Miracle-dz/UniFAR-FTUs huggingface dataset:
Introduction to Self-Assembling DNA Nanostructures for Computation and Nanofabrication

Introduction. DNA, well-known as the predominant chemical for duplication and storage of genetic information in biology, has also recently been shown to be highly useful as an engineering material for construction of special purpose computers and micron-scale objects with nanometer-scale feature resolution. Properly designed synthetic DNA can be thought of as a programmable glue which, via specific hybridization of complementary sequences, will reliably self-organize to form desired structures and superstructures. Such engineered structures are inherently information-rich and are suitable for use directly as computers or as templates for imposing specific patterns on various other materials. In theory, DNA can be used to create any desired pattern in two or three dimensions and simultaneously to guide the assembly of a wide variety of other materials into any desired patterned structure. Given diverse mechanical, chemical, catalytic, and electronic properties of these specifically patterned materials, DNA self-assembly techniques hold great promise for bottom-up nanofabrication in a large number of potential applications in wide ranging fields of technology. Starting with background for understanding why the physical, chemical, and biological properties of DNA make it extremely useful as a "smart" material for nanoengineering projects, this chapter traces the historic development of DNA-based nanofabrication, outlines its major successes, and presents some possible future applications in fields as diverse as electronics, combinatorial chemistry, nano-robotics, and gene therapy,. DNA-based nanoengineering as a field is related to computational biology, bioinformatics, and genome informatics rather tangentially; it is more closely allied with biomolecular computation (BMC) – the engineering of biological macromolecules for production of artificial information processing systems. Rather than using binary, electronic computers for analyzing information extracted from biological systems, BMC seeks to utilize biomolecules directly as active parts of engineered computers. The concluding section of this chapter contains some speculation into the possibility of coming full circle and applying BMC and DNA-based nanoengineering principles and systems to the extraction and processing of information directly from biological DNA, that is, the possible use of natural DNA molecules as inputs for artificial DNA-based machines.
Optical Communications Investigation into the significance of failure rate calculations for erbium - doped fiber amplifiers in view of the reliability of communication networks

This paper deals with the impact of erbium-doped fiber amplifier (EDFAs) on the reliability of communication networks. It is shown that failure rates calculated for EDFAs have only limited significance in view of the reliability of the complete network. Standard amplifier setups using a single pump per stage are compared with setups making use of pump sharing. The analysis reveals that differences with respect to downtime and mean time to repair of networks using these types of amplifiers are much smaller than it is expected from the failure rate calculations. This is due to the fact that standard amplifiers can compensate the failure of an intermediate pump for several operating conditions by increasing the power emitted by the other pumps, whereas compensation capabilities of setups based on pump sharing are strongly constrained. Copyright © 2008 John Wiley & Sons, Ltd.
SPOT-4 (Take 5): Simulation of Sentinel-2 Time Series on 45 Large Sites

This paper presents the SPOT-4 (Take 5) experiment, aimed at providing time series of optical images simulating the repetitivity, the resolution and the large swath of Sentinel-2 images. The aim was to help users set up and test their applications and methods, before Sentinel-2 mission data become available. In 2016, when both Sentinel-2 satellites are operational, and for at least fifteen years, users will have access to high resolution time series of images systematically acquired every five days, over the whole Earth land surfaces. Thanks to Sentinel-2’s high revisit frequency, a given surface should be observed without clouds at least once a month, except in the most cloudy periods and regions. In 2013, the Centre National d’Etudes Spatiales (CNES) lowered the orbit altitude of SPOT-4, to place it on a five-day repeat cycle orbit for a duration of five months. This experiment started on 31 January 2013 and lasted until 19 June 2013. SPOT-4 images were acquired every fifth day, over 45 sites scattered in nearly all continents and covering very diverse biomes for various applications. Two ortho-rectified products were delivered for each acquired image that was not fully cloudy, expressed either as top of atmosphere reflectance (Level 1C) or as surface reflectance (Level 2A). An extensive validation campaign was held to check the performances of these products with regard to the multi-temporal registration, the quality of cloud masks, the accuracy of aerosol optical thickness estimates and the quality of surface reflectances. Despite high a priori geo-location errors, it was possible to register the images with an accuracy better than 0.5 pixels in the large majority of cases. Despite the lack of a blue band on the SPOT-4 satellite, the cloud and shadow detection yielded good results, while the aerosol optical thickness was measured with a root mean square error better than 0.06. The surface reflectances after atmospheric correction were compared with in situ data and other satellite data showing little bias and the standard deviation of surface reflectance errors in the range (0.01–0.02). The Take 5 experiment is being repeated in 2015 with the SPOT-5 satellite with an enhanced resolution.
Parcellation of the cingulate cortex at rest and during tasks: a meta-analytic clustering and experimental study

Anatomical, morphological, and histological data have consistently shown that the cingulate cortex can be divided into four main regions. However, less is known about parcellations of the cingulate cortex when involved in active tasks. Here, we aimed at comparing how the pattern of clusterization of the cingulate cortex changes across different levels of task complexity. We parcellated the cingulate cortex using the results of a meta-analytic study and of three experimental studies. The experimental studies, which included two active tasks and a resting state protocol, were used to control the results obtained with the meta-analytic parcellation. We explored the meta-analytic parcellation by applying a meta-analytic clustering (MaC) to papers retrieved from the BrainMap database. The MaC is a meta-analytic connectivity driven parcellation technique recently developed by our group which allowed us to parcellate the cingulate cortex on the basis of its pattern of co-activations during active tasks. The MaC results indicated that the cingulate cortex can be parcellated into three clusters. These clusters covered different percentages of the cingulate parenchyma and had a different density of foci, with the first cluster being more densely connected. The control experiments showed different clusterization results, suggesting that the co-activations of the cingulate cortex are highly dependent on the task that is tested. Our results highlight the importance of the cingulate cortex as a hub, which modifies its pattern of co-activations depending on the task requests and on the level of task complexity. The neurobiological meaning of these results is discussed.
The neural system that bridges reward and cognition in humans: An fMRI study

We test the hypothesis that motivational and cognitive processes are linked by a specific neural system to reach maximal efficiency. We studied six normal subjects performing a working memory paradigm (n-back tasks) associated with different levels of monetary reward during an fMRI session. The study showed specific brain activation in relation with changes in both the cognitive loading and the reward associated with task performance. First, the working memory tasks activated a network including the dorsolateral prefrontal cortex [Brodmann area (BA) 9/46] and, in addition, in the lateral frontopolar areas (BA 10), but only in the more demanding condition (3-back task). This result suggests that lateral prefrontal areas are organized in a caudo-rostral continuum in relation with the increase in executive requirement. Second, reward induces an increased activation in the areas already activated by working memory processing and in a supplementary region, the medial frontal pole (BA 10), regardless of the level of cognitive processing. It is postulated that the latter region plays a specific role in monitoring the reward value of ongoing cognitive processes. Third, we detected areas where the signal decreases (ventral-BA 11/47 and subgenual prefrontal cortices) in relation with both the increase of cognitive demand and the reward. The deactivation may represent an emotional gating aimed at inhibiting adverse emotional signals to maximize the level of performance. Taken together, these results suggest a balance between increasing activity in cortical cognitive areas and decreasing activity in the limbic and paralimbic structures during ongoing higher cognitive processing.
Postglacial recolonization of eastern Blacknose Dace,Rhinichthys atratulus(Teleostei: Cyprinidae), through the gateway of New England

During the last ice age, much of North America far south as 40°N was covered by glaciers (Hewitt 2000). About 20,000 years ago, as the glaciers retreated, the hydrologic landscape changed dramatically creating waterways for fish dispersal. The number of populations responsible for recolonization and the regions from which they recolonized are unknown for many freshwater fishes living in New England and southeastern Canada. The Blacknose Dace,Rhinichthys atratulus, is one of the freshwater fish species that recolonized this region. We hypothesize that the earliest deglaciated region, modern-day Connecticut, was recolonized byR. atratulusvia a single founding event by a single population. In this paper, we test this hypothesis phylogenetically with regard to the major drainage basins within Connecticut. The mitochondrial DNA exhibits low nucleotide diversity, high haplotype diversity, and a dominant haplotype found across the state. A small percentage of individuals in the Housatonic drainage basin, however, share a haplotype with populations in New York drainage basins, a haplotype not found elsewhere in Connecticut's drainage basins. We calculated a range for the rate of divergence for NADH dehydrogenase subunit 2 (nd2) and control region (ctr) of 4.43–6.76% and 3.84–8.48% per million years (my), respectively. While this range is higher than the commonly accepted rate of 2% for mitochondrial DNA, these results join a growing list of publications finding high rates of divergence for various taxa (Peterson and Masel 2009). The data support the conclusion that Connecticut as a whole was recolonized initially by a single founding event that came from a single refugium. Subsequently, the Housatonic basin alone experienced a secondary recolonization event.
Long-term dietary compensation for added sugar: effects of supplementary sucrose drinks over a 4-week period

The long-term physiological effects of refined carbohydrates on appetite and mood remain unclear. Reported effects when subjects are not blind may be due to expectations and have rarely been studied for more than 24 h. The present study compared the effects of supplementary soft drinks added to the diet over 4 weeks on dietary intake, mood and BMI in normal-weight women (n 133). Subjects were categorised as ‘watchers’ or ‘non-watchers’ of what they ate then received sucrose or artificially sweetened drinks (4 × 250 ml per d). Expectancies were varied by labelling drinks ‘sugar’ or ‘diet’ in a counter-balanced design. Sucrose supplements provided 1800 kJ per d and sweetener supplements provided 67 kJ per d. Food intake was measured with a 7 d diary and mood with ten single Likert scales. By 4 weeks, sucrose supplements significantly reduced total carbohydrate intake (F(1,129) = 53·81; P < 0·001), fat (F(2,250) = 33·33; P < 0·001) and protein intake (F(2,250) = 28·04; P < 0·001) compared with sweetener supplements. Mean daily energy intake increased by just under 1000 kJ compared with baseline (t (67 df) = 3·82; P < 0·001) and was associated with a non-significant trend for those receiving sucrose to gain weight. There were no effects on appetite or mood. Neither dietary restraint status as measured by the Dutch Eating Behaviour Questionnaire nor the expectancy procedure had effects. Expectancies influenced mood only during baseline week. It is concluded that sucrose satiates, rather than stimulates, appetite or negative mood in normal-weight subjects.
Design of a Low-Power Differential Repeater Using Low Voltage and Charge Recycling

Advances in System-on-Chip (SoC) design have emphasized the need for driving long on-chip differential traces. The delay of long traces has traditionally been handled by inserting repeaters at periodic intervals. The repeater method reduces the delay at the expense of increased power consumption. At the same time, power is a major design consideration in SoC design, motivating a driver methodology that has comparable delay to the repeater approach, with lower power consumption. This paper presents the design of a differential driver using low-voltage swing and charge recycling. The low-voltage design is shown to reduce the overall power by 37% and the Power-Delay-Product by 32% compared to traditional full-swing differential repeaters. By including charge recycling, the power can be reduced by 43%, which includes the power consumed by the associated control circuitry. This indicates that the charge recycling low voltage differential driver methodology is valuable when power is a major design concern. Author(s) Biography Brock J. LaMeres received his BSEE from Montana State University in 1998 and his MSEE from the University of Colorado in 2001. He is currently a Ph.D. candidate at the University of Colorado where his research focus is VLSI Circuit Design and High-Speed I/O for next generation IC’s. For the past 7 years he has worked as a hardware design engineer for Agilent Technologies in Colorado Springs where he designs logic analyzer probes and acquisition boards. LaMeres has published over 30 technical articles in the area of signal integrity and holds a patent in the field of logic analyzer probing. LaMeres is a registered Professional Engineer in the State of Colorado. Sunil P. Khatri is an Assistant Professor in the Department of Electrical Engineering at Texas A&M University. He is affiliated with the VLSI CAD group. He completed his Ph.D. from the University of California, Berkeley in 1999. Before this, he worked with Motorola, Inc on the designs of the MC88110 and PowerPC 603 RISC Microprocessors. Khatri obtained his M.S from the University of Texas at Austin, which followed his B.Tech. from the Indian Institute of Technology, Kanpur. His research is in the areas of VLSI Design and VLSI CAD. Some recent areas of interest are design automation for datapath circuits, cross-talk avoidance in on-chip buses, leakage-power reduction, extreme low power circuit design, asynchronous circuit design methodologies, timing estimation, efficient test generation, fast logic simulation and cross-talk immune VLSI design.
Dynamics of Curved Bistable Reeled Composites

The vibration characteristics of cantilevered straight and curved carbon/epoxy bistable reeled composites (BRCs) have been investigated. The tube length, cross-section radius, subtending angle, longitudinal curvature and number of plies - design parameters were investigated for their effects on the vibration modes. The boom length affects the frequency the most, which is found to be inversely proportional to the square of boom length, in addition to ABAQUS simulation results showing that frequency is proportional to curvature. Short, three-ply carbon/epoxy samples were manufactured and tested. A regime change from short (48.5cm) to slender (≈150cm) tubes was observed, signified by curved tubes exhibiting higher vibration modes in a particular plane than the straight ones in simulation - highlighting the scalability of curved BRC applications. Recommendations for the upcoming CleanSpace One, EPFL space mission which uses curved tubes for its capture mechanism, are discussed. Dynamic stability analysis was performed by simulating increasing rotary accelerations, causing the cantilevered BRCs attached to a spacecraft to rotate. A failure point derived from the Budiansky-Hutchinson criterion was developed to determine the maximum rotation acceleration - the critical value by which the tube loses stability.
Protection of rat skeletal muscle fibers by either L-carnitine or coenzyme Q10 against statins toxicity mediated by mitochondrial reactive oxygen generation

Mitochondrial redox imbalance has been implicated in mechanisms of aging, various degenerative diseases and drug-induced toxicity. Statins are safe and well-tolerated therapeutic drugs that occasionally induce myotoxicity such as myopathy and rhabdomyolysis. Previous studies indicate that myotoxicity caused by statins may be linked to impairment of mitochondrial functions. Here, we report that 1-h incubation of permeabilized rat soleus muscle fiber biopsies with increasing concentrations of simvastatin (1–40 μM) slowed the rates of ADP-or FCCP-stimulated respiration supported by glutamate/malate in a dose-dependent manner, but caused no changes in resting respiration rates. Simvastatin (1 μM) also inhibited the ADP-stimulated mitochondrial respiration supported by succinate by 24% but not by TMPD/ascorbate. Compatible with inhibition of respiration, 1 μM simvastatin stimulated lactate release from soleus muscle samples by 26%. Co-incubation of muscle samples with 1 mM L-carnitine, 100 μM mevalonate or 10 μM coenzyme Q10 (Co-Q10) abolished simvastatin effects on both mitochondrial glutamate/malate-supported respiration and lactate release. Simvastatin (1 μM) also caused a 2-fold increase in the rate of hydrogen peroxide generation and a decrease in Co-Q10 content by 44%. Mevalonate, Co-Q10 or L-carnitine protected against stimulation of hydrogen peroxide generation but only mevalonate prevented the decrease in Co-Q10 content. Thus, independently of Co-Q10 levels, L-carnitine prevented the toxic effects of simvastatin. This suggests that mitochondrial respiratory dysfunction induced by simvastatin, is associated with increased generation of superoxide, at the levels of complexes-I and II of the respiratory chain. In all cases the damage to these complexes, presumably at the level of 4Fe-4S clusters, is prevented by L-carnitine.
Progesterone production in vitro by small and large ovine luteal cells.

Corpora lutea from cyclic ewes were dissociated by collagenase digestion and trypsin/EGTA treatment. Enriched fractions of endothelial cells, small luteal cells and large luteal cells were prepared on a stepped gradient of Ficoll 400. Progesterone was measured by radioimmunoassay and the results corrected so that progesterone production by each cell type could be determined. Endothelial cells did not produce significant amounts of progesterone, with or without LH stimulation, and endothelial cell contamination of small and large luteal cell fractions did not influence progesterone production by these fractions. Mean +/- s.e. m. basal progesterone production (n = 10) by large luteal cells was greater (P less than 0.001) on a per cell basis than that by small luteal cells (1.16 +/- 0.16 compared with 0.25 +/- 0.06 pg/h/cell). However LH, which stimulated a maximal 3-4-fold increase in progesterone production by small luteal cells (LH ED50 = 0.14 ng/ml), had no significant effect on production by large luteal cells, when contamination by small luteal cells was taken into account. The response of small luteal cells was specific to LH, other hormones having had no significant effect. Basal progesterone production by small luteal cells (0.12 +/- 0.03 fg/h/micron3) calculated per unit volume of cell was not significantly different from that of large luteal cells (0.17 +/- 0.02 fg/h/micron3). After LH stimulation, small luteal cells produced more progesterone than did large luteal cells (0.40 +/- 0.09 compared with 0.18 +/- 0.03 fg/h/micron3) (P less than 0.05). When the amounts of progesterone produced per cell were multiplied by the absolute numbers of large luteal (1 X 10(7] and small luteal (5 X 10(7] cells in the intact corpus luteum, basal progesterone production by large luteal cells (11.6 +/- 1.6 micrograms/h) was similar to that by small luteal cells (12.3 +/- 3.0 micrograms/h). However, under LH stimulation, progesterone production by the small luteal cell type (39.9 +/- 9.5 micrograms/h) was approximately 3 times greater than that by the large luteal cell type (12.3 +/- 1.6 micrograms/h) (P less than 0.05). We therefore conclude that small luteal cells may be the principal source of luteal progesterone production in the sheep.
Emirati speaker verification based on HMMls, HMM2s, and HMM3s

This work focuses on Emirati speaker verification systems in neutral talking environments based on each of First-Order Hidden Markov Models (HMMls), Second-Order Hidden Markov Models (HMM2s), and Third-Order Hidden Markov Models (HMM3s) as classifiers. These systems have been evaluated on our collected Emirati speech database which is comprised of 25 male and 25 female Emirati speakers using Mel-Frequency Cepstral Coefficients (MFCCs) as extracted features. Our results show that HMM3s outperform each of HMM1s and HMM2s for a text-independent Emirati speaker verification. The obtained results based on HMM3s are close to those achieved in subjective assessment by human listeners.