gebhart/patrepeval huggingface dataset:
Induction of human papillomavirus type 18 late gene expression and genomic amplification in organotypic cultures from transfected DNA templates (1997)

The genetic analysis of human papillomavirus (HPV) functions during the vegetative viral life cycle is dependent upon the ability to generate human keratinocyte cell lines which maintain episomal copies of transfected viral genomes. We have previously demonstrated that lipofection of normal human foreskin keratinocytes with recircularized cloned HPV-31 genomic sequences resulted in a high frequency of cell lines which maintained viral genomes as extrachromosomal elements (M.G. Frattini, H. Lim, and L.A. Laimins, Proc. Natl. Acad. Sci. USA 93:3062-3067, 1996). Following the growth of these cell lines in organotypic (raft) cultures, the differentiation-dependent expression of viral late genes, the amplification of viral genomes, and virion biosynthesis were observed. In the present study, we demonstrate that these methodologies are not restricted to HPV-31 but are applicable to other HPV types, including the oncogenic HPV-18. HPV-18 genomes were purified from bacterial vector sequences, religated, and transfected into normal human foreskin keratinocytes together with a neomycin-selectable marker. Following drug selection, resistant cells were expanded and examined for the state of the viral DNA. All cell lines examined were found to contain approximately 100 to 200 episomal copies of HPV-18 DNA per cell. Growth of these cell lines in raft cultures resulted in the differentiation-dependent expression of the E1 [symbol: see text] E4 and L1 capsid genes. In addition, viral genome amplification was observed in suprabasal cells following DNA in situ hybridization analysis of differentiated raft cultures. The induction of these late viral functions has previously been shown to be directly associated with differentiation-dependent virion biosynthesis. Our studies indicate the ability to perform a detailed genetic analysis of the various phases of the viral life cycle, including control of the differentiation-dependent late viral functions, using a second oncogenic HPV type.
Identification of Twelve O-Glycosylation Sites in Equine Chorionic Gonadotropin β and Equine Luteinizing Hormone β by Solid-Phase Edman Degradation1 (2001)

The O-glycosylation sites for equine LHss (eLHss) and eCGss were identified by solid-phase Edman degradation of four glycopeptides derived from the C-terminal region. Both subunits were O-glycosylated at the same 12 positions, rather than the 4-6 sites anticipated. These sites were partially glycosylated, with carbohydrate attachment ranging from 20% to 100% for eCGss and from 10% to 100% for eLHss. When the C-terminal peptide containing all but one of the O-linked oligosaccharides was removed by mild acid hydrolysis of either eLHss or eCGss, hybrid hormones could be obtained by reassociating eLHalpha,eFSHalpha, or eCGalpha with the truncated ss subunit derivatives. These hybrid hormones were identical in LH receptor-binding activity when des(121-149)eLHss or des(121-149)eCGss were combined with the same alpha subunit preparation. Thus, O-glycosylation appears to be responsible for the ss subunit contribution to the substantial difference in LH receptor-binding activity between eLH and eCG. Comparison of the equid LH/CGss sequences with those available for the primate CGss subunits indicated a greater conservation of glycosylation patterns in the former.
Isolation and characterization of HIV-2ben obtained from a patient with predominantly neurological defects (1990)

A HIV-2 strain named HIV-2ben was isolated from peripheral blood lymphocytes of a patient who, since 1984, had developed neurological symptoms such as Raynaud's syndrome, followed by paresthesia of extremities and ataxia, and finally paraparesis of the legs and incontinence. This new isolate could be distinguished from HIV-2rod by antibody-binding epitopes, peptide maps of core p24 and p18 polypeptides and restriction endonuclease cleavage pattern.
Active RNA Polymerases: Mobile or Immobile Molecular Machines? (2010)

It is widely assumed that active RNA polymerases track along their templates to produce a transcript. We test this using chromosome conformation capture and human genes switched on rapidly and synchronously by tumour necrosis factor alpha (TNFalpha); one is 221 kbp SAMD4A, which a polymerase takes more than 1 h to transcribe. Ten minutes after stimulation, the SAMD4A promoter comes together with other TNFalpha-responsive promoters. Subsequently, these contacts are lost as new downstream ones appear; contacts are invariably between sequences being transcribed. Super-resolution microscopy confirms that nascent transcripts (detected by RNA fluorescence in situ hybridization) co-localize at relevant times. Results are consistent with an alternative view of transcription: polymerases fixed in factories reel in their respective templates, so different parts of the templates transiently lie together.
Palmitoylation is required for signaling functions and membrane attachment of Gq alpha and Gs alpha. (1993)

We have identified the palmitoylated cysteine residues of alpha q and alpha s, alpha subunits of two heterotrimeric G proteins. Mutational substitutions of serines for cysteines 9 and 10 in alpha q and cysteine 3 in alpha s profoundly alter behavior of the subunits expressed in HEK293 cells. Neither mutant alpha subunit incorporates palmitate; both mutant proteins are found in the soluble rather than the particulate fraction; mutant alpha q or alpha s cannot couple a co-expressed receptor to stimulation of phospholipase C or adenylylcyclase, respectively; cysteine substitution prevents a mutationally activated alpha q (R183C) from stimulating phospholipase C directly, and reduces but does not abolish the ability of a similarly activated alpha s (R201C) to stimulate cAMP synthesis. Substitution of a myristoylation sequence for the palmitoylation sites leads to labeling of alpha q and alpha s by myristate, rather than by palmitate. Myristoylation restores the abilities of both nonpalmitoylated alpha q and alpha s to attach to membranes and, in the case of alpha q, restores its ability to stimulate phospholipase C, whether triggered by the R183C mutation or by receptor activation. These findings identify palmitoylation as a critical determinant of membrane attachment for alpha q and alpha s and show that this modification is required for normal signaling by these proteins.
Intensity discrimination of optical pulses with birefringent fibers (1982)

An intensity discriminator for optical pulses can be made with a birefringent fiber. Such a discriminator would be useful for separating the intense subpicosecond pulses formed by solitonlike compression from the weaker uncompressed background. The discriminator utilizes an intensity-dependent state of polarization out of the fiber.
Two‐component regulatory systems in <i>Pseudomonas aeruginosa</i>: an intricate network mediating fimbrial and efflux pump gene expression (2010)

Pseudomonas aeruginosa is responsible for chronic and acute infections in humans. Chronic infections are associated with production of fimbriae and the formation of a biofilm. The two-component system Roc1 is named after its role in the regulation of cup genes, which encode components of a machinery allowing assembly of fimbriae. A non-characterized gene cluster, roc2, encodes components homologous to the Roc1 system. We show that cross-regulation occurs between the Roc1 and Roc2 signalling pathways. We demonstrate that the sensors RocS2 and RocS1 converge on the response regulator RocA1 to control cupC gene expression. This control is independent of the response regulator RocA2. Instead, we show that these sensors act via the RocA2 response regulator to repress the mexAB-oprM genes. These genes encode a multidrug efflux pump and are upregulated in the rocA2 mutant, which is less susceptible to antibiotics. It has been reported that in cystic fibrosis lungs, in which P. aeruginosa adopts the biofilm lifestyle, most isolates have an inactive MexAB-OprM pump. The concomitant RocS2-dependent upregulation of cupC genes (biofilm formation) and downregulation of mexAB-oprM genes (antibiotic resistance) is in agreement with this observation. It suggests that the Roc systems may sense the environment in the cystic fibrosis lung.
Synthesis of new nitro and amino sterols; potential inhibitors of 4-methyl sterol oxidase (1988)

New 4-nitro and 4-amino 5α-steroids were made regioselectively from cholesterol via nitration of 3-acetoxy-5α-cholesta-l,3-diene (2). Nitration of enol acetate (2) gave 4α-nitro-5α-cholest-1-en-3-one (3), which was catalytically reduced to 4α-nitro-5α-cholestan-3-one (4). Sodium borohydride reduction of (4) gave 4α-nitro-5α-cholestan-3β-ol (5). Reduction of 4α-nitro-5α-cholestan-3β-ol with lithium aluminium hydride furnished 4-amino-3,4-seco-5α-cholestan-3β-ol (6), rather than the desired 4α-amino-5α-cholestan-3β-ol (8). The synthesis of compound (8) required prior derivatization of the 4α-nitro sterol as the 3-(tetrahydropyran-2-yl) ether. The related 4α-aminomethyl-5α-cholestan-3β-ol (12) has also been synthesized, via a 4α-formyl intermediate.
Segmentation of bladder tumors in cystoscopy images using a MAP approach in different color spaces (2017)

Nowadays the diagnosis of bladder lesions relies upon cystoscopic examination and depend on the interpreter's experience. State of the art of bladder tumor identification are based on 3D reconstruction, using CT images (Virtual Cystoscopy) or images where the structures are exalted with the use of pigmentations, but none uses white light cystoscopy images. Traditional cystoscopic images processing has a huge potential to improve early tumor detection and allow a more effective treatment. In this paper is described an initial approach to do segmentation of bladder cystoscopic images. This approach will be used in the future to automatically detect these types of lesions. It can be assumed that each region has a normal distribution with specific parameters, leading to the assumption that the distribution of intensities is a Gaussian Mixture Model (GMM). The most common bladder tumor type, with a cauliflower shape, appears with higher intensity than normal regions. The segmentation of these images is based on a Maximum A Posteriori (MAP) approach depending on pixel intensities of each three RGB and HSV channels, using the Expectation-Maximization (EM) algorithm to estimate the best GMM parameters. Experimental results show that the proposed method does bladder tumor segmentation in a more efficient way in RGB color space than in HSV, even in cases where the tumor shape is not well defined. Results also show that the channels with best results are the R component from RGB and the V component from HSV.
Detection of Server-side Web Attacks (2010)

Web servers and server-side applications constitute the key components of modern Internet services. We present a pattern recognition system to the detection of intrusion attempts that target such components. Our system is anomaly-based, i.e., we model the normal (legitimate) trac and intrusion attempts are identied as anomalous trac. In order to address the presence of attacks (noise) inside the training set we employ an ad-hoc outlier detection technique. This approach does not require supervision and allows us to accurately detect both known and unknown attacks against web services.
Defective development of the gall bladder and cystic duct in <i>Lgr4</i>‐ hypomorphic mice (2009)

Leucine-rich repeat (LRR) -containing G protein coupled receptor (LGR) family members are characterized by the presence of a seven-transmembrane domain and LRR motifs. We describe a new function for Lgr4 in the development of the gall bladder and cystic duct and in the epithelium-mesenchyme interaction. Lgr4 expression was observed in the gall bladder epithelium when the gall bladder primordium elongated ventrally. Although Lgr4 hypomorphic mutant (Lgr4(Gt/Gt)) embryos developed a normal gall bladder bud at embryonic day (E) 10.25, no further elongation was observed at later stages. At E12.5, the mesenchyme surrounding the gall bladder had completely disappeared in Lgr4(Gt/Gt) embryos, while the gall bladder remained unelongated. Neighboring tissues such as liver and pancreas were unaffected, as revealed by expression of marker genes. This is the first report of a mutant mouse that lacks a gall bladder and cystic duct without affecting the other tissues that derive from the same hepatic diverticulum.
The formation of reaction bonded silicon nitride from silane derived silicon powders (1989)

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 1989.
Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface (1999)

Overview of Natural Attenuation. Attenuation of Source Zones and Formation of Plumes. Abiotic Processes of Natural Attenuation. Overview of Intrinsic Bioremediation. Intrinsic Bioremediation of Petroleum Hydrocarbons. Intrinsic Bioremediation of Chlorinated Solvents. Evaluating Natural Attenuation. Modeling Natural Attenuation. Case Studies: Fuel Hydrocarbons. Case Studies: Chlorinated Solvents. Design of Long-Term Monitoring Programs. Appendices. Index.
Self-Assembly Approaches to Three-Dimensional Photonic Crystals (2001)

A brief review of the historical development of photonic bandgap (PBG) materials is provided and the fabrication methods employed are discussed with emphasis on self-assembly processes. The factors influencing the generation of a complete bandgap, from both an experimental and a calculational standpoint are then presented and discussed. The Figure shows a diamond-like 3D periodic structure.
An Electromagnetic Cycloid Motor. (1995)

A piezoelectric cycloid motor, which was proposed in a previous paper, is composed of an internal and external gear pair and four drive units containing piezoelectric actuators. The motor has hence some merits which arise from gear drive: no slip motion, long life, and precise motion. It has moreover an excellent characteristics that it rotates steadily and keeps its rotational speed up to its maximum output torque at any rotational speed. The efficiency increases as the rotational speed and the load increase. The motor, however, is subject to a drawback in that it is very difficult to miniaturize because the motor requires four magnifying lever mechanisms to increase the very small displacement, l0μm, of a piezoelectric actuator. In this paper, an electromagnetic cycloid motor is proposed, which is directly driven by four electromagnetic linear actuators instead of the four drive units. The motor rotates based on the same principle as the piezoelectric cycloid motor, but is not subject to the drawback. The output characteristics are experimentally and theoretically investigated.
Multiresolution stereo image matching using complex wavelets (2002)

This paper describes a multiresolution image-matching strategy, based on the complex discrete wavelet transform (CDWT), to derive a dense disparity field with hierarchical (coarse-to-fine) refinement. The CDWT feature space efficiently provides fractionally accurate matching results which are robust to typical image formation perturbations such as offsets, global scaling, and additive noise. At each level of the hierarchy, the disparity field is regularised to provide a global compromise between feature similarity and disparity field continuity, resulting in feature-sensitive smoothing. The algorithm is well suited to analysing facial images, for which we demonstrate striking reconstruction results.
A Comprehensive Panel of Three-Dimensional Models for Studies of Prostate Cancer Growth, Invasion and Drug Responses (2010)

Prostate epithelial cells from both normal and cancer tissues, grown in three-dimensional (3D) culture as spheroids, represent promising in vitro models for the study of normal and cancer-relevant patterns of epithelial differentiation. We have developed the most comprehensive panel of miniaturized prostate cell culture models in 3D to date (n = 29), including many non-transformed and most currently available classic prostate cancer (PrCa) cell lines. The purpose of this study was to analyze morphogenetic properties of PrCa models in 3D, to compare phenotypes, gene expression and metabolism between 2D and 3D cultures, and to evaluate their relevance for pre-clinical drug discovery, disease modeling and basic research. Primary and non-transformed prostate epithelial cells, but also several PrCa lines, formed well-differentiated round spheroids. These showed strong cell-cell contacts, epithelial polarization, a hollow lumen and were covered by a complete basal lamina (BL). Most PrCa lines, however, formed large, poorly differentiated spheroids, or aggressively invading structures. In PC-3 and PC-3M cells, well-differentiated spheroids formed, which were then spontaneously transformed into highly invasive cells. These cell lines may have previously undergone an epithelial-to-mesenchymal transition (EMT), which is temporarily suppressed in favor of epithelial maturation by signals from the extracellular matrix (ECM). The induction of lipid and steroid metabolism, epigenetic reprogramming, and ECM remodeling represents a general adaptation to 3D culture, regardless of transformation and phenotype. In contrast, PI3-Kinase, AKT, STAT/interferon and integrin signaling pathways were particularly activated in invasive cells. Specific small molecule inhibitors targeted against PI3-Kinase blocked invasive cell growth more effectively in 3D than in 2D monolayer culture, or the growth of normal cells. Our panel of cell models, spanning a wide spectrum of phenotypic plasticity, supports the investigation of different modes of cell migration and tumor morphologies, and will be useful for predictive testing of anti-cancer and anti-metastatic compounds.
Microwave Filters of Coupled Lines and Lumped Capacitances (Correspondence) (1970)

Two frequency transformations are given which enable microwave filters to be realized with coupled lines and lumped capacitances from a characteristic prototype lumped network to a good approximation. The procedore includes filters originally proposed by Matthaei and CristaI, and enables realizations for large bandwidths. A number of examples demonstrate the efficiency of the procedures.
[Characteristics of pathogenesis of acute leukemia in children]. (1991)

The main components of acute leukemia pathogenesis have been considered from the current positions: origination of the leukemic clone, characteristics of leukemia tumor histogenesis, mechanisms of proliferation and differentiation of leukemic cells. The main pathogenetic differences of acute leukemia in children and adults have been traced. The importance of these differences for the clinical picture, prognosis and response to chemotherapy has been analyzed.
Foye's Principles of Medicinal Chemistry (2012)

Acclaimed by students and instructors alike, Foye's Principles of Medicinal Chemistry is now in its Seventh Edition, featuring updated chapters plus new material that meets the needs of today's medicinal chemistry courses. This latest edition offers an unparalleled presentation of drug discovery and pharmacodynamic agents, integrating principles of medicinal chemistry with pharmacology, pharmacokinetics, and clinical pharmacy. All the chapters have been written by an international team of respected researchers and academicians. Careful editing ensures thoroughness, a consistent style and format, and easy navigation throughout the text.
Can we measure snow depth with GPS receivers? (2009)

Snow is an important component of the climate system and a critical storage component in the hydrologic cycle. However, in situ observations of snow distribution are sparse, and remotely sensed products are imprecise and only available at a coarse spatial scale. GPS geodesists have long recognized that snow can affect a GPS signal, but it has not been shown that a GPS receiver placed in a standard geodetic orientation can be used to measure snow depth. In this paper, it is shown that changes in snow depth can be clearly tracked in the corresponding multipath modulation of the GPS signal. Results for two spring 2009 snowstorms in Colorado show strong agreement between GPS snow depth estimates, field measurements, and nearby ultrasonic snow depth sensors. Because there are hundreds of geodetic GPS receivers operating in snowy regions of the U.S., it is possible that GPS receivers installed for plate deformation studies, surveying, and weather monitoring could be used to also estimate snow depth.
Camera control and decoupled motion for teleoperation (2004)

Human judgment is an integral part of the teleoperation process that is often heavily influenced by a single video feed returned from the remote environment. This limitation on the perceptual links to the environment leaves the operator prone to cognitive mistakes and general disorientation. These faults may be enhanced or muted, depending on the camera mountings and control opportunities that are at the disposal of the operator. These issues form the basis for an experiment to assess the effectiveness of existing and potential teleoperation controls. Findings suggest that providing a camera that is controlled independently from the orientation of the vehicle may yield significant benefits.
ChemInform Abstract: Synthesis of Highly Ordered Carbon Molecular Sieves via Template‐Mediated Structural Transformation. (1999)

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.
Thromboxane synthase immunohistochemistry in inflammatory bowel disease (2002)

Increased thromboxane synthase expression in lamina propria cells occurs in active inflammatory bowel disease. It is possible that this results in increased thromboxane synthesis, which may in turn contribute to mucosal inflammation and intramucosal thrombogenesis.
Base-Mediated Conversion of Hydrazine to Diazene and Dinitrogen at an Iron Center (2008)

The treatment of the hydrazine complex cis-[Fe(N(2)H(4))(dmpe)(2)](2+) with base afforded the diazene complex cis-[Fe(N(2)H(2))(dmpe)(2)]. This reaction is reversed by the treatment of the diazene complex with a mild acid, while treatment of the hydrazine complex with a mixture of KOBu(t) and Bu(t)Li afforded the dinitrogen complex [Fe(N(2))(dmpe)(2)].