gebhart/patrepeval huggingface dataset:
Inhibition of human tumor growth in mice by an oncolytic herpes simplex virus designed to target solely HER-2-positive cells (2009)

Oncolytic virotherapy exploits the ability of viruses to infect, replicate into, and kill tumor cells. Among the viruses that entered clinical trials are HSVs. HSVs can be engineered to become tumor-specific by deletion of selected genes or retargeting to tumor-specific receptors. A clinically relevant surface molecule is HER-2, hyperexpressed in one fourth of mammary and ovary carcinomas, and associated with high metastatic ability. As a previously undescribed strategy to generate HSV recombinants retargeted to HER-2 and detargeted from natural receptors, we replaced the Ig-folded core in the receptor-binding virion glycoprotein gD with anti-HER-2 single-chain antibody. The recombinant entered cells solely via HER-2 and lysed HER-2-positive cancer cells. Because of the high specificity, its safety profile in i.p. injected mice was very high, with a LD(50) >5 x 10(8) pfu, a figure at least 10,000-fold higher than that of corresponding WT-gD carrying virus (LD(50) approximately 5 x 10(4) pfu). When administered intratumorally to nude mice bearing HER-2-hyperexpressing human tumors, it strongly inhibited progressive tumor growth. The results provide a generally applicable strategy to engineer HSV recombinants retargeted to a wide range of receptors for which a single-chain antibody is available, and show the potential for retargeted HSV to exert target-specific inhibition of human tumor growth. Therapy with HER-2-retargeted oncolytic HSV could be effective in combined or sequential protocols with monoclonal antibodies and small inhibitors, particularly in patients resistant to HER-2-targeted therapy because of alterations in HER-2 signaling pathway, or against brain metastases inaccessible to anti-HER-2 antibodies.
The time course of developmental cell death in phenotypically defined dopaminergic neurons of the substantia nigra (1997)

We have previously shown that apoptotic natural cell death occurs within the substantia nigra (SN) pars compacta of the rat postnatally. However, the occurrence of natural cell death in phenotypically defined dopaminergic neurons has not previously been identified, nor has its time course been defined in pre- or postnatal development. We therefore examined the SN at intervals from E19 to P28 using immunostaining for tyrosine hydroxylase with a Nissl counterstain to identify intranuclear apoptotic chromatin clumps. We have found that natural cell death in dopaminergic neurons is biphasic. An initial, broad peak begins at E20, reaches maximum at P2, and abates by P8. A second peak occurs at P14. We conclude that most of the natural cell death in this neuronal population occurs in the early postnatal period.
Perifollicular Transgenic Expression of Human Interleukin-1 Receptor Antagonist Protein following Topical Application of Novel Liposome-Plasmid DNA Formulations In Vivo (1997)

Expression plasmid DNA for the human interleukin-1 receptor antagonist (IL-1ra) protein was formulated with nonionic:cationic (NC) liposomes or phosphatidylcholine:cationic (PC) liposomes and applied to the auricular skin of hamsters in single- and multiple-dose protocols. Confocal microscopy identified delivery of plasmid DNA proximal to perifollicular cells, and successful transfection of perifollicular cells was identified by immunohistochemistry and ELISA. Skin treated for 3 days with the NC liposomes had statistically significant levels of transgenic IL-1ra present for 5 days post-treatment. Expression of transgenic IL-1ra was specific to areas of skin treated with NC liposomes but not PC liposomes. The results indicate that the NC liposomes can deliver expression plasmid DNA to perifollicular cells and mediate transient transfection in vivo.
Single-mode operation from an external cavity controlled vertical-cavity surface-emitting laser (1999)

Single-mode operation from an index-guided vertical-cavity surface-emitting laser (VCSEL) has been achieved by using a fiber Bragg grating (FBG) as an external selective wavelength reflector. The spectral characteristics of the external cavity controlled VCSEL under static and dynamic conditions have been studied. The FBG provided stable single mode operation under pseudorandom modulation with a sidemode suppression ratio of /spl sim/30 dB from 500 Mb/s up to 4 Gb/s at room temperature.
A Surface-Exposed Region of a Novel Outer Membrane Protein (P66) ofBorreliaspp. Is Variable in Size and Sequence (1998)

A model of the 66-kDa outer membrane protein (P66) of Lyme disease Borrelia spp. predicts a surface-exposed loop near the C terminus. This region contains an antigen commonly recognized by sera from Lyme disease patients. In the present study, this region of P66 and homologous proteins of other Borrelia spp. were further investigated by using monoclonal antibodies, epitope mapping of P66 of Borrelia burgdorferi, and DNA sequencing. A monoclonal antibody specific for B. burgdorferi bound to the portion of P66 that was accessible to proteolysis in situ. The linear epitope for the antibody was mapped within a variable segment of the surface-exposed region. To further study this protein, the complete gene of Borrelia hermsii for a protein homologous to P66 was cloned. The deduced protein was 589 amino acids in length and 58% identical to P66 of B. burgdorferi. The B. hermsii P66 protein was predicted to have a surface-exposed region in the same location as that of B. burgdorferi's P66 protein. With primers designed on the basis of conserved sequences and PCR, we identified and cloned the same regions of P66 proteins of Borrelia turicatae, Borrelia parkeri, Borrelia coriaceae, and Borrelia anserina. The deduced protein sequences from all species demonstrated two conserved hydrophobic regions flanking a surface-exposed loop. The loop sequences were highly variable between different Borrelia spp. in both sequence and size, varying between 35 and 45 amino acids. Although the actual function of P66 of Borrelia spp. is unknown, the results suggest that its surface-exposed region is subject to selective pressure.
Geometry of the Kimura-Georgiou parametrization of modelling filters (1989)

We discuss questions concerning the geometry of the Kimura-Georgiou para-metrizalion of the set ( + (n) of degree n positive real transfer functions with the first n coefficients in the Laurent expansion about infinity prescribed. For example, one interesting question which has been raised is whether this set is star-shaped about the maximum entropy solution. This, of course, would be implied by convexity and would imply that,( plus;(n) is diffeomorphic to euclidean n-space. All three of these geometric properties would be of interest, for example, when using geometric or optimization techniques to construct an n-dimensional modelling filter with variations about the maximum entropy filter. Our first main result, which also lends support to conjectures concerning convexity and star-shapedness, is that. ( plus;(n) is in fact diffeomorphic to euclidean n-space. Our proof makes use of certain results from differential topology. There are of course several intimate relations between positive reality and stability properties of both real and complex polynomials. On this basis we observe that the convexity of the parametrization implies the convexity of the set of real Schur polynomials of degree n and is implied by the convexity of the set of complex Schur polynomials of degree n. From this it immediately follows that ( plus;(n) is not convex for n ≥ 3 and that. ( plus;(n) is convex and hence star-shaped. The case n = 2 is especially interesting since the real Schur region is convex whereas the complex is not. Another of our main results is to refine the above observations to settle this question in general, showing that for n ≥ 3 there is an open set of Schur parameters for which, ( plus;(n) fails to be star-shaped about the maximum entropy filter.
Dielectric and electrical properties of sputter grown (Ba,Sr)TiO3 thin films (1999)

The dielectric behavior containing the film thickness dependent dielectric constant, capacitance–voltage (C–V) variation, and the electrical conduction behavior containing the film thickness dependent current density-electric field variation of rf sputter deposited (Ba,Sr)TiO3 (BST) thin films are analyzed based on a fully depleted film and a combined Schottky-tunneling conduction model. The fact that the capacitance values in C–V increase with the increasing film thickness clearly indicates that the films are fully depleted. Also, the decreasing and nonvariant dielectric constants of the BST film on the Pt and IrO2 electrodes, respectively, with decreasing film thickness are attributed to the intrinsic interfacial layers at the interfaces with electrodes which have low dielectric constants and very small thicknesses. The increased leakage current density of a thicker film under a given electric field originates from the increased interfacial field strength due to the high space charge density in the sputtered film. The leakage current density under the electric field strength smaller than 120 kV/cm is controlled by the Schottky conduction mechanism (thermionic emission), and over that field strength, the tunneling related mechanism (thermionic field emission) is predominant. The calculated leakage current density on the basis of the combined Schottky-tunneling conduction model fits well to the measured current density at various temperatures and over a wide field range. For all the calculations, the electric field dependent dielectric constant is always taken into account. The electric field dependent dielectric constant and high defect or space charge density of the BST film make the conventional analysis of the dielectric and conduction behavior based on the classical metal/semiconductor contact theory invalid. Therefore, a more comprehensive formalism is developed to take into account the field dependent dielectric properties and high charge density of the sputter deposited BST films.
Shigella flexneri invasion of HeLa cells induces NF-kappa B DNA-binding activity (1993)

Although information about the genetic basis and mechanisms of Shigella flexneri cellular invasion is accumulating, little is known about changes in cell signaling and their consequences following bacterium-host cell interactions. A general result of signal transduction is alterations in the levels and/or activities of transcription factors. Alterations in transcription factor binding activities were observed following challenge with S. flexneri. Changes in the DNA-binding activities of cellular transcription factors to AP1, AP2, cyclic AMP response element, CTF1/NF1, NF-kappa B/Rel, OCT1, and SP1 DNA-binding sites were investigated by electrophoretic mobility shift assays. NF-kappa B/Rel DNA-binding activity was enhanced more than 11-fold by cellular invasion; noninvasive S. flexneri strains induced low levels of kappa B DNA binding. Both subunits of the NF-kappa B transcription factor, p50 and p65, but not c-Rel (p85), are components of the kappa B DNA-binding activity. These data suggest that changes in cellular transcription factor binding activity are a consequence of S. flexneri invasion, and these changes could play a role in the initial host response or in the pathogenesis of the disease.
The Role of SOCS-3 in Leptin Signaling and Leptin Resistance (1999)

We earlier demonstrated that leptin induces expression of SOCS-3 mRNA in the hypothalamus. Furthermore, transfection data suggest that SOCS-3 is an inhibitor of leptin signaling. However, little is known about the regulation of SOCS-3 expression by leptin and the mechanism by which SOCS-3 inhibits leptin action. We here show that in CHO cells stably expressing the long form of the leptin receptor (CHO-OBRl), leptin induces transient expression of endogenous SOCS-3 mRNA but not of CIS, SOCS-1, or SOCS-2 mRNA. SOCS-3 protein levels were maximal after 2-3 h of leptin treatment and remained elevated at 20 h. Furthermore, in leptin-pretreated CHO-OBRl cells, proximal leptin signaling was blocked for more than 20 h after pretreatment, thus correlating with increased SOCS-3 expression. Leptin pretreatment did not affect cell surface expression of leptin receptors as measured by (125)I-leptin binding assays. In transfected COS cells, forced expression of SOCS-3 results in inhibition of leptin-induced tyrosine phosphorylation of JAK2. Finally, JAK2 co-immunoprecipitates with SOCS-3 in lysates from leptin-treated COS cells. These results suggest that SOCS-3 is a leptin-regulated inhibitor of proximal leptin signaling in vivo. Excessive SOCS-3 activity in leptin-responsive cells is therefore a potential mechanism for leptin resistance, a characteristic feature in human obesity.
Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87 (1993)

The DNA base sequence of the Pseudomonas sp. NK87 gene (P-nylB) for 6-aminohexanoate-dimer hydrolase (P-EII), a xenobiotic-compound-degrading enzyme, was determined. It has an open reading frame of 1188 bp, initiated by ATG and terminated by TAG, and coding for 396 amino acids. The base sequence of the open reading frame has 53% sequence similarity to that of the gene for the same enzyme of Flavobacterium sp. KI72 (F-nylB) and 35% sequence similarity with respect to the deduced amino acid sequence. The P-EII enzyme was purified from an Escherichia coli clone in which the P-EII gene was highly expressed. The P-EII enzyme was inhibited by a serine protease inhibitor, diisopropyl fluorophosphate, as was the F-EII enzyme. Double reciprocal plots obtained from various concentrations of 6-aminohexanoate-dimer indicated that the kcat value of the P-EII enzyme (9.2 s-1) was approximately half that of the F-EII enzyme (19 s-1), and the P-EII enzyme had higher affinity toward this substrate (Km for P-EII, 0.6 mM; Km for F-EII, 15 mM). The P-EII enzyme had a temperature optimum of 48 degrees C, and a pH optimum of 7.5. It is speculated that since the P-nylB and F-nylB genes are more diverged from each other than the corresponding nylA genes, the latter may have evolved more recently.
Real‐time magnetic resonance imaging of laser heat deposition in tissue (1991)

We applied diffusion-sensitive echo planar (Instascan) imaging to study thermal changes caused by a Nd:YAG laser. Images of phantom materials and normal rabbit brain tissue in vivo, acquired in 150 ms, every 2s, clearly showed the dynamics of temperature-related signal intensity changes in the regions irradiated by the laser.
Paragangliomas of the Neck (1992)

Between 1967 and 1990 inclusive, 28 patients with paragangliomas of the neck were diagnosed at the University of Alabama at Birmingham Affiliated Hospitals. There were 11 men and 17 women, whose ages ranged from 12 to 76 years (mean, 47 years). Tumor locations included the carotid bodies (19 cases), the vagus nerves (three), supraglottic larynx (two), the left lateral pharyngeal wall (one), posterior to the right jugular vein (not otherwise defined) (one), subcutaneous neck tissue (one), and a cervical lymph node with unknown primary (one). Diagnostic workup included angiography (23 cases) with preoperative embolization (three), computed tomography (one), magnetic resonance imaging (two), and urinary catecholamine assay (four). All 28 patients underwent resection of the lesions. Cranial nerve damage occurred in 11 patients (39%). There were no perioperative deaths or cerebrovascular accidents, although one of two saphenous vein grafts became thrombotic after carotid body tumor resection.
Collagen‐based structures containing the peptoid residue N‐isobutylglycine (Nleu): Synthesis and biophysical studies of Gly‐Pro‐Nleu sequences by circular dichroism, ultraviolet absorbance, and optical rotation (1996)

A peptoid residue N-isobutylglycine (Nleu) was introduced as a proline surrogate in collagen-like triple helical structures. A series of single chain and template-assembled collagen-based peptide-peptoid structures composed of Gly-Pro-Nleu sequences were prepared by solid-phase segment condensation methods. Both a synthetic route in solution and a solid phase method were employed to couple the KTA (cis,cis-1,3,5-trimethylcyclohexane-1,3,5-tricarboxylic acid, also known as the Kemp triacid) based template, KTA-(Gly-OH)3, to peptide-peptoid chains. Biophysical studies using CD, uv absorbance, and optical rotation measurements demonstrated that these compounds form triple-helical structures when the chains are longer than critical lengths. Results from melting curve measurements indicated that the Gly-Pro-Nleu sequence is comparable to the Gly-Pro-Pro sequence in stabilizing a triple-helical conformation. The KTA-based template stabilized triple-helical structures as can be seen by the increased melting temperatures as compared to equivalent single chain molecules. In addition, the template reduced the minimum chain length necessary to form a triple helix from six to only three trimer repeats. © 1996 John Wiley & Sons, Inc.
The Representation and Matching of Pictorial Structures (1973)

The primary problem dealt with in this paper is the following. Given some description of a visual object, find that object in an actual photograph. Part of the solution to this problem is the specification of a descriptive scheme, and a metric on which to base the decision of "goodness" of matching or detection.
Wood‐Plastic Composites Need Protection, Too (2007)

Plastics Engineering is the official publication of the Society of Plastics Engineers (SPE). We provide plastics professionals with a wealth of information about machinery, technological advances, materials innovations, sustainability, and more.
Radiofrequency multielectrode catheter ablation in the atrium (1999)

We developed a temperature-controlled radiofrequency (RF) system which can ablate by delivering energy to up to six 12.5 mm long coil electrodes simultaneously. Temperature feedback was obtained from temperature sensors placed at each end of coil electrodes, in diametrically opposite positions. The coil electrodes were connected in parallel, via a set of electronic switches, to a 150 W 500 kHz temperature-controlled RF generator. Temperatures measured at all user-selected coil electrodes were processed by a microcontroller which sent the maximum value to the temperature input of the generator. The generator adjusted the delivered power to regulate the temperature at its input within a 5 degrees C interval about a user-defined set point. The microcontroller also activated the corresponding electronic switches so that temperatures at all selected electrodes were controlled within a 5 degrees C interval with respect to each other. Physical aspects of tissue heating were first analysed using finite element models and current density measurements. Results from these analyses also constituted design input. The performance of this system was studied in vitro and in vivo. In vitro, at set temperatures of 70 degrees C, 85% of the lesions were contiguous. All lesions created at set temperatures of 80 and 90 degrees C were contiguous. The lesion length increased almost linearly with the number of electrodes. Power requirements to reach a set temperature were larger as more electrodes were driven by the generator. The system impedance decreased as more electrodes were connected in the ablation circuit and reached a low of 45.5 ohms with five coil electrodes in the circuit. In vivo, right atrial lesions were created in eight mongrel canines. The power needed to reach 70 degrees C set temperature varied between 15 and 114 W. The system impedance was 105+/-16 ohms, with one coil electrode in the circuit, and dropped to 75+/-12 ohms when two coil electrodes were simultaneously powered. The length and the width of the lesion set varied between 17.6+/-6.1 and 59.2+/-11.7 mm and 5.9+/-0.7 and 7.1+/-1.2 mm respectively. No sudden impedance rises occurred and 75% of the lesions were contiguous. From the set of contiguous lesions, 90% were potentially therapeutic as they were transmural and extended over the entire target region. The average total procedure and fluoroscopy times were 83.4 and 5.9 min respectively. We concluded that the system can safely perform long and contiguous lesions in canine right atria.
Marine bacterial, archaeal and protistan association networks reveal ecological linkages (2011)

Microbes have central roles in ocean food webs and global biogeochemical processes, yet specific ecological relationships among these taxa are largely unknown. This is in part due to the dilute, microscopic nature of the planktonic microbial community, which prevents direct observation of their interactions. Here, we use a holistic (that is, microbial system-wide) approach to investigate time-dependent variations among taxa from all three domains of life in a marine microbial community. We investigated the community composition of bacteria, archaea and protists through cultivation-independent methods, along with total bacterial and viral abundance, and physico-chemical observations. Samples and observations were collected monthly over 3 years at a well-described ocean time-series site of southern California. To find associations among these organisms, we calculated time-dependent rank correlations (that is, local similarity correlations) among relative abundances of bacteria, archaea, protists, total abundance of bacteria and viruses and physico-chemical parameters. We used a network generated from these statistical correlations to visualize and identify time-dependent associations among ecologically important taxa, for example, the SAR11 cluster, stramenopiles, alveolates, cyanobacteria and ammonia-oxidizing archaea. Negative correlations, perhaps suggesting competition or predation, were also common. The analysis revealed a progression of microbial communities through time, and also a group of unknown eukaryotes that were highly correlated with dinoflagellates, indicating possible symbioses or parasitism. Possible 'keystone' species were evident. The network has statistical features similar to previously described ecological networks, and in network parlance has non-random, small world properties (that is, highly interconnected nodes). This approach provides new insights into the natural history of microbes.
A Facile and Efficient Synthesis of 4-Hydroxy-2,6-cis-tetrahydropyrans via Tandem Cross-Metathesis/Thermal SN2′ Reaction: Protecting-Group-Free Synthesis of (±)-Diospongin A (2009)

The tandem cross-metathesis/thermal S(N)2' reaction was explored for the facile and efficient synthesis of 4-hydroxy-2,6-cis-tetrahydropyrans. The mildness of the thermal conditions allowed for the synthesis of 4-hydroxy-2,6-cis-tetrahydropyrans from base-sensitive substrates without the use of protecting groups. The tandem reaction enabled a protecting-group-free synthesis of (+/-)-diospongin A.