gebhart/patrepeval huggingface dataset:
Signatures of copy number alterations in human cancer (2022)

Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy<sup>1,2</sup>. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance<sup>3-5</sup>. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas<sup>6</sup> revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.
Light irradiation and applied voltage history sensors using amorphous In-Ga-Zn-O thin-film transistors exposed to ozone annealing and fabricated under high oxygen pressure (2014)

We have developed light irradiation and applied voltage history sensors using amorphous In-Ga-Zn-O (oc-IGZO) thin-film transistor (TFTs) exposed to ozone annealing and fabricated under high oxygen pressure. These a-IGZO TFTs have an interesting property; the Ids-Vgs characteristic shifts positively and becomes steep when gate voltage is applied whereas it recover the initial one with a small threshold voltage and a large subthreshold swing upon light illumination. Therefore, these a-IGZO TFTs can be used as light irradiation history sensors; first, the gate voltage is applied to initialize the Ids-Vgs characteristic, next, the light is irradiated and finally, the Ids-Vgs characteristic is measured which depends on the light irradiation history. Moreover, these a-IGZO TFTs can be also used as applied voltage history sensors; first, the light is irradiated to initialize the Ids-Vgs characteristic, next, the gate voltage is applied and finally, the Ids-Vgs characteristic is measured which depends on the value or time of the applied voltage.
UV-Induced DNA Interstrand Cross-Linking and Direct Strand Breaks from a New Type of Binitroimidazole Analogue (2015)

Four novel photoactivated binitroimidazole prodrugs were synthesized. These agents produced DNA interstrand cross-links (ICLs) and direct strand breaks (DSB) upon UV irradiation, whereas no or very few DNA ICLs and DSBs were observed without UV treatment. Although these four molecules (1-4) contain the same binitroimidazole moiety, they bear four different leaving groups, which resulted in their producing different yields of DNA damage. Compound 4, with nitrogen mustard as a leaving group, showed the highest ICL yield. Surprisingly, compounds 1-3, without any alkylating functional group, also induced DNA ICL formation, although they did so with lower yields, which suggested that the binitroimidazole moiety released from UV irradiation of 1-3 is capable of cross-linking DNA. The DNA cross-linked products induced by these compounds were completely destroyed upon 1.0 M piperidine treatment at 90 °C (leading to cleavage at dG sites), which revealed that DNA cross-linking mainly occurred via alkylation of dGs. We proposed a possible mechanism by which alkylating agents were released from these compounds. HRMS and NMR analysis confirmed that free nitrogen mustards were generated by UV irradiation of 4. Suppression of DNA ICL and DSB formation by a radical trap, TEMPO, indicated the involvement of free radicals in the photo reactions of 3 and 4 with DNA. On the basis of these data, we propose that UV irradiation of compounds 1-4 generated a binitroimidazole intermediate that cross-links DNA. The higher ICL yield observed with 4 resulted from the amine effector nitrogen mustard released from UV irradiation.
The fluorouridine insensitive 1 (fur1) mutant is defective in equilibrative nucleoside transporter 3 (ENT3), and thus represents an important pyrimidine nucleoside uptake system in Arabidopsis thaliana (2007)

The fluorouridine insensitive 1 (fur1) locus in Arabidopsis thaliana (L.) Heynh. has previously been identified in a screen for growth resistance towards the toxic compound fluorouridine. Mutation of this locus by ethylmethane sulfonate (EMS) allows mutants to grow on this uridine analogue. We identified that the A. thaliana equilibrative nucleoside transporter (AtENT3) was encoded by the fur1 locus. T-DNA insertional mutant plants for AtENT3 resemble the fur1 mutant phenotype: i.e. they grow on fluorouridine, and seedlings as well as leaf discs exhibit a markedly reduced uptake capacity for uridine and cytidine, but a less pronounced reduced uptake for adenosine and guanosine. These results indicate that AtENT3 is an important pyrimidine nucleoside transporter in Arabidopsis. In addition, we identified the mutation in fur1 as a single base-pair exchange, guanine --> adenine, leading to an amino acid exchange G --> R at position 281. Furthermore, we showed that this mutation is indeed responsible for the observed alterations in nucleoside transport in the fur1-1 line, because the introduction of this mutation in AtENT3 promoted fluorouridine resistance in yeast cells expressing this mutated protein. The biochemical characterization of AtENT3 expressed in Xenopus oocytes identified a proton-coupled concentrative mode of nucleoside transport, although this carrier possesses structural features characteristic for equilibrative nucleoside carriers.
Ambivalence, Uncertainty, and Processes of Candidate Evaluation (2003)

The on‐line and memory‐based processing models of candidate evaluation can be better understood by incorporating the concepts of ambivalence and uncertainty, both as subjective feeling states and as objective properties of information. An experiment was designed to address three questions: What are the relationships between ambivalence and uncertainty? What are the informational foundations of subjective ambivalence and uncertainty, and to what extent are they rooted in on‐line (time of exposure) and memory‐based (time of judgment) processes? What are the consequences of ambivalence and uncertainty for candidate evaluation? The results suggest that (1) subjective uncertainty is more strongly rooted in information about the candidate than is subjective ambivalence; (2) subjective uncertainty and (to a lesser extent) ambivalence are associated with an increased propensity to engage in memory‐based processing; and (3) subjective ambivalence and uncertainty result in more negative evaluations, particularly among less sophisticated people. These results suggest ways in which the on‐line and memory‐based models might productively be combined.
Spectroscopic study of quantized breakdown voltage states of the quantum Hall effect (1994)

Quantized breakdown voltage states are observed in a second, wide, high-quality GaAs/AlGaAs sample made from another wafer, demonstrating that quantization of the longitudinal voltage drop along the sample is a general feature of the quantum Hall effect in the breakdown regime. The voltage states are interpreted in a simple energy conservation model as occurring when electrons are excited to higher Landau levels and then return to the original level. A spectroscopic study of these dissipative voltage states reveals how well they are quantized. The statistical variations of the quantized voltages increase linearly with quantum number.
Variation in Three Single Nucleotide Polymorphisms in the Calpain-10 Gene Not Associated With Type 2 Diabetes in a Large Finnish Cohort (2002)

Variations in the calpain-10 gene have recently been reported to be associated with type 2 diabetes in a Mexican-American population. We typed three single nucleotide polymorphisms (SNPs) in the calpain-10 gene (SNPs 43, 56, and 63) to test for association between variation at these loci and type 2 diabetes and diabetes-related traits in 1,603 Finnish subjects: two samples of 526 (Finland-U.S. Investigation of NIDDM Genetics [FUSION] 1) and 255 (FUSION 2) index case subjects with type 2 diabetes, 185 and 414 unaffected spouses and offspring of FUSION 1 index case subjects or their affected siblings, and 223 elderly normal glucose-tolerant control subjects. We found no significant differences in allele, genotype, haplotype, or haplogenotype frequencies between index case subjects with diabetes and the elderly and spouse control populations (all P > 0.087). Although variation in these three SNPs was associated with variation in some type 2 diabetes-related traits within each of the case and control groups, no consistent pattern of the implicated variant or combination of variants was discerned. We conclude that variation in these three SNPs in the calpain-10 gene is unlikely to confer susceptibility to type 2 diabetes in this Finnish cohort.
Driven ring oscillators as FPGA entropy sources (2019)

We show various degrees of complex behavior in driven ring oscillators on inexpensive FPGA student evaluation boards. Although ring oscillators typically give periodic behavior, they provide unpredictable, aperiodic behavior when driven at certain frequencies. Various non-ideal effects permit positive entropy due to the dynamics of this arrangement. The resulting topology is a driven, Boolean network consisting of long-established oscillator configurations. We implement ring oscillators driven by a variable frequency square wave generator. The resulting spectrum and autocorrelation illustrate various degrees of complex behavior. This work gives an accessible method for studying the complex dynamics found in Boolean networks through the combination of a simple, well-known network topology paired with convenient FPGA hardware.
Las Cámaras de Comercio durante el franquismo: el caso salmantino (1992)

Este libro que ahora presentamos ofrece los resultados de una intensa investigacion sobre unas instituciones de dilatada a la vez que poco estudiada trayectoria, las Camaras de Comercio. Pese a su presencia en la mayoria de los paises del mundo, pese a su actividad desplegada en el nuestro desde hace ya mas de 100 anos, realmente muy pocas veces se ha abordado su labor desde perspectivas que fueran mas alla de la mera descripcion o la facil apologia. En estos momentos, en los que sus funciones y caracter vuelven a estar -de nuevo sometidos a discusion. Puede ser de interes reflexionar sobre su compleja e interesante historia.Numero de Paginas: 289.
Polymer-clay nanocomposites (2000)

Contributors. Series Preface. Preface. Polymer-clay Intercalates. Layered Silicate-Polymer Intercalation Compounds. Electroactive Polymers Intercalated in Clays and Related Solids. Polymer-Clay Nanocomposites Derived from Polymer-Silicate Gels. Polymerization of Organic Monomers and Biomolecules on Hectorite. Nanocomposite Synthesis and Properties. Polymer-Clay Nanocomposites. In Situ Polymerization Route to Nylon 6-Clay Nanocomposites. Epoxy-Clay Nanocomposites. Polypropylene-Clay Nanocomposites. Polyethylene Terephthalate-Clay Nanocomposites. Special Properties and Applications. Polymer-Layered Silicate Nanocomposites with Conventional Flame Retardants. Nanocomposite Technology for Enhancing the Gas Barrier of Polyethylene Terephthalate. Structure and Rheology. Structural Characterization of Polymer-Layered Silicate Nanocomposites. New Conceptual Model for Interpreting Nanocomposite Behavior. Modeling the Phase Behavior of Polymer-Clay Nanocomposites. Rheological Properties of Polymer-Layered Silicate Nanocomposites. Index.
Physical and electrical characteristics of silicon oxynitride films with various refractive indices (2009)

This study explores the relationship between both the physical and the electrical characteristics of silicon oxynitride (SiON) films and the refractive index. The single wafer rapid thermal process modules were used for low pressure chemical vapour deposition of SiON films. A series of SiON films with refractive index between 1.50 and 1.83 were fabricated. Fourier transform infrared absorption spectroscopy and x-ray photoelectron spectroscopy identified the chemical bonding configurations of different SiON films: the Si–N bonds are replaced by Si–O bonds as the refractive index of the SiON films declines. Moreover, the Si atomic ratio is kept between 35% and 40% while the oxygen atomic ratio increases and the nitrogen atomic ratio decreases as the refractive index of the SiON film declines. The electrical characteristics of different SiON-based silicon–oxide–nitride–oxide–silicon (SONOS) devices suggest that (1) the dielectric constant increases with increasing refractive index of the SiON film and (2) the charge-trap density is inversely proportional to the oxygen concentration in the SiON film. Based on these results, the SiON films with various refractive indices can provide a wider application for silicon-based devices, such as SONOS and MOS devices.
Fast Node Overlap Removal in Graph Layout Adjustment (2022)

Most graph layout algorithms in the field of graph drawing treat nodes as points. The problem of node overlap removal is to adjust the layout generated by such methods so that nodes of non-zero width and height do not overlap, yet are as close as possible to their original positions. We give an O(n log n) algorithm for achieving this assuming that the number of nodes overlapping any single node is bounded by some constant. This method has two parts, a constraint generation algorithm which generates a linear number of “separation” constraints and an algorithm for finding a solution to these constraints “close” to the original node placement values. We also extend our constraint solving algorithm to give an active set based algorithm which is guaranteed to find the optimal solution but which has considerably worse theoretical complexity. We compare our method with convex quadratic optimization and force scan approaches and find that it is faster than either, gives results of better quality than force scan methods and similar quality to the quadratic optimisation approach.
Lespedeza capitata Michx. (2005)

https://thekeep.eiu.edu/herbarium_specimens_byname/13615/thumbnail.jpg
Mechanics of Fluids (2012)

MECHANICS OF FLUIDS presents fluid mechanics so that students gain an understanding of and an ability to analyze the important phenomena encountered by practicing engineers. The authors succeed in this through the use of several pedagogical tools (Margin Notes, Chapter Outlines, Summaries, and a nomenclature list) that help students visualize the many difficult-to-understand phenomena of fluid mechanics. Potter and Wiggert base their explanations on basic physical concepts and mathematics which are accessible to undergraduate engineering students, such as differential equations and vector algebra.
A homogeneous scintillation proximity assay for acetyl coenzyme A carboxylase coupled to fatty acid synthase (2006)

We have devised a rapid and sensitive homogeneous assay for acetyl CoA carboxylase (ACC) in a scintillation proximity assay format suitable for high-throughput screening. In this assay, ACC is coupled to fatty acid synthase (FAS). Malonyl CoA, the product of the ACC reaction, and acetyl CoA serve as substrates for FAS to synthesize palmitic acid. When [3H]acetyl CoA is used in the ACC/FAS coupled system, [3H]palmitic acid, the final product, is readily detected by scintillation proximity in a FlashPlate or Image FlashPlate coated with phospholipid. The [3H]palmitic acid binds to the coated phospholipid through hydrophobic interaction which brings it into close proximity of the scintillant on the FlashPlate or the Image FlashPlate, yielding photons that are read in a TopCount or LeadSeeker, respectively. The current assay consists of simple reagent addition, incubation, and detection of signal. The signal is ∼30-fold over the background and the Z′ value is ∼0.80, suggesting that this assay is robust and highly reproducible. To our knowledge this ACC/FAS coupled scintillation proximity assay is the only assay format that is compatible with high-throughput screening for systematic search of inhibitors against mammalian ACC.
Distributed collaborative localization of multiple vehicles from relative pose measurements (2009)

We propose a distributed algorithm for estimating the poses (positions and orientations) of multiple autonomous vehicles in GPS denied scenarios when pairs of vehicles can measure each other's relative pose in their local coordinates. Currently, navigation of an autonomous vehicle in GPS denied scenarios is achieved by integrating relative pose measurements between successive time instants that are obtained from onboard sensors, such as cameras and IMUs. However, this suffers from a high rate of error growth over time. We seek methods to ameliorate this error growth by using cooperation among a group of vehicles. Measurements of relative pose between certain pairs of vehicles provide extra information on their poses, which can be used for improving localization accuracy. We designed a distributed algorithm to fuse all the relative pose measurements to compute a more accurate estimate of all the vehicles' poses than what is possible by the vehicles individually. The algorithm is fully distributed since only neighboring vehicles need to exchange information periodically. Monte Carlo simulations show that the error in the location estimates obtained by using this algorithm is significantly lower than what is achieved when vehicles estimate their poses without cooperation.
Ebola Hemorrhagic Fever, Kikwit, Democratic Republic of the Congo, 1995: Risk Factors for Patients without a Reported Exposure (1999)

In 1995, 316 people became ill with Ebola hemorrhagic fever (EHF) in Kikwit, Democratic Republic of the Congo. The exposure source was not reported for 55 patients (17%) at the start of this investigation, and it remained unknown for 12 patients after extensive epidemiologic evaluation. Both admission to a hospital and visiting a person with fever and bleeding were risk factors associated with infection. Nineteen patients appeared to have been exposed while visiting someone with suspected EHF, although they did not provide care. Fourteen of the 19 reported touching the patient with suspected EHF; 5 reported that they had no physical contact. Although close contact while caring for an infected person was probably the major route of transmission in this and previous EHF outbreaks, the virus may have been transmitted by touch, droplet, airborne particle, or fomite; thus, expansion of the use of barrier techniques to include casual contacts might prevent or mitigate future epidemics.
Detection of the Jaagsiekte Sheep Retrovirus by RT-PCR in naturally ovine pulmonary adenocarcinoma-affected sheep and in apparently healthy in contact-sheep. (2009)

L'adenocarcinome pulmonaire ovin est une tumeur du poumon contagieuse probablement causee par le retrovirus de la Jaagsiekte (JSRV) qui ressemble au carcinome bronchiolo-alveolaire chez l'homme et pour lequel seul un diagnostic histopathologique ne peut etre fait que quand les symptomes cliniques sont deja apparents. Des examens macroscopiques et microscopiques de meme qu'une recherche du JSRV par RT-PCR ont ete effectues sur les poumons preleves d'une part sur 10 moutons issus de croisements de la province de Fars (Iran) spontanement atteints d'adenocarcinome pulmonaire (ces animaux presentaient une detresse respiratoire, de la toux et un jetage muqueux important ainsi que des nodules et masses fermes et grisâtres des lobes pulmonaires) et d'autre part sur 10 moutons apparemment sains mais en contact avec des sujets malades au sein des memes troupeaux. Des masses tumorales pulmonaires siegeant sur le lobe crânio-ventral ou sur le lobe caudal ont ete trouvees chez tous les animaux malades et le diagnostic d'a-denocarcinome a ete confirme par histologie (cellules cubiques ou en colonnes formant eventuellement des structures adenomateuses ou papillaires jouxtant les alveoles ou les epitheliums des bronchioles). Le JSRV a ete detecte dans les poumons par RT-PCR dans 100% des cas. D'autre part, bien qu'aucune lesion n'ait ete observee chez les moutons apparemment sains, 4 d'entre eux ont presente un resultat positif a la PCR. Ces resultats confirment le role du JSRV dans le developpement de l'adenocarcinome ovin pulmonaire mais suggerent aussi que l'infection surviendrait avant l'installation visible d'une tumeur.
Synthesis of a novel poly(aryl ether) with pendent N-phenylimide groups (1998)

A novel monomer with two N-phenylimide activating groups for the preparation of poly(aryl ether)s was investigated. A poly(aryl ether) was prepared by nucleophilic halide displacement from an aromatic dihalide monomer containing two N-phenylimide groups by sodium salts of bisphenol A. The monomers and the resulting polymer were characterized by FT-IR and 1H NMR spectroscopy, elemental analysis and differential scanning calorimetry (DSC). The prepared polymer with a molecular weight of 6 300 and a polydispersity of 1.37 determined by GPC is readily soluble in polar aprotic solvents, e. g. dimethylformamide (DMF), dimethylacetamide (DMAc), dimethylsulfoxide (DMSO), and N-methyl-2-pyrrolidone (NMP). Despite the low molecular weight the polymer is thermally stable up to 390°C and has a glass transition temperature of 218°C which is identical to that of ULTEM® poly(ether imide). Ein neuartiges Monomeres mit N-Phenylimid-Aktivierungsfunktionen zur Herstellung von Polyarylethern wurde untersucht. Ein Polyarylether wurde durch nukleophile Substitution an Dihalogenaromaten mit zwei N-Phenylimid-Funktionen mit dem Dinatriumsalz von Bisphenol A hergestellt. Die Monomeren und das daraus hergestellte Polymere wurden mit FT-IR- und 1H NMR-Spektroskopie, Elementaranalyse und Differentialkalorimetrie (DSC) charakterisiert. Der erhaltene Polyarylether mit einem Molekulargewicht von 6 300 und einer Uneinheitlichkeit von 1.37 (GPC) ist gut löslich in polaren aprotischen Lösemitteln wie Dimethylformamid, Dimethylacetamid, Dimethylsulfoxid und N-Methyl-2-pyrrolidon. Trotz des niedrigen Molekulargewichts ist das Polymere bis 390°C thermisch stabil und hat eine Glastemperatur von 218°C, die identisch mit der von ULTEM®-Polyetherimid ist.
Tradeoffs in targeted fuzzing of cyber systems by defenders and attackers (2011)

research-article Share on Tradeoffs in targeted fuzzing of cyber systems by defenders and attackers Authors: Jackson Mayo View Profile , Robert Armstrong View Profile Authors Info & Claims CSIIRW '11: Proceedings of the Seventh Annual Workshop on Cyber Security and Information Intelligence ResearchOctober 2011 Article No.: 37Pages 1https://doi.org/10.1145/2179298.2179339Online:12 October 2011Publication History 2citation218DownloadsMetricsTotal Citations2Total Downloads218Last 12 Months14Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access