Temperature 1 Self-Assembly: Deterministic Assembly in 3D and Probabilistic Assembly in 2D

We investigate the power of the Wang tile self-assembly model at temperature 1, a threshold value that permits attachment between any two tiles that share even a single bond. When restricted to deterministic assembly in the plane, no temperature 1 assembly system has been shown to build a shape with a tile complexity smaller than the diameter of the shape. In contrast, we show that temperature 1 self-assembly in 3 dimensions, even when growth is restricted to at most 1 step into the third dimension, is capable of simulating a large class of temperature 2 systems, in turn permitting the simulation of arbitrary Turing machines and the assembly of $n\times n$ squares in near optimal $O(\log n)$ tile complexity. Further, we consider temperature 1 probabilistic assembly in 2D, and show that with a logarithmic scale up of tile complexity and shape scale, the same general class of temperature $\tau=2$ systems can be simulated with high probability, yielding Turing machine simulation and $O(\log^2 n)$ assembly of $n\times n$ squares with high probability. Our results show a sharp contrast in achievable tile complexity at temperature 1 if either growth into the third dimension or a small probability of error are permitted. Motivated by applications in nanotechnology and molecular computing, and the plausibility of implementing 3 dimensional self-assembly systems, our techniques may provide the needed power of temperature 2 systems, while at the same time avoiding the experimental challenges faced by those systems

Therapeutic and chemopreventive potential of luteolin against growth and metastasis of breast cancer

Breast cancer is the second leading cause of cancer-related death in older women. Many postmenopausal women undergo hormone replacement therapy (HRT) to alleviate the symptoms of menopause. Recent studies implicate the progestin component of HRT as being most likely responsible for elevated breast cancer risk and increased mortality. Using animal models and cell culture we explored the preventive and therapeutic potential of luteolin (LU), a naturally-occurring compound found commonly in fruits and vegetables, and examined its ability to both prevent the onset of breast cancer, and inhibit its growth and metastasis. LU effectively blocked progestin (P)-induced intratumoral vascularization in our animal models when given preventatively or therapeutically. LU blocked P-stimulated effects in cultured human breast cancer cells, including inhibiting the enrichment of a subpopulation of human breast cancer cells that are believed to be responsible for tumor initiation. Such cells are difficult to treat by conventional methods. Progestins not only elevate the risk of breast cancer in postmenopausal women but have also been implicated in making tumor cells metastatic, increasing their ability to spread from the breast to distant sites around the body. With this in mind we utilized a hormone-independent model of lung metastasis, since most hormone-dependent cancer cells ultimately become hormone-resistant and lose therapeutic markers. LU significantly reduced the formation of lung colonies arising from these human breast cancer cells, with little or no animal toxicity. Overall, these studies provide compelling evidence that LU possesses chemopreventive, therapeutic, and anti-metastatic properties which might be harnessed to combat breast cancer

Time variability in the bipolar scattered light nebula of L1527 IRS: A possible warped inner disk

Context. The bipolar outflows associated with low-mass protostars create cavities in the infalling envelope. These cavities are illuminated by the central protostar and inner disk, creating a bipolar scattered light nebula at near-infrared and mid-infrared wavelengths. The variability of the scattered light nebula in both total intensity and intensity as a function of position in the scattered light nebula can provide important insights into the structure of the inner disk that cannot be spatially resolved. Aims. We aim to determine the likelihood that a warped inner disk is the origin of the surface brightness variability in the bipolar scattered light nebula associated with L1527 IRS. Methods. We present results from near-IR imaging conducted over the course of seven years, with periods of monthly cadence monitoring. We used Monte Carlo radiative transfer models to interpret the observations. Results. We find a time varying, asymmetrical brightness in the scattered light nebulae within the outflow cavities of the protostar. Starting in 2007, the surface brightnesses of the eastern and western outflow cavities were roughly symmetric. Then, in 2009, the surface brightnesses of the cavities were found to be asymmetric, with a substantial increase in surface brightness and a larger increase in the eastern outflow cavity. More regular monitoring was conducted from 2011 to 2014, revealing a rotating pattern of surface brightness variability in addition to a slow change of the eastern and western outflow cavities toward symmetry, but still not as symmetric as observed in 2007. We find that an inner disk warp is a feasible mechanism to produce the rotating pattern of surface brightness variability.Comment: 14 pages, 7 figures. Accepted for publication in Astronomy & Astrophysic

Beneficial physiological effects with blackcurrant intake in endurance athletes

Blackcurrant contains anthocyanins, known to influence vasorelaxation and peripheral blood flow. We examined the effects of 7 days intake of Sujon New Zealand blackcurrant powder (6g/day) on the lactate curve, maximum oxygen uptake, and cardiovascular responses at rest and during cycling. Thirteen trained triathletes with >3 yrs experience (8 men, age: 38±8 yrs, body mass: 71±9 kg, BF%: 19±5%, mean±SD) performed two incremental cycling protocols with recording of physiological and cardiovascular responses (Portapres® Model 2). Cardiovascular function was also measured in rest. Experimental design was double-blind, placebo-controlled, randomized and cross-over (wash-out 4 wks). Data was analysed with two-tailed t-tests and 2-way ANOVA and significance accepted at p<0.05. Plasma lactate was lower at 40%, 50%, 60% and 70% of maximum power by 27%, 22%, 17% and 13%. Intensity at 4 mmol∙L-1 OBLA was 6% higher with blackcurrant without effect on heart rate and oxygen uptake. Maximum values of oxygen uptake, heart rate and power were not affected by blackcurrant, but obtained with 14% lower lactate. In rest, blackcurrant increased stroke volume and cardiac output by 25% and 26%, and decreased total peripheral resistance by 16%, with no changes in blood pressure and heart rate. Cardiovascular responses during exercise at 40%, 50%, 60%, 70% and 80% intensity were not affected. Sujon New Zealand blackcurrant powder affects lactate production and/or clearance during exercise. Sujon New Zealand blackcurrant powder affects physiological and cardiovascular responses in rest and during exercise that may have implications for exercise performance

Effect of New Zealand Blackcurrant Extract on Substrate Oxidation and Cycling Performance in Normobaric Hypoxia

Blackcurrant is high in anthocyanin content. We have shown enhanced whole-body fat oxidation and increased time trial performance during cycling, in addition to increased femoral artery diameter during a sustained submaximal isometric contraction of the m.quadriceps with intake of New Zealand blackcurrant (NZBC) extract in normobaric normoxia (Cook et al., 2015, 2017). The effect of blackcurrant on metabolic and physiological responses and performance during cycling in normobaric hypoxia are not known. PURPOSE: To examine the effect of NZBC extract on intensity-dependent physiological and metabolic responses and 16.1-km cycling time trial in trained cyclists in normobaric hypoxia. METHODS: The study used a double-blind randomized cross-over design. Eleven healthy men from cycling and triathlon clubs with at least 3 yrs experience and cycling 8-10 hr·wk−1 (age: 38±11 yrs, height: 179±4 cm, body mass: 76±8 kg, V̇O2max: 47±5 mL·kg−1·min−1, maximum power: 398±38 W, mean±SD) ingested NZBC extract (600 mg·day−1 containing 220 mg anthocyanins) or placebo (PL) for 7 days (washout 14 days). Participants performed bouts of 10 min at 45, 55 and 65% V̇O2max, using indirect calorimetry and blood sampling, followed by a 16.1 km timetrial on a SRM ergometer (SRM International, Germany). Participants were familiarized for the time-trial. All testing took place in a temperature controlled (15°C) normobaric hypoxic chamber set at an altitude of ~2500 m (15% FiO2) (TIS Services, Medstead, UK) in morning sessions. Data was analysed using paired t-tests. RESULTS: At each intensity, NZBC extract had no effect on metabolic and physiological responses (e.g. at 65% V̇O2max, heart rate - PL: 133±12, NZBC; 132±12 beats·min-1); fat oxidation - PL: 0.24±0.12, NZBC: 0.20±0.16 g·min-1; carbohydrate oxidation - PL: 2.34±0.42, NZBC: 2.48±0.35 g·min-1; lactate - PL: 1.37±0.45, NZBC: 1.56±0.57 mmol·L-1). No improvements in 16.1 km time-trial performance were observed (PL: 1685±92, NZBC: 1685±99 sec). CONCLUSION: Seven day intake of New Zealand blackcurrant extract does not change whole-body fat oxidation and 16.1 km time-trial performance during cycling in normobaric hypoxia

Effect of New Zealand Blackcurrant Extract on Cycling Performance and Substrate Oxidation in Normobaric Hypoxia in Trained Cyclists

This study explored New Zealand blackcurrant (NZBC) extract for enhanced exercise-induced fat oxidation and 16.1 km cycling time trial (TT) performance in normobaric normoxia. The effect of NZBC extract on physiological and metabolic responses was examined during steady state cycling and a 16.1 km TT in normobaric hypoxia. This study used a randomized, double-blind, crossover design. Eleven healthy male cyclists (age: 38 ± 11 y, height: 179 ± 4 cm, body mass: 76 ± 8 kg, V ˙ O2max: 47 ± 5 mL·kg−1·min−1, mean ± SD) ingested NZBC extract (600 mg·day−1 CurraNZ® containing 210 mg anthocyanins) or a placebo (600 mg microcrystalline cellulose M102) for seven days (washout 14 days) and performed a steady state cycling test (3 × 10 min at 45%, 55% and 65% V ˙ O2max) followed by a 16.1 km TT at a simulated altitude of ~2500 meters (~15% of O2). Indirect calorimetry was used to measure substrate oxidation during steady state cycling. Intake of NZBC extract had no effect on blood glucose and lactate, heart rate, substrate oxidation, and respiratory exchange ratio during steady state cycling at 45%, 55% and 65% V ˙ O2max, and on 16.1 km TT performance (placebo: 1685 ± 92 s, NZBC extract: 1685 ± 99 s, P = 0.97). Seven days intake of New Zealand blackcurrant extract does not change exercise-induced metabolic responses and 16.1 km cycling time trial performance for moderately endurance-trained men in normobaric hypoxia

Recurrent miscalling of missense variation from short-read genome sequence data

Background: Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases ofgenomic variation. Results: We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of sequencing error approaches the sequence diversity between redundant regions. We find the resultant miscalled variants to be sensitive to small sequence variations between genomes, and thereby are often intrinsic to an individual, pedigree, strain or human ethnic group. In human exome sequences, we identify 2–300 recurrent false positive variants per individual, almost all of which are present in public databases of human genomic variation. From the exomes of non-reference strains of inbred mice, we identify 3–5000 recurrent false positive variants per mouse – the number of which increasing with greater distance between an individual mouse strain and the reference C57BL6 mouse genome. We show that recurrently miscalled variants may be reproduced for a given genome from repeated simulation rounds of read resampling, realignment and recalling. As such, it is possible to identify more than two-thirds of false positive variation from only ten rounds of simulation. Conclusion: Identification and removal of recurrent false positive variants from specific individual variant sets will improve overall data quality. Variant miscalls arising are highly sequence intrinsic and are often specific to an individual, pedigree or ethnicity. Further, read length is a strong determinant of whether given false variants will be called for any given genome – which has profound significance for cohort studies that pool datasets collected and sequenced at different points in time

Computing the Complete Gravitational Wavetrain from Relativistic Binary Inspiral

We present a new method for generating the nonlinear gravitational wavetrain from the late inspiral (pre-coalescence) phase of a binary neutron star system by means of a numerical evolution calculation in full general relativity. In a prototype calculation, we produce 214 wave cycles from corotating polytropes, representing the final part of the inspiral phase prior to reaching the ISCO. Our method is based on the inequality that the orbital decay timescale due to gravitational radiation is much longer than an orbital period and the approximation that gravitational radiation has little effect on the structure of the stars. We employ quasi-equilibrium sequences of binaries in circular orbit for the matter source in our field evolution code. We compute the gravity-wave energy flux, and, from this, the inspiral rate, at a discrete set of binary separations. From these data, we construct the gravitational waveform as a continuous wavetrain. Finally, we discuss the limitations of our current calculation, planned improvements, and potential applications of our method to other inspiral scenarios.Comment: 4 pages, 4 figure

Distributed System Contract Monitoring

The use of behavioural contracts, to specify, regulate and verify systems, is particularly relevant to runtime monitoring of distributed systems. System distribution poses major challenges to contract monitoring, from monitoring-induced information leaks to computation load balancing, communication overheads and fault-tolerance. We present mDPi, a location-aware process calculus, for reasoning about monitoring of distributed systems. We define a family of Labelled Transition Systems for this calculus, which allow formal reasoning about different monitoring strategies at different levels of abstractions. We also illustrate the expressivity of the calculus by showing how contracts in a simple contract language can be synthesised into different mDPi monitors.Comment: In Proceedings FLACOS 2011, arXiv:1109.239

Effect of New Zealand Blackcurrant Extract on Force Steadiness of the Quadriceps Femoris Muscle during Sustained Submax-imal Isometric Contraction

Intake of anthocyanin-rich New Zealand blackcurrant (NZBC) can alter physiological responses that enhance exercise performance. In two studies, we examined the effects of NZBC extract on the force steadiness during a sustained submaximal isometric contraction of the quad-riceps femoris muscle. With repeated measures designs, male participants in study one (n=13) and study two (n=19) performed a 120-second submaximal (30%) isometric contraction of the quadriceps femoris muscle following 7-day intake of NZBC extract and placebo (study one) and following 0 (control), 1, 4 and 7-day intake of NZBC extract (study two). Participants for both studies were different. In study one, NZBC extract enhanced isometric force steadiness during the 120-second contraction (placebo: 6.58±2.24%, NZBC extract: 6.05±2.24%, P=0.003), with differ-ences in the third (60-89 s) and fourth quartile (90-120 s) of the contraction. In study two, isomet-ric force steadiness was not changed following 1 and 4 days but was enhanced following 7-day intake of NZBC extract in comparison to control. In study two, the enhanced isometric force steadiness following 7-day intake did occur in the second (30-59 s), third (60-89 s) and fourth (90-120 s) quartiles. Daily supplementation of anthocyanin-rich NZBC extract can enhance force steadiness of the quadriceps femoris muscle during a sustained submaximal isometric contrac-tion. Our observations may have implications for human tasks that require postural stability