gebhart/patrepeval huggingface dataset:
Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit‐solvent model (2011)

In recent years, all-atom and coarse-grained models have been developed and applied to simulations of micelles and biological membranes. Here, we explore the question of whether a combined all-atom representation of surfactant molecules and continuum description of solvent based on the generalized Born model can be used to study surfactant micelles. Specifically, we report the parameterization of the GBSW model with a surface-area dependent nonpolar solvation energy term for dodecyl sulfate, dodecyl tetramethylammonium, and dodecyl triethyleneglycol ether molecules. In the parameterization procedure,the atomic Born radii were derived from the radial distribution functions of solvent charge and refined targeting the potential of mean force of dimer interactions from explicit-solvent simulations. The optimized radii were then applied in molecular dynamics simulations of the ionic and nonionic micelles.We found that the micelles are stable but more compact and rigid than in explicit solvent as a consequence of the drastic reduction in solvation and mobility of surfactant monomers within the micelle. Based on these data and our previous work, we suggest that in addition to a more accurate description of the nonpolar solvation energy, the ruggedness in the short-range interactions due to solvent granularity is a critical feature that needs to be taken into account to accurately model processes such as micelle formation and protein folding in implicit solvent. Finally, the explicit-solvent data presented here offers new insights into different conformational behavior of ionic and nonionic micelles which is valuable for understanding hydrophobic assemblies and of interest to the detergent industry.
Traumatic Fractures of Heterotopic Bone in Patients Who Have Fibrodysplasia Ossificans Progressiva (1994)

Fibrodysplasia ossificans progressiva is an extremely rare genetic disorder characterized by the formation of a heterotopic skeleton that is histologically, biomechanically, and metabolically indistinguishable from the normotopic skeleton. Isolated cases of traumatic and pathologic fractures have been reported in the normotopic skeleton of patients who have fibrodysplasia ossificans progressiva, but to the authors' knowledge there have been no detailed reports of traumatic fractures in the heterotopic skeleton of patients who have this disease. Reported here are 2 children with fibrodysplasia ossificans progressiva who sustained traumatic fractures of heterotopic bone around the elbows. In both children, the fractures healed uneventfully with normal-appearing callus. These 2 extremely rare cases suggest that the biologic response to fractures in the heterotopic skeleton appears indistinguishable from that in the normotopic skeleton in patients who have fibrodysplasia ossificans progressiva.
A two-step blocking scheme learner for scalable link discovery (2014)

Abstract. A two-step procedure for learning a link-discovery blocking scheme is presented. Link discovery is the problem of linking entities be-tween two or more datasets. Identifying owl:sameAs links is an impor-tant, special case. A blocking scheme is a one-to-many mapping from en-tities to blocks. Blocking methods avoid O(n2) comparisons by clustering entities into blocks, and limiting the evaluation of link specifications to entity pairs within blocks. Current link-discovery blocking methods use blocking schemes tailored for owl:sameAs links or that rely on assump-tions about the underlying link specifications. The presented framework learns blocking schemes for arbitrary link specifications. The first step of the algorithm is unsupervised and performs dataset mapping between a pair of dataset collections. The second supervised step learns blocking schemes on structurally heterogeneous dataset pairs. Application to RDF is accomplished by representing the RDF dataset in property table form. The method is empirically evaluated on four real-world test collections ranging over various domains and tasks.
Transmission of SDH signals through future satellite channels using high-level modulation techniques (1992)

The authors discuss the possibility of transmitting synchronous digital hierarchy (SDH) signals through two-link nonlinear satellite channels. Transmitting such high bit rate signals through a standard 54 MHz or 36 MHz transponder bandwidth requires the use of high-level modulation schemes. The techniques and technologies needed to make the use of 16-ary quadrature amplitude modulation (QAM) and 64-ary QAM transmissions feasible for future satellite communication systems are examined. It is shown that it is possible to transmit a synchronous transport module-level 1 (STM-1) signal through a standard 54 or 36 MHz transponder bandwidth using 16-ary QAM or 64-ary QAM transmission, respectively, for the 6/4 GHz band. However, for higher frequency bands, due to high fade margins needed to achieve the high availability and performance for SDH systems, is not practical to transmit the STM-1 signal through such standard transponder bandwidths.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: Synthesis and Structure‐Activity Relationships of Some Novel Oxetane Carbapenems. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comprehensive Highly Multiplexed Single-Tube Liquid Bead Microarray Assay for Constitutively Activated Tyrosine Kinases in Chronic Myeloproliferative Disorders. (2007)

Abstract Chronic Myeloproliferative disorders (CMPDs) are malignancies characterized by excessive proliferation of one or more of the myeloid lineages driven by constitutively activated tyrosine kinases (CATKs). CATKs are increasingly serving as targets for cancer-specific therapy and newer and more potent TK inhibitors are becoming available for clinical use. CATKs in CMPDs may result from karyotypically evident or cryptic chromosomal translocations leading to TK gene fusions or from karyotypically silent gain-of-function point mutations. More than ten CATK genes have been shown to result in CMPDs by imparting a demonstrable positive growth drive. CATK inhibitors important in the treatment of CMPDs have different inhibitory profiles, making it critical to identify the specific mutation involved in patients receiving targeted therapy. Of these TK genes, ABL, PDGFRB, PDGFRA, FGFR1, ETV6, JAK2 and MPL are the most frequently involved. Since most of these TK genes can participate in chromosome translocations with a large number of partner genes, the resulting number of possible CATKs is rather large, making detection and identification a challenging task. To date, two classic (B2A2 and B3A2) and seven less common fusions of the ABL and BCR genes have been described. In addition, over twenty non-BCR-ABL mutations have been shown to have pathogenetic relevance in CMPDs. We have developed a simple, high-throughput assay with a fast turnaround time that solves the complex problem of detecting and identifying multiple translocations and point mutations. Two steps are involved in this expandable assay. The first is a multiplex RT-PCR reaction that amplifies fusion transcripts and point mutations described in CMPDs from peripheral blood or bone marrow. This PCR reaction employs internal specific primers targeted to each of eight BCR-ABL mutations (E1A2, E1A3, B2A2, B3A2, E6A2, E8A2, E15A2, E19A2) eight non-BCR-ABL mutations (FIP1L1-PDGFRA, BCR-PDGFRA, BCR-FGFR1, MYO18A-FGFR1, CDK5RAP2-PDGFRA, ETV6-PDGFRB, RABAPTIN-5-PDGFRB, H4-PDGFRB) and two gain of function mutations (JAK2V617F and MPLW515L) and a biotinylated common primer set to increase amplification efficiency. The second is a liquid bead microarray (Luminex) which uses optically encoded beads to detect probes specific for multiple known translocations in a single tube. To date, we have selectively detected four BCR-ABL and three non-BCR-ABL mutations from cloned patient samples and the cell lines SupB15 (E1A2 p190 BCR-ABL fusion), K562 (B3A2 p210 BCR-ABL fusion) and BV173 (B2A2 p210 BCR-ABL fusion). Dilution studies using these cell lines demonstrate detection down to between 1/1000 and 1/100000 cell equivalents without significant cross-talk. Figure Figure Figure Figure
Quantitative analysis of properties and spatial relations of fuzzy image regions (1993)

Properties of objects and spatial relations between objects play an important role in rule-based approaches for high-level vision. The partial presence or absence of such properties and relationships can supply both positive and negative evidence for region labeling hypotheses. Similarly, fuzzy labeling of a region can generate new hypotheses pertaining to the properties of the region, its relation to the neighboring regions, and, finally, hypotheses pertaining to the labels of the neighboring regions. A unified methodology that can be used to characterize both properties and spatial relationships of object regions in a digital image is presented. The methods proposed for computing the properties and relations of image regions can be used to arrive at more meaningful decisions about the contents of the scene.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electron Microscopy, Nanoscopy, and Scanning Micro‐ and NanoanalysisUpdate based on the original article by Vladimir Oleshko, Renaat Gijbels and Severin Amelinckx,<i>Encyclopedia of Analytical Chemistry</i>, © 2000, John Wiley &amp; Sons, Ltd (2013)

Abstract The article considers the history and stages of development of electron microscopy (EM) and scanning microanalysis, including theoretical aspects of electron beam–solid interactions, instrumentation, methodology of particular techniques and image analysis, sample preparation, and some typical applications as well. Major classes of EM techniques, i.e. stationary beam (transmission) and scanning beam EM methods, analytical electron microscopy (AEM), in situ EM, holography, and tomography are overviewed. In AEM, several imaging, diffraction, and analytical modes are integrated in a design to provide analytical synergism having obvious advantages over any single instrument. The subject of EM is to determine the morphology, crystallinity, defect structure, phase and elemental compositions, and electronic properties of a material using the focused electron beam and signals generated in the course of its interaction with the specimen. Various electron–specimen interactions generate a great deal of structural and analytical information in the form of emitted electrons and/or photons and internally produced signals, such as elastically and inelastically scattered electrons, Auger electrons (AEs), X‐rays, and cathodoluminescence (CL), which can be analyzed in different operating modes. Imaging of solid materials is essentially due to elastic scattering (diffraction) of electrons by the periodic arrangement of atoms in crystals (diffraction contrast) and/or interference of several diffracted and transmitted beams (phase contrast). High‐resolution imaging in scanning transmission mode is possible by using incoherently scattered electrons (Z‐contrast). Inelastic interactions form the basis for all chemical analytical techniques (energy‐dispersive (EDS) and wavelength‐dispersive (WDS) X‐ray spectroscopy, electron energy‐loss spectroscopy (EELS) energy‐filtering transmission electron microscopy (EFTEM), AE‐, and CL‐spectroscopy). The introduction of aberration‐corrected and monochromatic electron optics during the last decade opened a new era of nanoscopy and nanoanalysis at sub‐0.1 nm lateral resolution and sub‐electronvolt energy resolution levels with improved signal‐to‐noise ratio (SNR). Basic data characterizing the current state‐of‐the‐art and trends in development of electron nanoscopy and nanoanalysis are presented.
Anti-inflammatory activity of phosphodiesterase (PDE)-IV inhibitors in acute and chronic models of inflammation (1995)

Inhibitors of cyclic nucleotide phosphodiesterases are known to suppress lipopolysaccharide (LPS)-induced tumour necrosis factor-alpha (TNF-alpha) production in vitro in human monocytes. The most potent of these have selectivity for type IV PDEs, suggesting that this class of PDE is the major type involved in the regulation of human TNF-alpha production. Using compounds of two distinct chemical structural classes, a quinazolinedione (CP-77059) and a 4 arylpyrrolidinone (rolipram), we show here that PDE-IV-specific inhibitors are also potent in suppressing LPS-induced TNF-alpha production in vitro in sodium periodate-elicited murine macrophages (IC50s of 1 and 33, respectively). We then report the in vivo anti-inflammatory effect of PDE-IV inhibition in five murine models of inflammation: (i) elevation of serum TNF-alpha induced by a sublethal LPS injection; (ii) LPS-induced endotoxic shock; (iii) LPS/galactosamine-induced endotoxic shock; (iv) carrageenan-induced paw oedema; and (v) adjuvant arthritis. Following a sublethal (5 micrograms/mouse) injection of LPS, serum TNF-alpha levels in mice peaked sharply, reaching concentrations of 3-12 ng/ml 90 min after injection. In this sublethal LPS assay, CP-77059 was about 30 times more potent than rolipram, with a minimum effective dose of 0.1 mg/kg versus 3 mg/kg for rolipram. This rank order is in keeping with the relative in vitro IC50s for CP-77059 and rolipram, as well as their relative Ki against the human PDE-IV enzyme (46 nM and 220 nM, respectively). In LPS-induced endotoxic shock, rolipram and CP-77059 at relatively high doses of 30 and 10 mg/kg, respectively, significantly reduced serum TNF-alpha levels, and also inhibited mortality 66%. In the LPS/galactosamine shock model, in which mice are rendered exquisitely sensitive to LPS by co-injection with galactosamine, only 0.1 microgram of LPS/mouse is necessary for serum TNF-alpha elevation and death. Both rolipram and the CP-77059 caused dose-dependent reduction of serum TNF-alpha and lethality. In the carrageenan-induced paw oedema model, in which there is a pronounced local TNF-alpha response (without a serum TNF-alpha elevation), rolipram significantly inhibited paw swelling as well as localized TNF-alpha levels in the paw. In the adjuvant arthritis model, a chronic model of inflammation also possessing localized TNF-alpha elevation in the inflamed paw, rolipram and CP-77059 suppressed ankle swelling and radiological evidence of joint damage. These data are consistent with a major role for PDE-IV in regulation of TNF-alpha production and inflammatory responses in murine systems.(ABSTRACT TRUNCATED AT 400 WORDS)
Compact and scalable polarimetric self-coherent receiver using dielectric metasurface (2023)

The polarimetric self-coherent system using a direct-detection-based Stokes-vector receiver (SVR) is a promising technology to meet both the cost and capacity requirements of the short-reach optical interconnects. However, conventional SVRs require a number of optical components to detect the state of polarization at high speed, resulting in substantially more complicated receiver configurations compared with the current intensity-modulation-direct-detection (IMDD) counterparts. Here, we demonstrate a simple and compact polarimetric self-coherent receiver based on a thin dielectric metasurface and a photodetector array (PDA). With a single 1.05-$μ$m-thick metasurface device fabricated on a compact silicon-on-quartz chip, we implement functionalities of all the necessary passive components: a 1$\times$3 splitter, three polarization beam splitters with different polarization bases, and six focusing lenses. Combined with a high-speed PDA, we demonstrate self-coherent transmission of 20-GBd 16-ary quadrature amplitude modulation (16QAM) and 50-GBd quadrature phase-shift keying (QPSK) signals over a 25-km single-mode fiber. Owing to the surface-normal configuration, it can easily be scaled to receive spatially multiplexed channels from a multicore fiber or a fiber bundle, enabling compact and low-cost receiver modules for the future highly parallelized self-coherent systems.
Measurement of thermally ablated lesions in sonoelastographic images using level set methods (2008)

The capability of sonoelastography to detect lesions based on elasticity contrast can be applied to monitor the creation of thermally ablated lesion. Currently, segmentation of lesions depicted in sonoelastographic images is performed manually which can be a time consuming process and prone to significant intra- and inter-observer variability. This work presents a semi-automated segmentation algorithm for sonoelastographic data. The user starts by planting a seed in the perceived center of the lesion. Fast marching methods use this information to create an initial estimate of the lesion. Subsequently, level set methods refine its final shape by attaching the segmented contour to edges in the image while maintaining smoothness. The algorithm is applied to <i>in vivo</i> sonoelastographic images from twenty five thermal ablated lesions created in porcine livers. The estimated area is compared to results from manual segmentation and gross pathology images. Results show that the algorithm outperforms manual segmentation in accuracy, inter- and intra-observer variability. The processing time per image is significantly reduced.
Mechanism of cell death induced by magnetic hyperthermia with nanoparticles of γ-MnxFe2–xO3 synthesized by a single step process (2007)

Magnetic nanoparticles of γ-MnxFe2–xO3 (0 ≤ x ≤ 1.3) have been synthesized successfully using a single step process wherein the respective inorganic salts were thermally decomposed in ethylene glycol at 200 °C. Single phase formation is evident in the as prepared dried samples without any further treatment. XRD line broadening along with TEM suggest that the particle size is below 30 nm. Both the magnetic and XRD data support the substitution of Mn3+ ions at the tetrahedral site of γ-Fe2O3. Improved magnetization value (78 emu g–1) is obtained for the sample with x = 0.2 compared to one with x = 0 (62 emu g–1) if measured at 20 kOe. Aqueous suspensions of the sample with x = 0.2 were prepared using a polymer, Acrypol 934, with an aim to examine the possible use of these suspensions in the magnetic hyperthermia treatment of cancer. These suspensions were found to be biocompatible at concentration as high as 3.75 mg mL–1 of culture media. Hyperthermia induced by the application of an AC magnetic field in the presence of the above suspension caused HeLa cell death. The cell death was found to be proportional to the quantity of the particles and the duration of application of the AC magnetic field. Following hyperthermia treatment, cells showed varying degrees of membrane blebbing with significant disruption of the actin and tubulin cytoskeletons. The apparent disruption of the actin and microtubule cytoskeletons of cells might be responsible for the death of cells following hyperthermia treatment. These observations suggest that the suspension of these particles may be evaluated for magnetic hyperthermia treatment of cancer.
Asymmetrical effects of cortical ablation on brain monoamines in mice (1991)

Neurochemical changes induced by right or left cortical ablation which have previously been described to have immunological effects were investigated in mice. Catecholamine and indolamine levels were determined in the contralateral cortex and in subcortical structures involved in immunoregulation 14 and 60 days after unilateral cortical ablation. Unilateral cortical ablation induced profound and widespread changes in the contralateral cortex but also in subcortical regions of both sides at 14 days after surgery. Lesions of the left neocortex appeared mainly to affect the activity of serotoninergic inputs to the right neocortex, whereas ablations of the right cortex influenced the activity of the catecholaminergic inputs to the left. Sixty days after surgery, modifications in monoamine levels were observed only in the ipsilateral, but not contralateral, subcortical regions, the only exception being that DA turnover in the tuberoinfundibular system remained lowered in both hemispheres after either right or left cortical ablations. Furthermore, some asymmetrical effects of cortical lesions depended on functional brain lateralization as assessed by paw preference. It may be hypothesized that some neurochemical modifications induced by unilateral cortical lesions are, at least partially, responsible for the immunological perturbations observed after cortical ablation.
Urban Mobility Lab Amsterdam: Begrijpen hoe mobiliteit werkt (2015)

Bereikbaarheid en daarmee mobiliteit en transport systemen zijn van vitaal belang van onze steden en regio’s. Verkeer en vervoer spelen een cruciale rol in het mogelijk maken van activiteiten voor mensen en bedrijven. Maatregelen, ingrepen en innovaties laten historisch een verbetering van de bereikbaarheid zien en daarmee van de vrijheid van het uitvoeren van activiteiten op de plaats en tijdstip naar keuze. Dit faciliteert economische groei. Tegelijk staat de groei van mobiliteit op gespannen voet met de leefbaarheid, veiligheid en uiteindelijk ook bereikbaarheid. De relaties tussen economische ontwikkeling, stedelijke planning en bereikbaarheid zijn complex en dynamisch. Belangrijkste reden omdat ze afhangen van gedrag en keuzes van miljoenen kleine en grote keuzes van mensen in de rol van bijv. forens, inwoner, toerist, maar ook politicus en bestuurder. De complexe interacties tussen alle mensen en daarbij hun beslissingen maken het moeilijk keuzes te baseren op verwachtingen voor de toekomst. Om onze inzichten op dit front te vergroten en daarmee beter te kunnen inschatten wat effecten van keuzes speelt data naar onze mening een cruciale rol. Om die reden hebben we het Urban Mobility Lab ontwikkeld. Dit is een project van de derde universiteit van onze hoofdstad: het Amsterdam Institute voor Advanced Metropolitan Solutions (AMS). Het urban mobility lab is een proeftuin vol data over vervoerpatronen in Amsterdam. Daar leren studenten en onderzoekers de kracht van het bewerken, combineren en visualiseren van data. Het Urban Mobility Lab verzamelt zoveel mogelijk data over voetgangers, fietsers, autoverplaatsingen en ov. Multimodaal dus. Belangrijk doel is het interpreteren van de data en kennis ontwikkelen over ons mobiliteitsgedrag. Waarom kiezen mensen voor de auto of de fiets? Welke variabelen spelen een rol bij routekeuze binnen het ov? Hoe werkt de keten fiets-ov? Hoe gedragen mensen zich als ze naar werk gaan, of een evenement bezoeken? Na deze belangrijke stap volgt theorievorming en modellering: hoe kunnen we ons gedrag (wiskundig) beschrijven en modelleren ter vereenvoudiging van de complexe werkelijkheid? Met andere woorden: we gaan vooruitkijken en kunnen gaan sturen. Uiteraard ontwikkelt het Urban Mobility Lab geen alwetende glazen bol. Helaas niet. Steeds realistischere what-if-analyses levert het lab wel. Wat gebeurt er als we een bus vervangen door een tram of andersom? Wat is de invloed van de automatische auto op ov- en fietsgebruik? Tijdens het CVS zal er in de presentatie naast de aanpak uitgebreid stil worden gestaan bij de eerste resultaten en vervolgstappen.