gebhart/patrepeval huggingface dataset:
Aberrant 5′ splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization (2007)

Despite a growing number of splicing mutations found in hereditary diseases, utilization of aberrant splice sites and their effects on gene expression remain challenging to predict. We compiled sequences of 346 aberrant 5 0 splice sites (5 0 ss) that were activated by mutations in 166 human disease genes. Mutations within the 5 0 ss consensus accounted for 254 cryptic 5 0 ss and mutations elsewhere activated 92 de novo 5 0 ss. Point mutations leading to cryptic 5 0 ss activation were most common in the first intron nucleotide, followed by the fifth nucleotide. Substitutions at position +5 were exclusively G4A transitions, which was largely attributable to high mutability rates of C/G4T/A. However, the frequency of point mutations at position +5 was significantly higher than that observed in the Human Gene Mutation Database, suggesting that alterations of this position are particularly prone to aberrant splicing, possibly due to a requirement for sequential interactions with U1 and U6 snRNAs. Cryptic 5 0 ss were best predicted by computational algorithms that accommodate nucleotide dependencies and not by weight-matrix models. Discrimination of intronic 5 0 ss from their authentic counterparts was less effective than for exonic sites, as the former were intrinsically stronger than the latter. Computational prediction of exonic de novo 5 0 ss was poor, suggesting that their activation critically depends on exonic splicing enhancers or silencers. The authentic counterparts of aberrant 5 0 ss were significantly weaker than the average human 5 0 ss. The development of an online database of aberrant 5 0 ss will be useful for studying basic mechanisms of splice-site selection, identifying splicing mutations and optimizing splice-site prediction algorithms.
[Dependable fertility control: hazards and barriers (author's transl)]. (1982)

This survey of attitudes toward contraception is taken from a document concerning psychological aspects of 233 women seeking pregnancy terminations. 87.12% had utilized a method of contraception at some time, of which 66.5% had used pills, 29.6% had used natural methods, 23.6% had used local methods, and 11.16% had used IUDs. 33.47% of the total sample had refused pills, in 83.65% of cases because of fears for health, and in the remainder because of infrequent intercourse, fears for unborn children, lack of information, belief that women shouldn't be responsible for contraception, or fear of forgetting. 64.38% of the women in the total sample had discontinued use of pills, about 2/3 of them for personal reasons such as nervousness, changes in the relationship, nausea, menstrual changes, frigidity, and depression, which are difficult to evaluate objectively. In most cases of termination of pill use for external reasons, the cause was opposition by the physician. Personality traits of the sample women which could impede responsible fertility control included passivity and inconsistency in 16.47%, dependency in 47.64%, and immaturity and poorly structured personality in 40.34%. Personality disorders among the latter included enjoyment of risk, impulsivity and lack of capacity to anticipate, emotional instability, and significant egocentrism and narcissism. 21.89% had depressive tendencies, 22.75% had sadomasochistic tendencies, and 28.33% had tendencies toward somatization, each of which is often correlated with unconscious choice. The unconscious elements are often more significant than the conscious and apparent motives. More effective contraception and a prevention of abortions might result from making women aware of their unconscious motivations.
Active microrheology of soft particle glasses (2014)

We study the forced motion of a tagged soft particle through a jammed suspension of identical soft particles using particle simulations. We relate the local particle dynamics, microstructure, and microrheology to the bulk rheological properties of the suspension. At small forces, the tagged particle is trapped in a cage of other particles that resist the external force whereas at larger forces the tagged particle breaks free of its cage. This is indicative of the macroscopic yielding behavior in these materials. The threshold force from microrheology is quantitatively related to the macroscopic yield stress. The computed microviscosity also follows the shear thinning nature of these glasses and matches the exponent of 0.5 observed in bulk measurements. The semiquantitative agreement between the micro and bulk viscosity is discussed by comparing the microstructural processes involved in both. In microrheology, at moderate forces, the probe displacement causes an accumulation of particles in the direction of motion and a depleted wake behind. In bulk rheology, there are accumulation and depletion of particles along the compression and extension axes, respectively. Despite these differences, the average number of contacts and the elastic contact force on the particles are similar, which justifies why microrheology measurements match bulk rheology data.
Inverse-Based Power Control in Domestic Induction-Heating Applications (2013)

The wide variability of the load is the main problem of domestic induction-heating technology. The considered power control strategy should guarantee stability and regulation with a suitable response time and no overshoot independently of any perturbation or load variation. In addition to this, it has to ensure the operation under safety conditions. This paper is focused on the power control applied to one heating unit by means of continuous modulations. An inverse-based power controller is proposed for dealing with load uncertainties. The proposed power control combines different variable frequency pulsewidth modulation strategies (constant duty cycle, constant on-time, and constant off-time modulations) for reaching the target power level while minimizing the switching frequency. Finally, simulation and experimental results compared with other techniques in a prototype of an induction-heating system are presented in order to validate the proposed control strategy.
DNA Complexing Lipopolythiourea (2004)

We present a neutral lipopolythiourea (DTTU) as a potential DNA-binding agent. Light scattering experiments showed that mixing a lipopolythiourea with dipalmitoylphosphatidylcholine (DPPC/DTTU) led to small particles with sizes ranging from 100 to 150 nm at optimum conditions. Setting a fixed DNA amount, an increasing amount of DTTU/DPPC or DPPC lipids was added. Particle size increased only with DTTU/DPPC, indicating that interaction occurred between the DTTU/DPPC particles and DNA. In the same way, only DTTU/DPPC limited the ethidium bromide accessibility to plasmid DNA. These data suggest that DTTU/DPPC liposomes associate to DNA, which was confirmed by agarose gel experiments. To prove the active part of the DTTU lipid itself in DNA compaction, pegoylated-lipid was used. Cholesterol-PEG(2000) alone was not able to condense DNA. In contrast, DTTU/PEG-cholesterol was able to retain plasmid DNA on an agarose gel. In vivo injection of DTTU/DPPC/complexes was studied. Circulation time increase for noncationic particles as compared to cationic. More obvious was the lack of nonspecific accumulation in the lung, where a gain of 3 to 40 fold was measured.
Broadband tunable phase shifter for microwaves (2020)

We implement a broadly tunable phase shifter for microwaves based on superconducting quantum interference devices (SQUIDs) and study it both experimentally and theoretically. At different frequencies, a unit transmission coefficient, |S21| = 1, can be theoretically achieved along a curve where the phase shift is controllable by the magnetic flux. The fabricated device consists of three equidistant SQUIDs interrupting a transmission line. We model each SQUID embedded at different positions along the transmission line with two parameters, capacitance and inductance, the values of which we extract from the experiments. In our experiments, the tunability of the phase shift varies from 0.07 × π to 0.14 × π radians along the full-transmission curve with the input frequency ranging from 6.00 GHz to 6.28 GHz. The reported measurements are in good agreement with simulations, which is promising for future design work of phase shifters for different applications.
Synthesis of cycloSal‐(Glycopyranosyl‐6)‐phosphates as Activated Sugar Phosphates (2013)

Abstract The synthesis of cyclo Sal‐masked glycopyranosyl phosphates demands suitably protected precursors. A highly regioselective strategy for the preparation of cyclo Sal‐(1,2,3,4‐tetra‐ O ‐acetylglycopyranosyl‐6)‐phosphates was developed. Intermediate introduction of the Fmoc‐group allowed the isolation of the 1,2,3,4‐tetra‐ O ‐acetyl glycopyranoses to be skipped, thus, no isomerization occurred. Glycopyranoses were first converted into the 6‐ O ‐TBDMS‐1,2,3,4‐tetra‐ O ‐acetyl derivatives then, in a one‐pot reaction, the silyl ether was cleaved and the resulting 1,2,3,4‐tetra‐ O ‐acetyl glycopyranoses were trapped with Fmoc‐chloride. In this exchange of protecting groups no acetyl group migration occurred. The 6‐ O ‐Fmoc‐protected intermediates were selectively converted into the cyclo Sal‐masked glycopyranosyl phosphates in a one‐pot reaction. Finally, the reactivity of these activated glycopyranosyl‐6‐phosphates was demonstrated in the synthesis of 1,6‐diglycopyranosyl‐phosphates.
α-Actinin-4 Is Required for Normal Podocyte Adhesion (2006)

Mutations in the alpha-actinin-4 gene ACTN4 cause an autosomal dominant human kidney disease. Mice deficient in alpha-actinin-4 develop a recessive phenotype characterized by kidney failure, proteinuria, glomerulosclerosis, and retraction of glomerular podocyte foot processes. However, the mechanism by which alpha-actinin-4 deficiency leads to glomerular disease has not been defined. Here, we examined the effect of alpha-actinin-4 deficiency on the adhesive properties of podocytes in vivo and in a cell culture system. In alpha-actinin-4-deficient mice, we observed a decrease in the number of podocytes per glomerulus compared with wild-type mice as well as the presence of podocyte markers in the urine. Podocyte cell lines generated from alpha-actinin-4-deficient mice were less adherent than wild-type cells to glomerular basement membrane (GBM) components collagen IV and laminin 10 and 11. We also observed markedly reduced adhesion of alpha-actinin-4-deficient podocytes under increasing shear stresses. This adhesion deficit was restored by transfecting cells with alpha-actinin-4-GFP. We tested the strength of the integrin receptor-mediated linkages to the cytoskeleton by applying force to microbeads bound to integrin using magnetic pulling cytometry. Beads bound to alpha-actinin-4-deficient podocytes showed greater displacement in response to an applied force than those bound to wild-type cells. Consistent with integrin-dependent alpha-actinin-4-mediated adhesion, phosphorylation of beta1-integrins on alpha-actinin-4-deficient podocytes is reduced. We rescued the phosphorylation deficit by transfecting alpha-actinin-4 into alpha-actinin-4-deficient podocytes. These results suggest that alpha-actinin-4 interacts with integrins and strengthens the podocyte-GBM interaction thereby stabilizing glomerular architecture and preventing disease.
High-aspect-ratio periodical twin structure for QPM SHG in quartz (2004)

We demonstrate periodic twins propagating with high aspect ratio of 11:2:1 and 3rd- and 2nd-order QPM SHG of a Nd:YAG laser The normalized conversion efficiency is 0.63 %/W/cm/sup 2/ in 2nd-order QPM with 4.9 nsec pulsewidth.
Development of acoustic optics tunable filter and its application to strain sensing system (2009)

A highly accurate strain sensing system has been developed by combining an acoustic optic tunable filter (AOTF), an optical fiber, and fiber Bragg gratings (FBGs). The AOTF is composed of an interdigital transducer (IDT) to generate surface acoustic wave (SAW), a SAW guide, and polarization beam splitters (PBSs) for separating TE and TM modes from a light with both modes and optical waveguides consisting of a Li-diffused layer on a Y-X LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> substrate. The AOTF outputs only the wavelength of light corresponding to the applied SAW frequency. The AOTF operates as an optical spectrum analyzer by applying the swept SAW frequency to the AOTF. A highly accurate strain sensing system has been contributed by combining the optical fiber, the fiber Bragg gratings (FBGs), and the AOTF used instead of a conventional optical spectrum analyzer. The each FBG has each period of the grating in the fiber. The only wavelength of the light corresponding to the period of grating of FBG reflects when the light with wide range wavelength is inputted. The AOTF measures the reflected wavelength. When the strain is applied to the FBG, the only reflected wavelength corresponding to the strained grating period of its FGB shifts. The strength of the strain can be obtained from the shift value of the wavelengths measured by the AOTF. The place, where the strain is received, can also be measured at the same time by setting up a lot of FBGs having different period of grating. The strain accuracy of 0.9 ppm was measured by using this method at the room temperature. But a temperature characteristic of the AOTF is not good, it is necessary to improve the temperature characteristic of this sensing system. Adopting additional FBGs for reference, measured accuracy of standard deviation of 0.63 pm was obtained under the temperature change from -20 to 70degC. This strain sensing system would be able to apply to monitoring or watching a fall of rock, a landslide, an earthquake, a vibration of a building or a bridge, a trespasser, a water level of river, and so on.
Minimally invasive 3D endoscope using the structured light technique and its pattern (2011)

info:eu-repo/semantics/nonPublished
Solution–Liquid–Solid Growth and Catalytic Applications of Silica Nanorod Arrays (2020)

As an analogue to the vapor-liquid-solid process, the solution-liquid-solid (SLS) method offers a mild solution-phase route to colloidal 1D nanostructures with controlled sizes, compositions, and properties. However, direct growth of 1D nanostructure arrays through SLS processes remains in its infancy. Herein, this study shows that SLS processes are also suitable for the growth of nanorod arrays on the substrate. As a proof of concept, seedless growth of silica nanorod arrays on a variety of hydrophilic substrates such as pristine and oxide-modified glass, metal sheets, Si wafers, and biaxially oriented polypropylene film are demonstrated. Also, the silica nanorod arrays can be used as a new platform for the fabrication of catalysts for photothermal CO<sub>2</sub> hydrogenation and the reduction of 4-nitrophenol reactions. This work offers some fundamental insight into the SLS growth process and opens a new avenue for the mild preparation of functional 1D nanostructure arrays for various applications.
Interfacial characteristics of fully depleted SiGe-on-insulator (SGOI) substrate fabricated by modified Ge condensation (2005)

A fully depleted SiGe-on-insulator (SGOI) substrate has been fabricated by a modified Ge condensation technique. The characteristics of the SiGe/buried-oxide (BOX) interface and the influence on the electrical performance of the SGOI substrate are investigated. The long oxidation time during the fabrication of the fully depleted (FD) SGOI substrate leads to Ge atom pileup at the SiGe/BOX interface, and consequently a large number of interfacial trapped charges are produced. Furthermore, our results disclose that Ge diffusion into the BOX increases the interfacial trapped charges and the fixed oxide charges during oxidation. As a result, the electrical properties of the FD-SGOI substrate degrade due to the poor SiGe/BOX interface.
ANALYSIS OF SINGLE PARTICLE TRAJECTORIES: FROM NORMAL TO ANOMALOUS DIFFUSION ∗ (2009)

With modern experimental tools it is possible to track the motion of single nanoparticles in real time, even in complex environments such as biological cells. The quest is then to reliably evaluate the time series of individual trajectories. While this is straightforward for particles performing normal Brownian motion, interesting subtleties occur in the case of anomalously diffusing particles: it is no longer granted that the long time average equals the ensemble average. We here discuss for two different models of anomalous diffusion the detailed behaviour of time averaged mean squared displacement and related quantities, and present possible criteria to analyse single particle trajectories. An important finding is that although the time average may suggest normal diffusion the actual process may in fact be subdiffusive.
Visualization of spherical objects in a reflection acoustic microscope (1993)

An expression for the output signal of a reflection acoustic microscope corresponding to a spherical object is presented in this paper as spherical function expansion. The character of the image is shown to depend on the focal plane position with respect to spherical objects center. The size of spherical objects image is smaller than a real particle dimension at any focal plane position. Experimental data agree with the theory.
Critical Role of Kupffer Cell-Derived IL-10 for Host Defense in Septic Peritonitis (2001)

Intra-abdominal infection in patients following major visceral surgery is associated with high mortality. Using a macrophage depletion technique, we demonstrate that in murine septic peritonitis, Kupffer cells are a major source of systemic IL-10 levels. Kupffer cell-depleted mice were highly susceptible to the lethal effects of septic peritonitis and exhibited an increased bacterial load. Kupffer cell-depleted mice were protected by the administration of an IL-10-Fc fusion protein. Loss of Kupffer cell-derived IL-10 was associated with a weak increase in serum IL-12 levels, whereas TNF, IL-1alpha, and IL-18 levels were not significantly elevated, suggesting that the loss of Kupffer cell-derived IL-10 did not result in a toxic cytokine release syndrome. Instead, loss of Kupffer cell-derived IL-10 was associated with a reduced splenocyte production of IFN-gamma that is required for immune protection in murine septic peritonitis. Therefore, the results suggest that the protective function of IL-10 in septic peritonitis may not be restricted to the anti-inflammatory activities of IL-10.
A Discussion on some Key Issues for Seismic Design of Concentrically Braced Frames According to Canadian and Chinese Codes (2010)

To gain further insight into the seismic design of concentrically braced frames as defined by the Canadian and Chinese codes, a comparison of the main design requirements contained in each code is carried out in this paper. The comparison emphasizes on the differences existing in these two code provisions, and the reasons behind them. The issues that are examined include the seismic force resisting systems for braced frames, the height restrictions, the force transferred to the beams in chevron configurations, the slenderness ratios of the bracing members, the width-to-thickness ratios of the brace sections, and the influence of brace connections on the columns. Some additional issues that still remain undefined on the seismic response of these systems and some proposals for further studies are also discussed. It is concluded through this comparison that a number of modifications are still required in order to fully implement a capacity design approach of these systems in both codes.
Design of organically functionalised hybrid silica fibres through the use of anthracenic organogelatorsElectronic supplementary information (ESI) available: SEM images of other non-calcined/unwashed hybrid samples prepared using DDOA (non-hydrolytic conditions) and DAP organogelators (Fig. S1); additional SEM images of calcined/washed organosilicas (Fig. S2); 29Si MAS NMR spectra of samples A and B (Fig. S3). See http://www.rsc.org/suppdata/jm/b2/b212465n/ (2003)

Organically functionalised hybrid silica fibres with accessible and modifiable functionalities have been reproducibly obtained for the first time through the use of organogelators as structure-directing agents.
Two Novel Natural Flavonoids from Primula palinuri (2006)

The farinose exudate produced by Primula palinuri was found to consist of 12 flavones at least. Two of them are novel natural compounds, 2′-hydroxy-2-methoxychalcone and 8,2′,5′-trihydroxyflavone 5′-benzoate. The structure was determined by analysis of MS and 2D NMR spectral data and spectral comparison with the known compounds.
On-Wafer Seamless Integration of GaN and Si (100) Electronics (2009)

The high thermal stability of nitride semiconductors allows for the on-wafer integration of (001)Si CMOS electronics and electronic devices based on these semiconductors. This paper describes the technology developed at MIT to seamlessly integrate GaN and Si transistors in very close proximity (<5 mum). This integration, the first of any III-V field effect transistor with (001) Si electronics, enables tremendous new possibilities to circuit and system designers. For example, we will study the use of hybrid GaN-Si circuits to improve the power distribution networks in Si microprocessors.
A rev1–vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev–vpu–env cassettes and reduces virion infectivity in pseudotyping assays (2020)

Functional studies of HIV-1 envelope glycoproteins (Envs) commonly include the generation of pseudoviruses, which are produced by co-transfection of rev-vpu-env cassettes with an env-deficient provirus. Here, we describe six Env constructs from transmitted/founder HIV-1 that were defective in the pseudotyping assay, although two produced infectious virions when expressed from their cognate proviruses. All of these constructs exhibited an unusual gene arrangement in which the first exon of rev (rev1) and vpu were in the same reading frame without an intervening stop codon. Disruption of the rev1-vpu fusion gene by frameshift mutation, stop codon, or abrogation of the rev initiation codon restored pseudovirion infectivity. Introduction of the fusion gene into wildtype Env cassettes severely compromised their function. The defect was not due to altered env and rev transcription or a dominant negative effect of the expressed fusion protein, but seemed to be caused by inefficient translation at the env initiation codon. Although the rev1-vpu polymorphism affects Env expression only in vitro, it can cause problems in studies requiring Env complementation, such as analyses of co-receptor usage and neutralization properties, since 3% of subtype A, 20% of subtype C and 5% of CRF01_A/E viruses encode the fusion gene. A solution is to eliminate the rev initiation codon when amplifying rev-vpu-env cassettes since this increases Env expression irrespective of the presence of the polymorphism.
Analytical model for RESET operation of Phase Change Memory (2008)

We present a novel analytical model for the RESET operation of Phase Change Memory (PCM) that explicitly describes the dependency of the programming current on various cell dimensions and material parameters. This model also explains, for the first time, the fundamental physics behind the inverse relationship between dynamic resistance(R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> ) and the amplitude of the programming current.
Response to “Comment on ‘Enhanced optical field intensity distribution in organic photovoltaics using external coatings’” [Appl. Phys. Lett. 91, 266103 (2007)] (2007)

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