gebhart/patrepeval huggingface dataset:
The requirement for eukaryotic initiation factor 4A (eIF4A) in translation is in direct proportion to the degree of mRNA 5′ secondary structure (2001)

Eukaryotic initiation factor (elF) 4A functions as a subunit of the initiation factor complex elF4F, which mediates the binding of mRNA to the ribosome. elF4A possesses ATPase and RNA helicase activities and is the prototype for a large family of putative RNA helicases (the DEAD box family). It is thought that the function of elF4A during translation initiation is to unwind the mRNA secondary structure in the 5' UTR to facilitate ribosome binding. However, the evidence to support this hypothesis is rather indirect, and it was reported that elF4A is also required for the translation of mRNAs possessing minimal 5' UTR secondary structure. Were this hypothesis correct, the requirement for elF4A should correlate with the degree of mRNA secondary structure. To test this hypothesis, the effect of a dominant-negative mutant of mammalian elF4A on translation of mRNAs with various degrees of secondary structure was studied in vitro. Here, we show that mRNAs containing stable secondary structure in the 5' untranslated region are more susceptible to inhibition by the elF4A mutant. The mutant protein also strongly inhibits translation from several picornavirus internal ribosome entry sites (IRES), although to different extents. UV crosslinking of elF4F subunits and elF4B to the mRNA cap structure is dramatically reduced by the elF4A mutant and RNA secondary structure. Finally, the elF4A mutant forms a more stable complex with elF4G, as compared to the wild-type elF4A, thus explaining the mechanism by which substoichiometric amounts of mutant elF4A inhibit translation.
A comparative transport study of Bi2Se3 and Bi2Se3/yttrium iron garnet (2014)

Bilayers of 20 quintuple layer Bi2Se3 on 30 nm thick yttrium iron garnet (YIG) have been grown with molecular beam epitaxy in conjunction with pulsed laser deposition. The presence of the ferri-magnetic insulator YIG causes additional scattering to the surface states of the Bi2Se3 topological insulator layer, as indicated by the temperature dependence of the resistivity. From the two-channel analysis of the Hall data, we find that the surface contribution in the bilayer samples is greatly reduced. Furthermore, the weak antilocalization effect from the surface states is clearly suppressed due to the presence of the YIG layer.
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition (2017)

We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with differential abundance directly from the raw data files. This enables the retrieval of virtually all variation present in an RNA-seq data set. This variation is subsequently assigned to biological events or entities such as differential long non-coding RNAs, splice and polyadenylation variants, introns, repeats, editing or mutation events, and exogenous RNA. Applying DE-kupl to human RNA-seq data sets identified multiple types of novel events, reproducibly across independent RNA-seq experiments.
Spin-orbit torque induced magnetization switching in nano-scale Ta/CoFeB/MgO (2015)

We study the device size dependence of spin-orbit torque induced magnetization switching in a Ta/CoFeB/MgO structure with perpendicular easy axis. The miniaturization of the device from micrometer-sized wire to 80-nm dot results in the increase of the threshold current density Jth by one order, whereas Jth increases only slightly with further reducing the device size down to 30 nm. No significant increase in Jth is seen, as the current pulse width decreases from 100 ms down to 3 ns. We reveal that the switching in devices at reduced size is reasonably well explained by the macrospin model, in which the effects of both the Slonczewski-like torque and field-like torque are included.
Effects of oxybutynin transdermal system on health-related quality of life and safety in men with overactive bladder and prostate conditions (2007)

Oxybutynin transdermal system treatment of men with OAB was effective and well tolerated, regardless of history of prostate condition.
Comparing bleed frequency and factor concentrate use between haemophilia A and B patients (2011)

Haemorrhagic manifestations in patients with haemophilia A and B are considered quite similar for comparable level of factor deficiency. We investigated the bleeding frequency and factor usage between HA and HB patients with comparable disease severities. We collected data on frequency of bleeds and factor concentrate utilization over 3 years, from January 2001 to December 2003. Information was gathered from home infusion logs recorded by patients or their parents, and treatment records from the Hemophilia Clinic or the Hospital Emergency Department. Data were available on 58 patients with severe HA (FVIII < 0.01 U mL(-1)), 10 with moderate HA (FVIII < 0.05 U mL(-1)), 15 with severe HB, and five with moderate HB who required treatment for episodic bleeds, postoperative haemostasis and for primary or secondary prophylaxis. The HA patients bled more frequently than HB patients (14.4 vs. 8.63 bleeds/patient/year), but used similar amounts of concentrate per year. HA patients underwent surgical procedures 3.2 times more frequently than HB patients to correct musculoskeletal complications. A total of 21,363,409 IU of recombinant FVIII was used by patients with HA (104,722 IU/patient/year) and 6,430, 960 IU of recombinant factor IX, by patients with HB (107,182 IU/patient/year). The difference in factor concentrate usage is not statistically significant (P > 0.05). The decrease in bleed frequency in haemophilia B indicates that the conclusions from randomized trials of prophylaxis in HA may not be accurately applied to HB.
Serum microRNA expression patterns that predict early treatment failure in prostate cancer patients (2014)

We aimed to identify microRNA (miRNA) expression patterns in the serum of prostate cancer (CaP) patients that predict the risk of early treatment failure following radical prostatectomy (RP). Microarray and Q-RT-PCR analyses identified 43 miRNAs as differentiating disease stages within 14 prostate cell lines and reflectedpublically available patient data. 34 of these miRNA were detectable in the serum of CaP patients. Association with time to biochemical progression was examined in a cohort of CaP patients following RP. A greater than two-fold increase in hazard of biochemical progression associated with altered expression of miR-103, miR-125b and miR-222 (p<.0008) in the serum of CaP patients. Prediction models based on penalized regression analyses showed that the levels of the miRNAs and PSA together were better at detecting false positives than models without miRNAs, for similar level of sensitivity. Analyses of publically available data revealed significant and reciprocal relationships between changes in CpG methylation and miRNA expression patterns suggesting a role for CpG methylation to regulate miRNA. Exploratory validation supported roles for miR-222 and miR-125b to predict progression risk in CaP. The current study established that expression patterns of serum-detectable miRNAs taken at the time of RP are prognostic for men who are at risk of experiencing subsequent early biochemical progression. These non-invasive approaches could be used to augment treatment decisions.
A Current Look at the Federal Drinking Water Regulations (1992)

In response to mandates of the 1986 Safe Drinking Water Act amendments, the US Environmental Protection Agency is developing, proposing, and adopting new drinking water regulations that are significantly changing water treatment practices and water utility operations. In February 1990, the author summarized the history, content, status, and schedule of regulations as of January 1990. In this article, the author presents updated information on the regulations covered in the February 1990 article and summarizes new and anticipated regulations as of January 1992.
Multipole imaging of an elongated magnetic source (2000)

This paper describes a mathematical method for modeling the magnetic field from an elongated source, a method that is relevant to the reduction of the magnetic signature of a marine vessel. We seek the magnetic multipole image (MMI), the set of coefficients in a prolate spheroidal harmonic expansion of magnetic scalar potential U, which describes the magnetic source. The MMI is useful for efficient and accurate modeling of the magnetic field outside the source and for developing methods of reducing the magnetic signature. We model an elongated complex source by consideration of elementary internal sources, which consist of concentrated eccentric dipoles (located away from the origin) inside the spheroidal boundary and coils on the spheroidal surfaces (bounded by longitudes and latitudes). For the internal dipole sources, the scalar magnetic potential U is expanded in prolate spheroidal coordinates in terms of associated Legendre functions. The Green function F=1/R, R being the distance between the source and evaluation point, is also expressed In terms of Legendre functions of the first and second kind. Since U of an elementary dipole is proportional to the gradient of F, comparison of the expansion coefficients is used to determine the MMI of the source. In the same way, an integration of the gradient of F over the virtual surface dipoles inside the coil boundaries is used to determine the MMI of each elementary coil.
Nonsense Mutations in cspA Cause Ribosome Trapping Leading to Complete Growth Inhibition and Cell Death at Low Temperature in Escherichia coli (2001)

CspA, the major cold shock protein of Escherichia coli, is dramatically induced immediately after cold shock. CspA production is transient and reduces to a low basal level when cells become adapted. Here we show that expression from multicopy plasmids of mutant cspA mRNAs bearing nonsense mutations in the coding region caused sustained high levels of the mutant mRNAs at low temperature, resulting in complete inhibition of cell growth ultimately leading to cell death. We demonstrate that the observed growth inhibition was caused by largely exclusive occupation of cellular ribosomes by the mutant cspA mRNAs. Such sequestration of ribosomes even occurs without a single peptide bond formation, implying that the robust translatability of the cspA mRNA is determined at the step of initiation. Further analysis demonstrated that the downstream box of the cspA mRNA was dispensable for the effect, whereas the upstream box of the mRNA was essential. Our system may offer a novel means to study sequence or structural elements involved in the translation of the cspA mRNA and may also be utilized to regulate bacterial growth at low temperature.
Obsidian: A Safer Blockchain Programming Language (2017)

Blockchain platforms, such as Ethereum, promise to facilitate transactions on a decentralized computing platform among parties that have not established trust. Recognition of the unique challenges of blockchain programming has inspired developers to create domain-specific languages, such as Solidity, for programming blockchain systems. Unfortunately, bugs in Solidity programs have recently been exploited to steal money. We propose a new programming language, Obsidian, to make it easier for programmers to write correct programs.
Determination of the Orientation of Adsorbed Pyridine and γ-MPS on Alumina Surface by Photoacoustic FT-IR Spectroscopy (1986)

Fourier transform infrared photoacoustic spectroscopy has been applied to determine the structure and orientation of pyridine and γ-Metacryl-oxypropyltriethoxysilane (γ-MPS) on γ-Al 2 O 3 surface. Adsorption of pyridine on activated γ-Al 2 O 3 leads to formation of a pyridinium ion (pyN + -H) and pyridine N-oxide. The orientation of pyridinium ion on the alumina surface is random, whereas the pyridine N-oxide is parallel with respect to the surface. The adsorption of oligomers of γ-MPS gives parallel layers on the alumina surface. At low γ-MPS surface coverage, the carbonyl groups interact with the surface hydroxyl groups. Increasing surface coverage leads to an excess of the free C=O species.
Distribution of distances between DNA barcode labels in nanochannels close to the persistence length (2015)

We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.
Theory of Interferometric Analysis of Laser Phase Noise* (1966)

The line width of a well-stabilized laser operating far above threshold is determined by random fluctuations of the phase. This paper discusses several types of experiments which can give information about the details of this phase random process. In order to study the laser phase noise experimentally the laser signal (containing phase noise only) must be passed through some type of interferometer which will convert the phase noise to intensity noise. The various properties of this derived intensity noise which may then be determined are its probability density, first and second moments, autocorrelation function, and spectrum. These measurable quantities depend on two factors; the first and more fundamental is the joint probability distribution for the change in phase in a given time. The second factor is the manner of operation of the interferometer in changing phase to intensity noise. We discuss both two-beam and multiple-beam interferometers and derive theoretical expressions for the above-mentioned properties of the output intensity fluctuations. It is interesting that although in both cases the output intensity fluctuations are nongaussian random processes, it is nevertheless possible to derive a number of useful theoretical results.
<i>Escherichia coli</i> DnaA forms helical structures along the longitudinal cell axis distinct from MreB filaments (2009)

DnaA initiates chromosomal replication in Escherichia coli at a well-regulated time in the cell cycle. To determine how the spatial distribution of DnaA is related to the location of chromosomal replication and other cell cycle events, the localization of DnaA in living cells was visualized by confocal fluorescence microscopy. The gfp gene was randomly inserted into a dnaA-bearing plasmid via in vitro transposition to create a library that included internally GFP-tagged DnaA proteins. The library was screened for the ability to rescue dnaA(ts) mutants, and a candidate gfp-dnaA was used to replace the dnaA gene of wild-type cells. The resulting cells produce close to physiological levels of GFP-DnaA from the endogenous promoter as their only source of DnaA and somewhat under-initiate replication with moderate asynchrony. Visualization of GFP-tagged DnaA in living cells revealed that DnaA adopts a helical pattern that spirals along the long axis of the cell, a pattern also seen in wild-type cells by immunofluorescence with affinity purified anti-DnaA antibody. Although the DnaA helices closely resemble the helices of the actin analogue MreB, co-visualization of GFP-tagged DnaA and RFP-tagged MreB demonstrates that DnaA and MreB adopt discrete helical structures along the length of the longitudinal cell axis.
The Temporal Delay Hypothesis: Natural, Vocoded and Synthetic Speech (2015)

Including disfluencies in synthetic speech is being explored as a way of making synthetic speech sound more natural and conversational. How to measure whether the resulting speech is actually more natu-ral, however, is not straightforward. Conventional approaches to synthetic speech evaluation fall short as a listener is either primed to prefer stimuli with filled pauses or, when they aren’t primed they prefer more fluent speech. Psycholinguistic reaction time experiments may circumvent this issue. In this pa-per, we revisit one such reaction time experiment. For natural speech, delays in word onset were found to facilitate word recognition regardless of the type of delay; be they a filled pause (um), silence or a tone. We expand these experiments by examining the effect of using vocoded and synthetic speech. Our results partially replicate previous findings. For natural and vocoded speech, if the delay is a silent pause, significant increases in the speed of word recognition are found. If the delay comprises a filled pause there is a significant increase in reaction time for vocoded speech but not for natural speech. For synthetic speech, no clear effects of delay on word recognition are found. We hypothesise this is be-cause it takes longer (requires more cognitive re-sources) to process synthetic speech than natural or vocoded speech.
Twenty Years of Naproxen Technology (1997)

This review includes (1) a discussion of marketing and manufacturing of optically pure pharmaceuticals including naproxen, (2) an historical overview of Syntex naproxen manufacturing technology, (3) a comparison of classical resolution and asymmetric technologies specific to naproxen manufacture, (4) a cost comparison of naproxen starting materials, (5) data on the Syntex resolution technology and the impact of continuous process research and development on that technology, and (6) some environmental aspects of naproxen manufacturing.
Field programmable analogue array based on MOSFET transconductors (1992)

An area efficient and parasitic insensitive technique for the implementation of a field programmable analogue array is proposed. The connections between configurable analogue blocks are realised using MOSFET transconductors. The conductance is controlled by varying the gate voltages defined by a multivalued memory system or external/internal signals.
Charisma, Coercion, and Comic Form in The Taming of the Shrew (1984)

Modern critics tend to view Shakespearean comedy either as a cel ebration of social harmony or as an ironic, quiet subversion of that harmony. Critical disagreement typically focuses on resolutions of comedies: critics who see a restored and renewed community point to marriages, banquets, and festivity of endings, while critics who view resolutions as ironic commentary argue that presence of Shylock, Don John, Malvolio, or Jacques is often dis ruptive of social harmony; irony is measured by what certain critics take to be a gap between social harmony presumed by char acters and sense that this harmony is achieved provi sionally and at great cost.1 Despite this disagreement, all of these critics share a central assumption about social function of comedies: purpose of comedies is to resolve social conflicts conclusively, though for ironic critics they may fail to do so. I want to suggest that comedies have a different social function. Commu nity is formed and affirmed not by putting an end to social conflicts, but by managing and controlling them so that social norms are con tinually reinforced. This function is disclosed by form of Shake speare's endings. Although critics tend to believe that comedies have formal unity, they have been troubled by dramatic closure be cause it violates formal unity in most spectacular manner: closure is generally extremely artificial and arbitrary, often straining bounds of credibility. Northrop Frye argues, for example, that the drive towards a comic conclusion is so powerful that it breaks all chains of probability in plot, in habit and in characters, even of expectation in audience.2 Similarly, Louis Adrian Montrose argues that to view the happy endings of romantic comedies as symbolic assimilations of potential disorder by a norma tive system is inadequate because Shakespeare's romantic com edies conclude on threshold of marriage and parenthood. They end without consummations and procreation which guarantee continuity of socio-economic order; and without comic soci
Model of a TDI line scan camera and its electronics (2004)

This paper proposes a model of a TDI line scan camera and its electronics. The model consists of three parts, the camera geometric model, the TDI CCD line scan sensor model and the electronics model. The camera geometric model gives a perspective transformation from continuous known objects to a discrete image on the TDI CCD sensor. The mathematical relationship between the amount of incident light and the analog output signal of a TDI CCD sensor is established. Finally, the camera electronics including pre amplifier, DC restore, correlated double sampling (CDS), gain amplifier, and A/D converter are modeled. The model of a TDI line scan camera and its electronics is useful to design and evaluate the electronics of the camera, to develop the virtual CCD camera and to research the methods of enhancing the image quality.
Ubiquitin-Activating/Conjugating Activity of TAF <sub>II</sub> 250, a Mediator of Activation of Gene Expression in <i>Drosophila</i> (2000)

Ubiquitination of histones has been linked to the complex processes that regulate the activation of eukaryotic transcription. However, the cellular factors that interpose this histone modification during the processes of transcriptional activation are not well characterized. A biochemical approach identified the Drosophila coactivator TAFII250, the central subunit within the general transcription factor TFIID, as a histone-specific ubiquitin-activating/conjugating enzyme (ubac). TAFII250 mediates monoubiquitination of histone H1 in vitro. Point mutations within the putative ubac domain of TAFII250 abolished H1-specific ubiquitination in vitro. In the Drosophila embryo, inactivation of the TAFII250 ubac activity reduces the cellular level of monoubiquitinated histone H1 and the expression of genes targeted by the maternal activator Dorsal. Thus, coactivator-mediated ubiquitination of proteins within the transactivation pathway may contribute to the processes directing activation of eukaryotic transcription.
GuessWhat?! Visual Object Discovery through Multi-modal Dialogue (2017)

We introduce GuessWhat?!, a two-player guessing game as a testbed for research on the interplay of computer vision and dialogue systems. The goal of the game is to locate an unknown object in a rich image scene by asking a sequence of questions. Higher-level image understanding, like spatial reasoning and language grounding, is required to solve the proposed task. Our key contribution is the collection of a large-scale dataset consisting of 150K human-played games with a total of 800K visual question-answer pairs on 66K images. We explain our design decisions in collecting the dataset and introduce the oracle and questioner tasks that are associated with the two players of the game. We prototyped deep learning models to establish initial baselines of the introduced tasks.
An evaluation of ribonuclease protection assays for the detection of beta-cardiac myosin heavy chain gene mutations. (1994)

We conclude that RNase protection is a sensitive method for screening for mutations within the beta-cardiac MHC gene. Further, mutations in the noncoding regions of the beta-MHC gene and mutations in the alpha-cardiac MHC gene are not a common cause of FHC. Negative RNase protection assays of affected individuals suggest that their FHC is due to mutations at other loci.