gebhart/patrepeval huggingface dataset:
An intron splicing enhancer containing a G-rich repeat facilitates inclusion of a vertebrate micro-exon. (1996)

The average length of a vertebrate axon is approximately 130 nt. Decreasing the size of an internal axon to less than 51 nt induces axon skipping, implying a minimal size for exons. A few constitutively included internal exons, however, are extremely small. To investigate if such micro-exons require special mechanisms for their inclusion, we studied the sequences necessary for inclusion of a 6-nt axon from chicken cardiac troponin T (cTNT). In vivo, the cTNT micro-exon was not included in mRNA unless accompanied by a 134-nt sequence located next to the micro-exon in the downstream intron. Increasing the length of the micro-exon alleviated the requirement for the intron element, indicating that the lack of inclusion of the micro-exon in the absence of a facilitating sequence was due to its small size, rather than suboptimal splice sites. The intron element contained six copies of a G-rich 7-nt sequence. Multimers of the repeat supported exon inclusion, indicating that the repeat sequence is an important part of the intron element. The entire intron element activated inclusion of a heterologous 7-nt exon, suggesting that the intron element is a general enhancer for the splicing of micro-exons. In vitro, the intron element and the repeated sequence facilitated splicing of a heterologous exon. Because of the ability of the cTNT intron element to facilitate the splicing of heterologous exons, we have termed the element an intron splicing enhancer (ISE). Interestingly, the ISE demonstrated position independence in that it facilitated inclusion of the heterologous micro-exon when placed either upstream or downstream of the micro-exon. In vitro, the ISE or copies of the ISE G-rich repeat stimulated splicing of an adjacent intron. The ISE thus becomes one of only a few characterized ISEs containing a G-rich repeat and the first to work both upstream and downstream of a target axon.
MudskipperPeriophthalmodon schlosseri can repay oxygen debts in air but not in water (1999)

We determined aerial and aquatic oxygen uptake rates (&Mdot;o(2)) of Periophthalmodon schlosseri at rest and after exhaustive exercise at 30 degrees C. Resting &Mdot;o(2) in air (3.16 +/- 0.10 [SE] &mgr;mol/g/hr) was significantly higher than that in air saturated water (2.41 +/- 0.06 &mgr;mol/g/hr). When the fish was placed in air after 2 min exhaustive exercise, &Mdot;o(2) immediately increased about 2.5 times, thereby repaying oxygen debt of 5.0 &mgr;mol/g. In contrast, &Mdot;o(2) failed to show any significant elevation from the resting level as long as the fish was confined in water after exercise. However, when the fish was subsequently emerged, &Mdot;o(2) did increase above the resting level, amounting to an excess oxygen uptake of 5.5 &mgr;mol/g. These results demonstrated that the gas transport system of P. schlosseri is better adapted to air breathing and the mode of adaptation limited the capability for water breathing. J. Exp. Zool. 284:265-270, 1999. Copyright 1999 Wiley-Liss, Inc.
Path-programmable water droplet manipulations on an adhesion controlled superhydrophobic surface (2015)

Here, we developed a novel and facile method to control the local water adhesion force of a thin and stretchable superhydrophobic polydimethylsiloxane (PDMS) substrate with micro-pillar arrays that allows the individual manipulation of droplet motions including moving, merging and mixing. When a vacuum pressure was applied below the PDMS substrate, a local dimple structure was formed and the water adhesion force of structure was significantly changed owing to the dynamically varied pillar density. With the help of the lowered water adhesion force and the slope angle of the formed dimple structure, the motion of individual water droplets could be precisely controlled, which facilitated the creation of a droplet-based microfluidic platform capable of a programmable manipulation of droplets. We showed that the platform could be used in newer and emerging microfluidic operations such as surface-enhanced Raman spectroscopy with extremely high sensing capability (10(-15) M) and in vitro small interfering RNA transfection with enhanced transfection efficiency of ~80%.
Modifications to the copper strip corrosion test for the measurement of sulfur-related corrosion (2007)

The copper strip corrosion test (CSCT) is used to measure the corrosivity of sulfur compounds in hydrocarbon fluids. The CSCT is performed by immersing a strip of cleaned, polished copper in a hydrocarbon fluid at a specified temperature for a predetermined time, then ‘rating’ the strip against a standard. In this work, instead of using the usual large, oblong strips designed to measure 30 mL fluid samples, we used small circular Cu ‘coupons’ as an alternative method for carrying out CSCTs on microscale samples of fluid. The motivations for reducing the scale include: applicability to small samples, ability to archive the small and inexpensive coupons, reduced waste, and potential for automated analysis using autosampler vials as reaction vessels. Moreover, the symmetric circular geometry facilitates the analysis of the images with mathematical color spaces. Mixtures of n-decane:n-tetradecane with varying concentrations of H2S (from a distillation column) were used as a source of microscale samples of corrosive fluid to demonstrate the viability of the smaller scale CSCT. Additional experimental details concerning the lighting conditions and digital photography of the coupons, measurement of corrosion using color space, and quantification of the sulfur content of the distillate are also described.
Targeting of LcrV virulence protein from Yersinia pestis to dendritic cells protects mice against pneumonic plague (2010)

To help design needed new vaccines for pneumonic plague, we targeted the Yersinia pestis LcrV protein directly to CD8α(+) DEC-205(+) or CD8α(-) DCIR2(+) DC along with a clinically feasible adjuvant, poly IC. By studying Y. pestis in mice, we could evaluate the capacity of this targeting approach to protect against a human pathogen. The DEC-targeted LcrV induced polarized Th1 immunity, whereas DCIR2-targeted LcrV induced fewer CD4(+) T cells secreting IFN-γ, but higher IL-4, IL-5, IL-10, and IL-13 production. DCIR-2 targeting elicited higher anti-LcrV Ab titers than DEC targeting, which were comparable to a protein vaccine given in alhydrogel adjuvant, but the latter did not induce detectable T-cell immunity. When DEC- and DCIR2-targeted and F1-V+ alhydrogel-vaccinated mice were challenged 6 wk after vaccination with the virulent CO92 Y. pestis, the protection level and Ab titers induced by DCIR2 targeting were similar to those induced by F1-V protein with alhydrogel vaccination. Therefore, LcrV targeting to DC elicits combined humoral and cellular immunity, and for the first time with this approach, also induces protection in a mouse model for a human pathogen.
An advanced tool for optimised design of power electronic circuits (2002)

This article gives an introduction to optimised design of power electronic circuits. The use of mathematical optimisation routines in connection with general purpose circuit simulators is discussed. A tool which connects the circuit simulator SABER with optimisation routines in MATLAB is developed. A detailed description of the optimisation of a gate-drive for an inverter leg in a frequency converter is given.
Verification of Mechanical Leaf Gap Error and VMAT Dose Distribution on Varian VitalBeam™ Linear Accelerator (2018)

The proper position of a multi-leaf collimator (MLC) is essential for the quality of intensity-modulated radiation therapy (IMRT) and volumetric modulated arc radiotherapy (VMAT) dose delivery. Task Group (TG) 142 provides a quality assurance (QA) procedure for MLC position. Our study investigated the QA validation of the mechanical leaf gap measurement and the maintenance procedure. Two VitalBeamTM systems were evaluated to validate the acceptance of an MLC position. The dosimetric leaf gaps (DLGs) were measured for 6 MV, 6 MVFFF, 10 MV, and 15 MV photon beams. A solid water phantom was irradiated using 10×10 cm2 field size at source-to-surface distance (SSD) of 90 cm and depth of 10 cm. The portal dose image prediction (PDIP) calculation was implemented on a treatment planning system (TPS) called EclipseTM. A total of 20 VMAT plans were used to confirm the accuracy of dose distribution measured by an electronic portal imaging device (EPID) and those predicted by VMAT plans. The measured leaf gaps were 0.30 mm and 0.35 mm for VitalBeam 1 and 2, respectively. The DLG values decreased by an average of 6.9% and 5.9% after mechanical MLC adjustment. Although the passing rates increased slightly, by 1.5% (relative) and 1.2% (absolute) in arc 1, the average passing rates were still within the good dose delivery level (>95%). Our study shows the existence of a mechanical leaf gap error caused by a degenerated MLC motor. This can be recovered by reinitialization of MLC position on the machine control panel. Consequently, the QA procedure should be performed regularly to protect the MLC system.
A low-power true random number generator using random telegraph noise of single oxide-traps (2006)

A true random number generator is realized by utilizing the noise produced by single oxide traps in small-area MOSFETs in combination with built-in redundancy. The circuit has an area of 0.009mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 0.12μm CMOS and consumes 50μW at 200kb/s random output data. The concept is robust against environmental noise and supply-voltage variations and is thus suitable for operation within security controllers
Capture of Complexity of Specialty Care in Pediatric Cardiology by Work RVU Measures (2013)

Time, skill, and stress inherent to performing catheterization procedures for congenital heart disease are not captured by measurement of RVU alone.
Corneal Neuro-Regenerative Effect of Transcutaneous Electrical Stimulation in Rabbit Lamellar Keratectomy Model (2022)

This study shows how application of TES to the eyes that exhibit corneal nerve damage can improve corneal nerve regeneration examined by histologic analysis.
Effect of dithiocarbamate thiram on Wistar rat growth plate and articular cartilage (2012)

Avaliou-se o efeito do tirame, ditiocarbamato largamente utilizado na agricultura como antifúngico e repelente de roedores, na ossificação endocondral de mamíferos, usando, como modelo, ratos Wistar. Não foram observadas lesões na cartilagem articular, nem nas placas de crescimento, o que pode ser atribuído à dose utilizada e à duração do ensaio. A diminuição da altura da placa de crescimento nos animais aos quais foi administrado o tirame parece traduzir o atraso verificado no crescimento em geral, e não um efeito específico na cartilagem, uma vez que as diferentes zonas da placa epifisária mantiveram as proporções dos animais do grupo-controle. Embora não tenham sido verificados, no presente trabalho, os efeitos registrados para outras espécies nos tecidos cartilaginosos, sugere-se a avaliação dos efeitos crónicos do tirame no crescimento e no desenvolvimento dos ossos longos em mamíferos.
VTint: Protecting Virtual Function Tables' Integrity (2015)

Author(s): Chao Zhang, Chengyu Songz, Kevin Zhijie Chen, Zhaofeng Cheny, Dawn Song Download: Paper (PDF) Date: 8 Feb 2015 Document Type: Briefing Papers Additional Documents: Slides Associated Event: NDSS Symposium 2015 Abstract: Since researchers have proposed lots of defenses to protect control data (e.g., return addresses saved on the stack) from corruption, most traditional control … Continued
A New Platelet‐Specific Antigen, Naka, Involved in the Refractoriness of HLA‐Matched Platelet Transfusion (1989)

Serum from a thrombocytopenic patient who was refractory to the transfusions of HLA-matched platelets contained a platelet-specific alloantibody, anti-Naka. Immunofluorescence analyses revealed that the Naka antigen defined by the serum was expressed exclusively on platelets and its distribution was different from P1A1, Baka, Yuka or Yukb. Analysis by Dr. von dem Borne's group revealed the Naka was also different from Koa, Kob or Zwb. Family studies showed that the Naka antigen was inherited as an autosomal codominant trait. Its antigen frequency in the Japanese population was over 97%. The results of the enzyme immunoassay using monoclonal antibodies for antigen immobilization showed that the Naka epitope did not appear to reside on GPIIb/IIIa or Ib. The transfusions of Naka-compatible platelets improved the patient's thrombocytopenia.
Mechanical stretch and shear flow induced reorganization and recruitment of fibronectin in fibroblasts (2011)

It was our objective to study the role of mechanical stimulation on fibronectin (FN) reorganization and recruitment by exposing fibroblasts to shear fluid flow and equibiaxial stretch. Mechanical stimulation was also combined with a Rho inhibitor to probe their coupled effects on FN. Mechanically stimulated cells revealed a localization of FN around the cell periphery as well as an increase in FN fibril formation. Mechanical stimulation coupled with chemical stimulation also revealed an increase in FN fibrils around the cell periphery. Complimentary to this, fibroblasts exposed to fluid shear stress structurally rearranged pre-coated surface FN, but unstimulated and stretched cells did not. These results show that mechanical stimulation directly affected FN reorganization and recruitment, despite perturbation by chemical stimulation. Our findings will help elucidate the mechanisms of FN biosynthesis and organization by furthering the link of the role of mechanics with FN.
Solvent Additive Effects on Small Molecule Crystallization in Bulk Heterojunction Solar Cells Probed During Spin Casting (2013)

Solvent additive processing can lead to drastic improvements in the power conversion efficiency (PCE) in solution processable small molecule (SPSM) bulk heterojunction solar cells. In situ grazing incidence wide-angle X-ray scattering is used to investigate the kinetics of crystallite formation during and shortly after spin casting. The additive is shown to have a complex effect on structural evolution invoking polymorphism and enhanced crystalline quality of the donor SPSM.
A class of analysis-by-synthesis predictive coders for high quality speech coding at rates between 4.8 and 16 kbit/s (1988)

The general structure of this class of coders is reviewed, and the particulars of its members are discussed. The different analysis procedures are described, and the contributions of the various coder parameters to the performance of the coder are examined. Quantization procedures for each transmitted parameter are given along with examples of bit allocations. The speech quality produced by these coders is high at 16 kb/s and good at 8 kb/s, but only fair at 4.8 kb/s. The use of postprocessing techniques changes the performance at lower rates, but more research is needed to further improve the coders.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mild Sialoadenitis: A Common Finding in Patients with Hepatitis C Virus Infection (1994)

Sialoadenitis of HCV-related liver disease is common but differs from SS with regard to predisposing genetic factors, expression of autoimmune markers, and histopathologic severity.
Piston-Liner Crevice Geometry Effect on HCCI Combustion by Multi-Zone Analysis (2002)

&lt;div class="htmlview paragraph"&gt;A multi-zone model has been developed that accurately predicts HCCI combustion and emissions. The multi-zone methodology is based on the observation that turbulence does not play a direct role on HCCI combustion. Instead, chemical kinetics dominates the process, with hotter zones reacting first, and then colder zones reacting in rapid succession. Here, the multi-zone model has been applied to analyze the effect of piston crevice geometry on HCCI combustion and emissions. Three different pistons of varying crevice size were analyzed. Crevice sizes were 0.26, 1.3 and 2.1 mm, while a constant compression ratio was maintained (17:1).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The results show that the multi-zone model can predict pressure traces and heat release rates with good accuracy. Combustion efficiency is also predicted with good accuracy for all cases, with a maximum difference of 5% between experimental and numerical results. Carbon monoxide emissions are underpredicted, but the results are better than those obtained in previous publications. The improvement is attributed to the use of a 40-zone model, while previous publications used a 10-zone model. Hydrocarbon emissions are well predicted. For cylinders with wide crevices (1.3 and 2.1 mm), HC emissions do not decrease monotonically as the relative air/fuel ratio (λ) increases. Instead, maximum HC emissions are obtained for an intermediate value of λ. The model predicts this relative air/fuel ratio for maximum HC emissions with very good accuracy. The results show that the multi-zone model can successfully predict the effect of crevice geometry on HCCI combustion, and therefore it has applicability to the design of HCCI engines with optimum characteristics for high efficiency, low emissions and low peak cylinder pressure.&lt;/div&gt;
On the Pressure and Force Field on a Circular Cylinder Oscillating in the Lock-In Region at Sub-Critical Reynolds Number (2006)

The vortex induced vibration of a rigid cylinder has been studied in the subcritical Reynolds range in terms of motion parameters and also in terms of instantaneous pressure distribution on the cylinder surface. The resulting force field has been analyzed as a function of the fundamental parameters z* (non-dimensional amplitude) and Un (critical velocity ratio) showing a possible systematic modelization of the force component synchronous with the oscillation frequency, responsible for the power input in the lock-in region. The magnitude and the phase of the synchronous force component have been studied analyzing build-up events as well as steady state constant amplitude oscillation events. A very close correspondence has been highlighted among the two different analyzed cases, confirming that a quasi-steady model of the force field is a robust and reliable representation of the flow-cylinder interaction force field. This interaction is responsible for the typical transient build-up oscillations of technical interest. The pressure distribution monitored at different locations along the oscillating cylinder axial coordinate allowed finally to show a direct link between the incoming flow velocity distribution and the correlation characteristics of the vortex shedding force distribution along the cylinder axis.
ChemInform Abstract: N‐Benzylpyridinium Salts as New Useful Catalysts for Transformation of Epoxides (I) to Cyclic Acetals (III), Orthoesters (Va), (Vc), and Orthocarbonates (Vb). (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies (2011)

These studies demonstrate how subclonal heterogeneity, prevalent in tumor samples, is reflected in aggregate signals measured by high-throughput techniques. Our proposed approach yields high robustness in detecting copy number alterations using high-throughput technologies and has the potential to identify specific subclonal markers from next-generation sequencing data.
Calcium influx and signaling in cytotoxic T‐lymphocyte lytic granule exocytosis (2009)

Cytotoxic T lymphocytes (CTLs) kill targets by releasing cytotoxic agents from lytic granules. Killing is a multi-step process. The CTL adheres to a target, allowing its T-cell receptors to recognize antigen. This triggers a signal transduction cascade that leads to the polarization of the microtubule cytoskeleton and granules towards the target, followed by exocytosis that occurs specifically at the site of contact. As with cytokine production by helper T cells (Th cells), target cell killing is absolutely dependent on Ca2+ influx, which is involved in regulating both reorientation and release. Current evidence suggests that Ca2+ influx in CTLs, as in Th cells, occurs via depletion-activated channels. The molecules that couple increases in Ca2+ to reorientation are unknown. The Ca2+/calmodulin-dependent phosphatase calcineurin, which plays a critical role in cytokine production by Th cells, is also involved in lytic granule exocytosis, although the relevant substrates remain to be identified and calcineurin activation is only one Ca2+-dependent step involved. There are thus striking similarities and important differences between Ca2+ signals in Th cells and CTLs, illustrating how cells can use similar signal transduction pathways to generate different functional outcomes.
Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease (2016)

In chronic kidney disease (CKD), the decline in the glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has been extensively studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential for sensitive nucleic acid biomarkers in various human diseases. Therefore, in this study we aimed to identify urinary exosomal ncRNAs as novel biomarkers for diagnosis of CKD. Since up to now most approaches have focused on the class of miRNAs, we extended our analysis to several other noncoding RNA classes, such as tRNAs, tRNA fragments (tRFs), mitochondrial tRNAs, or lincRNAs. For their computational identification from RNA-seq data, we developed a novel computational pipeline, designated as ncRNASeqScan. By these analyses, in CKD patients we identified 30 differentially expressed ncRNAs, derived from urinary exosomes, as suitable biomarkers for early diagnosis. Thereby, miRNA-181a appeared as the most robust and stable potential biomarker, being significantly decreased by about 200-fold in exosomes of CKD patients compared to healthy controls. Using a cell culture system for CKD indicated that urinary exosomes might indeed originate from renal proximal tubular epithelial cells.
Cycle detection in repair-based railway scheduling system (2002)

Proposes an approach for railway scheduling based on iterative repair, a technique that starts with a complete but possibly flawed schedule and searches through the space of possible repairs. The search is guided by an earliest-conflict-first heuristic that attempts to repair the earliest constraint violation while minimizing the value of objective function. Since cycles may exist among a sequence of repairs during the repair process, a cycle detection and resolution scheme is proposed to prevent infinite loops. Experimental results show that the efficiency of the repair algorithm improves significantly when cycle detection is incorporated.