gebhart/patrepeval huggingface dataset:
A two-step approach to qPCR experimental design and software for data analysis (2010)

Materials and methods For screening, a single biological sample is used for each control and treatment group. If screening shows interesting findings, confirmation follows with more biological replicates and a definitive statistical analysis using pooled data from the screening and confirmation steps. This experimental design for qPCR reduces reagent cost and labor without sacrificing sensitivity. To quantitate gene expression, we selected the comparative Ct method due to its simplicity, intuitiveness, and popularity. For statistical analysis, however, this two-step approach raised an interesting question; which parameter should be used for statistical analysis of the data from the screening step. With a single biological sample, the statistical analysis relies on the technical replicates of qPCR. Even though it is natural to assume a normal distribution of the relative gene expression levels of biological replicates based on the central limit theorem, it is unknown for technical replicates because the Ct values of the technical replicates have been non-linearly transformed to obtain relative gene expression levels. Hence, we studied the distribution of delta-Ct and relative gene expression levels from our qPCR data and found that the distribution of delta-Ct is symmetrical and approximately normal while the distribution of relative gene expression levels is skewed. Therefore, we chose deltaCt as our parameter for statistical analysis of the technical replicates from the screening step. To automate the data analysis of the screening step, we developed REALPLOT. A text file is used to enter Ct values and gene/ group information into REALPLOT that calculates relative gene expression, performs statistical analysis, and graphically displays the screening step data. To automate the data analysis after the confirmation step, we developed REALPOOL that pools the data from both the screening and confirmation steps, performs the final statistical analysis, and generates a publishable graphical representation. REALPLOT and REALPOOL were developed using the open-source statistical R environment. They are compatible with all major computer operating systems.
Broker-based Cross-Cloud Federation Manager (2013)

Cloud federation is the next step in creating a new cloud computing ecosystem. The absence of suitable business models for federation managers is hindering the wide deployment of this critical feature. In this paper we will study existing federation managers, specifically CCFM (Cross-Cloud Federation Manager) and analyze its strengths and limitations. To overcome its limitations and make cloud federation more competitive in the current business trends, we introduce a new node called "broker" which will play a significant role in the enhanced CCFM mechanisms. The discovery and match-making agents in CCFM wil be modified to enforce a new business model which is more interesting for private investors. Finally, our new business model will be discussed and possible versions are stated.
Lineage II of Southeast Asian/American DENV-2 is Associated with a Severe Dengue Outbreak in the Peruvian Amazon (2014)

During 2010 and 2011, the Loreto region of Peru experienced a dengue outbreak of unprecedented magnitude and severity for the region. This outbreak coincided with the reappearance of dengue virus-2 (DENV-2) in Loreto after almost 8 years. Whole-genome sequence indicated that DENV-2 from the outbreak belonged to lineage II of the southeast Asian/American genotype and was most closely related to viruses circulating in Brazil during 2007 and 2008, whereas DENV-2 previously circulating in Loreto grouped with lineage I (DENV-2 strains circulating in South America since 1990). One amino acid substitution (NS5 A811V) in the 2010 and 2011 isolates resulted from positive selection. However, the 2010 and 2011 DENV-2 did not replicate to higher titers in monocyte-derived dendritic cells and did not infect or disseminate in a higher proportion of Aedes aegypti than DENV-2 isolates previously circulating in Loreto. These results suggest that factors other than enhanced viral replication played a role in the severity of this outbreak.
&lt;title&gt;Scene segmentation from vector-valued images using anisotropic diffusion&lt;/title&gt; (1998)

Scene segmentation is a pre-processing step for many vision systems. We are concerned with segmentation as a precursor to 3D scene modeling. Segmentation of a scene for this purpose usually involves dividing an image into areas that are relatively uniform in some value (e.g. intensity, range, or curvature). This single segmented image represents the analogous segmented scene. This paper presents a segmentation method that uses features to indicate boundaries or edges between regions. We incorporate features from multiple images types to obtain an more accurate segmentation of objects or object parts in the scene. Multiple features are not only combined directly to improve segmentation results, but they are also used to guide a smoothing operation. This smoothing technique preserves features representing edges while smoothing noise in the images.
The Role of Metal-Catalyzed Chemical Etching Black Silicon in the Reduction of Light- and Elevated Temperature-Induced Degradation in P-Type Multicrystalline Wafers (2021)

Light- and elevated temperature-induced degradation (LeTID) of silicon wafers reduces the energy yield of photovoltaic modules in the field. A previous study demonstrated that this degradation is greatly reduced in samples with a surface textured with black silicon formed via reactive ion etching. However, the reason for this reduction is currently not understood. This article extends that result to a range of nano-textures formed using commercial metal-catalyzed chemical etching. Lifetime test structures are fabricated on multicrystalline wafers with six different chemical nano-textures and the results are compared to planar reference samples. The article demonstrates a reduction in the extent of light-induced degradation compared to planar reference samples for all six textures. The extent of LeTID is observed to reduce with decreasing front surface reflectance and increasing front surface area. The article finds that wafer thickness, phosphorus gettering, and fast-firing cannot explain the result.
Oxidation of <scp>L</scp>‐amino acids by metal ion (Mn<sup>3+</sup>) in sulfuric acid medium: Effect of nucleophilicity and hydrophobicity on reaction rate (2011)

Abstract The kinetics of oxidation of L ‐amino acids (AAs) glycine( 1a ), alanine( 1b ), valine( 1c ), isoleucine( 1d ), leucine( 1e ), proline( 1f ), and phenylalanine( 1g ) by a transition metal ion (Mn 3+ ) was studied in the presence of sulfuric acid medium at 26°C by a spectrophotometrical (λ max = 500 nm) method. In all cases, the kinetics of reactions was of first‐order with respect to each [AA] and [Mn 3+ ]. Increased [H + ], [Mn 2+ ] (the reduction product of Mn 3+ ), sulfate, and chloride had no effect on the reaction rate. However, the reaction rate increased with increased dielectric constant of the medium. Oxidation rate increased for 1a–g and an apparent correlation was observed between the rate of oxidation and nucleophilicty of AAs except for 1a and 1g . The reaction rate also linearly depended on the hydrophobicity of AAs except for 1f and 1g . The thermodynamic parameters for AA‐metal ion complex formation and activation parameters for the rate‐limiting steps have been evaluated. Analysis of the oxidation products indicated that the AAs underwent oxidative deamination and decarboxylation to form corresponding aldehydes. Based on these data, plausible mechanisms involved in the oxidation of AAs are proposed. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 43: 599–607, 2011
Effect of Warm Laser Shock Peening on the Tensile Strength and Ductility of Aluminum Alloys (2012)

In this study, aluminum alloy 7075 (AA 7075) is processed by WLSP and compared with LSP at room temperature (RT-LSP). The microstructure of AA 7075 after processing is characterized by transmission electron microscopy (TEM) and X-ray diffraction (XRD). Tensile test and hardness test were carried out to investigate the effect of WLSP to material strength and ductility. It has been found that highly dense nanoscale precipitate particles are generated after WLSP. These nanoscale precipitate particles effectively block dislocations and thus increase the material strength.
Capillary Electrophoretic Analysis of Somatostatin Analog Peptides. Effect of Organic Solvents as Buffer Modifiers (1992)

Abstract Capillary electrophoretic (CE) method utilizing triethylammonium phosphate/organic modifier solvents as CE buffer was developed for analysis of new proprietary Somatostatin analog peptides synthetized in our laboratory. Acetonitrile, methanol, ethanol and i-propanol were applied as organic modifiers. Applicability of the systems in the analysis of Somatostatin analog peptides was evaluated and optimum conditions of the separation were determined. The effects of the organic solvents on the migration times of the S-analog peptides, elution order and selectivity in the CE systems were investigated. The migration time, elution order and selectivity can be influenced modifying the composition of the electrophoretic buffer with organic solvents. Applying different organic solvents as modifiers the elution order of the peptides can be changed in different ways. The effect of the alcohols on the CE migration time of the peptides is quite opposite to that of the acetonitrile. The degree of the effect of the alcohols at a given concentration depends on the nature of the alcohol: the longer the carbon chain of the alcohol the greater the increase of the CE migration time of the peptide comparing to the migration time obtained in buffer not containing organic solvents.
Severe pruritus in a patient with urticaria pigmentosa treated with topical 5% urea and 3% polidocanol cream (2003)

(2003). Severe pruritus in a patient with urticaria pigmentosa treated with topical 5% urea and 3% polidocanol cream. Journal of Dermatological Treatment: Vol. 14, No. 3, pp. 190-191.
Strength of joints subjected to combined action of bending moments and axial forces (1999)

peer reviewed
Spectrophotometry techniques for the characterisation of yeast cell suspensions (1999)

The use of spectrophotometers for the measurement of cell concentration in yeast suspension is critically discussed. Corrections are derived which take into account cell size, shape, cell aggregation (flocculation) and non linear effects related to sample thickness (cell piling)
Additively Manufactured 3D Micro-bioelectrodes for Enhanced Bioelectrocatalytic Operation (2023)

The drive toward miniaturization of enzyme-based bioelectronics established a need for three-dimensional (3D) microstructured electrodes, which are difficult to implement using conventional manufacturing processes. Additive manufacturing coupled with electroless metal plating enables the production of 3D conductive microarchitectures with high surface area for potential applications in such devices. However, interfacial delamination between the metal layer and the polymer structure is a major reliability concern, which leads to device performance degradation and eventually device failure. This work demonstrates a method to produce a highly conductive and robust metal layer on a 3D printed polymer microstructure with strong adhesion by introducing an interfacial adhesion layer. Prior to 3D printing, multifunctional acrylate monomers with alkoxysilane (-Si-(OCH<sub>3</sub>)<sub>3</sub>) were synthesized via the thiol-Michael addition reaction between pentaerythritol tetraacrylate (PETA) and 3-mercaptopropyltrimethoxysilane (MPTMS) with a 1:1 stoichiometric ratio. Alkoxysilane functionality remains intact during photopolymerization in a projection micro-stereolithography (PμSLA) system and is utilized for the sol-gel reaction with MPTMS during postfunctionalization of the 3D printed microstructure to build an interfacial adhesion layer. This leads to the implementation of abundant thiol functional groups on the surface of the 3D printed microstructure, which can act as a strong binding site for gold during electroless plating to improve interfacial adhesion. The 3D conductive microelectrode prepared by this technique exhibited excellent conductivity of 2.2 × 10<sup>7</sup> S/m (53% of bulk gold) with strong adhesion between a gold layer and a polymer structure even after harsh sonication and an adhesion tape test. As a proof-of-concept, we examined the 3D gold diamond lattice microelectrode modified with glucose oxidase as a bioanode for a single enzymatic biofuel cell. The lattice-structured enzymatic electrode with high catalytic surface area was able to generate a current density of 2.5 μA/cm<sup>2</sup> at 0.35 V, which is an about 10 times increase in current output compared to a cube-shaped microelectrode.
Intravenous Delivery of miR-21 Inhibitor in Mice With Head and Neck Squamous Cell Carcinoma (2023)

Intravenous delivery of a miR-21 inhibitor with lipid nanoparticles is a promising approach for miRNA-targeted therapy of head and neck squamous cell carcinoma.
Model identification for FES supported standing up and sitting down (2004)

This paper is focused on closed loop control of standing up and sitting down of paraplegics using Functional Electrical Stimulation (FES). The sit to stand movement is obtained by feedback controlled stimulation of the vasti muscles. The design of a feedback control loop on the gastrocnemius stimulation is strongly advisable in view of reducing the vasti stimulation and consequently the effect of the fatigue phenomenon on this muscular group. Thus, in this paper, as a first step towards the design of a closed loop controller, a black-box model for the dynamic relationship between gastrocnemius stimulation and knee joint angle is estimated.
Critical Fluid Velocities for Removing Cuttings Bed Inside Horizontal and Deviated Wells (2010)

Abstract This study aims to estimate the critical fluid flow velocity for preventing the development of a stationary bed using empirical correlations valid for horizontal and highly inclined wellbores that can be easily used at the field. For this purpose, experiments have been conducted at METU-PETE Cuttings Transport Flow Loop for various conditions. Observations showed that a stationary bed is developed when the fuid velocity is less than 6.0 ft/s, and a critical fluid velocity of 8.0 ft/s is required to establish a no-bed condition. Results showed that the critical velocity and the thickness of the stationary bed, if developed, could be estimated with a reasonable accuracy.
Turbofan Engine Sizing and Tradeoff Analysis via Signomial Programming (2017)

This paper presents a full one-dimensional core and fan flowpath turbofan optimization model, based on first principles, and meant to be used during aircraft conceptual design optimization. The model is formulated as a signomial program, which is a type of optimization problem that can be solved locally using sequential convex optimization. Signomial programs can be solved reliably and efficiently and are straightforward to integrate with other optimization models in an all-at-once manner. To demonstrate this, the turbofan model is integrated with a simple commercial aircraft sizing model. The turbofan model is validated against the Transport Aircraft System Optimization turbofan model as well as two Georgia Institute of Technology Numerical Propulsion System Simulation turbofan models. Four integrated engine/aircraft parametric studies are performed, including a multimission optimization with over 2400 variables that solves in under 4 s.
High-Dynamic-Range Receivers forDigital BeamForming RadarSystems (2007)

A microwave S-Band receiver wasdeveloped for designed assuming there wasapre-amplifier withthis gain studying dynamic rangeissues indigital beamforming (DBF), andnoisefigure atitsinput, andthiswassimulated inthe phased-array radar systems withmultiple receivers. Particular laboratory withdiscrete components. Thisallowed ustoset attention waspaidtounderstanding thebalance between the thenoise level attheinput oftheanalog-to-digital converter analog andtheanalog-digital conversion segments ofthereceiver(ADC) inasimilar wayaswouldbedoneinarealistic system. tomaximize itsdynamic range.Measurements ofspuriousTwo noiselevelsettings were designed thatresulted in signals weremadewellbelowthereceiver noise floor togainan understanding ofwhichspurs, ifcorrelated amongthereceivers receiver noise figure increases caused bytheADC of1dB inaDBFsystem, might appear above thenoise level attheoutput(highdynamicrangemode)and0.1dB (highsensitivity ofthedigital beamformer.
Phylogenetic history of hominoid DRB loci and alleles inferred from intron sequences (1999)

The evolutionary relationships among the MHC class II DRB4, DRB5 and DRB6 loci as well as the allelic lineages and alleles of the DRB1 locus were studied based on intron 1 and intron 2 sequences from humans, chimpanzee (Pan troglodytes), bonobo (Pan paniscus) and gorilla (Gorilla gorilla). The phylogenetic trees for these sequences indicate that most of the DRB1 allelic lineages predate the separation of the hominoid species studied, consistent with previous analysis of the coding sequences of these lineages. However, the intron sequence variation among alleles within DRB1 allelic lineages is very limited, consistent with the notion that the majority of the contemporary alleles have been generated within the last 250,000 years. The clustering of the DRB1 allelic lineages *08 and *12 with *03 supports a common ancestry for the DR8 and DR52 haplotypes. Similarly, the clustering of DRB1 allelic lineages *15 and *01 with the DRB3 locus is consistent with a common ancestry for the DR1 and DR51 haplotypes. Two cases of recombination around the second exon were observed: 1) the HLA-DRB6 locus appears to have been generated through a recombination between a DRB5 allele and an ancestral DRB6 allele, and 2) the gorilla sequence Gogo-DRB1 *03 appears to have been generated through a recombination between the DRB3 locus and an allele from the DRB1 *03 allelic lineage. The nucleotide substitution rate of DRB introns was estimated to 0.85-1.63 x 10(-9) per site per year, based on comparisons between the most closely related sequences from different hominoid species. This estimate is similar to the substitution rate for other intronic regions of the primate genome.
Prospective of Semiconductor Memory Devices: from Memory System to Materials (2015)

The ever‐increasing demand for higher‐capacity digital memory shows no sign of declining. The conventional strategy for meeting such demand, i.e. shrinking of the memory cell size, will no longer be useful at some point in the future, owing to economic reasons and performance degradation. Nevertheless, performance of computing systems will keep improving for the next generation information technology. This indicates the necessity to consider a fundamentally disparate approach to enhance memory technology. Here, the current status of computer memory chips is reviewed and the pros and cons of the present technology are discussed from computing system, fabrication technology, and materials points of view. Based on this knowledge, the limitations of the present technologies are described, and the possible solutions suggested up to now are reassessed. Finally, a shift in the fundamental computational paradigm from von Neumann computing to other alternatives such as neuromorphic computing and material implication, is commented upon.
Nanoparticle-Based Combination Therapy for Cancer Treatment (2015)

In recent years, combination of different types of therapies using nanoparticles has emerged as an advanced strategy for cancer treatment. Most of all, combination of chemotherapeutic drug and siRNA in nanoformulation has shown a great potential, because siRNA-mediated specific gene silencing can compensate for the incomplete anti-cancer actions of chemotherapy. In this article, nanoparticle-based combination therapy for cancer treatment is introduced to be focused on the therapeutic chemical and siRNA combination. It is classified into 3 groups: 1) general chemotherapy combined with siRNA carrying nanoparticle, 2) co-delivery of chemical and siRNA therapeutics within a single nanoparticle, and 3) Use of multiple nanoparticles for chemical and siRNA therapeutics. The purpose of the combination and the mechanisms of anti-cancer action was described according to the categories. Examples of some recent developments of nanotechnology-based chemo- and siRNA- therapeutics combination therapy are summarized for better understanding of its practical application.
Diagnosing and optimizing water treatment processes by using particle counter: a case study in Korea (2002)

The goal of the flocculation process is to change the particle size distribution to best suit the subsequent processes. Although several methods exist to evaluate the flocculation process, no single universally accepted method has yet to be developed. The purpose of this paper is to present experiences whereby particle counting was used in the diagnosis and optimization of the flocculation process. A commercially available on-line continuous particle counter has been used in evaluating the design and the operation of this process at two conventional Water Treatment Plants. The evaluation is based on particle dynamics, i.e., the change of the number of small and large particles. Some design deficiencies in the distribution channel and flocculation process have been identified from this method, and thus some operational parameters are suggested for optimum performance. Because the optimum condition may be site-specific, the method presented in this paper will be beneficial in the evaluation of the flocculation process at other water treatment plants.
Carbon Nanotube-Based High Temperature Vacuum Microelectronics for E&amp;P Applications (2012)

Abstract Field emission from carbon nanotube (CNT) bundles has been applied to develop new class of computational vacuum microelectronics for harsh environment applications. CNTs have demonstrated superior field emission performance because of their low emission threshold, high current density, and are conducive for monolithic integration with silicon structures to develop microelectronic/microsensor systems. In this paper we present high-temperature tolerant "digital" vacuum electronics using CNTs. This technology is applicable to in situ sensor electronics for down-hole applications where the operating environment is high temperature, high pressure, and has corrosive chemicals. The digital and analog electronic devices developed using CNT-vacuum microelectronic technology can be integrated with sensor systems to achieve prolonged stand-alone operation during E&amp;P. NASA-JPL has developed high performance cold cathodes using arrays of carbon nanotube bundles that produce &amp;gt; 15 A/cm2 at applied fields of 6 to 8 V/μm. They have exhibited robust operation in poor vacuums of 10‒7 to 10‒4 Torr-a typically achievable range inside hermetically sealed microcavities. By monolithically integrating CNT cathodes with micromachined Si multi-gate structures we have demonstrated a new class of programmable "vacuum" logic gates. We have achieved switching operation at temperatures up to 700° C. The initial design, operation, and the potential performance in an improved design will be presented in this paper along with vacuum packaging techniques to make stand alone devices for circuit board integration. CNT-vacuum microelectronics opens up a new regime of in situ electronics for novel sensor/electronics systems because of their inherent high-temperature tolerance, and corrosion resistance. Unlike traditional vacuum tubes, these are low power, miniature, and potentially as fast as their solid-state counterparts while exhibiting superior reverse bias or leakage current characteristics. These devices offer potential to significantly enhance E&amp;P operation.