gebhart/patrepeval huggingface dataset:
Atomic Layer Deposition on Self-Assembled-Monolayers (2013)

Atomic layer deposition (ALD) is an advanced technique for growing thin film structures. ALD was developed by Tuomo Suntola and co workers in 1974. At first, the method was called Atomic layer epitaxy (ALE). However, today the name “ALD” is more common. The motiva‐ tion behind developing ALD was the desire to achieve a technique for creating thin film electroluminescent (TFEL) flat panel displays. [1][7]
Positive and negative association of HLA-DR genotypes with Japanese rheumatoid arthritis. (1996)

DRB1*0405 and DRB1*0802, which are both rare alleles in Caucasians, are positively and negatively correlated, respectively, with the pathogenesis of RA in Japan.
Reliable cooling of high-power laser diode arrays (2008)

Northrop Grumman/Cutting Edge Optronics has developed a line of microchannel-cooled laser diode arrays in which the coolant is electrically isolated from the current path. As a result, these arrays do not require the use of deionized water. The thermal performance of these arrays is presented and, in one case, shown to far exceed the performance of standard copper microchannel-cooled packages. This sets them apart from other non-DI microchannel coolers currently on the market which typically have worse thermal performance than copper MCCs. These newly-developed coolers are compatible with other technologies developed by NGCEO that enable long lifetimes under harsh operating conditions. In particular, these arrays can be assembled using hard-solder technology that enables power-cycled and high-current operation. The soldering technology also generates arrays that are easily lensed and satisfy a wide range of direct diode needs, including welding, marking, and complex line generation applications. These microchannel-cooled arrays represent an important next step in the solid state laser industry. They allow for much simpler (non-deionized) cooling systems while maintaining excellent thermal performance and lifetime.
Mission Task Element Development Process: An Approach to FAA Handling Qualities Certification (2020)

Development of new air vehicles (e.g., personal air vehicles, urban taxis, etc.) have led to a proliferation of Vertical Takeoff and Landing (VTOL) vehicle concepts including electric vehicles, many of which are well funded and are in various stages of prototype development and test. These vehicles will almost exclusively feature fly-by-wire flight control systems that may feature advanced response-types. The processes and requirements needed to certify these disparate vehicles for operation within the National Airspace System are still emerging. To aid in the requirements and certification process, a mission-oriented approach is being applied to define handling qualities mission task elements that will serve as a means of compliance with Part 23 certification requirements.
5-Alpha reductase type 2 deficiency: a case report (2012)

Remnant endangered saltmarsh communities in Australia often occur in urbanised estuaries where industrial processes have contaminated sediments with metal(loid)s. Despite this issue, virtually nothing is known on local plant species exposure to metal contaminants, nor their ability to uptake and translocate metal(loid)s from contaminated estuarine sediment. In the current study, we assessed the accumulation and partitioning of the metal(loid)s Zn, Cu, Pb, Cd and Se in the dominant saltmarsh primary producer, Sporobolus virginicus, across three urbanised estuaries in NSW Australia. Lake Macquarie was the most contaminated estuary, while Sydney Olympic Park, Port Jackson exhibited intermediate metal(loid) loadings and Hunter Wetlands exhibited the lowest loadings among estuaries. Essential metals (Zn and Cu) were more mobile, with sediment:root bioconcentration factors (BCFs) greater than unity and translocation among plant organs greater than, or equal to, unity. Other metal(loid)s were less mobile, with BCFs equal to unity and translocation factors among organs much reduced. Despite these barriers to translocation, all metal(loid)s were accumulated to roots with dose, and further accumulative relationships between metal(loid)s in roots and culms, and culms and leaves, were evidenced (with the exception of Cu). Along with sediment metal(loid)s, increases in sediment pH predicted Cu uptake in roots and increases in soil organic matter predicted Se uptake in roots. Although significant positive linear relationships were observed between sediment metal(loid)s and plant organ metal(loid)s(withholding Cu), the variance explained was low to intermediate for most metal(loid)s suggesting employing S. virginicus as an accumulative bioindicator would be impractical.
The use of rapamycin to treat vascular tumours and malformations: A single-centre experience (2019)

Rapamycin is safe and efficacious in most children with select vascular tumours and malformations. Young children appear to respond better, suggesting that early initiation of rapamycin should be considered.
Energy expenditure and body composition in growth hormone deficient adults on exogenous growth hormone (1994)

Summary OBJECTIVES We assessed whether the obesity observed in growth hormone deficient adults is maintained by a reduction in energy expenditure. We studied the effects of exogenous growth hormone on energy expenditure and body composition. DESIGN We performed an open study with growth hormone administered at 0 5 units per kilogram ideal body weight per week for 3 months. PATIENTS Seven growth hormone deficient adults were studied. Thirty‐eight healthy volunteers had their resting metabolic rate measured, with seven of them proceeding to have their total energy expenditure assessed. MEASUREMENTS Total energy expenditure was measured by the doubly labelled water method (D 2 0 18 ), resting metabolic rate by ventilated hood indirect calorimetry, and fat free mass from the dilution volume of oxygen‐18. Body composition and components of energy expenditure were assessed before, at 2 weeks and at the end of the 3‐month treatment period on exogenous growth hormone. RESULTS Growth hormone deficient adults did not have a low total energy expenditure compared to healthy controls (13 12 vs 12 75 MJ/24 h) with only one patient expending less than 10 MJ/24 h. None had a resting metabolic rate lower than the 95% confidence limits of normality. The amount of energy expended on physical activity and thermogenesis was significant (6 54 MJ/24 h) and was similar to healthy controls (6 47 MJ/24 h). Resting metabolic rate increased by 15 9% after 14 days on exogenous growth hormone and was elevated 12‐1% after 3 months treatment but the ratio to fat‐free mass remained unaltered. Total energy expenditure increased by 13 4% after 14 days therapy. Fat‐free mass increased significantly after 3 months treatment by (mean) 4 5 kg with no change in fat mass and no loss in body weight. CONCLUSIONS Obesity maintenance in growth hormone deficient adults is not a consequence of reduced total energy expenditure or a reduced exercise energy output. There was also no evidence for an energy sparing mechanism. Energy expenditure was increased by exogenous growth hormone but was not associated with a loss in fat mass or body weight suggesting the need for dietetic advice for those already obese at the outset of therapy.
Low latency and efficient optical flow control for intra data center networks (2014)

We experimentally demonstrate a highly spectral efficient optical flow control technique for intra data center networks. A bi-directional system is implemented for generating flow control signal by reusing label wavelength and the transmission link within the same WDM channel. Dynamic operation shows high-quality flow control signal with 265 ns latency including 220 ns propagation delay and 500 mV amplitude with low input power and low bias current. Error free operation with 0.5 dB penalty for 40 Gb/s payload indicates that no distortion has been caused due the transmission of label and flow control signal.
Performance of 32-Gbaud PDM-QPSK in nonlinear transport regimes with different phase recovery methods (2011)

We experimentally investigate the performance of WDM coherent polarization-division multiplexed-return to zero-quadrature phase shift keying (PDM-RZ-QPSK) network in nonlinear transport regimes. Seven, 28 or 32-Gbaud PDM-RZ- QPSK channels are employed on a 50-GHz grid and transmitted over 1600-km fiber on an all-EDFA recirculating loop without any dispersion compensation module (DCM). The transmission link is configured entirely of either standard single-mode fiber (AllWave), medium dispersion fiber (TrueWave REACH), or ultra-large area fiber (ULAF). We sweep the launch power of the center channel and side channels together to measure the nonlinear effects of self-phase modulation (SPM), cross-phase modulation (XPM), and cross-polarization modulation (XPolM) on the center channel's BER performance. Furthermore, for all link configurations, we employ three different carrier phase recovery methods in the demodulation routine - Viterbi-Viterbi, Viterbi-Viterbi with a minimum mean-squared error (MMSE) filter, and the Optametra/Tektronix Weiner filter - to ascertain their relative performance in the presence of nonlinear effects.
Targeting the Raft-Associated Akt Signaling in Hepatocellular Carcinoma (2014)

Caveolin-1 and flotillin-1 are considered as markers of lipid rafts which can be regarded as sorting platforms for targeted transport of transmembrane proteins and are involved in fundamental cellular events such as signal transduction, cell adhesion, lipid/protein sorting, and human cancer. We addressed caveolin-1 and flotillin-1 expression in 90 human hepatocellular carcinoma (HCC) and adjacent noncancerous tissues (ANT) samples by SDS-PAGE and immunoblotting with specific antibodies. Significant caveolin-1 and flotillin-1 overexpression was found in HCC tissues compared to ANT and was confirmed by immunohistochemistry. Raft-associated Akt signaling pathway components involved in the regulation of cell survival were altered by western blotting in HCC microdomain-enriched subcellular fractions purified from paired HCC and ANT samples. Our results demonstrated that the activity of raft-associated but not total membrane Akt determines its cellular functions. Lipid rafts differ in different types of tissues, which allows for the possibility of tissue-type-specific targeting for cell survival.
A Review on Methods for Measurement of Free Water Surface (2023)

Turbulent free-surface flows are encountered in several engineering applications and are typically characterized by the entrainment of air bubbles due to intense mixing and surface deformation. The resulting complex multiphase structure of the air-water interface presents a challenge in precise and reliable measurements of the free-water-surface topography. Conventional methods by manometers, wave probes, point gauges or electromagnetic/ultrasonic devices are proven and reliable, but also time-consuming, with limited accuracy and are mostly intrusive. Accurate spatial and temporal measurements of complex three-dimensional free-surface flows in natural and man-made hydraulic structures are only viable by high-resolution non-contact methods, namely, LIDAR-based laser scanning, photogrammetric reconstruction from cameras with overlapping field of view, or laser triangulation that combines laser ranging with high-speed imaging data. In the absence of seeding particles and optical calibration targets, sufficient flow aeration is essential for the operation of both laser- and photogrammetry-based methods, with local aeration properties significantly affecting the measurement uncertainty of laser-based methods.
Ultrahigh resolution retinal imaging by visible light OCT with longitudinal achromatization (2018)

Chromatic aberrations are an important design consideration in high resolution, high bandwidth, refractive imaging systems that use visible light. Here, we present a fiber-based spectral/Fourier domain, visible light OCT ophthalmoscope corrected for the average longitudinal chromatic aberration (LCA) of the human eye. Analysis of complex speckles from <i>in vivo</i> retinal images showed that achromatization resulted in a speckle autocorrelation function that was ~20% narrower in the axial direction, but unchanged in the transverse direction. In images from the improved, achromatized system, the separation between Bruch's membrane (BM), the retinal pigment epithelium (RPE), and the outer segment tips clearly emerged across the entire 6.5 mm field-of-view, enabling segmentation and morphometry of BM and the RPE in a human subject. Finally, cross-sectional images depicted distinct inner retinal layers with high resolution. Thus, with chromatic aberration compensation, visible light OCT can achieve volume resolutions and retinal image quality that matches or exceeds ultrahigh resolution near-infrared OCT systems with no monochromatic aberration compensation.
Use of soluble CD27 as a marker of disease burden and the effect of rituximab-induced IgM flare and plasmapheresis in patients with Waldenström’s macroglobulinemia (2008)

8585 Backgound: Waldenstrom’s macroglobulinemia (WM) is a B-cell, IgM-secreting lymphoplasmacytic lymphoma. In this disease, serum IgM levels are used to assess both progression and response to treatment. Rituximab is an important therapeutic, but one frequently associated with an induced IgM flare, which may complicate response assessment (Treon et al, Ann Oncol 2004). In addition, plasmapheresis is commonly employed and can further complicate this evaluation. We, therefore, sought to identify a novel marker of disease burden which could evade these common clinical challenges. Soluble CD27 (sCD27) is a TNF-family member secreted by WM cells, elevated in patients with WM, and supports tumor cell growth through the induction of CD40L on bone marrow mast cells (Ho et al, Blood 2008). As such, we attempted to delineate its potential as a faithful marker of disease burden in WM. Methods: sCD27 levels were serially measured in 31 WM patients whose clinical outcomes (responder, stable disease, or progressive disease) were determined using consensus panel criteria based on concurrently-measured changes in serum IgM levels. Moreover, sCD27 levels were serially measured in 8 patients who had a rituximab-induced IgM flare, and in one patient, pre- and 48-hours post- plasmapheresis. Results: Serial changes in sCD27 levels paralleled those of serum IgM levels in all outcome categories, and highly-correlated to serial changes in serum IgM levels (r= 0.9760; p<0.0001 by Pearson’s correlation test). Moreover, in 8 patients who experienced an IgM flare related to rituximab, and eventually responded to therapy, IgM levels acutely rose from 3,515 to 5,270 mg/dL (p=0.016), while sCD27 levels declined from 174.1 to 155.9 U/mL (p=0.10). For the one patient undergoing plasmapheresis, IgM levels obtained 48 hours later declined from 4,770 to 2,370 mg/dL, whereas sCD27 levels showed minimal change (125.3 to 123.5 U/mL). Conclusion: sCD27 is a faithful marker of disease burden and is unaffected by the rituximab-induced IgM flare, as well as, plasmapheresis in WM. The use of this marker may aid in correctly predicting clinical outcome in patients undergoing treatment with rituximab and/or plasmapheresis in WM. No significant financial relationships to disclose.
Brief Report: In Search of a Candidate Pathogen for Giant Cell Arteritis: Sequencing‐Based Characterization of the Giant Cell Arteritis Microbiome (2014)

DNA sequencing of temporal artery biopsy specimens from GCA cases, in comparison with non-GCA controls, showed no evidence of previously identified candidate GCA pathogens. A single pathogen was not clearly and consistently associated with GCA in this case series.
Branched peptides for enzymatic supramolecular hydrogelation (2017)

Here we show the use of branched peptides (i.e., isopeptides) as the substrates of proteases for generating supramolecular hydrogels via enzymatically clipping the branch off the peptides. As the first report of using a protease to cut branched peptides to enable a molecular process for converting nanostructures, this work illustrates a fundamentally new molecular motif for exploring the applications of protease-instructed self-assembly for soft materials.
The role of the backbone torsion in protein folding (2016)

This article was reviewed by Frank Eisenhaber, Igor Berezovsky and Michael Gromiha.
Glatiramer acetate triggers PI3Kδ/Akt and MEK/ERK pathways to induce IL-1 receptor antagonist in human monocytes (2010)

Glatiramer acetate (GA), an immunomodulator used in multiple sclerosis (MS) therapy, induces the production of secreted IL-1 receptor antagonist (sIL-1Ra), a natural inhibitor of IL-1β, in human monocytes, and in turn enhances sIL-1Ra circulating levels in MS patients. GA is a mixture of peptides with random Glu, Lys, Ala, and Tyr sequences of high polarity and hydrophilic nature that is unlikely to cross the blood-brain barrier. In contrast, sIL-1Ra crosses the blood-brain barrier and, in turn, may mediate GA anti-inflammatory activities within the CNS by counteracting IL-1β activities. Here we identify intracellular signaling pathways induced by GA that control sIL-1Ra expression in human monocytes. By using kinase knockdown and specific inhibitors, we demonstrate that GA induces sIL-1Ra production via the activation of PI3Kδ, Akt, MEK1/2, and ERK1/2, demonstrating that both PI3Kδ/Akt and MEK/ERK pathways rule sIL-1Ra expression in human monocytes. The pathways act in parallel upstream glycogen synthase kinase-3α/β (GSK3α/β), the knockdown of which enhances sIL-1Ra production. Together, our findings demonstrate the existence of signal transduction triggered by GA, further highlighting the mechanisms of action of this drug in MS.
In situ high-pressure and high-temperature X-ray microtomographic imaging during large deformation: A new technique for studying mechanical behavior of multiphase composites (2011)

International audience
Cytotoxicity of Superoxide Dismutase 1 in Cultured Cells Is Linked to Zn2+ Chelation (2012)

Neurodegeneration in protein-misfolding disease is generally assigned to toxic function of small, soluble protein aggregates. Largely, these assignments are based on observations of cultured neural cells where the suspect protein material is titrated directly into the growth medium. In the present study, we use this approach to shed light on the cytotoxic action of the metalloenzyme Cu/Zn superoxide dismutase 1 (SOD1), associated with misfolding and aggregation in amyotrophic lateral sclerosis (ALS). The results show, somewhat unexpectedly, that the toxic species of SOD1 in this type of experimental setting is not an aggregate, as typically observed for proteins implicated in other neuro-degenerative diseases, but the folded and fully soluble apo protein. Moreover, we demonstrate that the toxic action of apoSOD1 relies on the protein's ability to chelate Zn(2+) ions from the growth medium. The decreased cell viability that accompanies this extraction is presumably based on disturbed Zn(2+) homeostasis. Consistently, mutations that cause global unfolding of the apoSOD1 molecule or otherwise reduce its Zn(2+) affinity abolish completely the cytotoxic response. So does the addition of surplus Zn(2+). Taken together, these observations point at a case where the toxic response of cultured cells might not be related to human pathology but stems from the intrinsic limitations of a simplified cell model. There are several ways proteins can kill cultured neural cells but all of these need not to be relevant for neurodegenerative disease.
Cytokinins Secreted byAgrobacteriumPromote Transformation by Repressing a Plant Myb Transcription Factor (2013)

Agrobacterium-mediated transformation is the most widely used technique for generating transgenic plants. However, many crops remain recalcitrant. We found that an Arabidopsis myb family transcription factor (MTF1) inhibited plant transformation susceptibility. Mutating MTF1 increased attachment of several Agrobacterium strains to roots and increased both stable and transient transformation in both susceptible and transformation-resistant Arabidopsis ecotypes. Cytokinins from Agrobacterium tumefaciens decreased the expression of MTF1 through activation of the cytokinin response regulator ARR3. Mutating AHK3 and AHK4, genes that encode cytokinin-responsive kinases, increased the expression of MTF1 and impaired plant transformation. Mutant mtf1 plants also had increased expression of AT14A, which encodes a putative transmembrane receptor for cell adhesion molecules. Plants overexpressing AT14A exhibited increased susceptibility to transformation, whereas at14a mutant plants exhibited decreased attachment of bacteria to roots and decreased transformation, suggesting that AT14A may serve as an anchor point for Agrobacteria. Thus, by promoting bacterial attachment and transformation of resistant plants and increasing such processes in susceptible plants, treating roots with cytokinins may help engineer crops with improved features or yield.
Implementation and Evaluation of a Hardware Decentralized Synchronization Lock for MPSoCs (2020)

International audience
Mining the Blogosphere for Contributors' Sentiments. (2006)

We propose a domain-independent approach to blog analysis for an assessment of bloggers ’ sentiments. The generic methodol-ogy to detect specific attitudes of human agents is based on rep-resentation of conflict scenarios by means of communicative actions (which express sentiments) and causal/argumentative links between their subjects (which may support these senti-ments). This methodology is applied to textual data on inter-human interactions including conflicts in opinions of bloggers. Evaluation is conducted in the domain of customer complaints.1
Probing the magnetic ground state of theDX−center inCd1−xMnxTe:Inusing muon spin relaxation (2006)

Muon spin relaxation $(\ensuremath{\mu}\mathrm{SR})$ measurements have been made on ${\mathrm{Cd}}_{0.85}{\mathrm{Mn}}_{0.15}\mathrm{Te}:\mathrm{In}$ and ${\mathrm{Cd}}_{0.86}{\mathrm{Mn}}_{0.14}\mathrm{Te}:\mathrm{Al}$. The spin glass transition region has been studied using $\ensuremath{\mu}\mathrm{SR}$ and low-temperature magnetic susceptibility measurements. Persistent photoconductivity (PPC) has been shown to exist only in the In-doped sample, the effect of PPC on the spin glass transition temperature using bulk magnetic susceptibility has also been studied, indicating the presence of bound magnetic polarons. $\ensuremath{\mu}\mathrm{SR}$ on the Al-doped sample clearly shows the spin glass transition, however, the presence of the DX center, which causes PPC when doping with In donors, perturbs the muon response. Particular attention is paid to the possibility of the DX center trapping muonium, preventing the detection of the spin glass transition. PPC does not induce a change in the muon response, however, we find continuous illumination of the sample allows the observation of the spin glass transition. We suggest that these results can be explained by assuming the presence of multiple DX centers. The muon acting as a local magnetic probe of the DX center also suggests the ground state is diamagnetic.