gebhart/patrepeval huggingface dataset:
DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes (2020)

We present DeepVesselNet, an architecture tailored to the challenges faced when extracting vessel trees and networks and corresponding features in 3-D angiographic volumes using deep learning. We discuss the problems of low execution speed and high memory requirements associated with full 3-D networks, high-class imbalance arising from the low percentage (<3%) of vessel voxels, and unavailability of accurately annotated 3-D training data-and offer solutions as the building blocks of DeepVesselNet. First, we formulate 2-D orthogonal cross-hair filters which make use of 3-D context information at a reduced computational burden. Second, we introduce a class balancing cross-entropy loss function with false-positive rate correction to handle the high-class imbalance and high false positive rate problems associated with existing loss functions. Finally, we generate a synthetic dataset using a computational angiogenesis model capable of simulating vascular tree growth under physiological constraints on local network structure and topology and use these data for transfer learning. We demonstrate the performance on a range of angiographic volumes at different spatial scales including clinical MRA data of the human brain, as well as CTA microscopy scans of the rat brain. Our results show that cross-hair filters achieve over 23% improvement in speed, lower memory footprint, lower network complexity which prevents overfitting and comparable accuracy that does not differ from full 3-D filters. Our class balancing metric is crucial for training the network, and transfer learning with synthetic data is an efficient, robust, and very generalizable approach leading to a network that excels in a variety of angiography segmentation tasks. We observe that sub-sampling and max pooling layers may lead to a drop in performance in tasks that involve voxel-sized structures. To this end, the DeepVesselNet architecture does not use any form of sub-sampling layer and works well for vessel segmentation, centerline prediction, and bifurcation detection. We make our synthetic training data publicly available, fostering future research, and serving as one of the first public datasets for brain vessel tree segmentation and analysis.
Can Patients with Parkinson’s Disease Use Dry Powder Inhalers during Off Periods? (2015)

Because of its rapid onset of action, pulmonary administration of levodopa is an interesting alternative to oral administration for the rescue treatment of Parkinson's disease patients in an off period. We studied the ability of Parkinson's disease patients to operate a dry powder inhaler (DPI) correctly during an off period. We used an instrumented test inhaler with three different resistances to air flow to record flow curves and computed various inhalation parameters. We observed that all (13) patients were able to generate pressure drops > 2 kPa over the highest resistance and 10 out of 13 patients achieved at least 4 kPa. Inhaled volumes (all resistances) varied from 1.2 L to 3.5 L. Total inhalation time and the time to peak inspiratory flow rate both decreased with decreasing inhaler resistance. Twelve out of thirteen patients could hold their breath for at least five seconds after inhalation and nine could extend this time to ten seconds. The data from this study indicate that patients with Parkinson's disease will indeed be able to use a dry powder inhaler during an off period and they provide an adequate starting point for the development of a levodopa powder inhaler to treat this particular patient group.
Synthese von N‐Maleoyl‐aminosäuren und ‐peptiden (1985)

Synthesis of N‐Maleoyl‐aminoacids and ‐peptides N‐Maleoyl‐aminoacid‐N′‐hydroxysuccinimidesters 3 or N‐maleoyl‐aminobenzoic acids 5 are synthesized from N‐maleyl‐aminoacids 1 on different ways. N‐maleoyl‐aminobenzoic‐4‐nitro‐phenyl‐,‐2‐nitro‐phenyl‐or 2,4‐dinitro‐phenylesters 6 , 7 and 8 will be obtained from 1 or 5 . o‐Mercapto‐aniline, thiourea or cysteine react with 5 to benzothiazines 9 , thiazolidines 10 and 1,4‐thiazines 11 . from 5 the peptides 12 are yielded. The pentapeptide 13 are formed from 12 by addition of glutathione.
Android hacker's handbook (2014)

The first comprehensive guide to discovering and preventing attacks on the Android OS As the Android operating system continues to increase its share of the smartphone market, smartphone hacking remains a growing threat. Written by experts who rank among the world's foremost Android security researchers, this book presents vulnerability discovery, analysis, and exploitation tools for the good guys. Following a detailed explanation of how the Android OS works and its overall security architecture, the authors examine how vulnerabilities can be discovered and exploits developed for various syst
Catalytic action of azolium salts. I. Aroylation of 4-chloro-1H-pyrazolo(3,4-d)pyrimidines with aromatic aldehydes catalyzed by 1,3-dimethylbenzimidazolium iodide. (1990)

When a mixture of 4-chloro-1-phenyl-1H-pyrazolo[3, 4-d]pyrimidine (9), aromatic aldehyde (5), sodium hydride, and a catalytic amount of 1, 3-dimethylbenzimidazolium iodide (4) in tetrahydrofuran was refluxed, the nucleophilic aroylation occurred, resulting in the formation of the aryl 1-phenyl-1H-pyrazolo[3, 4-d]pyrimidin-4-yl ketones (11).Similar reaction of 4-chloro-1-methyl-1H-pyrazolo[3, 4-d]pyrimidine (10) gave the corresponding aryl 1-methyl-1H-pyrazolo[3, 4-d]pyrimidin-4-yl ketones (12) in moderate yields. Use of dimethylformamide or dimethyl sulfoxide in the above reaction reduced the necessary reaction time and reaction temperature. A plausible reaction pathway for the formation of the ketones 11 and 12 involving the catalytic action of 4 is proposed.
Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease (2011)

The attachment of ubiquitin (Ub) and the Ub-like (Ubl) molecule interferon-stimulated gene 15 (ISG15) to cellular proteins mediates important innate antiviral responses. Ovarian tumor (OTU) domain proteases from nairoviruses and arteriviruses were recently found to remove these molecules from host proteins, which inhibits Ub and ISG15-dependent antiviral pathways. This contrasts with the Ub-specific activity of known eukaryotic OTU-domain proteases. Here we describe crystal structures of a viral OTU domain from the highly pathogenic Crimean-Congo haemorrhagic fever virus (CCHFV) bound to Ub and to ISG15 at 2.5-Å and 2.3-Å resolution, respectively. The complexes provide a unique structural example of ISG15 bound to another protein and reveal the molecular mechanism of an ISG15 cross-reactive deubiquitinase. To accommodate structural differences between Ub and ISG15, the viral protease binds the β-grasp folds of Ub and C-terminal Ub-like domain of ISG15 in an orientation that is rotated nearly 75° with respect to that observed for Ub bound to a representative eukaryotic OTU domain from yeast. Distinct structural determinants necessary for binding either substrate were identified and allowed the reengineering of the viral OTU protease into enzymes with increased substrate specificity, either for Ub or for ISG15. Our findings now provide the basis to determine in vivo the relative contributions of deubiquitination and deISGylation to viral immune evasion tactics, and a structural template of a promiscuous deubiquitinase from a haemorrhagic fever virus that can be targeted for inhibition using small-molecule-based strategies.
Culture and adenoviral infection of adult mouse cardiac myocytes: methods for cellular genetic physiology (2000)

Rapid development of transgenic and gene-targeted mice and acute genetic manipulation via gene transfer vector systems have provided powerful tools for cardiovascular research. To facilitate the phenotyping of genetically engineered murine models at the cellular and subcellular levels and to implement acute gene transfer techniques in single mouse cardiomyocytes, we have modified and improved current enzymatic methods to isolate a high yield of high-quality adult mouse myocytes (5.3 +/- 0.5 x 10(5) cells/left ventricle, 83.8 +/- 2.5% rod shaped). We have also developed a technique to culture these isolated myocytes while maintaining their morphological integrity for 2-3 days. The high percentage of viable myocytes after 1 day in culture (72.5 +/- 2.3%) permitted both physiological and biochemical characterization. The major functional aspects of these cells, including excitation-contraction coupling and receptor-mediated signaling, remained intact, but the contraction kinetics were significantly slowed. Furthermore, gene delivery via recombinant adenoviral infection was highly efficient and reproducible. In adult beta(1)/beta(2)-adrenergic receptor (AR) double-knockout mouse myocytes, adenovirus-directed expression of either beta(1)- or beta(2)-AR, which occurred in 100% of cells, rescued the functional response to beta-AR agonist stimulation. These techniques will permit novel experimental settings for cellular genetic physiology.
Synthesis and reactivity of a bis-sultone cross-linker for peptideconjugation and [<sup>18</sup>F]-radiolabelling via unusual “double click” approach (2011)

A novel homobifunctional cross-linker based on a bis-sultone benzenic scaffold was synthesised. The potential utility of this bioconjugation reagent was demonstrated through the preparation of an original prosthetic group suitable for the [(18)F]-labelling of peptides. The labelling strategy is based on the nucleophilic fluorination via the ring-opening of a first sultone moiety followed by the nucleophilic ring-opening of the second remanent sultone by a reactive amine of the biopolymer. Beyond the one-step radiolabelling of the peptide, the second main advantage of this strategy is the release of free sulfonic acid moieties making the separation of the targeted [(18)F]-tagged sulfonated compound from its non-sulfonated precursor easier and thus faster. This first report of the successful use of a bis-sultone moiety as a versatile bioconjugatable group was demonstrated through a comprehensive reactivity study involving various nucleophiles, especially those commonly found in biopolymers. An illustrative example, highlighting the potential of this unusual and promising "double click" conjugation approach, was devoted to the radiolabelling of a biological relevant peptide.
Optimized configuration of a tactile sensor system for flexible grippers (2017)

Autonomous grasping operations in dynamical environments are key elements of solutions for Factory-of-the-Future scenarios. The manipulator has to cope with a broad variety of objects with different shapes, materials and uncertain poses but at the same time it should provide reliable grasping and placement operations. Within this context, tactile sensors mounted directly on the grippers are a promising solution for monitoring the grasping process. They operate independently from light or line of sight configurations, thus offer a new object detection modality, besides optical-based systems. We receive an imprint of the grasped object with a spatial resolution according to the sensor pattern. However, in case of grippers with a flexible structure and material, this method generates spurious measurements if the gripper is deformed during a manipulation process. This effect disturbs the evaluation of the gripper's state or object position. In this paper, we develop the specification of a tailored tactile sensor configuration able to handle gripper deformations. Based on the results we present a proof-of-concept implementation.
Mechanical Properties Analysis of Super Early-Strength Composite Fiber Concrete after High Temperature (2014)

Experimental method is applied to analysis the mechanical properties of super early-strength composite fiber concrete on high temperature. Specimen are heated to in the stove at different temperatures for 30 Minutes, then the axial compressive strength can be measured. The experimental results showed that: the high temperature mechanical properties of materials decreased significantly; compared to ordinary concrete specimen, the mechanical properties of super early-strength composite fiber concrete decline slower.
Hybrid solvation models for bulk, interface, and membrane: Reference interaction site methods coupled with density functional theory (2017)

We present two hybrid solvation models for the calculation of the solvation structure with model 1 in a confined nanospace in bulk materials and model 2 at solid/liquid interfaces where an electrode is in contact with an electrolyte and a membrane is immersed into a solution. The hybrid theory is based on the reference interaction site method (RISM) for the solvent region. The electronic structure of a bulk material, an electrode, and a membrane is treated by density functional theory with the plane-wave basis and pseudopotentials technique. For model 1, we use the three-dimensional RISM (3D-RISM) by imposing a 3D periodic boundary condition on the system. However, for model 2, we reformulate the RISM by means of a two-dimensional boundary condition parallel to the surface and an open boundary condition normal to the surface. Four benchmark calculations are performed for the formaldehyde-water system, water packed into a zeolite framework, a NaCl solution in contact with an Al electrode, and an Al thin film immersed in a NaCl solution with different concentrations. The calculations are shown to be efficient and stable. Because of the flexibility of the RISM theory, the models are considered to be applicable to a wide range of solid/liquid interfaces.
The effect of cicloxolone sodium on the replication in cultured cells of adenovirus type 5, reovirus type 3, poliovirus type 1, two bunyaviruses and Semliki Forest virus (1992)

The effect of cicloxolone sodium (CCX) on the replication of typical representatives of different virus families [adenovirus type 5 (Ad-5), reovirus type 3 (Reo-3), Bunyamwera and Germiston viruses, poliovirus type 1 (Polio-1) and Semliki Forest virus (SFV)] in tissue culture was investigated. The Golgi apparatus inhibitor monensin (Mon) and CCX were shown to have analogous effects on some aspects of virus replication. Although the Mon-like effect of CCX played no role in the antiviral activity against Ad-5, Reo-3 or Polio-1, it could entirely account for the antiviral activity against the Bunyamwera and Germiston viruses, for which inhibition of glycoprotein processing was responsible for the antiviral activity. In the case of SFV, the Mon-like activity of CCX caused cytoplasmic assembly of fully infectious SFV within vacuoles and thus impaired virus release without altering total infectious virus yield. Fewer Ad-5 and Reo-3 progeny were produced in the presence of the drug. CCX had a dose-dependent biphasic effect on the particle:p.f.u. ratio of the Reo-3 yield. At low CCX concentration (<50 µm) the virus yield contained poor quality, non-infectious virus, but at higher CCX concentration (⩾ 100 µm) low quality virus could no longer be successfully assembled. We conclude that the antiviral effect can be manifested in three ways: (i) by a reduction in the virus particle yield produced; (ii) by a loss of quality (relative infectivity); (iii) by a virucidal effect of the drug. We have previously defined three CCX sensitivity classes. Mechanisms (i), (ii) and (iii) operate against viruses belonging to class CCXs-1 [herpes simplex virus (HSV) type 1, HSV-2 and vesicular stomatitis virus], but essentially only (i) and (ii) affect Reo-3 (CCXs-2), whereas (i) and possibly (iii) affect Ad-5 (CCXs-2). In the case of SFV (CCXs-3) none of these mechanisms operate, but relocation of assembled virus is found.
Constructing Mie‐Scattering Porous Interface‐Fused Perovskite Films to Synergistically Boost Light Harvesting and Carrier Transport (2017)

Abstract Light harvesting (LH) and carrier transport abilities of a photoactive layer, which are both crucial for optoelectronic devices such as solar cells and photodetectors (PDs), are typically hard to be synergistically improved. Taking perovskite as an example, a freeze‐drying recrystallization method is used to construct porous films with improvements of both LH and carrier transport ability. During the freeze‐drying casting process, the rapid solvent evaporation produces massive pores, the sizes of which can be adjusted to exploit the Mie scattering for enhancement of the LH ability. Meanwhile, owing to the strong iconicity, the interface between perovskite nanocrystals fused during recrystallization, which favors carrier transport. Subsequently, PDs based on these Mie porous and interface‐fused films show a high on/off ratio of more than 10 4 and an external quantum efficiency value of 658 % under 9 V bias and 520 nm light irradiation.
Tree-Structured Multiple Description Coding for Multiview Mobile TV and Camera-Phone Networks (2011)

Since multiview video communications facilitate the selection of several camera views of a given scene, it may be deemed to be a promising technique for mobile television and camera-phone networks. Similar to conventional single-view video, multiview video also suffers from packet loss events imposed by network congestion. Multiple description coding (MDC) constitutes an attractive candidate solution for mitigating the packet loss events in conventional video communications. Hence it may also be deemed to be an attractive solution for multiview video. In this paper, we propose a novel tree-structured MDC (T-MDC) scheme, which can be readily implemented with the aid of arbitrary video codecs, including multiview codecs. Moreover, the proposed philosophy enables the flexible creation of a variable number of unequal importance descriptions. Finally, we will conceive a joint multiple description coding and multiview video coding (MVC) scheme. We compare two specific tree- structured MDC schemes, namely a so-called height- one complete tree-structured MDC (HOCT-MDC) and a binary tree-structured MDC (BT-MDC) scheme, which we benchmarked against simulcasting aided single description coding in the context of both single and multiview video.
Styrene 4‐vinylbenzocyclobutene copolymer for microelectronic applications (2008)

Abstract Styrene and 4‐vinylbenzocyclobutene (vinyl‐BCB) random copolymers were prepared by free radical polymerization and studied for suitability as a dielectric material for microelectronic applications. The percentage of vinyl‐BCB in the copolymer was varied from 0 to 26 mol % to optimize the physical and mechanical properties of the cured copolymer as well as the cost. Copolymer in which 22 mol % of vinyl‐BCB was incorporated along with styrene produced a thermoset polymer which, after cure, did not show a T g before decomposition at about 350 °C. The polymeric material has a very low dielectric constant, dissipation factor, and water uptake. The fracture toughness of the copolymer was improved with the addition of 20 wt % of a star‐shaped polystyrene‐ block ‐polybutadiene. Blends of the poly(styrene‐ co ‐vinyl‐BCB) with the thermoplastic elastomer provided material that maintained high T g of the cured copolymer with only a slight decrease in thermal stability. The crosslinked styrenic polymer and toughened blends possess many properties that are desirable for high frequency‐high speed mobile communication applications. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2799–2806, 2008
The microRNA cluster miR-106b~25 regulates adult neural stem/progenitor cell proliferation and neuronal differentiation (2011)

In adult mammals, neural stem cells (NSCs) generate new neurons that are important for specific types of learning and memory. Controlling adult NSC number and function is fundamental for preserving the stem cell pool and ensuring proper levels of neurogenesis throughout life. Here we study the importance of the microRNA gene cluster miR-106b~25 (miR-106b, miR-93, and miR-25) in primary cultures of neural stem/progenitor cells (NSPCs) isolated from adult mice. We find that knocking down miR-25 decreases NSPC proliferation, whereas ectopically expressing miR-25 promotes NSPC proliferation. Expressing the entire miR-106b~25 cluster in NSPCs also increases their ability to generate new neurons. Interestingly, miR-25 has a number of potential target mRNAs involved in insulin/insulin-like growth factor-1 (IGF) signaling, a pathway implicated in aging. Furthermore, the regulatory region of miR-106b~25 is bound by FoxO3, a member of the FoxO family of transcription factors that maintains adult stem cells and extends lifespan downstream of insulin/IGF signaling. These results suggest that miR-106b~25 regulates NSPC function and is part of a network involving the insulin/IGF-FoxO pathway, which may have important implications for the homeostasis of the NSC pool during aging.
Aircraft Electric Propulsion Systems Applied Research at NASA (2015)

Researchers at NASA are investigating the potential for electric propulsion systems to revolutionize the design of aircraft from the small-scale general aviation sector to commuter and transport-class vehicles. Electric propulsion provides new degrees of design freedom that may enable opportunities for tightly coupled design and optimization of the propulsion system with the aircraft structure and control systems. This could lead to extraordinary reductions in ownership and operating costs, greenhouse gas emissions, and noise annoyance levels. We are building testbeds, high-fidelity aircraft simulations, and the first highly distributed electric inhabited flight test vehicle to begin to explore these opportunities.
“Squirrel” Primer-Based PCR Assay for Direct and Targeted Sanger Sequencing of Short Genomic Segments (2017)

Currently, short DNA segments of sub-100 bp can be sequenced either directly by next-generation sequencing and pyrosequencing, which are expensive, or indirectly, <i>via</i> Sanger sequencing combined with the cumbersome and failure-prone plasmid cloning. To circumvent these issues, we have generated a novel sequencing-purposed PCR assay using long-tailed primers (squirrel primers) to Sanger sequence directly sub-100 bp genomic amplicons. Squirrel primers, 40-65 nt in length, were used to amplify 51-93 bp long genomic sequences of <i>KRAS</i> exons 2 and 3, <i>BRAF</i> exon 15, <i>PI3K catalytic subunit alpha</i> exon 20, and <i>phosphatase and tensin homolog</i> exon 3 from colorectal cancer (CRC) cell lines and preamplified clinical CRC samples with known mutation status by PCR. Following this, a short second pair of primers that bind at the 5' region of the long tails was used for sequencing on the 3130 × l ABI Prism Genetic Analyzer. The sequencing data were analyzed <i>via</i> FinchTV software. High-quality sequencing data were obtained from 51 to 93 bp long genomic sequences with our novel PCR assay, with capture of all of the target sequences in all of the samples in both the forward and reverse directions and confirmation of the mutation status of the CRC samples. Whereas the sequencing quality was independent of the template type, it showed a squirrel primer tail length-dependent pattern. Our novel PCR assay for direct and targeted Sanger sequencing of short genomic segments has potential applications in focused molecular/genetic profiling of cancer in research and diagnostics fields in which fragmented DNA, such as circulating tumor DNA and archival tissue DNA, are used as starting templates.