gebhart/patrepeval huggingface dataset:
Piezoelectric transducer based miniature catheter for ultrahigh speed endoscopic optical coherence tomography (2011)

We developed a piezoelectric transducer (PZT) based miniature catheter with an outer diameter of 3 mm for ultrahigh speed endoscopic optical coherence tomography (OCT) using Fourier domain modelocked (FDML) laser at a 480 kHz axial scan rate. The miniaturized PZT bender actuates a fiber to provide high scanning speed. The side-viewing probe can be pulled back for a long distance to acquire three-dimensional (3D) dataset covering a large area on the specimen. Operating with a high speed data acquisition (DAQ) system, OCT imaging with 6.5 mm imaging range, 10 &mu;m axial resolution, 20 &mu;m lateral resolution, and frame rate of 480 frames per second (fps) is demonstrated.
Activin Acutely Sensitizes Dorsal Root Ganglion Neurons and Induces Hyperalgesia via PKC-Mediated Potentiation of Transient Receptor Potential Vanilloid I (2007)

Pain hypersensitivity is a cardinal sign of tissue damage, but how molecules from peripheral tissues affect sensory neuron physiology is incompletely understood. Previous studies have shown that activin A increases after peripheral injury and is sufficient to induce acute nociceptive behavior and increase pain peptides in sensory ganglia. This study was designed to test the possibility that the enhanced nociceptive responsiveness associated with activin involved sensitization of transient receptor potential vanilloid I (TRPV1) in primary sensory neurons. Activin receptors were found widely distributed among adult sensory neurons, including those that also express the capsaicin receptor. Whole-cell patch-clamp recording from sensory neurons showed that activin acutely sensitized capsaicin responses and depended on activin receptor kinase activity. Pharmacological studies revealed that the activin sensitization of capsaicin responses required PKCepsilon signaling, but not PI3K (phosphoinositide 3-kinase), ERK (extracellular signal-regulated protein kinase), PKA, PKCalpha/beta, or Src. Furthermore, activin administration caused acute thermal hyperalgesia in wild-type mice, but not in TRPV1-null mice. These data suggest that activin signals through its own receptor, involves PKCepsilon signaling to sensitize the TRPV1 channel, and contributes to acute thermal hyperalgesia.
Ad hoc networking: an introduction (2001)

In recent years, mobile computing has enjoyed a tremendous rise in popularity. The continued miniaturization of mobile computing devices and the extraordinary rise of processing power available in mobile laptop computers combine to put more and better computer-based applications into the hands of a growing segment of the population. At the same time, the markets for wireless telephones and communication devices are experiencing rapid growth. Projections have been made that, by the year 2002, there will be more than a billion wireless communication devices in use, and more than 200 million wireless telephone handsets will be purchased annually. The rise of wireless telephony will change what it means to be “in touch”; already many people use their office telephone for taking messages while they are away and rely on their mobile telephone for more important or timely messages. Indeed, mobile phones are used for tasks as simple and as convenient as finding one’s associates in a crowded shopping mall or at a conference. A similar transformation awaits mobile computer users, and we can expect new applications to be built for equally mundane but immediately convenient uses. Much of the context for the transformation has to do with keeping in touch with the Internet. We expect to have “the network” at our disposal for the innumerable little conveniences that we have begun to integrate into our professional lives. We might wish to download a roadmap on the spur of the moment so that we can see what is available in the local area. We might wish to have driving suggestions sent to us, based on information from the global positioning system (GPS) in our car, using the services offered by various web sites. The combination of sufficiently fast and inexpensive wireless communication links and cheap mobile computing devices makes this a reality for many people today. In the future, the average traveler is likely to take such services for granted.
Optimization for fast‐scanning irradiation in particle therapy (2007)

In three-dimensional irradiation with pencil beam scanning, an extra dose is inevitably delivered to the irradiated site due to the finite reaction times of the beam delivery system, and it causes a severe distortion of the dose distribution in the target region. Since the amount of the extra dose is proportional to the beam intensity, the dose uniformity deteriorates as the beam intensity is increased in order to shorten the treatment time. In order to overcome this problem and shorten the treatment time, we have developed an optimization method in which the extra dose is integrated into the optimization process of the best weighting matrix. The effectiveness and applicability of the optimization method for spot and raster scanning irradiation were confirmed with computer simulations and also confirmed using irradiation experiments for spot scanning irradiation. The treatment time could be shortened to about one sixth of the time needed without taking the extra dose into account while obtaining the same degree of dose homogeneity in the target volume. A typical treatment time with the proposed method is about 15 s for the irradiation of a spherical target with an 80 mm diameter at 3 GyE.
Transcription Factor YB-1 Mediates DNA Polymerase α Gene Expression (2004)

Y-box protein-1 involvement in cyclin A and B1 gene regulation has recently been demonstrated. A more generalized role of this protein for cell replication is hypothesized as numerous regulatory sequences of cell cycle-related genes contain putative binding sites. In the present study the DNA polymerase alpha (DPA) gene is identified as another YB-1-responsive gene with a Y-box and 3' inverted repeat sequence, designated DPA RE-1, in the serum-responsive promoter region. Overexpressed YB-1 concentration-dependently trans-activated DPA gene expression in reporter assays and Southwestern blotting as well as DNA binding analyses revealed binding of distinct endogenous proteins to the RE-1 with molecular sizes of 26, 32 and 52 kDa. Among these, YB-1 binding was confirmed using recombinant as well as endogenous proteins, with preferential single-stranded DNA binding. Early serum growth response in mesangial cells was accompanied by a nuclear YB-1 shift and nucleocomplex formation at the RE-1. Fine mapping of the DPA RE-1 sequence unraveled a dependence on co-factors for trans-regulation with gene activation in the context of a heterologous SV40 promoter but suppression in the context of the abbreviated homologous promoter sequence. A YB-1 knock down resulted in decreased DPA transcription rates and abrogated the serum-dependent induction of DPA transcription. These results link YB-1 with serum responsiveness of DPA gene expression and provide insight into the required sequence and protein binding context.
Kraepelin Was Right: A Latent Class Analysis of Symptom Dimensions in Patients and Controls (2010)

Phenotypic heterogeneity within patients and controls may explain why the genetic variants contributing to schizophrenia risk explain only a fraction of the heritability. The aim of this study is to investigate quantitative and qualitative differences in psychosis symptoms in a sample including psychosis patients, their relatives, and community controls. We combined factor analysis and latent class analysis to analyze variation in Comprehensive Assessment of Symptoms and History lifetime-rated symptoms in 4286 subjects. The Wechsler Adult Intelligence Scale-Intelligence Quotient (N = 2663) and the Camberwell Assessment of Need rating scale (N = 625) were assessed in a subsample. Variation in 5 continuous dimensions (disorganization, positive, negative, mania, and depression) was accounted for by the presence of 7 homogeneous classes (Kraepelinian schizophrenia, affective psychosis, manic-depression, deficit nonpsychosis, depression, healthy, and no symptoms). Eighty-five percent of the schizophrenia patients was assigned to the Kraepelinian schizophrenia class (characterized by high scores on the 5 dimensions, low IQ, and poor outcome) while 15% was assigned to the affective psychosis class (relatively low disorganization and negative scores, normal IQ, and good outcome). In bipolar patients (91% bipolar I), 41% was assigned to the Kraepelinian schizophrenia class, 44% to the affective psychosis class, and 10% to the manic-depression class. Latent class membership was associated with intelligence in psychosis patients and in their relatives but not in community controls. In conclusion, symptom heterogeneity is more pronounced in bipolar disorder compared with schizophrenia. Reducing phenotypic heterogeneity within psychosis patients and controls may facilitate etiological research.
Isolation and Characterization of Carnocyclin A, a Novel Circular Bacteriocin Produced by Carnobacterium maltaromaticum UAL307 (2008)

Carnobacterium maltaromaticum UAL307, isolated from fresh pork, exhibits potent activity against a number of gram-positive organisms, including numerous Listeria species. Three bacteriocins were isolated from culture supernatant, and using matrix-assisted laser desorption ionization-time of flight mass spectrometry and Edman sequencing, two of these bacteriocins were identified as piscicolin 126 and carnobacteriocin BM1, both of which have previously been described. The remaining bacteriocin, with a molecular mass of 5,862 Da, could not be sequenced by traditional methods, suggesting that the peptide was either cyclic or N-terminally blocked. This bacteriocin showed remarkable stability over a wide temperature and pH range and was unaffected by a variety of proteases. After digestion with trypsin and alpha-chymotrypsin, the peptide was de novo sequenced by tandem mass spectrometry and a linear sequence deduced, consisting of 60 amino acids. Based on this sequence, the molecular mass was predicted to be 5,880 Da, 18 units higher than the observed molecular mass, which suggested that the peptide has a cyclic structure. Identification of the genetic sequence revealed that this peptide is circular, formed by a covalent linkage between the N and C termini following cleavage of a 4-residue peptide leader sequence. The results of structural studies suggest that the peptide is highly structured in aqueous conditions. This bacteriocin, named carnocyclin A, is the first reported example of a circular bacteriocin produced by Carnobacterium spp.
Design, synthesis and properties of polyurethane hydrogels for tissue engineering (2002)

Due to their similarity to natural soft tissues, water-swellable polymeric materials (hydrogels) are, in principle, ideal candidates for scaffolds/matrices in tissue engineering. Polyurethanes (PU), hydrophilic but water-insoluble, can be obtained by the incorporation of hydrophilic soft segments, e.g. poly(ethylene oxide) (PEO). These materials possess the favorable characteristics of the family of PUs as well as the ability to mimic soft tissues. In this work, new crosslinked PU-hydrogels were prepared in a one-step bulk polymerization process using an aliphatic diisocyanate, PEO, a low molecular weight diol, and a tri-functional crosslinking agent. A porous structure was also obtained by air-incorporation under mechanical stirring at a controlled high speed during the polymerization. Structural characteristics of the compact (PU-HyC) and the porous (PU-HyP) material were investigated. Molecular weight between cross-links, M(c), and crosslinking density, rho(x), were typical of a low crosslinking degree. A homogeneous distribution of non-interconnecting pores (phi100 microm) was observed in PU-HyP. Both materials showed a high water adsorption. The swelling behavior and weight loss in water was affected by porosity. For their mechanical behavior in the swollen state, the novel PU hydrogels can be considered for biomedical applications where good mechanical properties are required (i.e. 3D scaffold for tissue engineering).
CD25+ CD4+ T Cells, Expanded with Dendritic Cells Presenting a Single Autoantigenic Peptide, Suppress Autoimmune Diabetes (2004)

In the nonobese diabetic (NOD) mouse model of type 1 diabetes, the immune system recognizes many autoantigens expressed in pancreatic islet beta cells. To silence autoimmunity, we used dendritic cells (DCs) from NOD mice to expand CD25+ CD4+ suppressor T cells from BDC2.5 mice, which are specific for a single islet autoantigen. The expanded T cells were more suppressive in vitro than their freshly isolated counterparts, indicating that DCs from autoimmune mice can increase the number and function of antigen-specific, CD25+ CD4+ regulatory T cells. Importantly, only 5,000 expanded CD25+ CD4+ BDC2.5 T cells could block autoimmunity caused by diabetogenic T cells in NOD mice, whereas 10(5) polyclonal, CD25+ CD4+ T cells from NOD mice were inactive. When islets were examined in treated mice, insulitis development was blocked at early (3 wk) but not later (11 wk) time points. The expanded CD25+ CD4+ BDC2.5 T cells were effective even if administered 14 d after the diabetogenic T cells. Our data indicate that DCs can generate CD25+ CD4+ T cells that suppress autoimmune disease in vivo. This might be harnessed as a new avenue for immunotherapy, especially because CD25+ CD4+ regulatory cells responsive to a single autoantigen can inhibit diabetes mediated by reactivity to multiple antigens.
Administration of a soluble activin type IIB receptor promotes skeletal muscle growth independent of fiber type (2010)

This is the first report that inhibition of negative regulators of skeletal muscle by a soluble form of activin type IIB receptor (ACE-031) increases muscle mass independent of fiber-type expression. This finding is distinct from the effects of selective pharmacological inhibition of myostatin (GDF-8), which predominantly targets type II fibers. In our study 8-wk-old C57BL/6 mice were treated with ACE-031 or vehicle control for 28 days. By the end of treatment, mean body weight of the ACE-031 group was 16% greater than that of the control group, and wet weights of soleus, plantaris, gastrocnemius, and extensor digitorum longus muscles increased by 33, 44, 46 and 26%, respectively (P<0.05). Soleus fiber-type distribution was unchanged with ACE-031 administration, and mean fiber cross-sectional area increased by 22 and 28% (P<0.05) in type I and II fibers, respectively. In the plantaris, a predominantly type II fiber muscle, mean fiber cross-sectional area increased by 57% with ACE-031 treatment. Analysis of myosin heavy chain (MHC) isoform transcripts by real-time PCR indicated no change in transcript levels in the soleus, but a decline in MHC I and IIa in the plantaris. In contrast, electrophoretic separation of total soleus and plantaris protein indicated that there was no change in the proportion of MHC isoforms in either muscle. Thus these data provide optimism that ACE-031 may be a viable therapeutic in the treatment of musculoskeletal diseases. Future studies should be undertaken to confirm that the observed effects are not age dependent or due to the relatively short study duration.
Wnt co-receptors Lrp5 and Lrp6 differentially mediate Wnt3a signaling in osteoblasts (2017)

Wnt3a is a major regulator of bone metabolism however, very few of its target genes are known in bone. Wnt3a preferentially signals through transmembrane receptors Frizzled and co-receptors Lrp5/6 to activate the canonical signaling pathway. Previous studies have shown that the canonical Wnt co-receptors Lrp5 and Lrp6 also play an essential role in normal postnatal bone homeostasis, yet, very little is known about specific contributions by these co-receptors in Wnt3a-dependent signaling. We used high-throughput sequencing technology to identify target genes regulated by Wnt3a in osteoblasts and to elucidate the role of Lrp5 and Lrp6 in mediating Wnt3a signaling. Our study identified 782 genes regulated by Wnt3a in primary calvarial osteoblasts. Wnt3a up-regulated the expression of several key regulators of osteoblast proliferation/ early stages of differentiation while inhibiting genes expressed in later stages of osteoblastogenesis. We also found that Lrp6 is the key mediator of Wnt3a signaling in osteoblasts and Lrp5 played a less significant role in mediating Wnt3a signaling.
Focused ultrasound-facilitated brain drug delivery using optimized nanodroplets: vaporization efficiency dictates large molecular delivery (2017)

Focused ultrasound with nanodroplets could facilitate localized drug delivery after vaporization with potentially improved in vivo stability, drug payload, and minimal interference outside of the focal zone compared with microbubbles. While the feasibility of blood-brain barrier (BBB) opening using nanodroplets has been previously reported, characterization of the associated delivery has not been achieved. It was hypothesized that the outcome of drug delivery was associated with the droplet's sensitivity to acoustic energy, and can be modulated with the boiling point of the liquid core. Therefore, in this study, octafluoropropane (OFP) and decafluorobutane (DFB) nanodroplets were used both in vitro for assessing their relative vaporization efficiency with high-speed microscopy, and in vivo for delivering molecules with a size relevant to proteins (40 kDa dextran) to the murine brain. It was found that at low pressures (300-450 kPa), OFP droplets vaporized into a greater number of microbubbles compared to DFB droplets at higher pressures (750-900 kPa) in the in vitro study. In the in vivo study, successful delivery was achieved with OFP droplets at 300 kPa and 450 kPa without evidence of cavitation damage using ¼ dosage, compared to DFB droplets at 900 kPa where histology indicated tissue damage due to inertial cavitation. In conclusion, the vaporization efficiency of nanodroplets positively impacted the amount of molecules delivered to the brain. The OFP droplets due to the higher vaporization efficiency served as better acoustic agents to deliver large molecules efficiently to the brain compared with the DFB droplets.
Organic Electron Transfer Systems, II Substituted Triarylamine Cation‐Radical Redox Systems – Synthesis, Electrochemical and Spectroscopic Properties, Hammet Behavior, and Suitability as Redox Catalysts (1991)

Abstract 21 triarylamines ( 1n – 1z , 1za , 1zb ) and triarylamine analogs ( 2a , 2b , 3a , 3b , 4a , 4b ) with substituents in at least all three p positions and some of their cation‐radical hexachloroantimonates have been synthesized. The electrochemical behavior has been studied by cyclic voltammetry. Most of the compounds show chemically and electrochemically reversible first oxidation waves in the formation of the cation radicals. With the exception of 4a and 4b , the second wave for the formation of the dication is chemically irreversible. The UV spectra of the triarylamine cation radicals have been obtained in the presence of a slight excess of SbCl 5 . A good Hammett correlation between the first anodic potential of only p‐substituted triarylamines and the σ/σ values has been established. Some redox‐catalytic properties of triarylamine cation radicals are described.
A transgene containing lacZ is expressed in primary sensory neurons in zebrafish (1992)

In order to screen for developmentally active chromosomal domains during zebrafish embryogenesis, we generated transgenic fish by microinjecting two different lacZ reporter constructs into fertilized eggs. Transgenic fish were screened among the progeny of injected fish (F0) crossed to non-injected fish. Groups of 15 to 20 progeny of each cross were tested for lacZ expression and/or transmission of injected sequences using PCR and Southern hybridizations. Progeny from 2 of 102 fish injected with supercoiled constructs containing Rous sarcoma virus promoter sequences showed apparently spatially regulated beta-galactosidase (beta-Gal) activity. However, we were not able to detect this reporter construct in DNA from fins of F1 fish. Injections of a linear reporter construct containing mouse heat-shock promoter sequences revealed transmission of injected sequences to F1 progeny in about 6% of cases (8 of 129 fish, tested with PCR). We found one lacZ-expressing line that showed a spatially and temporally restricted expression of lacZ and, therefore, features typical characteristics of "enhancer trap" lines. In this line, lacZ expression starts at 16 hours post-fertilization in trigeminal ganglion cells. At about 24 hours lacZ expression can be detected in trigeminal ganglion neurons and Rohon-Beard neurons, indicating that the development of these two cell types shows common features. The reporter gene has integrated as a single copy. The founder fish was mosaic: 19% of its offspring (3 of 16 tested animals) carried the reporter construct in their fins; about 51% (13 of 27 tested animals) of the progeny of F1 fish were beta-Gal positive indicating full hemizygosity.(ABSTRACT TRUNCATED AT 250 WORDS)
Spamming botnets (2008)

In this paper, we focus on characterizing spamming botnets by leveraging both spam payload and spam server traffic properties. Towards this goal, we developed a spam signature generation framework called AutoRE to detect botnet-based spam emails and botnet membership. AutoRE does not require pre-classified training data or white lists. Moreover, it outputs high quality regular expression signatures that can detect botnet spam with a low false positive rate. Using a three-month sample of emails from Hotmail, AutoRE successfully identified 7,721 botnet-based spam campaigns together with 340,050 unique botnet host IP addresses. Our in-depth analysis of the identified botnets revealed several interesting findings regarding the degree of email obfuscation, properties of botnet IP addresses, sending patterns, and their correlation with network scanning traffic. We believe these observations are useful information in the design of botnet detection schemes.
Glycosaminoglycans that bind cold-insoluble globulin in cell-substratum adhesion sites of murine fibroblasts. (1980)

Glycosaminoglycans (GAGs) and glycoprotein-derived glycopeptide from mouse BALB/c3T3 and simian virus 40-transformed 3T3 whole cells or their adhesion sites, which are left bound to the serum-coated tissue culture substratum after detachment of cells mediated by [ethylenebis-(oxyethylenenitrilo]tetraacetic acid (EGTA), were analyzed for specific binding to Sepharose columns derivatized with cold-insoluble globulin (CIg). CIg is the serum-contained form of fibronectin and is required for the adhesion of these fibroblasts to the substratum. Of the various GAGs present in these fractions of either cell type, only the highly N-sulfated sequences of heparan sulfate and a small subset of dermatan sulfate bind to CIg-Sepharose. There was no detectable binding of glycopeptide, undersulfated heparan sulfate, the various chondroitin species, or hyaluronate. Adhesion sites from newly attaching cells were greatly enriched in CIg-binding heparan sulfate when compared to long-term-growth adhesion sites or EGTA-detached cells. Various properties of binding were determined. The reference standard standard GAGs heparin (or heparan sulfate) and dermatan sulfate were able to displace bound radiolabeled adhesion site GAG from the column, whereas the other GAGs had no effect. CIg has been shown to be the only adhesion-promoting activity in the serum layer of this culture system. Because these fibroblast adhesion sites do not contain collagen, which could potentially mediate adhesion to the substratum-bound CIg, these data support other evidence that multivalent heparan sulfate proteoglycans mediate substratum adhesion of these cells by coordinate binding to fibronectin on the cell surface and CIg on the substratum.