gebhart/patrepeval huggingface dataset:
Fractionation of stable isotopes in perchlorate and nitrate during in situ biodegradation in a sandy aquifer (2009)

Environmental context. Perchlorate (ClO4–) and nitrate (NO3–) are common co-contaminants in groundwater, with both natural and anthropogenic sources. Each of these compounds is biodegradable, so in situ enhanced bioremediation is one alternative for treating them in groundwater. Because bacteria typically fractionate isotopes during biodegradation, stable isotope analysis is increasingly used to distinguish this process from transport or mixing-related decreases in contaminant concentrations. However, for this technique to be useful in the field to monitor bioremediation progress, isotope fractionation must be quantified under relevant environmental conditions. In the present study, we quantify the apparent in situ fractionation effects for stable isotopes in ClO4– (Cl and O) and NO3– (N and O) resulting from biodegradation in an aquifer. Abstract. An in situ experiment was performed in a shallow alluvial aquifer in Maryland to quantify the fractionation of stable isotopes in perchlorate (Cl and O) and nitrate (N and O) during biodegradation. An emulsified soybean oil substrate that was previously injected into this aquifer provided the electron donor necessary for biological perchlorate reduction and denitrification. During the field experiment, groundwater extracted from an upgradient well was pumped into an injection well located within the in situ oil barrier, and then groundwater samples were withdrawn for the next 30 h. After correction for dilution (using Br– as a conservative tracer of the injectate), perchlorate concentrations decreased by 78% and nitrate concentrations decreased by 82% during the initial 8.6 h after the injection. The observed ratio of fractionation effects of O and Cl isotopes in perchlorate (?18O/?37Cl) was 2.6, which is similar to that observed in the laboratory using pure cultures (2.5). Denitrification by indigenous bacteria fractionated O and N isotopes in nitrate at a ratio of ~0.8 (?18O/?15N), which is within the range of values reported previously for denitrification. However, the magnitudes of the individual apparent in situ isotope fractionation effects for perchlorate and nitrate were appreciably smaller than those reported in homogeneous closed systems (0.2 to 0.6 times), even after adjustment for dilution. These results indicate that (1) isotope fractionation factor ratios (?18O/?37Cl, ?18O/?15N) derived from homogeneous laboratory systems (e.g. pure culture studies) can be used qualitatively to confirm the occurrence of in situ biodegradation of both perchlorate and nitrate, but (2) the magnitudes of the individual apparent ? values cannot be used quantitatively to estimate the in situ extent of biodegradation of either anion.
Aqueous Micellar Medium in Organic Synthesis: Alkylations and Michael Reactions of Benzotriazole (2001)

Abstract The feasibility of aqueous micelles of cetyltrimethylammonium bromide in catalyzing C–N bond formation has been studied with respect to N-alkylations of benzotriazole (Bt). Alkylations with various alkylating agents and the addition of Bt across activated double bonds in the Michael fashion occurred successfully in fair-to-good yields in the aqueous micellar regime. These reactions provided a mixture of N-1 and N-2 alkylated products, with a marked preference for N-1 over N-2 isomers. Micellar catalysis has been evaluated experimentally to indicate over a 50% micellar contribution to these alkylations in contrast to their aqueous counterparts. Since, N-alkyl benzotriazoles are of potential biological interest, the present micellar procedure offers a convenient alternative to other available methods.
Proton pump inhibitors are associated with hypersensitivity reactions to drugs in hospitalized patients: a nested case‐control in a retrospective cohort study (2012)

In hospitalized patients, the use of proton pump inhibitors was associated with a significant increase risk of drug hypersensitivity reactions along with a personal history of drug allergies and long hospitalization time.
Image-based clothes transfer (2011)

Virtual dressing rooms for the fashion industry and digital entertainment applications aim at creating an image or a video of a user in which he or she wears different garments than in the real world. Such images can be displayed, for example, in a magic mirror shopping application or in games and movies. Current solutions involve the error-prone task of body pose tracking. We suggest an approach that allows users who are captured by a set of cameras to be virtually dressed with previously recorded garments in 3D. By using image-based algorithms, we can bypass critical components of other systems, especially tracking based on skeleton models. We rather transfer the appearance of a garment from one user to another by image processing and image-based rendering. Using images of real garments allows for photo-realistic rendering quality with high performance.
Pain sensitivity alterations as a function of lesion location in the parasylvian cortex (1999)

Six patients with lesions involving parasylvian cerebral cortex were evaluated for their pain thresholds using contact heat (all six) and sharp probes that evoke pin-prick pain (4/6). Without knowledge of the sensory status of the individuals, two of the authors evaluated the MRIs of these patients, and determined to what extent the following cerebral regions were involved in the lesion: anterior insula, posterior insula, retroinsula, and parietal operculum. Each patient's lesion encompassed at least two of these regions. Three individuals demonstrated significant laterality differences in pain sensitivity, with elevated thresholds on the hand contralateral to his/her lesion. The common feature in these cases was the inclusion of the parietal operculum and posterior insula. The three other cases showed no evidence of abnormal pain thresholds. The common feature of these cases was the apparent sparing of the parietal operculum. Thus, this series of cases points to the significance of the parietal operculum, either alone or with adjacent posterior insula, for normal pain thresholds. In comparison, extensive involvement of the anterior insula in two cases was not associated with abnormal pain thresholds. Four of the six patients were also evaluated with a cold pain tolerance test, which presumably involves more affective/motivational aspects of pain than threshold tests. Only two of these patients showed greater tolerance contralaterally versus ipsilaterally, and theirs were the two lesions of the four with involvement of a large part of the insula. This result supports the theory that the insula's involvement in nociceptive processing is related to the affective/motivational aspect of pain.
Lipid peroxidation and antioxidant enzyme levels in patients with schizophrenia and bipolar disorder (2002)

Recent data from several reports indicate that free radicals are involved in aetiopathogenesis of many human pathologies including neuropsychiatric disorders such as schizophrenia, bipolar disorder etc. In the present study, we aimed at determining and evaluating levels of malondialdehyde (MDA), a product of lipid peroxidation, and antioxidant enzyme superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity levels in patients diagnosed with schizophrenia (n = 25) and bipolar disorder (n = 23). The control group was composed of 20 healthy subjects. There was a significant increase in MDA levels of patients with schizophrenia and bipolar disorder compared with controls. SOD and GSH-Px activity levels were significantly higher in the schizophrenic group compared with controls. SOD activity levels in bipolar the group were significantly higher than controls whereas there were no significant changes in GSH-Px activity levels in the bipolar group and controls. Significant differences between lipid peroxidation product and antioxidant enzyme (SOD and GSH-Px) activity levels in schizophrenic and bipolar disorder patients compared with controls leads us to believe that these differences are related to the heterogenities in aetiologies of these disorders.
The Diamond Laplace for Polygonal and Polyhedral Meshes (2021)

Abstract We introduce a construction for discrete gradient operators that can be directly applied to arbitrary polygonal surface as well as polyhedral volume meshes. The main idea is to associate the gradient of functions defined at vertices of the mesh with diamonds: the region spanned by a dual edge together with its corresponding primal element — an edge for surface meshes and a face for volumetric meshes. We call the operator resulting from taking the divergence of the gradient Diamond Laplacian. Additional vertices used for the construction are represented as affine combinations of the original vertices, so that the Laplacian operator maps from values at vertices to values at vertices, as is common in geometry processing applications. The construction is local, exactly the same for all types of meshes, and results in a symmetric negative definite operator with linear precision. We show that the accuracy of the Diamond Laplacian is similar or better compared to other discretizations. The greater versatility and generally good behavior come at the expense of an increase in the number of non‐zero coefficients that depends on the degree of the mesh elements.
Deformylation and protein biosynthesis (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDeformylation and protein biosynthesisDavid M. Livingston and Philip LederCite this: Biochemistry 1969, 8, 1, 435–443Publication Date (Print):January 1, 1969Publication History Published online1 May 2002Published inissue 1 January 1969https://pubs.acs.org/doi/10.1021/bi00829a059https://doi.org/10.1021/bi00829a059research-articleACS PublicationsRequest reuse permissionsArticle Views157Altmetric-Citations89LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Timing and kinematics of quadrupedal walking pattern (2002)

Improved walking of completely paralyzed paraplegic subjects assisted by multichannel functional electrical stimulation (FES) and crutches is proposed. In the resulting quadrupedal gait the center of body (COB) is both actively and passively transferred in the direction of progression. Active transfer of the COB is accomplished by electrical stimulation of ankle plantarflexors of the trailing leg. Passive displacement of the COB occurs during the unstable state when the paraplegic person is only supported by a single foot and the contralateral crutch. Comparison of the time parameters measured during human crawling on knees and arms with the crutch assisted walking is presented. Results of kinematic modeling of the present and the improved FES and crutch assisted walking are displayed in the form of supporting polygons with the trajectory of the COB projected to the ground.
Structural analysis of the lipopolysaccharide from Chlamydophila psittaci strain 6BC (2000)

The lipopolysaccaride of Chlamydophila psittaci 6BC was isolated from tissue culture-grown elementary bodies using a modified phenol/water procedure followed by extraction with phenol/chloroform/light petroleum. Compositional analyses indicated the presence of 3-deoxy-Dmanno-oct-2-ulosonic acid, GlcN, organic bound phosphate and fatty acids in a molar ratio of approximately 3. 3 : 2 : 1.8 : 4.6. Deacylated lipopolysaccharide was obtained after successive microscale treatment with hydrazine and potassium hydroxide, and was then separated by high performance anion-exchange chromatography into two major fractions, the structures of which were determined by 600 MHz NMR spectroscopy as alpha-Kdo-(2-->8)-alpha-Kdo-(2-->4)-alpha-Kdo-(2-->6)-beta-D-GlcpN -(1 -->6)-alpha-D-GlcpN 1,4'-bisphosphate and alpha-Kdo-(2-->4)-[alpha-Kdo-(2-->8)]-alpha-Kdo-(2-->4)-alpha-Kdo-(2- ->6)-beta-D-GlcpN-(1-->6)-alpha-D-GlcpN 1,4'-bisphosphate. The distribution of fatty acids in lipid A was determined by compositional analyses and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry experiments on lipid A and de-O-acylated lipid A. It was shown that the carbohydrate backbone of lipid A is replaced by a complex mixture of fatty acids, including long-chain and branched (R)-configured 3-hydroxy fatty acids, the latter being exclusively present in an amide linkage.
Antibiotic Susceptibility Testing of the Gram-Negative Bacteria Based on Flow Cytometry (2016)

Rapidly treating infections with adequate antibiotics is of major importance. This requires a fast and accurate determination of the antibiotic susceptibility of bacterial pathogens. The most frequently used methods are slow because they are based on the measurement of growth inhibition. Faster methods, such as PCR-based detection of determinants of antibiotic resistance, do not always provide relevant information on susceptibility, particularly that which is not genetically based. Consequently, new methods, such as the detection of changes in bacterial physiology caused by antibiotics using flow cytometry and fluorescent viability markers, are being explored. In this study, we assessed whether Alexa Fluor® 633 Hydrazide (AFH), which targets carbonyl groups, can be used for antibiotic susceptibility testing. Carbonylation of cellular macromolecules, which increases in antibiotic-treated cells, is a particularly appropriate to assess for this purpose because it is irreversible. We tested the susceptibility of clinical isolates of Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa, to antibiotics from the three classes: β-lactams, aminoglycosides, and fluoroquinolones. In addition to AFH, we used TO-PRO®-3, which enters cells with damaged membranes and binds to DNA, and DiBAC4 (3), which enters cells with depolarized membranes. We also monitored antibiotic-induced morphological alterations of bacterial cells by analyzing light scattering signals. Although all tested dyes and light scattering signals allowed for the detection of antibiotic-sensitive cells, AFH proved to be the most suitable for the fast and reliable detection of antibiotic susceptibility.
A Coupled-Waveguide TE/TM Mode Splitter (1980)

A novel channel waveguided TE/TM mode splitter is presented. This splitter can spatially separate the TE and TM mode components and is compatible with single mode fiber systems. The operation principle is as follows. Two straight waveguides are formed closely parallel to each other on c -plate LiNbO 3 by preferential Ti diffusion. An Al strip loaded on waveguide 2 induces a large change in the propagation constant for the TM mode, so that the TM mode component, fed into waveguide 1, cannot couple to waveguide 2 (“straight-through state”). By applying external voltages V 1 and V 2 to the two planar electrodes, formed on waveguide 1 with an Al 2 O 3 buffer layer in-between, a complete power transfer from waveguide 1 to waveguide 2 takes place for the TE mode (“crossover state”). Less than -20 dB crosstalk was realized at 1.15 µm wavelength for V 1 =20 V and V 2 =-15 V. The insertion loss was 1.7 dB.
Clonal hematopoiesis associated with TET2 deficiency accelerates atherosclerosis development in mice (2017)

Human aging is associated with an increased frequency of somatic mutations in hematopoietic cells. Several of these recurrent mutations, including those in the gene encoding the epigenetic modifier enzyme TET2, promote expansion of the mutant blood cells. This clonal hematopoiesis correlates with an increased risk of atherosclerotic cardiovascular disease. We studied the effects of the expansion of <i>Tet2</i>-mutant cells in atherosclerosis-prone, low-density lipoprotein receptor-deficient (<i>Ldlr</i><sup>-/-</sup>) mice. We found that partial bone marrow reconstitution with TET2-deficient cells was sufficient for their clonal expansion and led to a marked increase in atherosclerotic plaque size. TET2-deficient macrophages exhibited an increase in NLRP3 inflammasome-mediated interleukin-1β secretion. An NLRP3 inhibitor showed greater atheroprotective activity in chimeric mice reconstituted with TET2-deficient cells than in nonchimeric mice. These results support the hypothesis that somatic <i>TET2</i> mutations in blood cells play a causal role in atherosclerosis.
A field and laboratory method for monitoring the concentration and isotopic composition of soil CO 2 (2008)

The stable isotope composition of nmol size gas samples can be determined accurately and precisely using continuous flow isotope ratio mass spectrometry (IRMS). We have developed a technique that exploits this capability in order to measure delta13C and delta18O values and, simultaneously, the concentration of CO2 in sub-mL volume soil air samples. A sampling strategy designed for monitoring CO2 profiles at particular locations of interest is also described. This combined field and laboratory technique provides several advantages over those previously reported: (1) the small sample size required allows soil air to be sampled at a high spatial resolution, (2) the field setup minimizes sampling times and does not require powered equipment, (3) the analytical method avoids the introduction of air (including O2) into the mass spectrometer thereby extending filament life, and (4) pCO2, delta13C and delta18O are determined simultaneously. The reproducibility of measurements of CO2 in synthetic tank air using this technique is: +/-0.08 per thousand (delta13C), +/-0.10 per thousand (delta18O), and +/-0.7% (pCO2) at 5550 ppm. The reproducibility for CO2 in soil air is estimated as: +/-0.06 per thousand (delta13C), +/-0.06 per thousand (delta18O), and +/-1.6% (pCO2). Monitoring soil CO2 using this technique is applicable to studies concerning soil respiration and ecosystem gas exchange, the effect of elevated atmospheric CO2 (e.g. free air carbon dioxide enrichment) on soil processes, soil water budgets including partitioning evaporation from transpiration, pedogenesis and weathering, diffuse solid-earth degassing, and the calibration of speleothem and pedogenic carbonate delta13C values as paleoenvironmental proxies.
Interstitial OH Radicals in F2-Laser-Irradiated Bulk Amorphous SiO2 (2006)

An interstitial hydroxyl radical (HO*) has been generated in bulk amorphous SiO2 (a-SiO2) loaded with interstitial H2O molecules and exposed to F2 laser light (hnu = 7.9 eV, lambda = 157 nm) at 77 K. F2 laser light dissociates an O-H bond of interstitial H2O into a pair of hydrogen atom (H0) and HO*. The resultant H0 disappears below 150 K, whereas HO* is detectable after thermal annealing at 200 K. The electron paramagnetic resonance (EPR) signal of the interstitial HO* recorded at 77 K is similar to that formed in amorphous ice, indicating that HO* is confined in an orthorhombic field by hydrogen bonding, probably with adjacent H2O molecules, silanol (SiOH) groups, and bridging oxygen atoms in the a-SiO2 network.
Replication Data for: Electrically and Thermally Tunable Smooth Silicon Metasurfaces for Broadband Terahertz Antireflection (2021)

Replication data for this paper published in Adv. Optical Mater. including raw data, processed data and figures. DOI: 10.1002/adom.201800928
Particle RRT for Path Planning with Uncertainty (2007)

This paper describes a new extension to the rapidly-exploring random tree (RRT) path planning algorithm. The particle RRT algorithm explicitly considers uncertainty in its domain, similar to the operation of a particle filter. Each extension to the search tree is treated as a stochastic process and is simulated multiple times. The behavior of the robot can be characterized based on the specified uncertainty in the environment, and guarantees can be made as to the performance under this uncertainty. Extensions to the search tree, and therefore entire paths, may be chosen based on the expected probability of successful execution. The benefit of this algorithm is demonstrated in the simulation of a rover operating in rough terrain with unknown coefficients of friction
Designing with Midwives: Improving Prenatal Care in Low Resource Regions (2013)

This paper describes the early design of a diagnostic system to support prenatal care of rural pregnant women. Our design is based on interviews and feedback from midwives who have worked in developed and developing countries. Based on the interviews we identified key issues in prenatal care and pro
Finite-Element Modeling of the Electric Double-Layer and Its Application to the Prediction of Supercapacitor Charging Dynamics (2013)

Abstract not Available.
Serum microRNA panel for early diagnosis of the onset of hepatocellular carcinoma (2017)

Unique change of circulating microRNAs (miRNAs) was recognized to occur in early oncogenesis, which conferred it the potential as biomarkers for early detection of cancer. However, its diagnostic capability for hepatocellular carcinoma (HCC) has not been fully understood. In this study, microarray analysis was applied to screen the initial candidate miRNA from both the supernatants of anoikis-resistant cellular models and the sera samples of HCC patients. The selected differentially expressed miRNAs were further verified in 115 HCC patients and 40 health controls by qRT-PCR. Among these, 4 miRNAs (miR-16-2-3p, 92a-3p, 107, and 3126-5p) were significantly changed in HCC patients compared with controls. Logistic regression analysis identified a 3-miRNA panel (miR-92-3p, miR-107, and miR-3126-5p) as valuable diagnostic marker for HCC, especially for early stage patients (AUC = 0.975) and for low-level AFP HCC patients (AUC = 0.971). In addition, the combination of 3-miRNA panel and AFP was even more effective for discriminating the early stage HCC patients (AUC = 0.988) and low-level AFP HCC patients (AUC = 0.989) from control. In conclusion, diagnostic efficacy of the combination of 3-miRNA panel and AFP was powerful for HCC diagnosis, especially in early tumor screening and low-level AFP patients.
High rate anaerobic fixed bed reactor with floating supports for the treatment of effluents from agro-food industries - Session PP3C – Biofilms (2007)

International audience
Effect of chromosomal proteins extractable with low concentrations of NaCl on chromatin structure of resting and proliferating cells. (1975)

When quiescent WI-38 cells are stimulated to proliferate by nutritional changes, the chromatin of stimulated cells shows an increased ellipticity in circular dichroism spectra and an increased ability to bind ethidium bromide. The differences between the chromatins of quiescent and stimulated cells are abolished if both chromatins are treated with 0.25 M NaCl. However, when salt-treated chromatins are reconstituted by dialysis agains 10 mM Tris-HCl, the difference in circular dichroism spectra and ethidium bromide binding re-appear. Furthermore, addition of the 0.25 M NaCl extract from chromatin of stimulated cells to chromatin of quiescent cells causes an increased ellipticity in circular dichroism spectra similar to that of stimulated chromatin. Since only proteins (mostly nonhistones) are detectable in the 0.25 M NaCl extract, these results strongly suggest that the chromosomal proteins extractable with low concentrations of salt are responsible for the functional and structural changes occurring in chromatin of WI-38 cells stimulated to proliferate.