gebhart/patrepeval huggingface dataset:
A Bayesian Markov-Chain-Based Heteroscedastic Regression Model for the Analysis of <sup>18</sup>O-Labeled Mass Spectra (2011)

To reduce the influence of the between-spectra variability on the results of peptide quantification, one can consider the (18)O-labeling approach. Ideally, with such labeling technique, a mass shift of 4 Da of the isotopic distributions of peptides from the labeled sample is induced, which allows one to distinguish the two samples and to quantify the relative abundance of the peptides. It is worth noting, however, that the presence of small quantities of (16)O and (17)O atoms during the labeling step can cause incomplete labeling. In practice, ignoring incomplete labeling may result in the biased estimation of the relative abundance of the peptide in the compared samples. A Markov model was developed to address this issue (Zhu, Valkenborg, Burzykowski. J. Proteome Res. 9, 2669-2677, 2010). The model assumed that the peak intensities were normally distributed with heteroscedasticity using a power-of-the-mean variance funtion. Such a dependence has been observed in practice. Alternatively, we formulate the model within the Bayesian framework. This opens the possibility to further extend the model by the inclusion of random effects that can be used to capture the biological/technical variability of the peptide abundance. The operational characteristics of the model were investigated by applications to real-life mass-spectrometry data sets and a simulation study.
ChemInform Abstract: Methyl Formate as a Carbonylating Agent for the Catalytic Conversion of Phenol to Methyl Phenyl Carbonate. (2013)

Abstract A new protocol for the formation of methyl phenyl carbonate by oxidative carbonylation of phenol with methyl formate is developed, which does not require the use of toxic CO gas.
High Pressure NMR Investigation of 3M Fuel Cell Ionomers (2014)

Nuclear Magnetic Resonance (NMR) measurements were obtained for polymer electrolyte membranes (PEM) provided by 3M Corp. through the courtesy of Dr. Steve Hamrock. These membranes have potential for use within PEM Fuel Cells (PEMFCs) and can operate at somewhat lower relative humidity than NAFION. NMR spin-lattice relaxation (T 1 ) and static gradient self-diffusion measurements were obtained as a function of applied hydrostatic pressure for three different equivalent weight (EW) membranes at several values of water content. T 1 measurements allow us to study the rotational molecular motion of water within the membranes, whereas diffusion directly probes translational motion (1). By measuring both T 1 and self-diffusion, possible relationships between rotational and translational motion within the membranes can be observed and effects due to water content or EW can be found. The membranes studied had EWs of 700, 825, and 1000, and each was prepared with both 10% and 20% water content (wt. %). Measurements were conducted at several temperatures. For T 1 measurements, we used deuteron NMR in membranes equilibrated with D 2 O because of the high sensitivity of nuclear quadrupole relaxation to rotational motions (2). In order to measure diffusion (using proton NMR on samples equilibrated with H 2 O) in samples contained within a high pressure Cu/Be cell, it was necessary to use a spin-echo pulse sequence in the static gradient in the fringe field of a 7.3 T superconducting magnet. Figure 1 displays isothermal variable pressure T 1 results obtained for the 700 EW membrane with 20 wt. % D 2 O. It can be seen that T 1 values increase with temperature and decrease with pressure. The results for different membranes also suggest that values for T 1 increase with higher membrane EW and with higher D 2 O content. It is found that there is an increase in activation volume, Δv, with lower water content and lower temperatures, which was calculated using Δv = -kT[lnT 1 /P] T [1] Table 1 displays the activation volume of each membrane at various temperatures with 20 wt. % D 2 O. Measurements of water self-diffusion as a function of pressure for each sample at different water content are underway. Diffusion activation volumes will thus be obtained and compared with those for deuteron spin-lattice relaxation. Such comparison will shed light on the relationship between water translational and rotational motion inside the ionomer, and hopefully lead to insight into the proton transport mechanism. REFERENCES 1. Jayakody, JRP, Stallworth, PE, Mananga, ES, Farrington-Zapata, J, and Greenbaum, SG. J. Phys. Chem. B 108 , 4260 (2004). 2. Fontanella, JJ, Wintersgill, MC, Chen, RS, Wu, Y, and Greenbaum, SG. Electrochimica Acta 40 , 2321 (1995). This work was supported by the Office of Naval Research.
The Interlayer Collapse During Dehydration of Synthetic Na<sub>0.7</sub>-Beidellite: A <sup>23</sup>Na Solid-State Magic-Angle Spinning NMR Study (1992)

Abstract The dehydration and migration of the interlayer cation of the synthetic beidellite Na 0.7 Al 4.7 Si 7.3 O 20 -(OH) 4 ·nH 2 O, were studied with solid-state 23 Na and 27 Al MAS-NMR, heating stage XRD, and thermogravimetric analyses (TGA, DTA). The 23 Na MAS-NMR of Na-beidellite at 25°C displays a chemical shift of 0.2 ppm, which indicates a configuration comparable with that of Na + in solution. Total dehydration proceeds reversibly in two temperature ranges. Four water molecules per Na + are gradually removed from 25° to 85°C. As a result, the basal spacing decreases from 12.54 Å to 9.98 Å and the Na + surrounded by the two remaining water molecules is relocated in the hexagonal cavities of the tetrahedral sheet. The chemical shift of 1.5 ppm exhibited after the first dehydration stage illustrates the increased influence of the tetrahedral sheet. The high local symmetry is maintained throughout the entire first dehydration stage. During the second dehydration, which proceeds in a narrow temperature range around 400°C, the remaining two water molecules are removed reversibly without any change of the basal spacing.
Progresses and emerging trends of arsenic research in the past 120 years (2020)

Arsenic has been used for various purposes throughout human history, such as medicinal and industrial applications, while its health risks have only been gradually recognized in the 20th century and have raised global concerns since the 1990s. Reviewing the progress of arsenic research from a scientometric viewpoint is of great value and importance to predict future trends in arsenic studies. Unfortunately, such review is lacking, which could possibly lead to a biased understanding of the role of arsenic in human health. In this study, we collected 61,988 published literatures on arsenic research in the past 120 years from Web of Science, on which scientometric analysis using CiteSpace and subsequent review were conducted. Our scientometric-based review demonstrated the progress in the past 120 years of arsenic research and identified emerging trends in recent years, emphasizing the health risks posed by arsenic, arsenic applications, and their interaction. The information summarized in this study will shed light on the wise and extensive use of arsenic, which could be a double-edged sword in human health.
Ultrathin Surface Chemistry to Delay Anion Fouling (2015)

The unwanted fouling of surfaces by ionic adsorption has received little research attention. In this context, ultrathin organic adlayer surface chemistry-featuring monoethylene glycol based molecular residues-is described that is capable of noticeably decreasing the rate of anion depletion from solution. The strategy is exemplified with glass as the substrate material and fluoride as the anion foulant.
Modelling the observed oscillations in the adsorption kinetics of propyltrimethoxysilane on iron and aluminium oxide surfaces (2000)

The growth kinetics of surface films of propyltrimethoxysilane (PTMS) deposited on aluminium and iron oxide surfaces exhibit oscillatory adsorption. This phenomenon involves non-linear oscillations in surface coverage of the adsorbate, as measured by x-ray photoelectron spectroscopy (XPS), as a function of exposure time and solution concentration. In this paper, a mathematical model is presented to describe the experimentally observed time-dependent behaviour. The oscillatory nature of the adsorption can be modelled by a superposition of adsorption and desorption processes. The model quantitatively describes the rate and non-linearity of these processes. Using this model, the influence of the substrate upon the various adsorption processes is described quantitatively. A model for the physical origins of the three processes is presented. Copyright © 2000 John Wiley & Sons, Ltd.
Optical properties of Ge-rich<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi mathvariant="normal">G</mml:mi><mml:msub><mml:mi mathvariant="normal">e</mml:mi><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>x</mml:mi></mml:mrow></mml:msub><mml:mi mathvariant="normal">S</mml:mi><mml:msub><mml:mi mathvariant="normal">i</mml:mi><mml:mi>x</mml:mi></mml:msub></mml:mrow></mml:math>alloys: Compositional dependence of the lowest direct and indirect gaps (2016)

Ge-rich $\mathrm{G}{\mathrm{e}}_{1\ensuremath{-}x}\mathrm{S}{\mathrm{i}}_{x}$ alloys have been investigated using spectroscopic ellipsometry and photoluminescence at room temperature. Special emphasis was placed on the compositional dependence of the lowest-energy interband transitions. For $x\ensuremath{\le}0.05$, a compositional range of particular interest for modern applications, we find ${E}_{0}=0.799(1)+3.214(45)x+0.080(44){x}^{2}$ (in eV) for the lowest direct gap. The compositional dependence of the indirect gap is obtained from photoluminescence as ${E}_{\mathrm{ind}}=0.659(4)+1.18(17)x$ (in eV). We find no significant discrepancies between these results and the extrapolations from measurements at higher Si concentrations. Such discrepancies had been suggested by recent work on $\mathrm{G}{\mathrm{e}}_{1\ensuremath{-}x}\mathrm{S}{\mathrm{i}}_{x}$ films on Si. Accurate knowledge of the interband transition energies is an important requirement for the design of devices incorporating Ge-rich $\mathrm{G}{\mathrm{e}}_{1\ensuremath{-}x}\mathrm{S}{\mathrm{i}}_{x}$ alloys and for the understanding of more complex systems, such as ternary $\mathrm{G}{\mathrm{e}}_{1\ensuremath{-}x\ensuremath{-}y}\mathrm{S}{\mathrm{i}}_{x}\mathrm{S}{\mathrm{n}}_{y}$ alloys, in terms of its binary constituents.
Monomer Molecule (2021)

The present document provides recommendations for (i) definitions of terms related to dendrimers with regular dendrons and to hyperbranched polymers, and (ii) nomenclature for naming these complex compounds on the basis of structure-based nomenclature for regular and irregular organic polymers, including adjustments required for specifying dendritic and hyperbranched macromolecular structures. The recommendations and the examples deal with organic-chemical structures only. Nevertheless, the general principles described in this document can similarly be applied to inorganic and to hybrid inorganic-organic dendrimers and hyperbranched macromolecules.
Arsenic Trioxide Exerts Antitumor Activity through Regulatory T Cell Depletion Mediated by Oxidative Stress in a Murine Model of Colon Cancer (2012)

Immunotherapy is a promising antitumor strategy that can successfully be combined with current anticancer treatment. In this study, arsenic trioxide (As(2)O(3)) was shown to increase the antitumor immune response in CT26 colon tumor-bearing mice through the modulation of regulatory T cell (T(reg)) numbers. As(2)O(3) induced T(reg)-selective depletion in vitro. In vivo, tumor-bearing mice injected with 1 mg/kg As(2)O(3) showed a significant decrease in the T(reg)/CD4 cell ratio and in absolute T(reg) count versus controls. As(2)O(3) exerted antitumor effects only in immunocompetent mice and enhanced adoptive immunotherapy effects. Inhibition of As(2)O(3)-induced T(reg) depletion by the NO synthase inhibitor N(G)-nitro-l-arginine methyl ester and the superoxide dismutase mimic manganese [III] tetrakis-(5, 10, 15, 20)-benzoic acid porphyrin suggested that it was mediated by oxidative and nitrosative stress. The differential effect of As(2)O(3) on T(reg) versus other CD4 cells may be related to differences in the cells' redox status, as indicated by significant differences in 2'7'dichlorodihydrofluorescein diacetate and 4,5-diaminofluorescein diacetate fluorescence levels. In conclusion, these results show for the first time, to our knowledge, that low doses As(2)O(3) can delay solid tumor growth by depleting T(regs) through oxidative and nitrosative bursts, and suggest that As(2)O(3) could be used to enhance the antitumor activity of adoptive immunotherapy strategies in human cancer.
SCWO Characteristics of Organics in a Vertical Type Continuous Reactor. (2000)

覗窓, 混合ノズル設置ダウンフロー型式の完全連続反応器において, 2-プロパノール, ヘキサン, ビフェニル溶液の超臨界水酸化挙動を調べた. 2-プロパノールは安定した連続酸化挙動を示し, 反応器温度維持のために有効な補助燃料であることが確認できた. 空気比1.1においてもCO, NO, NO2, すすを発生せずに高分解率維持連続反応が可能であった. また, 広範囲な空気比において排ガス組成は酸化反応式から求まる値とほぼ一致していた. 投入空気量を空気比1.8以上とした場合, 断続的な火炎発生を伴う酸化反応が進行することが確認された. この火炎発生現象は2-プロパノール特有では無く, ヘキサン, ビフェニル溶液でも同じく確認された.
Fine-Grained Lesion Annotation in CT Images With Knowledge Mined From Radiology Reports (2019)

In radiologists' routine work, one major task is to read a medical image, e.g., a CT scan, find significant lesions, and write sentences in the radiology report to describe them. In this paper, we study the lesion description or annotation problem as an important step of computer-aided diagnosis (CAD). Given a lesion image, our aim is to predict multiple relevant labels, such as the lesion's body part, type, and attributes. To address this problem, we define a set of 145 labels based on RadLex to describe a large variety of lesions in the DeepLesion dataset. We directly mine training labels from the lesion's corresponding sentence in the radiology report, which requires minimal manual effort and is easily generalizable to large data and label sets. A multi-label convolutional neural network is then proposed for images with multi-scale structure and a noise-robust loss. Quantitative and qualitative experiments demonstrate the effectiveness of the framework. The average area under ROC curve on 1,872 test lesions is 0.9083.
Structure and Hydrogen Sensing Properties of Plasma Electrochemically Oxidized Titanium Foils (2012)

Plasma electrochemical oxidation (PEO) of titanium foils is the key step in the production of platinum/TiO2/Ti sandwich structures that can be used as hydrogen sensors. If a voltage is applied between the platinum contact and the supporting Ti foil, the structures indicate current–voltage curves that depend on the H2 concentration in air. The sensing mechanism, based on catalytic oxidation of H2 and hydrogen doping of TiO2, is fast and reversible in a broad temperature regime. Particularly the devices can operate at room-temperature and hence do not require an additional heating. A suitable porosity enables a high surface area combined with a good accessibility of the reacting H2 and O2. Thermal stability is mandatory because catalytic heat is released during sensor operation at higher concentrations of hydrogen. Another important feature of the sandwich structures concerns the mechanical and electrical stability of the oxide film since the operation voltages are typically in a range of ± 10 V. Our structural study serves as an important contribution towards an understanding of the interplay between process parameters and sensor properties.
Bioluminescence Potential Modeling and Forecasting (2013)

Abstract : Bioluminescence in the ocean is the result of light produced by a chemical reaction within organisms. There is a long documented history of brilliant displays of bioluminescence in the wakes of ships, breaking waves, around the bodies of rapidly moving fish and mammals, and from simple agitation of the water with one's hand or a stick. Predictions of the location, timing and intensity of bioluminescence (BL) potential and intensity of bioluminescence water leaving radiance (BLw) are critical for numerous naval operations, including preventing detection of covert operations, as well as in aiding detection of enemy incursions. Risks and opportunities from bioluminescence radiance directly depend on the Inherent Optical Properties (IOPs), as the propagation of BL radiance depends on the optical properties of the water. Therefore, joint modeling and predictions of BL potential and IOPs are very important for Navy objectives. Combining predictions from physical, bio-optical and bioluminescence models, a methodology for estimating the BL potential and night time water leaving radiance is demonstrated and evaluated. Modeling and data assimilation with nested, coupled physical, bio-optical models are computationally-demanding, and realistic, high-resolution simulations cannot be performed without the resources.
Novel phase-shifting algorithm to achieve high-speed long-depth range probing by frequency domain optical coherence tomography (2003)

There has been a long discussion if Fourier Domain Optical Coherence Tomography (FDOCT) is competitive to nowadays standard time domain systems. Still the main points were autocorrelation terms that obscured the object information and degraded the sensitivity and signal to noise ratio. By exploiting the phase information of the interferograms, it was possible to remove those autocorrelation terms and to double the measurement range. However standard phase retrieval algorithms need three to five interferograms. We present a novel technique that allows removing the coherent noise terms together with doubling the measurement range with only two recorded interferograms. In addition the measured system sensitivity of 94dB shows that the performance of FDOCT is comparable to that of time domain OCT (TDOCT) setups.
Intra-articular infusion (2016)

Bactericidal levels of antibiotics are difficult to achieve in infected total joint arthroplasty when intravenous antibiotics or antibiotic-loaded cement spacers are used, but intra-articular (IA) delivery of antibiotics has been effective in several studies. This paper describes a protocol for IA delivery of antibiotics in infected knee arthroplasty, and summarises the results of a pharmacokinetic study and two clinical follow-up studies of especially difficult groups: methicillin-resistant Staphylococcus aureus and failed two-stage revision. In the pharmacokinetic study, the mean synovial vancomycin peak level was 9242 (3956 to 32 150; sd 7608 μg/mL) among the 11 patients studied. Serum trough level ranged from 4.2 to 25.2 μg/mL (mean, 12.3 μg/mL; average of 9.6% of the joint trough value), which exceeded minimal inhibitory concentration. The success rate exceeded 95% in the two clinical groups. IA delivery of antibiotics is shown to be safe and effective, and is now the first option for treatment of infected total joint arthroplasty in our institution.
Abnormal Thyroid Regulation in Chickens with Autoimmune Thyroiditis* (1979)

The obese strain of chicken (OS) in which virtually all individuals spontaneously develop autoimmune thyroiditis was developed by selection from the Cornell strain (CS). Lymphocytes start infiltrating the thyroid gland 1 week after hatching. One possibility explaining this infiltration postulates preexisting abnormalities or defects of the target organ. The present study examines one parameter of thyroid function, uptake of 131I- under conditions in which TSH secretion is minimized. This was accomplished by supplementation of feed with T4 from hatching until sacrifice. Serum T4 levels were monitored by RIA. Twenty-hour thyroidal iodide uptakes were determined at autopsy by counting the radioactivity in the extirpated thyroid lobes. Dietary T4 supplementation increased serum T4 levels many times above normal. This drastically decreased thyroid function in four normal chicken strains; thyroidal uptake of 131I- was suppressed 97.5-99.2%. OS chickens were incompletely suppressed; mean values ranged between 80.9-94.2% suppression. CS chickens were the most poorly suppressible, with values ranging between 62.3-68.5%. The incomplete suppression of the OS and CS is probably not due to a thyroid-stimulating immunoglobulin, since pretreatment with cyclophosphamide had no effect on thyroid suppression. An analysis of the intrathyroidal coupling reaction to form iodothyronines from iodotyrosines likewise revealed a marked resistance to suppression induced by T4 feeding in the OS and CS chickens. Thus, the OS chicken and its progenitor CS strain have an abnormality of thyroid function reflected by significant thyroidal uptakes and iodotyrosine coupling in the presence of serum T4 levels which are adequate for suppression in control chickens. The poor suppressibility is not likely due to persistent TSH secretion by the pituitary, since OS and CS chickens have normal serum and thyroidal T4 and T3 values on a regular feed. An abnormality of the thyroid gland is more likely to cause this dysfunction.
Phase II study of cemiplimab in patients (pts) with advanced cutaneous squamous cell carcinoma (CSCC): Longer follow-up. (2020)

10018 Background: Cemiplimab monotherapy achieves clinically meaningful activity in pts with advanced CSCC (metastatic [mCSCC] or locally advanced [laCSCC] not amenable to curative surgery or curative radiation) and has a safety profile consistent with other anti–PD-1 agents. Based on initial data (median follow-up of 9.4 months in the pivotal study, NCT02760498), cemiplimab (cemiplimab-rwlc in the US) was approved for the treatment of pts with advanced CSCC. Historical data shows median overall survival (OS) of approximately 15 months with conventional chemotherapy or EGFR inhibitors (ASCO 2019, e21033). We present ~1-year additional follow-up from the largest prospective data set in advanced CSCC. Methods: Pts received cemiplimab 3 mg/kg Q2W (Group [Gp] 1; mCSCC; Gp 2, laCSCC) or cemiplimab 350 mg Q3W (Gp 3, mCSCC). The primary endpoint was objective response rate (ORR; complete response + partial response) per independent central review (ICR). Data presented here are per investigator review (INV); ICR data will be available at the meeting. Results: 193 pts were enrolled (Gp 1, n = 59; Gp 2, n = 78; Gp 3, n = 56). 128 pts had received no prior anti-cancer systemic therapy, 65 pts were previously treated. As of Oct 11, 2019 (data cut-off), median duration of follow-up was 15.7 months (range: 0.6–36.1) among all pts; 18.5 months (range: 1.1–36.1) for Gp 1, 15.5 months (range: 0.8–35.0) for Gp 2, and 17.3 months (range: 0.6–26.3) for Gp 3. ORR per INV was 54.4% (95% CI: 47.1–61.6) for all pts; 50.8% (95% CI: 37.5–64.1) for Gp 1, 56.4% (95% CI: 44.7–67.6) for Gp 2, and 55.4% (95% CI: 41.5–68.7) for Gp 3. ORR per INV was 57.8% (95% CI: 48.8–66.5) among treatment-naïve pts and 47.7% (95% CI: 35.1–60.5) among previously treated pts. Median duration of response (DOR) has not been reached (observed DOR range: 1.8–34.2 months). In responding pts, estimated proportion of pts with ongoing response at 24 months was 76.0% (95% CI: 64.1–84.4). Median OS has not been reached. Estimated OS at 24 months was 73.3% (95% CI: 66.1–79.2). The most common treatment-emergent adverse events (TEAEs) by any grade were fatigue (34.7%), diarrhea (27.5%), and nausea (23.8%). The most common grade ≥3 TEAEs were hypertension (4.7%) and anemia and cellulitis (each 4.1%). Conclusions: For pts with advanced CSCC, cemiplimab achieves ORRs, DOR and survival superior to what has been reported with other agents. Clinical trial information: NCT02760498.