gebhart/patrepeval huggingface dataset:
Issues in reduced-resolution decoding of MPEG video (2003)

Given a high resolution compressed video, we investigate the problem of simplifying the memory and computational requirements of the decoder, when the intended playback resolution is less than the encoded resolution. We show that significant savings can be obtained in the amount of temporary storage space used, memory bandwidth between the processor and local memory, and raw computational complexity, while not incurring a significant loss in perceptual quality. Most video compression standards make special adjustments to deal with interlaced video. We explore how the proposed solution adapts to these situations and suggest modifications which improve the quality of the reconstructed video. Results from using these algorithms on a number of test sequences compressed with the MPEG-2 standard are presented.
Mathematical design of prokaryotic clone-based microarrays (2005)

Validation of these equations shows that they form reliable tools supporting optimal design of prokaryotic clone-based microarrays.
High-quality, deterministic parallel placement for FPGAs on commodity hardware (2008)

In this paper, we describe the application of two parallelization strategies to the Quartus II FPGA placer. The first uses a pipelining approach and achieves speedups of 1.3x on two processing cores. The second uses a parallel moves approach and achieves speedups of 2.2x on four cores. Unlike all previous parallel moves algorithms, ours is deterministic and always gives the same answer as the serial version of the algorithm, without any significant reduction in performance.
DBCG: The Danish Breast Cancer Cooperative Group – a 30-year struggle for better breast cancer treatment in Denmark (2008)

Udgivelsesdato: 2008-null
High-Level Immunogenicity Is Achieved Vaccine With Adjuvanted Pandemic H1N12009and Improved With Booster Dosing in a Randomized Trial of HIV-Infected Adults (2012)

High-level immunogenicity was achieved with a single dose of this adjuvanted vaccine. Immunogenicity was further improved with booster dosing. Use of this adjuvanted vaccine and booster represent an important approach to increasing immunogenicity in this vaccine hypo-responsive population.
ChemInform Abstract: Decavanadate Ion‐Pillared Hydrotalcite: Spectroscopic Studies of the Thermal Decomposition Process. (1990)

Abstract The thermal decomposition of samples prepared by intercalation of V 10 O 2 6‐ 8 ions into the layers of Mg 2 Al(OH) 6 is followed over the range 20‐650 °C by means of XRD, Raman spectroscopy, and X‐ray absorption near‐edge spectroscopy (XANES).
Low-temperature nitride transformation reactions (2011)

This study illustrates a novel method of transforming between two refractory nitrides at temperatures well below their respective melting points. Silicon nitride (Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) is an excellent thermal and electronic insulator, with applications in the microelectronic, automotive and technical ceramic industries. Thermodynamically, there is a significant decrease in the Gibb's Free Energy inherent in the transformation between Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> and a number of refractory metal nitrides; however, these transformation reactions are limited in the pure state by a kinetic barrier at any temperature appreciably lower than the melting point of Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> (~2173 K). Results of this study illustrate the successful conversion of powdered amorphous Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> to TiN. The transformation is made possible by a liquid phase present in a number of Ti-based alloys at temperatures in the vicinity of 800°C. Since both nitrides (SiN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> and TiN) are refractory, the presence of the liquid phase provides a high-diffusivity pathway, thus overcoming the kinetic barrier associated with the otherwise thermodynamically favorable reaction.
Cascaded all-optical sub-channel add/drop multiplexing from a 1-Tb/s MB-OFDM or N-WDM super-channel with ultra-low guard-bands (2017)

We show cascaded 100-Gb/s sub-channel add/drop from a 1-Tb/s MB-OFDM or Nyquist-WDM super-channel having ultra-low inter-sub-channel guard-bands within a recirculating loop via a hierarchical ROADM using high-resolution filters, showcasing up to 1000-km transmission reach and five ROADM node passages for the add/drop sub-channel when hybrid Raman-EDFA is used.
The Construction and Use of Cloning Vectors (1990)

This chapter contains sections titled: The Commercially Available Vectors The Construction of Vectors for Use with the Clostridia References Appendix I: Addresses of Suppliers of Cloning Vectors Appendix II: Addresses of Suppliers of Other Products Useful for Molecular Biology
Bactericidal Efficacy of Nitric Oxide-Releasing Silica Nanoparticles (2020)

The utility of nitric oxide (NO)-releasing silica nanoparticles as a novel antibacterial is demonstrated against Pseudomonas aeruginosa. Nitric oxide-releasing nanoparticles were prepared via co-condensation of tetraalkoxysilane with aminoalkoxysilane modified with diazeniumdiolate NO donors, allowing for the storage of large NO payloads. Comparison of the bactericidal efficacy of the NO-releasing nanoparticles to 1-[2-(carboxylato)pyrrolidin-1-yl]diazen-1-ium-1,2-diolate (PROLI/NO), a small molecule NO donor, demonstrated enhanced bactericidal efficacy of nanoparticle-derived NO and reduced cytotoxicity to healthy cells (mammalian fibroblasts). Confocal microscopy revealed that fluorescently-labeled NO-releasing nanoparticles associated with the bacteria, providing rationale for the enhanced bactericidal efficacy of the nanoparticles. Intracellular NO concentrations were measurable when the NO was delivered from nanoparticles as opposed to PROLI/NO. Collectively, these results demonstrate the advantage of delivering NO via nanoparticles for antimicrobial applications.
Applications of Lentiviral Vectors in Noninvasive Molecular Imaging (2008)

Noninvasive imaging of molecular-genetic and cellular processes is an effective way to determine the location(s), magnitude, and time variation of action of gene products used for many therapeutic strategies. Lentiviral vectors provide effective means for the delivery, integration, and expression of transgenes in cultured mammalian cells as well as in vivo. Therefore, the combination of lentiviral vector-mediated therapeutic and imaging-targeted reporter gene delivery to various target organs holds promise for the future treatment of diseases. In this chapter, we provide protocols for developing lentiviral vectors that can be utilized for noninvasive monitoring/imaging of reporter gene expression. We have described the procedures to perform cellular assays and animal imaging based on positron emission tomography (PET), optical bioluminescence, and fluorescence reporter genes. The protocols described here are standardized for mouse models, which can also be adapted for other small animal models (e.g., rats).
Inhibition of Formation of Calcium Phosphate Deposits on Teeth and Dental Materials: Recent Advances (1995)

The inorganic composition of dental calculi from teeth and dentures has been characterized by x-ray diffraction, electron microprobe, and infrared absorption spectroscopy. They consist of carbonated hydroxylapatite (CHA), dicalcium phosphate dihydrate (DCPD), octacalcium phosphate (OCP), and magnesium-substituted beta-tricalcium phosphate (6-TCMP). The calculi on denture surfaces are principally CHA. Formulations have been developed to inhibit formation of these calculi in humans. The active inhibitors are pyrophosphate, pyrophosphate plus polymer, and zinc salts. These agents inhibit calculus formation in humans by preventing the formation of hydroxyapatite crystals. The new formulations include multiple-benefits products containing fluoride and antimicrobial and/or desensitizing agents. These provide not only reduction in calculus formation in humans but also reduced plaque, gingivitis, and/or dentinal hypersensitivity. Recent studies have also indicated a relationship between gingival recession and supragingival calculus in the Thai population, and the use of an anticalculus formulation has shown significant improvement in gingival recession in this population.
Engineering a Minimal 1185 Bp Cloning Vector from a Puc18 Plasmid Backbone with an Extended Multiple Cloning Site (2018)

Minimal plasmids play an essential role in many intermediate steps in molecular biology. They can for example be used to assemble building blocks in synthetic biology or be used as intermediate cloning plasmids that are ideal for PCR-based mutagenesis methods. A small backbone also opens up for additional unique restriction enzyme cloning sites. Here we describe the generation of a ~1kb fully functional cloning plasmid with an extended multiple cloning site (MCS). To our knowledge, this is the smallest high-copy cloning vector ever described.
A Pyramid Of Image Generating Functions (1987)

An image is modeled by a two-parameter stochastic process generated by splitting a pixel into a block of 2 X 2 pixels thereby obtaining a higher resolution image. This sequential reproduction process is achieved by using a sequence of random variables as multipliers. In the analysis of image structure we apply the model in the reverse order, i.e. estimate the sequence of random variables which generates the image. The size of matrices representing the stochastic processes show a pyramidal structure when increasing or decreasing the resolution. The features characterizing an image are provided by analysis of the properties of estimated stochastic processes at each level of the pyramid, and by comparison of properties characteristic of consecutive levels of the pyramid. As a byproduct of this image structure analysis, our approach suggests a new method for data compression.
Protein binding and biological evaluation of a polymer-anchored cobalt(iii) complex containing a 2,2′-bipyridine ligand (2014)

The molecular interaction of polymer-anchored cobalt(III) complex, cis-[Co(bpy)2(BPEI)Cl]Cl2·4H2O (bpy = 2,2′-bipyridine, BPEI = branched polyethyleneimine) with two plasma proteins, human serum albumin (HSA) and bovine serum albumin (BSA) using various spectrophotomeric techniques has been investigated. The steady-state and time-resolved fluorescence spectra clearly demonstrated the static quenching mechanism. The calculated thermodynamic parameters revealed that the interaction between the polymer–cobalt(III) complex and HSA/BSA was driven mainly by van der Waals forces and hydrogen bonds. The results observed from three dimensional fluorescence and circular dichorism (CD) spectral studies manifested the conformational changes of HSA/BSA upon addition of the polymer–cobalt(III) complex. Furthermore, the antimicrobial result showed that the polymer–cobalt(III) complex exhibits good antibacterial and antifungal activities against certain human pathogenic microorganisms. In addition, the antiproliferative properties of the polymer–cobalt(III) complex on the HEp-2 human larynx cancer cells were determined using the MTT assay. The mode of cell death induced by the complex following treatment was analyzed adopting specific staining techniques. MTT assay revealed that the viability of the cells thus treated was significantly decreased and the cells succumbed to apoptosis as well as necrosis as reflected in changes in the nuclear morphology and cytoplasmic features by AO & EB and Hoechst staining methods.
Expression of Hepatocyte Growth Factor and c-Met Receptor in Gastric Mucosa during Gastric Ulcer Healing (2000)

Recent studies have shown that hepatocyte growth factor (HGF) has a mitogenic and motogenic activity for gastric mucosal cells. The aim of this study is to ascertain the clinical significance of the expression of HGF and its receptor (c-met) during the course of gastric ulcer healing.Ten patients who underwent endoscopic mucosal resection (EMR) and developed acute gastric ulcer and 20 patients with peptic ulcer of the stomach were enrolled in this study. Tissue samples were serially obtained from both the edge of the ulcer and its neighboring mucosa 0, 2, and 8 weeks after EMR or diagnosis. Gene expression of HGF, c-met, c-myc, and proliferating cell nuclear antigen (PCNA) was semiquantitatively examined by reverse transcription polymerase chain reaction (RT-PCR) using beta-actin as an internal control. In addition, expression of HGF and c-met mRNA with regard to the presence or absence of Helicobacter pylori infection was studied.In patients after EMR HGF, c-met, c-myc, and PCNA mRNA in the ulcer lesion at 0 week was at the peak of its expression and then decreased with time (P < 0.01, P < 0.05, P < 0.05, and P < 0.05, respectively). In patients who underwent EMR the intensity of HGF mRNA was correlated with that of c-met, c-myc, and PCNA mRNA (P < 0.0001, P = 0.0095, and P = 0.0009, respectively) and that of c-met mRNA was correlated with that of c-myc and PCNA mRNA (P = 0.012 and P < 0.0001, respectively). In patients with peptic ulcer, expression of HGF mRNA decreased with time (0 week versus 8 weeks, P < 0.05; 0 week versus 8 weeks, P < 0.01). c-Met expression was lower at 8 weeks than at 0 week (P < 0.05). The intensity of c-met mRNA was correlated with that of PCNA mRNA (P < 0.0001). H. pyiori-infected mucosa had a higher level of HGF mRNA than non-infected mucosa.The present study suggests that HGF is one of the growth factors acting together during healing of gastric ulcer.
Electrochemical Upgrading of Bio-Oil (2017)

Bio-oil produced by fast pyrolysis of biomass is a potential source of low carbon, renewable hydrocarbon fuel. However, the properties such as low heating value, incomplete volatility, acidity, instability, and incompatibility with standard fuels restrict its use. The undesirable properties of pyrolysis oil result from its chemical composition that mostly consists of different classes of oxygenated organic compounds. Current process of Hydrodeoxygenation to remove oxygen involves high-temperature, high-pressure processing in the presence of hydrogen and catalyst. An alternative process of deoxygenation of bio-oil using solid-state, oxygen conductor based electrochemical cell is under investigation. The electrolysis process removes oxygen from the oxygenated organic molecule as well from steam to produce hydrogen in-situ allowing for a distributed, small scale integrated upgrading unit. Mixtures of model compounds and a slip stream of pyrolysis vapor were tested. The results show the potential for integrating a pyrolyzer and an electrochemical device for stabilizing pyrolysis oil.
Deep Information Propagation (2016)

We study the behavior of untrained neural networks whose weights and biases are randomly distributed using mean field theory. We show the existence of depth scales that naturally limit the maximum depth of signal propagation through these random networks. Our main practical result is to show that random networks may be trained precisely when information can travel through them. Thus, the depth scales that we identify provide bounds on how deep a network may be trained for a specific choice of hyperparameters. As a corollary to this, we argue that in networks at the edge of chaos, one of these depth scales diverges. Thus arbitrarily deep networks may be trained only sufficiently close to criticality. We show that the presence of dropout destroys the order-to-chaos critical point and therefore strongly limits the maximum trainable depth for random networks. Finally, we develop a mean field theory for backpropagation and we show that the ordered and chaotic phases correspond to regions of vanishing and exploding gradient respectively.
Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages (2019)

Abstract Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromere DNA sequences are diverse and often repetitive, making them challenging to assemble and identify. Here, we describe centromeres in an oomycete Phytophthora sojae by combining long-read sequencing-based genome assembly and chromatin immunoprecipitation for the centromeric histone CENP-A followed by high-throughput sequencing (ChIP-seq). P. sojae centromeres cluster at a single focus at different life stages and during nuclear division. We report an improved genome assembly of the P. sojae reference strain, which enabled identification of 15 enriched CENP-A binding regions as putative centromeres. By focusing on a subset of these regions, we demonstrate that centromeres in P. sojae are regional, spanning 211 to 356 kb. Most of these regions are transposon-rich, poorly transcribed, and lack the histone modification H3K4me2 but are embedded within regions with the heterochromatin marks H3K9me3 and H3K27me3. Strikingly, we discovered a Copia -like transposon (CoLT) that is highly enriched in the CENP-A chromatin. Similar clustered elements are also found in oomycete relatives of P. sojae , and may be applied as a criterion for prediction of oomycete centromeres. This work reveals a divergence of centromere features in oomycetes as compared to other organisms in the Stramenopila-Alveolata-Rhizaria (SAR) supergroup including diatoms and Plasmodium falciparum that have relatively short and simple regional centromeres. Identification of P. sojae centromeres in turn also advances the genome assembly. Author summary Oomycetes are fungal-like microorganisms that belong to the stramenopiles within the Stramenopila-Alveolata-Rhizaria (SAR) supergroup. The Phytophthora oomycetes are infamous as plant killers, threatening crop production worldwide. Because of the highly repetitive nature of their genomes, assembly of oomycete genomes presents challenges that impede identification of centromeres, which are chromosomal sites mediating faithful chromosome segregation. We report long-read sequencing-based genome assembly of the Phytophthora sojae reference strain, which facilitated the discovery of centromeres. P. sojae harbors large regional centromeres fully embedded in heterochromatin, and enriched for a Copia -like transposon that is also found in discrete clusters in other oomycetes. This study provides insight into the oomycete genome organization, broadens our knowledge of the centromere structure, function and evolution in eukaryotes, and may help elucidate the high frequency of aneuploidy during oomycete reproduction.
EUV patterning successes and frontiers (2016)

The feature scaling and patterning control required for the 7nm node has introduced EUV as a candidate lithography technology for enablement. To be established as a front-up lithography solution for those requirements, all the associated aspects with yielding a technology are also in the process of being demonstrated, such as defectivity process window through patterning transfer and electrical yield. This paper will review the current status of those metrics for 7nm at IBM, but also focus on the challenges therein as the industry begins to look beyond 7nm. To address these challenges, some of the fundamental process aspects of holistic EUV patterning are explored and characterized. This includes detailing the contrast entitlement enabled by EUV, and subsequently characterizing state-of-the-art resist printing limits to realize that entitlement. Because of the small features being considered, the limits of film thinness need to be characterized, both for the resist and underlying SiARC or inorganic hardmask, and the subsequent defectivity, both of the native films and after pattern transfer. Also, as we prepare for the next node, multipatterning techniques will be validated in light of the above, in a way that employs the enabling aspects of EUV as well. This will thus demonstrate EUV not just as a technology that can print small features, but one where all aspects of the patterning are understood and enabling of a manufacturing-worthy technology.
Origin and Emission of Volatile Biomarkers in Skin (2022)

Skin volatile biomarkers have great potential to become a field-oriented approach for evaluating health conditions. The profiles of biomarkers are highly dependent on the sampled skin area because the distribution of the skin glands is not homogeneous, creating a large number of potential sampling points to gain better profiling of volatile compounds. This chapter reviews the different origins of the volatile organic compounds (VOCs) and currently available literature on the detection of skin VOCs in the diagnosis and monitoring of diseases. Mass spectrometry and sensor-based systems for capturing skin VOCs are presented and discussed, as well as the expectation of their becoming medical devices to be used in medical or in-field settings.
A metasurface optical modulator using voltage-controlled population of quantum well states (2018)

The ability to control the light-matter interaction with an external stimulus is a very active area of research since it creates exciting new opportunities for designing optoelectronic devices. Recently, plasmonic metasurfaces have proven to be suitable candidates for achieving a strong light-matter interaction with various types of optical transitions, including intersubband transitions (ISTs) in semiconductor quantum wells (QWs). For voltage modulation of the light-matter interaction, plasmonic metasurfaces coupled to ISTs offer unique advantages since the parameters determining the strength of the interaction can be independently engineered. In this work, we report a proof-of-concept demonstration of a new approach to voltage-tune the coupling between ISTs in QWs and a plasmonic metasurface. In contrast to previous approaches, the IST strength is here modified via control of the electron populations in QWs located in the near field of the metasurface. By turning on and off the ISTs in the semiconductor QWs, we observe a modulation of the optical response of the IST coupled metasurface due to modulation of the coupled light-matter states. Because of the electrostatic design, our device exhibits an extremely low leakage current of ∼6 pA at a maximum operating bias of +1 V and therefore very low power dissipation. Our approach provides a new direction for designing voltage-tunable metasurface-based optical modulators.