gebhart/patrepeval huggingface dataset:
Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing (2015)

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM- EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes- ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.
7.6 A 512&#x00D7;424 CMOS 3D Time-of-Flight image sensor with multi-frequency photo-demodulation up to 130MHz and 2GS/s ADC (2014)

Interest in 3D depth cameras has been piqued by the release of the Kinect motion sensor for the Xbox 360 gaming console. This paper presents the pixel and 2GS/s signal paths in a state-of-the-art Time-of-Flight (ToF) sensor suitable for use in the latest Kinect sensor for Xbox One. ToF cameras determine the distance to objects by measuring the round trip travel time of an amplitude-modulated light from the source to the target and back to the camera at each pixel. ToF technology provides an accurate high pixel resolution, low motion blur, wide field of view (FoV), high dynamic range depth image as well as an ambient light invariant brightness image (active IR) that meets the highest quality requirements for 3D motion detection.
Effect of Automatic Ball Balancer on Unbalanced Rotor Vibration (2017)

Rotor vibration due to unbalance causes a lot of problems during operation. One of the simplest ways to reduce rotor vibration is the passive balancing. Unbalanced vertical rotor is modeled by a two degrees of freedom system considering Jeffcott model assumption. A (2+n) degrees of freedom mathematical model is derived with respect to a Cartesian co-ordinate system for the unbalanced rotor with the automatic ball balancer. The model equations are expressed as state equations then solved numerically to calculate vibration amplitudes and angular positions of balancing balls. Model validation is achieved by comparing these results with a three-dimensional model. The effect of the automatic ball balancer on vibration amplitudes is explained at different speed ranges. A parametric study is done to explain the effect of the system damping coefficient on the ball balancer behaviors.
A multiple shared memory switch (2002)

One of the problems that shared memory switches have is that in order to build large switches the memory access requirements become stringent. One way to overcome this is to utilize multiple buffers which space division multiplex the input lines and thereby alleviate the memory access requirements. However, previous attempts to implement multi-buffered shared memory switches have suffered from serious limitations. The authors describe in this work a multi-buffered architecture that offers tremendous potential. It is able to fully share the buffer, it guarantees the minimum delay switching of all cells, it can accomplish multi-cast and multi-channel switching, it can accommodate various priorities and classes of traffic while maintaining high performance on account of very efficient buffer utilization.
Analysis of the binding of C-reactive protein to chromatin subunits (1991)

C-reactive protein (CRP) is an acute phase serum protein in man. The functional activities of CRP, like Ig, include complement activation and enhancement of phagocytosis. CRP binding to several substrates, including phosphocholine, individual denatured histones, and chromatin, has been demonstrated. We previously demonstrated that CRP binding to chromatin is dependent on the presence of histone H1, despite the fact that CRP binds to purified individual histones H2A and H2B, as well as to H1. In this report we examined the binding of CRP to native sub-nucleosomal chromatin fragments. CRP binding to the H2A-H2B dimer and (H3-H4)2 tetramer was demonstrated and these reactions were inhibited by phosphocholine. However, no binding to the subnucleosome complexes (H2A-H2B)-DNA and (H3-H4)2-DNA was seen. Similarly, CRP binding to H1 was eliminated when H1 was reconstituted with DNA. The reconstitution of H1-depleted chromatin with H1 restored CRP binding. CRP binding to nucleosome core particles, as previously demonstrated by others, was confirmed. Therefore, the interaction of CRP with individual core histones does not appear to be responsible for the binding of CRP to native chromatin. However, binding to core particles could be mediated by differentially exposed determinants on H2A and H2B.
Cyclic hydroxamates, especially multiply substituted [1,2]oxazinan-3-ones (2003)

Routes to putative N-acyl-D-ala-D-ala surrogates, beginning with the conversion of 4-, 5-, and 6-membered lactones into 5-, 6-, and 7-membered cyclic hydroxamates, are reported. The key step of the synthesis is trimethylaluminium-promoted cyclization of an ω-aminooxyester. The 7-membered cyclic hydroxamate crystallizes in a chair conformation. Extension of the reaction sequence to homoserine or homoserine lactone leads to cyclocanaline and N-acylated cyclocanalines. The 4-phenylacetamido derivative of cyclocanaline crystallizes in a boat conformation. The attachment of a 2-carboxypropyl substituent to the ring nitrogen of a 4-acylaminocyclocanaline has been effected, prior to cyclization, by coupling of the acyclic aminooxyester precursor to the triflate of benzyl lactate or, after cyclization, by coupling to tert-butyl α-bromopropionate in the presence of potassium fluoride  alumina, followed by removal of the protecting group in each case. A six-membered homolog of the antibiotic lactivicin has been synthesized by the reaction of 4-phenylacetamidocyclocanaline with benzyl 2-oxoglutarate in the presence of carbodiimide, followed by hydrogenolysis. Starting with methyl 2,4-dibromo-2,4-dideoxy-L-erythronate, which is available in two steps from L-ascorbic acid, these reaction sequences have been applied to the stereospecific synthesis of a D-alanine derivative whose nitrogen atom is enclosed within a 3,4-disubstituted [1,2]oxazinan-3-one. Key words: D-ala-D-ala surrogate, cyclocanaline, homolactivicin, peptidoglycan, trimethylaluminium.
Magnetic guidance of ferrofluidic nanoparticles in an<i>in vitro</i>model of intraocular retinal repair (2003)

Agarose gel at a concentration of 0.6% was used to simulate the vitreous body of the eye during the infusion of a ferrofluid and the subsequent magnetic concentration of it onto a surrogate retinal surface. The 10 nm Fe3O4 particles in the ferrofluid served to mimic the cobalt particles in a silicone magnetic fluid that is being developed for use as a tamponading agent in magnetic fluid therapies designed to alleviate retinal detachments and other types of retinopathy. Magnetically guided interstitial diffusion of the nanoparticles through up to 20 mm of the gel over periods of 72 h was shown to be possible, thus demonstrating that essentially all points on the retinal surface are reachable from elsewhere in the ocular interior. The nanodynamics of the magnetic and viscous forces at work on the particles during movement through the gel are discussed; in particular the diffusion speeds of the particles are estimated and compared with observations.
Analgetics Based on the Pyrrolidine Ring. II. (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalgetics Based on the Pyrrolidine Ring. II.J. F. Cavalla, R. A. Selway, J. Wax, L. Scotti, and C. V. WinderCite this: J. Med. Chem. 1962, 5, 3, 441–451Publication Date (Print):May 1, 1962Publication History Published online1 May 2002Published inissue 1 May 1962https://pubs.acs.org/doi/10.1021/jm01238a004https://doi.org/10.1021/jm01238a004research-articleACS PublicationsRequest reuse permissionsArticle Views79Altmetric-Citations4LEARN 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 options Get e-Alerts
Collagen-bound von Willebrand Factor Has Reduced Affinity for Factor VIII (1999)

von Willebrand factor (vWf) is a multimeric adhesive glycoprotein that serves as a carrier for factor VIII in plasma. Although each vWf subunit displays a high affinity binding site for factor VIII in vitro, in plasma, only 2% of the vWf sites for factor VIII are occupied. We investigated whether interaction of plasma proteins with vWf or adhesion of vWf to collagen may alter the affinity or availability of factor VIII-binding sites on vWf. When vWf was immobilized on agarose-linked monoclonal antibody, factor VIII bound to vWf with high affinity, and neither the affinity nor binding site availability was influenced by the presence of 50% plasma. Therefore, plasma proteins do not alter the affinity or availability of factor VIII-binding sites. In contrast, when vWf was immobilized on agarose-linked collagen, its affinity for factor VIII was reduced 4-fold, with KD increasing from 0.9 to 3.8 nM. However, one factor VIII-binding site remained available on each vWf subunit. A comparable reduction in affinity for factor VIII was observed when vWf was a constituent of the subendothelial cell matrix and when it was bound to purified type VI collagen. In parallel with the decreased affinity for factor VIII, collagen-bound vWf displayed a 6-fold lower affinity for monoclonal antibody W5-6A, with an epitope composed of residues 78-96 within the factor VIII-binding motif of vWf. We conclude that collagen induces a conformational change within the factor VIII-binding motif of vWf that lowers the affinity for factor VIII.
Depot‐Specific Expression of Fibroblast Growth Factors in Human Adipose Tissue (2002)

We show that several members of the FGF family are expressed in human adipose tissue, and that the expression for some of the FGFs differs between sc and om adipose tissue. Taken together with previously published reports on the biological effects of FGFs on adipose cells, our results suggest that locally expressed FGFs could play role in the regulation of regional adipose tissue mass.
Isolation and Laboratory Maintenance of <i>Treponema pallidum</i> (2007)

The spirochetal bacteria that cause syphilis, yaws, and bejel cannot be cultivated in vitro. This unit describes methods for the isolation of subspecies of Treponema pallidum and other pathogenic treponemes from clinical specimens, the propagation of these isolates in rabbits, isolation of clonal populations of T. pallidum, and techniques for maintenance of frozen stocks of these treponemes.
Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food (2011)

Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.
Fuel Optimal Powertrain Control for Heavy Trucks Utilizing Look Ahead (2009)

The road topography in highways affects the powertrain control of a heavy truck substantially since the engine power is low in relation to the vehicle weight. In large road gradients constant speed is not possible to keep, which would have been beneficial otherwise, and in some uphills shifting gears becomes inevitable. If information about the road ahead, i.e. look ahead information, is available, then the powertrain can be controlled in a more fuel efficient way. Trial runs are performed, where the velocity trajectory that minimizes energy consumption, is calculated and communicated in real time as set points to the conventional cruise control. This look ahead control gives significant fuel consumption reductions compared to a standard cruise control, while keeping to the same mean speed. The results are the inspiration to further studies in how powertrain control can benefit from look ahead information. An engine with a non-linear fuel map is studied to understand its impact on fuel optimal speed. It is shown that for a significant fuel map non-linearity, quantified by a threshold value, constant speed in small road gradients is no longer optimal. Further, an automated manual transmission (AMT) optimal gear control is studied. It is shown that the reduced propulsion of a typical AMT gear-shifting process must be considered when choosing when to shift gears. Thus, additional reductions of fuel consumption are obtained with a look ahead control based on knowledge of engine and transmission characteristics.
Performance assessment of the Optical Transient Detector and Lightning Imaging Sensor (2007)

We describe the clustering algorithm used by the Lightning Imaging Sensor (LIS) and the Optical Transient Detector (OTD) for combining the space‐based observations of lightning pulse data into events, groups, flashes, and areas. Events are single pixels that exceed the LIS/OTD background level during a single frame (2 ms). Groups are clusters of events that occur within the same frame and in adjacent pixels. Flashes are clusters of groups that occur within 330 ms and either 5.5 km (for LIS) or 16.5 km (for OTD) of each other. Areas are clusters of flashes that occur within 16.5 km of each other. The flash data from LIS/OTD are currently being used for lightning and thunderstorm processes and climatological studies; therefore we test how variations in the algorithms for the event‐group and group‐flash clustering affect the flash count for a subset of the LIS and OTD data. We divided the subset into areas with low (1–3), medium (4–15), high (16–63), and very high (64+) flash counts to see how changes in the clustering parameters affect the flash rates in these different sizes of areas. We found that as long as the cluster parameters are within about a factor of two of the current values, the overall flash counts do not change by more than about 20%. Therefore the flash clustering algorithm used by the LIS and OTD sensors are robust and create flash rates that are relatively insensitive to reasonable variations in the clustering algorithms.
Cuenesics (2014)

Most of today's public displays only show predefined contents that passers-by are not able to change. We argue that interactive public displays would benefit from immediately usable mid-air techniques for choosing options, expressing opinions or more generally selecting one among several items. We propose a design space for hand-gesture based mid-air selection techniques on interactive public displays, along with four specific techniques that we evaluated at three different locations in the the field. Our findings include: 1) if no hint is provided, people successfully use Point+Dwell for selecting items, 2) the user representation could be switched from Mirror to Cursor after registration without causing confusion, 3) people tend to explore items before confirming one, 4) in a public context, people frequently interact inadvertently (without looking at the screen). We conclude by providing recommendations for designers of interactive public displays to support immediate usability for mid-air selection.
Comportamiento de la infección experimental por aislamientos colombianos de Giardia duodenalis en el modelo animal del gerbo (Meriones unguiculatus). (2005)

Introduction. Natural and experimental Giardia infections have been reported from bovines, equines, goats, canines, felines and rodents such as mice, rats and gerbils. The latter have provided successful animal models for Giardia duodenalis and Giardia muris experimental infections.Objective. The gerbil model was used to establish the pattern of infection of Colombian Giardia human isolates.Materials And Methods. Giardia cysts were obtained from stool specimens of symptomatic giardiasis patients by means of sucrose-percoll gradients. Animal inoculation was performed by gastric intubation and injection with 5 x 10(3) Giardia cysts. The course of infection was established by counting cysts every day and trophozoites weekly throughout a period of 30 days.Results. The pattern of cyst excretion was found to be intermittent. Cysts were released during the second and third weeks of infection but not during the first or fourth weeks. The mean minimal number of cysts released per 2-hr collection period was 79 and the mean maximum number was 17,943. Colonization of the small intestine by trophozoites was observed with a mean number ranging from 15,000 to 6,577,778 trophozoites/ml.Discussion And Conclusions. Gerbils inoculated with G. duodenalis isolates obtained from geographical areas outside Colombia resolved the infection between 86 and 114 days after infection, whereas gerbils infected with Colombian G. duodenalis isolates resolved the infection at 30 days. The gerbil proved to be a good animal model for experimental infection with Colombian isolates of G. duodenalis. Experimental Giardia infection of gerbils permit a sufficient yield of cysts and trophozoites to be used as antigens for the immunization of other animals and to obtain Giardia antibodies that could be used for Giardia antigen detection assays in stool specimens.
Detecting and Quantifying a Massive Invasion of Floating Aquatic Plants in the Río de la Plata Turbid Waters Using High Spatial Resolution Ocean Color Imagery (2018)

The massive development of floating plants in floodplain lakes and wetlands in the upper Middle Paraná river in the La Plata basin is environmentally and socioeconomically important. Every year aquatic plant detachments drift downstream arriving in small amounts to the Río de la Plata, but huge temporary invasions have been observed every 10 or 15 years associated to massive floods. From late December 2015, heavy rains driven by a strong El Niño increased river levels, provoking a large temporary invasion of aquatic plants from January to May 2016. This event caused significant disruption of human activities via clogging of drinking water intakes in the estuary, blocking of ports and marinas and introducing dangerous animals from faraway wetlands into the city. In this study, we developed a scheme to map floating vegetation in turbid waters using high-resolution imagery, like Sentinel-2/SMI (MultiSpectral Imager), Landsat-8/OLI (Operational Land Imager), and Aqua/MODIS (MODerate resolution Imager Spectroradiometer)-250 m. A combination of the Floating Algal Index (that make use of the strong signal in the NIR part of the spectrum), plus conditions set on the RED band (to avoid misclassifying highly turbid waters) and on the CIE La*b* color space coordinates (to confirm the visually “green” pixels as floating vegetation) were used. A time-series of multisensor high resolution imagery was analyzed to study the temporal variability, covered area and distribution of the unusual floating macroalgae invasion that started in January 2016 in the Río de la Plata estuary.
Solution-Phase Synthesis of Cu<sub>2</sub>O Nanocubes (2002)

We report here the solution-phase synthesis of highly uniform and monodisperse cubic Cu2O nano- and microcubes. Copper(II) salts in water are reduced with sodium ascorbate in air, in the presence of a surfactant. The average edge length of the cubes varies from 200 to 450 nm, as a function of surfactant concentration. Transmission electronic microscopy suggests that these cubes are composed of small nanoparticles and appear to be hollow.
Clinical use of HCG and hCG beta determinations. (1993)

Recent advances in our understanding of hCG/hCG beta synthesis by trophoblastic and nontrophoblastic tissues together with improved techniques for measuring hCG have helped to define the role of hCG as a clinical marker. HCG determination by sensitive immunometric assay enables detection of hCG immunoreactivity in normal men and women. It facilitates early detection of normal pregnancy and significantly contributes to the diagnosis of various pregnancy-related disorders, such as ectopic pregnancy, spontaneous abortion, hydatidiform mole, choriocarcinoma or Trisomy 21. Further, determination of this marker is immensely helpful to guide curative intervention in testicular cancer. For diagnosis and follow-up of patients with testicular cancer, a method measuring both hCG and hCG beta or separate methods for each component are recommended, because a significant portion of seminoma exclusively secrete free hCG beta. Also, hCG beta production by other than trophoblastic malignancies has been well recognized. A possible clinical use of hCG beta as a marker of cancers of the bladder, pancreas or biliary tract is currently debated.