gebhart/patrepeval huggingface dataset:
Yttrium(III)-Containing Tungstoantimonate(III) Stabilized by Tetrahedral WO42− Capping Unit, [{Y(α-SbW9O31(OH)2)(CH3COO)(H2O)}3(WO4)]17− (2010)

The yttrium(III)-containing tungstoantimonate(III) [{Y(α-SbW(9)O(31)(OH)(2))(CH(3)COO)(H(2)O)}(3)(WO(4))](17-) (1) has been synthesized in a simple one-pot reaction of Y(3+) ions with [α-SbW(9)O(33)](9-) and WO(4)(2-) in a 3:3:1 molar ratio in 1 M LiOAc/AcOH buffer at pH 5.3. Polyanion 1 is composed of three (α-SbW(9)O(33)) units linked by three Y(3+) ions and a capping, tetrahedral WO(4)(2-) capping unit, resulting in an assembly with C(3v) symmetry. The hydrated ammonium-sodium salt of 1 was investigated in the solid state by single-crystal XRD, FT-IR spectroscopy, thermogravimetric and elemental analyses, and in solution by multinuclear NMR spectroscopy.
New Catalysts for the Hydrogen and Oxygen Evolution Reactions (2015)

We have recently introduced corrole metal complexes (metallocorroles) as catalysts for various reactions, including those that are of prime importance for water splitting into its elements- the hydrogen and oxygen evolution reactions. A careful choice of substituents on the corrole ligand and the kind of metal ion chelated by them allows for lowering of the electrocatalytic overpotential and increasing reactivity. An arsenal of electrochemical and spectroscopic methodologies, which in the case of metallocorroles is very rich, was applied for acquiring highly valuable information about the mechanisms of action (see upper part of the Figure for the hydrogen evolution reaction). Preliminary results regarding water oxidation with the aid of immobilized catalysts (see lower part of the Figure) will be presented as well. REFERENCES “Cobalt Corrole Catalyst for Efficient Hydrogen Evolution Reaction from H 2 O under Ambient Conditions: Reactivity, Spectroscopy and DFT Calculations”, Inorg. Chem. 2013 , 52 , 3381-3387. "The Cobalt Corrole Catalyzed Hydrogen Evolution Reaction: Surprising Electronic Effects and Characterization of Key Reaction Intermediates" Chem. Commun. 2014 , 50 , 2725-2727. Figure 1
Measurement of the production cross section for W-bosons in association with jets in pp collisions at √s = 7 TeV with the ATLAS detector (2011)

This Letter reports on a first measurement of the inclusive W+jets cross section in proton-proton collisions at a centre-of-mass energy of 7 TeV at the LHC, with the ATLAS detector. Cross sections, in both the electron and muon decay modes of the W-boson, are presented as a function of jet multiplicity and of the transverse momentum of the leading and next-to-leading jets in the event. Measurements are also presented of the ratio of cross sections σ(W+≥n)/σ(W+≥n-1) for inclusive jet multiplicities n=1-4. The results, based on an integrated luminosity of 1.3 pb-1, have been corrected for all known detector effects and are quoted in a limited and well-defined range of jet and lepton kinematics. The measured cross sections are compared to particle-level predictions based on perturbative QCD. Next-to-leading order calculations, studied here for n≤2, are found in good agreement with the data. Leading-order multiparton event generators, normalized to the NNLO total cross section, describe the data well for all measured jet multiplicities. © 2011 CERN Elsevier B.V.
High-Pressure Studies for Iron-Based Superconductors (2011)

Electrical and magnetic measurements for 1111 type Ca(Fe 1- x Co x )AsF and 11 type Fe(Se 1- x Te x ) have been performed under high pressure. Superconductivity appeared with Co substitution for Ca(Fe 1- x Co x )AsF. For superconducting Ca(Fe 1- x Co x )AsF, pressure does not enhance the superconductivity so much. Disorder induced by the Co substitution in the FeAs superconducting layer is considered to be related to the pressure dependence of T c . Pressure-induced superconductivity was observed for x = 0.0 and 0.05. For Fe(Se 1- x Te x ), T c exhibits the maximum value at x = 0.5 and decreases with increasing Te concentration. The enhancement of T c with pressure was suppressed by increasing Te concentration for Fe(Se 1- x Te x ) ( x ≧0.5). For non-superconducting FeTe, pressure-induced superconductivity was not detected under high pressure up to 19 GPa.
Guided model checking for programs with polymorphism (2009)

Exhaustive model checking search techniques are ineffective for error discovery in large and complex multi-threaded software systems. Distance estimate heuristics guide the concrete execution of the program toward a possible error location. The estimate is a lower-bound computed on a statically generated abstract model of the program that ignores all data values and only considers control flow. In this paper we describe a new distance estimate heuristic that efficiently computes a tighter lower-bound in programs with polymorphism when compared to the state of the art distance heuristic. We statically generate conservative distance estimates and refine the estimates when the targets of dynamic method invocations are resolved. In our empirical analysis the state of the art approach is computationally infeasible for large programs with polymorphism while our new distance heuristic can quickly detect the errors.
Using genetic algorithms to improve the visual quality of fractal plants generated with CSG-PL-Systems (1996)

To confirm the predictive value of calcifications in thyroid nodules as a risk factor for malignancy and to detect specific aspects for tumours, in a set of 175 patients--30 papillary carcinoma (PC) and 145 multinodular goiters (MNG) with dominant nodule--calcifications were detected by ultrasound scan. Calcifications were significantly more frequent in PC than in MNG (40% vs 20.7% p < 0.05) but their considered characteristics (size, number, position, location in the gland, sonographic features of the nodule) did not show any particular difference between PC and MNG. The frequency of calcifications in our series was higher in older patients (mean age 58.7 +/- 13.3 vs 51.1 +/- 12.7 in patients without calcifications, p < 0.001) and this could imply that their onset is time-dependent. Calcifications can be a useful indicator of enhanced risk, to be considered in the overall process of surgical decision making.
In Vitro and In Vivo Osteogenesis of Porcine Skin-Derived Mesenchymal Stem Cell–like Cells with a Demineralized Bone and Fibrin Glue Scaffold (2009)

In vitro and in vivo osteogenesis of skin-derived mesenchymal stem cell-like cells (SDMSCs) with a demineralized bone (DMB) and fibrin glue scaffold were compared. SDMSCs isolated from the ears of adult miniature pigs were evaluated for the expression of transcriptional factors (Oct-4, Sox-2, and Nanog) and MSC marker proteins (CD29, CD44, CD90, and vimentin). The isolated SDMSCs were cocultured in vitro with a mixed DMB and fibrin glue scaffold in a nonosteogenic medium for 1, 2, and 4 weeks. Osteonectin, osteocalcin, and Runx2 were expressed during the culture period and reached maximum at 2 weeks after in vitro coculture. von Kossa-positive bone minerals were also noted in the cocultured medium at 4 weeks. Autogenous porcine SDMSCs (1 x 10(7)) labeled with a tracking dye, PKH26, were grafted into the maxillary sinus with a DMB and fibrin glue scaffold. In the contralateral side, only a scaffold was grafted without SDMSCs (control). In vivo osteogenesis was evaluated from two animals euthanized at 2 and 4 weeks after grafting. In vivo PKH26 staining was detected in all the specimens at both time points. Trabecular bone formation and osteocalcin expression were more pronounced around the grafted materials in the SDMSC-grafted group compared with the control group. New bone generation was initiated from the periphery to the center of the grafted material. The number of proliferating cells increased over time and reached a peak at 4 weeks in both in vivo and in vitro specimens. These findings suggest that autogenous SDMSC grafting with a DMB and fibrin glue scaffold can serve as a predictable alternative to bone grafting in the maxillary sinus floor.
Linkage of scapuloperoneal spinal muscular atrophy to chromosome 12q24.1-q24.31 (1996)

Scapuloperoneal (SP) syndromes are heterogeneous neuromuscular disorders which are characterized by weakness in the distribution of shoulder girdle and peroneal muscles. SP syndromes can resemble facioscapulohumeral muscular dystrophy (FSH) due to scapular weakness or Charcot-Marie-Tooth disease (CMT) due to atrophy of peroneal muscles. Both neurogenic and myopathic SP syndromes have been described. Locus for the myopathic form of SP syndrome (scapuloperoneal muscular dystrophy, SPMD) has recently been assigned to chromosome 12q. We previously described a large New England kindred exhibiting an autosomal dominant neurogenic SP syndrome (scapuloperoneal spinal muscular atrophy, SPSMA). Disease expression was more severe and progressive in successive generations, which suggested genetic anticipation. We performed genetic linkage analysis of this family with microsatellite markers and excluded the loci for FSH, CMT, SPMD and SMA (spinal muscular atrophy) in our family. Linkage in our SPSMA family (lod score > 3) was established to seven microsatellite markers that map to chromosome 12q24.1-q24.31. The highest lod score with two-point linkage analysis was 6.67 (theta = 0.00) with marker D12S353. Multipoint analysis gave maximum lod scores of 7.38 between D12S354 and D12S79, and also 7.38 between D12S369 and NOS1 (neuronal nitric oxide synthase). The gene for SPSMA lies within the 19 cM interval between D12S338 and D12S366. This report establishes a locus for the neurogenic form of SP syndrome approximately 20 cM telomeric to the one described for the myopathic form of SP syndrome.
A Neuro-Inspired Autoencoding Defense Against Adversarial Perturbations (2020)

Deep Neural Networks (DNNs) are vulnerable to adversarial attacks: carefully constructed perturbations to an image can seriously impair classification accuracy, while being imperceptible to humans. While there has been a significant amount of research on defending against such attacks, most defenses based on systematic design principles have been defeated by appropriately modified attacks. For a fixed set of data, the most effective current defense is to train the network using adversarially perturbed examples. In this paper, we investigate a radically different, neuro-inspired defense mechanism, starting from the observation that human vision is virtually unaffected by adversarial examples designed for machines. We aim to reject L^inf bounded adversarial perturbations before they reach a classifier DNN, using an encoder with characteristics commonly observed in biological vision: sparse overcomplete representations, randomness due to synaptic noise, and drastic nonlinearities. Encoder training is unsupervised, using standard dictionary learning. A CNN-based decoder restores the size of the encoder output to that of the original image, enabling the use of a standard CNN for classification. Our nominal design is to train the decoder and classifier together in standard supervised fashion, but we also consider unsupervised decoder training based on a regression objective (as in a conventional autoencoder) with separate supervised training of the classifier. Unlike adversarial training, all training is based on clean images. Our experiments on the CIFAR-10 show performance competitive with state-of-the-art defenses based on adversarial training, and point to the promise of neuro-inspired techniques for the design of robust neural networks. In addition, we provide results for a subset of the Imagenet dataset to verify that our approach scales to larger images.
Draft Genome Assemblies of Ionic Liquid-Resistant Yarrowia lipolytica PO1f and Its Superior Evolved Strain, YlCW001 (2020)

Adaptive laboratory evolution of <i>Yarrowia lipolytica</i> PO1f in the benchmark ionic liquid (IL; 1-ethyl-3-methylimidazolium acetate) produced a superior IL-tolerant microorganism, strain YlCW001. Here, we report the genome sequences of PO1f and YlCW001 to study the robustness of <i>Y. lipolytica</i> and its potential use as a microbial platform for producing fuels and chemicals.
SLIC superpixels for efficient graph-based dimensionality reduction of hyperspectral imagery (2015)

Nonlinear graph-based dimensionality reduction algorithms such as Laplacian Eigenmaps (LE) and Schroedinger Eigenmaps (SE) have been shown to be very effective at yielding low-dimensional representations of hyperspectral image data. However, the steps of graph construction and eigenvector computation required by LE and SE can be prohibitively costly as the number of image pixels grows. In this paper, we propose pre-clustering the hyperspectral image into Simple Linear Iterative Clustering (SLIC) superpixels and then performing LE- or SE-based dimensionality reduction with the superpixels as input. We then investigate how different superpixel size and regularity choices yield trade-offs between improvements in computational efficiency and accuracy of subsequent classification using the low-dimensional representations.
Percutaneous right ventricular assist device–supported ventricular tachycardia ablation in a patient with severe right ventricular dysfunction (2019)

Catheter ablation is an established therapy for the management of ventricular tachycardia (VT) but can be complicated by hemodynamic decompensation. Left ventricular assist devices (LVADs) have been used to support VT ablation. Percutaneous right ventricular assist devices (pRVADs) are a recent addition to the therapeutic armamentarium for the treatment of patients with right ventricular (RV) failure and there is no published literature for their use during VT ablation. Here, we present a first report of a patient treated with pRVAD-supported ablation for refractory RV VT in the setting of severe RV dysfunction.
Further polymers derived from bisazlactones and tetraamino compounds (1989)

Abstract New polymers containing benzimidazole in the polymeric backbone were obtained from the reaction of bis(oxazolones) with known and with a novel aromatic tetraamine. The polymers have inherent viscosities in the range of 0.1‐0.4 dL/g (in DMF 30°C).
Analysis of the Pulmonary Vein Ostia using Cardiac 4DCT for Radiosurgical Ablation (2007)

A software tool to analyze 4D cardiac CT data sets for planning radiosurgical ablations in the heart is presented. Volume rendering and data processing are performed using a GPU. The user visualizes the data from inside the left atrium and defines the target in 3D using an intuitive user interface. A haptic input device lets the user measure motion at the ostia of the pulmonary veins for radiosurgical treatment planning. This tool has been used effectively for generating radiation treatment plans for animal studies.
Physicochemical Properties Altered by the Tail Group of Lipid Membranes Influence Huntingtin Aggregation and Lipid Binding (2022)

Huntington's disease is a neurodegenerative disorder caused by an expanded polyglutamine (polyQ) domain within the huntingtin protein (htt) that initiates toxic protein aggregation. Htt directly interacts with membranes, influencing aggregation and spurring membrane abnormalities. These interactions are facilitated by the 17 N-terminal residues (Nt17) that form an amphipathic α-helix implicated in both lipid binding and aggregation. Here, the impact of unsaturation in phospholipid tails on htt-lipid interaction and htt aggregation was determined. There was no correlation between the degree of htt-lipid complexation and the degree of htt aggregation in the presence of each lipid system, indicating that lipid systems with different properties uniquely alter the membrane-mediated aggregation mechanisms. Also, the association between Nt17 and membrane surfaces is determined by complementarity between hydrophobic residues and membrane defects and how easily the peptide can partition into the bilayer. Our results provide critical insights into how membrane physical properties influence downstream htt aggregation.
Bionanofabrication of Ordered Nanoparticle Arrays:  Effect of Particle Properties and Adsorption Conditions (2004)

Arrays of Au nanoparticles were created using the inherent repeating patterns of bacterial S-layer proteins. Bacterial self-assembling S-layer protein lattices display a highly repetitive surface structure that makes them particularly suitable as biotemplates to fabricate metallic/semiconducting nanostructures and arrays. One interesting S-layer for nanoparticle templating is the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans. This S-layer, displaying hexagonal (p6) symmetry, is comprised of a hexameric protein core unit with a central pore, surrounded by six relatively large openings ("vertex points"). In this work, the influences of particle properties and adsorption conditions on the formation of ordered arrays of 5-nm Au nanoparticles using HPI S-layers were investigated. Using transmission electron microscopy (TEM), it was found that the templating of citrate-capped Au nanoparticles on HPI layers under low ionic strength conditions resulted in hexagonal-packed ordered arrays with ∼18-nm interparticle spacings that corresponded with the pore-to-pore distance of the S-layer. Interestingly, nanoparticle binding occurs at the vertex points on the HPI layer and, due to repulsion forces, adsorption tends to be favored at every second vertex point. Upon increasing the ionic strength, ordered packing is still observed. However, because interparticle repulsions are less prominent, adsorption of nanoparticles occurs in virtually every available vertex point, resulting in the formation of a honeycomb-like pattern of nanoparticles extending throughout the HPI monolayer sheet. Combined with the results of additional investigations using either uncharged hydroxy-terminated particles or positively charged ferritin molecules, the experimental data suggest that the creation of ordered arrays through biotemplating of Au nanoparticles onto HPI S-layers depends on the electrostatic interactions between individual nanoparticles as well as the interaction with the HPI layer.
Poster - Thur Eve - 70: Automatic lung bronchial and vessel bifurcations detection algorithm for deformable image registration assessment (2014)

Purpose: To investigate an automatic bronchial and vessel bifurcations detection algorithm for deformable image registration (DIR) assessment to improve lung cancer radiation treatment. Methods: 4DCT datasets were acquired and exported to Varian treatment planning system (TPS) EclipseTM for contouring. The lungs TPS contour was used as the prior shape for a segmentation algorithm based on hierarchical surface deformation that identifies the deformed lungs volumes of the 10 breathing phases. Hounsfield unit (HU) threshold filter was applied within the segmented lung volumes to identify blood vessels and airways. Segmented blood vessels and airways were skeletonised using a hierarchical curve-skeleton algorithm based on a generalized potential field approach. A graph representation of the computed skeleton was generated to assign one of three labels to each node: the termination node, the continuation node or the branching node. Results: 320 ± 51 bifurcations were detected in the right lung of a patient for the 10 breathing phases. The bifurcations were visually analyzed. 92 ± 10 bifurcations were found in the upper half of the lung and 228 ± 45 bifurcations were found in the lower half of the lung. Discrepancies between ten vessel trees were mainly ascribed to large deformation and in regions where the HU varies. Conclusions: We established an automatic method for DIR assessment using the morphological information of the patient anatomy. This approach allows a description of the lung's internal structure movement, which is needed to validate the DIR deformation fields for accurate 4D cancer treatment planning.
Modified equivalent time sampling for improving precision of time-of-flight based localization (2013)

Applications based on precise indoor and urban area localization are becoming quite popular. The integration of localization in currently existing wireless data communication systems is especially interesting. The popularity comes from the possibility to economically use the same analog front-end for data communication and localization. In indoor environments, where the precision should be under 1 m, because of the limited sample rate of the A/D converters, range binning becomes the main source of errors. Noise is not so much a problem, because for systems used mainly in indoor scenarios, the SNR is usually quite good. One solution, which is used to mitigate range binning is oversampling. Since oversampling requires additional hardware complexity, we propose here a “modified equivalent time sampling” approach. With this approach, no oversampling data converters are needed. The same data converters used for data communication can be used for ranging, but some signal processing before transmission and after reception of the signal is needed. The achieved resolution of the distance measurements is comparable to the solution with oversampling data converters.
Transconductance Linearity Analysis of 1-D, Nanowire FETs in the Quantum Capacitance Limit (2013)

The impact of channel material and dimensionality on the linearity of nanowire transistors is studied theoretically. This paper also evaluates various scattering mechanisms in this context. While operating under 1-D transport conditions in the quantum capacitance limit, the achievable device linearity strongly depends on the details of the scattering mechanisms limiting the transport. Interestingly, it is not only the scattering length that determines the third-order intercept point but also the particular energy dependence of the dominant-scattering mechanism that needs to be considered. Our results provide critical insights for the choice of material to obtain the desired device linearity.
The same 50-kDa cellular protein binds to the negative regulatory elements of the interleukin 2 receptor alpha-chain gene and the human immunodeficiency virus type 1 long terminal repeat. (1989)

We have investigated the biochemical basis for negative regulation of interleukin 2 receptor alpha-chain (IL-2R alpha) gene expression. Transient transfection studies employing internally deleted forms of the IL-2R alpha promoter localized a negative regulatory element (NRE) between nucleotides -400 and -368 relative to the major distal transcription start (cap) site. This 31-base-pair (bp) element is involved in the attenuation of both basal and inducible IL-2R alpha promoter activity. Comparison of this IL-2R alpha NRE with other known regulatory motifs revealed an 11-bp core element (TTCATCCCAGG) that was strikingly similar to a protein-binding domain within the long terminal repeat of the type 1 human immunodeficiency virus (HIV-1). This viral domain has been previously implicated in the negative control of HIV-1 gene expression. In vitro protein-DNA binding studies demonstrated that the same constitutively expressed approximately 50-kDa protein (SP-50) specifically bound to both the IL-2R alpha and HIV-1 NRE core elements. Mutation of the 11-bp IL-2R alpha NRE core element, which disrupted protein binding, significantly augmented basal as well as Tax protein- or phorbol ester-induced IL-2R alpha promoter activity in vivo, suggesting that SP-50 functions as a transcriptional silencer.