gebhart/patrepeval huggingface dataset:
Evaluation of moisture ingress from the perimeter of photovoltaic modules (2013)

ABSTRACT Many thin film photovoltaic (PV) technologies can be sensitive to corrosion induced by the presence of water vapor in the packaging materials. Typically impermeable front and backsheets are used in conjunction with an edge‐seal around the perimeter to prevent water vapor ingress. These edge‐seal materials are often made of a polyisobutylene resin filled with desiccant, which dramatically increases the time for moisture to reach sensitive module components. While edge‐seals can prevent moisture ingress, even the lowest diffusivity transparent encapsulant materials are insufficient for the lifetime of a module. To evaluate the performance of edge‐seal and encapsulant materials in a manner that simulates their function in a PV module, an optical method was devised where ingress is detected by reaction of a Ca film with water. Using this method, we have exposed test samples to heat and humidity allowing quantitative comparison of different edge‐seal and encapsulant materials. Next, we use measurements of polymer diffusivity and solubility to evaluate the ability to model this moisture ingress. Here, we find good agreement between these two methods highlighting the much greater ability of polyisobutylene materials to keep moisture out as compared with typical encapsulant materials used in the PV industry. Copyright © 2013 John Wiley &amp; Sons, Ltd.
Complete genome sequence of Cryptobacterium curtum type strain (12-3T) (2009)

Cryptobacterium curtum Nakazawa etal. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodontitis, inflammations and abscesses. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Negative Self-Regulation of TLR9 Signaling by Its N-Terminal Proteolytic Cleavage Product (2014)

TLR signaling is essential to innate immunity against microbial invaders and must be tightly controlled. We have previously shown that TLR9 undergoes proteolytic cleavage processing by lysosomal proteases to generate two distinct fragments. The C-terminal cleavage product plays a critical role in activating TLR9 signaling; however, the precise role of the N-terminal fragment, which remains in lysosomes, in the TLR9 response is still unclear. In this article, we report that the N-terminal cleavage product negatively regulates TLR9 signaling. Notably, the N-terminal fragment promotes the aspartic protease-mediated degradation of the C-terminal fragment in endolysosomes. Furthermore, the N-terminal TLR9 fragment physically interacts with the C-terminal product, thereby inhibiting the formation of homodimers of the C-terminal fragment; this suggests that the monomeric C-terminal product is more susceptible to attack by aspartic proteases. Together, these results suggest that the N-terminal TLR9 proteolytic cleavage product is a negative self-regulator that prevents excessive TLR9 signaling activity.
Selection of Microbial T-Cell Epitopes for Immune-Diagnosis, Immune- Therapy and Vaccine Design (2005)

The ability to induce and/or monitor an immune response to a broad repertoire of epitopes universally recognized across continents and genetic backgrounds is considered a critical characteristic of an effective vaccine and diagnostic tool. Opportunities for epitope identification are expanding as the number of entirely sequenced pathogens approaches 500 and access to this data improves. The pace of vaccine design will accelerate as bioinformatics are systematically applied to whole genomes and used in combination with in vitro methods for screening and confirming epitopes. Given access to bioinformatic tools, epitope-driven diagnostic tools and both preventive and therapeutic vaccines (for infectious diseases of worldwide impact such as tuberculosis and HIV) are now within our reach. This review describes the structural basis of the bioinformatic tools for epitope prediction methods as well as the recent use of these approaches at genomic level in the development of diagnostic tools and vaccine design as example of structural bioinformatic system applied to pharmacogenomics. Keywords: Human Leukocyte Antigen, therapeutical tools, transcriptional adaptation, Tuberculosis, Malaria, Intracellular Cytokine Staining
Kinetics of DNA-mediated docking reactions between vesicles tethered to supported lipid bilayers (2007)

Membrane-membrane recognition and binding are crucial in many biological processes. We report an approach to studying the dynamics of such reactions by using DNA-tethered vesicles as a general scaffold for displaying membrane components. This system was used to characterize the docking reaction between two populations of tethered vesicles that display complementary DNA. Deposition of vesicles onto a supported lipid bilayer was performed by using a microfluidic device to prevent mixing of the vesicles in bulk during sample preparation. Once tethered onto the surface, vesicles mixed via two-dimensional diffusion. DNA-mediated docking of two reacting vesicles results in their colocalization after collision and their subsequent tandem motion. Individual docking events and population kinetics were observed via epifluorescence microscopy. A lattice-diffusion simulation was implemented to extract from experimental data the probability, P(dock), that a collision leads to docking. For individual vesicles displaying small numbers of docking DNA, P(dock) shows a first-order relationship with copy number as well as a strong dependence on the DNA sequence. Both trends are explained by a model that includes both tethered vesicle diffusion on the supported bilayer and docking DNA diffusion over each vesicle's surface. These results provide the basis for the application of tethered vesicles to study other membrane reactions including protein-mediated docking and fusion.
Distributed Algorithms for Spectrum Access in Cognitive Radio Relay Networks (2012)

We develop distributed algorithms for efficient spectrum access strategies in cognitive radio relay networks. In our setup, primary users permit secondary users access to the resource (spectrum) as long as they consent to aiding the primary users as relays in addition to transmitting their own data. Given a pool of primary and secondary users, we desire to optimize overall network utility by determining the best configuration/pairing of secondary users with primary users. This optimization can be stated in a form similar to the maximum weighted matching problem. Given such formulation, we develop an algorithm based on affinity propagation technique that is completely distributed in its structure. We demonstrate the convergence of the developed algorithm and show that it performs close to the optimal centralized scheme.
The Effect of Air Bubbles and Headspace on the Aqueous Concentrations of Volatile Organic Compounds in Sampling Vials (2001)

Abstract The presence of headspace and air bubbles in volatile organic analysis sampling vials lowers the actual aqueous concentration of these compounds due to the partitioning of solutes into the gaseous phase. This could make the sample invalid for analysis. In this work, the effects of air bubbles and headspace on the aqueous concentration of 60 volatile organic compounds listed in U.S.Environmental Protection Agency (U.S. EPA) Method 8260 were evaluated experimentally and theoretically. The results showed that for air to water ratios of 1 to 20 and less, there was no significant effect on the aqueous concentrations of target organic solutes in the sampling vials. When the air to water ratio was increased to 1 to 10, the recovery rates of four organic compounds were lower than the control. Laboratory experiments on sampling vials showed that the presence of air bubbles or headspace with the volumetric air to water ratios of 1 to 20 and less do not produce any significant effect on the original concentrations for most targeted volatile organic compounds. The experimental results also indicated that in 40 mL sampling vials with headspace range of 2 to 8 mL, the recovery rates of most volatile organic compounds with high values of Henry's law constant (&gt; 0.01 Atm m 3 /mol. at 25°C) were larger than the calculated rates.
SiGe bipolar 5.5 GHz dual-modulus prescaler (1999)

A SiGe bipolar dual-modulus ÷64/65, ÷32/33 prescaler implemented in commercially available Infineon SiGe bipolar technology is presented. A maximum operational frequency of 5.5 GHz has been measured for a supply current of 6 mA at 3.3 V. For a reduced supply current of 3.5 mA, a maximum frequency of 4.0 GHz has been obtained. A comparison with a purely-Si prescaler clearly demonstrates the enhanced speed-power product of the SiGe technology.
Effect of viscous damping devices on the response of seismically isolated structures (2014)

Summary Viscous and other damping devices are often used as elements of seismic isolation systems. Despite the widespread application of nonlinear viscous systems particularly in Japan (with fewer applications in the USA and Taiwan), the application of viscous damping devices in isolation systems in the USA progressed intentionally toward the use of supplementary linear viscous devices due to the advantages offered by these devices. This paper presents experimental results on the behavior of seismically isolated structures with low damping elastomeric (LDE) and single friction pendulum (SFP) bearings with and without linear and nonlinear viscous dampers. The isolation systems are tested within a six‐story structure configured as moment frame and then again as braced frame. Emphasis is placed both on the acquisition of data related to the structural system (drifts, story shear forces, and isolator displacements) and on non‐structural systems (floor accelerations, floor spectral accelerations, and floor velocities). Moreover, the accuracy of analytical prediction of response is investigated based on the results of a total of 227 experiments, using 14 historic ground motions of far‐fault and near‐fault characteristics, on flexible moment frame and stiff braced frame structures isolated with LDE or SFP bearings and linear or nonlinear viscous dampers. It is concluded that when damping is needed to reduce displacement demands in the isolation system, linear viscous damping results in the least detrimental effect on the isolated structure. Moreover, the study concludes that the analytical prediction of peak floor accelerations and floor response spectra may contain errors that need to be considered when designing secondary systems. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Maximum Entropy Models of Surace Reflectance Spectra (2006)

We investigate the use of a maximum entropy spectral model for surface spectra from photoreceptor measurements. We compare the accuracy of maximum entropy models againts those provided by the stand linear PCA-based models. We show that the maximum entropy models have similar performance to the linear models, even though they require no a priori information.
LINKAGE OF MUTATIONS AFFECTING MINUS FLAGELLAR MEMBRANE AGGLUTINABILITY TO THE <i>mt</i> - MATING-TYPE LOCUS OF CHLAMYDOMONAS (1981)

Two independently isolated mutant strains, imp-10 and imp-12, were obtained by UV irradiation of wild-type mating-type minus (wt(-)). Each fails to agglutinate sexually with gametes of either mating type, but mating and zygote formation can be elicited by agglutinating either strain to wt(+) gametes by means of anti-flagellar antiserum. Tetrad analysis of the resultant zygotes shows that both imp-10 and imp-12 are very closely linked to mt(-), with no recombinants observed. Diploid strains constructed between imp-10 or imp-12 and wt(+) gametes are wt(-), that is, they agglutinate and fuse like normal minus cells. Tetrad analysis of triploids from imp-10 diploid x wt(+) haploid crosses shows that only imp-10 and wt(+) products are recovered. A model is proposed to account for these results.
Fundamental Issues in Manual Control Cybernetics (2016)

Manual control cybernetics aims to understand and describe how humans control vehicles and devices, such that more effective human-machine interfaces can be designed. Current cybernetics theory is primarily based on technology and analysis methods developed in the 1960s and has shown to be limited in its capability to capture the full breadth of human cognition and control. This paper summarizes some of the main fundamental limitations in cybernetics and provides a possible road-map to advance the theory and its applications. Central in this agenda will be a shift from the current linear time-invariant modeling approach, to the use of linear parameter-varying system models. Recent progress in identification methods of these latter models may allow us, for the first time, to mathematically model and identify time-varying, adaptive human control, opening up many opportunities to systematically optimize our human control interfaces and training. New foundations for cybernetics will impact all domains that involve humans in manual and semi-automatic control.
Quantitative Assessment of Postsurgical Breakdown of the Blood-Aqueous Barrier (1983)

Breakdown and reestablishment of the blood-aqueous barrier (BAB) following experimental surgical trauma was evaluated by anterior segment slitlamp fluorophotometry. Substantially more fluorescein leakage was caused by 6-mm limbal incisions for at least the first four postoperative days than was produced by 3-mm incisions. Following 3-mm corneal incisions, leakage of fluorescein closely paralleled that of fluorescein-labeled dextran 70 (molecular weight, 70,000) for the first three postoperative days. On the fourth postoperative day, the BAB appeared reestablished to fluorescein-labeled dextran 70 but was still abnormally permeable to fluorescein. Thus, it appears that although fluorescein is the most sensitive technique of demonstrating breakdown of BAB, it may not always be an indicator of large-molecule permeability.
A closer look at high‐resolution electron holography (2016)

In the recent years high‐resolution off‐axis electron holography made huge advancements. Electron microscopes with increased numbers of electron optical biprisms and electron lenses allow more flexible ray paths. Due to the combination of double biprism holography and higher magnification at the lower biprism, holograms in the high resolution regime are now recorded with negligible artifacts [1]. Furthermore, smart averaging schemes for hologram series allow to prolong the effective exposure time for a hologram to time scales, where the experimental errors are not dominated by the shot noise anymore [2]. One of the advantages of holography is the posterior correction of residual aberrations. However, the aberrations still have to be sufficiently known. By quantitative comparison of reconstructed wave functions with calculations the imaging parameters can be retrieved with sufficient precision allowing the reconstruction of aberration corrected exit‐wave functions. Thus nowadays holograms with (sub‐)angstrom resolution can be obtained on a regular basis. In off‐axis holography only the side‐band channel of the information recorded in the hologram is reconstructed. As hologram series are recorded and the reconstructed wave function can be propagated to arbitrary defocus values anyway, also focal series of conventional images (center‐band) can be obtained in the same measurement. In the figures the reconstructed exit waves of a GaAs wedge, obtained by inline and off‐axis holography are shown [3, 4]. While differences in the low‐frequency reconstruction are expected, also significant differences in thicker specimen parts are found. The latter can be easily recognized on the left side of the linescan profiles, where the amplitudes signals at the columns positions exhibit different behaviours. There are several possible reasons for this discrepancy. The numerical inversion of the imaging process within the inline method becomes worse conditioned since the thicker parts exhibit stronger non‐linear imaging. Thus the reconstruction algorithm might converge in a wrong minimum of the overall error figure. Also, any changes of the object during the acquisition of the series will exhibit different behaviour in the measurement. Furthermore, both channels (side‐band and center‐band) refer to different parts of the density matrix due to the different quantum‐mechanical nature of the underlying interference experiment.
pH‐stat fed‐batch process to enhance the production of <i>cis</i>, <i>cis</i>‐muconate from benzoate by <i>Pseudomonas putida</i> KT2440‐JD1 (2011)

Pseudomonas putida KT2440-JD1 is able to cometabolize benzoate to cis, cis-muconate in the presence of glucose as growth substrate. P. putida KT2440-JD1 was unable to grow in the presence of concentrations above 50 mM benzoate or 600 mM cis, cis-muconate. The inhibitory effects of both compounds were cumulative. The maximum specific uptake rate of benzoate was higher than the specific production rate of cis, cis-muconate during growth on glucose in the presence of benzoate, indicating that a benzoate derivative accumulated in the cells, which is likely to be catechol. Catechol was shown to reduce the expression level of the ben operon, which encodes the conversion of benzoate to cis, cis-muconate. To prevent overdoses of benzoate, a pH-stat fed-batch process for the production of cis, cis-muconate from benzoate was developed, in which the addition of benzoate was coupled to the acidification of the medium. The maximum specific production rate during the pH-stat fed-batch process was 0.6 g (4.3 mmol) g dry cell weight(-1) h(-1), whereas 18.5 g L(-1) cis, cis-muconate accumulated in the culture medium with a molar product yield of close to 100%. Proteome analysis revealed that the outer membrane protein H1 was upregulated during the pH-stat fed-batch process, whereas the expression of 10 other proteins was reduced. The identified proteins are involved in energy household, transport, translation of RNA, and motility.
Towards a translational health information language (2014)

Recent calls in the EU and US for the creation of a "universal exchange language" for health information representation This paper calls for the development of a 'translational health information language' (THIL), which could serve the translational information continuum. Its backbone spans from the biological research results and new types of raw data coming from sources like omics assays, sensors data and imaging techniques, and then clinical trials data and on to clinical data. Alongside this backbone of information there are also contributions of economic, social and psychological considerations that quite often prevent a new and successful intervention at the bedside from scaling out to the community and policy. The main assumption of this paper is that given the current diversity of such a continuum, it is not reasonable to expect a simplified exchange language that covers all portions of that continuum. Instead, THIL strives to mix & match existing and emerging languages through fundamental touchpoints in order to enable the integration of patients' data through a conceptual workflow of continuous data encapsulation & bubbling up loop These processes lead to gradual distillation of the raw data that makes the data usable and useful at the point of care, or for early detection, prevention and well-being.
Therapeutic Potential of Vaccines for Alzheimer‘s Disease (2011)

The pathological hallmarks of Alzheimer's disease (AD) are amyloid-β (Aβ) plaques and Tau-containing neurofibrillary tangles. Although the relationship between neuronal loss and the presence of plaques/tangles is not well understood, the prevailing Aβ hypothesis posits that excessive accumulation of conformers and assemblies of Aβ protein precedes AD-related dementia and neuronal loss. Consequently, most disease-modifying immunotherapy approaches are directed towards modulating the levels of Aβ. The first AD vaccine clinical trial (AN1792) was suspended after the patients developed meningoencephalitis. In spite of the setback, the trial provided insights to refine development second-generation vaccines, which are attempting to resolve the side effects observed in the trial. This article provides an analysis of these efforts.
Wild-Type Kras Inhibits NrasQ61R/+-Induced Leukemias (2015)

Ras proteins belong to the super family of small GTPases. Although RAS mutations are oncogenic, it remains highly controversial whether wild-type (WT) RAS facilitates or inhibits tumorigenesis in the presence of oncogenic RAS. Previous studies suggest that this might depend on cell type, specific RAS isoforms, and/or stage of tumorigenesis (e.g. tumor initiation versus tumor progression). Recently, we found that deletion of WT Kras in oncogenic Kras mice promotes myeloidproliferative neoplasm (MPN) in a cell-autonomous manner. This is through promoting activation of all Ras isoforms and thus enhancing cytokine signaling in vivo. However, it remains unknown whether WT Kras plays a similar role in oncogenic Nras-induced leukemogenesis. To address this issue, we conditionally down-regulated WT Kras expression in a novel leukemia model induced by endogenous NrasQ61R/+. Detailed characterization of NrasQ61R allele reveals that NrasQ61R/+ displays an intermediate leukemogenic activity between NrasG12D/+ and NrasG12D/G12D. NrasQ61R/+ mice developed MPN (100%) and acute T-cell lymphoblastic leukemia/lymphoma (T-ALL) (~10%) at the moribund stage with a median survival of 197 days. Therefore, NrasQ61R/+ mice provide an excellent experimental system to test genetic lesions promoting or inhibiting oncogenic Nras-induced leukemogenesis. We observed that 3-weeks after activation of NrasQ61R/+ and deletion of WT Kras, the double mutant mice displayed more severe MPN phenotypes than NrasQ61R/+ mice, as demonstrated by more prominent hepatosplenomegaly and further expanded myeloid compartment in bone marrow and spleen. Consistent with these MPN phenotypes, NrasQ61R/+; Kras-/- myeloid progenitor and precursor cells showed prolonged and hyperactivated GM-CSF signaling compared to NrasQ61R/+ cells. In addition, NrasQ61R/+; Kras-/- mice displayed further expanded common lymphoid progenitor compartment and a less differentiated phenotype in thymic T-cells than NrasQ61R/+ mice. In NrasQ61R/+; Kras-/- mice, early thymic T cell progenitors demonstrated enhanced cell proliferation and stronger ERK1/2 signaling compared to NrasQ61R/+ cells. Consequently, NrasQ61R/+; Kras-/- mice survived significantly shorter than NrasQ61R/+ mice (median survival: 97 days; P &lt; 0.001) and 100% of them developed both MPN and T-ALL at the moribund stage. Preliminary results from bone marrow transplantation assay indicate that loss of WT Kras expression promoted NrasQ61R/+-induced MPN and T-ALL in a cell-autonomous manner. Taken together, our results suggest that loss of WT Kras promotes leukemogenesis in NrasQ61R/+ mice. We are currently studying on the underlying mechanisms. Disclosures No relevant conflicts of interest to declare.