gebhart/patrepeval huggingface dataset:
Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be? (2015)

In recent years, RNA-seq is emerging as a powerful technology in estimation of gene and/or transcript expression, and RPKM (Reads Per Kilobase per Million reads) is widely used to represent the relative abundance of mRNAs for a gene. In general, the methods for gene quantification can be largely divided into two categories: transcript-based approach and 'union exon'-based approach. Transcript-based approach is intrinsically more difficult because different isoforms of the gene typically have a high proportion of genomic overlap. On the other hand, 'union exon'-based approach method is much simpler and thus widely used in RNA-seq gene quantification. Biologically, a gene is expressed in one or more transcript isoforms. Therefore, transcript-based approach is logistically more meaningful than 'union exon'-based approach. Despite the fact that gene quantification is a fundamental task in most RNA-seq studies, however, it remains unclear whether 'union exon'-based approach for RNA-seq gene quantification is a good practice or not. In this paper, we carried out a side-by-side comparison of 'union exon'-based approach and transcript-based method in RNA-seq gene quantification. It was found that the gene expression levels are significantly underestimated by 'union exon'-based approach, and the average of RPKM from 'union exons'-based method is less than 50% of the mean expression obtained from transcript-based approach. The difference between the two approaches is primarily affected by the number of transcripts in a gene. We performed differential analysis at both gene and transcript levels, respectively, and found more insights, such as isoform switches, are gained from isoform differential analysis. The accuracy of isoform quantification would improve if the read coverage pattern and exon-exon spanning reads are taken into account and incorporated into EM (Expectation Maximization) algorithm. Our investigation discourages the use of 'union exons'-based approach in gene quantification despite its simplicity.
Tetrahydrobiopterin-Dependent Functional Recovery in 6-Hydroxydopamine-Treated Rats by Intracerebral Grafting of Fibroblasts Transfected with Tyrosine Hydroxylase cDNA (1992)

Fibroblasts (NRK-49F) were transfected with human type 2 tyrosine hydroxylase (TH; EC 1.14.16.29) cDNA, to clarify the mechanism involved in amelioration of parkinsonism by intracerebral grafting of catecholaminergic neurons and to investigate its possible use as a donor material. These genetically manipulated fibroblasts did not develop into a mass of tissue, and survived well in the host striatum. Expression of the TH minigene in the cells was successful even when they were transplanted into the host brain. Intracerebral microdialysis revealed that a measurable amount of L-3,4-dihydroxyphenylalanine (L-DOPA) was not spontaneously released from the implanted cells into the host striatum. However, release of a large amount of L-DOPA from the cells was observed when (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) was perfused through a dialysis probe. Finally, we investigated whether these BH4-dependent L-DOPA-secreting fibroblasts are able to ameliorate the abnormal behavior of 6-hydroxydopamine-treated rats. Apomorphine-induced rotating behavior was not reversed by the grafting alone, whereas a marked reduction in drug-induced circling was observed temporarily after BH4 was perfused around the implanted cells. These findings indicate that TH cDNA-transfected non-neuronal cells might be able to be used as donor material for intracerebral grafting and ameliorate the abnormal behavior of rats with experimental Parkinson's disease.
Cross-Linked and Shapeable Porous 3D Substrates from Freeze-Linked Cellulose Nanofibrils (2018)

Chemically cross-linked highly porous nanocellulose aerogels with complex shapes have been prepared using a freeze-linking procedure that avoids common post activation of cross-linking reactions and freeze-drying. The aerogel shapes ranged from simple geometrical three-dimensional bodies to swirls and solenoids. This was achieved by molding or extruding a periodate oxidized cellulose nanofibril (CNF) dispersion prior to chemical cross-linking in a regular freezer or by reshaping an already prepared aerogel by plasticizing the structure in water followed by reshaping and locking the aerogel into its new shape. The new shapes were most likely retained by new cross-links formed between CNFs brought into contact by the deformation during reshaping. This self-healing ability to form new bonds after plasticization and redrying also contributed to the mechanical resilience of the aerogels, allowing them to be cyclically deformed in the dry state, reswollen with water, and redried with good retention of mechanical integrity. Furthermore, by exploiting the shapeability and available inner structure of the aerogels, a solenoid-shaped aerogel with all surfaces coated with a thin film of conducting polypyrrole was able to produce a magnetic field inside the solenoid, demonstrating electromagnetic properties. Furthermore, by biomimicking the porous interior and stiff exterior of the beak of a toucan bird, a functionalized aerogel was created by applying a 300 μm thick stiff wax coating on its molded external surfaces. This composite material displayed a 10-times higher elastic modulus compared to that of the plain aerogel without drastically increasing the density. These examples show that it is possible to combine advanced shaping with functionalization of both the inner structure and the surface of the aerogels, radically extending the possible use of CNF aerogels.
Zero discharge desalination (2001)

Intensive energy consumption and concentrate management are major issues for desalination at inland areas. This work addresses these issues by examining a systems approach for desalination. The systems approach, called zero discharge desalination, combines multiple desalination processes and brine concentration with salinity gradient solar pond (SGSP) technology. In the zero discharge system, the concentrate from desalination processes is reused by solar ponds thereby negating brine disposal, and the solar ponds provide renewable energy to the desalination and brine concentration processes. A multi-effect multi stage (MEMS) desalination unit, a membrane distillation (MD) unit, and a brine concentration and recovery system (BCRS) were tested with the heat generated from the El Paso Solar Pond. The MEMS unit with three-effects and four stages was effectively operated at a first stage vapor temperature range of 60 ∼ 75°C, and at high concentration ratio. This unit produced high quality distillate with a total dissolved solids level of less than 5 mg/liter. Its distillate production rate ranged from 1.6 to 5.0 liter/min, and was significantly affected by flash range, concentration of reject brine, and first effect circulation rate. No significant scaling and fouling were found during the tests. An air gap MD unit with a membrane area of 2.94 m2 was tested with feedwaters in which salinity ranged from 0 to 19%, and operated with variable warm side temperature, transmembrane temperature drop, and circulation flow rate. The distillate flux ranged from 1 to 6 kg/m2-hr, and was strongly affected by the transmembrane temperature drop, instead of the warm side temperature. This observation suggests that heat transfer is the limiting factor for the flux rather than vapor diffusion. The MD unit can produce high quality distillate, however, membrane wetting has a major impact on the quality of product water. The BCRS uses moderate temperature heat to drive evaporative concentration of saline water, and recovers some fresh water. Slurry salt was produced by the BCRS unit, and recharged into the solar pond along with saturated brine. The operational experience and technical advancements of salinity gradient solar pond technology are also presented in this work.
Solid-Support Sample Loading for DNA Sequencing (2006)

We present a new method for simplified low-quantity DNA loading onto microelectrophoresis devices. The method is based on combined solid-phase extraction, purification, and transport of DNA reversibly bound on paramagnetic microspheres. DNA is adsorbed onto the microspheres, captured with a magnetized permalloy wire, and then directly injected as a highly focused sample plug into the separation channel. This method circumvents both the minimum volume requirement of pipettors (since only solid beads are transported) and the timing complications of double-T microfluidic injection. Injections from Sanger samples of <100 pg total suspended weight match the signal strength of our previous conventional injections at >10-times the starting DNA sample. Sequencing traces show a resolution that matches or exceeds double-T injections. A kinetic model reproduces the time-dependence of the injection signals and proves that total nonidealities in the method produce injection-broadened plugs of approximately 1-s duration. The method should be broadly extendable to DNA and protein separations in both microdevice and capillary electrophoresis.
The Campeche Bay Blow Out: A Strict Liability Approach to Damages Resulting from Offshore Drilling Accidents (1979)

Examines what avenues are open to establish a legal procedure to ensure compensation for parties injured as the result of accidents caused by offshore drilling rigs. Concludes that there is a need to impose strict liability standard on those parties engaged in offshore drilling for damages caused by such activities.
Plasmonic nanostructures for light trapping in organic photovoltaic devices (2014)

Over the past decade, we have witnessed rapid advances in the development of organic photovoltaic devices (OPVs). At present, the highest level of efficiency has surpassed 10%, suggesting that OPVs have great potential to become competitive with other thin-film solar technologies. Because plasmonic nanostructures are likely to further improve the efficiency of OPVs, this Article reviews recent progress in the development of metal nanostructures for triggering plasmonic effects in OPVs. First, we briefly describe the physical fundamentals of surface plasmons (SPs). Then, we discuss recent approaches toward increasing the light trapping efficiency of OPVs through the incorporation of plasmonic structures. Finally, we provide a brief outlook into the future use of SPs in highly efficient OPVs.
<title>Methods for detecting compression wood in green and dry conditions</title> (1999)

The living softwood tree forms compression wood to compensate for external loads during growth, which creates wood fibers with higher longitudinal shrinking and swelling than normal wood at moisture content changes. This is often the cause of undesirable warping of sawn wood products after drying. An automatic detection of severe compression wood is thus useful to reject unwanted pieces. Detection in green condition is often preferred in a sawmill while detection in dry condition is needed in other applications. Three different non- destructive scanning methods were evaluated on both green and dry wood surfaces. The methods used were RGB (red, green, blue) color scanning, tracheid-effect scanning and x-ray scanning. The color and x-ray methods were evaluated on Southern yellow pine lumber, while the tracheid-effect scanning was tested on Norway spruce. For scanning in green condition detection of compression wood was good using the tracheid-effect and color scanning. X-ray scanning was not useful because of the uneven moisture distribution in green lumber. After drying the result changes, tracheid-effect and x-ray scanning have good detection ability while RGB color does not provide sufficient information for reliable detection.
Regulation of gonadotropin gene expression by Müllerian inhibiting substance (2003)

In addition to its role in causing Müllerian duct regression, Müllerian inhibiting substance (MIS) is implicated in the regulation of steroidogenesis, breast and prostate growth, and ovarian follicle recruitment, all of which are processes controlled or influenced by the hypothalamic-pituitary-gonadal axis. Whereas the direct effect of MIS on gonadal, prostate, and breast cells is under investigation, the ability of MIS to modulate pituitary function, thereby affecting those tissues indirectly, has not yet been studied. Using LbetaT2 cells, a murine gonadotrope-derived cell line, we have evaluated the effects of MIS on the expression of the gonadotropin genes. We show that both LbetaT2 cells and adult rat pituitaries express MIS type II receptor (MISRII) mRNA. Within 2 h, follicle-stimulating hormone beta subunit (FSHbeta) mRNA levels are significantly induced by addition of MIS to LbetaT2 cells and remain elevated through 8 h of treatment. Transcriptional activation of both the FSHbeta and luteinizing hormone beta subunit (LHbeta) gene promoters was observed by MIS, which enhances the effect of gonadotropin-releasing hormone (GnRH) agonist on the FSHbeta gene promoter and synergizes with the GnRH agonist to stimulate LHbeta gene promoter activity. Addition of MIS to LbetaT2 cells stimulates the activity of the rat LHbeta gene promoter with as little as 1 microg/ml and in a dose-dependent manner. These studies report both MISRII expression in rat pituitary cells and a gonadotrope-derived cell line and MIS-mediated activation of LHbeta and FSHbeta gene expression, and suggest that MIS may modulate the hypothalamic-pituitary-gonadal axis at more than one level.
The Power Doppler Velocity Index, Pulsatility Index, and Resistive Index Can Assist in Making a Differential Diagnosis of Primary Ovarian Carcinoma and Krukenberg Tumors (2007)

Transvaginal power Doppler sonography with spectral Doppler analysis is an effective method in evaluating intratumoral blood flow of Krukenberg tumors. Low impedance (PI, RI, and VeI) might assist us in making differential diagnoses between primary ovarian carcinoma and Krukenberg tumors according to our preliminary results.
Atmospheric water vapor absorption at 13 μm (1987)

Absolute absorption cross sections for water vapor and water vapor/air mixtures were measured in a frequency range encompassing that of the chemically pumped atomic iodine laser. Measurements were made with a temperature-controlled multipass absorption cell and a high-resolution Fourier transform spectrometer. The measurements covered a broad range of water vapor and air pressures. Several techniques of data analysis were used, and the absorption cross section of 2 kPa of water vapor in an atmosphere of air was determined to be 1.1 +/- 0.2 x 10(-24) cm(2) . In this paper, an expression is derived which allows estimation of the absorption cross section for any pressure of water vapor and air.
A Block-Floating-Point Processor for Rapid Application Development (2007)

This paper proposes an instruction set processor which uses hierarchical block-floating-point (H-BFP) arithmetic. H-BFP has been developed to provide efficient development approach for digital signal processing system. H-BFP offers highly abstracted computation model, and leads to cost-effective implementation. However, application development based on H-BFP is still time consuming task because of lacking high level programming language. In this paper, a processor architecture together with a set of instructions to support H-BFP are proposed. We also propose a related software development environment for efficient algorithm translation which generate high performance codes without any time consuming task. Experimental results show proposed environment achieves high performance signal processing systems with H-BFP processors.
Nanoemulsion Formation by Phase Inversion Emulsification:  On the Nature of Inversion (2006)

Emulsification processes are usually characterized by the way they allow the surfactants, as well as the dispersed phase, to be incorporated into emulsions. A model cyclohexane-in-water emulsion using a pair of polyoxyethylene nonylphenyl ether surfactants, one oil-soluble and one water-soluble, was considered. Two surfactant mixing approaches consisting of mixed surfactants (agent-in-oil and agent-in-water) and segregated surfactants (agent in corresponding oil and water phases) were used to produce the model emulsion. Formation of oil-in-water nanodroplets could be only achieved if emulsification was associated with the formation of a three-phase microemulsion structure (transitional phase inversion) across the path. This occurred only if segregated surfactants were used in a process in which water was added to oil. With decreasing surfactant concentration, a point was reached below which the inversion mechanism transformed from transitional to catastrophic, leading to the formation of large droplets. The transformation was also accompanied by a shift in the evolution of the drop size. Drop size variations showed a minimum at the inversion point for the transitional phase inversion, whereas they showed a maximum for the catastrophic phase inversion. The agent-in-oil technique followed a catastrophic phase inversion mechanism and ranked second in terms of drop size.
Adsorption Removal of Hydrogen Sulfide by Activated Coke Produced from Wood Pellet in the Recycle System of Biomass (2003)

Activated coke is produced from ligneous biomass molded pellets by different carbonization methods and conditions as the absorbents of hydrogen sulfide with the object of both the biomass recycle and the gas purification in a biomass gasification process. We clarified the differences of activated coke characteristics influenced by different production processes, such as the carbonization temperature, carbonization time and carbonization gases. The carbonization temperature was maintained from 723 to 1123 K, the carbonization time was set from 30 to 250 min and the carbonization gas used was either nitrogen or steam. The production process does not include the activation process for reducing the production steps and costs. The activated coke quality and characteristics that were evaluated were the specific surface area, pore size distribution, particle density and adsorption capacity of hydrogen sulfide. Other commercial adsorbents, such as activated carbon and activated char, were used to compare the adsorption performance. The measured adsorption performance of activated coke using the steam carbonization was better than that using the nitrogen carbonization. Comparing the activated coke with commercial absorbents, produced activated coke showed good adsorption results. There is a possibility of using activated coke in the gas purification process in a biomass recycling system instead of using expensive commercial adsorbents or other gas purification processes.
The Effect of Magnetic Field on Scale Prevention in the Industrial Boilers (2005)

We have investigated the effect of magnetic field on the scale formation in the industrial boilers. It was found that passing water through a static magnetic field about 6000 G reduces the scale formation and protects the boiler from internal corrosion. It seems that the presence of the magnetic field modifies the local ionic concentrations via Lorentz Force →× → BVq and therefore changes the morphology of the mineral crystals. This effect causes the shape of the crystals change from a dendristic form to a disk-shape form that is less likely to form a scale.
Transient Focal Cerebral Ischemia Induces a Dramatic Activation of Small Ubiquitin-Like Modifier Conjugation (2008)

This study was designed to investigate whether small ubiquitin-like modifier (SUMO) conjugation is activated after focal cerebral ischemia. Transient ischemia induced a dramatic increase in SUMO2/3 protein conjugates. The most pronounced changes were found in the parietal cortex. SUMO2/3 conjugation was particularly high in neurons located at the border of the middle cerebral artery territory where sumoylated proteins translocated to the nucleus. Considering the marked effect of SUMO conjugation on the function of target proteins, it is very likely that the postischemic activation of sumoylation has a significant effect on the fate of neurons exposed to transient ischemia.
Cancer epigenetics drug discovery and development: the challenge of hitting the mark (2014)

Over the past several years, there has been rapidly expanding evidence of epigenetic dysregulation in cancer, in which histone and DNA modification play a critical role in tumor growth and survival. These findings have gained the attention of the drug discovery and development community, and offer the potential for a second generation of cancer epigenetic agents for patients following the approved "first generation" of DNA methylation (e.g., Dacogen, Vidaza) and broad-spectrum HDAC inhibitors (e.g., Vorinostat, Romidepsin). This Review provides an analysis of prospects for discovery and development of novel cancer agents that target epigenetic proteins. We will examine key examples of epigenetic dysregulation in tumors as well as challenges to epigenetic drug discovery with emerging biology and novel classes of drug targets. We will also highlight recent successes in cancer epigenetics drug discovery and consider important factors for clinical success in this burgeoning area.
Stiffness and inelastic deformation in acrylic‐titanium composite implant materials under compression (1983)

A variety of acrylic bone cement-metal composite materials were prepared and tested in simple compression at 37 degrees C in order to evaluate the mechanical behavior of these materials for possible use in bone replacement. The stiffness of the composite was of particular concern, and a simple rule of mixture was used to raise the modulus of acrylic bone cement. The reinforcement of the cement was accomplished by titanium and Ti-6Al-4V in different forms, e.g., wire, sheet, wire mesh, and powder. Test results demonstrated that the stiffness of the bone cement could indeed be increased by a desired amount to that of bone. A 16% volume fraction consisting of 25 0.10 cm diam Ti-6Al-4V wires increased the modulus of the bone cement by 380% to a value comparable to the modulus of cortical bone. Titanium sheet was nearly as effective as wires in increasing the modulus of bone cement, while titanium mesh was not a significantly effective reinforcing material. The amount of titanium powder added to the bone cement did not alter the compliance of the matrix material. In addition, as the flow strength increased, the strain to the point of load instability decreased. It was concluded that the extent of stiffening was governed by nonuniform deformation in the metal and the adjacent matrix which could be explained on the basis of geometrical considerations. Some of the limitations of the test results as well as methods of predicting the composite implant material behavior are also outlined.