gebhart/patrepeval huggingface dataset:
Endoscopic imaging of white matter fiber tracts using polarization-sensitive optical coherence tomography (2022)

Polarization sensitive optical coherence tomography (PSOCT) has been shown to image and delineate white matter fibers in a label-free manner by revealing optical birefringence within the myelin sheath using a microscope setup. In this proof-of-concept study, we adapt recent advancements in endoscopic PSOCT to perform depth-resolved imaging of white matter structures deep inside intact porcine brain tissue ex-vivo, through a small, rotational fiber probe. The probe geometry is comparable to microelectrodes currently used in neurosurgical interventions. The presented imaging system is mobile, robust, and uses biologically safe levels of optical radiation making it well suited for clinical translation. In neurosurgery, where accuracy is imperative, endoscopic PSOCT through a narrow-gauge fiber probe could provide intra-operative feedback on the location of critical white matter structures.
The rate of water vapor evaporation from ice substrates in the presence of HCl and HBr: Implications for the lifetime of atmospheric ice particles (2003)

Abstract. Using a multidiagnostic approach the rate Rev or flux Jevof evaporation of H2O and its condensation, kcond, on a 1mm thick ice film have been studied in the temperature range 190 to 240 K as well as in the presence of small amounts of HCl and HBr that left the vapor pressure of H2O on ice unchanged. The resulting Arrhenius expressions with RT in kcal mol-1 for pure ice are Jev=1.6×1028+/−1·exp({−10.3+\\−1.2}/{RT}) [molec cm−2 s−1], kcond=1.7×10−2+\\-1×exp({+1.6+\\−1.5}/{RT}) [s−1], in the presence of an HCl mole fraction in the range 3.2×10−5-6.4×10−3: Jev=6.4×1026+/−1×exp({−9.7+/−1.2}/{RT}) [molec cm−2 s−1], kcond=2.8×10−2+/-1×exp({+1.5+/−1.6}/{RT}) [s−1], and an HBr mole fraction smaller than 6.4×10−3:Jev=7.4×1025+/−1×exp({−9.1+/−1.2}/{RT}) [molec cm−2 s−1], kcond=7.1×10−5+\\−1×exp({+2.6+/−1.5}/{RT}) [s−1]}. The small negative activation energy for H2O condensation on ice points to a precursor mechanism. The corresponding enthalpy of sublimation is DHsubl=Eev-Econd=11.9+/−2.7 kcal mol−1, DHsubl=11.2+/−2.8 kcal mol−1, and DHsubl=11.7+/−2.8 kcal mol−1 whose values are identical within experimental uncertainty to the accepted literature value of 12.3 kcal mol−1. Interferometric data at 633 nm and FTIR absorption spectra in transmission support the kinetic results. The data are consistent with a significant lifetime enhancement for HCl- and HBr-contaminated ice particles by a factor of 3–6 and 10–20, respectively, for submonolayer coverages of HX.
Supplementary Figure 1 from Identification and Characterization of NVP-BKM120, an Orally Available Pan-Class I PI3-Kinase Inhibitor (2023)

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Human Papillomavirus Triage for Young Women With Atypical Squamous Cells of Undetermined Significance (2006)

III.
Sensitivity of a High-Resolution Fluid-Density Sensor in Multiphase Flow (2010)

Abstract An important objective of wireline formation testing is the accurate determination of in-situ fluid properties, including density. However, sensors are frequently subjected to multiphase flow when sampling, which can lead to inaccurate determination of the fluid properties and ambiguity in sample contamination analysis. In this paper, we study the behavior of multiphase flow using a density sensor and the implications for the determination of in-situ fluid properties and sample contamination, together with other downhole sensors. A vibrating-tube density sensor operates under the physical premise that its resonance frequency is directly related to the density of fluid within the tube. In reality, however, because of its high sensitivity, the sensor response is influenced by multiple factors, including sensor temperature, pressure, and specific mechanical design configuration. A theoretical study of the physics of a vibrating tube density sensor was performed using a first principle-based approach to optimize sensor characterization and accuracy. By considering all forces acting on the sensor under downhole conditions, a comprehensive theoretical model was established for the vibrating density sensor. This theoretical model is validated using experimental measurements in which we contrast theoretically predicted sensor responses with laboratory-measured responses. We compare these results with log examples using downhole fluid sample results and densities. This paper includes the conclusions derived about the accuracy of measuring fluid densities with this new sensor and a comparison of this measurement with traditional data sources.
Regulation and Physiological Roles of Serum- and Glucocorticoid-Induced Protein Kinase Isoforms (2001)

Serum- and glucocorticoid-induced protein kinase 1 (SGK1) was identified in 1993 as an immediate early gene whose mRNA levels increase dramatically within 30 minutes when cells are exposed to serum or glucocorticoids, or both. Subsequently, many other agonists, acting through a variety of signal transduction pathways, have been shown to induce SGK1 gene transcription in cells and tissues. SGK1 is a member of the "AGC" subfamily, which includes protein kinases A, G, and C, and its catalytic domain is most similar to protein kinase B (PKB). Like PKB, SGK1 is activated by phosphorylation in response to signals that stimulate phosphatidylinositol 3-kinase, and this is mediated by 3-phosphoinositide-dependent protein kinase 1 (PDK1) and another protein kinase that has yet to be identified. Thus, SGK1 is remarkable in being activated at both the transcriptional and posttranslational levels by a huge number of extracellular signals. In contrast, little is known about the transcriptional regulation of the two closely related isoforms SGK2 and SGK3, although they can be activated by phosphorylation. The substrate specificity of SGK isoforms superficially resembles that of PKB in that serine and threonine residues lying in Arg-Xaa-Arg-Xaa-Xaa-Ser/Thr sequences (where Xaa is a variable amino acid) are phosphorylated. However, although they may have some substrates in common, evidence is emerging that SGK1 and PKB phosphorylate distinct proteins and have different functions in vivo. In particular, SGK1 plays an important role in activating certain potassium, sodium, and chloride channels, suggesting an involvement in the regulation of processes such as cell survival, neuronal excitability, and renal sodium excretion. Moreover, sustained high levels of SGK1 protein and activity may contribute to conditions such as hypertension and diabetic nephropathy. This raises the possibility that specific inhibitors of SGK1 may have therapeutic potential for the treatment of several diseases.
ChemInform Abstract: New 4 + 1 Radical Annulations. A Formal Total Synthesis of (.+‐.)‐ Camptothecin. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Molecular motion, morphology, and thermal properties of multiwall carbon nanotube/polysilsesquioxane composite (2008)

Abstract Diglycidyl ether of bisphenol A (DGEBA)‐bridged polyorganosiloxane precursors have been prepared successfully by reacting diglycidyl ether of bisphenol A epoxy resin with 3‐aminopropyltriethoxysilane. Acid‐modified and unmodified multiwalled carbon nanotube (MWCNT) were dispersed in the diglycidyl ether of bisphenol A‐bridged polyorganosiloxane precursors and cured to prepare the carbon nanotube/diglycidyl ether of bisphenol A‐bridged polysilsesquioxane (MWCNT/DGEBA‐PSSQ) composites. The molecular motion of MWCNT/DGEBA‐PSSQ nanocomposites was studied by high‐resolution solid‐state 13 C NMR. Acid‐modification can improve the affinity between MWCNT and the polymer matrix. The molecular motion of the DGEBA‐PSSQ decreased with acid‐modified MWCNT content. However, when unmodified MWCNT was used, the molecular motion of the DGEBA‐PSSQ was increased. SEM and TEM microphotographs confirm that acid‐modified MWCNT exhibits better dispersion than unmodified MWCNT in DGBEA‐PSSQ. The dynamic mechanical properties of acid‐modified MWCNT/DGBEA‐PSSQ composites are more favorable than those of unmodified MWCNT. T g of the DGEBA‐PSSQ decreased from 174.0 °C (neat DGEBA‐PSSQ) to 159.0 °C (1 wt % unmodified MWCNT) and 156.0 °C (1 wt % acid‐modified MWCNT). The storage modulus (at 30 °C) of the DGEBA‐PSSQ increased from 1.23 × 10 9 Pa (neat DGEBA‐PSSQ) to 1.65 × 10 9 Pa (1 wt % acid‐modified MWCNT). However, when unmodified MWCNT was used, the storage modulus of the DGEBA‐PSSQ decreased to 6.88 × 10 8 Pa (1 wt % unmodified MWCNT). At high temperature, above 150 °C, storage modulus of nanocomposites was higher than that of neat polymer system. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 472–482, 2008
Thermoacoustic instabilities: Modeling and control (2003)

The goal of this study was twofold. First, modeling strategies were proposed to characterize the dynamics driving the thermoacoustic instabilities in a swirl-stabilized premixed burner. Second, this model was used to synthesize controllers in order to apply active control strategies to suppress this phenomenon. An experimental combustor model based on acoustic properties of the combustion chamber was derived. This model separates the combustor into a four-block linear system. Acoustic and fuel modulations were used to obtain the frequency response of each block representing a part of the combustor test-rig. Using this linear representation H/sub /spl infin// disturbance rejection and H/sub /spl infin// loop-shaping controllers were computed and tested for a set of different working conditions of the chamber for the robustness of the resulting controllers. Standard phase-delay control was used as baseline control strategy to judge the performance of the proposed controllers. Experimental results show the advantages of these model-based control strategies to suppress thermoacoustic instabilities in the test-rig.
Two-colour In0.5Ga0.5As quantum dot infrared photodetectors on silicon (2018)

An InGaAs quantum dot (QD) photodetector is directly grown on a silicon substrate. GaAs-on-Si virtual substrates with a defect density in the order of 106 cm−2 are fabricated by using strained-layer superlattice as dislocation filters. As a result of the high quality virtual substrate, fabrication of QD layer with good structural properties has been achieved, as evidenced by transmission electron microscopy and x-ray diffraction measurements. The InGaAs QD infrared photodetector is then fabricated on the GaAs-on-Si wafer substrate. Dual-band photoresponse is observed at 80 K with two response peaks around 6 and 15 μm.
Enhancing Fairness in Face Detection in Computer Vision Systems by Demographic Bias Mitigation (2022)

Fairness has become an important agenda in computer vision and artificial intelligence. Recent studies have shown that many computer vision models and datasets exhibit demographic biases and proposed mitigation strategies. These works attempt to address accuracy disparity, spurious correlations, or unbalanced representations in datasets in tasks such as face recognition, verification and expression and attribute classification. These tasks, however, all require face detection as the first preprocessing step, and surprisingly, there has been little effort in identifying or mitigating biases in face detection. Biased face detectors themselves pose a threat against fair and ethical AI systems, and their biases may be further passed on to subsequent downstream tasks such as face recognition in a computer vision pipeline. This paper therefore investigates the problem of biases in face detection, focusing on accuracy disparity of detectors between demographic groups including gender, age group, and skin tone. We collect perceived demographic attributes on a popular face detection benchmark dataset, WIDER FACE, report skewed demographic distributions, and compare detection performance between groups. In order to mitigate the biases, we apply three mitigation methods that have been introduced in the recent literature and also propose two novel methods. Experimental results show that these methods are effective in reducing demographic biases. We also discuss how the effectiveness varies by demographic attributes, detection easiness, and multiple detectors, which will shed light on this new topic of addressing face detection bias.
Evidence of Neutralizing and Non-Neutralizing Anti-Glucosaminidase Antibodies in Patients With S. Aureus Osteomyelitis and Their Association With Clinical Outcome Following Surgery in a Clinical Pilot (2022)

<i>Staphylococcus aureus</i> osteomyelitis remains a very challenging condition; recent clinical studies have shown infection control rates following surgery/antibiotics to be ~60%. Additionally, prior efforts to produce an effective <i>S. aureus</i> vaccine have failed, in part due to lack of knowledge of protective immunity. Previously, we demonstrated that anti-glucosaminidase (Gmd) antibodies are protective in animal models but found that only 6.7% of culture-confirmed <i>S. aureus</i> osteomyelitis patients in the AO Clinical Priority Program (AO-CPP) Registry had basal serum levels (>10 ng/ml) of anti-Gmd at the time of surgery (baseline). We identified a small subset of patients with high levels of anti-Gmd antibodies and adverse outcomes following surgery, not explained by Ig class switching to non-functional isotypes. Here, we aimed to test the hypothesis that clinical cure following surgery is associated with anti-Gmd neutralizing antibodies in serum. Therefore, we first optimized an <i>in vitro</i> assay that quantifies recombinant Gmd lysis of the <i>M. luteus</i> cell wall and used it to demonstrate the 50% neutralizing concentration (NC<sub>50</sub>) of a humanized anti-Gmd mAb (TPH-101) to be ~15.6 μg/ml. We also demonstrated that human serum deficient in anti-Gmd antibodies can be complemented by TPH-101 to achieve the same dose-dependent Gmd neutralizing activity as purified TPH-101. Finally, we assessed the anti-Gmd physical titer and neutralizing activity in sera from 11 patients in the AO-CPP Registry, who were characterized into four groups <i>post-hoc</i>. Group 1 patients (n=3) had high anti-Gmd physical and neutralizing titers at baseline that decreased with clinical cure of the infection over time. Group 2 patients (n=3) had undetectable anti-Gmd antibodies throughout the study and adverse outcomes. Group 3 (n=3) had high titers +/- neutralizing anti-Gmd at baseline with adverse outcomes. Group 4 (n=2) had low titers of non-neutralizing anti-Gmd at baseline with delayed high titers and adverse outcomes. Collectively, these findings demonstrate that both neutralizing and non-neutralizing anti-Gmd antibodies exist in <i>S. aureus</i> osteomyelitis patients and that screening for these antibodies could have a value for identifying patients in need of passive immunization prior to surgery. Future prospective studies to test the prognostic value of anti-Gmd antibodies to assess the potential of passive immunization with TPH-101 are warranted.
Superior Oxygen Electrocatalysis on RuSex Nanoparticles for Rechargeable Air Cathodes (2017)

Abstract A one‐step, facile supercritical‐ethanol‐fluid synthesis of Se‐modified Ru nanoparticles nucleated on carbon defects is reported, and it is demonstrated that these nanoparticles provide, with &gt;70% efficiency at 1 A g −1 , a highly active and reversible oxygen‐reduction/oxygen‐evolution reaction on an air cathode in a nonaqueous electrolyte. The Se modification not only prevents Ru oxidation during charge/discharge cycling, but also improves the catalytic activity by promoting Li 2 O 2 versus Li 2 O deposited on the Ru particles during discharge. A computational calculation with density functional theory supports the role of a larger electron transfer to the oxygen of Li 2 O 2 adsorbed on a surface layer of RuSe 2− δ than on a surface layer of RuO 2 , thereby shifting the more stable adsorbent from Li 2 O to Li 2 O 2 .
Challenges and procedures for experiments with steady and unsteady model velocities in a water towing tank (2021)

Abstract Challenges for steady and unsteady model motion in a large water towing tank and procedures to overcome them are the focus of the presented work. Some challenges are attributed to experiments conducted in water, whereas others are uniquely ascribed to a towing tank facility. Data convergence and outlier detection are studied based on the phase averaged pressure in order to ensure proper data quality. Pressure measurements are performed with non-surface mounted sensors. Therefore, inertia effects are detrimental when the attached tubing is not fully de-aired. A procedure for de-airing the pressure sensor cavity and its tubing is described. An iterative approach is developed that compensates for nonlinear distortion of the model’s velocity profile. Further, vibration effects are examined by distinguishing mechanical and flow-induced frequencies that scale with the instantaneous model velocity. Sloshing waves are excited, which are a function of the water basin size. The first sloshing mode defines the required sensor offset time in between test cases when prevailing sloshing waves have not fully decayed. This appropriate selection of sensor offset time reduces data scatter and enables a reasonable waiting time in between test cases. A skim plate installed just below the water surface offers a potential solution to alleviate surface wave effects over the model.
Synthesis and characterization of biodegradable and charged salen‐based polymers (2006)

Abstract The goal of this study was to synthesize novel biodegradable charged polymers for medical applications. The polymers synthesized were metal‐coordinated salicylidene‐based copolymers. The linear copolymers were prepared by polycondensation of the metal‐coordinated salicylidene monomer with acyl or aryl dichloride. Structure analysis was carried out by 1 H and 13 C NMR, FTIR, and elemental analysis. Physicochemical evaluation was carried out using DSC and thermogravimetry. The surface properties were analyzed by contact angle measurements and the crystallinity was determined by polarizing microscopy and AFM. Finally, polymer electrical conductivity and biocompatibility were examined. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 2568–2577, 2006
Improving Protein and Proteome Coverage through Data-Independent Multiplexed Peptide Fragmentation (2010)

Performance differences in protein and proteome characterization achieved by data-independent acquisition (DIA) LC/MS(E) and data-dependent acquisition (DDA) LC/MS/MS approaches were investigated. LC/MS(E) is a novel mode of generating product ion data for all coeluting precursors in parallel as opposed to LC/MS/MS where coeluting precursors must be serially fragmented one at a time. During LC/MS(E) analysis, alternating MS scans of "normal" and "elevated" collision energy are collected at regular intervals, providing nearly a 100% duty cycle for precursor detection and fragmentation because all precursors are fragmented across their full chromatographic elution profile. This is in contrast to DDA-based MS/MS where serial selection of precursor ions is biased toward interrogation and detection of the highest abundance sample components by virtue of the intensity-driven interrogation scheme employed. Both modes of acquisition were applied to a simple four-protein standard mixture with a 16-fold dynamic range in concentration, an in-gel digest of the Arabidopsis thaliana protein FLS2 purified by immunoprecipitation, and a solution-digested tomato leaf proteome sample. Dramatic improvement for individual protein sequence coverage was obtained for all three samples analyzed by the DIA approach, particularly for the lowest abundance sample components. In many instances, precursors readily detected and identified during DIA were either interrogated by MS/MS during DDA at inopportune points in their chromatographic elution profiles resulting in poor quality product ion spectra or not interrogated at all. Detailed evaluation of both DDA and DIA raw data and timing of the MS-to-MS/MS switching events clearly revealed the fundamental limitations of serial MS/MS interrogation and the advantages of parallel fragmentation by DIA for more comprehensive protein identification and characterization which holds promise for enhanced isoform and post-translational modification analysis.
Dual role of PKA in phenotypic modulation of vascular smooth muscle cells by extracellular ATP (2004)

Extracellular ATP is released from activated platelets and endothelial cells and stimulates proliferation of vascular smooth muscle cells (VSMC). We found that ATP stimulates a profound but transient activation of protein kinase A (PKA) via purinergic P2Y receptors. The specific inhibition of PKA by adenovirus-mediated transduction of the PKA inhibitor (PKI) attenuates VSMC proliferation in response to ATP, suggesting a positive role for transient PKA activation in VSMC proliferation. By contrast, isoproterenol and forskolin, which stimulate a more sustained PKA activation, inhibit VSMC growth as expected. On the other hand, the activity of serum response factor (SRF) and the SRF-dependent expression of smooth muscle (SM) genes, such as SM-alpha-actin and SM22, are extremely sensitive to regulation by PKA, and even transient PKA activation by ATP is sufficient for their downregulation. Analysis of the dose responses of PKA activation, VSMC proliferation, SRF activity, and SM gene expression to ATP, with or without PKI overexpression, suggests the following model for the phenotypic modulation of VSMC by ATP, in which the transient PKA activation plays a critical role. At low micromolar doses, ATP elicits a negligible effect on DNA synthesis but induces profound SRF activity and SM gene expression, thus promoting the contractile VSMC phenotype. At high micromolar doses, ATP inhibits SRF activity and SM gene expression and promotes VSMC growth in a manner dependent on transient PKA activation. Transformation of VSMC by high doses of ATP can be prevented and even reversed by inhibition of PKA activity.
CAMR: Coded Aggregated MapReduce (2019)

Many big data algorithms executed on MapReduce-like systems have a shuffle phase that often dominates the overall job execution time. Recent work has demonstrated schemes where the communication load in the shuffle phase can be traded off for the computation load in the map phase. In this work, we focus on a class of distributed algorithms, broadly used in deep learning, where intermediate computations of the same task can be combined. Even though prior techniques reduce the communication load significantly, they require a number of jobs that grows exponentially in the system parameters. This limitation is crucial and may diminish the load gains as the algorithm scales. We propose a new scheme which achieves the same load as the state-of-the-art while ensuring that the number of jobs as well as the number of subfiles that the data set needs to be split into remain small.
Changes in beta-adrenergic receptivity during human left ventricular hypertrophy due to pressure overload (1993)

Galinier, Michel; Sénard, Jean-Michel; Valet, Philippe; Glock, Yves; Fournial, Gérard; Massabuau, Pierre; Puel, Jacques; Montastruc, Jean-Louis; Bounhoure, Jean-Paul Author Information