gebhart/patrepeval huggingface dataset:
The Unreasonable Effectiveness of Deep Features as a Perceptual Metric (2018)

While it is nearly effortless for humans to quickly assess the perceptual similarity between two images, the underlying processes are thought to be quite complex. Despite this, the most widely used perceptual metrics today, such as PSNR and SSIM, are simple, shallow functions, and fail to account for many nuances of human perception. Recently, the deep learning community has found that features of the VGG network trained on ImageNet classification has been remarkably useful as a training loss for image synthesis. But how perceptual are these so-called "perceptual losses"? What elements are critical for their success? To answer these questions, we introduce a new dataset of human perceptual similarity judgments. We systematically evaluate deep features across different architectures and tasks and compare them with classic metrics. We find that deep features outperform all previous metrics by large margins on our dataset. More surprisingly, this result is not restricted to ImageNet-trained VGG features, but holds across different deep architectures and levels of supervision (supervised, self-supervised, or even unsupervised). Our results suggest that perceptual similarity is an emergent property shared across deep visual representations.
Highly Conserved Protective Epitopes on Influenza B Viruses (2012)

Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.
Tuning the properties of a novel short cell-penetrating peptide by intramolecular cyclization with a triazole bridge (2015)

Cell-penetrating peptides (CPPs) present a versatile alternative to viral gene delivery vectors, addressing the still challenging task to suitably transport the desired gene to the target cell. In this work, the rational design of triazole-bridged CPPs and their detailed investigation concerning peptide/lipid interactions, using also NMR-based structure calculations, are reported.
Neurotrophin-3 production promotes human neuroblastoma cell survival by inhibiting TrkC-induced apoptosis (2010)

Tropomyosin-related kinase receptor C (TrkC) is a neurotrophin receptor with tyrosine kinase activity that was expected to be oncogenic. However, it has several characteristics of a tumor suppressor: its expression in tumors has often been associated with good prognosis; and it was recently demonstrated to be a dependence receptor, transducing different positive signals in the presence of ligand but inducing apoptosis in the absence of ligand. Here we show that the TrkC ligand neurotrophin-3 (NT-3) is upregulated in a large fraction of aggressive human neuroblastomas (NBs) and that it blocks TrkC-induced apoptosis of human NB cell lines, consistent with the idea that TrkC is a dependence receptor. Functionally, both siRNA knockdown of NT-3 expression and incubation with a TrkC-specific blocking antibody triggered apoptosis in human NB cell lines. Importantly, disruption of the NT-3 autocrine loop in malignant human neuroblasts triggered in vitro NB cell death and inhibited tumor growth and metastasis in both a chick and a mouse xenograft model. Thus, we believe that our data suggest that NT-3/TrkC disruption is a putative alternative targeted therapeutic strategy for the treatment of NB.
Identification of two cysteine residues involved in the binding of UDP‐GalNAc to UDP‐GalNAc:polypeptide N‐acetylgalactosaminyltransferase 1 (GalNAc‐T1) (2002)

Biosynthesis of mucin-type O-glycans is initiated by a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which contain several conserved cysteine residues among the isozymes. We found that a cysteine-specific reagent, p-chloromercuriphenylsulfonic acid (PCMPS), irreversibly inhibited one of the isozymes (GalNAc-T1). Presence of either UDP-GalNAc or UDP during PCMPS treatment protected GalNAc-T1 from inactivation, to the same extent. This suggests that GalNAc-T1 contains free cysteine residues interacting with the UDP moiety of the sugar donor. For the functional analysis of the cysteine residues, several conserved cysteine residues in GalNAc-T1 were mutated individually to alanine. All of the mutations except one resulted in complete inactivation or a drastic decrease in the activity, of the enzyme. We identified only Cys212 and Cys214, among the conserved cysteine residues in GalNAc-T1, as free cysteine residues, by cysteine-specific labeling of GalNAc-T1. To investigate the role of these two cysteine residues, we generated cysteine to serine mutants (C212S and C214S). The serine mutants were more active than the corresponding alanine mutants (C212A and C214A). Kinetic analysis demonstrated that the affinity of the serine-mutants for UDP-GalNAc was decreased, as compared to the wild type enzyme. The affinity for the acceptor apomucin, on the other hand, was essentially unaffected. The functional importance of the introduced serine residues was further demonstrated by the inhibition of all serine mutant enzymes with diisopropyl fluorophosphate. In addition, the serine mutants were more resistant to modification by PCMPS. Our results indicate that Cys212 and Cys214 are sites of PCMPS modification, and that these cysteine residues are involved in the interaction with the UDP moiety of UDP-GalNAc.
Intrinsic Disorder in Transcription Factors (2006)

Intrinsic disorder (ID) is highly abundant in eukaryotes, which reflect the greater need for disorder-associated signaling and transcriptional regulation in nucleated cells. Although several well-characterized examples of intrinsically disordered proteins in transcriptional regulation have been reported, no systematic analysis has been reported so far. To test for the general prevalence of intrinsic disorder in transcriptional regulation, we used the predictor of natural disorder regions (PONDR) to analyze the abundance of intrinsic disorder in three transcription factor datasets and two control sets. This analysis revealed that from 94.13 to 82.63% of transcription factors possess extended regions of intrinsic disorder, relative to 54.51 and 18.64% of the proteins in two control datasets, which indicates the significant prevalence of intrinsic disorder in transcription factors. This propensity of transcription factors to intrinsic disorder was confirmed by cumulative distribution function analysis and charge-hydropathy plots. The amino acid composition analysis showed that all three transcription factor datasets were substantially depleted in order-promoting residues and significantly enriched in disorder-promoting residues. Our analysis of the distribution of disorder within the transcription factor datasets revealed that (a) the AT-hooks and basic regions of transcription factor DNA-binding domains are highly disordered; (b) the degree of disorder in transcription factor activation regions is much higher than that in DNA-binding domains; (c) the degree of disorder is significantly higher in eukaryotic transcription factors than in prokaryotic transcription factors; and (d) the level of alpha-MoRF (molecular recognition feature) prediction is much higher in transcription factors. Overall, our data reflected the fact that eukaryotes with well-developed gene transcription machinery require transcription factor flexibility to be more efficient.
Metal Binding and Oxidation of Amyloid-β within Isolated Senile Plaque Cores:  Raman Microscopic Evidence (2003)

Alzheimer's disease (AD) is characterized by the deposition of amyloid plaques in the parenchyma and vasculature of the brain. Although previous analytical studies have provided much information about the composition and structure of synthetic amyloid-beta fibrils, there is, surprisingly, a dearth of data on intact amyloid plaques from AD brain. Therefore, to elucidate the structure and detailed composition of isolated amyloid plaque cores, we utilized a high-resolution, nondestructive technique, Raman microscopy. The data are of very high quality and contain detailed information about protein composition and conformation, about post-translational modification, and about the chemistry of metal binding sites. Remarkably, spectra obtained for senile plaque (SP) cores isolated from AD brain are essentially identical both within and among brains. The Raman data show for the first time that the SP cores are composed largely of amyloid-beta and confirm inferences from X-ray studies that the structure is beta-sheet with the additional possibility that this may be present as a parallel beta-helix. Raman bands characteristic of methionine sulfoxide show that extensive methionine oxidation has occurred in the intact plaques. The Raman spectra also demonstrate that Zn(II) and Cu(II) are coordinated to histidine residues in the SP cores, at the side chains' N(tau) and N(pi) atoms, respectively. Treatment of the senile plaques with the chelator ethylenediaminetetraacetate reverses Cu binding to SP histidines and leads to a broadening of amide features, indicating a "loosening" of the beta-structure. Our results indicate that Abeta in vivo is a metalloprotein, and the loosening of the structure following chelation treatment suggests a possible means for the solubilization of amyloid deposits. The results also reveal a direct chemical basis for oxidative damage caused by amyloid-beta protein in AD.
Improving the Solubility and Pharmacological Efficacy of Curcumin by Heat Treatment (2007)

Lipid peroxidation has been implicated in a variety of diseases. 4-Hydroxy-2-nonenal (HNE), a major oxidation by-product, is cytotoxic, mutagenic, and genotoxic, being involved in disease pathogenesis. Naturally occurring pharmacologically active small molecules are very attractive as natural nonsteroidal anti-inflammatory agents. Interest has greatly increased recently in the pharmacotherapeutic potential of curcumin, the yellow pigment found in the rhizomes of the perennial herb Curcuma longa (turmeric). Curcumin is efficacious against colon cancer, cystic fibrosis, and a variety of other disorders. Curcumin's full pharmacological potential is limited owing to its extremely limited water solubility. We report here that the water solubility of curcumin could be increased from 0.6 microg/ml to 7.4 microg/ml (12-fold increase) by the use of heat. Spectrophotometric (400-700 nm) and mass spectrometric profiling of the heat-extracted curcumin displays no significant heat-mediated disintegration of curcumin. Using an enzyme-linked immunosorbent assay that employed HNE modification of solid-phase antigen, we found that the heat-solubilized curcumin inhibited HNE-protein modification by 80%. Thus, inhibition of HNE modification may be a mechanism by which curcumin exerts its effect. We also report a simple assay to detect curcumin spectrophotometrically. Curcumin was solubilized in methanol and serially diluted in methanol to obtain a set of standards that were then read for optical density at 405 nm. Curcumin in the heat-solubilized samples was determined from this standard. Heat-solubilized curcumin should be considered in clinical trials involving curcumin, especially in the face of frustrating results obtained regarding curcumin-mediated correction of cystic fibrosis defects.
Phase I Trial of Intravesical Docetaxel in the Management of Superficial Bladder Cancer Refractory to Standard Intravesical Therapy (2006)

Intravesical docetaxel exhibited minimal toxicity and no systemic absorption in the first human intravesical clinical trial. This suggests that docetaxel is a safe agent for further evaluation of efficacy in a phase II trial.
Localization of antigen on lymph node dendritic cells after exposure to the contact sensitizer fluorescein isothiocyanate. Functional and morphological studies. (1987)

We have examined the cells involved in the development of contact sensitivity to FITC in CBA mice. After skin painting with antigen, the number of dendritic cells (DC) in the draining lymph nodes increased by 30 min, was maximal at 48 h, and returned to normal by 6 d. Derivation of some DC from Langerhans' cells of the skin was indicated from the presence of Birbeck granules observed in some DC isolated 24 h after skin painting. The DC acquired FITC and by 8 h there were two populations, one highly fluorescent and the other less fluorescent. The highly fluorescent cells were present between 8 h and 3 d after sensitization, and during this period the DC were potent at initiating primary proliferative responses of normal syngeneic T lymphocytes in vitro. Between days 3 and 5 the numbers of lymphocytes in the draining lymph node increased. During this period purified T lymphocytes did not express detectable levels of antigen, but enriched B cell populations expressed antigen transiently on day 1, 2, or 3 after exposure to antigen. The results showed that, during a 3-d period after exposure to antigen, DC expressed antigen and stimulated T cell proliferation. We speculate that low amounts of FITC binding selectively to veiled cells or lymph node DC in the first hours after exposure to antigen are not immunogenic but that Langerhans' cells acquire high levels of antigen, enter the nodes, and initiate immune responses.
The reaction between isatin and some amines (1972)

In acidic aqueous solution 2-(3,4-dimethoxyphenyl)ethylamine and isatin reacted to give 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline-1-spiro-3′-(2′-oxoindoline)(1a); 2-(3-hydroxy-4-methoxyphenyl)ethylamine gave a mixture of the analogous 6-hydroxy-7-methoxyspiran (1b) and the isomeric 8-hydroxy-7-methoxyspiran (1c). In neither case was a derivative of 1-benzyl-1,2,3,4-tetrahydroisoquinoline detected. A mixture of 2-(3-hydroxy-4-methoxyphenyl)ethylamine and benzylamine reacted with isatin to form, in addition to the spirans, some 6-hydroxy-7-methoxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline (3b); but when a mixture of 2-(3,4-dimethoxyphenyl)-ethylamine and benzylamine was used, no 6,7-dimethoxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline was detected.
Effect of shear on the death of two strains of mammalian tissue cells (1971)

Abstract This study reports some findings on the death of mammalian cells occurring from fluid dynamic effects when they are pumped through capillaries. The cell strains used were human HeLa S3 and mouse L929, grown in monolayer culture. Cells were harvested and suspensions were pumped through various lengths and diameters of stainless steel capillary tubing. Viability of the cells was assayed by the dye exclusion test. Cell deaths occurred and could be correlated with either average wall shear or power dissipation within the capillary tube. L929 cells were found to be more sensitive than HeLa S3 cells at all shear rates tested.
Managing distributed shared arrays in a bulk‐synchronous parallel programming environment (2004)

Abstract NestStep is a parallel programming language for the BSP (bulk‐hronous parallel) programming model. In this article we describe the concept of distributed shared arrays in NestStep and its implementation on top of MPI. In particular, we present a novel method for runtime scheduling of irregular, direct remote accesses to sections of distributed shared arrays. Our method, which is fully parallelized, uses conventional two‐sided message passing and thus avoids the overhead of a standard implementation of direct remote memory access based on one‐sided communication. The main prerequisite is that the given program is structured in a BSP‐compliant way. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Monocycle shapes for ultra wideband system (2003)

Ultra wideband (UWB) is a promising technique for wireless communications. It is a carrier-free (base-band) technique, which can greatly reduce the complexity and cost of the transceiver. In contrast with conventional communication systems using the "sine wave", UWB information is carried in a very short pulse, which covers an extremely wide spectrum bandwidth. Several candidate monocycle (narrow pulse) shapes are investigated, their spectrum characteristics and BER performance in AWGN using pulse position modulation (PPM) are simulated, and the results are compared. Their performances in the fading multipath channel are also investigated.
Melatonin‐induced increased activity of the respiratory chain complexes I and IV can prevent mitochondrial damage induced by ruthenium red in vivo (2000)

Melatonin displays antioxidant and free radical scavenger properties. Due to its ability with which it enters cells, these protective effects are manifested in all subcellular compartments. Recent studies suggest a role for melatonin in mitochondrial metabolism. To study the effects of melatonin on this organelle we used ruthenium red to induce mitochondrial damage and oxidative stress. The results show that melatonin (10 mg/kg i.p.) can increase the activity of the mitochondrial respiratory complexes I and IV after its administration in vivo in a time-dependent manner; these changes correlate well with the half-life of the indole in plasma. Melatonin administration also prevented the decrease in the activity of complexes I and IV due to ruthenium red (60 microg/kg i.p.) administration. At this dose, ruthenium red did not induce lipid peroxidation but it significantly reduced the activity of the antioxidative enzyme glutathione peroxidase, an effect also counteracted by melatonin. These results suggest that melatonin modulates mitochondrial respiratory activity, an effect that may account for some of the protective properties of the indoleamine. The mitochondria-modulating role of melatonin may be of physiological significance since it seems that the indoleamine is concentrated into normal mitochondria. The data also support a pharmacological use of melatonin in drug-induced mitochondrial damage in vivo.
Synthetic SAR Image Generation using Sensor, Terrain and Target Models (2016)

A tool to generate synthetic SAR images of objects set on a clutter background is described. The purpose is to generate images for training Automatic Target Recognition and Identification algorithms. The tool employs a commercial electromagnetic simulation program to calculate radar cross sections of the object using a CAD-model. The raw measurements are input to a SAR system and terrain model, which models thermal noise, terrain clutter, and SAR focusing to produce synthetic SAR images. Examples of SAR images at 0.3m and 0.1m resolution, and a comparison with real SAR imagery from the MSTAR dataset is presented.
Smart thermo-triggered squirting capsules for nanoparticle delivery (2010)

A squirting capsule is designed to deliver nanoparticles inspired by the squirting cucumber ejecting its seeds. The capsule has a thermo-sensitive hydrogel shell, and encapsulates nanoparticles by emulsifying the nanoparticle aqueous suspension in the water-in-oil emulsion core. The squirting capsule can completely squirt out the encapsulated nanoparticles with a high momentum, just like a nanoparticle bomb, by the dramatic shrinkage and sudden rupture of the capsule membrane upon heating.
Label‐Free Affinity Assays by Rapid Detection of Immune Complexes in Submicrometer Pores (2006)

Resistance movement: A submicrometer conical pore was used for the single-aggregate detection and characterization of immune complexes consisting of proteins such as staphylococcal enterotoxin B and antibodies. The developed assay is rapid, label-free, requires no immobilization or modification of the antibody or antigen, and can be performed with antibodies or proteins in serum. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z502862_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Efficient protocol for qubit initialization with a tunable environment (2017)

Abstract We propose an efficient qubit initialization protocol based on a dissipative environment that can be dynamically adjusted. Here, the qubit is coupled to a thermal bath through a tunable harmonic oscillator. On-demand initialization is achieved by sweeping the oscillator rapidly into resonance with the qubit. This resonant coupling with the engineered environment induces fast relaxation to the ground state of the system, and a consecutive rapid sweep back to off resonance guarantees weak excess dissipation during quantum computations. We solve the corresponding quantum dynamics using a Markovian master equation for the reduced density operator of the qubit-bath system. This allows us to optimize the parameters and the initialization protocol for the qubit. Our analytical calculations show that the ground-state occupation of our system is well protected during the fast sweeps of the environmental coupling and, consequently, we obtain an estimate for the duration of our protocol by solving the transition rates between the low-energy eigenstates with the Jacobian diagonalization method. Our results suggest that the current experimental state of the art for the initialization speed of superconducting qubits at a given fidelity can be considerably improved.
Does Distance Matter in the Age of the Internet? (2010)

This study is part of the broad debate about the role of distance and technology for interpersonal contact. To the best of the authors’ knowledge, this is the first study that systematically and explicitly compares the role of distance in social networks pre- and post-Internet. An analysis is made of the effect of distance on the frequency of e-mail, phone, face-to-face and overall contact in personal networks, and the findings are compared with their pre-Internet counterpart whose data were collected in 1978 in the same East York, Toronto locality. Multilevel models with a spline specification are used to examine the non-linear effects of distance on the frequency of contact. These effects are compared for both very close and somewhat close ties, and for different role relationships: immediate kin, extended kin, friends and neighbours. The results show that e-mail contact is generally insensitive to distance, but tends to increase for transoceanic relationships greater than 3000 miles apart. Face-to-face contact remains strongly related to short distances (within five miles), while distance has little impact on how often people phone each other at the regional level (within 100 miles). The study concludes that e-mail has only somewhat altered the way people maintain their relationships. The frequency of face-to-face contact among socially close friends and relatives has hardly changed between the 1970s and the 2000s, although the frequency of phone contact has slightly increased. Moreover, the sensitivity of these relationships to distance has remained similar, despite the communication opportunities of the Internet and low-cost telephony.