Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and temporal variation in barnacle growth in a coastal upwelling system

Recent studies suggest that large-scale variation in nearshore primary productivity may strongly influence the dynamics of rocky intertidal communities. Among the hypothesized effects is a link between phytoplankton abundance and the growth of barnacles and other suspension feeders. We tested the strength of this association on the central coast of Oregon, USA, by quantifying water- column chlorophyll a (chl a) concentration and the growth of 2 intertidal barnacles (Balanus glandula and Chthamalus dalli). Barnacles were photographed at 13 d intervals on mid-intertidal growth plates attached in wave-exposed and wave-protected habitats at 2 sites differing in nearshore pro- ductivity: Strawberry Hill (SH) and Boiler Bay (BB), Oregon. B. glandula grew more rapidly in wave- exposed areas than wave-protected habitats, presumably because higher flows delivered more food to passively feeding barnacles. After several months, individuals of both species attained a larger size at SH, the site with consistently higher chl a concentrations. Surprisingly, short-term growth rates only partially matched spatial and temporal variations in phytoplankton. Growth rates were low dur- ing a persistent upwelling event, and increased 2- to 3-fold during the subsequent upwelling relax- ation. At SH, this increase coincided with a major phytoplankton bloom, but growth rates remained high well after chl a concentrations decreased. Moreover, parallel increases in growth were observed at BB, despite the fact that no bloom was recorded at this site. These results imply that factors other than phytoplankton contributed to variation in barnacle growth. Records of barnacle settlement sug- gest that water-column concentrations of larvae increased dramatically at both sites during the period of high barnacle growth. Published analyses of stomach contents indicate that zooplankton may be an important food source in other barnacle species. Yet another factor, water temperature, was also elevated during the period of sustained barnacle growth. Increased barnacle growth during the upwelling relaxation may thus have arisen from the combined benefits of more phytoplankton, more zooplankton, and warmer water temperatures. Incorporating the influence of zooplankton and water temperature into studies of bottom-up influences may improve our ability to explain variation among intertidal communities.
Exploring system performance using elastic traces: Fast, accurate and portable

Simulation tools are indispensable to computer architects. Detailed execution-driven CPU models offer high accuracy, but at the cost of simulation speed. Trace-driven simulation is widely adopted to alleviate this problem, especially for studies focusing on memory-system exploration. Ideally, trace-driven core models will mimic out-of-order processors executing full-system workloads to enable computer architects to evaluate modern systems. Additionally, to be useful to the broader community the tracing and replay models should be publicly available. However, existing trace-driven approaches are limited in their applicability and availability. We propose elastic traces in which we accurately capture data and load/store order dependencies by instrumenting a detailed out-of-order processor model. In contrast to existing work, we do not rely on offline analysis of timestamps, and instead use accurate dependency information tracked inside the processor pipeline. We thereby account for the effects of speculation and branch misprediction resulting in a more accurate trace playback. We provide a trace player that honours the dependencies and thus adapts its execution time to memory-system changes, as would the actual CPU. Compared to the detailed CPU, our trace player achieves a speed-up of 6–8 times. When modifying the memory-system parameters, the average error in absolute execution time is 7% for SPEC 2006 benchmarks on a bare metal system and 17% for HPC benchmarks on Linux. Relative performance is predicted with less than 3% error, achieving fast and accurate system performance exploration. We make this functionality available to the broader community via a widely-used open source full-system simulator.
Modeling the benefits of mixed data and task parallelism

Mixed task and data parallelism exists naturally in many applications, but utilizing it may require sophisticated scheduling algorithms and software support. Recently, significant research effort has been applied to exploiting mixed parallelism in both theory and systems communities. In this paper, we ask how much mixed parallelism will improve performance in practzce, and how architectural evolution impacts these est imat es. First, we build and validate a performance model for a class of mixed task and data parallel problems based on machine and problem parameters. Second, we use this model to estimate the gains from mixed parallelism for some scientific applications on current machines. This quantifies our intuition that mixed parallelism is best when either communication is slow or the number of processors is large. Third, we show that, for balanced divide and conquer trees, a simple one-time switch between data and task parallelism gets most of the benefit of general mixed parallelism. Fourth, we establish upper bounds to the benefits of mixed parallelism for irregular task graphs. Apart from these detailed analyses, we provide a framework in which other applications and machines can be evaluated.
Knowledge acquisition for new product development with the use of an ERP database

Nowadays, a considerable number of enterprises develop new products using an Enterprise Resource Planning (ERP) system. One of the modules of a typical ERP system concerns project management. Functionalities of this module consist of defining resources, company calendars, sequence of project tasks, task duration etc. in order to obtain a project schedule. These parameters can be defined by the employees according to their knowledge, or they can be connected with data from previous completed projects. The paper investigates using an ERP database to identify critical factors, i.e. variables that significantly influence on new product development. Project duration and cost is estimated by a fuzzy neural system that uses data of completed projects stored in an ERP system.
Incidence of the Major Stroke Subtypes: Initial Findings From the North East Melbourne Stroke Incidence Study (NEMESIS)

Background and Purpose— Population-based stroke incidence studies are the only accurate way to determine the number of strokes that occur in a given society. Because the major stroke subtypes have different patterns of incidence and outcome, information on the natural history of stroke subtypes is essential. The purpose of the present study was to determine the incidence and case-fatality rate of the major stroke subtypes in a geographically defined region of Melbourne, Australia. Methods— All suspected strokes that occurred among 133 816 residents of suburbs north and east of Melbourne, Australia, during a 12-month period of 1996 and 1997 were identified and assessed. Multiple overlapping sources were used to ascertain cases, and standard criteria for stroke and case-fatality were used. Stroke subtypes were defined by CT, MRI, and autopsy. Results— Three hundred eighty-one strokes occurred among 353 persons during the study period, with 276 (72%) being first-ever-in-a-lifetime strokes. Of these, 72.5% (95% CI 67.2% to 77.7%) were cerebral infarction, 14.5% (95% CI 10.3% to 18.6%) were intracerebral hemorrhage, 4.3% (95% CI 1.9% to 6.8%) were subarachnoid hemorrhage, and 8.7% (95% CI 5.4% to 12.0%) were stroke of undetermined type. The 28-day case-fatality rate was 12% (95% CI 7% to 16%) for cerebral infarction, 45% (95% CI 30% to 60%) for intracerebral hemorrhage, 50% (95% CI 22% to 78%) for subarachnoid hemorrhage, and 38% (95% CI 18% to 57%) for stroke of undetermined type. Conclusions— The overall distribution of stroke subtypes and 28-day case-fatality rates are not significantly different from those of most European countries or the United States. There may, however, be some differences in the incidence of subtypes within Australia.
Silicon Nano-Photonic Devices

This thesis deals with the design, fabrication and characterization of nano-photonic devices including ridge waveguide components, microring resonators, and photonic crystal components, and explore the potential for these devices in different applications ranging from optical communication to microwave systems and biosensing devices. An ultra-low loss inverse taper coupler for interfacing silicon ridge waveguides and optical fibers is introduced and insertion losses of less than 1 dB are achieved for both transverse-electric (TE) and transversemagnetic (TM) polarizations. Integrated with the couplers, a silicon ridge waveguide is utilized in nonlinear all-optical signal processing for optical time division multiplexing (OTDM) systems. Record ultra-highspeed error-free optical demultiplexing and waveform sampling are realized and demonstrated for the first time. Microwave phase shifters and notch filters based on tunable microring resonators are proposed and analyzed. Based on a single microring resonator, a maximum radio frequency (RF) phase shift of 336◦ is obtained, but with large power variation. By utilizing a dual-microring resonator, a RF phase shifting range larger than 2π is achieved with small power variation. A widely tunable microwave notch filter is also experimentally demonstrated at 40GHz. Other application such as pulse repetition rate multiplication by using microring resonator is also presented. Photonic crystal components are studied. Two different types of photonic crystal structures are analyzed concerning index sensitivity, dispersion engineering, and slow-light coupling. Several photonic crystal devices such as index sensor, slow-light coupler, and all-optical tunable cavity are presented.
Impact of LTE Operating in Unlicensed Spectrum on Wi-Fi Using Real Equipment

The proliferation of mobile devices and the exponential growth of data transmitted over the air pushed the wireless community to find solutions in order to increase network capacity and fully exploit the available spectrum. Recently, 3GPP announced the operation of LTE in the unlicensed spectrum in order to offload the limited and expensive licensed spectrum. Concurrently, leading parties of the wireless community examine standalone operation of LTE in unlicensed spectrum. LTE was initially designed to operate in licensed spectrum and does not use any channel estimation mechanism to determine ongoing transmissions by other co-located networks. This introduces important coexistence challenges in unlicensed spectrum between LTE deployments and the current, well-established technologies, such as IEEE 802.11 (a.k.a. Wi-Fi). In this paper, we discuss the core differences between LTE and Wi-Fi, which lead to significant coexistence issues. We verify and showcase the problem by analyzing the performance degradation of Wi-Fi, when a traditional LTE network is co-located and operates in the same unlicensed frequency without any coexistence mechanism. The experiments are performed using open- source LTE and Wi-Fi implementations on real equipment in a fully controlled wireless environment. We conclude with showing the need for coexistence mechanisms, following the work that is being done within the standardization activities.
Socioeconomic inequalities in oral health in different European welfare state regimes

Background There is very little information about the relationship between welfare regimes and oral health inequalities. We compared socioeconomic inequalities in adults’ oral health in five European welfare-state regimes: Scandinavian, Anglo-Saxon, Bismarckian, Southern and Eastern. Methods Using data from the oral health module of the Eurobarometer 72.3 survey, we assessed inequalities in two self-reported oral health measures: no functional dentition (less than 20 natural teeth) and edentulousness (no natural teeth). Occupational social class, education and subjective social status (SSS) were included as socioeconomic position indicators. We estimated age-standardised prevalence rates, ORs, the Relative Index of Inequality (RII) and the Slope Index of Inequality (SII). Results The Scandinavian regime showed the lowest prevalence rates of the two oral health measures while the Eastern showed the highest. In all welfare regimes there was a general pattern of social gradients by occupational social class and education. Relative educational inequalities in no functional dentition were largest in the Scandinavian welfare regime (RII=3.81; 95% CI 2.68 to 5.42). The Scandinavian and Southern regimes showed the largest relative inequalities in edentulousness by occupation and education, respectively. There were larger absolute inequalities in no functional dentition in the Eastern regime by occupation (SII=42.16; 95% CI 31.42 to 52.89) and in the Southern by SSS (SII=27.92; 95% CI 17.36 to 38.47). Conclusions Oral health inequalities in adults exist in all welfare-state regimes, but contrary to what may be expected from theory, they are not smaller in the Scandinavian regime. Future work should examine the potential mechanisms linking welfare provision and oral health inequalities.
Semiquantitative analysis of atherosclerotic plaque using optical coherence tomography and time-of-flight secondary ion mass spectrometry

Atherosclerosis is the underlying vascular pathology that initiates arterial thromboembolic occlusions (myocardial infarctions, strokes and peripheral vessel blockage). Two imaging modalities, Optical Coherence Tomography (OCT) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), were investigated for detection and compositional analysis of unstable plaque associated with plaque erosion and sudden occlusion. OCT produces high resolution images whereas mass spectrometry images provide information on the spatial distribution of chemical elements. Diseased carotid arteries taken from patients with high-risk lesions were imaged with OCT and ToF-SIMS to give molecular and metabolic information, and matched with histopathology. OCT results show clear indications of vascular remodeling by the presence of fatty acid deposits, fibrous tissue and calcifications. ToF-SIMS further characterized changes based on secondary ion topography analysis where a high 23Na/39K ratio was indicative of arterial tissue degradation and the amount of 40Ca corresponded with late stage atherosclerosis. This pilot experiment has demonstrated that in vitro OCT imaging and ToF-SIMS of diseased carotid arteries have scientific merit for targeting clinically relevant morphology and metabolic changes to compare stable and unstable plaque. These optical techniques provide complimentary metabolic and molecular information on unstable plaque, specifically cell break-down with altered ion ratios of 23Na, 39K and 40Ca.
Chloroplast Signaling and LESION SIMULATING DISEASE1 Regulate Crosstalk between Light Acclimation and Immunity in Arabidopsis[W]

Plants are simultaneously exposed to abiotic and biotic hazards. Here, we show that local and systemic acclimation in Arabidopsis thaliana leaves in response to excess excitation energy (EEE) is associated with cell death and is regulated by specific redox changes of the plastoquinone (PQ) pool. These redox changes cause a rapid decrease of stomatal conductance, global induction of ASCORBATE PEROXIDASE2 and PATHOGEN RESISTANCE1, and increased production of reactive oxygen species (ROS) and ethylene that signals through ETHYLENE INSENSITIVE2 (EIN2). We provide evidence that multiple hormonal/ROS signaling pathways regulate the plant's response to EEE and that EEE stimulates systemic acquired resistance and basal defenses to virulent biotrophic bacteria. In the Arabidopsis LESION SIMULATING DISEASE1 (lsd1) null mutant that is deregulated for EEE acclimation responses, propagation of EEE-induced programmed cell death depends on the plant defense regulators ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4). We find that EDS1 and PAD4 operate upstream of ethylene and ROS production in the EEE response. The data suggest that the balanced activities of LSD1, EDS1, PAD4, and EIN2 regulate signaling of programmed cell death, light acclimation, and holistic defense responses that are initiated, at least in part, by redox changes of the PQ pool.
Integrating Pareto Optimization into Dynamic Programming

Pareto optimization combines independent objectives by computing the Pareto front of the search space, yielding a set of optima where none scores better on all objectives than any other. Recently, it was shown that Pareto optimization seamlessly integrates with algebraic dynamic programming: when scoring schemes A and B can correctly evaluate the search space via dynamic programming, then so can Pareto optimization with respect to A and B. However, the integration of Pareto optimization into dynamic programming opens a wide range of algorithmic alternatives, which we study in substantial detail in this article, using real-world applications in biosequence analysis, a field where dynamic programming is ubiquitous. Our results are two-fold: (1) We introduce the operation of a “Pareto algebra product” in the dynamic programming framework of Bellman’s GAP. Users of this framework can now ask for Pareto optimization with a single keystroke. Careful evaluation of the implementation alternatives by means of an extended Bellman’s GAP compiler demonstrates the dependence of the best implementation choice on the application at hand. (2) We extract from our experiments several pieces of advice to programmers who do not use a system such as Bellman’s GAP, but who choose to hand-craft their dynamic programming recurrences, incorporating Pareto optimization from scratch.
The energetics of lactation in cooperatively breeding meerkats Suricata suricatta

Species may become obligate cooperative breeders when parents are unable to raise their offspring unassisted. We measured the daily energy expenditure of mothers, helpers and offspring during peak lactation in cooperatively breeding meerkats Suricata suricatta using the doubly labelled water technique. Lactating mothers expended more energy per day than allo–lactating subordinate females, non–lactating females or suckling offspring. Metabolizable energy intakes of lactating mothers were calculated from isotope–based estimates of offspring milk energy intake, and were not significantly different from the previously suggested maximal limit for mammals. Allo–lactating females were the only category of animals that lost weight during the period of study, probably because they spent more time babysitting than non–lactating females. Daily energy expenditure (DEE) of lactating mothers increased with litter size but decreased with the number of helpers. Calculations show that for every 10 helpers, even in the absence of allo–lactators, mothers are able to reduce their DEE during peak lactation by an amount equivalent to the energy cost of one pup. These results indicate that helpers have beneficial energetic consequences for lactating mothers in an obligate cooperatively breeding mammal.
A level set based segmentation approach for point-sampled surfaces *

Segmenting a complex 3D surface model into some visually meaningful sub-parts is one of the fundamental problems in digital geometry processing. In this paper, a novel segmentation approach of point-sampled surfaces is proposed, which is based on the level set evolution scheme. To segment the model so as to align the patch boundaries with high curvature zones, the driven speed function for the zero level set inside narrow band is defined by the extended curvature field, which approaches zero speed as the propagating front approaches high curvature zone. The effectiveness of the proposed approach is demonstrated by our experimental results. Furthermore, two applications of model segmentation are illustrated, such as piecewise parameterization and local editing for point-sampled geometry.
Human NDR Kinases Are Rapidly Activated by MOB Proteins through Recruitment to the Plasma Membrane and Phosphorylation

ABSTRACT Human nuclear Dbf2-related kinases (NDRs) are up-regulated in certain cancer types, yet their precise function(s) and regulatory mechanism(s) still remain to be defined. Here, we show that active (phosphorylated on Thr444) and inactive human NDRs are both mainly cytoplasmic. Moreover, NDR kinases colocalize at the plasma membrane with human MOBs (hMOBs), which are recently described coactivators of human NDR in vitro. Strikingly, membrane targeting of NDR results in a constitutively active kinase due to phosphorylation on Ser281 and Thr444 that is further activated upon coexpression of hMOBs. Membrane-targeted hMOBs also robustly promoted activation of NDR. We further demonstrate that the in vivo activation of human NDR by membrane-bound hMOBs is dependent on their interaction and occurs solely at the membrane. By using a chimeric molecule of hMOB, which allows inducible membrane translocation, we found that NDR phosphorylation and activation at the membrane occur a few minutes after association of hMOB with membranous structures. We provide insight into a potential in vivo mechanism of NDR activation through rapid recruitment to the plasma membrane mediated by hMOBs.
Comparison of bluetongue virus detection and quantitation methods in south India.

INTRODUCTION Bluetongue (BT), a vector-borne viral disease, primarily affects sheep. Of the 26 serotypes of BTV identified so far, 22 are reported to be circulating in India. Due to an increase in vector population and delays in disease diagnosis, the BT control program heavily relies on rapid and confirmatory diagnosis. Polymerase chain reaction (PCR)-based real-time detection assays may be an ideal method to detect the BTV genome in animal blood at an early stage of infection. METHODOLOGY In this study, a SYBR green-based real-time RT-PCR assay was evaluated, validated, and compared with conventional RT-PCR. The specificity and sensitivity of an assay using BTV-2 RNA extracted from tenfold serially diluted (starting from 1.0 TCID50/mL) cell culture virus was also evaluated. RESULTS While conventional RT-PCR could detect 3.16 × 10(2) TCID50 of virus/mL, the real-time PCR test had a detection limit of 3.16 × 10(-4) TCID50/mL. Melting curve analysis indicated the absence of non-specific amplification (R(2) = 0.987). Out of the 32 infected blood samples examined, 24 tested positive for BTV RNA. Seven that were found negative through conventional PCR tested positive through real-time PCR. CONCLUSIONS These results showed that the SYBR green-based real-time PCR assay is rapid, sensitive, and equally specific in the diagnosis of BT in BTV-affected animals.
Condition Assessment of Power Transformer on-Load Tap-Changers Using Wavelet Analysis and Self-Organizing Map: Field Evaluation

An on-load tap-changer (OLTC) is the most maintenance-intensive subassembly on a power transformer. Vibration monitoring is an effective technique that can be used to assess the condition of an OLTC effectively and nonintrusively. The authors have developed a condition monitoring system for common types of OLTCs that enables the condition of tap changer contacts and associated drive system to be inferred from vibration signals. A number of prototype systems have been installed onto OLTCs in distribution zone substations for field trials. Particular emphasis has been given to the detection of faults in a particular type of older tap-changer that had been prone to a range of faults associated with the switching contacts and drive mechanism. For this type of tap-changer, it is possible to determine not only that the tap-changer is aging but also to identify the particular part that is degrading.