Miracle-dz/UniFAR-FTUs huggingface dataset:
Consequences of Secondary Calibrations on Divergence Time Estimates

Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.
Ordered‐subset analysis (OSA) for family‐based association mapping of complex traits

Association analysis provides a powerful tool for complex disease gene mapping. However, in the presence of genetic heterogeneity, the power for association analysis can be low since only a fraction of the collected families may carry a specific disease susceptibility allele. Ordered‐subset analysis (OSA) is a linkage test that can be powerful in the presence of genetic heterogeneity. OSA uses trait‐related covariates to identify a subset of families that provide the most evidence for linkage. A similar strategy applied to genetic association analysis would likely result in increased power to detect association. Association in the presence of linkage (APL) is a family‐based association test (FBAT) for nuclear families with multiple affected siblings that properly infers missing parental genotypes when linkage is present. We propose here APL‐OSA, which applies the OSA method to the APL statistic to identify a subset of families that provide the most evidence for association. A permutation procedure is used to approximate the distribution of the APL‐OSA statistic under the null hypothesis that there is no relationship between the family‐specific covariate and the family‐specific evidence for allelic association. We performed a comprehensive simulation study to verify that APL‐OSA has the correct type I error rate under the null hypothesis. This simulation study also showed that APL‐OSA can increase power relative to other commonly used association tests (APL, FBAT and FBAT with covariate adjustment) in the presence of genetic heterogeneity. Finally, we applied APL‐OSA to a family study of age‐related macular degeneration, where cigarette smoking was used as a covariate. Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.
Instance Weighting for Neural Machine Translation Domain Adaptation

Instance weighting has been widely applied to phrase-based machine translation domain adaptation. However, it is challenging to be applied to Neural Machine Translation (NMT) directly, because NMT is not a linear model. In this paper, two instance weighting technologies, i.e., sentence weighting and domain weighting with a dynamic weight learning strategy, are proposed for NMT domain adaptation. Empirical results on the IWSLT English-German/French tasks show that the proposed methods can substantially improve NMT performance by up to 2.7-6.7 BLEU points, outperforming the existing baselines by up to 1.6-3.6 BLEU points.
A social ecological exploration of community adult playground use among seniors in Northern Ontario

iii Acknowledgements . iv Chapter 1: Introduction . 1 Description of the Setting . 5 Wymont and Deer Park . 7 Contribution to Public Health and the Community . 10 Literature Review . 11 Outdoor Adult Playgrounds . 12 Older Adults and Physical Activity Initiatives . 16 Socioeconomic and Environmental Influences on Physical Activity . 20 Methodology . 23 Situating the Researcher . 24 Case Study Methodology . 25 Social Ecological Model . 26 Ethical Approval . 29 Data Collection . 30 Data Analysis . 35 Thesis Format . 36 Chapter 2: Outdoor Adult Playgrounds: A Case for Social Ecological Development . 39 Outdoor Adult Playgrounds . 42 Setting . 44
Bmc Complementary and Alternative Medicine Mediterranean Diet or Extended Fasting's Influence on Changing the Intestinal Microflora, Immunoglobulin a Secretion and Clinical Outcome in Patients with Rheumatoid Arthritis and Fibromyalgia: an Observational Study

Background: Alterations in the intestinal bacterial flora are believed to be contributing factors to many chronic inflammatory and degenerative diseases including rheumatic diseases. While microbiological fecal culture analysis is now increasingly used, little is known about the relationship of changes in intestinal flora, dietary patterns and clinical outcome in specific diseases. To clarify the role of microbiological culture analysis we aimed to evaluate whether in patients with rheumatoid arthritis (RA) or fibromyalgia (FM) a Mediterranean diet or an 8-day fasting period are associated with changes in fecal flora and whether changes in fecal flora are associated with clinical outcome.
Dosimetric validation for an automatic brain metastases planning software using single-isocenter dynamic conformal arcs.

An automatic brain-metastases planning (ABMP) software has been installed in our institution. It is dedicated for treating multiple brain metastases with radiosurgery on linear accelerators (linacs) using a single-setup isocenter with noncoplanar dynamic conformal arcs. This study is to validate the calculated absolute dose and dose distribution of ABMP. Three types of measurements were performed to validate the planning software: 1, dual micro ion chambers were used with an acrylic phantom to measure the absolute dose; 2, a 3D cylindrical phantom with dual diode array was used to evaluate 2D dose distribution and point dose for smaller targets; and 3, a 3D pseudo-in vivo patient-specific phantom filled with polymer gels was used to evaluate the accuracy of 3D dose distribution and radiation delivery. Micro chamber measurement of two targets (volumes of 1.2 cc and 0.9 cc, respectively) showed that the percentage differences of the absolute dose at both targets were less than 1%. Averaged GI passing rate of five different plans measured with the diode array phantom was above 98%, using criteria of 3% dose difference, 1 mm distance to agreement (DTA), and 10% low-dose threshold. 3D gel phantom measurement results demonstrated a 3D displacement of nine targets of 0.7±0.4 mm (range 0.2 ~ 1.1 mm). The averaged two-dimensional (2D) GI passing rate for several region of interests (ROI) on axial slices that encompass each one of the nine targets was above 98% (5% dose difference, 2 mm DTA, and 10% low-dose threshold). Measured D95, the minimum dose that covers 95% of the target volume, of the nine targets was 0.7% less than the calculated D95. Three different types of dosimetric verification methods were used and proved the dose calculation of the new automatic brain metastases planning (ABMP) software was clinical acceptable. The 3D pseudo-in vivo patient-specific gel phantom test also served as an end-to-end test for validating not only the dose calculation, but the treatment delivery accuracy as well. PACS number(s): 87.53. Lv, 87.55. km, 87.55. Qr.
Respiratory Muscle Fatigue After an Ultra-Marathon Measured as Inspiratory Task Failure

Controversial literature exists concerning the occurrence of inspiratory muscle fatigue during efforts performed outside a laboratory. The purpose of this study was to assess inspiratory muscle strength and endurance time measured as Tlim, the length of time a subject can endure a task before the onset of fatigue, in ultra-marathon runners by simple non-invasive techniques before and after an ultra-marathon (87 km). Ten runners, (8 males and 2 females), who had normal clinical evaluation and lung function underwent inspiratory muscle assessment by measurement of maximal inspiratory mouth pressures and sustained inspiratory mouth pressures at a given target pressure and a given duty cycle. The measurements were performed prior to the race and 3 days after the race. No significant difference was observed in the inspiratory muscle strength 3 days after the race (p > 0.37), but the inspiratory muscle endurance time as measured by Tlim, was significantly lower (p < 0.002), with an overall decrease of 26.5%. Inspiratory muscle strength was normal 3 days after the race, however the inspiratory muscle endurance time as measured by sustained inspiratory pressure was still impaired 3 days after the race.
Cognitive Functioning Is Related to Physical Functioning in a Longitudinal Study of Women at Midlife

Background: Studies have reported declines with age in cognitive or physical functioning, but rarely identify whether these are parallel or linked events in the same study. Furthermore, most research in this area has focused on persons in late life rather than midlife. Objective: The objective of the study was to determine (1) if cognitive functioning was related to physical functioning and whether this relationship persisted after adjustment for age, menopause status, metabolic status, depression and socioeconomic resources, and (2) if changes in physical functioning were associated with changes in cognitive functioning over a 4-year follow-up period. Methods: Data were from the Study of Women’s Health Across the Nation (SWAN), a multi-site, longitudinal study of women aged 46–56 years at follow-up examination 4. Three follow-up examinations (study years 04, 06 and 08) included measures of physical functioning perception (MOS SF-36) and cognitive functioning [Symbol Digit Modality Test (SDMT), Digit Span Backward Test (DSBT), and East Boston Memory Test (EBMT)] (n = 2,405). Results: Women with lower cognitive functioning scores also had lower perceived physical functioning scores. While adjustment for covariates attenuated the association between perceived physical functioning and both the SDMT and EBMT cognitive measures, these associations remained statistically significant. Additionally, the 4-year change in perceived physical functioning was significantly associated with the 4-year change in the EBMT. Conclusions: At midlife, there were associated declines in cognitive and perceived physical functioning scores, commencing at midlife in women.
EXECUTER1- and EXECUTER2-dependent transfer of stress-related signals from the plastid to the nucleus of Arabidopsis thaliana

Shortly after the release of singlet oxygen (1O2), drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. In contrast to retrograde control of nuclear gene expression by plastid signals described earlier, the primary effect of 1O2 generation in the flu mutant is not the control of chloroplast biogenesis but the activation of a broad range of signaling pathways known to be involved in biotic and abiotic stress responses. This activity of a plastid-derived signal suggests a new function of the chloroplast, namely that of a sensor of environmental changes that activates a broad range of stress responses. Inactivation of the plastid protein EXECUTER1 attenuates the extent of 1O2-induced up-regulation of nuclear gene expression, but it does not fully eliminate these changes. A second related nuclear-encoded protein, dubbed EXECUTER2, has been identified that is also implicated with the signaling of 1O2-dependent nuclear gene expression changes. Like EXECUTER1, EXECUTER2 is confined to the plastid. Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple mutant is sufficient to suppress the up-regulation of almost all 1O2-responsive genes. Retrograde control of 1O2-responsive genes requires the concerted action of both EXECUTER proteins within the plastid compartment.
Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes

ABSTRACT Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h−1) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during hydrological events and then decay once there.
Relationship Between HAART Adherence and Adipose Tissue Alterations

Summary: Adipose tissue alterations (ATA), which are common among persons treated with highly active antiretroviral therapy (HAART), can have substantial psychologic repercussions, with a subsequent negative impact on the patient's quality of life and on HAART adherence. However, the cross‐sectional nature of the studies precludes establishing the direction and causality of the relationship. The authors evaluated the longitudinal relationship between ATA and adherence to HAART. The analysis included all participants in the AdICoNA and the LipoICoNA substudies of the Italian Cohort Naive Antiretrovirals (ICoNA). Adherence was assessed using a 16‐item self‐administered questionnaire, which also included a question on self‐perceived fat accumulation experienced during the past 4 weeks. ATA was diagnosed by physicians at enrollment and evaluated every 6 months thereafter. There were 207 patients, with a median age of 35 years; 73% were men; and 34% acquired HIV through injection drug use. At baseline, nonadherence was reported by 63% of participants, and ATA was self‐perceived by 15% and clinically diagnosed in 25%. Using Cox regression analysis, patients with good adherence at baseline were more likely to develop ATA (RH = 2.58; 95% CI, 1.09‐6.11) and developed it sooner. Self‐perceived ATA at baseline was independently related to subsequent nonadherence (OR, 4.67; 95% CI, 1.01‐22.4), but clinically diagnosed ATA was not (OR, 0.77; 95% CI, 0.37‐1.61). Patients' adherence to HAART is a dynamic process that interacts with ATA. Better adherence is associated with a higher risk of subsequent occurrence of ATA, while patient‐perceived onset of morphologic alterations can reduce adherence to antiretroviral therapy.
Heinz Lehmann Award paper Cytochrome P 450 – mediated drug metabolism in the brain

Cytochrome P450 enzymes (CYPs) are found throughout the animal and plant kingdoms and are responsible for the oxidative metabolism of a wide variety of both exogenous and endogenous compounds. A large proportion of therapeutic drugs acting on the central nervous system (CNS) are metab ol ized by CYPs, primarily by members of the CYP2 family, to either active or inactive metabolites. For example, CYP2D6 activates codeine to morphine, inactivates the antidepressant desipramine and converts the active antipsychotic parent drug risperidone to an equally active metabolite. There is a great deal of variation in individual responses to centrally acting drugs, and in some cases the plasma levels of these drugs and/or their metabolites do not predict their therapeutic effect. Drug metabolism by CYPs takes place primarily in the liver, but CYP enzymes are also found in many other tissues, including brain. It is predicted that local brain metabolism of centrally acting drugs at their site of action can influence their therapeutic efficacy independently of liver metabolism, and differences in brain levels of CYP enzymes can contribute to the observed interindividual variation in drug response. There are many isoforms of CYPs, and these are classified into 18 families and 57 subfamilies based on their amino acid identity. Members of families 1, 2 and 3 primarily metabolize xenobiotics, such as drugs and environmentally derived compounds, and some endogenous substrates, whereas other vertebrate CYP family members primarily metabolize endogenous compounds. The CYP2 family metabolizes a large proportion of CNS-acting pharmacologics, such as antidepressants and antipsychotics; drugs of abuse, such as amphetamine and ethanol; and some endogenous neurochem icals, such as dopamine and serotonin. Some examples are presented in Tables 1 and 2. As in the liver, the expression levels of brain CYP forms vary greatly among individuals. This can be caused by factors that affect both brain and liver CYP expression levels, including genetic variation, which can result in differences in the plasma levels of drugs and their
Strategies and Operating Point Optimization of STATCOM Control for Voltage Unbalance Mitigation in Three-Phase Three-Wire Systems

Reactive power control through the static compensator (STATCOM) has gained wide attentions due to its outstanding performance. But for a STATCOM with traditional control strategies, unbalanced utility voltages will greatly affect the performance of the STATCOM and, in severe cases, may even cause the shutdown of the STATCOM for overcurrent protection. This paper proposes novel control strategies to ensure normal operation of STATCOM in three-phase three-wire systems when severe system voltage unbalance occurs and, furthermore, to mitigate voltage unbalance at the point of common coupling (PCC) whether it is caused by the utility or load. The control laws, operation principles, compensation characteristics, and operating point optimization of the proposed control strategies are analyzed and compared in detail. The power flow in the STATCOM and corresponding dc-side voltage-control schemes for these control strategies are also introduced. It is shown that the proposed voltage-controlled current source (VCCS) strategy and modified voltage-controlled voltage source strategy are valid for voltage unbalance compensation, especially the VCCS strategy for low rating under the same performance. Finally, the simulation and experimental investigations were carried out with these three parameter-optimized control strategies, respectively, for light and heavy load conditions. The results verified that the current passing through the STATCOM is under control and the voltage at the PCC is more balanced than before compensation. The compensation performance of the STATCOM is thus proven satisfactory
Key Management for Wireless Sensor Networks Using Trusted Neighbors

Establishing and maintaining secure communication paths in a wireless sensor network poses mathematical and technical challenges. We suggest to use random nonces to set up secure communication links after the network deployment phase. This idea exploits some of the inherent features of sensor networks, e.g.: nodes are densely deployed; the wireless communication areas of neighbouring nodes have a large overlap. We outline the analytical properties of such a scheme and show simulation results which corroborate them for practical purposes.
Physiological strategies during animal diapause: lessons from brine shrimp and annual killifish

ABSTRACT Diapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana and annual killifish Austrofundulus limnaeus share strikingly similar life histories that include embryonic diapause as a means to synchronize the growth and reproduction phases of their life history to favorable environmental conditions. In both species, respiration rate is severely depressed during diapause and thus alterations in mitochondrial physiology are a key component of the suite of characters associated with cessation of development. Here, we use these two species to illustrate the basic principles of metabolic depression at the physiological and biochemical levels. It is clear that these two species use divergent molecular mechanisms to achieve the same physiological and ecological outcomes. This pattern of convergent physiological strategies supports the importance of biochemical and physiological adaptations to cope with extreme environmental stress and suggests that inferring mechanism from transcriptomics or proteomics or metabolomics alone, without rigorous follow-up at the biochemical and physiological levels, could lead to erroneous conclusions. Summary: The apparent convergent evolution of diapause in brine shrimp and annual killifish has occurred at the physiological level, via unique molecular mechanisms. This review underscores the central importance of physiological, rather than molecular, responses to environmental stress.