Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing for the Markov Property in Time Series Testing for the Markov Property in Time Series

participants at Queen's University for their comments and discussions. Any remaining errors are solely ours. Abstract The Markov property is a fundamental property in time series analysis and is often assumed in economic and …nancial modelling. We develop a test for the Markov property using the conditional characteristic function embedded in a frequency domain approach, which checks the implication of the Markov property in every conditional moment (if exist) and over many lags. The proposed test is applicable to both univariate and multivariate time series with discrete or continuous distributions. Simulation studies show that with the use of a smoothed nonparametric transition density-based bootstrap procedure, the proposed test has reasonable sizes and all-around power against non-Markov alternatives in …nite samples. We apply the test to a number of high-frequency …nancial time series and …nd strong evidence against the Markov property.
Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica

Abstract We examine the population genetic structure and divergence among the regional populations of the Japanese honeybee, Apis cerana japonica, by re‐sequencing the genomes of 105 individuals from the three main Japanese islands with diverse climates. The genetic structure results indicated that these individuals are distinct from the mainland Chinese A. cerana samples. Furthermore, population structure analyses have identified three genetically distinct geographic regions in Japan: Northern (Tohoku‐Kanto‐Chubu districts), Central (Chugoku district), and Southern (Kyushu district). In some districts, “possible non‐native” individuals, likely introduced from other regions in recent years, were discovered. Then, genome‐wide scans were conducted to detect candidate genes for adaptation by two different approaches. We performed a population branch statistics (PBS) analysis to identify candidate genes for population‐specific divergence. A latent factor mixed model (LFMM) was used to identify genes associated with climatic variables along a geographic gradient. The PBSmax analysis identified 25 candidate genes for population‐specific divergence whereas the LFMM analysis identified 73 candidate genes for adaptation to climatic variables along a geographic gradient. However, no common genes were identified by both methods.
Flow regulation by dams affecting ichthyoplankton: the case of the Porto Primavera Dam, Paraná River, Brazil

The effects of a dam closure (Porto Primavera Dam) on reproduction of the main species that use the floodplain located below a nursery area were determined. Specifically, we examined, before and after the closure of the dam, the spatial distribution of larvae and the differences in density according to life strategy (migratory and non‐migratory species). Fifteen points distributed along the channels of the Paraná, Ivinheima and Paranapanema rivers were sampled, between 1997 and 2001, (October 1997 to December 1998—pre; and between January 1999 to March 2001—post closure), during the spawning period of most fish species found in the region (October to March). Samplings were always conducted at night, using a conical‐cylindrical plankton net (0.5 mm mesh) with a flowmeter attached. There were significant differences in larvae densities between pre and post dam closure for several species. Also, there were significant differences between the pre and post‐closure periods for densities of migratory and non‐migratory species, and between sampling sites. These findings indicate decline in densities and number of taxa caught after the closure of the dam. Larvae of migratory species, formerly common in the entire study area, were registered only in points influenced by the non dammed rivers (such as the Ivinheima River), indicating that the closure of Porto Primavera caused negative impacts on fish reproduction downstream of the dam. Copyright © 2006 John Wiley & Sons, Ltd.
Exploring the Relationships Between Rehabilitation and Survivors of Intimate Partner Violence: A Scoping Review

Intimate partner violence (IPV) is a public health crisis affecting one in three women and one in ten men in their lifetimes. Rehabilitation professionals are highly likely to encounter survivors of IPV in their practice; yet, there exists no formal review assessing the relationship between IPV and rehabilitation. Our objective was to understand the types and contexts of rehabilitation care currently available for survivors of IPV, opportunities identified in the literature for rehabilitation care, and IPV awareness and education among rehabilitation providers. A search strategy related to IPV and four rehabilitation professionals of interest (occupational therapy, physiotherapy, speech-language pathology/therapy, and physiatry) was developed across 10 databases and complemented by a gray literature search. Two reviewers independently assessed articles for inclusion. In all, 44 articles met inclusion criteria, ranging from primary research articles (48%) to clinical newsletters. Included articles predominantly focused on opportunities for rehabilitation care (68%) and occupational therapists as a profession (68%). A minority of studies examined specific interventions for IPV survivors (18%) or assessed for knowledge and attitudes about IPV (16%) among rehabilitation professionals. To our knowledge, this is the first scoping review exploring the rehabilitation literature for IPV survivors. These findings show an awareness of IPV among rehabilitation professionals, the importance of identifying IPV in clients, and the ways in which rehabilitation professionals are uniquely situated to support survivors of IPV. There remains an opportunity to explore interventions designed specifically for IPV survivors.
Autoactivation of mycorrhizal symbiosis signaling through gibberellin deactivation in orchid seed germination

Abstract Orchids parasitically depend on external nutrients from mycorrhizal fungi for seed germination. Previous findings suggest that orchids utilize a genetic system of mutualistic arbuscular mycorrhizal (AM) symbiosis, in which the plant hormone gibberellin (GA) negatively affects fungal colonization and development, to establish parasitic symbiosis. Although GA generally promotes seed germination in photosynthetic plants, previous studies have reported low sensitivity of GA in seed germination of mycoheterotrophic orchids where mycorrhizal symbiosis occurs concurrently. To elucidate the connecting mechanisms of orchid seed germination and mycorrhizal symbiosis at the molecular level, we investigated the effect of GA on a hyacinth orchid (Bletilla striata) seed germination and mycorrhizal symbiosis using asymbiotic and symbiotic germination methods. Additionally, we compared the transcriptome profiles between asymbiotically and symbiotically germinated seeds. Exogenous GA negatively affected seed germination and fungal colonization, and endogenous bioactive GA was actively converted to the inactive form during seed germination. Transcriptome analysis showed that B. striata shared many of the induced genes between asymbiotically and symbiotically germinated seeds, including GA metabolism- and signaling-related genes and AM-specific marker homologs. Our study suggests that orchids have evolved in a manner that they do not use bioactive GA as a positive regulator of seed germination and instead autoactivate the mycorrhizal symbiosis pathway through GA inactivation to accept the fungal partner immediately during seed germination.
Future treatment of vascular calcification in chronic kidney disease

ABSTRACT Introduction Cardiovascular disease (CVD) is one of the global leading causes of morbidity and mortality in chronic kidney disease (CKD) patients. Vascular calcification (VC) is a major cause of CVD in this population and is the consequence of complex interactions between inhibitor and promoter factors leading to pathological deposition of calcium and phosphate in soft tissues. Different pathological landscapes are associated with the development of VC, such as endothelial dysfunction, oxidative stress, chronic inflammation, loss of mineralization inhibitors, release of calcifying extracellular vesicles (cEVs) and circulating calcifying cells. Areas covered In this review, we examined the literature and summarized the pathophysiology, biomarkers and focused on the treatments of VC. Expert opinion Even though there is no consensus regarding specific treatment options, we provide the currently available treatment strategies that focus on phosphate balance, correction of vitamin D and vitamin K deficiencies, avoidance of both extremes of bone turnover, normalizing calcium levels and reduction of inflammatory response and the potential and promising therapeutic approaches liketargeting cellular mechanisms of calcification (e.g. SNF472, TNAP inhibitors). Creating novel scores to detect in advance VC and implementing targeted therapies is crucial to treat them and improve the future management of these patients.
Probabilistic dynamics of soil nitrate: Coupling of ecohydrological and biogeochemical processes

In this paper we analyze the probabilistic dynamics resulting from a simplified model of soil moisture and nitrate mass in relatively arid environments, which accounts for relevant hydrologic and biogeochemical processes and for the random characters of rainfall. The soil nitrate balance includes uptake through transpiration, mineralization, nitrification, and denitrification. To allow an exact mathematical treatment, all nitrate fluxes are assumed to be linear functions of the state variables, namely, soil moisture and nitrate mass stored in soils. The range of applicability of the above simplification is investigated by means of numerical Monte Carlo simulations, showing that the linear approach is meaningful in relatively arid environments, where soil moisture contents are generally low. The moment‐generating function of the joint probability distribution (pdf) of soil nitrate and water content is derived, thereby allowing a linkage between the main features of soil nitrate statistics and the underlying soil, vegetation, rainfall, and biogeochemical parameters. Exact expressions for the moments of the nitrate pdf and for the covariance of soil moisture and nitrate mass are derived. The pdf of the nitrate mass in storage within the soil is shown to be reasonably approximated by a gamma distribution in many cases of practical interest. Interestingly, nitrogen limitation for the ecosystem is shown to be directly related to low values of the product between the rate of rainfall arrivals and the characteristic time of nitrate removal.
Assessing Juvenile Native Fish Demographic Responses to a Steady Flow Experiment in a Large Regulated River

The Colorado River below Glen Canyon Dam, Arizona, is part of an adaptive management programme which optimizes dam operations to improve various resources in the downstream ecosystem within Grand Canyon. Understanding how populations of federally endangered humpback chub Gila cypha respond to these dam operations is a high priority. Here, we test hypotheses concerning temporal variation in juvenile humpback chub apparent survival rates and abundance by comparing estimates between hydropeaking and steady discharge regimes over a 3‐year period (July 2009–July 2012). The most supported model ignored flow type (steady vs hydropeaking) and estimated a declining trend in daily apparent survival rate across years (99.90%, 99.79% and 99.67% for 2009, 2010 and 2011, respectively). Corresponding abundance of juvenile humpback chub increased temporally; open population model estimates ranged from 615 to 2802 individuals/km, and closed model estimates ranged from 94 to 1515 individuals/km. These changes in apparent survival and abundance may reflect broader trends, or simply represent inter‐annual variation. Important findings include (i) juvenile humpback chub are currently surviving and recruiting in the mainstem Colorado River with increasing abundance; (ii) apparent survival does not benefit from steady fall discharges from Glen Canyon Dam; and (iii) direct assessment of demographic parameters for juvenile endangered fish are possible and can rapidly inform management actions in regulated rivers. Copyright © 2015 John Wiley & Sons, Ltd.
Tyrosine hydroxylase phosphorylation is under the control of serine 40

Tyrosine hydroxylase catalyzes the initial and rate‐limiting step in the biosynthesis of the neurotransmitter dopamine. The phosphorylation state of Ser40 and Ser31 is believed to exert a direct effect on the enzymatic activity of tyrosine hydroxylase. Interestingly, some studies report that Ser31 phosphorylation affects Ser40 phosphorylation, while Ser40 phosphorylation has no effect on Ser31 phosphorylation, a process named hierarchical phosphorylation. Here, we provide a detailed investigation into the signal transduction mechanisms regulating Ser40 and Ser31 phosphorylation in dopaminergic mouse MN9D and Neuro2A cells. We find that cyclic nucleotide signaling drives Ser40 phosphorylation, and that Ser31 phosphorylation is strongly regulated by ERK signaling. Inhibition of ERK1/2 with UO126 or PD98059 reduced Ser31 phosphorylation, but surprisingly had no effect on Ser40 phosphorylation, contradicting a role for Ser31 in the regulation of Ser40. Moreover, to elucidate a possible hierarchical mechanism controlling tyrosine hydroxylase phosphorylation, we introduced tyrosine hydroxylase variants in Neuro2A mouse neuroblastoma cells that mimic either phosphorylated or unphosphorylated serine residues. When we introduced a Ser40Ala tyrosine hydroxylase variant, Ser31 phosphorylation was completely absent. Additionally, neither the tyrosine hydroxylase variant Ser31Asp, nor the variant Ser31Ala had any significant effect on basal Ser40 phosphorylation levels. These results suggest that tyrosine hydroxylase is not controlled by hierarchical phosphorylation in the sense that first Ser31 has to be phosphorylated and subsequently Ser40, but, conversely, that Ser40 phosphorylation is essential for Ser31 phosphorylation. Overall our study suggests that Ser40 is the crucial residue to target so as to modulate tyrosine hydroxylase activity.
Water balance of the Sudanese savannah woodland region

Abstract The annual water balance for 39 grid cells covering the savannah woodland region of Sudan (10–16°N; 21–36°E) was determined and regional maps produced. Long-term (1961–1990) mean monthly climate data, National Forest Inventory data and Harmonized World Soil Database data for arenosols and vertisols, the two dominant soil types in the region, were used. Model validation was performed using daily data from a site in one of the grid cells and inter-annual (1961–1990) variation examined for another grid cell. Rainfall varied from 147 to 732 mm and only exceeded evapotranspiration for 18 of the grid cells, resulting in a small increase in soil moisture and runoff. Evapotranspiration accounted for, on average, 96% of rainfall and there was little difference between soil types. Drainage only occurred from AR soils and for four of the grid cells. Runoff varied from 0 to 89 mm for arenosols and from 0 to 109 mm for vertisols. The study provided useful insights into the spatial variability in water balance components across the region. Editor D. Koutsoyiannis; Associate editor D. Gerten
Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints

Abstract Gene duplication is recognized as a critical process in genome evolution; however, many questions about this process remain unanswered. Although gene duplicability has been observed to differ by duplication mechanism and evolutionary rate, there is so far no broad characterization of its determinants. Many features correlate with this difference in duplicability; however, our ability to exploit these observations to advance our understanding of the role of duplication in evolution is hampered by limitations within existing work. In particular, the existence of methodological differences across studies impedes meaningful comparison. Here, we use consistent definitions of duplicability in the human lineage to explore these associations, allow resolution of the impact of confounding factors, and define the overall relevance of individual features. Using a classifier approach and controlling for the confounding effect of duplicate longevity, we find a subset of gene features important in differentiating genes duplicable by small-scale duplication from those duplicable by whole-genome duplication, revealing critical roles for gene dosage and expression costs in duplicability. We further delve into patterns of functional enrichment and find a lack of constraint on duplicate retention in any context for genes duplicable by small-scale duplication.
Implications for the Dating of Wisconsinan (Weichselian) Late-Glacial Events of Systematic Radiocarbon Age Differences between Terrestrial Plant Macrofossils from a Site in SW Ireland

Abstract AMS radiocarbon dates were obtained from Salix herbacea leaves, Carex seeds, and bulk organic detritus from a lake sediment profile of Wisconsinan (Weichselian) Lateglacial age in SW Ireland. There is a systematic age difference between the dated series from the two types of macrofossils, with ages obtained from Salix herbacea leaves being 900 to 1500 14C years younger than those obtained from Carex seeds. The latter tend to be more in accord with dates from the total organic detritus in the lake sediment, although the bulk organic fraction invariably registered the older ages. Intact survival of the fragile Salix leaves indicates that they are unlikely to have been physically transferred within the sediment matrix and/or otherwise reworked from the surrounding catchment. Hence, these macrofossils are the more likely to be contemporaneous with the time of deposition. However, there is no significant correlation between measured 14C age and depth in the Salix values, which scatter over a range of 700 14C years. In contrast, the age/depth relationship for Carex shows a significant reversal, possibly reflecting the redeposition of these macrofossils, and therefore giving radiocarbon ages that are anomalously old. The data have important implications for the dating of lake sediment sequences by AMS radiocarbon measurement of terrestrial plant macrofossils.
Pharmacokinetics of pimobendan after oral administration to dogs with myxomatous mitral valve disease

Abstract Background Pimobendan is an important therapy for dogs with myxomatous mitral valve disease (MMVD). The pharmacokinetics are reported in healthy dogs but not in dogs with heart disease. Hypothesis/Objectives To determine if dog characteristics such as age, breed, body condition score, ACVIM stage of heart disease or biochemical laboratory value alter the pharmacokinetics of orally administered pimobendan and its metabolite in a cohort of dogs with naturally occurring MMVD. Animals Fifty‐seven client‐owned dogs with MMVD ACVIM Stage B2, C, or D and administered pimobendan to steady state blood concentrations. Methods Prospective, observational study. Samples were collected using a sparse‐sampling protocol at specific intervals after administration of pimobendan. Plasma pimobendan and the active metabolite (O‐desmethyl‐pimobendan, ODMP) concentrations were determined via high‐pressure liquid chromatography and fluorescence detection. Data was analyzed via a population pharmacokinetic approach and nonlinear mixed effects modeling (NLME). Numerous covariates were examined in the NLME model. Results The absorption and elimination half‐lives (t 1/2) were approximately 1.4 and 1 hour for pimobendan and 1.4 and 1.3 hours for ODMP, respectively. Pharmacokinetic parameters were highly variable, especially the values for pimobendan absorption and elimination rate, and absorption rate of ODMP with coefficients of variation of 147.84%, 64.51% and 64.49%, respectively. No covariate evaluated was a significant source of variability. Conclusions and Clinical Importance The pharmacokinetic parameters were highly variable among this group of dogs with MMVD. The variability was not associated with the dog's age, body weight or condition score, stage of heart disease, dose, serum creatinine, or alkaline phosphatase.
The Relational Care Framework: Promoting Continuity or Maintenance of Selfhood in Person-Centered Care

Abstract We argue that contemporary conceptualizations of “persons” have failed to achieve the moral goals of “person-centred care” (PCC, a model of dementia care developed by Tom Kitwood) and that they are detrimental to those receiving care, their families, and practitioners of care. We draw a distinction between personhood and selfhood, pointing out that continuity or maintenance of the latter is what is really at stake in dementia care. We then demonstrate how our conceptualization, which is one that privileges the lived experiences of people with dementia, and understands selfhood as formed relationally in connection with carers and the care environment, best captures Kitwood’s original idea. This conceptualization is also flexible enough to be applicable to the practice of caring for people at different stages of their dementia. Application of this conceptualization into PCC will best promote the well-being of people with dementia, while also encouraging respect and dignity in the care environment.
Caracterização e classificação de solos desenvolvidos de arenitos da formação Aquidauana-MS

The Aquidauana geological formation consists of a set of up to 500 m thick sediments predominantly composed of sandstone with fine to medium grain size, interspersed with sandy conglomerates. In this environment, the topography is one of the main conditioning factors of the formation of different soil types in the landscape. The objective of this study was to characterize and classify soils developed from these sandstones. Four soils profiles along a representative toposequence of gentle slopes were sampled and studied. The profiles were located on the shoulder (P1), backslope (P2), footslope ( P3) and toeslope (P4). The soil profiles were morphologically described and physical and chemical properties of their horizons evaluated. The sand fraction was predominant in all profiles (> 680 g kg-1), with textures ranging from sandy loam (P4) to clay sandy loam. The water pH values ranged from 4.2 to 6.5. The cation exchange capacity values ranged from 1.6 cmolc kg-1(in P4) to 10.3 cmolc kg-1 (in P2), with a predominance of hydrogen ions in P1 and P4, and calcium in profile P2 and P3. The P1 and P4 pedons were dystrophic, whereas in P2 and P3, a high base saturation status evidenced an eutrophic character. Except in P2, the profiles presented low activity clays. In all soil profiles the morphological, physical, chemical and mineralogical properties were conditioned by the parent material and relief, demonstrating the influence of these factors on the pedogenesis.