Miracle-dz/UniFAR-FTUs huggingface dataset:
Lycopene Stability During Food Processing

Abstract Accumulating epidemiological evidence continues to show that lycopene, found in tomatoes, grapefruits and watermelons, is associated with a reduced risk of developing certain chronic diseases and cancers. With respect to lycopene in tomato products, the effect of thermal processing on its stability has not yet been rigorously addressed. This paper assesses the effect of several different heat treatments on lycopene's isomeric distribution in a variety of tomato products, as well as in organic solvent mixtures containing all-trans lycopene. Experimental results indicate that in contrast to β-carotene, lycopene remained relatively resistant to heat-induced geometrical conversion during typical food processing of tomatoes and related products. The presence of fat, the change in percentage of solids, and the severity of heat treatment were not contributing factors in the formation of lycopene isomers in tomato products, except at extreme conditions not regularly employed in the food industry or during food preparation. However, lycopene in organic solvent isomerized readily as a function of time even in the absence of light and the presence of antioxidants. These findings suggest that while lycopene is stable in the tomato matrix, sample handling techniques should be carefully evaluated to minimize the formation of lycopene cis isomers in organic solutions.
The Extinction Dynamics of Bacterial Pseudogenes

Pseudogenes are usually considered to be completely neutral sequences whose evolution is shaped by random mutations and chance events. It is possible, however, for disrupted genes to generate products that are deleterious due either to the energetic costs of their transcription and translation or to the formation of toxic proteins. We found that after their initial formation, the youngest pseudogenes in Salmonella genomes have a very high likelihood of being removed by deletional processes and are eliminated too rapidly to be governed by a strictly neutral model of stochastic loss. Those few highly degraded pseudogenes that have persisted in Salmonella genomes correspond to genes with low expression levels and low connectivity in gene networks, such that their inactivation and any initial deleterious effects associated with their inactivation are buffered. Although pseudogenes have long been considered the paradigm of neutral evolution, the distribution of pseudogenes among Salmonella strains indicates that removal of many of these apparently functionless regions is attributable to positive selection.
The Avian Song System in Comparative Perspective

Abstract: The song system of oscine birds has become a versatile model system that is used to study diverse problems in neurobiology. Because the song system is often studied with the intention of applying the results to mammalian systems, it is important to place song system brain nuclei in a broader context and to understand the relationships between these avian structures and regions of the mammalian brain. This task has been impeded by the distinctiveness of the song system and the vast apparent differences between the forebrains of birds and mammals. Fortunately, accumulating data on the development, histochemistry, and anatomical organization of avian and mammalian brains has begun to shed light on this issue. We now know that the forebrains of birds and mammals are more alike than they first appeared, even though many questions remain unanswered. Furthermore, the song system is not as singular as it seemed—it has much in common with other neural systems in birds and mammals. These data provide a firmer foundation for extrapolating knowledge of the song system to mammalian systems and suggest how the song system might have evolved.
On permutation operations in cipher design

New and emerging applications can change the mix of operations commonly used within computer architectures. It is sometimes surprising when instruction-set architecture (ISA) innovations intended for one purpose are used for other (initially unintended) purposes. We consider recent proposals for the processor support of families of bit-level permutations. From a processor architecture point of view, the ability to support very fast bit-level permutations may be viewed as a further validation of the basic word-orientation of processors, and their ability to support next-generation secure multimedia processing. However, bitwise permutations are also fundamental operations in many cryptographic primitives and we discuss the suitability of these new operations for cryptographic purposes.
Zebrafish forebrain and temporal conditioning

The rise of zebrafish as a neuroscience research model organism, in conjunction with recent progress in single-cell resolution whole-brain imaging of larval zebrafish, opens a new window of opportunity for research on interval timing. In this article, we review zebrafish neuroanatomy and neuromodulatory systems, with particular focus on identifying homologies between the zebrafish forebrain and the mammalian forebrain. The neuroanatomical and neurochemical basis of interval timing is summarized with emphasis on the potential of using zebrafish to reveal the neural circuits for interval timing. The behavioural repertoire of larval zebrafish is reviewed and we demonstrate that larval zebrafish are capable of expecting a stimulus at a precise time point with minimal training. In conclusion, we propose that interval timing research using zebrafish and whole-brain calcium imaging at single-cell resolution will contribute to our understanding of how timing and time perception originate in the vertebrate brain from the level of single cells to circuits.
Biophysical properties of presynaptic short-term plasticity in hippocampal neurons: insights from electrophysiology, imaging and mechanistic models

Hippocampal neurons show different types of short-term plasticity (STP). Some exhibit facilitation of their synaptic responses and others depression. In this review we discuss presynaptic biophysical properties behind heterogeneity in STP in hippocampal neurons such as alterations in vesicle priming and docking, fusion, neurotransmitter filling and vesicle replenishment. We look into what types of information electrophysiology, imaging and mechanistic models have given about the time scales and relative impact of the different properties on STP with an emphasis on the use of mechanistic models as complementary tools to experimental procedures. Taken together this tells us that it is possible for a multitude of different mechanisms to underlie the same STP pattern, even though some are more important in specific cases, and that mechanistic models can be used to integrate the biophysical properties to see which mechanisms are more important in specific cases of STP.
SPARE‐ICE: Synergistic ice water path from passive operational sensors

This article presents SPARE‐ICE, the Synergistic Passive Atmospheric Retrieval Experiment‐ICE. SPARE‐ICE is the first Ice Water Path (IWP) product combining infrared and microwave radiances. By using only passive operational sensors, the SPARE‐ICE retrieval can be used to process data from at least the NOAA 15 to 19 and MetOp satellites, obtaining time series from 1998 onward. The retrieval is developed using collocations between passive operational sensors (solar, terrestrial infrared, microwave), the CloudSat radar, and the CALIPSO lidar. The collocations form a retrieval database matching measurements from passive sensors against the existing active combined radar‐lidar product 2C‐ICE. With this retrieval database, we train a pair of artificial neural networks to detect clouds and retrieve IWP. When considering solar, terrestrial infrared, and microwave‐based measurements, we show that any combination of two techniques performs better than either single‐technique retrieval. We choose not to include solar reflectances in SPARE‐ICE, because the improvement is small, and so that SPARE‐ICE can be retrieved both daytime and nighttime. The median fractional error between SPARE‐ICE and 2C‐ICE is around a factor 2, a figure similar to the random error between 2C‐ICE ice water content (IWC) and in situ measurements. A comparison of SPARE‐ICE with Moderate Resolution Imaging Spectroradiometer (MODIS), Pathfinder Atmospheric Extended (PATMOS‐X), and Microwave Surface and Precipitation Products System (MSPPS) indicates that SPARE‐ICE appears to perform well even in difficult conditions. SPARE‐ICE is available for public use.
Iridescence: a functional perspective

In animals, iridescence is generated by the interaction of light with biological tissues that are nanostructured to produce thin films or diffraction gratings. Uniquely among animal visual signals, the study of iridescent coloration contributes to biological and physical sciences by enhancing our understanding of the evolution of communication strategies, and by providing insights into physical optics and inspiring biomimetic technologies useful to humans. Iridescent colours are found in a broad diversity of animal taxa ranging from diminutive marine copepods to terrestrial insects and birds. Iridescent coloration has received a surge of research interest of late, and studies have focused on both characterizing the nanostructures responsible for producing iridescence and identifying the behavioural functions of iridescent colours. In this paper, we begin with a brief description of colour production mechanisms in animals and provide a general overview of the taxonomic distribution of iridescent colours. We then highlight unique properties of iridescent signals and review the proposed functions of iridescent coloration, focusing, in particular, on the ways in which iridescent colours allow animals to communicate with conspecifics and avoid predators. We conclude with a brief overview of non-communicative functions of iridescence in animals. Despite the vast amount of recent work on animal iridescence, our review reveals that many proposed functions of iridescent coloration remain virtually unexplored, and this area is clearly ripe for future research.
Biogeochemical interfaces in natural and artificial soil systems: specific surface area, phenanthrene sorptive properties and formation of organo-mineral associations

The effect of different components on the properties of biogeochemical interfaces in soil was examined in natural arable soils and artificial soils composed of different mixtures of clean model materials, manure as organic carbon source and a microbial inoculum. In the natural soils, iron oxides were found to be important providers of interfaces, and phenanthrene sorption showed that both the surface area available in soil and the organic matter content determined the sorption interface for hydrophobic organic chemicals. The incubated artificial soils developed quickly from mixtures of clean model materials into soil-like systems where minerals, organic matter and microorganisms were closely associated. Overall, the results presented in this dissertation demonstrate that biogeochemical interfaces in soil are not only determined by the different components present, but foremost by the interaction between these components.
Views and attitudes of oral contraceptive users towards their availability without a prescription in the Republic of Ireland

Background: Previous studies show that provision of oral contraceptive pill (OCs) without a prescription is safe, feasible and effective and that users are interested in obtaining contraception in this way, especially if a pharmacist screening is involved. A recent national survey conducted in the Republic of Ireland has highlighted that unintended pregnancy resulting from the failure of OCs could be linked to poor compliance due to costs and difficulty of access. Objective: To evaluate views and attitudes of OC users towards the availability of OCs without a prescription in the Republic of Ireland. Methods: A cross sectional survey was conducted using an opportunistic sample of OC users aged 18 to 50 years. Sixty community pharmacists were recruited nationwide. Data were collected using self-completed questionnaires. The questionnaires comprised information on: demographic data, need of the service, views on the availability of OCs without prescription, advantages and concerns around the service, role of pharmacists and cost implications for private and public patients. Results: A total of 488 eligible OC users completed the survey. The majority of the respondents (71.7%;n = 350/488) reported to have missed a pill for reasons connected to the OCs prescription status and 55.5% (n = 268/488) of the respondents reported to have felt distressed on at least one occasion because they could not renew their OC prescription. A total of 87.9% (n = 429/488) of the respondents said they were in favour of OCs being available without prescription and 92% (n = 448/488) said they were likely to obtain OCs without prescription if available. Convenience and ease of access were indicated as the main advantages of availing of OCs without prescription, while safety was the biggest concern reported. Over 88% (n = 430/488) of the respondents indicated that pharmacists would be able to safely supply OCs without prescription. Private patients expected to save an average of 27.3% on their OC if obtained without prescription. Conclusions: OC users in the Republic of Ireland are in favour of OCs being available without prescription and are willing to obtain it this way, providing that pharmacists supply them according to protocols that facilitate the safety and the efficacy of the supply. An easier and more convenient access to OCs could also reduce the likelihood of missed pills and bring considerable savings to users.
The multi-adaptor proto-oncoprotein Cbl is a key regulator of Rac and actin assembly

The induction of protein tyrosine kinase signaling pathways is a principal mechanism for promoting cellular activation. Biochemical and genetic analyses have implicated the multi-adaptor proto-oncogene protein Cbl as a key negative regulator of activated protein tyrosine kinases. By inhibiting the function of Cbl as a multi-domain adaptor protein, through expression of a truncated form (480-Cbl), we demonstrate that Cbl is a potent negative regulator of actin assembly in response to receptor tyrosine kinase (RTK) activation. Expression of 480-Cbl dramatically enhances RTK-dependent induction of actin dorsal ruffles, which correlates with a pronounced increase in Rac activation. By contrast, mitogenic signaling by RTK targets, such as PI 3-kinase and MAP kinases, as well as RTK-mediated tyrosine phosphorylation do not appear to be affected by 480-Cbl expression. Further, we determined that Cbl undergoes a striking RTK-activation-dependent translocation to sites of active actin dorsal ruffle nucleation. Hence, the selective regulation of RTK signaling to the actin cytoskeleton appears to result from recruitment of signaling proteins on a Cbl template bound to the actin cytoskeleton.
UvA-DARE ( Digital Academic Repository ) X-ray bursts at extreme mass accretion rates from GX 17 + 2

We report on ten type I X-ray bursts originating from GX 17+2 in data obtained with the RXTE/PCA in 1996–2000. Three bursts were short in duration (∼10 s), whereas the others lasted for ∼6–25 min. All bursts showed spectral softening during their decay. There is no evidence for high-frequency (>100Hz) oscillations at any phase of the bursts. We see no correlations of the burst properties with respect to the persistent X-ray spectral properties, suggesting that in GX 17+2 the properties of the bursts do not correlate with inferred mass accretion rate. The presence of short bursts in GX 17+2 (and similar bright X-ray sources) is not accounted for in the current X-ray bursts theories at the high mass accretion rates encountered in this source. We obtain satisfactory results if we model the burst emission with a black body, after subtraction of the persistent pre-burst emission. The twocomponent spectral model does not fit the total burst emission whenever there is a black-body component present in the persistent emission. We conclude that in those cases the black-body contribution from the persistent emission is also present during the burst. This implies that, contrary to previous suggestions, the burst emission does not arise from the same site as the persistent black-body emission. The black-body component of the persistent emission is consistent with being produced in an expanded boundary layer, as indicated by recent theoretical work. Five of the long bursts showed evidence of radius expansion of the neutron star photosphere (independent of the spectral analysis method used), presumably due to the burst luminosity reaching the Eddington value. When the burst luminosity is close to the Eddington value, slight deviations from pure black-body radiation are seen at energies below 10 keV. Similar deviations have been seen during (long) X-ray bursts from other sources; they can not be explained by spectral hardening models. The total persistent flux just before and after the radius expansion bursts is inferred to be up to a factor of 2 higher than the net peak flux of the burst. If both the burst and persistent emission are radiated isotropically, this would imply that the persistent emission is up to a factor of 2 higher than the Eddington luminosity. This is unlikely and we suggest that the persistent luminosity is close to the Eddington luminosity and that the burst emission is (highly) anisotropic (ξ ∼ 2). Assuming that the net burst peak fluxes equal the Eddington limit, applying standard burst parameters (1.4 M neutron star, cosmic composition, electron scattering opacity appropriate for high temperatures), and taking into account gravitational redshift and spectral hardening, we derive a distance to GX 17+2 of ∼8 kpc, with an uncertainty of up to ∼30%.
Diffusion neutral and diffusion dependent patterning

In this paper a connection between reaction-diffusion systems with small diffusion coefficients and the corresponding shorted systems (where diffusion is removed) is investigated. We obtain new sufficient conditions showing when solutions are completely defined by the corresponding shorted system and when, in contrast to this, pattern formation depends on diffusion. We call the two situations, diffusion neutral and diffusion dependent patterning. We also discuss the consequences of being in one or in the other of the two situations and present examples from developmental biology and from fluid mechanics.
Mechanisms of urodele limb regeneration

Abstract This review explores the historical and current state of our knowledge about urodele limb regeneration. Topics discussed are (1) blastema formation by the proteolytic histolysis of limb tissues to release resident stem cells and mononucleate cells that undergo dedifferentiation, cell cycle entry and accumulation under the apical epidermal cap. (2) The origin, phenotypic memory, and positional memory of blastema cells. (3) The role played by macrophages in the early events of regeneration. (4) The role of neural and AEC factors and interaction between blastema cells in mitosis and distalization. (5) Models of pattern formation based on the results of axial reversal experiments, experiments on the regeneration of half and double half limbs, and experiments using retinoic acid to alter positional identity of blastema cells. (6) Possible mechanisms of distalization during normal and intercalary regeneration. (7) Is pattern formation is a self‐organizing property of the blastema or dictated by chemical signals from adjacent tissues? (8) What is the future for regenerating a human limb?
Linear Precoding for Relay Networks with Finite-Alphabet Constraints

In this paper, we investigate the optimal precoding scheme for relay networks with finite-alphabet constraints. We show that the previous work utilizing various design criteria to maximize either the diversity or the transmission rate with the Gaussian inputs assumption may lead to significant loss for a practical system with finite constellation set constraint. A linear precoding scheme is proposed to maximize the transmission rate, i.e., the mutual information, for relay networks. We exploit the structure of the optimal precoding matrix, and develop a unified two-step iterative algorithm utilizing the theory of convex optimization and optimization on the complex Stiefel manifold. Numerical examples show that this novel iterative algorithm achieves significant gains compared to its conventional counterpart.
Fairness-aware thread scheduling for multithreaded program using Intel® Software Guarded Extensions

Intel® Software Guarded Extensions was introduced to protect sensitive information of computer systems. It provides isolated execution area named enclave. The security enhancing feature (i.e. enclave) of Intel® Software Guarded Extensions allows only serialized multithreaded execution for a program. In this paper, we propose fairness-aware thread scheduling method to solve the problems that can be caused by serialized access on the enclave. To guarantee fairness among threads, the scheduler records occupation time on enclave and controls access priority to enclave. With this scheduling method, monopolization and starvation problems on enclave are handled. The average speedup is achieved as 7.76% compared to the non-scheduled execution in our model.
An Ultracompact Polarization-Insensitive Silicon-Based Strip-to-Slot Power Splitter

An ultracompact and polarization-insensitive silicon-based strip-to-slot power splitter based on multimode interference is proposed, where an inverse-tapered subwavelength grating (SWG) structure is embedded in the center of the multimode waveguide and two strip-to-slot mode converters are integrated at the end. With the optimized SWG structure, the length of the multimode waveguide is reduced by nearly half against without such a structure and polarization-insensitive transmission can be achieved. Tapered and cut-right-angled waveguides are also introduced to enhance the performance. Simulation results show that a length of 1.92 μm for the multimode region with an insertion loss of 0.39 dB (polarization-dependent loss (PDL) = 0), the reflection losses of -30.51 dB (transverse-electric mode) and -33.62 dB (transverse-magnetic mode) are obtained at 1.55 μm, and the bandwidth can be enlarged to ~105 nm for a PDL <; 0.1 dB. In addition, fabrication tolerances and mode-field evolution are also presented.
A Universal Crease Pattern for Folding Orthogonal Shapes

Abstract : We present a universal crease pattern--known in geometry as the tetrakis tiling and in origami as box pleating--that can fold into any object made up of unit cubes joined face-to-face (polycubes). More precisely, there is one universal finite crease pattern for each number n of unit cubes that need to be folded. This result contrasts previous universality results for origami, which require a different crease pattern for each target object, and confirms intuition in the origami community that box pleating is a powerful design technique.
Slow Crack Growth in Single-Crystal Silicon

Time-dependent crack growth has been measured on a precracked, single-crystal silicon cantilever beam 75 micrometers long that was excited at resonance. Growth of the precrack changes the resonant frequency of the beam, which is correlated to crack length. The measured steady-state crack growth rate was as slow as 2.9 x 10–13 meter per second, although the apparatus can measure crack growth rates as low as 10–15 meter per second. It is postulated that static fatigue of the native surface silica layer is the mechanism for crack growth. These experiments demonstrate the possibility of rate-dependent failure of silicon devices and the applicability of linear elastic fracture mechanics to small-scale micromechanical devices. The results indicate that slow crack growth must therefore be considered when evaluating the reliability of thin-film silicon structures.