gebhart/patrepeval huggingface dataset:
Human cancers express a mutator phenotype (2006)

Cancer cells contain numerous clonal mutations, i.e., mutations that are present in most or all malignant cells of a tumor and have presumably been selected because they confer a proliferative advantage. An important question is whether cancer cells also contain a large number of random mutations, i.e., randomly distributed unselected mutations that occur in only one or a few cells of a tumor. Such random mutations could contribute to the morphologic and functional heterogeneity of cancers and include mutations that confer resistance to therapy. We have postulated that malignant cells exhibit a mutator phenotype resulting in the generation of random mutations throughout the genome. We have recently developed an assay to quantify random mutations in human tissue with unprecedented sensitivity. Here, we report measurements of random single-nucleotide substitutions in normal and neoplastic human tissues. In normal tissues, the frequency of spontaneous random mutations is exceedingly low, less than 1 x 10(-8) per base pair. In contrast, tumors from the same individuals exhibited an average frequency of 210 x 10(-8) per base pair, an elevation of at least two orders of magnitude. Our data document tumor heterogeneity at the single-nucleotide level, indicate that accelerated mutagenesis prevails late into tumor progression, and suggest that elevation of random mutation frequency in tumors might serve as a novel prognostic indicator.
Image-Guided Tumor Ablation: Emerging Technologies and Future Directions (2010)

As the trend continues toward the decreased invasiveness of medical procedures, image-guided percutaneous ablation has begun to supplant surgery for the local control of small tumors in the liver, kidney, and lung. New ablation technologies, and refinements of existing technologies, will enable treatment of larger and more complex tumors in these and other organs. At the same time, improvements in intraprocedural imaging promise to improve treatment accuracy and reduce complications. In this review, the latest advancements in clinical and experimental ablation technologies will be summarized, and new applications of image-guided tumor ablation will be discussed.
Netalyzr (2010)

In this paper we present Netalyzr, a network measurement and debugging service that evaluates the functionality provided by people's Internet connectivity. The design aims to prove both comprehensive in terms of the properties we measure and easy to employ and understand for users with little technical background. We structure Netalyzr as a signed Java applet (which users access via their Web browser) that communicates with a suite of measurement-specific servers. Traffic between the two then probes for a diverse set of network properties, including outbound port filtering, hidden in-network HTTP caches, DNS manipulations, NAT behavior, path MTU issues, IPv6 support, and access-modem buffer capacity. In addition to reporting results to the user, Netalyzr also forms the foundation for an extensive measurement of edge-network properties. To this end, along with describing Netalyzr 's architecture and system implementation, we present a detailed study of 130,000 measurement sessions that the service has recorded since we made it publicly available in June 2009.
Effect of thermal expansion on shape memory behavior of polyurethane and its nanocomposites (2008)

Abstract The effects of thermal expansion on shape memory performance of shape memory polyurethanes and their nanocomposites with organoclay, carbon nanofiber (CNF), silicon carbide (SiC), and carbon black (CB) were evaluated. The shape memory test cycle involved tensile deformation at above the trigger temperature to initiate shape memory function, cooling to room temperature to fix the shape, and shape recovery induced by heating to above the trigger temperature. Phenomenological models were used to interpret the experimental data on coefficient of thermal expansion (CTE). It was found that Kerner model showed good fit for composites of SiC and CB, and Halpin model gave better fit for composites of organoclay and CNF. It was observed that thermal expansion exerts negative effect on recovered strain, the extent of which depends on the magnitude of temperature gradient, CTE, and the level of tensile strain. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1437–1449, 2008
Hydrazine Detection Using a Tyrosinase-Based Inhibition Biosensor (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleHydrazine Detection Using a Tyrosinase-Based Inhibition BiosensorJoseph. Wang and Liang. ChenCite this: Anal. Chem. 1995, 67, 20, 3824–3827Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ac00116a035https://doi.org/10.1021/ac00116a035research-articleACS PublicationsRequest reuse permissionsArticle Views371Altmetric-Citations71LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Binding of the virion protein mediating alpha gene induction in herpes simplex virus 1-infected cells to its cis site requires cellular proteins. (1987)

In herpes simplex virus 1-infected cells, the transcription of alpha genes, the first set of genes to be expressed, is induced by a virion component, the alpha-trans-induction factor, and requires a cis site. Homologs of the cis site are present in the promoter-regulatory domains of all alpha genes and bind two cellular proteins designated as alpha H1 and alpha H2-alpha H3. We report that alpha-trans-induction factor, synthesized in vitro or present in nuclear extracts of infected cells, forms complexes with viral DNA fragments containing its cis-acting site only in the presence of cellular proteins and only under conditions that also enable the binding of the alpha H1 protein to the DNA. The induction of alpha genes by alpha-trans-induction factor appears, therefore, to be mediated by the interaction of the viral protein with cellular proteins at its cis-acting site.
Lawyer Distress: Alcohol-Related Problems and Other Psychological Concerns Among a Sample of Practicing Lawyers (1995)

Holding that an "attorney suffering from depression was suspended from the practice of law for a period of 120 days; suspension was to ensure there would be evidence of a meaningful and sustained recovery before the attorney was allowed to return to practice.”
Endogenous DNA double-strand breaks: Production, fidelity of repair, and induction of cancer (2003)

This article extends our previous quantitative analysis of the relationship between the dynamics of the primary structure of DNA and mutagenesis associated with single-strand lesions to an analysis of the production and processing of endogenous double-strand breaks (EDSBs) and to their implications for oncogenesis. We estimate that in normal human cells approximately 1% of single-strand lesions are converted to approximately 50 EDSBs per cell per cell cycle. This number is similar to that for EDSBs produced by 1.5-2.0 Gy of sparsely ionizing radiation. Although EDSBs are usually repaired with high fidelity, errors in their repair contribute significantly to the rate of cancer in humans. The doubling dose for induced DSBs is similar to doubling doses for mutation and for the induction of carcinomas by ionizing radiation. We conclude that rates of production of EDSBs and of ensuing spontaneous mitotic recombination events can account for a substantial fraction of the earliest oncogenic events in human carcinomas.
Preparation and Characterization of Cholic Acid-Derived Antimicrobial Agents with Controlled Stabilities (2000)

[reaction: see text] Novel cholic acid-derived antimicrobial agents that decompose under mildly basic conditions have been prepared. These compounds range in biological properties from potent antibacterial activity to effective permeabilization of the outer membranes of Gram-negative bacteria.
Fourier-domain digital holographic optical coherence imaging of living tissue (2007)

Digital holographic optical coherence imaging is a full-frame coherence-gated imaging approach that uses a CCD camera to record and reconstruct digital holograms from living tissue. Recording digital holograms at the optical Fourier plane has advantages for diffuse targets compared with Fresnel off-axis digital holography. A digital hologram captured at the Fourier plane requires only a 2D fast Fourier transform for numerical reconstruction. We have applied this technique for the depth-resolved imaging of rat osteogenic tumor multicellular spheroids and acquired cross-section images of the anterior segment and the retinal region of a mouse eye. A penetration depth of 1.4 mm for the tumor spheroids was achieved.
Applications of EcR gene switch technology in functional genomics (2007)

Genetic engineering of plants using transgenic technology is targeted to enhance agronomic performance or improved quality traits in a wide variety of plant species, and has become a fundamental tool for basic research in plant biotechnology. Constitutive promoters are presently the primary means used to express transgenes in plants. However, inducible gene regulation systems based on specific chemicals have many potential applications in agriculture and for enhancing the basic understanding of gene function. As a result, several gene switches have been developed. The ecdysone receptor gene switch is one of the best inducible gene regulation systems available, because the chemical, methoxyfenozide, required for its regulation is registered for field use. An EcR gene switch with a potential for use in large-scale field applications has been developed by adopting a two-hybrid format. In a two-hybrid switch format, the GAL4 DNA binding domain (GAL4 DBD) was fused to the ligand binding domain (LBD) of the Choristoneura fumiferana ecdysone receptor (CfEcR); and, the VP16 activation domain (VP16 AD) was fused to the LBD of Locust migratoria retinoid X receptor (LmRXR). The sensitivity of the CfEcR gene switch was improved from micromolar to nanomolar concentrations of ligand by using the CfEcR:LmRXR two-hybrid switch. In this report, we demonstrate the utility of CfEcR:LmRXR two-hybrid gene switch in functional genomics applications for regulating the expression of a Superman-like single zinc finger protein 11 (ZFP11) gene in both Arabidopsis and tobacco transgenic plants.
A transient calcium‐dependent potassium component of the epileptiform burst after‐hyperpolarization in rat hippocampus. (1988)

1. The epileptiform burst potential produced by picrotoxin is a model of the interictal spike potential seen in epilepsy. We have studied the epileptiform burst after-hyperpolarization (epileptiform burst AHP) using intracellular recording from rat CA1 hippocampal pyramidal cells in the slice preparation. In most experiments burst potentials were induced by electrical stimulation of afferent fibres, but in some experiments bursts that arose spontaneously were also investigated. 2. Previous evidence suggested that the epileptiform burst AHP has two slow K+-dependent components and that both components would be blocked by phorbol esters that activate protein kinase C. We found that phorbol esters indeed blocked the slow components, but also uncovered a transient hyperpolarizing component of the epileptiform burst AHP. This phorbol-ester-insensitive component (the transient AHP) peaked approximately 65 ms after the onset of the stimulus and lasted approximately 150 ms. The transient AHP is K+ dependent since its reversal potential shifted in elevated [K+]o, whereas Cl- loading of the cell had no effect on either its development or reversal potential. 3. The transient AHP was either greatly reduced or abolished by 5-10 mM-tetraethylammonium (TEA) and by 15-20 nM-charybdotoxin (CTX), both of which block a particular Ca2+-dependent K+ current. Concomitant with the block of the transient AHP was a significant increase in burst duration. The transient AHP was not blocked by up to 1 mM-4-aminopyridine (4-AP), 1 mM-N'-2'-O-dibutyryl-adenosine 3':5'-cyclic monophosphate (dBcAMP) or 50 microM-carbamylcholine (carbachol), and burst duration was relatively unaffected by these agents. 4. The transient AHP is Ca2+ dependent: (1) it was often associated with the occurrence of a slow, Ca2+-dependent spike; (2) its amplitude was increased in either elevated [Ca2+] saline or in (3) Bay K 8644 (5-10 microM), a compound that prolongs the open time of certain Ca2+ channels. 5. We conclude that a Ca2+-dependent K+ conductance is transiently activated by the epileptiform burst potential. Its distinctive pharmacological profile indicates that it is fundamentally different from the slow Ca2+-dependent K+ conductance. The Ca2+-dependent K+ current, IC, may mediate the transient AHP. Our data also suggest that the transient AHP conductance plays an important role in repolarizing the membrane after bursts of action potentials.
rev protein of human immunodeficiency virus type 1 affects the stability and transport of the viral mRNA. (1989)

rev (trs/art) is an essential human immunodeficiency virus type 1 (HIV-1) regulatory protein. rev increases the levels of the gag- and env-producing mRNAs via a cis-acting element in the env region of HIV-1, named rev-responsive element. Our results show that rev increases the stability of the unspliced viral mRNA, while it does not affect the stability of the multiply spliced viral mRNAs that do not contain the rev-responsive element. The study of mutated proviral constructs producing mRNA that cannot be spliced revealed that the effect of rev on stability is independent of splicing. Our experiments also indicate that rev promotes the transport of the viral mRNA containing the rev-responsive element from the nucleus to the cytoplasm. The proposed functions of rev are consistent with its nuclear localization as shown by immunofluorescence. The selective effects of rev on the levels of the viral mRNA suggest a model for feedback regulation by rev leading to a steady state of viral expression.
A Cytoplasmic Substrate of Mitogen-Activated Protein Kinase Is Responsible for Estrogen Receptor-α Down-Regulation in Breast Cancer Cells: The Role of Nuclear Factor-κB (2004)

Estrogen receptor alpha (ERalpha) negative breast tumors often present with enhanced expression and/or activation of growth factor receptors, resulting in increased growth factor signaling and hyperactivation of MAPK (ERK1 and ERK2). We have pre-viously shown that ERalpha(+) MCF-7 cells with elevated growth factor signaling lose expression of ERalpha without any ligand-independent transcriptional activation, and this is a reversible effect attributable to ERK1/2 hyperactivation. Here, we show that down-regulation of ERalpha is not mediated by a specific ERK-1 vs. ERK-2 substrate. Despite up-regulated activator protein-1 activity in response to ERK1/2 activation, and in ERalpha(-) and hormone-independent breast cancers, we find that increased activator protein-1 activity is not responsible for ERalpha down-regulation. Interestingly, our findings implicate a cytoplasmic substrate of ERK1/2. However, RSK1, the best-characterized cytoplasmic ERK1/2 substrate, does not down-regulate ERalpha in our models. On the other hand, inhibition of nuclear factor-kappaB (which is linked to chemoresistance in cancer in general and has elevated activity in hormone-independent and ERalpha- breast cancer) significantly enhances ERalpha activity, suggesting that indirect elevation in nuclear factor-kappaB activity (due to hyperactive ERK1/2) is at least partially responsible for ERalpha down-regulation in these cell line models.
Maps of optical differential pathlength factor of human adult forehead, somatosensory motor and occipital regions at multi-wavelengths in NIR (2002)

The optical differential pathlength factor (DPF) is an important parameter for physiological measurement using near infrared spectroscopy, but for the human adult head it has been available only for the forehead. Here we report measured DPF results for the forehead, somatosensory motor and occipital regions from measurements on 11 adult volunteers using a time-resolved optical imaging system. The optode separation was about 30 mm and the wavelengths used were 759 nm, 799 nm and 834 nm. Measured DPFs were 7.25 for the central forehead and 6.25 for the temple region at 799 nm. For the central somatosensory and occipital areas (10 mm above the inion), DPFs at 799 nm are 7.5 and 8.75, respectively. Less than 10% decreases of DPF for all these regions were observed when the wavelength increased from 759 nm to 834 nm. To compare these DPF maps with the anatomical structure of the head, a Monte Carlo simulation was carried out to calculate DPF for these regions by using a two-layered semi-infinite model and assuming the thickness of the upper layer to be the sum of the thicknesses of scalp and skull, which was measured from MRI images of a subject's head. The DPF data will be useful for quantitative monitoring of the haemodynamic changes occurring in adult heads.
The Drosophila rhodopsin cytoplasmic tail domain is required for maintenance of rhabdomere structure (2006)

The ninaE-encoded Rh1 rhodopsin is the major light-sensitive pigment expressed in Drosophila R1-6 photoreceptor cells. Rh1 rhodopsin localizes to and is essential for the development and maintenance of the rhabdomere, the specialized membrane-rich organelle that serves as the site of phototransduction. We showed previously that the vertebrate bovine rhodopsin (Rho) is expressed and properly localized in Drosophila photoreceptor cells. Drosophila photoreceptors expressing only Rho have normal rhabdomere structure at young ages, but the rhabdomeres are not maintained and show extensive disorganization by 7-10 days of age. A series of Rho-Rh1 opsin chimeric rhodopsins were used to identify Rh1 domains required for maintenance of rhabdomeric structure. The results show that the Rh1 rhodopsin cytoplasmic tail domain, positioned to interact with cytoplasmic structural components, plays a major role in promoting rhabdomeric organization.
A novel tripodal tris-hydroxypyrimidinone sequestering agent for trivalent hard metal ions: synthesis, complexation and in vivo studies (2012)

A new tripodal hexadentate ligand, NTP(PrHPM)(3), having three hydroxypyrimidinone (HPM) chelating units attached to a nitrilotripropionic acid (NTP) has been prepared and studied in terms of thermodynamic stability of the complexes with iron, aluminium and gallium and it has been subsequently in vivo assayed for its capacity to remove hard metal ions from an animal model overloaded with (67)Ga. The anchoring of the HPM units to the NTP scaffold revealed to be an interesting alternative to the reported hexadentate tris(3-hydroxy-4-pyridinone) analogue, NTP(PrHP)(3), because the new tris-HPM ligand still keeps high chelating capacity for hard metal ions and presents better water-solubility (log P = -1.51). The in vivo studies show that NTP(PrHPM)(3) induces a faster clearance from main organs and an enhancement of overall excretion, as compared with the commercial drug, DFP, or the bidentate HPM compound (HOPY-PrN), albeit slightly lower than the tris-hydroxypyridinone analogue, NTP(PrHP)(3). The solution and in vivo results herein presented encourage further studies envisaging the potential clinical applications of hexadentate HPM derivatives as metal sequestering agents.
Leidenfrost Point Reduction on Micropatterned Metallic Surfaces (2012)

Droplets are able to levitate when deposited over a hot surface exceeding a critical temperature. This is known as the Leidenfrost effect. This phenomenon occurs when the surface is heated above the so-called Leidenfrost point (LFP), above which the vapor film between the droplet and hot surface is able to levitate the droplet. Such a critical temperature depends on several factors. One of the most studied parameters has been the surface roughness. Almost all of the experimental studies in the literature have concluded that the LFP increases with the roughness. According to these results, it seems that the roughness is detrimental for the stability of the vapor film. In contrast with these results, we present here a micropatterned surface that significantly reduces the LFP. The temperature increase, relative to the boiling point, required to reach the LFP is 70% lower than that on the flat surface. The reasons for such an effect are qualitatively and quantitatively discussed with a simple semiempirical model. This result can be relevant to save energy in applications that take advantage of the Leidenfrost effect for drop control or drag reduction.
The HIV-1 Aspartyl Protease: Maturation and Substrate Specificity (1990)

In all retroviruses, the viral aspartyl protease is first translated as part of a large polyprotein precursor, the 160 kilodalton gag-pol polyprotein in the case of HIV-1 (Rey et al, 1987; Jacks et al, 1988). Experimental evidence strongly suggests that HIV-1 viral particles initially bud out of the host cell with an immature structure and composition, containing unprocessed PrSSgag and Pr160gag-Pol polyproteins (Hockley et al, 1988; Gottlinger et al, 1989, Peng et al, 1989). The question of when and how the protease actually processes these polyproteins is important for the understanding of the viral life cycle but remains to be answered. In an effort to gain information on this process, we undertook a series of genetic studies in Escherichia coli on the maturation of the protease from its precursor forms and on this protease substrate preferences. This information should not only contribute to our understanding of the viral maturation process, but also assist us in the design of inhibitors of this essential viral enzyme.