gebhart/patrepeval huggingface dataset:
Pharmacogenomics and transplantation: Where are we? (2004)

Before pharmacogenomics became a common word, it was known that a small percentage of the population developed a severe reaction to azathioprine, leading to agranulocytosis and occasionally death. In the late 1980s, it was realized that this small percentage of the population had poor function of the metabolizing enzyme thiopurine S-methyltransferase (TPMT), and could only metabolize substrates, such as azathioprine, very slowly (1). The ability to predict who would have this reaction made it safer to give aziothioprine.
The pH sensitive properties of carboxymethyl chitosan nanoparticles cross-linked with calcium ions (2017)

In environmental applications the applied materials are required to be non-toxic and biodegradable. Carboxymethyl chitosan nanoparticles cross-linked with Ca<sup>2+</sup> ions (CMC-Ca) fulfill these requirements, and they are also renewable. These nanoparticles were applied to oil-spill treatment in our previous study and here we focused on enhancing their properties. It was found that while the divalent Ca<sup>2+</sup> ions are crucial for the formation of the CMC-Ca, the attractive interaction between NH<sub>3</sub><sup>+</sup> and COO<sup>-</sup> groups contributed significantly to the formation and stability of the CMC-Ca. The stability decreased as a function of pH due to the deprotonation of the amino groups. Therefore, the nanoparticles were found to be fundamentally pH sensitive in solution, if the pH deviated from the pH (7-9) that was used in the synthesis of the nanoparticles. The pH sensitive CMC-Ca synthesized in pH 7 and 8 were most stable in the studied conditions and could find applications in oil-spill treatment or controlled-release of substances.
Phytophthora Disease of Some Ornamental Foliage Plants as New Records in Taiwan (2000)

Eight new Phytophthora diseases of ornamental foliage plants were described. Phytophthora parasitica was detected from five species of plants. It caused blight and wilt of painted nettle and peperomia, leaf and stem blight of compact dracaena and fatsia, and root rot of croton. P. citrophthora was isolated from pathos and Malabar chestnut. The fungus infected the whole plants of the former and the young seedlings of the latter. P. palmivora attacked leaves, petioles, and rhizomes of maidenhair fern and induced wilt of the affected plants. Similar diseases were reproduced when seedlings, cuttings or plantings of each host were inoculated with zoospore suspension of their respective isolates of Phytophthora species in pathogenicity tests. Same species of Phytophthora was reisolated from all artificially infected tissues. All eight citrophthora on pothos and Malabar chestnut, and P. palmivora on maidenhair fern have not been described in any other places.
Synthetic antibodies as therapeutics (2006)

Synthetic antibody libraries, whose repertoires are designed, have advanced in the last decade to rival natural repertoire-based libraries. Many types of diversity design have been shown to generate highly functional libraries. Defined template and defined diversity in synthetic antibody libraries improve the process of discovering and optimizing new antibodies. Synthetic libraries with different diversity design have targeted different epitopes on antigens, including epitopes that are unlikely to be targeted by immunization and hybridoma. Cross-species binding antibodies are prime examples of products generated by synthetic antibody libraries, and they are becoming the tools of choice to validate the selection of targeted molecules in therapeutic development. Synthetic antibody libraries complement the existing natural repertoire-based antibody libraries and hybridoma approach to maximize the potentials of antibodies as therapeutics.
Racial Disparities in End-of-Life Communication and Preferences among Chronic Kidney Disease Patients (2016)

As Black and White patients with advanced CKD differ in areas of EOL communication, preferences, and hospice knowledge, future efforts should aim to improve patient understanding and promote informed decision-making.
Les différents lasers : un tour d’horizon (2010)

Les lasers sont multiples : en fonction de leurs caractéristiques physiques intrinsèques (quel milieu à gain ? quelle cavité ? quel pompage ?), ils produisent des rayonnements couvrant des plages extrêmement vastes, tant du point de vue spectral – de l’extrême ultraviolet au lointain infrarouge – que temporel – du régime continu aux attosecondes – ou encore énergétique – du nano au mégajoule. C’est de cette impressionnante diversité que les lasers tirent leur capacité à répondre à tant d’applications différentes.Nous vous proposons dans cet article de faire un rapide tour d’horizon des différents types de lasers existants et de leurs performances.
Detailed process analysis for sub-resolution assist features introduction (2004)

Sub-Resolution Assists Features (SRAF) is a well known and well described method for process window improvement. The introduction of such a technique is not always an easy task for two reasons. On one hand the SRAF placement rules must be defined very well and on the other hand an empirical resist model must be created, which describes the process. Model based Optical and Process effects correction (MB-OPC) is using an empirical model so called black box, which must be able to predict properly the printing feature for any kind of complex design configuration. When SRAF are implemented in the design, the degree of freedom for the MB-OPC can be reduced. Beside that effort to predetermine as required as possible the target layer, SRAF placement rules and SRAF printing restrictions will limit the OPC. MB-OPC has to cover both the parameters space corresponding to areas in which SRAF are placed and the parameter space for which no SRAF has been implemented. Of course, it could also be possible to apply the correction of the proximity effect of a complex design with SRAF by an extensive rule-based OPC. Nevertheless the advantage of MB-OPC exists in the possibility to verify the design after Data Preparation by simulating it with the help of the calibrated model. However one should not trust the simulation alone, always a verification of the design on silicon would be necessary, by comparing simulation to SEM images. Beside the advantages of MB-OPC also weaknesses exist in the meantime, which could require a combination of rule-based and model-based OPC, so called “hybrid OPC”. Empirical models are very often only able to predict the proximity behavior due to a certain range, which is called the optical range of a model. Distances bigger than this range will be covered by extrapolations. This procedure would be correct, if the proximity behavior was as constant as in the area inside the optical range. We generated an empirical model with the Calibre Workbench from Mentor Graphics. For the model calibration we chose structures with SRAF placement rules, which we applied to the design as well as SRAF placement rules which were not applied to the design. Afterwards, we performed simulations of critical lines over pitch including SRAF. Beside the MB-OPC, we will also describe in this paper the process steps how to generate the SRAF placement rules. The restrictions resulting from the SRAF rules are presented. Subsequently, the experimental results will show that both for symmetrical and asymmetrical structures an improvement of the process window has been obtained. Also weaknesses become clear, which place either the model or the SRAF rule-set questionable. Finally two solutions will be compared, a pure MB-OPC including the isolated lines outside of the optical range and a combination of MB-OPC with a rule-based OPC table for the isolated lines.
Design of a wavelength-tunable optical fiber tweezer (Conference Presentation) (2017)

We present for the first time a wavelength tunable fiber-based optical tweezer using a graded index multimode optical fiber (GIMF). Optical fiber tweezer is a viable replacement for the bulky objective-based tweezers because of the low-cost and user-friendly operation and maneuverability. The proposed optical fiber tweezer consists of a GIMF spliced to a single mode fiber into which a wavelength tunable laser is launched. The exit field at the end-facet of the GIMF is used for tweezing. The GIMF setup is capable of generating a tunable-distance optical trap over a hundred microns by just tuning the laser wavelength. The position of the optical trap can also be customized with the proper design of the GIMF and straining the fiber. The length of the GIMF also plays an important role in the operation of the device. This length needs to be fined-tuned only over less than 500 microns due to the self-imaging properties of the beam propagating in a GIMF; therefore, the necessary length adjustments can be easily done by polishing the end-facet of the fiber. The numerical results also show that as the optical trap moves farther away from the GIMF tip, the optical trap gets weaker. The results also show that the minimum input power to meet the stability conditions for a particle with a radius of 0.1 micron is around 400 mW.
Chaos in Motion: Measuring Visual Pollution with Tangential View Landscape Metrics (2020)

Visual pollution (VP) in the form of outdoor advertisements (OA) is a threat to landscape physiognomy. Despite their proven usefulness in landscape aesthetic studies, landscape metrics have not yet been applied to address the phenomenon of VP. To fill this knowledge gap, a methodological framework for the measurement of VP using tangential view landscape metrics is proposed, which is accompanied by statistically significant proofs. Raster products derived from aerial laser scanning data were used to characterize two study areas with different topographic conditions in the city of Lublin, East Poland. The visibility of the cityscape in motion was simulated through viewshed measurements taken at equal intervals in the forwards and backwards directions along pedestrian walkways. The scrutinized tangential view landscape metrics (visible area, maximum visible distance, skyline, Shannon depth, view depth line) was the object of a two-fold interpretation wherein the spatial occurrence of VP as well as its impacts on the visual landscape character (VLC) were examined. The visible area metrics were found to be highly sensitive VP indicators. The maximum visible distance metrics provided evidence for the destructive effect of OA on view corridors. The Shannon depth and depth line metrics were not found to be statistically significant indicators of VP. Results from directional viewshed modelling indicate that distortion in the analyzed cityscape physiognomy depends on the view direction. The findings allow for particular recommendations with practical implementations in land use planning, which are discussed along with limitations to our proposed methods.
Thyroid Antigen-Antibody Nephritis: Possible Involvement of Fucosyl-GM1 as the Antigen. (1987)

Hyperthyroidism, microscopic hematuria, and proteinuria developed in an 11-year-old girl. Proteinuria decreased during treatment of hyperthyroidism with an antithyroid drug. On admission, serum anti-thyroglobulin antibody, antimicrosomal antibody, and immune complex were present. The thyrotropin binding inhibitory immunoglobulin (TBII) level was low. On the other hand, an antibody to the ganglioside component (fucosyl-GM1) was detected by an enzyme linked immunosolvent assay (ELISA). A thyroid biopsy specimen showed massive lymphocytic infiltration and interstitial fibrosis. A renal biopsy specimen showed marked proliferation of mesangial cells and increased mesangial matrix with focal segmental capillary wall abnormality. Electron microscopec studies demonstrated mild paramesangial dense deposits. By indirect immunofluorescence, granular glomerular basement membrane and mesangial staining were not detected with rabbit antibody to thyroglobulin, but were detected with rabbit antibody to fucosyl GM1. Fucosyl GM1 was also seen along the basilar aspect of the thyroid follicular epithelial cells. These observation suggests the development of glomerulonephritis mediated by thyroid antigen, particularly ganglioside component.
On a Cognitive Radio Network's Random Access Game With a Poisson Number of Secondary Users (2015)

In this letter a random access algorithm based on game theory for cognitive radio networks with random number of secondary users is investigated. The scenario examines a non-cooperative game in which all the players are unaware of the total number of devices participating (population uncertainty). We proposed a scheme where failed attempts to transmit (collisions) are penalized and, consequently, the optimum penalization in mixed strategies is calculated. Furthermore, an analytical approximation for the corresponding Pareto fronts which maximizes the throughput of individual secondary users is obtained. Finally, the impact that the presence of primary users have on the optimal access strategy is assessed.
Epstein-Barr Virus Induces Erosive Arthritis in Humanized Mice (2011)

Epstein-Barr virus (EBV) has been implicated in the pathogenesis of rheumatoid arthritis (RA) on the basis of indirect evidence, such as its presence in affected joint tissues, antigenic cross reactions between EBV and human proteins, and elevated humoral and cellular anti-EBV immune responses in patients. Here we report development of erosive arthritis closely resembling RA in humanized mice inoculated with EBV. Human immune system components were reconstituted in mice of the NOD/Shi-scid/IL-2Rγ(null) (NOG) strain by transplantation with CD34(+) hematopoietic stem cells isolated from cord blood. These humanized mice were then inoculated with EBV and examined pathologically for the signs of arthritis. Erosive arthritis accompanied by synovial membrane proliferation, pannus formation, and bone marrow edema developed in fifteen of twenty-three NOG mice transplanted with human HSC and inoculated with EBV, but not in the nine NOG mice that were transplanted with HSC but not inoculated with EBV. This is the first report of an animal model of EBV-induced arthritis and strongly suggest a causative role of the virus in RA.
Electrically Tunable Multiterminal SQUID-on-Tip (2016)

We present a new nanoscale superconducting quantum interference device (SQUID) whose interference pattern can be shifted electrically in situ. The device consists of a nanoscale four-terminal-four-junction SQUID fabricated at the apex of a sharp pipet using a self-aligned three-step deposition of Pb. In contrast to conventional two-terminal-two-junction SQUIDs that display optimal sensitivity when flux biased to about a quarter of the flux quantum, the additional terminals and junctions allow optimal sensitivity at arbitrary applied flux, thus eliminating the magnetic field "blind spots". We demonstrate spin sensitivity of 5 to 8 μ<sub>B</sub>/Hz<sup>1/2</sup> over a continuous field range of 0 to 0.5 T with promising applications for nanoscale scanning magnetic imaging.
Low complexity list successive cancellation decoding of polar codes (2014)

The authors propose a low complexity list successive cancellation (LCLSC) decoding algorithm, where the advantages of the successive cancellation (SC) decoding and the list successive cancellation (LSC) decoding are both considered. In the proposed decoding, SC decoding instead of LSC decoding is implemented when all information bits from bad subchannels are received reliably. While the reliability of each information bit is estimated by its likelihood ratio (LR), the bit channel quality is measured via its Bhattacharyya parameter. To achieve this goal, the authors introduce two thresholds: LR threshold and Bhattacharyya parameter threshold. Also, the methods to determine them are both elaborated. The numerical results suggest that the complexity of LCLSC decoding is much lower than LSC decoding and can be close to that of SC decoding, while the error performance is almost equal to that of LSC decoding. Especially, when the code rate is in low region, the advantage of our decoding is more obvious.
Cultivation media for lactic acid bacteria used in dairy products (2019)

This review aims to familiarize the reader with research efforts on the cultivation media of lactic acid bacteria (LAB). We have also included a brief discussion on standard ingredients used in LAB media and chemically defined media as related to bacterial growth requirements. Recent research has focused on modifying standard media for the enumeration, differentiation, isolation, and identification of starter cultures and probiotics. Even though large numbers of these media have been developed to serve dairy microbial control, they have failed to provide consistent results. The research consequently points to the need to develop a reliable lactobacilli growth medium for the dairy industry.
TRPM8-expressing dorsal root ganglion neurons project dichotomizing axons to both skin and bladder in rats (2010)

To reveal the mechanism of urinary urgency evoked by cold sensation, we investigated the convergence of the primary sensory afferents of the skin and bladder. Dichotomizing afferents of L6-S1 dorsal root ganglion neurons that innervate the skin and bladder was constantly observed with retrograde neuron tracers in rats. In-situ hybridization revealed that approximately 8.0% of the double-labelled cells expressed transient receptor potential channel melastatin member 8 (TRPM8) transcripts in the dorsal root ganglions. Cold and menthol stimuli to the skin generated bladder nerve responses conducted through dichotomizing axons, which significantly decreased in the presence of the TRPM8 blocker BCTC. Taken together, TRPM8-expressing sensory neurons with dichotomizing axons projecting to the skin and bladder may be responsible for the urinary urgency evoked by cold sensation.
Repetitive stress in mice causes migraine-like behaviors and calcitonin gene-related peptide-dependent hyperalgesic priming to a migraine trigger (2020)

Migraine is one of the most disabling disorders worldwide but the underlying mechanisms are poorly understood. Stress is consistently reported as a common trigger of migraine attacks. Here, we show that repeated stress in mice causes migraine-like behaviors that are responsive to a migraine therapeutic. Adult female and male mice were exposed to 2 hours of restraint stress for 3 consecutive days, after which they demonstrated facial mechanical hypersensitivity and facial grimace responses that were resolved by 14 days after stress. Hypersensitivity or grimace was not observed in either control animals or those stressed for only 1 day. After return to baseline, the nitric oxide donor sodium nitroprusside (SNP; 0.1 mg/kg) elicited mechanical hypersensitivity in stressed but not in control animals, demonstrating the presence of hyperalgesic priming. This suggests the presence of a migraine-like state, because nitric oxide donors are reliable triggers of attacks in migraine patients but not controls. The stress paradigm also caused priming responses to dural pH 7.0 treatment. The presence of this primed state after stress is not permanent because it was no longer present at 35 days after stress. Finally, mice received either the calcitonin gene-related peptide monoclonal antibody ALD405 (10 mg/kg) 24 hours before SNP or a coinjection of sumatriptan (0.6 mg/kg). ALD405, but not sumatriptan, blocked the facial hypersensitivity due to SNP. This stress paradigm in mice and the subsequent primed state caused by stress allow further preclinical investigation of mechanisms contributing to migraine, particularly those caused by common triggers of attacks.
Science performance of the Pupil-mapping Exoplanet Coronagraphic Observer (PECO) (2009)

The Pupil-mapping Exoplanet Coronagraphic Observer (PECO) medium-class mission concept is a 1.4-m space-based optical telescope with a high-performance Phase-Induced Amplitude Apodization (PIAA) coronagraph. PECO detects and characterizes exoplanets and their host systems at 2 &lambda;/D (0.15") separation at high contrast (~1e-10). The optical design images in 16 filter bands from 400-800 nm, producing simultaneous low-resolution target spectra. PECO will characterize terrestrial planets in the habitable zones of ~20 nearby F, G, K stars at spectral resolution of R~15, as well as over a dozen radial-velocity planets and over a hundred gas giants and exozodiacal dust disks. We discuss PECO's expected science performance and simulated data products over its three-year mission lifetime.
Chemistry of 99mTc tracers. II. In vitro conversion of tagged HEDP and pyrophosphate (bone-seekers) into gluconate (renal agent). Effects of Ca and Fe (ii) on in vivo distribution. (1976)

Sodium gluconate transforms the bone-seekers 99mTc-HEDP and 99mTc-pyrophosphate into the renal agent 99mTc-gluconate. In these in vitro processes, pyrophosphate is displaced faster than HEDP, while the HEDP reaction is accelerated by calcium ions. The in vivo distributions of these bone and kidney agents are altered by the prior local injection of calcium or iron(II). These transformation and translocation phenomena are explained in terms of the mechanistic behavior of Tc(IV) complexes.
Targeting Pro-Invasive Oncogenes with Short Chain Fatty Acid-Hexosamine Analogues Inhibits the Mobility of Metastatic MDA-MB-231 Breast Cancer Cells (2008)

Per-butanoylated N-acetyl-D-mannosamine (Bu(4)ManNAc), a SCFA-hexosamine cancer drug candidate with activity manifest through intact n-butyrate-carbohydrate linkages, reduced the invasion of metastatic MDA-MB-231 breast cancer cells unlike per-butanoylated-D-mannose (Bu(5)Man), a clinically tested compound that did not alter cell mobility. To gain molecular-level insight, therapeutic targets implicated in metastasis were investigated. The active compound Bu(4)ManNAc reduced both MUC1 expression and MMP-9 activity (via down-regulation of CXCR4 transcription), whereas "inactive" Bu(5)Man had counterbalancing effects on these oncogenes. This divergent impact on transcription was linked to interplay between HDACi activity (held by both Bu(4)ManNAc and Bu(5)Man) and NF-kappaB activity, which was selectively down-regulated by Bu(4)ManNAc. Overall, these results establish a new therapeutic end point (control of invasion) for SCFA-hexosamine hybrid molecules, define relative contributions of molecular players involved in cell mobility and demonstrate that Bu(4)ManNAc breaks the confounding link between beneficial HDACi activity and the simultaneous deleterious activation of NF-kappaB often found in epigenetic drug candidates.