A different algebraic analysis of the ZUC stream cipher

Existing algebraic analyses of the ZUC cipher indicate that the cipher should be secure against algebraic attacks. In this paper, we present an alternative algebraic analysis method for the ZUC stream cipher, where a combiner is used to represent the nonlinear function and to derive equations representing the cipher. Using this approach, the initial states of ZUC can be recovered from 2^97 observed words of keystream, with a complexity of 2^282 operations. This method is more successful when applied to a modified version of ZUC, where the number of output words per clock is increased. If the cipher outputs 120 bits of keystream per clock, the attack can succeed with 219 observed keystream bits and 2^47 operations. Therefore, the security of ZUC against algebraic attack could be significantly reduced if its throughput was to be increased for efficiency.

Time-dependent rates of molecular evolution

For over half a century, it has been known that the rate of morphological evolution appears to vary with the time frame of measurement. Rates of microevolutionary change, measured between successive generations, were found to be far higher than rates of macroevolutionary change inferred from the fossil record. More recently, it has been suggested that rates of molecular evolution are also time dependent, with the estimated rate depending on the timescale of measurement. This followed surprising observations that estimates of mutation rates, obtained in studies of pedigrees and laboratory mutation-accumulation lines, exceeded long-term substitution rates by an order of magnitude or more. Although a range of studies have provided evidence for such a pattern, the hypothesis remains relatively contentious. Furthermore, there is ongoing discussion about the factors that can cause molecular rate estimates to be dependent on time. Here we present an overview of our current understanding of time-dependent rates. We provide a summary of the evidence for time-dependent rates in animals, bacteria and viruses. We review the various biological and methodological factors that can cause rates to be time dependent, including the effects of natural selection, calibration errors, model misspecification and other artefacts. We also describe the challenges in calibrating estimates of molecular rates, particularly on the intermediate timescales that are critical for an accurate characterization of time-dependent rates. This has important consequences for the use of molecular-clock methods to estimate timescales of recent evolutionary events.

Review ["Telling the Evolutionary Time : Molecular Clocks and the Fossil Record" edited by Philip C. J. Donoghue and M. Paul Smith]

Determining the temporal scale of biological evolution has traditionally been the preserve of paleontology, with the timing of species originations and major diversifications all being read from the fossil record. However, the ages of the earliest (correctly identified) records will underestimate actual origins due to the incomplete nature of the fossil record and the necessity for lineages to have evolved sufficiently divergent morphologies in order to be distinguished. The possibility of inferring divergence times more accurately has been promoted by the idea that the accumulation of genetic change between modern lineages can be used as a molecular clock (Zuckerkandl and Pauling, 1965). In practice, though, molecular dates have often been so old as to be incongruent even with liberal readings of the fossil record. Prominent examples include inferred diversifications of metazoan phyla hundreds of millions of years before their Cambrian fossil record appearances (e.g., Nei et al., 2001) and a basal split between modern birds (Neoaves) that is almost double the age of their earliest recognizable fossils (e.g., Cooper and Penny, 1997).

Time dependency of molecular rate estimates and systematic overestimation of recent divergence times

Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

Relaxed phylogenetics and dating with confidence

In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas

The semiaquatic platypus and terrestrial echidnas (spiny anteaters) are the only living egg-laying mammals (monotremes). The fossil record has provided few clues as to their origins and the evolution of their ecological specializations; however, recent reassignment of the Early Cretaceous Teinolophos and Steropodon to the platypus lineage implies that platypuses and echidnas diverged >112.5 million years ago, reinforcing the notion of monotremes as living fossils. This placement is based primarily on characters related to a single feature, the enlarged mandibular canal, which supplies blood vessels and dense electrosensory receptors to the platypus bill. Our reevaluation of the morphological data instead groups platypus and echidnas to the exclusion of Teinolophos and Steropodon and suggests that an enlarged mandibular canal is ancestral for monotremes (partly reversed in echidnas, in association with general mandibular reduction). A multigene evaluation of the echidna–platypus divergence using both a relaxed molecular clock and direct fossil calibrations reveals a recent split of 19–48 million years ago. Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas had aquatically foraging ancestors that reinvaded terrestrial ecosystems. This ecological shift and the associated radiation of echidnas represent a recent expansion of niche space despite potential competition from marsupials. Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode. Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

The relationship between cognitive ability, insight and self-regulatory behaviors: Findings from the older driver population

Self-regulation is often promoted as a coping strategy that may allow older drivers to drive safely for longer. Self-regulation depends upon drivers making an accurate assessment of their own ability and having a willingness to practice self-regulatory behaviors to compensate for changes in ability. The current study explored the relationship between older drivers’ cognitive ability, their driving confidence and their use of self-regulation. An additional study aim was to explore the relationship between these factors and older drivers’ interest in driving programs. Seventy Australian drivers aged 65 years and over completed a questionnaire about their driving and a brief screening measure of cognitive ability (an untimed Clock Drawing Test). While all participants reported high levels of confidence regarding their driving ability, and agreed that they would continue driving in the foreseeable future, a notable proportion performed poorly on the Clock Drawing Test. Compared to older drivers who successfully completed the Clock Drawing Test, those who failed the cognitive test were significantly less likely to report driving self-regulation, and showed significantly less interest in being involved in driving programs. Older drivers with declining cognitive abilities may not be self-regulating their driving. This group also appears to be unlikely to self-refer to driving programs.

Evaluation of precision time synchronisation methods for substation applications

Many substation applications require accurate time-stamping. The performance of systems such as Network Time Protocol (NTP), IRIG-B and one pulse per second (1-PPS) have been sufficient to date. However, new applications, including IEC 61850-9-2 process bus and phasor measurement, require accuracy of one microsecond or better. Furthermore, process bus applications are taking time synchronisation out into high voltage switchyards where cable lengths may have an impact on timing accuracy. IEEE Std 1588, Precision Time Protocol (PTP), is the means preferred by the smart grid standardisation roadmaps (from both the IEC and US National Institute of Standards and Technology) of achieving this higher level of performance, and integrates well into Ethernet based substation automation systems. Significant benefits of PTP include automatic path length compensation, support for redundant time sources and the cabling efficiency of a shared network. This paper benchmarks the performance of established IRIG-B and 1-PPS synchronisation methods over a range of path lengths representative of a transmission substation. The performance of PTP using the same distribution system is then evaluated and compared to the existing methods to determine if the performance justifies the additional complexity. Experimental results show that a PTP timing system maintains the synchronising performance of 1-PPS and IRIG-B timing systems, when using the same fibre optic cables, and further meets the needs of process buses in large substations.

Parents’ experience of time distortion following diagnosis of a serious or lethal fetal anomaly

PURPOSE: To explore the experience of couples who continued pregnancy following a diagnosis of serious or lethal fetal anomaly. STUDY DESIGN: Thirty-one male and female participants were recruited from a high-risk maternal–fetal medicine clinic in Washington State. Data were collected using in-depth interviews during pregnancy and after the birth of their baby. Transcribed interviews were thematically analyzed through the phenomenological lens of Merleau-Ponty. FINDINGS: Participants described how time became reconfigured and reconstituted as they tried to compress a lifetime of love for their future child into a limited period. Participants’ concepts of time became distorted and were related to their perceptual lived experience rather than the schedule-filled,regimented, linear clock time that governed the health professionals. CONCLUSION: Living in distorted time may be a mechanism parents use to cope with overwhelming and disorienting feelings when their unborn baby is diagnosed with a fetal anomaly.

Quantitative assessment of fault tolerant precision timing for electricity substations

Advanced substation applications, such as synchrophasors and IEC 61850-9-2 sampled value process buses, depend upon highly accurate synchronizing signals for correct operation. The IEEE 1588 Precision Timing Protocol (PTP) is the recommended means of providing precise timing for future substations. This paper presents a quantitative assessment of PTP reliability using Fault Tree Analysis. Two network topologies are proposed that use grandmaster clocks with dual network connections and take advantage of the Best Master Clock Algorithm (BMCA) from IEEE 1588. The cross-connected grandmaster topology doubles reliability, and the addition of a shared third grandmaster gives a nine-fold improvement over duplicated grandmasters. The performance of BMCA mediated handover of the grandmaster role during contingencies in the timing system was evaluated experimentally. The 1 µs performance requirement of sampled values and synchrophasors are met, even during network or GPS antenna outages. Slave clocks are shown to synchronize to the backup grandmaster in response to degraded performance or loss of the main grandmaster. Slave disturbances are less than 350 ns provided the grandmaster reference clocks are not offset from one another. A clear understanding of PTP reliability and the factors that affect availability will encourage the adoption of PTP for substation time synchronization.

One night stand : only you

Technical: This looped video work is made up from a number of still images animated in a sequence, not intended to be a smooth action, but syncopated. The gaps in real time suggest blinking, lapses in technology, warps in time and distance. The still images have been manipulated in photoshop and imported into an animation software program, showing subtle emphasis on various aspects of the features of the face and location from the screen shots. Content: Obsession is one of the most constant expressions of love, whether it is a negative attribute, such as stalking, or the need to see or stroke the beloved, or telling and re-telling the story of first meeting. “like the beat, beat, beat of the tom tom when the jungle shadows fall like the tick, tick, tock of the stately clock as it stands against the wall like the drip, drip drip of the rain drops when the summer shower’s through a voice within me keeps repeating you, you, you… only you...” (Cole Porter, Night and Day) My desire to immerse myself in my newly-met adult daughter as a reality is as obsessive as any new parent. The primary means of contact is video cam, which has become a kind of surveillance for me. I stare at her mouth as it moves, her ear as she moves her head, her smile, her grimaces, her high cheekbones, her eyes that are like mine, the shape of her head, her teeth that are like her father’s… hundreds of candid pictures screen shot over a year and a half were the source of the video images.

Fast scanning electron microscope (FSEM)

High magnification and large depth of field with a temporal resolution of less than 100 microseconds are possible using the present invention which combines a linear electron beam produced by a tungsten filament from an SX-40A Scanning Electron Microscope (SEM), a magnetic deflection coil with lower inductance resulting from reducing the number of turns of the saddle-coil wires, while increasing the diameter of the wires, a fast scintillator, photomultiplier tube, photomultiplier tube base, and signal amplifiers and a high speed data acquisition system which allows for a scan rate of 381 frames per second and 256.times.128 pixel density in the SEM image at a data acquisition rate of 25 MHz. The data acquisition and scan position are fully coordinated. A digitizer and a digital waveform generator which generates the sweep signals to the scan coils run off the same clock to acquire the signal in real-time.

Evaluation of primary epidermal lamellar density in the forefeet of near-term fetal Australian feral and domesticated horses

Objective: To investigate the density of the primary epidermal lamellae (PEL) around the solar circumference of the forefeet of near-term fetal feral and nonferal (ie, domesticated) horses. Sample: Left forefeet from near-term Australian feral (n = 14) and domesticated (4) horse fetuses. Procedures: Near-term feral horse fetuses were obtained from culled mares within 10 minutes of death; fetuses that had died in utero 2 weeks prior to anticipated birth date and were delivered from live Thoroughbred mares were also obtained. Following disarticulation at the carpus, the left forefoot of each fetus was frozen during dissection and data collection. In a standard section of each hoof, the stratum internum PEL density was calculated at the midline center (12 o'clock) and the medial and lateral break-over points (11 and 1 o'clock), toe quarters (10 and 2 o'clock), and quarters (4 and 6 o'clock). Values for matching lateral and medial zones were averaged and expressed as 1 density. Density differences at the 4 locations between the feral and domesticated horse feet were assessed by use of imaging software analysis. Results: In fetal domesticated horse feet, PEL density did not differ among the 4 locations. In fetal feral horse feet, PEL density differed significantly among locations, with a pattern of gradual reduction from the dorsal to the palmar aspect of the foot. The PEL density distribution differed significantly between fetal domesticated and feral horse feet. Conclusions and Clinical Relevance: Results indicated that PEL density distribution differs between fetal feral and domesticated horse feet, suggestive of an adaptation of feral horses to environment challenges.

Long summer days : grounded learning of words for the uneven cycles of real world events

Time and space are fundamental to human language and embodied cognition. In our early work we investigated how Lingodroids, robots with the ability to build their own maps, could evolve their own geopersonal spatial language. In subsequent studies we extended the framework developed for learning spatial concepts and words to learning temporal intervals. This paper considers a new aspect of time, the naming of concepts like morning, afternoon, dawn, and dusk, which are events that are part of day-night cycles, but are not defined by specific time points on a clock. Grounding of such terms refers to events and features of the diurnal cycle, such as light levels. We studied event-based time in which robots experienced day-night cycles that varied with the seasons throughout a year. Then we used meet-at tasks to demonstrate that the words learned were grounded, where the times to meet were morning and afternoon, rather than specific clock times. The studies show how words and concepts for a novel aspect of cyclic time can be grounded through experience with events rather than by times as measured by clocks or calendars