gebhart/patrepeval huggingface dataset:
Heparin promotes fibrillation of most phenol-soluble modulin virulence peptides from Staphylococcus aureus (2021)

Phenol-soluble modulins (PSMs), such as α-PSMs, β-PSMs, and δ-toxin, are virulence peptides secreted by different Staphylococcus aureus strains. PSMs are able to form amyloid fibrils, which may strengthen the biofilm matrix that promotes bacterial colonization of and extended growth on surfaces (e.g., cell tissue) and increases antibiotic resistance. Many components contribute to biofilm formation, including the human-produced highly sulfated glycosaminoglycan heparin. Although heparin promotes S. aureus infection, the molecular basis for this is unclear. Given that heparin is known to induce fibrillation of a wide range of proteins, we hypothesized that heparin aids bacterial colonization by promoting PSM fibrillation. Here, we address this hypothesis using a combination of thioflavin T-fluorescence kinetic studies, CD, FTIR, electron microscopy, and peptide microarrays to investigate the mechanism of aggregation, the structure of the fibrils, and identify possible binding regions. We found that heparin accelerates fibrillation of all α-PSMs (except PSMα2) and δ-toxin but inhibits β-PSM fibrillation by blocking nucleation or reducing fibrillation levels. Given that S. aureus secretes higher levels of α-PSM than β-PSM peptides, heparin is therefore likely to promote fibrillation overall. Heparin binding is driven by multiple positively charged lysine residues in α-PSMs and δ-toxins, the removal of which strongly reduced binding affinity. Binding of heparin did not affect the structure of the resulting fibrils, that is, the outcome of the aggregation process. Rather, heparin provided a scaffold to catalyze or inhibit fibrillation. Based on our findings, we speculate that heparin may strengthen the bacterial biofilm and therefore enhance colonization via increased PSM fibrillation.
Pulse electrodeposition of 2.4 T Co/sub 37/Fe/sub 63/ alloys at nanoscale for magnetic recording application (2006)

Pulse deposition of 2.4 T Co/sub 37/Fe/sub 63/ alloy in photoresist features with 40 nm critical dimension and high aspect ratio is presented. The design of the pulse deposition parameters is described in terms of the transport limitations through the diffusion layer, electrochemical interface stability with respect to Fe(OH)/sub 3/ precipitation, and the optimum conditions for additive (Saccharin) adsorption. The alloy grain size and crystal structure in the nanoconfined electrode geometry is compared versus the thin film and relevant implications for magnetic recording are discussed. The 2.4 T Co/sub 38/Fe/sub 61/Pd/sub 1/ alloy is introduced as a possible way to improve the corrosion properties of 2.4 T Co/sub 37/Fe/sub 63/ alloy.
Investigations of an improved esophageal cancer diagnostics approach. (2015)

e15059 Background: For esophageal cancer, no viable non-invasive detection technologies are available today. In this investigation, a newly developed IVD cancer diagnostic technology named Cancer Differentiation Analysis Technology (CDA) was investigated for esophageal cancer detection. In a CDA technology, multi-level and multi-parameter information is collected using a medical device fabricated by Anpac Bio-Medical Science Co., Ltd. which measures information relating to both protein fragments and cellular signals in blood samples in a single test. Methods: Blood samples were collected in EDTA vacutainer tubes, with 49 esophageal cancer patients and 303 healthy individuals (control group). CDA data was then collected, and analysis was carried out. Results: The results showed significant statistical difference between esophageal cancer and control groups with P value < 0.05 (Table 1). Also, CDA values at different stages of esophageal cancer samples showed possible effectiveness using CDA technology for early stage esophageal cancer detection (P value < 0.05 between stage I esophageal cancer and control groups). In addition, using a reasonable cut-off value, its sensitivity and specificity are about 70% and 90%, respectively. Conclusions: CDA technology is a promising approach for esophageal cancer diagnostics including early stage diagnostics. Keywords: Esophageal Cancer; CDA Table 1 CDA Test Results. Group Sample Size CDA Mean (rel. units) CDA STDEV (rel. units) Control Group 303 33.7 9.1 Esophageal Cancer Group 49 52.4 11.0
Human Tissue Kallikrein Gene Transfer Induces Angiogenesis (2000)

74 Angiogenesis therapy is emerging as a new strategy for treatment of vascular disease, not susceptible of revascularization. As kinins are implicated in vascular protection and repair, we hypothesized that targeted potentiation of kinin-nitric oxide (NO) pathway may stimulate neo-vascularization. CD1 mice were IM injected with 3.6x10 8 plaque forming units of adenovirus (Ad) harboring human tissue kallikrein (HK) or β-galactosidase (LacZ) gene under the control of cytomegalovirus enhancer/promoter (CMV). Successful transduction of injected adductor skeletal muscle was documented at mRNA and protein level. HK expression reached a peak between 3 and 7 d and then declined to become undetectable at 28 d. Contralateral muscles and liver were not transduced. Immunohistochemical identification of endothelial cell antigen factor VIII combined with blinded morphometric analysis of capillary density revealed a marked angiogenic effect in HK-transduced muscle (1013±18 vs 518±15 n cap /mm 2 in LacZ-injected muscle at 28 d, P&lt;.001), whereas no angiogenic effect was seen in ipsilateral gastrocnemious or contralateral muscles. HK increased muscular kinin (60±12 vs 20±6 pg/g tissue in controls at 3 d, P&lt;.05), cAMP (1.02±0.06 vs 0.48±0.04 ng/mg prot, P&lt;.01) and cGMP levels (99±5 vs 68±5 fmol/mg prot, P&lt;.01). HK-induced angiogenic response was completely prevented by pharmacologic blockade of kinin B 1 or B 2 receptors, or inhibition of NO synthase, but not by cycloxygenase inhibition. Neovascularization was associated with a transient increase in muscular blood flow as determined by laser Doppler flowmetry. HK-induced neo-vascularization was stable and functionally utilitarian, as surgical induction of hindlimb ischemia 28 d after gene tranfer was followed by accelerated hemodynamic recovery of HK-injected muscle (perfusion ratio: 0.84±0.05 vs 0.68±0.03 in LacZ-injected muscle at 14 d, P&lt;.05). We conclude that (a) HK acts as an angiogenic factor via kinin-mediated stimulation of NO release, (b) neo-vascularization can preserve tissue from supervening ischemia. The discovery that HK has angiogenic activity may represent an important advancement in vascular medicine for therapeutic benefit.
Higher-Dimensional Signal Processing via Multiscale Geometric Analysis (2010)

Abstract : This project pursued a general theory for complex-valued multiscale signal and image modeling, processing, and analysis that is matched to singularity-rich data. Higher-dimensional signals that feature geometric manifold structures were of particular interest in developing theory and a practical toolset for analysis and processing. We pursued a three-pronged approach in creating new multiscale transforms, new geometric statistical models, and new manifold-based signal representations. The results of our research include (1) the Dual Tree Quaternion Wavelet, an efficient transform and analysis tool that features near shift invariance and linear computational complexity; (2) a geometric hidden Markov tree wavelet model, which accounts for geometric regularity by capturing the dependencies between complex wavelet coefficients along a contour; and (3) surflet representations of signal discontinuities with near optimal rate-distortion performance. These new tools have led to significant performance gains immediately applicable to a number of important Navy-relevant applications, including target detection and classification, image segmentation and fusion, and computer network traffic modeling.
Use of Ambulance Dispatch Calls for Surveillance of Severe Acute Respiratory Infections (2019)

Ambulance dispatches for respiratory syndromes reflect incidence of influenza-like illness in primary care. Associations are highest in children (15%-34% of respiratory calls attributable to influenza), out-of-office hours (9%), and highest urgency-level calls (9%-11%). Ambulance dispatches might be an additional source of data for severe influenza surveillance.
CanHap 501: Learning Haptic UX Design in Remote Teams (2021)

We describe the graduate-level CanHap 501 (wiki.canhaptics.ca) course, an introduction to the inception, creation and evaluation of haptic and multimodal human-computer interfaces. The course covers perceptual and attentional foundations, and emphasizes control and/or display of computed sensations and environments through haptic devices to users’ sense of touch for the purpose of haptic communication—e.g., signalling, social and affective touch, and sharing of control between humans and smart systems.
Mutation of chicken anemia virus VP2 differentially affects serine/threonine and tyrosine protein phosphatase activities (2005)

Novel dual-specificity protein phosphatases (DSPs), which catalyse the removal of phosphate from both phosphotyrosine and phosphoserine/phosphothreonine substrates, have recently been identified in two viruses within the family Circoviridae. Viral protein 2 (VP2) of chicken anemia virus (CAV) and ORF2 of TT virus have been shown to possess DSP activity in vitro. CAV VP2 is unusual in possessing two vicinal cysteines within the protein phosphatase signature motif. The first cysteine residue (C95) within the motif has been identified by mutagenesis as the essential catalytic cysteine. In this study, it was shown that virus mutated at this residue displayed a marked inhibition of growth, with titres reduced 10(4)-fold, and reduced cytopathogenic effect in cell culture, indicating that viral DSP activity may be significant during infection. As with virus mutated at the first cysteine residue, mutation of the second cysteine (C97) within the motif resulted in a marked reduction in viral growth and attenuation of cytopathogenicity in infected cell cultures. However, mutagenesis of this second cysteine only reduced phosphotyrosine phosphatase activity to 70 % of that of wild-type VP2, but increased phosphoserine/phosphothreonine phosphatase activity by as much as 700 %. The differential effect of the C97S mutation on VP2 activity does not appear to have parallels in other DSPs and suggests a unique role for the second cysteine in the function of these viral proteins, particularly in vivo.
ChemInform Abstract: A Convenient Access to 16‐Methylene and 16β‐Methyl Corticosteroids by a Novel Transformation of Geminal Bis( phenylsulfinyl) Intermediates. (1993)

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.
Activity-dependent local protection and lateral inhibition control synaptic competition in developing mitral cells in mice (2023)

In developing brains, activity-dependent remodeling facilitates the formation of precise neuronal connectivity. Synaptic competition is known to facilitate synapse elimination; however, it has remained unknown how different synapses compete with one another within a post-synaptic cell. Here, we investigate how a mitral cell in the mouse olfactory bulb prunes all but one primary dendrite during the developmental remodeling process. We find that spontaneous activity generated within the olfactory bulb is essential. We show that strong glutamatergic inputs to one dendrite trigger branch-specific changes in RhoA activity to facilitate the pruning of the remaining dendrites: NMDAR-dependent local signals suppress RhoA to protect it from pruning; however, the subsequent neuronal depolarization induces neuron-wide activation of RhoA to prune non-protected dendrites. NMDAR-RhoA signals are also essential for the synaptic competition in the mouse barrel cortex. Our results demonstrate a general principle whereby activity-dependent lateral inhibition across synapses establishes a discrete receptive field of a neuron.
PT-symmetric interface states based on synthetic 4D topological space (Conference Presentation) (2018)

In recent years, topological insulator and topological semimetal have drawn much attention, due to the novel properties such as robust edge states, chiral anomaly, diverging local density of states and so on. However, the dimension of momentum space is less than three, which limits the exploration the physics in higher dimensions. Take advantage of the concept of synthetic dimension, we can construct higher dimensional spaces to realize more amazing phenomenon including Weyl surface in 5D space, 4D Quantum Hall effect and so on. Some works also focused on probing the topological physics of non-Hermitian systems, which leads to additional novel consequences such as the transformation of the Weyl point into an exceptional ring when introducing a non-Hermitian term. In this work, we give a flexible platform to investigate the PT-symmetric topological physics in 4D synthetic space. Here, based on 1D photonic crystal with a complex seven-layer unit cell, we construct a 4D synthetic space with two momentum vectors and two geometric parameters. Before introducing the non-Hermitian term, the system shows a 2D Nodal-hyperedge in 4D space. If we add gain and loss in to the PCs but preserving PT symmetry, the 2D hyperedge will be transformed into a 3D exceptional hypersurface, on which the Hamiltonian becomes defective. Such 3D exceptional hypersurface also guarantees the unidirectional reflectionless resonance in 1D PCs even with oblique incidence. Furthermore, we also find the existence of PT-symmetric interface states in our systems, which will give rise to the strong field enhancement, and is quite useful in nonlinear and quantum optics.
Evaluation of the effect of expansion and shear stress on a self-assembled endothelium mimicking nanomatrix coating for drug eluting stents in vitro and in vivo (2014)

Coating stability is increasingly recognized as a concern impacting the long-term effectiveness of drug eluting stents (DES). In particular, unstable coatings have been brought into focus by a recently published report (Denardo et al 2012 J. Am. Med. Assoc. 307 2148-50). Towards the goal of overcoming current challenges of DES performance, we have developed an endothelium mimicking nanomatrix coating composed of peptide amphiphiles that promote endothelialization, but limit smooth muscle cell proliferation and platelet adhesion. Here, we report a novel water evaporation based method to uniformly coat the endothelium mimicking nanomatrix onto stents using a rotational coating technique, thereby eliminating residual chemicals and organic solvents, and allowing easy application to even bioabsorbable stents. Furthermore, the stability of the endothelium mimicking nanomatrix was analyzed after force experienced during expansion and shear stress under simulated physiological conditions. Results demonstrate uniformity and structural integrity of the nanomatrix coating. Preliminary animal studies in a rabbit model showed no flaking or peeling, and limited neointimal formation or restenosis. Therefore, it has the potential to improve the clinical performance of DES by providing multifunctional endothelium mimicking characteristics with structural integrity on stent surfaces.
Submitochondrial Protein Translocation in Thermogenic Regulation (2023)

Mitochondrial stress regulates energy utilization by forcing translocation of IM-bound proteins into the matrix.
Im2Vec: Synthesizing Vector Graphics without Vector Supervision (2021)

Vector graphics are widely used to represent fonts, logos, digital artworks, and graphic designs. But, while a vast body of work has focused on generative algorithms for raster images, only a handful of options exists for vector graphics. One can always rasterize the input graphic and resort to image-based generative approaches, but this negates the advantages of the vector representation. The current alternative is to use specialized models that require explicit supervision on the vector graphics representation at training time. This is not ideal because large-scale high-quality vector-graphics datasets are difficult to obtain. Furthermore, the vector representation for a given design is not unique, so models that supervise on the vector representation are unnecessarily constrained. Instead, we propose a new neural network that can generate complex vector graphics with varying topologies, and only requires indirect supervision from readily-available raster training images (i.e., with no vector counterparts). To enable this, we use a differentiable rasterization pipeline that renders the generated vector shapes and composites them together onto a raster canvas. We demonstrate our method on a range of datasets, and provide comparison with state-of-the-art SVG-VAE and DeepSVG, both of which require explicit vector graphics supervision. Finally, we also demonstrate our approach on the MNIST dataset, for which no groundtruth vector representation is available. Source code, datasets and more results are available at http://geometry.cs.ucl.ac.uk/projects/2021/Im2Vec/.
Erratum for Chu et al., Function of the Borrelia burgdorferi FtsH Homolog Is Essential for Viability both In Vitro and In Vivo and Independent of HflK/C (2016)

Volume 7, no. 2, doi:[10.1128/mBio.00404-16][1], 2016. The present address should have appeared as shown above.

 [1]: /lookup/doi/10.1128/mBio.00404-16
HAPADEP: Human Asisted Pure Audio Device Pairing. (2007)

The number and diversity of electronic gadgets has been steadily increasing and they are becoming indispensable to more and more professionals and non-professionals alike. At the same time, there has been fairly little progress in secure pairing of such devices. The pairing challenge revolves around establishing on-the-fly secure communication without any trusted (onor off-line) third parties between devices that have no prior association. The main security issue is the danger of so-called Man-in-the-Middle (MiTM) attacks, whereby an adversary impersonates one of the devices by inserting itself into the pairing protocol. One basic approach to countering these MiTM attacks is to involve the user in the pairing process. Therein lies the usability challenge since it is natural to minimize user burden. Previous research yielded some interesting secure pairing techniques, some of which ask too much of the human user, while others assume availability of specialized equipment (e.g., wires, photo or video cameras) on devices. Furthermore, all prior methods assumed the existence of a common digital (humanimperceptible) communication medium, such as Infrared, 802.11 or Bluetooth. In this paper we introduce a very simple technique called HAPADEP (Human-Assisted Pure Audio Device Pairing). It places very little burden on the human user and requires no common means of electronic communication. Instead, HAPADEP uses the audio channel to exchange both data and verification information among devices. It makes secure pairing possible even if devices are equipped only with a microphone and a speaker. Despite its simplicity, a number of interesting issues arise in the design of HAPADEP. We discuss design and implementation highlights as well as usability features and limitations.
Force Measurement Improvements to the National Transonic Facility Sidewall Mounted Support System (2016)

The National Transonic Facility is a transonic pressurized cryogenic facility. The development of the high Reynolds number semi-span capability has advanced over the years to include transonic active flow control and powered testing using the sidewall model support system. While this system can be used in total temperatures down to -250Â F for conventional unpowered configurations, it is limited to temperatures above -60Â F when used with powered models that require the use of the high-pressure air delivery system. Thermal instabilities and non-repeatable mechanical arrangements revealed several data quality shortfalls by the force and moment measurement system. Recent modifications to the balance cavity recirculation system have improved the temperature stability of the balance and metric model-to-balance hardware. Changes to the mechanical assembly of the high-pressure air delivery system, particularly hardware that interfaces directly with the model and balance, have improved the repeatability of the force and moment measurement system. Drag comparisons with the high-pressure air system removed will also be presented in this paper.
A hierarchical domain model for safety-critical cyber-physical systems in process automation (2015)

Cyber-physical systems (CPS) integrate computation with physical processes. For the last years, CPS have been in the focus of research and are getting adopted in multiple domains like health care, automotive and smart factories. The use of CPS promises dynamic adaption of systems to changing environmental and economic conditions through autonomous CPS decisions based on the physical process. In industrial process automation, research and adoption of CPS have to account for the severe safety restrictions that dominate the system design in this domain. To transfer the benefits of CPS application to process automation, the CPS must be able to formally verify the safety of its autonomous reconfiguration decisions. This paper proposes a domain model for safety-critical CPS in industrial process automation to serve as foundation for formal CPS algorithms.
Shortest wavelength (607 nm) operations of GaInP/AlInP distributed Bragg reflector lasers (1992)

Visible light GaInP/AlInP distributed Bragg reflector (DBR) lasers with second order gratings (184.7 nm period) were fabricated by gas source molecular beam epitaxy (GSMBE) and the conventional interference method for the first time. Single mode operations of GaInP/AlInP DBR lasers were maintained up to over 1.8 times the threshold currents with a wavelength of 607 nm at 140 K and a wavelength shift of 0.033 nm/K. No mode hopping was observed in a temperature range from 120 to 165 K.
Andrographolide nanophytosomes exhibit enhanced cellular delivery and pro-apoptotic activities in HepG2 liver cancer cells (2023)

Andrographolide (AG), a major active constituent of <i>Andrographis paniculata,</i> is known to hinder proliferation of several types of cancer cells. However, its poor solubility and cellular permeability restrict its use in clinical applications. In this study, AG-loaded phytosomes (AG-PTMs) were formulated and optimized with respect to particle size using l-α-phosphatidylcholine (PC):AG ratio and sonication time (ST) as independent variables. The optimized formula was prepared at 1:2.7 for AG:PC molar ratio and 4.9 min for ST and exhibited a particle size of 243.7 ± 7.3 nm, polydispersity index (PDI) of 0.310 and entrapment efficiency of 72.20 ± 4.53. Also, the prepared formula showed a slow release of AG over 24-h period. The antiproliferative activity of AG-PTMs was investigated against the liver cancer cell line HepG2. AG-PTMs significantly repressed the growth of HepG2 cells with an IC<sub>50</sub> value of 4.02 ± 0.14 µM. AG uptake by HepG2 cells was significantly enhanced in incubations containing the optimized formula. AG-PTMs also caused G2-M cell cycle phase arrest and increased the fraction of apoptotic cells in pre-G1 phase. These effects were associated with induction of oxidative stress and mitochondrial dysfunction. In addition, AG-PTMs significantly upregulated mRNA expression of <i>BAX</i> and downregulated that of <i>BCL2.</i> Furthermore, AG-PTMs significantly enhanced the concentration of caspase-3 in comparison to raw AG. These data indicate that the phytosomal delivery of AG significantly inhibited HepG2 cell proliferation through enhanced cellular uptake, arresting cell cycle at the G2-M phase and inducing mitochondrial-dependent apoptosis.