gebhart/patrepeval huggingface dataset:
Expected Improvements in the Quantitative Remote Sensing of Optically Complex Waters with the Use of an Optically Fast Hyperspectral Spectrometer—A Modeling Study (2015)

Using simulated data, we investigated the effect of noise in a spaceborne hyperspectral sensor on the accuracy of the atmospheric correction of at-sensor radiances and the consequent uncertainties in retrieved water quality parameters. Specifically, we investigated the improvement expected as the F-number of the sensor is changed from 3.5, which is the smallest among existing operational spaceborne hyperspectral sensors, to 1.0, which is foreseeable in the near future. With the change in F-number, the uncertainties in the atmospherically corrected reflectance decreased by more than 90% across the visible-near-infrared spectrum, the number of pixels with negative reflectance (caused by over-correction) decreased to almost one-third, and the uncertainties in the retrieved water quality parameters decreased by more than 50% and up to 92%. The analysis was based on the sensor model of the Hyperspectral Imager for the Coastal Ocean (HICO) but using a 30-m spatial resolution instead of HICO's 96 m. Atmospheric correction was performed using Tafkaa. Water quality parameters were retrieved using a numerical method and a semi-analytical algorithm. The results emphasize the effect of sensor noise on water quality parameter retrieval and the need for sensors with high Signal-to-Noise Ratio for quantitative remote sensing of optically complex waters.
Mediastinal cysts: diagnosis by CT and needle aspiration (1988)

Five patients with bronchogenic or enteric cysts were diagnosed by using a combination of CT and transbronchial or transesophageal needle aspiration. Serous or mucoid fluid was successfully aspirated in each case. Cultures of the fluid were negative for pathogens, and cytologic examinations showed no malignancy. Mediastinoscopy and thoracotomy were avoided in all patients, including one symptomatic patient whose symptoms resolved after needle aspiration. CT with transbronchial or transesophageal needle aspiration represents a practical alternative to surgery in the evaluation of congenital mediastinal cysts.
Ultraviolet picosecond optical pulse generation from a mode-locked InGaN laser diode (2001)

Ultraviolet optical pulses were generated by actively mode locking an external cavity InGaN laser at a wavelength of 409 nm with a temporal pulse duration of 30 ps. The average power was 2 mW and the time–bandwidth product was 1.2. Dynamic detuning plays a major role in pulse development.
FORMATION AND IDENTIFICATION OF INTERSTELLAR MOLECULE LINEAR C5H FROM PHOTOLYSIS OF METHANE DISPERSED IN SOLID NEON (2009)

Photolysis of methane dispersed (1/1000) in solid Ne at 3 K with vacuum-ultraviolet light from a synchrotron produced infrared absorption lines of several products, including new lines at 3319.3 and 1955.5 cm−1. Based on experiments with isotopic labeling and results of quantum-chemical calculations, these lines are assigned to the C–H stretching and C=C stretching modes, respectively, of interstellar molecule linear C5H radicals.
An Environmental Sentinel Biomonitor System for Drinking Water Protection (2008)

Toxic industrial chemicals (TICs) are a potential threat to field drinking water supplies, but capabilities for rapid field testing of water are limited to relatively few chemicals. The Environmental Sentinel Biomonitor (ESB) system will significantly augment current detection methods by rapidly identifying toxicity from chemicals that currently cannot be rapidly detected in water samples in the field. The ESB system utilizes two toxicity sensors – a cell-based electrical impedance sensor and an enzyme-based acetylcholinesterase (AChE) inhibition sensor – to rapidly respond to a wide range of TICs. Future improvements to the ESB system under evaluation include the use of non-mammalian vertebrate cells to improve sensitivity and reduce logistical requirements and the development of an AChE inhibition sensor to provide more rapid detection with fewer steps and reagents.
PolypharmDB, a Deep Learning-Based Resource, Quickly Identifies Repurposed Drug Candidates for COVID-19 (2020)

&lt;p&gt;There is an immediate need to discover treatments for COVID-19, the pandemic caused by the SARS-CoV-2 virus. Standard small molecule drug discovery workflows that start with library screens are an impractical path forward given the timelines to discover, develop, and test clinically. To accelerate the time to patient testing, here we explored the therapeutic potential of small molecule drugs that have been tested to some degree in a clinical environment, including approved medications, as possible therapeutic interventions for COVID-19. Motivating our process is a concept termed polypharmacology, i.e. off-target interactions that may hold therapeutic potential. In this work, we used Ligand Design, our deep learning drug design platform, to interrogate the polypharmacological profiles of an internal collection of small molecule drugs with federal approval or going through clinical trials, with the goal of identifying molecules predicted to modulate targets relevant for COVID-19 treatment. Resulting from our efforts is PolypharmDB, a resource of drugs and their predicted binding of protein targets across the human proteome. Mining PolypharmDB yielded molecules predicted to interact with human and viral drug targets for COVID-19, including host proteins linked to viral entry and proliferation and key viral proteins associated with the virus life-cycle. Further, we assembled a collection of prioritized approved drugs for two specific host-targets, TMPRSS2 and cathepsin B, whose joint inhibition was recently shown to block SARS-CoV-2 virus entry into host cells. Overall, we demonstrate that our approach facilitates rapid response, identifying 30 prioritized candidates for testing for their possible use as anti-COVID drugs. Using the PolypharmDB resource, it is possible to identify repurposed drug candidates for newly discovered targets within a single work day. We are making a complete list of the molecules we identified available at no cost to partners with the ability to test them for efficacy, in vitro and/or clinically.&lt;/p&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;
A Novel Dural Reconstruction Method Following Spinal Tumor Resection (2014)

Objective: This report describes a new method for reducing the risk of postoperative obliteration of the subdural space and spinal cord tethering that frequently occurs following resection of intradural spinal tumors. Methods: A 66-year-old patient underwent resection of a T1 to T2 intradural meningioma. A duraplasty procedure was performed to reconstruct the thecal sac and create a capacious cerebrospinal fluid (CSF)-filled space around the spinal cord. To prevent subsequent inward compression of the thecal sac from dorsally located soft tissue, a titanium strap was fashioned to span the laminectomy defect. Dural tack-up stitches were secured to the titanium strap and the laminoplasty construct was secured in place using standard bone screws. Results: The combined duraplasty-titanium laminoplasty procedure was technically straightforward and there were no complications following surgery. Postoperative MR imaging 6 weeks following surgery demonstrated that the goal of creating a capacious CSF-filled space around the spinal cord, without inward compression of the thecal sac by scar tissue, was achieved. MR images of the spinal cord and dura were not degraded by the presence of the overlying titanium strap. Conclusions: This simple method that combines a duraplasty and titanium laminoplasty procedure seems to be a safe and effective approach to achieving the objective of maintaining a capacious CSF-filled space surrounding the spinal cord following intradural surgery.
NCoR1 restrains thymic negative selection by repressing Bim expression to spare thymocytes undergoing positive selection (2017)

Thymocytes must pass both positive and negative selections to become mature T cells. Negative selection purges thymocytes whose T-cell receptors (TCR) exhibit high affinity to self-peptide MHC complexes (self pMHC) to avoid autoimmune diseases, while positive selection ensures the survival and maturation of thymocytes whose TCRs display intermediate affinity to self pMHCs for effective immunity, but whether transcriptional regulation helps conserve positively selected thymocytes from being purged by negative selection remains unclear. Here we show that the specific deletion of nuclear receptor co-repressor 1 (NCoR1) in T cells causes excessive negative selection to reduce mature thymocyte numbers. Mechanistically, NCoR1 protects positively selected thymocytes from negative selection by suppressing Bim expression. Our study demonstrates a critical function of NCoR1 in coordinated positive and negative selections in the thymus.Thymocytes are screened by two processes, termed positive and negative selections, which are permissive only for immature thymocytes with intermediate avidity to the selecting ligands. Here the authors show that the nuclear receptor NCoR1 suppresses Bim1 to inhibit negative selection and promote thymocyte survival.
Spectroscopic ellipsometry of oxygen-ion-implanted silicon-on-insulator annealed at different temperatures (2003)

Summary form only given. The effect of annealing temperature on the various layers in a SIMOX (separation by implantation of oxygen) wafer has been nondestructively characterized using spectroscopic ellipsometry. Four different samples have been probed, which were all implanted under similar conditions but annealed at temperatures of 1150 degrees C, 1200 degrees C, 1250 degrees C, and 1300 degrees C. A modeling scheme has been developed to include the effect of the transition regions between the top Si and the buried oxide increases with anneal temperature, as expected, since more oxygen is pumped from Si and forms SiO/sub 2/. The interlayer between the top Si and the buried oxide becomes very sharp, indicating that the oxide precipitates present at the boundary merge with the buried oxide, and thus the top Si layer is effectively repaired for subsequent device fabrication. The lower transition region between the buried oxide and the substrate is also reduced by high temperature anneal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Graphene oxide/oxidized carbon nanofiber/mineralized hydroxyapatite based hybrid composite for biomedical applications (2017)

Hydroxyapatite (Ca10(PO4)6(OH)2, HAP), a multi-mineral substituted calcium phosphate is the main mineral component of tooth enamel and bone, has become an important biomaterial for biomedical applications. However, as-synthesized HAP has poor mechanical properties and inferior wear resistance, so it is not suitable to use in bone tissue engineering applications. We report the successful incorporation of oxidized carbon nanofibers (O-CNF) and graphene oxide (GO) into the mineralized hydroxyapatite (M-HAP) which showed excellent mechanical and biological properties. GO improved the high mechanical strength and corrosion protection of the substrate in simulated body fluid (SBF) solution and promoted the viability of osteoblasts MG63 cells. As-prepared M-HAP/O-CNF/GO composite showed materials characteristics that similar to natural bone (M-HAP) with high mechanical strength. The resultant M-HAP/O-CNF/GO composite was characterized out by x-ray diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), and Fourier-transform infrared spectroscopy (FT-IR), respectively. The mechanical strength of the material was determined by Vicker's micro-hardness method and it was found that M-HAP/O-CNF/GO (468 ± 4 Hv) composite has superior mechanical properties than M-HAP (330 ± 3 Hv) and M-HAP/GO (425 ± 5 Hv) samples. In addition, antibacterial activity of the composite was studied against Staphylococcus aureus and Escherichia coli. Furthermore, the cell viability of the composite was observed in vitro against osteoblast cells. All these studies confirmed that the M-HAP/O-CNF/GO composite can be considered as potential candidate for dental and orthopedic applications.
High-Density Power-Efficient Parallel Multi-Wavelength Optical Interconnect for Computer Systems (2005)

This paper describes a 3 W 500-Gbps (4⨉12⨉10.42-Gb/s) parallel wavelength-division multiplexed optical interconnect that uses a 12-fiber ribbon with 4 wavelengths per fiber. The transmitter and receiver are each 5mm ⨉ 8 mm chip-scale packages.
Vibrio splendidus persister cells induced by host coelomic fluids show a similar phenotype to antibiotic‐induced counterparts (2021)

Persister cells are dormant variants of regular cells that are multidrug tolerant and have heterogeneous phenotypes; these cells are a potential threat to hosts because they can escape the immune system or antibiotic treatments and reconstitute infectious. Skin ulcer syndrome (SUS) frequently occurs in the sea cucumber (Apostichopus japonicus), and Vibrio splendidus is one of the main bacterial pathogens of SUS. This study found that the active cells of V. splendidus became persister cells more readily in the presence of A. japonicus coelomic fluids. We showed that the A. japonicus coelomic fluids plus antibiotics induce 100-fold more persister cells in V. splendidus compared with antibiotics alone via nine sets of experiments including assays for antibiotic resistance, metabolic activity, and single-cell phenotypes. Furthermore, the coelomic fluids-induced persister cells showed similar phenotypes as the antibiotic-induced persister cells. Further investigation showed that guanosine pentaphosphate/tetraphosphate (henceforth ppGpp) and SOS response pathway involved in the formation of persister cells as determined using real-time RT-PCR. In addition, single-cell observations showed that, similar to the antibiotic-induced V. splendidus persister cells, the coelomic fluids-induced persister cells have five resuscitation phenotypes: no growth, expansion, elongation, elongation and then division, and elongation followed by death/disappearance. In addition, dark foci formed in the majority of persister cells for both the antibiotic-induced and coelomic fluids-induced persister cells. Our results highlight that the pathogen V. splendidus might escape from the host immune system by entering the persister state during the process of infection due to exposure to coelomic fluids.
Manufacturing of roughness standard samples based on ACF/PSD model programming (2018)

International audience
MLO spreading codes for CDMA systems using DCT/DST (2009)

We propose the use of the discrete cosine transform (DCT) and discrete sine transform (DST), as well as their inverses, for spreading in multi-carrier (MC) code division multiple access (CDMA) systems. The DCT matrix works as a multi-level orthogonal (MLO) spreading code set. More generally, the DCT can be used in any spread spectrum system including single-carrier CDMA systems, MC-CDMA and MC direct sequence (DS) CDMA. The use of the DCT in MC-CDMA is shown to yield better system performance than traditional binary spreading codes.
Evolution and function of the epithelial cell-specific ER stress sensor IRE1β (2021)

Barrier epithelial cells lining the mucosal surfaces of the gastrointestinal and respiratory tracts interface directly with the environment. As such, these tissues are continuously challenged to maintain a healthy equilibrium between immunity and tolerance against environmental toxins, food components, and microbes. An extracellular mucus barrier, produced and secreted by the underlying epithelium plays a central role in this host defense response. Several dedicated molecules with a unique tissue-specific expression in mucosal epithelia govern mucosal homeostasis. Here, we review the biology of Inositol-requiring enzyme 1β (IRE1β), an ER-resident endonuclease and paralogue of the most evolutionarily conserved ER stress sensor IRE1α. IRE1β arose through gene duplication in early vertebrates and adopted functions unique from IRE1α which appear to underlie the basic development and physiology of mucosal tissues.
Structure-activity relationship of carboxin-related carboxamides as fungicide (2011)

Various carboxamides were synthesized and their structure-activity relationships were examined as fungicides. The fungicidal activity and spectrum depended on the aromatic ring and N-substituent at the amide moiety. Among them, N-(biphenyl-2-yl)-2-chloropyridine-3-carboxamide exhibited high activity against gray mold, and the corresponding 3-CF3-pyrazole-4-carboxamide exhibited higher activity. Moreover, it was found that compounds with hydrophobic branched alkyl groups at the ortho position of the N-phenyl group exhibited high and broad-spectrum fungicidal activity. The benzene ring of the N-phenyl group can be replaced with a thiophene ring, and optimization of the alkyl groups on the thiophene ring led to penthiopyrad (1); N-[2-(1,3-dimethylbutyl)-3-thienyl]-1-methyl-3-(trifluoromethyl)pyrazole-4-carboxamide, which proved to be very effective against various diseases.
Breast Cancer: Effectiveness of Computer-aided Diagnosis—Observer Study with Independent Database of Mammograms (2002)

Computer-aided diagnosis can potentially help radiologists improve their diagnostic accuracy in the task of differentiating between benign and malignant masses seen on mammograms.
Dose-Dependent Effects of Intranasal Insulin on Resting-State Brain Activity (2017)

Nasal insulin dose-dependently modulated regional brain activity with the strongest effects after 160 U. However, this dose was accompanied by a transient increase in circulating insulin concentrations due to a spillover into circulation. Our current results may serve as a basis for future studies with nasal insulin to untangle brain insulin effects in health and disease.
Spirometers: a field test evaluation. (1987)

The need for performance control of spirometers has been studied in Helsinki hospitals. The performance of 27 instruments was measured using 11 technical test parameters. The performance was assessed by calculating figures of merit (FM) determined as a weighted sum of the test results. 55% of the devices failed the test. Performance was specific for each instrument, was dependent on maintenance but independent of instrument age. Specific attention to accuracy is recommended in measuring rapid forced expiratory parameters with wedge-type volume meters sealed with bellows. Although daily calibration is helpful, it is not sufficient to maintain optimal performance. Device maintenance should start from acceptance trials to detect manufacturing problems and be complemented by periodic technical performance tests.
Changes in mucin-type O-linked glycosylation in cancer (2013)

One of the definitions of mucins is that greater than 50% of their weight must be due to the presence of O-linked glycans. Another is the presence of tandemly repeated amino acids rich in serine and/or threonine that form a scaffold for the attachment of many of the O-linked glycans. Therefore, mucins are heavily glycosylated molecules, and many of the properties and functions of mucins are dependent on their glycosylation, which can be dramatically changed in cancer. In this chapter, we discuss mucin-type O-linked glycosylation, the changes that occur in cancer and how this affects the function of these molecules.
Mechanical coupling and tuned anisotropic elasticity: Numerical and experimental material design for shear-normal and shear-shear interactions (2023)

Mechanical coupling in architectured materials has been traditionally investigated in the context of generalized continuum mechanics and is often assumed to be non-existent in the framework of classical continuum mechanics. In this paper, we challenge this misconception and study an anisotropic architectured material exhibiting shear-shear and shear-normal coupling from the standpoint of classical continuum mechanics. The material is non-regular tetrahedron lattice, a potential candidate for biomedical implants, but the lack of understanding about its anisotropic behavior and mechanical couplings has limited its application. We exploited the unit-cell definition with periodic boundary conditions and performed elastic and elastoplastic homogenizations. Non-zero coupling sub-matrices appeared in the homogenized elasticity matrix, which we further transformed into material’s natural coordinate system using elastic distance function. This allowed for anisotropy identification and determination of all the coupling parameters. Next, compression tests are conducted on laser powder bed fused Al-12Si (mass%) lattice samples with different relative densities and spatial orientations. Employing test data, mechanical anisotropy and shear-normal couplings are experimentally characterized. Both numerical and experimental results confirmed the presence of mechanical couplings and predicted a similar anisotropic tendency in the material. Finally, the role of manufacturing defects in deterioration of as-designed mechanical properties is discussed.
Upper Limb Strength and Muscle Volume in Healthy Middle-Aged Adults (2015)

Our purpose was to characterize shoulder muscle volume and isometric moment, as well as their relationship, for healthy middle- aged adults. Muscle volume and maximum isometric joint moment were assessed for 6 functional muscle groups of the shoulder, elbow, and wrist in 10 middle-aged adults (46&ndash;60 y, 5M, 5F). Compared with young adults, shoulder abductors composed a smaller percentage of total muscle volume (P = .0009) and there was a reduction in shoulder adductor strength relative to elbow flexors (P = .012). We observed a consistent ordering of moment-generating capacity among functional groups across subjects. Although total muscle volume spanned a 2.3-fold range, muscle volume was distributed among functional groups in a consistent manner across subjects. On average, 72% of the variation in joint moment could be explained by the corresponding functional group muscle volume. These data are useful for improved modeling of upper limb musculoskeletal performance in middle-aged subjects, and may improve computational predictions of function for this group.
Optimizing societal benefit using a systems engineering approach for implementation of the GEOSS space segment (2008)

The Group on Earth Observations (GEO) is driving a paradigm shift in the Earth Observation community, refocusing Earth observing systems on GEO Societal Benefit Areas (SBA). Over the short history of space-based Earth observing systems most decisions have been made based on improving our scientific understanding of the Earth with the implicit assumption that this would serve society well in the long run. The space agencies responsible for developing the satellites used for global Earth observations are typically science driven. The innovation of GEO is the call for investments by space agencies to be driven by global societal needs. This paper presents the preliminary findings of an analysis focused on the observational requirements of the GEO Energy SBA. The analysis was performed by the Committee on Earth Observation Satellites (CEOS) Systems Engineering Office (SEO) which is responsible for facilitating the development of implementation plans that have the maximum potential for success while optimizing the benefit to society. The analysis utilizes a new taxonomy for organizing requirements, assesses the current gaps in spacebased measurements and missions, assesses the impact of the current and planned space-based missions, and presents a set of recommendations.