gebhart/patrepeval huggingface dataset:
SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus) (2012)

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.
Fast Sol–Gel Preparation of Silicon Carbide–Silicon Oxycarbide Nanocomposites (2011)

Silicon carbide nanofiber dispersion within a silicon oxycarbide glassy ceramic was achieved through a combination of a fast sol–gel procedure for in situ ceramic matrix synthesis and nanofiber conversion from sacrificial multiwalled carbon nanotube templates. Nanotubes were dispersed using both surfactant adsorption and a covalent sidewall modification scheme with gel‐grafting capabilities. The combination of high temperature processing and silicon monoxide precursor concentrations allowed substantial carbothermal reduction of the nanotube templates, yielding silicon carbide nanofibers. The resulting nanocomposites were examined for density, Vickers microhardness, Young's modulus, and fracture toughness. The surfactant‐assisted route inhibited ceramic densification, offering virtually no mechanical property enhancement. In contrast, the covalently functionalized nanotube templates at 0.8 wt% loading enhanced tensile modulus of 77% while simultaneously maintaining both Vickers microhardness and fracture toughness. These results indicate strong interfacial adhesion between the nanofiber surface and host matrix despite the abrupt chemical changes experienced during the high temperature processing.
Value of Information in Feedback Control: Global Optimality (2022)

The rate-regulation tradeoff, defined between two objective functions, one penalizing the packet rate and one the regulation cost, can express the fundamental performance bound of networked control systems. However, the characterization of the set of globally optimal solutions in this tradeoff for multidimensional Gauss–Markov processes has been an open problem. In this article, we characterize a policy profile that belongs to this set without imposing any restrictions on the information structure or the policy structure. We prove that such a policy profile consists of a symmetric threshold triggering policy based on the value of information and a certainty-equivalent control policy based on a non-Gaussian linear estimator. These policies are deterministic and can be designed separately. Besides, we provide a global optimality analysis for the value of information <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mathbf{{VoI}}_{{\boldsymbol{k}}}$</tex-math></inline-formula> , a semantic metric that emerges from the rate-regulation tradeoff as the difference between the benefit and the cost of a data packet. We prove that it is globally optimal that a data packet containing sensory information at time <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">${\boldsymbol{k}}$</tex-math></inline-formula> be transmitted to the controller only if <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mathbf{{VoI}}_{{\boldsymbol{k}}}$</tex-math></inline-formula> becomes nonnegative. These findings have important implications in the areas of communication and control.
Electrochemical Deposition of Molybdenum Nanowires for Use as Sensors (2001)

Abstract Electrodeposition of molybdenum dioxide (using the step edges of highly oriented pyrolytic graphite as nucleation templates) is used to form precursor nanowires ranging in diameter from 10 nm to one micron with many exceeding one-half millimeter in length. Subsequent treatment with hydrogen gas above 500°C reduces the wires to conductive metallic molybdenum. (Science, December 15, 2000, 290 (5499) 2120, selected as cover story). Currently, this is the only method which exists to create millions of ordered nanowire arrays with such high aspect ratios. A film of either polystyrene or cyanoacrylate polymer is used to lift the wires off of the conductive graphite substrate making electronically isolated wires. Electronically isolated wires such as these hold promise to be sensors, electronic interconnects or as precursors for growing more complex electrodeposited circuitry. The discovery of a method to deposit nanowires is just the beginning. By using a piece of a double-sided copper-clad circuit board as a support, the polymer containing nanowires can be made into a robust sensor device.
Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles (2009)

HIV-1 can evolve HLA-specific escape variants in response to HLA-mediated cellular immunity. HLA alleles that are common in the host population may increase the frequency of such escape variants at the population level. When loss of viral fitness is caused by immune escape variation, these variants may revert upon infection of a new host who does not have the corresponding HLA allele. Furthermore, additional escape variants may appear in response to the nonconcordant HLA alleles. Because individuals with rare HLA alleles are less likely to be infected by a partner with concordant HLA alleles, viral populations infecting hosts with rare HLA alleles may undergo a greater amount of evolution than those infecting hosts with common alleles due to the loss of preexisting escape variants followed by new immune escape. This hypothesis was evaluated using maximum likelihood phylogenetic trees of each gene from 272 full-length HIV-1 sequences. Recent viral evolution, as measured by the external branch length, was found to be inversely associated with HLA frequency in nef (p < 0.02), env (p < 0.03), and pol (p < or = 0.05), suggesting that rare HLA alleles provide a disproportionate force driving viral evolution compared to common alleles, likely due to the loss of preexisting escape variants during early stages postinfection.
What Really Rigs Up RIG-I? (2016)

RIG-I (retinoic acid-inducible gene 1) is an archetypal member of the cytoplasmic DEAD-box dsRNA helicase family (RIG-I-like receptors or RLRs), the members of which play essential roles in the innate immune response of the metazoan cell. RIG-I functions as a pattern recognition receptor that detects nonself RNA as a pathogen-associated molecular pattern (PAMP). However, the exact molecular nature of the viral RNAs that act as a RIG-I ligand has remained a mystery and a matter of debate. In this article, we offer a critical review of the actual viral RNAs that act as PAMPs to activate RIG-I, as seen from the perspective of a virologist, including a recent report that the viral Leader-read-through transcript is a novel and effective RIG-I ligand.
Co‐Evaporated Bulk Heterojunction Solar Cells with >6.0% Efficiency (2012)

High power conversion efficiencies of over 6.0% are achieved with a squaraine compound from co-deposited photovoltaic cells with a simple device structure, in which the efficiency is insensitive to blending ratios and thicknesses of photoactive layers. It demonstrates the huge potential of low molecular weight materials in photovoltaic cells via vacuum processes.
Potential Future Aviation Communication Technologies (2019)

Aviation growth is occurring in all sectors of the industry: numbers of commercial passenger, freight, experimental, and especially unmanned flights are rising steadily. This requires advances in aeronautics as well as in air traffic management (ATM). Multiple organizations worldwide are working on research and development for future ATM, including NASA and the FAA, EuroControl, major airlines, aviation support industries, and academia. Three key elements underlying efficient ATM are communications, navigation, and surveillance (CNS). In this paper we focus on communications for future ATM. As part of a University Leadership Initiative project sponsored by NASA, we are investigating current and future communications technologies that can be applied to enhance ATM, specifically air traffic safety and efficiency. These technologies pertain to air-ground (AG), air-air (AA), and terrestrial communications at aerodromes (airports, airstrips, etc.). One portion of our work addresses more “futuristic” approaches, and this is the subject of this paper. After a brief review of current and currently planned aviation communications technologies, we describe several potential future aviation communication technologies and tools. This includes techniques that are used at present, but largely in non-aviation settings, such as free-space optical communications, troposcatter communications, and near-vertical incidence skywave (NVIS) communications in the HF band. We also discuss some very new techniques still under investigation by the communications research community: orbital angular momentum transmission, orthogonal time-frequency-space (OTFS) modulation, and the application of machine learning to ATM in functions such as dynamic spectrum allocation and spatial trajectory planning. A short review of these techniques is provided, along with an estimate of their potentials and application areas for future air traffic management.
Fast feature-based preclassification of segments in continuous digit recognition (2005)

This paper describes the preclassification part of a real time speaker dependent continuous digit recognition system. The system's main characteristic is a fast feature-based word hypothesizer employing a combination of knowledge-based methods and pattern matching. This provides for a more reasonable behaviour, avoiding unintuitive errors typically found in conventional pattern matching systems. The processing can be broken up into four components: on-line segmentation according to four coarse phonetic classes, feature based matching focusing on voiced segments, word candidate generation and pruning and finally, candidate-adaptive pattern matching for decision making. The digit accuracy of the preclassifier, which includes the first 3 steps was found to be 96% in experiments using a total of 540 digit strings with an average length of 4 digits, collected from six speakers (4 male, 2 female).
A Tutorial on Impedance Spectroscopy (1998)

Abstract Electrochemical impedance spectroscopy is a powerful and general technique suitable for in-situ characterization of electrochemical systems. The fundamental concepts of impedance spectroscopy are presented in the context of a hierarchy of electrochemical methods. As, in theory, time-domain and frequency-domain transient techniques provide the same information concerning the system under study, the selection between the two must be based on the frequency range that can be sampled and on the associated error structure. In the context of error structure, the advantages of impedance spectroscopy are that the integration at a single frequency over many cycles greatly reduces stochastic errors and that the measurement of a complex impedance allows use of the Kramers-Kronig relations to identify experimental bias errors.
Validation of the Acenocoumarol EU-PACT Algorithms: Similar Performance in the Rotterdam Study Cohort as in the Original Study (2012)

The EU-PACT acenocoumarol algorithm performs just as accurately in this study as in the original study, which implies applicability in various populations.
Specific proteolytic cleavage of agrin regulates maturation of the neuromuscular junction (2010)

During the initial stage of neuromuscular junction (NMJ) formation, nerve-derived agrin cooperates with muscle-autonomous mechanisms in the organization and stabilization of a plaque-like postsynaptic specialization at the site of nerve-muscle contact. Subsequent NMJ maturation to the characteristic pretzel-like appearance requires extensive structural reorganization. We found that the progress of plaque-to-pretzel maturation is regulated by agrin. Excessive cleavage of agrin via transgenic overexpression of an agrin-cleaving protease, neurotrypsin, in motoneurons resulted in excessive reorganizational activity of the NMJs, leading to rapid dispersal of the synaptic specialization. By contrast, expression of cleavage-resistant agrin in motoneurons slowed down NMJ remodeling and delayed NMJ maturation. Neurotrypsin, which is the sole agrin-cleaving protease in the CNS, was excluded as the physiological agrin-cleaving protease at the NMJ, because NMJ maturation was normal in neurotrypsin-deficient mice. Together, our analyses characterize agrin cleavage at its proteolytic α- and β-sites by an as-yet-unspecified protease as a regulatory access for relieving the agrin-dependent constraint on endplate reorganization during NMJ maturation.
Chain-Scission and Bleaching in Heterophasic Ethylene-Propylene Copolymers (1996)

The variations in the viscosity and gloss (yellowness and whiteness index) in isotactic polypropylene, heterophasic E-P copolymers and polyethylene were measured during photo-oxidation. The samples underwent extensive reduction in intrinsic viscosity [[UNKNOWN]] upon U.V. irradiation. The kinetics of oxidative degradation have also been studied using polychromatic light at 60°C in air. These parameters appear to be a sensitive criteria to characterize the photo-oxidative transformation of polymers. The course of degradation is random and the yellowing process brought by the short wavelength U.V. light is accompanied by a photobleaching reaction which is caused by the light of longer wavelengths.
Evidence that the Type‐2 Gonadotrophin‐Releasing Hormone (GnRH) Receptor Mediates the Behavioural Effects of GnRH‐II on Feeding and Reproduction in Musk Shrews (2005)

Gonadotrophin-releasing hormone (GnRH) is a regulatory neuropeptide of which there are multiple structural variants. In mammals, a hypothalamic form (GnRH-I) controls gonadotrophin secretion whereas a midbrain form (GnRH-II) appears to have a neuromodulatory role affecting feeding and reproduction. In female musk shrews and mice, central administration of GnRH-II reinstates mating behaviour previously inhibited by food restriction. In addition, GnRH-II treatment also decreases short-term food intake in musk shrews. GnRH-II can bind two different mammalian GnRH receptors (type-1 and type-2), and thus it is unclear which receptor subtype mediates the behavioural effects of this peptide. Adult female musk shrews implanted with i.c.v. cannula were food restricted or fed ad lib and then tested for sexual behaviour or food intake. One hour before testing, animals were pretreated with vehicle or Antide, a potent type-1 GnRH receptor antagonist (at a dose that blocks GnRH-I or -II mediated ovulation). Twenty minutes before testing, females were infused a second time with either GnRH-II or vehicle. Additional females were tested after an infusion of 135-18, a type-1 receptor antagonist that displays agonist actions at the primate type-2 receptor. GnRH-II treatment increased sexual behaviour in underfed female shrews; pretreatment with Antide did not block this action, suggesting that the effects of GnRH-II are not mediated via the type-1 receptor. Similarly, the inhibitory effects of GnRH-II on short-term food intake were not prevented by pretreatment with Antide. The behavioural effects of the type-2 receptor agonist 135-18 were similar to those seen in GnRH-II-treated females, with 135-18 promoting sexual behaviour and decreasing food intake. Collectively, these results indicate that GnRH-II does not act via the type-1 GnRH receptor to regulate mammalian behaviour but likely activates the type-2 GnRH receptor.
Impedance Analysis Of Ultrathin Platinum Film Immunosensors With Different Thickness And Macro Geometry (2005)

SUMMARY An impedance based immunosensor has been prepared by using an ultrathin platinum film with an immobilized layer of anti-SEB. Effect of the film morphology on the impedance spectra as well as the sensing properties of the sensors has been discussed.
Histology of porous-coated acetabular components: 25 cementless cups retrieved after arthroplasty (1993)

25 hemispherical acetabular components retrieved from patients who had a total hip arthroplasty (THA) were studied histologically. All of the components had titanium fiber metal porous coatings and were implanted with adjuvant screw fixation, 18 in primary THA and 7 in revision THA. None of the cups had been removed because of infection or failure of fixation. The components had been in place an average of 30 (1-140) weeks. 18 cups had bone ingrowth into the porous coating. Up to one third of the available void space within the porous coating was occupied by bone, while the maximal proportion of the area of the bone-implant interface with bone ingrowth was over 80 percent. Bone ingrowth was more often observed at the dome and in the vicinity of sites of screw fixation than elsewhere. Peripherally, bone ingrowth was less consistent, and in isolated areas fibrocartilage and mineralized fibrocartilage were occasionally observed. The longer-term cases had more bone ingrowth than the shorter-term cases. Apparent metallic debris was observed within histiocytes adjacent to screw holes, and the amount of this material increased with duration of implantation.
Defining the transcriptome of accelerated and replicatively senescent keratinocytes reveals links to differentiation, interferon signaling, and Notch related pathways (2006)

Epidermal keratinocytes (KCs) undergo highly orchestrated morphological and molecular changes during transition from proliferative compartment into growth arrested early and late differentiation layers, prior to dying in outermost cornified layers of normal skin. Creation of stratum corneum is vital to barrier function protecting against infection. Transcriptional events in KCs regulating complex processes of differentiation and host defense required to maintain constant epidermal thickness and resistance to infection in either young or aged skin are largely unknown. Furthermore, as terminal differentiation is characterized by irreversible loss of replicative potential culminating in dead layers at the skin surface, this process may be viewed as a form of senescence. However, a complete transcriptional profile of senescent (SN) human KCs has not been previously defined to permit delineation of molecular boundaries involving differentiation and senescence. To fill this void, we utilized global transcriptional analysis of KCs maintained in vitro as either cultures of proliferating (PR) cells, early and late confluent (LC) (accelerated senescence) cultures, or KCs undergoing replicative senescence. Global gene expression profiling revealed early confluent (EC) KCs were somewhat similar to PR KCs, while prominent differences were evident when compared to LC KCs; which were also distinct from replicatively SN KCs. While confluent KCs have in common several genes regulating differentiation with replicatively SN KCs, the latter cells expressed elevated levels of genes involved in interferon signaling and inflammatory pathways. These results provide new insights into cell autonomous transcriptional-based programs operative within KCs contributing to replicative senescence, with partial sharing of genes involved in differentiation. In addition, regulation of KC senescence may involve participation of interferon signaling pathways derived from the important role of KCs in protecting skin from infection. Integrating all of the transcriptional data revealed a key role for Notch receptor mediated signaling in the confluency induced differentiation phenotype using this model system.
An Improved Left Ventricular Cannula for Chronic Dynamic Blood Pump Support (1995)

Ventricular unloading with dynamic blood pumps can be markedly affected by the geometry of the cannula tip within the ventricular chamber. Due to the ability of these pumps to develop significant negative inflow pressure, existing cannula tips designed for passively filling blood pumps can be predisposed to inflow occlusion by intraventricular anatomic structures. A novel "trumpet" mouth cannula was constructed to overcome this limiting problem. This design was based on two criteria: to provide additional stenting to the ventricular apex, and to assure placement of the tip opening relative to the endocardial surface. This prototype cannula was evaluated in vivo against conventional caged, blunt, and tapered designs to assess anatomic and hemodynamic interaction within the ventricular apex. Post mortem examination revealed the inflow tract to be devoid of myocardial obstruction in all cases. These initial studies indicate that a trumpet mouth cannula can provide satisfactory hemodynamic performance required by dynamic blood pumps.
Selective COX-2 inhibition prevents progressive dopamine neuron degeneration in a rat model of Parkinson's disease. (2004)

Several lines of evidence point to a significant role of neuroinflammation in Parkinson's disease (PD) and other neurodegenerative disorders. In the present study we examined the protective effect of celecoxib, a selective inhibitor of the inducible form of cyclooxygenase (COX-2), on dopamine (DA) cell loss in a rat model of PD. We used the intrastriatal administration of 6-hydroxydopamine (6-OHDA) that induces a retrograde neuronal damage and death, which progresses over weeks. Animals were randomized to receive celecoxib (20 mg/kg/day) or vehicle starting 1 hour before the intrastriatal administration of 6-OHDA. Evaluation was performed in vivo using micro PET and selective radiotracers for DA terminals and microglia. Post mortem analysis included stereological quantification of tyrosine hydroxylase, astrocytes and microglia. 12 days after the 6-OHDA lesion there were no differences in DA cell or fiber loss between groups, although the microglial cell density and activation was markedly reduced in animals receiving celecoxib (p < 0.01). COX-2 inhibition did not reduce the typical astroglial response in the striatum at any stage. Between 12 and 21 days, there was a significant progression of DA cell loss in the vehicle group (from 40 to 65%) that was prevented by celecoxib. Therefore, inhibition of COX-2 by celecoxib appears to be able, either directly or through inhibition of microglia activation to prevent or slow down DA cell degeneration.