gebhart/patrepeval huggingface dataset:
Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives (2014)

Background Studies of ancestry are difficult in tomato because it crosses with many wild relatives and species in the tomato clade have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using coding sequence from Solanum lycopericum , S. galapagense , S. pimpinellifolium , S. corneliomuelleri , and S. tuberosum and genomic sequence from two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium , as well as an heirloom line, S. lycopersicum ‘Yellow Pear’, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato. Results Divergence date estimates suggest divergence of S. lycopersicum , S. galapagense , and S. pimpinellifolium happened less than 0.5 MYA . Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense , although two secondary trees are also highly represented . A total of 29 genes in our analysis showed evidence of selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these accessions, likely as a result of incomplete lineage sorting and introgression, a primary phylogenetic history was strongly supported. Conclusions Based on analysis of these accessions, S. galapagense appears to be closely related to S. lycopersicum , suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.
Konstitution und Lichtabsorption, II. Mitteil. Diacetylen‐Verbindungen (1951)

Abstract Es werden einige Kohlenwasserstoffe dargestellt, die in einer Kette konjugierter C:C‐Bindungen die Diacetylengruppe eingebaut enthalten. Die Absorptionspektren sind in den Anfangsgliedern „anomal”︁ und gehen bei größerer Anzahl von C:C‐Bindungen wieder weitgehend in „normale”︁ Spektren über, doch sind die Maxima gegenüber den entsprechenden Äthylenverbindungen ins Kurzwellige verschoben und die Extinktionen erheblich erniedrigt.
Microstructure and Mechanical Properties of Surfactant Templated Nanoporous Silica Thin Films: Effect of Methylsilylation (2003)

Microstructural and mechanical properties of organic surfactant templated nanoporous thin silica films have been studied by X-ray diffraction, Fourier transform infrared spectroscopy, and nanoindentation. Compared with many other porous low-k dielectrics, the self-assembled molecularly templated nanoporous silica films demonstrate better mechanical properties. This is ascribed to the presence of a well-ordered pore channel structure in the nanoporous silica thin films. Hardness and elastic modulus are strongly dependent on film preparation and modification methods. Trimethylsilylation by hexamethylsilazane vapor treatment effectively enhances the mechanical strength of the nanoporous silica films. When the sol precursor solution is mixed with trimethylchlorosilane (TMCS), the resulting nanoporous films have a weaker mechanical strength. The pore channel structure of the nanoporous silica film becomes less ordered for the TMCS derivatized nanoporous films. In addition, the chemical structure in the silica solid matrix of the TMCS derivatized films is more disordered than those without TMCS modification. The nanoindentation measurement results are discussed in terms of the pore microstructure of the nanoporous silica network and the springback effect due to the presence of trimethylsilyl groups in the nanopores. © 2003 The Electrochemical Society. All rights reserved.
The Genetics of Alzheimer’s Disease (2007)

The genetics of Alzheimer’s disease is produced by 3 essentially interactive gene groups: (1) APP and presenilin 1 and 2; (2) APOE E2, E3, and E4; (3) genes on chromosomes 9, 10, 12, etc. If any gene in (1) mutates, beta amyloid (Aβ) increases sharply beyond what the genes of (3) can remove, with early-onset Alzheimer’s disease the result. With retention of Aβ by E4 in (2), Alzheimer’s disease might result even though (1) and (3) are normal. If any gene in (3) mutates, the level of Aβ will rise, but because many genes are involved in Aβ removal, late-onset Alzheimer’s disease would be detected only eventually.
Dispersion-flattened photonic crystal fiber with large effective area and low confinement loss (2005)

A photonic crystal fiber (PCF) can realize a flat dispersion over a wide wavelength range that cannot be realized with a conventional single-mode fiber. However, the confinement loss tends to increase in a conventional dispersion-flattened PCF (DF-PCF) that has uniform air holes. In this paper, a novel PCF that has two cladding layers with different effective indices is proposed. The authors numerically show that the proposed PCF can achieve an ultralow dispersion variation of less than 0.8 ps/nm/spl middot/km in all telecommunication bands, with both a large effective area greater than 100 /spl mu/m/sup 2/ and a low confinement loss less than 0.01 dB/km.
Human Identities and Nation Building: Comparative Analysis, Markets, and the Modern University (2014)

The purpose of this article is to discuss the dilemma of the multi-university in sustainable education, research, and outreach by addressing some of the ways in which universities, must generate actions that seek to address these challenges, develop strategic relationships, and maximize their potential in the areas of teaching, research and service to society. Significantly, we examine how sustainability is experienced by nations—in our case Mexico—by analyzing higher education and its mission in developing citizens and economic sovereignty. The author’s goal is to establish a new paradigm by which practitioners and researchers can collaborate to produce the ideas that stimulate sustainable development.
Effect of Tungsten on the Purification of Few-Walled Carbon Nanotubes Synthesized by Thermal Chemical Vapor Deposition Methods (2006)

Few-walled carbon nanotubes (FWNTs) were synthesized by the methane chemical vapor deposition (CVD) method using binary catalysts Co/Mo and Co/W supported on MgO. It was found that Mo was not only a promoter for FWNT growth but also active in the formation of multiwalled carbon nanotubes (MWNTs) in our CVD process. W was found to be a better promoter since it was much less active in producing MWNT impurities. As a result, the raw FWNT materials prepared from W-containing catalysts were much more easily purified than those from Mo-containing catalysts. Scanning electron microscopy, thermogravimetric analysis, X-ray photoelectron spectroscopy, and transmission electron microscopy were used to characterize both raw materials and purified samples.
A novel architecture for low-power design of parallel multipliers (2002)

In this paper, a new architecture for low-power design of parallel multipliers is proposed. Reduction of power consumption is achieved by reducing the circuit activity at the architecture level by dividing the multiplication circuit into clusters of smaller multipliers. By applying clock gating techniques and preprocessing operations on the input pattern using simple logic functions, some of these clusters that are producing a zero result can be disabled and hence saving the switching power component that could be consumed by these clusters. The amount of power savings is dependent on the nature of the input pattern, which varies according to the application. Analysis of the input pattern is performed. For testing purposes, A 8-bit multiplier prototype is constructed in 0.35 micron double metal CMOS technology using Cadence development tools. For the average case when all the input combinations have an equal probability of occurrence, HSPICE simulation results at 3.3 V and 500 MHz frequency show that the proposed architecture results in 13.4% power savings.
Caching search engine results over incremental indices (2010)

A Web search engine must update its index periodically to incorporate changes to the Web, and we argue in this work that index updates fundamentally impact the design of search engine result caches. Index updates lead to the problem of cache invalidation: invalidating cached entries of queries whose results have changed. To enable efficient invalidation of cached results, we propose a framework for developing invalidation predictors and some concrete predictors. Evaluation using Wikipedia documents and a query log from Yahoo! shows that selective invalidation of cached search results can lower the number of query re-evaluations by as much as 30% compared to a baseline time-to-live scheme, while returning results of similar freshness.
Decisions About Dendritic Cells: Past, Present, and Future (2012)

A properly functioning adaptive immune system signifies the best features of life. It is diverse beyond compare, tolerant without fail, and capable of behaving appropriately with a myriad of infections and other challenges. Dendritic cells are required to explain how this remarkable system is energized and directed. I frame this article in terms of the major decisions that my colleagues and I have made in dendritic cell science and some of the guiding themes at the time the decisions were made. As a result of progress worldwide, there is now evidence of a central role for dendritic cells in initiating antigen-specific immunity and tolerance. The in vivo distribution and development of a previously unrecognized white cell lineage is better understood, as is the importance of dendritic cell maturation to link innate and adaptive immunity in response to many stimuli. Our current focus is on antigen uptake receptors on dendritic cells. These receptors enable experiments involving selective targeting of antigens in situ and new approaches to vaccine design in preclinical and clinical systems.
In Vitro Analysis of Mutations Causing Myoclonus Epilepsy with Ragged-Red Fibers in the Mitochondrial tRNA<sup>Lys</sup> Gene: Two Genotypes Produce Similar Phenotypes (1995)

Cytoplasts from patients with myoclonus epilepsy with ragged-red fibers harboring a pathogenic point mutation at either nucleotide 8344 or 8356 in the human mitochondrial tRNA(Lys) gene were fused with human cells lacking endogenous mitochondrial DNA (mtDNA). For each mutation, cytoplasmic hybrid (cybrid) cell lines containing 0 or 100% mutated mtDNAs were isolated and their genetic, biochemical, and morphological characteristics were examined. Both mutations resulted in the same biochemical and molecular genetic phenotypes. Specifically, cybrids containing 100% mutated mtDNAs, but not those containing the corresponding wild-type mtDNAs, exhibited severe defects in respiratory chain activity, in the rates of protein synthesis, and in the steady-state levels of mitochondrial translation products. In addition, aberrant mitochondrial translation products were detected with both mutations. No significant alterations were observed in the processing of polycistronic RNA precursor transcripts derived from the region containing the tRNA(Lys) gene. These results demonstrate that two different mtDNA mutations in tRNA(Lys), both associated with the same mitochondrial disorder, result in fundamentally identical defects at the cellular level and strongly suggest that specific protein synthesis abnormalities contribute to the pathogenesis of myoclonus epilepsy with ragged-red fibers.
A Prospective Study of Ripple Mapping in Atrial Tachycardias (2016)

RM helps to define activation through low-voltage regions and aids ablation of atrial tachycardias.
PHOTORESPONSIVE MEMBRANES. REGULATION OF MEMBRANE PROPERTIES BY PHOTOREVERSIBLE cis–trans ISOMERIZATION OF AZOBENZENES (1980)

Abstract Photoresponsive membranes have been constructed by incorporating the amphiphatic alkylammonium salts containing azobenzene chromophores into dipalmitoylphosphatidylcholine liposomes.
A Hardware-Agnostic OPC UA Skill Model for Robot Manipulators and Tools (2019)

The current trend to lot-size-one production requires reduced integration effort and easy reuse of available devices inside the production line. These devices have to offer a uniform interface to fulfill these requirements.This paper presents a hardware-agnostic skill model using the semantic modeling capabilities of OPC UA. The model provides a standardized interface to hardware or software functionality while offering an intuitive way of grouping multiple skills to a higher hierarchical abstraction.Our skill model is based on OPC UA Programs and modeled as an open source NodeSet. We hereby focus on the reusability of the skills for many different domains. The model is evaluated by controlling three different industrial robots and their tools through the same skill interface. The evaluation shows that our generic OPC UA skill model can be used as a standardized control interface for device and software components in industrial manufacturing. With our solution new components can easily be exchanged without changing the interface. This is not only true for industrial robots, but for any device which provides a controllable functionality.
RF challenges for 2.4 and 5 GHz WLAN deployment and design (2003)

With their low cost and high-speed data rate capabilities, IEEE 802.11-based wireless local area networks (WLANs) are growing exponentially. This paper discusses the interference impact from the co-channel interference on current 2.4 GHz WLAN application and addresses several RF design challenges for future 5 GHz frequency band operations. Coverage and migration issues from 2.4 GHz to 5 GHz are also included.
Substrate‐induced lateral micro‐phase separation of a diblock copolymer (1996)

“Ultra‐monomolecular” films of block copolymers , i.e., films whose surface concentration is so low that the substrate cannot be covered homogeneously without affecting the structure of the macromolecules very strongly, have been studied using tapping‐ and friction‐mode SFM. Two‐dimensional phase separation yielding an ordered pattern of polystyrene and poly‐2‐vinylpyridine surface domains is observed. SFM is shown to distinguish topological features and also to discriminate between chemically different components. The surface features generated and the formation mechanisms involved are discussed.
Triplex-Forming Oligonucleotides Can Modulate Aquaporin-5 Gene Expression in Epithelial Cells (1997)

Triplex-forming oligonucleotides (TFOs) may provide a useful approach to decrease gene transcription in vivo. We have identified two sequences in the rat aquaporin 5 (rAQP5) cDNA that are capable of forming a DNA triple helix. We designed four TFOs based on these sequences (a purine and a pyrimidine TFO per sequence). All four TFOs were able to bind to the rAQP5 cDNA at varying efficiencies in vitro as measured by using gel mobility shift assays. The TFOs were delivered to intact MDCK epithelial cells via adenovirus-polylysine complexes. Experiments with fluorescein-isothiocyanate-labeled oligonucleotides delivered in this way showed primarily a nuclear localization. Three of the four TFOs internalized by adenovirus-polylysine complexes were capable of decreasing rAQP5 expression in intact MDCK cells infected with a recombinant adenovirus encoding rAQP5. These data show that adenovirus-polylysine-TFO complexes can result in TFO delivery to the nucleus in intact epithelial cells and that TFOs may provide a useful way to selectively modulate rAQP5 gene expression.
Temperature-dependent near-infrared emission of highly concentrated Cu<sup>2+</sup>in CaCuSi<sub>4</sub>O<sub>10</sub>phosphor (2014)

CaCuSi4O10 (CCS4O) shows a 430–800 nm broad excitation band and an intense 918 nm near-infrared (NIR) emission peak at room temperature (RT). The electronic structure calculated by density functional theory (DFT) is discussed in an attempt to understand the small quenching effects in this highly concentrated Cu2+ material, which may be ascribed to the localization of 3d electrons of Cu2+ ion and weak interaction between Cu2+ ions. The assignments of photoluminescence excitation (PLE) and photoluminescence (PL) peaks are made based on the absorption spectrum and crystal field theory. In particular, we investigate the temperature-dependent PL spectra upon excitation by monochromatic light and simulated sunlight. The distinct variation in PL intensities with temperature upon the two means of excitation can be understood by configurational coordinate (CC) models, in which different thermal activation energies are considered. Furthermore, Ba2+-doped and Zn2+-doped series are used to illustrate the relation between the redshift of the PL peak and lattice expansion. The high thermal quenching temperature (555 K) and low concentration quenching (unchanged lifetimes when diluting Cu2+ ions) indicate that this phosphor has great potential as an inorganic dye for luminescent solar concentrator (LSC).
Neurovirulence Mutant of Vesicular Stomatitis Virus with an Altered Target Cell Tropism In Vivo (1980)

Intracerebral infection of weanling Swiss mice with a temperature-sensitive (ts) mutant of vesicular stomatitis virus (VSV), ts pi364, resulted in a unique neuropathological syndrome not previously described with other VSV mutants. Mice infected with wild-type VSV died from an acute encephalitis characterized by neuronal necrosis and efficient virus replication in both brain and spinal cord. In contrast, with VSV ts pi364, the most prominent histopathological feature was destruction of the ependyma of the lateral ventricles. Virus antigen was also limited to the leptomeninges and the lateral ventricles. Infected mice survived and developed hydrocephalus. Replication of ts pi364 in the brain was 10- to 100- fold less than that of wild-type VSV, and appearance of virus in the spinal cord was delayed. VSV ts pi364 was isolated from mouse cells persistently infected with VSV. Another VSV ts pi mutant, isolated from the same persistent infection, behaved in vivo like wild-type VSV, even though both mutants were very similar in plaque size, reversion frequency, cut-off temperature, and synthesis of virus-specific proteins at semipermissive temperature. These results strongly suggest that VSV ts pi364 has a second, non-ts mutation which results in a restricted target cell range in vivo; wild-type VSV can infect both neurons and ependymal cells, whereas ts pi364 does not replicate in neurons.
Simplification of the Mitsunobu Reaction. Di-<i>p</i>-chlorobenzyl Azodicarboxylate:  A New Azodicarboxylate (2006)

Di-p-chlorobenzyl azodicarboxylate (DCAD) is introduced as a novel, stable, solid alternative to DEAD and DIAD for a variety of Mitsunobu couplings. DCAD/Ph(3)P-mediated reactions in CH(2)Cl(2) generate a readily separable hydrazine byproduct. [reaction: see text]
A perspective on thermal energy storage systems for solar energy applications (1996)

The use of thermal energy storage (TES) systems is essential for solar power systems because of fluctuations in the solar energy input. Several classes of storage may be required for a single installation, depending on the type and scale of the solar power plant itself, and the nature of its integration with conventional utility systems. For heating and hot water applications, water and phase change materials (PCMs) constitute the principle storage media. Soil, rock and other solids are used as well. Water has the advantage of approximately 80% less volume than that of water for a temperature variation of 10°C, which is the difference between temperatures of a fully charged and a fully discharged storage tank. Some PCMs are viscous and corrosive, and must be segregated within the container in order to be used as a heat transfer medium. For heat storage, two PCMs must be available, unless heat pumping is employed. A variety of solids is also used; rock particles of 20 to 50 mm in size are most prevalent. Well-designed packed rock beds have several desirable characteristics for energy storage. The heat transfer coefficient between the air and the solid is high, the cost of the storage material is low, the conductivity of the bed is low when air flow is not present and a large heat transfer area can be achieved at low cost by reducing the size of particles. TES systems have also been suggested for storing thermal energy at medium (38–304°C) and high temperatures (120–566°C). For instance, systems in an oil-rock system for hot water and heat-recovery applications are examples of medium-temperature applications, while those in molten nitrate salt systems (an excellent storage medium) for steam production for process applications are for high temperatures. Oil-rock TES, in which the energy is stored in a mixture of oil and rock in a tank, is less expensive than molten nitrate salt TES, but is limited to low-temperature applications. However, this oil-rock TES has been proven successful for solar thermal applications. The selection of the type of TES depends on various factors such as the storage period (diurnal or seasonal), economic viability, operating conditions, etc. In this article, a study of TES systems (including materials) is presented particularly with solar thermal applications in mind. The evaluation of their performances, cost and economic viability, ease of installation, cleanliness, environmental impact, safety factors, technological usability and applicability are discussed.
In vitro detection of circulating tumor cells compared by the CytoTrack and CellSearch methods (2015)

Comparison of two methods to detect circulating tumor cells (CTC) CytoTrack and CellSearch through recovery of MCF-7 breast cancer cells, spiked into blood collected from healthy donors. Spiking of a fixed number of EpCAM and pan-cytokeratin positive MCF-7 cells into 7.5 mL donor blood was performed by FACSAria flow sorting. The samples were shipped to either CytoTrack or CellSearch research facilities within 48 h, where evaluation of MCF-7 recovery was performed. CytoTrack and CellSearch analyses were performed simultaneously. Recoveries of MCF-7 single cells, cells in clusters, and clusters were determined. The average numbers of MCF-7 cells/cells in clusters/clusters recovered from blood by the CytoTrack and CellSearch methods were 103 ± 5.9/27 ± 7.9/11 ± 3.5 (95 % CI) and 107 ± 4.4/20 ± 7.1/10 ± 3.5, respectively, with no difference between the two methods (p = 0.37/p = 0.23/p = 0.09). Overall, the recovery of CytoTrack and CellSearch was 68.8 ± 3.9 %/71.1 ± 2.9 %, respectively (p = 0.58). In spite of different methodologies, CytoTrack and CellSearch found similar number of CTCs, when spiking was performed with the EpCAM and pan cytokeratin-positive cell line MCF-7. The results suggest that CytoTrack and CellSearch have similar abilities to identify CTC in vitro.
Mixup: A Development and Runtime Environment for Integration at the Presentation Layer (2007)

Abstract. In this paper we present a development and runtime environment for creating composite applications by reusing existing presentation components. The granularity of components is that of stand-alone modules encapsulating reusable functionalities. The goal is to allow developers to easily create composite applications by combining the components &apos; individual user interfaces. 1