gebhart/patrepeval huggingface dataset:
ErpA, an iron–sulfur (Fe–S) protein of the A-type essential for respiratory metabolism in <i>Escherichia coli</i> (2007)

Understanding the biogenesis of iron-sulfur (Fe-S) proteins is relevant to many fields, including bioenergetics, gene regulation, and cancer research. Several multiprotein complexes assisting Fe-S assembly have been identified in both prokaryotes and eukaryotes. Here, we identify in Escherichia coli an A-type Fe-S protein that we named ErpA. Remarkably, erpA was found essential for growth of E. coli in the presence of oxygen or alternative electron acceptors. It was concluded that isoprenoid biosynthesis was impaired by the erpA mutation. First, the eukaryotic mevalonate-dependent pathway for biosynthesis of isopentenyl diphosphate restored the respiratory defects of an erpA mutant. Second, the erpA mutant contained a greatly reduced amount of ubiquinone and menaquinone. Third, ErpA bound Fe-S clusters and transferred them to apo-IspG, a protein catalyzing isopentenyl diphosphate biosynthesis in E. coli. Surprisingly, the erpA gene maps at a distance from any other Fe-S biogenesis-related gene. ErpA is an A-type Fe-S protein that is characterized by an essential role in cellular metabolism.
<i>Dyrk1A</i> Haploinsufficiency Affects Viability and Causes Developmental Delay and Abnormal Brain Morphology in Mice (2002)

DYRK1A is the human orthologue of the Drosophila minibrain (mnb) gene, which is involved in postembryonic neurogenesis in flies. Because of its mapping position on chromosome 21 and the neurobehavioral alterations shown by mice overexpressing this gene, involvement of DYRK1A in some of the neurological defects of Down syndrome patients has been suggested. To gain insight into its physiological role, we have generated mice deficient in Dyrk1A function by gene targeting. Dyrk1A(-/-) null mutants presented a general growth delay and died during midgestation. Mice heterozygous for the mutation (Dyrk1A(+/-)) showed decreased neonatal viability and a significant body size reduction from birth to adulthood. General neurobehavioral analysis revealed preweaning developmental delay of Dyrk1A(+/-) mice and specific alterations in adults. Brains of Dyrk1A(+/-) mice were decreased in size in a region-specific manner, although the cytoarchitecture and neuronal components in most areas were not altered. Cell counts showed increased neuronal densities in some brain regions and a specific decrease in the number of neurons in the superior colliculus, which exhibited a significant size reduction. These data provide evidence about the nonredundant, vital role of Dyrk1A and suggest a conserved mode of action that determines normal growth and brain size in both mice and flies.
A zooming Web browser (1996)

The World Wide Web (WWW) is becoming increasingly important for business, education, and entertainment. Popular web browsers make access to Internet information resources relatively easy for novice users. Simply by clicking on a link, a new page of information replaces the current one on the screen. Unfortunately however, after following a number of links, people can have difficulty remembering where they’ve been and navigating links they have followed. As one’s collection of web pages grows and as more information of interest populates the web, effective navigation becomes an issue of fundamental importance. We are developing a prototype zooming browser to explore alternative mechanisms for navigating the WWW. Instead of having a single page visible at a time, multiple pages and the links between them are depicted on a large zoomable information surface. Pages are scaled so that the page in focus is clearly readable with connected pages shown at smaller scales to provide context. As a link is followed the new page becomes the focus and existing pages are dynamically repositioned and scaled. Layout changes are animated so that the focus page moves smoothly to the center of the display surface while contextual information provided by linked pages scales down. While our browser supports multiscale representations of existing HTML pages, we have also extended HTML to support multiscale layout within a page. This extension, Multi-Scale Markup Language (MSML), is at an early stage of development. It currently supports inclusion within a page of variable-sized dynamic objects, graphics, and other interface mechanisms from our
Respiration uncoupling and metabolism in the control of energy expenditure (2005)

Metabolic energy expenditure negatively regulates energy balance. Metabolic and catabolic pathways contribute to energy expenditure. Catabolic pathways split C-containing molecules into small molecules and generate reduced coenzymes and ATP. For a given amount of substrate, any increase in energy expenditure requires either increased ATP hydrolysis or decreased ATP synthesis. In skeletal muscles substrate utilisation is coupled to ATP production, whereas ATP hydrolysis is activated during physical exercise and increases energy expenditure. In brown adipose tissue activation of cells during exposure to cold increases substrate utilisation in such a way that glucose and fatty acid oxidation detach from the orthodox coupling to ATP synthesis and result in thermogenesis. The unique mechanism of uncoupling respiration that occurs in brown adipocyte mitochondria represents an attractive strategy for promoting energy expenditure and decreasing the fat content of the body. Moreover, ectopic expression of brown fat uncoupling protein (UCP) 1 in mouse skeletal muscle and induction of UCP1 in mouse or human white adipocytes promote fatty acid oxidation and resistance to obesity. In normal conditions UCP2 and UCP3 do not seem to contribute substantially to energy expenditure. Whether the induction of UCP1, the induction of other UCP or chemical mild uncoupling represent promising strategies for attenuating nutrient efficiency and counteracting obesity should be considered.
Process variations aware area efficient negative bit-line voltage scheme for improving write ability of SRAM in nanometer technologies (2012)

The increased device variations, lower supply voltages have enforced the usage of write-assist circuits in static random access memory (SRAMs) in the nano-complementary metal oxide semiconductor (CMOS) regime. Negative bit-line scheme during write has been found one of the most promising write-assist solutions. A new low power, negative bit-line scheme is presented. The presented negative bit-line technique can be used to improve the write ability of 6 T single-port (SP) as well as 8 T dual-port (DP) and other multiport SRAM cells. Negative voltage is generated on-chip using capacitive coupling. Only the bit-line on which a ‘0’ is to be written is taken negative during write operation. The proposed circuit design topology does not affect the read operation for bit-interleaved architectures enabling high-speed operation. Simulation results and comparative study of the present scheme with state-of-the art conventional schemes proposed in the literature for 45 nm CMOS technology show that the proposed scheme is superior in terms of process-variations impact, area overhead, timings and dynamic power consumption.
Polymeric Membranes for Aromatic/Aliphatic Separation Processes (2002)

For the membrane-based separation of benzene/cyclohexane mixtures, the pervaporation properties of different 6FDA (4,4'-hexafluoroisopropylidene diphthalic anhydride) based copolyimide membranes have been investigated. In order to obtain high permeability as well as high selectivity copolyimides were synthesised using a combination of 4MPD (2,3,5,6-tetramethyl-1,4-phenylene diamine) and 6FpDA (4,4'-hexafluoro-isopropylidene dianiline) as well as DABA (3,5-diaminobenzoic acid) as monomers. Cross-linking is possible with this type of copolyimides and necessary to reduce swelling effects, which often occur with polymeric membranes and lead to a deterioration of the separation characteristics in aromatic/aliphatic separation processes. In order to find the most suitable membrane material, the polymer structure, the crosslinking agents, as well as the crosslinking methods have been varied. The separation characteristics have been determined by sorption and pervaporation experiments. Sorption experiments have been carried out at 60 degrees C using benzene, toluene and ethylbenzene as aromatic components and cyclohexane, cyclohexene, hexane and heptane as aliphatic solvents. Pervaporation experiments have been performed at 60 degrees C using benzene/cyclohexane mixtures with benzene concentrations covering the whole concentration range. It has been found that crosslinked copolyimide membranes show excellent chemical resistance, strongly reduced swelling behaviour and higher selectivity in aromatic/aliphatic separation compared to conventional membrane materials.
Oasis: Procedurally Generated Social Virtual Spaces from 3D Scanned Real Spaces (2017)

We present Oasis, a novel system for automatically generating immersive and interactive virtual reality environments for single and multiuser experiences. Oasis enables real-walking in the generated virtual environment by capturing indoor scenes in 3D and mapping walkable areas. It makes use of available depth information for recognizing objects in the real environment which are paired with virtual counterparts to leverage the physicality of the real world, for a more immersive virtual experience. Oasis allows co-located and remotely located users to interact seamlessly and walk naturally in a shared virtual environment. Experiencing virtual reality with currently available devices can be cumbersome due to presence of objects and furniture which need to be removed every time the user wishes to use VR. Our approach is new, in that it allows casual users to easily create virtual reality environments in any indoor space without rearranging furniture or requiring specialized equipment, skill or training. We demonstrate our approach to overlay a virtual environment over an existing physical space through fully working single and multiuser systems implemented on a Tango tablet device.
Illumination methods for optical wear detection (2007)

The paper presents some results of a study on optical wear detection. The focus of the paper is on the illumination, to optimize the contrast of the images. Various illumination methods are compared: bright field versus dark field illumination, and various kind of light sources: laser light, diffuse light and ring-light.
Additive effect of TRAIL and p53 gene transfer on apoptosis of human lung cancer cell lines (2004)

TRAIL is a cytokine that can induce tumor-specific apoptosis through its specific death receptors (DR4 and DR5) and p53 has been proven to increase the expression of death receptors. To examine their interaction in tumor suppression, p53 and TRAIL genes were inserted in recombinant adenovirus vectors and transferred simultaneously into non-small cell lung cancer cell lines (NCI-H157, NCI-H358, NCI-H460 and A549). Western blot assay demonstrated production of TRAIL protein in NCI-H157 and A549 cell lines. Increased expressions of DR4 and DR5 of NCI-H157 and DR4 of A549 after p53 overexpression were confirmed by flow cytometry. p53 or TRAIL gene transfer increased sub-G1 fraction in cell cycle analysis and inhibited the tumor growth dose-dependently and the degree was potentiated by co-transfer. But isobologram analysis indicated an additive effect. Together, these data indicate that p53 and TRAIL interact additively on tumor apoptosis despite theoretical synergism.
Dynamic Concept Composition for Zero-Example Event Detection (2016)

In this paper, we focus on automatically detecting events in unconstrained videos without the use of any visual training exemplars. In principle, zero-shot learning makes it possible to train an event detection model based on the assumption that events (e.g. birthday party) can be described by multiple mid-level semantic concepts (e.g. ``blowing candle'', ``birthday cake''). Towards this goal, we first pre-train a bundle of concept classifiers using data from other sources. Then we evaluate the semantic correlation of each concept w.r.t. the event of interest and pick up the relevant concept classifiers, which are applied on all test videos to get multiple prediction score vectors. While most existing systems combine the predictions of the concept classifiers with fixed weights, we propose to learn the optimal weights of the concept classifiers for each testing video by exploring a set of online available videos with free-form text descriptions of their content. To validate the effectiveness of the proposed approach, we have conducted extensive experiments on the latest TRECVID MEDTest 2014, MEDTest 2013 and CCV dataset. The experimental results confirm the superiority of the proposed approach.
Chloroquine inhibits cyclization of squalene oxide to lanosterol in mammalian cells. (1984)

Chloroquine inhibits the incorporation of [14C]acetate into sterols at a concentration of 10 microM or more in mouse L cells but has no effect on fatty acid synthesis and CO2 production from the same substrate even at a 10-fold higher concentration of the drug. The site of inhibition is distal to the formation of mevalonate since chloroquine also inhibits [14C]mevalonate metabolism to sterols and does not decrease the activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (EC 1.1.1.34) or the incorporation of [14C]acetate into the total nonsaponifiable lipids. Analyses by thin layer and high pressure liquid chromatography of the nonsaponifiable lipid fraction from cultures incubated with chloroquine show an accumulation of radioactivity in the region of squalene oxide. Identification of the radiolabeled lipid as squalene oxide has been established by: (a) its co-migration with the authentic squalene oxide standard; (b) its conversion into squalene glycol by acid hydrolysis; and (c) its further metabolism to desmosterol when chloroquine is removed from the medium. Addition of chloroquine (12.5-50 microM) to 20,000 X g supernatant fractions of mouse liver homogenates inhibits the incorporation of [14C]mevalonolactone into cholesterol and lanosterol, with corresponding increases of [14C]squalene oxides, in a concentration-dependent manner. It appears, therefore, that chloroquine inhibits the enzymatic step catalyzed by 2,3-oxidosqualene-lanosterol cyclase (EC 5.4.99.7). Incubation of cell cultures with chloroquine (50 microM) arrests cell growth and causes cell death after 1-3 days. However, simultaneous incubation of chloroquine with either cholesterol or lanosterol prevents cell death and permits cell growth. Uptake of chloroquine is not affected by exogenous sterols since intracellular chloroquine concentrations are the same in cells grown with or without added sterols. The cytotoxicity of chloroquine, under our experimental conditions, must, therefore, be due primarily to its inhibition of sterol synthesis. In addition to its well known effect on protein catabolism, chloroquine has been found to inhibit protein synthesis. The significance of these findings concerning the use of chloroquine in studying the regulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity is discussed.
Growth-dependent inhibition of CCAAT enhancer-binding protein (C/EBP alpha) gene expression during hepatocyte proliferation in the regenerating liver and in culture. (1992)

As an approach to understanding physiological mechanisms that control the proliferation of highly differentiated cells, we are addressing whether certain hepatic transcription factors participate in mechanisms that control the growth of hepatocytes. We have focused on CCAAT enhancer-binding protein (C/EBP alpha), a transcription factor which is highly abundant in normal liver and is considered to regulate expression of many genes, including some involved in energy metabolism (S. L. McKnight, M. D. Lane, and S. Gluecksohn-Walsh. Genes Dev. 3:2021-2024, 1989). Using Northern (RNA) blot analysis, we have examined the expression of C/EBP alpha mRNA during liver regeneration and in primary cultures of hepatocytes. C/EBP alpha mRNA levels decrease 60 to 80% within 1 to 3 h after partial hepatectomy as the cells move from G0 to G1 and decrease further when cells progress into S phase. Run-on transcription analysis is in agreement with the Northern blot data, thus suggesting that C/EBP alpha is transcriptionally regulated in regenerating liver. C/EBP alpha mRNA expression also decreases dramatically during the growth of freshly isolated normal hepatocytes cultured under conventional conditions (on dried rat tail collagen; stimulated to proliferate by epidermal growth factor [EGF] and insulin). Cultures of hepatocytes on rat tail collagen in the presence or absence of EGF clearly show that within 3 h, EGF depresses C/EBP alpha mRNA expression and that this effect is substantially greater by 4 h. Inhibition of protein synthesis in the liver by cycloheximide or in cultured hepatocytes by puromycin or cycloheximide effectively blocks the down-regulation of C/EBP alpha gene expression, apparently by stabilizing the normal rapid turnover of the C/EBP alpha mRNA (half-life of <2 h). This drop in C/EBP alpha gene expression in response to activation of hepatocyte growth is consistent with the proposal that C/EBP alpha has an antiproliferative role to play in highly differentiated cells (R. M. Umek, A. D. Friedman, and S. L. McKnight, Science 251: 288-292, 1991).
Distribution and Maturation of Skin Dendritic Cell Subsets in Two Forms of Cutaneous T-Cell Lymphoma: Mycosis Fungoides and Sézary Syndrome (2012)

Dendritic cells (DCs) critically regulate immune responses and the "immune-surveillance" of tumours. This study retrospectively analysed the distribution and maturation status of DC-subsets in T-cell lymphoma of the skin. Mycosis fungoides and Sézary syndrome (n = 25) were investigated immunohistochemically for DC subsets, based on C-type lectin receptor expression: Langerhans' cells (langerin/CD207+, DEC-205/CD205+), dermal DCs (DC-SIGN/CD209+, CD205+) and plasmacytoid DC (BDCA-2/CD303+). Maturation status was assessed by double-labelling for CD83 and CD208/DC-LAMP. DCs were interspersed between the neoplastic infiltrate, and a marked increase in numbers of all three subsets was noted, DC-SIGN+ dermal DCs constituting the majority. Substantial numbers of plasmacytoid DCs were consistently observed. Most DCs in epidermis and dermis were phenotypically immature. Amongst the relatively few mature DCs in the dermis, langerin+ cells predominated. There was a positive correlation between the histological intensity of the tumour infiltrate and DC numbers. It is possible that mature DCs reflect ongoing anti-tumour immune responses, and immature DCs the induction of tumour tolerance.
Targeting tumor microenvironment: crossing tumor interstitial fluidby multifunctional nanomedicines (2014)

The cancerous cells attain unique abilities to form its permissive microenvironment, wherein (a) extracellular pH is dysregulated towards acidification, (b) extracellular matrix (ECM) is deformed, (c) stromal cells are cooperative with cancer cells, (d) immune system mechanisms are defective, (e) non-integrated irregular microvasculature with pores (120-1200 nm) are formed, and (h) interstitial fluid pressure is high. All these phenomena are against cancer treatment modalities. As a result, to control such abnormal pathophysiologic traits, novel cancer therapy strategies need to be devised using multifunctional nanomedicines and theranostics.
Analysis of cerebellar function in Ube3a-deficient mice reveals novel genotype-specific behaviors (2008)

Angelman syndrome (AS) is a childhood-onset neurogenetic disorder characterized by functionally severe developmental delay with mental retardation, deficits in expressive language, ataxia, appendicular action tremors and unique behaviors such as inappropriate laughter and stimulus-sensitive hyperexcitibility. Most cases of AS are caused by mutations which disrupt expression of maternal UBE3A. Although some progress has been made in understanding hippocampal-related memory and learning aspects of the disorder using Ube3a deficient mice, the numerous motoric abnormalities associated with AS (ataxia, action tremor, dysarthria, dysphagia, sialorrhea and excessive chewing/mouthing behaviors) have not been fully explored with mouse models. Here we use a novel quantifiable analysis of fluid consumption and licking behavior along with a battery of motor tests to examine cerebellar and other motor system defects in Ube3a deficient mice. Mice with a maternally inherited Ube3a deficiency (Ube3a(m-/p+)) show defects in fluid consumption behavior which are different from Ube3a(m-/p-) mice. The rhythm of fluid licking and number of licks per visit were significantly different among the three groups (m-/p-, m-/p+, m+/p+) and indicate that not only was fluid consumption dependent on Ube3a expression in the cerebellum, but may also depend on low levels of Ube3a expression in other brain regions. Additional neurological testing revealed defects in both Ube3a(m-/p+) and Ube3a(m-/p-) mice in rope climbing, grip strength, gait and a raised-beam task. Long-term observation of fluid consumption behavior is the first phenotype reported that differentiates between mice with a maternal loss of function versus complete loss of Ube3a in the brain. The neuronal and molecular mechanisms underlying mouse fluid consumption defects specifically associated with maternally inherited Ube3a deficiency may reveal important new insights into the pathobiology of AS in humans.
Biofouling Growth in Cold Estuarine Waters and Evaluation of Some Chitosan and Copper Anti-Fouling Paints (2009)

Ecological concerns about antifouling paints containing non-green tin and copper compounds have highlighted the need for environmentally friendly alternatives. We report here a field test conducted in estuarine waters over two months designed to evaluate the efficiency of a number of active natural and man-made chemical ingredients added into a silicon-polyurethane marine paint. Early steps of biofouling in cold seawater of the St. Lawrence Estuary (Canada) were observed. Analyses, including dry biomass, flow cytometry and spectrofluorimetry, demonstrated a short-term antibacterial action of chitosan-based paints although no significant anti-algal action was observed. Cuprous oxide paints were efficient against bacteria and algae invasion in the first two weeks, especially those with added organic biocides such as isothiazolone and copper pyrithione. However, the overall dry biomass and chlorophyll a content were similar for all chitosan-and copper-based paints after 63 days. Microscopic observations revealed variation in the highly diverse benthic diatom population including species Navicula, Melosira, Cocconeis, Nitshzcia, Fragilaria and Amphora. Results suggest no real long-term efficiency for tested antifouling paints and highlight a particular need for green antifouling ingredients that are active under northern estuarine conditions.
Bismuth Subgallate–Epinephrine Paste in Adenotonsillectomies (2000)

OBJECTIVE:To evaluate the role of bismuth subgallate–epinephrine (BSE) paste as a hemostatic in adenotonsillectomies.DATA SOURCES:MEDLINE (January 1966–October 1999) and Current Contents (January 1997–October 1999) were searched, using bismuth subgallate, adenoidectomy, tonsillectomy, and adenotonsillectomy as search terms. A citation search was performed using Science Citation Index (January 1977–October 1999).DATA SYNTHESIS:Adenotonsillectomies are common procedures; although there are few complications, hemorrhage is a concern. Bismuth subgallate has historically been used as an astringent and hemostatic. An evaluation of studies of bismuth subgallate and BSE paste was conducted.CONCLUSIONS:There is minimal evidence to support this practice, but data suggest that epinephrine may be the active ingredient in BSE paste. BSE paste is inexpensive, poses little risk, and may decrease postoperative bleeding; therefore, it may be a reasonable hemostatic agent.