ions, which have a localized-electron ${d}^{3}$ configuration, also perturb the electron potential sufficiently to induce, at larger $x$, a $3d$-electron localization on the vanadium ions.
Fiber design and realization of point-by-point written fiber Bragg gratings in polymer optical fibers (2012)

An increasing interest in making sensors based on fiber Bragg gratings (FBGs) written in polymer optical fibers (POFs) has been seen recently. Mostly microstructured POFs (mPOFs) have been chosen for this purpose because they are easier to fabricate compared, for example, to step index fibers and because they allow to tune the guiding parameters by modifying the microstructure. Now a days the only technique used to write gratings in such fibers is the phase mask technique with UV light illumination. Despite the good results that have been obtained, a limited flexibility on the grating design and the very long times required for the writing of FBGs raise some questions about the possibility of exporting POF FBGs and the sensors based on them from the laboratory bench to the mass production market. The possibility of arbitrary design of fiber Bragg gratings and the very short time required to write the gratings make the point-by-point grating writing technique very interesting and would appear to be able to fill this technological gap. On the other end this technique is hardly applicable for microstructured fibers because of the writing beam being scattered by the air-holes. We report on the design and realization of a microstructured polymer optical fiber made of PMMA for direct writing of FBGs. The fiber was designed specifically to avoid obstruction of the writing beam by air-holes. The realized fiber has been used to point-by-point write a 5 mm long fourth order FBG with a Bragg wavelength of 1518 nm. The grating was inspected under Differential Interferometric Contrast microscope and the reflection spectrum was measured. This is, to the best of our knowledge, the first FBGs written into a mPOF with the point-by-point technique and also the fastest ever written into a polymer optical fiber, with less than 2.5 seconds needed.
Synthesis of chemisorbed imidazolium and phosphonium cations by reaction of ionic liquid precursors with silica (2010)

The reaction of four different basic ionic liquid precursors with Aerosil®300 is presented. Chemisorbed imidazolium and phosphonium cations, with silanolate anions as part of the silicatic support, were obtained and investigated with various solid state NMR techniques.
Abstract 430: Vascular Contrast Increases Permeability of Proximal Tubule Epithelium: A Possible Mechanism of Contrast-Induced Nephropathy (2012)

Objectives: Contrast Induced Nephropathy (CIN) is the third leading cause of hospital acquired renal failure and excludes numbers of patients from less invasive endovascular procedures. The mechanism of CIN is not fully understood. We investigated the hypotheses that CIN may result from direct toxicity or malfunction of kidney cells caused by contrast agent. Methods: Human kidney 2 (HK-2) cells were treated with Phosphate-Buffered Saline (PBS) or Iodixanol, a contrast agent, representing control and experimental groups. TUNEL assay was used to evaluate apoptosis. Cell proliferation was measured by BrdU incorporation. Expression of Claudin-2, a tight junction protein, was assessed by qRT-PCR and western blot. Intercellular gaps were measured using phase contrast microscopy and quantified by Image J software. Results: Iodixanol reduced tubule cell proliferation, but did not cause apoptosis. Phase contrast imaging of HK-2 cells demonstrated that intercellular gaps within the monolayer of cells were significantly increased by Iodixanol in a dose dependent manner. Western blot and qRT-PCR showed up-regulation of claudin-2 protein and mRNA expression. Both intercellular gap formation and up-regulation of claudin-2 expression are consistent with possible increase of permeability across proximal tubule epithelium, which is one of the known causes of renal failure. Conclusion: Our in vitro data do not support the hypothesis that direct kidney cell death from contrast agent is a major mechanism of CIN. However, increased permeability of proximal tubule epithelium caused by contrast may play an important role in CIN.
To alloy or not to alloy? : Cr modified Pt/C cathode catalysts for PEMfuel cells (2007)

The cathode electrocatalysts for proton exchange membrane (PEM) fuel cells are commonly platinum and platinum based alloy nanoparticles dispersed on a carbon support. Control over the particle size and composition has, historically, been attained empirically, making systematic studies of the effects of various structural parameters difficult. The controlled surface modification methodology used in this work has enabled the controlled modification of carbon supported Pt nanoparticles by Cr so as to yield nanoalloy particles with defined compositions. Subsequent heat treatment in 5% H2 in N2 resulted in the formation of a distinct Pt3Cr alloy phase which was either restricted to the surface of the particles or present throughout the bulk of the particle structure. Measurement of the oxygen reduction activity of the catalysts was accomplished using the rotating thin film electrode method and the activities obtained were related to the structure of the nanoalloy catalyst particles, largely determined using Cr K edge and Pt L3 edge XAS.
Steam Reforming of Methyl Fuel - Phase I (1977)

An experimental study was made on the effects of gasoline contamination of methanol relative to steam reforming of the mixture. At the conventional steam reforming temperature of 350-400 F soot was produced with a 90/10 mixture of methanol and gasoline (by weight). A parametric study was conducted to evaluate the effects of higher temperature and higher steam to carbon ratio with four different catalysts. Soot-free operation was obtained with Girdler catalyst T-2107 at an operating temperature of 750 F at a steam to (total) carbon ratio of 3.8. Essentially all the gasoline is converted into light gaseous hydrocarbons, primarily methane. A trace of light-yellow oil droplets could be detected in the cooled product gas condensate. A 100 hour test showed no deterioration of the T-2107 catalyst activity under the above conditions. (Author)
Magnesiation of Electron-Rich Aryl Bromides and Their Use in Nickel-Catalyzed Cross-Coupling Reactions (2007)

Electron-rich aryl bromides are rapidly converted to the corresponding lithium triarylmagnesiates with (n-Bu)3MgLi, which undergo efficient nickel-catalyzed Kumada-Corriu cross-coupling reactions with a variety of aryl and alkenyl bromides, chlorides, tosylates, and triflates.
Rational Design of Rod‐Like Liquid Crystals Exhibiting Two Nematic Phases (2017)

Recently, a polar, rod-like liquid-crystalline material was reported to exhibit two distinct nematic mesophases (termed N and N<sub>X</sub> ) separated by a weakly first-order transition. Herein, we present our initial studies into the structure-property relationships that underpin the occurrence of the lower-temperature nematic phase, and report several new materials that exhibit this same transformation. We have prepared material with significantly enhanced temperature ranges, allowing us to perform a detailed study of both the upper- and lower-temperature nematic phases by using small-angle X-ray scattering. We observed a continuous change in d spacing rather than a sharp change at the phase transition, a result consistent with a transition between two nematic phases, structures of which are presumably degenerate.
Towards Low-Power Machine Learning Architectures Inspired by Brain Neuromodulatory Signalling (2022)

We present a transfer learning method inspired by modulatory neurotransmitter mechanisms in biological brains and explore applications for neuromorphic hardware. In this method, the pre-trained weights of an artificial neural network are held constant and a new, similar task is learned by manipulating the firing sensitivity of each neuron via a supplemental bias input. We refer to this as neuromodulatory tuning (NT). We demonstrate empirically that neuromodulatory tuning produces results comparable with traditional fine-tuning (TFT) methods in the domain of image recognition in both feed-forward deep learning and spiking neural network architectures. In our tests, NT reduced the number of parameters to be trained by four orders of magnitude as compared with traditional fine-tuning methods. We further demonstrate that neuromodulatory tuning can be implemented in analog hardware as a current source with a variable supply voltage. Our analog neuron design implements the leaky integrate-and-fire model with three bi-directional binary-scaled current sources comprising the synapse. Signals approximating modulatory neurotransmitter mechanisms are applied via adjustable power domains associated with each synapse. We validate the feasibility of the circuit design using high-fidelity simulation tools and propose an efficient implementation of neuromodulatory tuning using integrated analog circuits that consume significantly less power than digital hardware (GPU/CPU).
S1575 The Use of Post-Prandial Breath Hydrogen to Monitor Antibiotic-Induced Changes in the Activity of the Gut Microbiome (2022)

Introduction: Small intestinal bacterial overgrowth (SIBO) is a common condition that is associated with a range of non-specific GI symptoms. Patients are often prescribed an empirical trial of antibiotics, however, response to treatment can vary. Due to the heterogeneous nature of symptoms experienced, post-prandial breath hydrogen (PPH2) may assist in identifying beneficial changes in the activity of the gut microbiome in those with a dysbiotic phenotype. Methods: Sixteen suspected SIBO patients measured their PPH2 using an at-home, app-connected breath analyzer (AIRE, FoodMarble). Readings were taken at 0, 30, 60, and 90 min after their morning and evening meals for 7 days pre and post-treatment. There were 14/16 patients who followed this protocol during antibiotic treatment. Six controls measured their PPH2 levels for 7 days. Gas normalization was defined as +2 SD of the mean PPH2 in controls. Results: Patients produced significantly more PPH2 (P=0.003), 27 ppm ± 22 ppm (mean ± SD) than controls (13 ppm ± 7 ppm). 5/14 patients saw a transient increase (P=0.2) of 23 ppm ± 23 ppm (mean delta ± SD) of PPH2 during treatment. Post-treatment, patients produced significantly less PPH2 (P=0.00001), 17 ppm ± 13 ppm, more closely matching that of healthy controls (Figure). Conclusion: For the first time, PPH2 was tracked before, during, and after antibiotic treatment. PPH2 was significantly greater in patients. Interestingly, for some patients, PPH2 increased during the treatment period, likely due to a dynamic rearrangement of certain microbial populations. Post-treatment, the level of PPH2 in patients was more similar to that of healthy volunteers. The collection of PPH2 data may be useful to identify those who produce elevated gas levels due to dysbiosis and to determine the normalization of their microbiome in response to antibiotics.Figure 1.: Post prandial breath hydrogen of suspected SIBO patients (n=16) before, during and after antibiotic treatment compared to healthy controls (n = 6)
Access to tough and transparent nanocomposites via Pickering emulsion polymerization using biocatalytic hybrid lignin nanoparticles as functional surfactants (2021)

Coating of lignin nanoparticles with chitosan and glucose oxidase allows for the green synthesis of acrylic and vinyl polymers in Pickering emulsions. The resulting dispersions offer a green route to tough composites equipped with antioxidant activity.
Active Guardband Management in Power7+ to Save Energy and Maintain Reliability (2013)

Microprocessor voltage levels traditionally include substantial margin to ensure reliable operation despite variations in manufacturing, workload, and environmental parameters. This margin allows the microprocessor to function correctly during worst-case conditions, but during typical operation it is larger than necessary and wastes energy. The authors present a mechanism that reduces excess voltage margin by introducing a critical-path monitor (CPM) circuit that measures available timing margin in real time; coupling the CPM output to the clock generation circuit to rapidly adjust clock frequency in response to excess or inadequate timing margin; and adjusting the processor voltage level periodically in firmware to achieve a specified average clock frequency target. They first demonstrated this mechanism in an IBM Power7 server and proved its effectiveness in the Power7+ product. Power consumption on the VDD rail was reduced by 11 percent for SPEC CPU2006 workloads with negligible performance loss yet increased protection against noise events.
Engineering Surface Structure of Spinel Oxides via High-Valent Vanadium Doping for Remarkably Enhanced Electrocatalytic Oxygen Evolution Reaction (2019)

Spinel oxides (AB<sub>2</sub>O<sub>4</sub>) with unique crystal structures have been widely explored as promising alternative catalysts for efficient oxygen evolution reactions; however, developing novel methods to fabricate robust, cost-effective, and high-performance spinel oxide based electrocatalysts is still a great challenge. Here, utilizing a complementary experimental and theoretical approach, pentavalent vanadium doping in the spinel oxides (i.e., Co<sub>3</sub>O<sub>4</sub> and NiFe<sub>2</sub>O<sub>4</sub>) has been thoroughly investigated to engineer their surface structures for the enhanced electrocatalytic oxygen evolution reaction. Specifically, when the optimal concentration of vanadium (ca. 7.7 at. %) is incorporated into Co<sub>3</sub>O<sub>4</sub>, the required overpotential to reach a certain <i>j</i><sub>GEOM</sub> and <i>j</i><sub>ECSA</sub> decreases dramatically for oxygen evolution reactions in alkaline media. Even after 30 h of chronopotentiometry, the required potential for V-doped Co<sub>3</sub>O<sub>4</sub> just increases by 16.3 mV, being much lower than that of the undoped one. It is observed that the pentavalent vanadium doping introduces lattice distortions and defects on the surface, which in turn exposes more active sites for reactions. DFT calculations further reveal the rate-determining step changing from the step of *-O to *-OOH to the step of *-OH to *-O, while the corresponding energy barriers decrease from 1.73 to 1.57 eV accordingly after high-valent V doping. Moreover, the oxygen intermediate probing method using methanol as a probing reagent also demonstrates a stronger OH* adsorption on the surface after V doping. When vanadium doping is performed in the inverse spinel matrix of NiFe<sub>2</sub>O<sub>4</sub>, impressive performance enhancement in the oxygen evolution reaction is as well witnessed. All these results clearly illustrate that the V doping process can not only efficiently improve the electrochemical properties of spinel transition metal oxides but also provide new insights into the design of high-performance water oxidation electrocatalysts.