gebhart/patrepeval huggingface dataset:
Laser Capture Microdissection (LCM): Preparation and Sectioning of Frozen Tissue Blocks and Purification of RNA from Isolated Cells (2006)

Capture Microdissection (LCM): Preparation and Sectioning of Frozen Tissue Blocks and Purification of RNA from Isolated Cells Motoko Morimoto, Masahiro Morimoto, Jeanette Whitmire, Robert A. Star, Joseph F. Urban, Jr., and William C. Gause This protocol was adapted from Laser Capture Microdissection, contributed by Motoko Morimoto, Masahiro Morimoto, Jeannette Whitmire, Robert A. Star, Joseph F. Urban, Jr., and William C. Gause, Chapter 11, in PCR Primer, 2nd edition (eds. Dieffenbach and Dveksler). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2003.
Solution and Solid-Phase Synthesis of Functionalized 3-Arylbenzofurans by a Novel Cyclofragmentation – Release Pathway (2000)

A diverse family of arylbenzofurans can be generated both in solution and on solid support from a novel reaction cascade starting from 2-hydroxybenzophenones. The key step is a 5-exo-trig cyclization to generate alkoxide intermediates, which collapse to form the 3-arylbenzofuran products (see scheme), an important class of compounds in biology and medicine. Not only are electron-donating and electron-withdrawing groups tolerated in the reaction, but pyridyl, naphthyl, and sterically hindered xylene analogues can also be obtained.
Sex and sexual health: A survey of Canadian youth and mothers (2008)

Most adolescents are responsible when it comes to sexuality, but there are still areas of concern. Adolescents identify barriers to getting information and lack knowledge about sexually transmitted infections. Parents should feel more comfortable when it comes to discussing sexuality, especially the more value-based issues. Health care professionals and teachers have a role to play, and should ensure that teens are getting correct information. It is important to have diverse sources of information. All teens are not ready at the same time to receive the information; thus, it should be repeated. Governments, health, education and public health authorities have an essential role to play to make sexual health information accurate, accessible, inclusive and salient to the reality of Canadian adolescents.
Diesel engine aftertreatment warm-up through early exhaust valve opening and internal exhaust gas recirculation during idle operation (2017)

A large fraction of diesel engine tailpipe NOx emissions are emitted before the aftertreatment components reach effective operating temperatures. As a result, it is essential to develop technologies to accelerate initial aftertreatment system warm-up. This study investigates the use of early exhaust valve opening (EEVO) and its combination with negative valve overlap to achieve internal exhaust gas recirculation (iEGR), for aftertreatment thermal management, both at steady state loaded idle operation and over a heavy-duty federal test procedure (HD-FTP) drive cycle. The results demonstrate that implementing EEVO with iEGR during steady state loaded idle conditions enables engine outlet temperatures above 400 °C, and when implemented over the HD-FTP, is expected to result in a 7.9% reduction in tailpipe-out NOx.
Prior COVID-19 Infection and Antibody Response to Single Versus Double Dose mRNA SARS-CoV-2 Vaccination (2021)

The double dose regimen for mRNA vaccines against SARS-CoV-2 presents both a hope and a challenge for global efforts to curb the COVID-19 pandemic. With supply chain logistics impacting the rollout of population-scale vaccination programs, increasing attention has turned to the potential efficacy of single versus double dose vaccine administration for select individuals. To this end, we examined response to Pfizer-BioNTech mRNA vaccine in a large cohort of healthcare workers including those with versus without prior COVID-19 infection. For all participants, we quantified circulating levels of SARS-CoV-2 anti-spike (S) protein IgG at baseline prior to vaccine, after vaccine dose 1, and after vaccine dose 2. We observed that the anti-S IgG antibody response following a single vaccine dose in persons who had recovered from confirmed prior COVID-19 infection was similar to the antibody response following two doses of vaccine in persons without prior infection (P≥0.58). Patterns were similar for the post-vaccine symptoms experienced by infection recovered persons following their first dose compared to the symptoms experienced by infection naïve persons following their second dose (P=0.66). These results support the premise that a single dose of mRNA vaccine could provoke in COVID-19 recovered individuals a level of immunity that is comparable to that seen in infection naïve persons following a double dose regimen. Additional studies are needed to validate our findings, which could allow for public health programs to expand the reach of population wide vaccination efforts.
Effect of Larval Density on Food Utilization Efficiency ofTenebrio molitor(Coleoptera: Tenebrionidae) (2015)

Crowding conditions of larvae may have a significant impact on commercial production efficiency of some insects, such as Tenebrio molitor L. (Coleoptera: Tenebrionidae). Although larval densities are known to affect developmental time and growth in T. molitor, no reports were found on the effects of crowding on food utilization. The effect of larval density on food utilization efficiency of T. molitor larvae was studied by measuring efficiency of ingested food conversion (ECI), efficiency of digested food conversion (EDC), and mg of larval weight gain per gram of food consumed (LWGpFC) at increasing larval densities (12, 24, 36, 48, 50, 62, 74, and 96 larvae per dm(2)) over four consecutive 3-wk periods. Individual larval weight gain and food consumption were negatively impacted by larval density. Similarly, ECI, ECD, and LWGpFC were negatively impacted by larval density. Larval ageing, measured as four consecutive 3-wk periods, significantly and independently impacted ECI, ECD, and LWGpFC in a negative way. General linear model analysis showed that age had a higher impact than density on food utilization parameters of T. molitor larvae. Larval growth was determined to be responsible for the age effects, as measurements of larval mass density (in grams of larvae per dm(2)) had a significant impact on food utilization parameters across ages and density treatments (in number of larvae per dm(2)). The importance of mass versus numbers per unit of area as measurements of larval density and the implications of negative effects of density on food utilization for insect biomass production are discussed.
Computational Analysis of Cerebrospinal Fluid Flow in the Normal and Obstructed Subarachnoid Space (2008)

Patients with Chiari I malformations have increased cerebrospinal fluid (CSF) velocities compared to subjects without the malformation. Improved methods of analyzing the CSF fluid dynamics are needed to evaluate the impact of increased fluid velocities on pressure differentials in the upper cervical spinal canal and the potential impact of surgery on flow dynamics in patient-specific geometries. Here, a numerical technique based on the boundary elements method (BEM) for modeling the CSF flow within the spinal canal is presented. Results for velocity and pressure throughout the spinal canal were obtained at flow rates representative of different phases of the cardiac cycle for a healthy geometry and a Chiari model. In the healthy geometry, peak CSF velocities occurred anterolateral to the spinal cord at all flow rates. Partially obstructing the subarachnoid space increased peak systolic and diastolic velocities and shear stresses anteriorly. In addition, in the obstructed (Chiari) model, stagnation regions were evident posteriorly. The effects of surgical treatment on these CSF flow patterns warrant further study.
Vinyl polymerization by carbon black V. Solvent effect and the kinetics of the polymerization of N‐vinylcarbazole (1985)

Abstract The polymerization of N ‐vinylcarbazole has been carried out at 60°C under nitrogen with different grades of carbon black, N220, N110, N330, and N660 as heterogeneous catalysts. The order of efficiency of the catalysts in regard to the polymerization is: N220 &gt; N110 &gt; N660 &gt; N330. Effect of solvent polarity on the polymerization has been studied with acetonitrile, 1,2‐dichloroethane, and toluene‐nitrobenzene mixtures. Nitrobenzene, with highest polarity, affords the highest rate, which decreases with decreasing nitrobenzene percentage in the solvent mixture. These features suggest the polymerization to be cationic in nature. The relative viscosities of the polymers are low, but tend to increase only slightly with increasing nitrobenzene content. The rate of polymerization can be expressed by the relation A suitable kinetic model has been presented in conformity with the experimental findings.
Cobalt Corrole Catalyst for Efficient Hydrogen Evolution Reaction from H2O under Ambient Conditions: Reactivity, Spectroscopy, and Density Functional Theory Calculations (2013)

The feasibility of a hydrogen-based economy relies very much on the availability of catalysts for the hydrogen evolution reaction (HER) that are not based on Pt or other noble elements. Significant breakthroughs have been achieved with certain first row transition metal complexes in terms of low overpotentials and large turnover rates, but the majority of reported work utilized purified and deoxygenated solvents (most commonly mixtures of organic solvents/acids). Realizing that the design of earth abundant metal catalysts that operate under truly ambient conditions remains an unresolved challenge, we have now developed an electronically tuned Co(III) corrole that can catalyze the HER from aqueous sulfuric acid at as low as -0.3 V vs NHE, with a turnover frequency of 600 s(-1) and ≫10(7) catalytic turnovers. Under aerobic conditions, using H2O from naturally available sources without any pretreatment, the same complex catalyzes the reduction of H(+) with a Faradaic Yield (FY) of 52%. Density functional theory (DFT) calculations indicate that the electron density on a putative hydride species is delocalized off from the H atom into the macrocycle. This makes the protonation of a [Co(III)-H](-) species the rate determining step (rds) for the HER consistent with the experimental data.
Wavelength-tunable OTDR using a mode- locked erbium-doped-fiber laser (1993)

Rare-earth-doped fibers can be used for laser light sources as well as for traveling-wave optical amplifiers. Doped-fiber lasers have many applications, such as optical communications and measurement equipment. Mode-locked operation has been demonstrated for erbium-doped-fiber (EDF) lasers.1,2 In this paper we demonstrate wavelength-tunable optical time-domain reflectometry (OTDR) using a mode-locked EDF ring laser as a light source.
Gold-standard diagnostics are tarnished by lytic bacteriophage (2020)

ABSTRACT Background A fundamental clinical and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. Methods Cholera was chosen as a model disease to investigate this important question. Patients with diarrheal disease were enrolled at two remote hospitals in Bangladesh. Diagnostic performance was assessed as a function of lytic bacteriophage detection, as well as exposure to the first-line antibiotic azithromycin detected by mass spectrometry. Results Among diarrheal samples positive by nanoliter quantitative PCR for Vibrio cholerae (n=78/849), the odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by 89% (OR 0.108; 95%CI 0.002-0.872) and 87% (OR 0.130; 95%CI 0.022-0.649) when lytic bacteriophage were detected, respectively. The odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by more than 99% (OR 0.00; 95% CI: 0.00-0.28) and 89% (OR 0.11; 95% CI: 0.03-0.44) when azithromycin was detected, respectively. Conclusions Estimations of cholera burden may improve by accommodating for the negative effect of antimicrobial exposure on diagnostic positivity. Furthermore, the findings herein challenge our current approach to interpreting and developing bacterial diagnostics given variable rates of lytic bacteriophage and antibiotic exposure.
Expert-prescribed weighting for support vector machine classification (2016)

Support Vector Machines (SVM) are a family of algorithms that are used in classification and regression tasks. Often, multiple SVMs are combined in a coding scheme to provide multi-class classification capabilities. Generally, multi-class classification systems are evaluated on their accuracy of producing a correct coding by using test data and successful predictions are counted as a percentage of the whole, assuming that the test data set is a “good” representation of what the classification algorithm will see in its applied use. However, in practical applications, there may be situations where certain mistakes/confusions in classification are inconsequential to system operation. In this work, a method for integration of expert-defined allowable confusions into SVM systems is introduced, with an example implementation in a least squares support vector machine (LS-SVM) tested on industrial data, and shown to improve overall performance of a multi-class classification system when an appropriate performance measurement method is formulated.
Synthesis and Spin‐Trapping Properties of a Trifluoromethyl Analogue of DMPO: 5‐Methyl‐5‐trifluoromethyl‐1‐pyrroline N‐Oxide (5‐TFDMPO) (2014)

The 5-diethoxyphosphonyl-5-methyl-1-pyrroline N-oxide superoxide spin adduct (DEPMPO-OOH) is much more persistent (about 15 times) than the 5,5-dimethyl-1-pyrroline N-oxide superoxide spin adduct (DMPO-OOH). The diethoxyphosphonyl group is bulkier than the methyl group and its electron-withdrawing effect is much stronger. These two factors could play a role in explaining the different half-lifetimes of DMPO-OOH and DEPMPO-OOH. The trifluoromethyl and the diethoxyphosphonyl groups show similar electron-withdrawing effects but have different sizes. We have thus synthesized and studied 5-methyl-5-trifluoromethyl-1-pyrroline N-oxide (5-TFDMPO), a new trifluoromethyl analogue of DMPO, to compare its spin-trapping performance with those of DMPO and DEPMPO. 5-TFDMPO was prepared in a five-step sequence by means of the Zn/AcOH reductive cyclization of 5,5,5-trifluoro-4-methyl-4-nitropentanal, and the geometry of the molecule was estimated by using DFT calculations. The spin-trapping properties were investigated both in toluene and in aqueous buffer solutions for oxygen-, sulfur-, and carbon-centered radicals. All the spin adducts exhibit slightly different fluorine hyperfine coupling constants, thereby suggesting a hindered rotation of the trifluoromethyl group, which was confirmed by variable-temperature EPR studies and DFT calculations. In phosphate buffer at pH 7.4, the half-life of 5-TFDMPOOOH is about three times shorter than for DEPMPO-OOH and five times longer than for DMPO-OOH. Our results suggest that the stabilization of the superoxide adducts comes from a delicate balance between steric, electronic, and hydrogen-bonding effects that involve the β group, the hydroperoxyl moiety, and the nitroxide.
Single Breath-Hold 3-Dimensional Magnetic Resonance Elastography Depicts Liver Fibrosis and Inflammation in Obese Patients (2023)

The single breath-hold 3D MRE sequence may be effective in measuring liver fibrosis and inflammation in obese patients.
The Rational Design of Drugs with Phos-phonic/phinic Acids as Enzyme Inhibitors Isosteric Receptor Ligands (2002)

Phosphonic/phosphinic acid analogs have been studied for inhibitory and ligand activity in farnesyl pyrophosphate synthase, prostaglandin, and other GPCR's.
Analyse comparative des classes en commutation (F, F-1, E) pour l'amplification de puissance en technologie GaN (2009)

National audience
Chronic inflammation induced by organic dust and related metabolic cardiovascular disease risk factors (2004)

Exposure to contaminated organic dust induces a chronic inflammation that is not associated with increased metabolic or acute-phase cardiovascular risk factors; this finding suggests that chronic inflammation per se may not be a cardiovascular risk factor in this group of pig farmers.
Repairing Inconsistent Curve Networks on Non‐parallel Cross‐sections (2018)

Abstract In this work we present the first algorithm for restoring consistency between curve networks on non‐parallel cross‐sections. Our method addresses a critical but overlooked challenge in the reconstruction process from cross‐sections that stems from the fact that cross‐sectional slices are often generated independently of one another, such as in interactive volume segmentation. As a result, the curve networks on two non‐parallel slices may disagree where the slices intersect, which makes these cross‐sections an invalid input for surfacing. We propose a method that takes as input an arbitrary number of non‐parallel slices, each partitioned into two or more labels by a curve network, and outputs a modified set of curve networks on these slices that are guaranteed to be consistent. We formulate the task of restoring consistency while preserving the shape of input curves as a constrained optimization problem, and we propose an effective solution framework. We demonstrate our method on a data‐set of complex multi‐labeled input cross‐sections. Our technique efficiently produces consistent curve networks even in the presence of large errors.
Broadband Silicon Photonic Packet-Switching Node for Large-Scale Computing Systems (2012)

We present a broadband packet-switching node that utilizes silicon photonic technology. The node design uses a silicon microring for switching functionality, leverages in-flight header processing for arbitration, and has a tunable driving circuit for thermal-effect mitigation. Moreover, these integrated microring switches are capable of scaling to tremendously high port counts in a compact area, which are attractive for data-center networks. We experimentally characterize the extinction ratio of the switch for varying packet durations, interarrival times, and driving voltages and demonstrate an error-free routing of 10-Gb/s wavelength-striped packets with lengths of up to 1536 ns. We further study the resonance thermal drifting for long-hold-time packet switching through carrier injection and show thermal-effect mitigation using a pre-emphasized gating signal.
Reproducibility and relative validity of a food-frequency questionnaire for French-speaking Swiss adults (2011)

This FFQ shows good reproducibility and can be used determining macronutrient intake in a French-speaking Swiss population in an epidemiological setting.
A Small-Vocabulary Shared Task for Medical Speech Translation (2008)

We outline a possible small-vocabulary shared task for the emerging medical speech translation community. Data would consist of about 2000 recorded and transcribed utterances collected during an evaluation of an English
16.6 An 800MHz-BW VCO-Based Continuous-Time Pipelined ADC with Inherent Anti-Aliasing and On-Chip Digital Reconstruction Filter (2020)

Modern wireless communication systems operating at tens of GHz have opened a near-GHz contiguous RF BW for various applications. Further, spectral efficiency has often necessitated such applications to use MIMO and beamforming, resulting in systems that are highly integrated and require tight power budgets. The ADC, being an indispensable element of these systems, has been thus pushed to digitize ever-increasing BWs (>500MHz) with low power dissipation and area, in an integration-friendly manner. Continuous-time (CT) ΔΣ ADCs have traditionally been used in integrated receiver applications because their oversampling and inherent anti-aliasing ease the frequency planning and make on-chip active filtering possible. Designing these CT ΔΣ ADCs for BW specifications of more than 500MHz, however, is challenging. Digitizing near-GHz RF BW with a typical oversampling ratio (OSR) of ~16 requires a very high sampling frequency with prohibitive power dissipation even in advanced process nodes. Using discrete-time (DT) ADCs is a possibility, but the ADC will still need to be oversampled to ease on-chip filtering and to prevent unwanted mixer terms from aliasing in-band. Thus, the power consumption and area penalties can be prohibitive.
Visual Function and Cortical Organization in Carriers of Blue Cone Monochromacy (2013)

Carriers of blue cone monochromacy have fewer cone photoreceptors than normal. Here we examine how this disruption at the level of the retina affects visual function and cortical organization in these individuals. Visual resolution and contrast sensitivity was measured at the preferred retinal locus of fixation and visual resolution was tested at two eccentric locations (2.5° and 8°) with spectacle correction only. Adaptive optics corrected resolution acuity and cone spacing were simultaneously measured at several locations within the central fovea with adaptive optics scanning laser ophthalmoscopy (AOSLO). Fixation stability was assessed by extracting eye motion data from AOSLO videos. Retinotopic mapping using fMRI was carried out to estimate the area of early cortical regions, including that of the foveal confluence. Without adaptive optics correction, BCM carriers appeared to have normal visual function, with normal contrast sensitivity and visual resolution, but with AO-correction, visual resolution was significantly worse than normal. This resolution deficit is not explained by cone loss alone and is suggestive of an associated loss of retinal ganglion cells. However, despite evidence suggesting a reduction in the number of retinal ganglion cells, retinotopic mapping showed no reduction in the cortical area of the foveal confluence. These results suggest that ganglion cell density may not govern the foveal overrepresentation in the cortex. We propose that it is not the number of afferents, but rather the content of the information relayed to the cortex from the retina across the visual field that governs cortical magnification, as under normal viewing conditions this information is similar in both BCM carriers and normal controls.
Engineered Human Lipocalin as an Antibody Mimetic: Application to Analysis of the Small Peptide Hormone Hepcidin (2014)

Item does not contain fulltext
Design and Process Considerations for a Tunneling Tip Accelerometer (1995)

In this paper, we discuss issues related to the fabrication of a bulk micromachined single axis accelerometer. The accelerometer is designed to have a full scale range of ten millig and a sensitivity of tens of nanog. During the process, three distinctly different die are fabricated. These are subsequently assembled using an ally bonding technique. During the bonding operation, electrical contacts are made between layers. The accelerometer is controlled by electrostatic force plates above and below the proof mass. The lower electrode has a dual role. In operation, it provides a necessary control electrode. When not in operation, it is used to clamp the proof mass and prevents its motion. Results of the fabrication process and initial testing of the clamping function are reported.