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Life satisfaction is vital for older adults' well‐being, impacting various life aspects. It is dynamic, necessitating nuanced approaches to capture its trajectories accurately. This study aimed to explore the diverse trajectories and predictors of life satisfaction among older adults in China using longitudinal data from the China Health and Retirement Longitudinal Study. Latent class growth modeling and growth mixture modeling were employed to identify distinct trajectories of life satisfaction. Machine learning (ML) models were developed to predict different trajectories and identify important predictors of different trajectories. Four distinct trajectories of life satisfaction were identified, showcasing nuanced patterns of life satisfaction that changed over time. ML models, especially random forest, effectively predicted these trajectories. Emotional experiences (particularly the frequency of happiness and loneliness), body mass index, and self‐report health emerged as significant predictors of different life satisfaction trajectories. Our finding revealed the importance of focusing on individuals or groups with consistently low life satisfaction and paying more attention to mental and physical health predictors. Our models might guide future targeted preventative treatments. [ABSTRACT FROM AUTHOR]

Background: Trajectories of asthma and allergy in children are heterogeneous and commonly derived from parental report of disease or clinical records. This study combined parental‐reported and register‐based dispensed medication data to characterize childhood trajectories of co‐existing asthma, allergic rhinitis, and eczema. Methods: From a Swedish population‐based birth cohort (N = 5654), survey responses collected at the age of 1, 4.5, 8, and 12 years were linked to dispensed medication register data for the period of 2–13 years. Trajectories were identified with latent class analysis. Statistical metrics and clinical interpretability guided the model selection. Results: Nine distinct trajectories were identified: three asthma‐dominated (early‐onset remitting [n = 189, 3.3%], late‐onset [n = 117, 2.1%], and persistent [n = 149, 2.6%]), two eczema‐dominated (persistent [n = 190, 3.4%] and remitting [n = 432, 7.6%]), one allergic rhinitis‐dominated (late‐onset [n = 259, 4.6%]), two multimorbidity (mid‐childhood asthma and late‐onset allergic rhinitis [n = 144, 2.5%], and persistent eczema and late‐onset allergic rhinitis [n = 90, 1.6%]), and one low‐disease burden trajectory (n = 4084, 72.2%). Differences were seen across the trajectories in the proportion of parental report of disease and dispensed medication as well as by class and quantity of medication dispensed. Conclusion: Combined parental‐reported and dispensed medication data enriches characterization of longitudinal trajectories of asthma and allergy in children by merging subjective experience of disease with healthcare utilization. The identified trajectories were characterized by distinct disease development and prescription patterns suggesting clinically differential morbidity burden. [ABSTRACT FROM AUTHOR]

Aims: The aim of this study was to measure trajectories of craving for methamphetamine during the course of pharmacotherapy trials for methamphetamine use disorder. Design, setting and participants: Craving trajectories were identified using Group‐Based Trajectory Modeling. The association of craving trajectories with drug use trajectories was examined using a dual trajectory model. Association of craving trajectories with other health and social outcomes was also examined. The study used pooled data from five randomized controlled pharmacotherapy trials for methamphetamine use disorder. A total of 866 adults with methamphetamine use disorder participated in randomized controlled pharmacotherapy trials. Measurement: Craving was assessed weekly using the Brief Substance Craving Scale. Drug use was assessed using urine toxicology. Alcohol‐ and drug‐related problems, as well as psychiatric, medical, legal, employment and relationship problems, were measured using the Addiction Severity Index. Findings: A three‐trajectory model with high, medium and low craving trajectories was selected as the most parsimonious model. Craving trajectories were associated with methamphetamine use trajectories in the course of trial; 88.4% of those in the high craving trajectory group had a consistently high frequency of methamphetamine use compared with 18.7% of those in the low craving group. High craving was also associated with less improvement in most other outcomes and higher rate of dropout from treatment. In turn, low craving was associated with a rapidly decreasing frequency of methamphetamine use, greater improvement in most other outcomes and a lower rate of dropout. Participants on modafinil daily and ondansetron 1 mg twice daily were less likely to be in the high craving group compared with those on placebo. Conclusions: Trajectories of methamphetamine craving in the course of clinical trials for methamphetamine use disorder appear to be both highly variable and strongly associated with greater frequency of drug use, other drug‐related outcomes and dropout from trials. Two medications, modafinil daily and ondansetron at a dose of 1 mg two times daily, appear to be associated with greater reduction in craving in the course of treatment compared with placebo. A decrease in methamphetamine craving shows promise as an early indicator of recovery from methamphetamine use disorder. [ABSTRACT FROM AUTHOR]

BACKGROUND: The beet webworm, Loxostege sticticalis, a worldwide pest of many crops, performs a seasonal migration, causing periodic outbreaks in Asia, Europe and North America. Although long‐distance migration is well documented in China, patterns of transboundary migration among China, Russia and Mongolia are largely unknown. We performed a phase analysis of L. sticticalis periodic outbreaks among three countries based on 30 years of historical population data, analyzed the wind systems during migration over boundary regions, and traced the migratory routes in a case study of outbreaks in 2008 by trajectory simulation. RESULTS: Highly synchronized outbreak years of L. sticticalis were observed between China and Mongolia, China and eastern Siberia, China and western Siberia, Mongolia and eastern Siberia, eastern Siberia and western Siberia from 1978 to 2008, indicating possible transboundary migration between these regions. Winds at 300–600 m altitude, where adult migration usually occurs, also showed a high probability of northwestern winds in Haila'er (China), Chita (Russia) and Choybalsan (Mongolia), favoring successful adult migration from these areas to northern and northeastern China. Back trajectory analysis further showed that the first‐generation adults that caused the severe outbreak of second‐generation larvae in 2008 originated from eastern Siberia, eastern Mongolia, and the boundary regions of China–Russia and China–Mongolia. CONCLUSION: Our findings demonstrated that the source of L. sticticalis outbreaks in northern China was closely related to the outbreaks in Siberia and Mongolia via long‐distance transboundary windborne migration. This information will help guide international monitoring and management strategies against this notorious pest. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

It is well known that medication adherence is critical to patient outcomes and can decrease patient mortality. The Pharmacy Quality Alliance (PQA) has recognized and identified medication adherence as an important indicator of medication‐use quality. Hence, there is a need to use the right methods to assess medication adherence. The PQA has endorsed the proportion of days covered (PDC) as the primary method of measuring adherence. Although easy to calculate, the PDC has however several drawbacks as a method of measuring adherence. PDC is a deterministic approach that cannot capture the complexity of a dynamic phenomenon. Group‐based trajectory modeling (GBTM) is increasingly proposed as an alternative to capture heterogeneity in medication adherence. The main goal of this paper is to demonstrate, through a simulation study, the ability of GBTM to capture treatment adherence when compared to its deterministic PDC analogue and to the nonparametric longitudinal K‐means. A time‐varying treatment was generated as a quadratic function of time, baseline, and time‐varying covariates. Three trajectory models are considered combining a cat's cradle effect, and a rainbow effect. The performance of GBTM was compared to the PDC and longitudinal K‐means using the absolute bias, the variance, the c‐statistics, the relative bias, and the relative variance. For all explored scenarios, we find that GBTM performed better in capturing different patterns of medication adherence with lower relative bias and variance even under model misspecification than PDC and longitudinal K‐means. [ABSTRACT FROM AUTHOR]

Aim: The aim of this study was to identify factors affecting overweight growth development using extended body mass index (BMI) data combined with birth and maternal records from Finnish national registries. Methods: The longitudinal data consist of growth measurements of 7372 from six birth cohorts in Finland: 1974 (n = 1109), 1981 (n = 983), 1991 (n = 607), 1994–1995 (n = 829), 2001 (n = 821), and 2003–2004 (n = 3023). Anthropometric data were collected from birth to age 15 years from the health records. Pregnancy health data were included for the four most recent birth cohorts (n = 2810). A statistical method called trajectory analysis was used to identify different BMI development trajectories. Factors associated with abnormal growth tracks were analysed using logistic regression models. Results: High pre‐pregnancy BMI, gestational diabetes mellitus, maternal smoking, and greater gestational weight gain than the Institute of Medicine (United States) recommendations were associated with the overweight growth track. Two of the trajectories didn't seem to follow the normal growth pattern: overweight growth track appeared to lead to overweight, while low birth BMI track showed accelerating growth after the adiposity rebound point of BMI growth. Conclusion: These findings suggest that maternal overweight before pregnancy, excessive gestational weight gain, gestational diabetes mellitus, and smoking could potentially be associated with the risk of obesity in children. [ABSTRACT FROM AUTHOR]

The southwest vortices (SWVs) are a unique type of mesoscale vortex that frequently induce torrential rainfall in China. In this study, we focused a long‐lived quasi‐stationary SWV, which was the primary system for producing an extremely heavy rainstorm within/around Sichuan (the maximum hourly precipitation was ~103.8 mm) in Mid July 2021. After reproduced the SWV's formation by using Weather Research and Forecasting model, we conducted trajectory analyses and topography sensitivity simulations to understand the effects of complicated topography on the vortex's formation. It is found that, the regions south and southwest of the SWV acted as the most important source regions for the air clusters that formed the SWV (proportion ≥ 65%), and the air clusters originated from the upper layer contributed the most (≥60%). Of these, the air clusters sourced from the upper layer southwest and south of the SWV played the most important role in the SWV's formation, as their increase in cyclonic vorticity and their contributions to trajectory number and vorticity were all much larger than those of the others. Sensitivity simulations indicated that, detailed topography features around the Sichuan Basin were crucial in determining the structure, intensity and precipitation of the SWV, whereas, the topography features were not a decisive factor for the SWV's formation. In summary, our findings are useful to enrich the current understanding of the SWVs' formation, which would be helpful to improve the related forecasts. [ABSTRACT FROM AUTHOR]

The grid inhomogeneous solvation theory (GIST) method requires the often time-consuming calculation of water-water and water-solute energy on a grid. Previous efforts to speed up this calculation include using OpenMP, GPUs, and particle mesh Ewald. This article details how the speed of this calculation can be increased by parallelizing it with MPI, where trajectory frames are divided among multiple processors. This requires very little communication between individual processes during trajectory processing, meaning the calculation scales well to large processor counts. This article also details how the entropy calculation, which must happen after trajectory processing since it requires information from all trajectory frames, is parallelized via MPI. This parallelized GIST method has been implemented in the freely-available CPPTRAJ analysis software. [ABSTRACT FROM AUTHOR]

The rapid increase in computational power with the latest supercomputers has enabled atomistic molecular dynamics (MDs) simulations of biomolecules in biological membrane, cytoplasm, and other cellular environments. These environments often contain a million or more atoms to be simulated simultaneously. Therefore, their trajectory analyses involve heavy computations that can become a bottleneck in the computational studies. Spatial decomposition analysis (SPANA) is a set of analysis tools in the Generalized‐Ensemble Simulation System (GENESIS) software package that can carry out MD trajectory analyses of large‐scale biological simulations using multiple CPU cores in parallel. SPANA applies the spatial decomposition of a large biological system to distribute structural and dynamical analyses into individual CPU cores, which reduces the computational time and the memory size, significantly. SPANA opens new possibilities for detailed atomistic analyses of biomacromolecules as well as solvent water molecules, ions, and metabolites in MD simulation trajectories of very large biological systems containing more than millions of atoms in cellular environments. [ABSTRACT FROM AUTHOR]

During 26–27 June 2022, mainly influenced by three mesoscale vortices, central‐eastern China (particularly for Henan and Shandong) experiences the first widespread torrential rainfall event of the 2022 flood season (maximum 24‐hr accumulated precipitation is ∼380.9 mm), resulting in severe social impacts. The three mesoscale vortices form and sustain under favorable background conditions, mainly including a strong upper‐level divergence, an intense middle‐level warm advection, and a powerful lower‐level convergence associated with a low‐level jet. Among the vortices, the vortex which forms over Shandong, lasts for ∼9 hr, and makes a much larger contribution than the other vortices to the accumulated precipitation, is defined as the primary vortex. More than a half of the hourly precipitation peaks in this event appear in the life span of the primary vortex, which is closely related to the variations of the vortex in its cyclonic‐vorticity and vertical extent. Backward trajectory analysis indicates that air particles originating from the lower troposphere southwest of the primary vortex contribute the most to its formation (∼82.7%). These air particles mainly experience a notable increase in their cyclonic‐vorticity due to convergence‐related vertical stretching, which directly renders the formation of primary vortex. During the whole life span of the primary vortex, convergence‐related vertical stretching is the most favorable factor for its development/sustainment, and the convection‐related vertical transport of cyclonic vorticity ranks second; whereas, the horizontal transport is the most detrimental factor. Moisture budget shows that Southeast China is the most important moisture source for this event (accounting for ∼48.9%). Plain Language Summary: Due to global warming, extreme weather and climate events occur with a higher frequency and a stronger intensity in China. Of these, a widespread heavy rainfall occurs in central‐eastern China during 26–27 June 2022, which causes severe impacts on society. Our attention is drawn to understand how the extreme rainstorm forms and where the main moisture sources are located. For this, we analyze this event by using automatic station data and reanalysis data and discover that three mesoscale vortices are the primary reason for the heavy rainfall. Among the vortices, the one with the longest life span contributes the most to the accumulated precipitation. The strong convergence in the lower troposphere dominates the formation/maintenance of the vortex. Southeast China continuously supplies moisture for the rainfall (∼48.9% in contribution). This research is helpful to enhance the understanding of this type of heavy rainfall event. Key Points: Affected by three mesoscale vortices, central‐eastern China experiences torrential rainfall, with a rainfall peak of ∼380.9 mm observedThe primary vortex, which is produced by vertical stretching, is directly related to more than a half of the hourly rainfall peaksSoutheast China provides ∼48.9% of the moisture for the rainfall, which is mainly transported by the Southwesterly/southerly wind [ABSTRACT FROM AUTHOR]

The Upper Jurassic-Lower Cretaceous sedimentary rocks in the Eastern Barents Sea Basin are up to 2 km thick and represent one of the least studied Arctic intervals. Here, for the first time, we present a detailed analysis of 43,000 km of 2D seismic profiles, as well as well-log and core data from 24 offshore wells with the aim to create a comprehensive sequence stratigraphic framework that can be integrated with the rest of the basin. Results show that (1) seven third-order sequences and five types of clinoforms can be identified based on integrated seismic and well data. The age of each sequence was established based on published biostratigraphic investigations along with new dinocyst interpretations included in this study; (2) the deep marine basin was gradually filled with sediments coming from north, east and south as a response to HALIP, Canada Basin opening and Cimmerian uplift of Novaya Zemlya, and was preserved only in the southwestern part of the Barents Sea Basin at the end of Early Cretaceous and (3) both Eastern Barents Sea and West Siberia Basin share similarities in sedimentary environments and tectonic setting, though the spatial distribution of clastic reservoirs in Upper Jurassic and Lower Cretaceous mega-sequence heavily depends on the source areas that require more provenance focused research. The results presented here can be used in further regional exploration in the area and to better understand the geodynamic evolution of the Greater Barents Sea Basin. [ABSTRACT FROM AUTHOR]

Establishing the path or trajectory of a fired bullet is an often recurring part of shooting incident reconstruction. The current study describes how gravitational pull causes a systemic error on the vertical component of a trajectory reconstruction. Bullet drop, drop angle, and vertical offset are explained and calculated for 10 different handgun/ammunition combinations over a range of distances up to 100 m. The presented results are intended to provide forensic firearm examiners with a reference frame for the magnitude of error introduced on handgun bullet trajectory reconstructions over distance. Threshold values of 20 and 30 m are proposed as conservative distances up to where bullet trajectories can be modeled as straight lines with subsonic/transonic handgun bullets and with supersonic handgun bullets respectively. Both the bullet drop and vertical offset will be below 5 cm at these distances for those categories. The drop angle will be below 0.3°. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to identify and describe trajectories of change in distress among highly challenging patients who had received long and intensive psychoanalytic psychotherapy. Methods: The longitudinal version of the K‐means algorithm was applied to the outcome measures data of 74 patients treated in four public mental health centers. The patients were measured five times at 6‐month intervals for three outcome measures. Results: For the OQ45 and Symptom Checklist‐90, one trajectory was marked by a lower initial distress level. In this trajectory, the improvement occurred in the first half of the measurements, with a plateau thereafter. A second trajectory was characterized by higher initial severity and an improvement, mainly in the second part of the measurements. For the Beck Depression Inventory, one trajectory was marked by lower initial distress. In this group, the improvement occurred throughout the entire period. The remaining patients were characterized by higher initial distress and a decreased level of distress in the last part of treatment. They began to improve only during the third year of therapy. Conclusion: The response to treatment is not uniform in long‐term treatment for highly challenging patients. A significant number of patients require a longer period of therapy to ignite improvement. [ABSTRACT FROM AUTHOR]

Warm conveyor belts (WCBs) are rapidly ascending air streams associated with extratropical cyclones. WCBs exert a substantial influence on the evolution of the large‐scale midlatitude flow and have previously been related to increased forecast uncertainty in case studies. This study provides a first systematic investigation of the role of WCBs for errors in medium‐range ensemble forecasts in the Atlantic–European region. The study is enabled through a unique data set, allowing for a Lagrangian detection of WCBs in three years of operational ensemble forecasts from the European Centre for Medium‐Range Weather Forecasts. By analysing the relationship between commonly used error metrics of variables that characterise the large‐scale flow and WCBs, the study aims to shed light on the question of the extent to which WCBs act as a source of forecast errors and as an amplifier of pre‐existing errors in a state‐of‐the‐art global operational numerical weather prediction model. We show that forecasts with high WCB activity are on average characterised by an amplified Rossby‐wave pattern and anticyclonic flow anomalies downstream. We find that the forecast skill is generally reduced when the WCB activity is high, and that WCB activity is particularly increased when the error growth is largest. To establish a causal relationship, we employ two composite approaches. The first focuses on the time of largest error growth and the second calculates normalised forecast error fields centered on WCB objects. Both approaches yield a consistent picture: anomalously high errors are initially associated with misrepresentations of an upstream trough. In regions of WCB ascent and outflow, the errors grow rapidly in terms of magnitude and scale and are projected onto the upper‐level large‐scale circulation. We also find indications that WCBs can cause errors even when the upstream flow is well represented. Notwithstanding, evidence is robust for WCBs acting as an amplifier of forecast uncertainty. [ABSTRACT FROM AUTHOR]

Based on potential vorticity (PV) thinking, northeast China cold vortex (NCCV) corresponds to an upper‐level high PV anomaly from stratospheric PV downward intrusion. Within a vortex, latent heating from precipitation would produce a vertical dipole of PV anomalies that would affect structures and evolution of the vortex. In this paper, three‐dimensional structures and evolution of NCCV and, effects of latent heating from precipitation along bent‐back, cold and warm fronts on them are investigated based on convection‐allowing simulations for an intense NCCV case during 8–17 June 2012. Trajectory analysis shows that the negative upper‐level diabatic PV anomaly from bent‐back frontal precipitation, near the vortex center, is the dominant contributor to erosion of high PV in the vortex core region as it is advected in, leading to the weakening of the vortex. The negative PV anomalies along the cold and warm fronts, at the east‐to‐southeast side of the vortex, are mostly advected downstream away from the NCCV. In the middle troposphere, positive PV anomalies are primarily generated along fronts and the accumulated positive PV anomalies filling the vortex region help to reinforce the low‐level cyclonic circulation. The lower‐level PV is affected by surface heating and cooling through their effects on static stability, but such effects are periodic and create mainly diurnal variations. The NCCV eventually decays as the upper‐level vortex weakens due to significant PV erosion. Plain Language Summary: Northeast China cold vortex (NCCV) is responsible for much of the warm season precipitation in northeast China. Based on convection‐allowing simulations of a characteristic case, the distribution and effects of latent heating release from precipitation in bent‐back, cold and warm frontal regions on the structures and evolution of potential vorticity (PV) within the NCCV are studied. Negative upper‐level PV anomalies generated at the bent‐back front are primarily responsible for the filamentation and erosion of high PV in the core of NCCV, leading to the weakening of the vortex. At middle‐to‐low levels, positive PV anomalies generated reinforce the low‐level circulations. However, the lower‐level PV exhibits a significant diurnal cycle, which is mainly affected by the surface heating and cooling through reducing static stability at daytime and increasing static stability during night. The overall system eventually decays as the upper‐level vortex weakens. Key Points: Precipitation in northeast China cold vortex produces negative upper‐level potential vorticity (PV) anomaly that weakens the upper level cold vortexNegative PV anomaly produced at the bent‐back front is the dominant contributor to the erosion of upper‐level high PV in the vortex centerLower‐level vortex is enhanced by positive PV anomaly from precipitation, and the PV has diurnal variations due to surface heating/cooling [ABSTRACT FROM AUTHOR]

The authors aimed to identify determinants of the clinical course of herpes zoster and immunological responses, focusing on pain trajectories. This prospective community‐based cohort study involved the analysis of responses to a valid pain survey provided by 375 patients diagnosed with herpes zoster based on clinical symptoms and virus identification by polymerase chain reaction. The authors analyzed most patients for humoral/cell‐mediated immune response against varicella‐zoster virus at the onset and 3 months post‐onset. Six months post‐initial visit, patients self‐reported pain on a scale of 0 (no pain) to 5 (extremely strong pain) at up to 18 time points. Moreover, the pain trajectories were traced using group‐based trajectory modeling. Subsequently, the authors used analysis of covariance to explore predictors and the humoral/cell‐mediated immune response according to the pain trajectories. In addition, humoral/cell‐mediated immune responses were assessed among each trajectory using paired t tests. Amon the five identified trajectories, two were isolated that particularly developed postherpetic neuralgia, with or without severe acute pain. Cancer therapy and corticosteroid use before herpes zoster onset specifically predicted postherpetic neuralgia without severe acute pain. In contrast, prescription of nonsteroidal anti‐inflammatory drugs was uniquely associated with postherpetic neuralgia accompanied by severe acute pain. The aforementioned trajectories with postherpetic neuralgia showed increased antibodies and decreased cell‐mediated immunity compared with those without postherpetic neuralgia. The authors could successfully distinguish between postherpetic neuralgia trajectories with and without severe acute pain. The identified key predictors and immunological responses against varicella‐herpes zoster contribute further evidence to our understanding of the clinical features of herpes zoster and postherpetic neuralgia. [ABSTRACT FROM AUTHOR]

The composition of ecological assemblages has changed rapidly over the past century. Compositional reorganization rates are high relative to rates of alpha diversity change, creating an urgent need to understand how this compositional reorganization is progressing. We developed a quantitative framework for comparing temporal trajectories of compositional reorganization and applied it to two long‐term bird and marine fish datasets. We then evaluated how the number and magnitude of short‐term changes relate to overall rates of change. We found varied trajectories of turnover across birds and fish, with linear directional change predominating in birds and non‐directional change more common in fish. The number of changes away from the baseline was a more consistent correlate of the overall rate of change than the magnitude of such changes, but large unreversed changes were found in both fish and birds, as were time series with accelerating compositional change. Compositional reorganization is progressing through a complex mix of temporal trajectories, including both threshold‐like behaviour and the accumulation of repeated, linear change. [ABSTRACT FROM AUTHOR]

Long‐term monitoring programs are fundamental to detect changes in ecosystem health and understand ecological processes. In the current context of increasing anthropogenic threats on marine ecosystems, understanding the dynamics and response of communities becomes essential. We used data collected over 14 years in the REBENT benthic coastal invertebrates monitoring program, at a regional scale in the North‐East Atlantic, covering a total of 26 sites and 979 taxa. Four distinct habitats were studied: two biogenic habitats associated with foundation species in the intertidal and subtidal zones and two bare sedimentary habitats in the same respective tidal zones. We used community trajectory analysis (CTA), a statistical approach that allows for quantitative measures and comparisons of temporal trajectories of ecosystems. We compared observed community trajectories to trajectories simulated under a non‐directional null model in order to better understand the dynamics of the communities, their potential drivers, and the role of the studied habitats in these dynamics. Despite strong differences in the community compositions between sites and habitats, the communities followed non‐directional dynamics during the 14 years monitored, which suggested stability at the regional scale. However, the shape, size, and direction of the trajectories of benthic communities were more similar within than among habitats, also suggesting the influence of the nature of the habitat on community dynamics. Results showed a higher variability in community composition the first years of the monitoring in the intertidal bare habitat and confirmed the role of biogenic habitats in maintaining temporal stability. They also highlighted the need to apprehend the role of transient and rare species and the scale of observation in temporal beta diversity analyses. Finally, our study confirmed the usefulness of CTA to link observed trajectory patterns to fundamental ecological processes. [ABSTRACT FROM AUTHOR]

Understanding how sedimentary rocks represent time is one of the significant challenges in sedimentology. Sedimentation rates retrieved from vertical sections are strongly timescale dependent, which means that we cannot use empirical rate data derived from vertical sections in modern environments to interpret the temporal structure of ancient sedimentary deposits. We use the Lower to Middle Campanian Blackhawk Formation deposits in eastern Utah and western Colorado as a natural laboratory to test a source‐to‐sink methodology circumventing this timescale dependence by relating modern progradation rates to the deltaic shoreline progradation of ancient siliciclastic rocks. Our objective is to quantify how much time is needed to account for the observed cumulative deltaic shoreline progradation recorded by the shallow‐marine sandstone bodies of the Blackhawk Formation in terms of progradation rates derived from comparable modern deltaic systems. By making the simplifying assumption that the Blackhawk Formation rocks were deposited along a linear coastline that only grew by aggradation and progradation, it is possible to argue that the stratigraphic completeness of two‐dimensional dip‐oriented stratigraphic cross‐sections through these deposits should be high. Furthermore, we hypothesise that delta progradation estimates capture a significant portion of the biostratigraphically and radiometrically constrained duration of the succession. By comparing the recorded progradation with modern progradation rates, we estimate that we need ca. 20% (median value, with minimum and maximum estimates of 2% and 300%) of the time available from biostratigraphic and radiometric dating to account for the progradation recorded by the sedimentary deposits. This indicates that long‐term progradation rates averaged over the entire duration of the Blackhawk Formation were only a factor of five times slower than the modern progradation rates derived from observations over periods that are five to six orders of magnitude shorter. We conclude that a significant amount of time is represented by prograding deltaic shoreline deposits and that by considering the cumulative shoreline progradation, we could limit the effects of timescale dependence on the rate estimates used in our analysis. [ABSTRACT FROM AUTHOR]

Aims: To determine diabetic retinopathy (DR) prevalence, incidence, and whether distinct trajectories are associated with DR‐complicating Type 2 diabetes. Methods: Retinal photographs from Fremantle Diabetes Study Phase II (FDS2) participants with Type 2 diabetes recruited in 2008–2011 and who attended biennial assessments for up to 6 years were graded as no DR, mild non‐proliferative DR (NPDR), moderate NPDR or severe NPDR/proliferative DR. Baseline DR prevalence, and the cumulative incidence of moderate NPDR or worse in those without DR at baseline, were calculated. Group‐based DR trajectory modelling was performed. Logistic regression determined independent associates of incident moderate NPDR or worse and trajectory group membership. Results: Of 1521 participants (mean age 65.6 years, 52.1% males, median diabetes duration 9.0 years; 98% of all FDS2 participants with Type 2 diabetes) with gradable baseline photographs, 563 (37.0%) had DR. During a median 6.1 years of follow‐up, 23 (3.2%) without baseline DR developed at least moderate NPDR (crude incidence 6.1/1000 person‐years) with HbA1c the sole independent predictor (odds ratio [95% CI]: 1.62 [1.30–2.02] per 1% [11 mmol/mol] increase). Trajectory analysis showed two distinct groups, those with baseline/persistent DR (20%) and those remaining DR free (80%). Longer diabetes duration, insulin use, higher mean HbA1c, higher mean systolic blood pressure and higher mean urinary albumin: creatinine ratio all increased the odds (p ≤ 0.014) of being in the persistent DR trajectory group. Conclusions: The low incidence of at least moderate NPDR reflects the trajectory analysis. The currently recommended biennial retinal screening frequency for individuals without DR could potentially be extended. [ABSTRACT FROM AUTHOR]

The growing trend of agricultural abandonment requires an understanding of the development of secondary forests on old fields in the context of restoration. However, few studies examine the regeneration trajectories of functional composition and functional diversity in afrotropical secondary forests. We tested how functional composition, diversity, and aboveground biomass (AGB) change with age and determined restoration success for a secondary forest restored through assisted natural regeneration in Uganda. We assessed the influence of distance to forests on regeneration. We sampled trees in 63 plots (2000 m2 each) in the secondary forest (16–22‐year old) and five plots in an old‐growth forest in 2011, 2014 and 2017. We computed functional composition (community‐weighted means—CWM) and diversity using categorical (habitat type, dispersal mode, fruit size, and successional group) and continuous traits (wood density and maximum height) of the species and calculated AGB. The secondary forest showed dissimilar trajectories of functional composition, diversity, and AGB. After 16–22 years, the secondary forest had not yet reached equivalent values of most attributes of functional composition, diversity and AGB in the old‐growth forest. The distance to forests had a negative effect on CWM of forest‐dependent species, nonpioneer light demanders, and functional divergence and a positive effect on CWM of pioneer species. We show that assisted natural regeneration can enhance the functional composition, functional diversity, and AGB of degraded forests and that continued monitoring is needed to attain full recovery. In planning passive restoration, sites closer to existing forests should be prioritized in order to achieve faster recovery. [ABSTRACT FROM AUTHOR]

The stochastically perturbed parametrisation tendency (SPPT) scheme is a well‐established technique in ensemble forecasting to address model uncertainty by introducing perturbations into the tendencies provided by the physics parametrisations. The magnitude of the perturbations scales with the local net parametrisation tendency, resulting in large perturbations where diabatic processes are active. Rapidly ascending air streams, such as warm conveyor belts (WCBs) and organized tropical convection, are often driven by cloud diabatic processes and are therefore prone to such perturbations. This study investigates the effects of SPPT and initial condition perturbations on rapidly ascending air streams by computing trajectories in sensitivity experiments with the European Centre for Medium‐Range Weather Forecasts (ECMWF) ensemble prediction system, which are set up to disentangle the effects of initial conditions and physics perturbations. The results demonstrate that SPPT systematically increases the frequency of rapidly ascending air streams. The effect is observed globally, but is enhanced in regions where the latent heating along the trajectories is larger. Despite the frequency changes, there are only minor modifications to the physical properties of the trajectories due to SPPT. In contrast to SPPT, initial condition perturbations do not affect WCBs and tropical convection systematically. An Eulerian perspective on vertical velocities reveals that SPPT increases the frequency of strong upward motions compared with experiments with unperturbed model physics. Consistent with the altered vertical motions, precipitation rates are also affected by the model physics perturbations. The unperturbed control member shows the same characteristics as the experiments without SPPT regarding rapidly ascending air streams. We make use of this to corroborate the findings from the sensitivity experiments by analyzing the differences between perturbed and unperturbed members in operational ensemble forecasts of ECMWF. Finally, we give an explanation of how symmetric, zero‐mean perturbations can lead to a unidirectional response when applied in a nonlinear system. [ABSTRACT FROM AUTHOR]

Objective: To examine the hypothesis that PTSD with delayed expression in some cases occurs without subthreshold PTSD symptoms above background levels bridging the gap between the traumatic exposure(s) and the clinical diagnosis. Methods: We performed systematic searches of peer‐reviewed papers in English referenced in Pubmed, Embase, or PsycINFO and ascertained 34 prospective studies of PTSD symptom trajectories identified by latent class growth statistical modeling. Studies with delayed and low‐stable trajectories provided appropriate data for this study. We computed the difference between the delayed trajectory PTSD symptom sumscore and the low‐stable PTSD sumscore at the observed points in time after the traumatic event(s). Results: In 29 study populations, the latent class growth analyses displayed delayed trajectories, and in these, we identified 110 data points (% PTSD sumscore difference/months since traumatic exposure). The median PTSD symptom sumscore was 25% higher during the initial 6 months among individuals in the delayed trajectory compared to those in low‐stable trajectory. From this level, the difference widened and reached a plateau of 40–50% higher. The variation was large, and the baseline participation rate and loss to follow‐up were exceeding 25% in the majority of the studies. Heterogeneity of populations, measures, and analyses precluded formal meta‐analysis. Conclusion: Delayed PTSD is preceded by PTSD symptoms during the first year in most cases. Still, few individuals may experience an asymptomatic delay. The results underpin the rationale for monitoring PTSD symptoms and may inform forensic assessments in that delayed PTSD without symptoms bridging the traumatic event is rare. [ABSTRACT FROM AUTHOR]

Objectives: To elaborately decipher the mouse and human bladders at single‐cell levels. Materials and Methods: We collected more than 50,000 cells from multiple datasets and created, up to date, the largest integrated bladder datasets. Pseudotime trajectory of urothelium and interstitial cells, as well as dynamic cell‐cell interactions, was investigated. Biological activity scores and different roles of signaling pathways between certain cell clusters were also identified. Results: The glucose score was significantly high in most urothelial cells, while the score of H3 acetylation was roughly equally distributed across all cell types. Several genes via a pseudotime pattern in mouse (Car3, Dkk2, Tnc, etc.) and human (FBLN1, S100A10, etc.) were discovered. S100A6, TMSB4X, and typical uroplakin genes seemed as shared pseudotime genes for urothelial cells in both human and mouse datasets. In combinational mouse (n = 16,688) and human (n = 22,080) bladders, we verified 1,330 and 1,449 interactive ligand‐receptor pairs, respectively. The distinct incoming and outgoing signaling was significantly associated with specific cell types. Collagen was the strongest signal from fibroblasts to urothelial basal cells in mouse, while laminin pathway for urothelial basal cells to smooth muscle cells (SMCs) in human. Fibronectin 1 pathway was intensely sent by myofibroblasts, received by urothelial cells, and almost exclusively mediated by SMCs in mouse bladder. Interestingly, the cell cluster of SMCs 2 was the dominant sender and mediator for Notch signaling in the human bladder, while SMCs 1 was not. The expression of integrin superfamily (the most common communicative pairs) was depicted, and their co‐expression patterns were located in certain cell types (eg, Itgb1 and Itgb4 in mouse and human basal cells). Conclusions: This study provides a complete interpretation of the normal bladder at single‐cell levels, offering an in‐depth resource and foundation for future research. [ABSTRACT FROM AUTHOR]

We present CHAMPION (Chalmers hierarchical atomic, molecular, polymeric, and ionic analysis toolkit): a software developed to automatically detect time‐dependent bonds between atoms based on their dynamics, classify the local graph topology around them, and analyze the physicochemical properties of these topologies by statistical physics. In stark contrast to methodologies where bonds are detected based on static conditions such as cut‐off distances, CHAMPION considers pairs of atoms to be bound only if they move together and act as a bound pair over time. Furthermore, the time‐dependent global bond graph is possible to split into dynamically shifting connected components or subgraphs around a certain chemical motif and thereby allow the physicochemical properties of each such topology to be analyzed by statistical physics. Applicable to condensed matter and liquids in general, and electrolytes in particular, this allows both quantitative and qualitative descriptions of local structure, as well as dynamical processes such as speciation and diffusion. We present here a detailed overview of CHAMPION, including its underlying methodology, implementation, and capabilities. [ABSTRACT FROM AUTHOR]

Background: Gallbladder cancer (GC) is a malignant disease characterized with highly cellular heterogeneity and poor prognosis. Determining the intratumoral heterogeneity and microenvironment (TME) can provide novel therapeutic strategies for GC. Methods: We performed the single‐cell RNA sequencing on the primary and lymph node metastatic gallbladder tumors and the adjacent normal tissues of five patients. The transcriptomic atlas and ligand–receptor‐based intercellular communication networks of the single cells were characterized. Results: The transcriptomic landscape of 24,887 single cells was obtained and characterized as 10 cellular clusters, including epithelial, neuroendocrine tumor cells, T&NK cells, B cells, RGS5+ fibroblasts, POSTN+ fibroblasts, PDGFRA+ fibroblasts, endothelial, myeloid cells, and mast cells. Different types of GC harbored distinct epithelial tumor subpopulations, and squamous cell carcinoma could be differentiated from adenocarcinoma cells. Abundant immune cells infiltrated into adenocarcinoma and squamous cell carcinoma, rather than neuroendocrine neoplasms, which showed significant enrichment of stromal cells. CD4+/FOXP3+ T‐reg and CD4+/CXCL13+ T helper cells with higher exhausting biomarkers, as well as a dynamic lineage transition of tumor‐associated macrophages from CCL20hi/CD163lo, CCL20lo/CD163hi to APOE+, were identified in GC tissues, suggesting the immunosuppressive and tumor‐promoting status of immune cells in TME. Two distinct endothelial cells (KDR+ and ACKR1+), which were involved in angiogenesis and lymphangiogenesis, showed remarkable ligand–receptor interactions with primary GC cells and macrophages in gallbladder tumors. Conclusions: This study reveals a widespread reprogramming across multiple cell populations in GC progression, dissects the cellular heterogeneity and interactions in gallbladder TME, and provides potential therapeutic targets for GC. [ABSTRACT FROM AUTHOR]

Many studies have validated cartilage thickness as a biomarker for knee osteoarthritis (OA); however, few studies investigate beyond cross‐sectional observations or comparisons across two timepoints. By characterizing the trajectory of cartilage thickness changes over 8 years in healthy individuals from the OA initiative data set, this study discovers associations between the dynamics of cartilage changes and OA incidence. A fully automated cartilage segmentation and thickness measurement method were developed and validated against manual measurements: mean absolute error = 0.11–0.14 mm (n = 4129 knees) and automatic reproducibility = 0.04–0.07 mm (n = 316 knees). The mean thickness for the medial and lateral tibia (MT, LT), central weight‐bearing medial and lateral femur (cMF, cLF), and patella (P) cartilage compartments were quantified for 1453 knees at seven timepoints. Trajectory subgroups were defined per cartilage compartment such as stable, thinning to thickening, accelerated thickening, plateaued thickening, thickening to thinning, accelerated thinning, or plateaued thinning. For tibiofemoral compartments, the stable (22%–36%) and plateaued thinning (22%–37%) trajectories were the most common, with an average initial velocity (μm/month), acceleration (μm/month2) for the plateaued thinning trajectories LT: −2.66, 0.0326; MT: −2.49, 0.0365; cMF: −3.51, 0.0509; and cLF: −2.68, 0.041. In the patella compartment, the plateaued thinning (35%) and thickening to thinning (24%) trajectories were the most common, with an average initial velocity, acceleration for each −4.17, 0.0424; 1.95, −0.0835. Knees with nonstable trajectories had higher adjusted odds of OA incidence than stable trajectories: accelerated thickening, accelerated thinning, and plateaued thinning trajectories of the MT had adjusted odds ratio (OR) of 18.9, 5.48, and 1.47, respectively; in the cMF, adjusted OR of 8.55, 10.1, and 2.61, respectively. [ABSTRACT FROM AUTHOR]

In the last decade, political and economic constraints have prompted many students to leave Iran. While Europe and North America have traditionally been Iranians' preferred destinations, selective entry procedures make direct access increasingly difficult. This article focuses on Iranian students' stepwise migration strategies to reach Western countries through Turkey. My research indicates that stepwise migration theory can be applied to international students, as visa restrictions and the selectivity of Western universities transformed Turkey into a stepwise migration corridor. The article also considers the advantages of the trajectory analysis method I developed. Trajectory analysis is a longitudinal and mobile method whereby migrants are followed over time and space. It enables the researcher to compare data about migrants who move stepwise and those who move crosswise by staying in Turkey. The research is based on interviews with 36 Iranians in Turkey, Europe, and the United States, of whom 15 moved in stepwise fashion. An important outcome is that students' academic capital is a crucial indicator for their ability to migrate to the West. This finding points to path dependency in students' trajectories along a hierarchy of destinations: not only in geographical terms but also in terms of the perceived level of educational institutions' reputations. [ABSTRACT FROM AUTHOR]

Summary: The performance of biomolecular molecular dynamics simulations has steadily increased on modern high‐performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations is becoming a bottleneck. To close this gap, we studied the performance of trajectory analysis with message passing interface (MPI) parallelization and the Python MDAnalysis library on three different Extreme Science and Engineering Discovery Environment (XSEDE) supercomputers where trajectories were read from a Lustre parallel file system. Strong scaling performance was impeded by stragglers, MPI processes that were slower than the typical process. Stragglers were less prevalent for compute‐bound workloads, thus pointing to file reading as a bottleneck for scaling. However, a more complicated picture emerged in which both the computation and the data ingestion exhibited close to ideal strong scaling behavior whereas stragglers were primarily caused by either large MPI communication costs or long times to open the single shared trajectory file. We improved overall strong scaling performance by either subfiling (splitting the trajectory into separate files) or MPI‐IO with parallel HDF5 trajectory files. The parallel HDF5 approach resulted in near ideal strong scaling on up to 384 cores (16 nodes), thus reducing trajectory analysis times by two orders of magnitude compared with the serial approach. [ABSTRACT FROM AUTHOR]

Motivated by the ongoing debates about the relative contribution of specific North African dust sources to the transatlantic dust transport to the Amazon Basin, the current study integrates a suite of satellite observations into a novel trajectory analysis framework to investigate dust transport from the leading two North African dust sources, namely, the Bodélé depression and El Djouf. In particular, this approach provides observation‐constrained quantification of the dust's dry and wet deposition along its transport pathways and is validated against multiple satellite observations. The current large ensemble trajectory simulations identify favorable transport pathways from the El Djouf across the Atlantic Ocean with respect to seasonal rain belts. The limited potential for long‐range transport of dust from the Bodélé depression is attributed to the currently identified extensive near‐source dust removal primarily by dry and wet deposition during boreal winter and summer, respectively. Plain Language Summary: North African deserts have been reported to export ~200 million tons of dust per year to the tropical Atlantic Ocean, degrading air quality over the Caribbean Islands in boreal summer and supplying nutrients to fertilize the Amazon Rainforest in boreal winter and spring through transatlantic dust transport. It has been assumed that the Bodélé depression is the main contributor to this transatlantic dust transport and Amazonian dust fertilization in boreal winter. However, these claims have not been supported by geochemical analysis. Here, we integrate a suite of satellite observations into a novel trajectory analysis framework to investigate dust transport from the leading two North African dust sources, namely, the Bodélé depression and El Djouf, and provide the first ever observation‐constrained quantification of the dust's dry and wet deposition along its transport pathways. The approach yields the novel observational finding that the El Djouf is the preferred source of intercontinental transport across the Atlantic Ocean rather than the Bodélé depression, bridging the geochemical impact of North African minerals on the Amazon Basin to the specific dust origin. Key Points: The current trajectory simulations quantify observation‐derived dust deposition and capture the observed three‐dimensional dust distributionEl Djouf is the preferred source of the transatlantic dust transport, due to favorable transport pathways with respect to seasonal rain beltsExtensive near‐source dust deposition supports the observed limited potential for long‐range transport of dust from the Bodélé depression [ABSTRACT FROM AUTHOR]

We developed a seismic geomorphology‐based procedure to enhance traditional trajectory analysis with the ability to visualize and quantify lateral variability along carbonate prograding‐margin types (ramps and rimmed shelves) in 3D and 4D. This quantitative approach analysed the shelf break geometric evolution of the Oligo‐Miocene carbonate clinoform system in the Browse Basin and delineated the feedback between antecedent topography and carbonate system response as controlling factor on shelf break rugosity. Our geometrical analysis identified a systematic shift in the large‐scale average shelf break strike direction over a transect of 10 km from 62° to 55° in the Oligo‐Miocene interval of the Browse Basin, which is likely controlled by far‐field allogenic forcing from the Timor Trough collision zone. Plotting of 3D shelf break trajectories represents a convenient way to visualize the lateral variability in shelf break evolution. Shelf break trajectories that indicate contemporaneous along‐strike progradation and retrogradation correlate with phases of autogenic slope system re‐organization and may be a proxy for morphological stability of the shelf break. Shelf break rugosity and shelf break trajectory rugosity are not inherited parameters and antecedent topography does not dictate long‐term differential movement of the shelf margin through successive depositional sequences. The autogenic carbonate system response to antecedent topography smooths high‐rugosity areas by filling accommodation and maintains a relatively constant shelf break rugosity of ~150 m. Color‐coding of the vertical component in the shelf break trajectory captures the creation and filling of accommodation, and highlights areas of the transect that are likely to yield inconsistent 2D sequence stratigraphic interpretations. [ABSTRACT FROM AUTHOR]

The fall armyworm, Spodoptera frugiperda (J.E. Smith), is an invasive pest species in the Old World. This species is originally native to the Americas. Since 2016, S. frugiperda has spread widely and rapidly throughout Africa, the Middle East, India, Southeast Asia and, most recently, to southern China. By May 2019, S. frugiperda had appeared in 13 provinces in southern China and will spread further into northern China. It is highly likely that S. frugiperda will enter Japan and Korea via overseas migrations as have many other migratory pests. To evaluate the risk of S. frugiperda invasion in Japan and the Korean Peninsula, we modelled the rate of expansion and future potential migratory range of the insect by a trajectory analytical approach using the flight behaviour of S. frugiperda and meteorological data of the past five years (2014–2018). If S. frugiperda can fly for up to 36 continuous hours over water, then our results predict migration from southern and eastern China into Japan and Korea. Most likely, Japan would be invaded from Fujian and Zhejiang in 1 June–15 July, and Kyushu, Shikoku and southwestern Honshu could face the highest risk of S. frugiperda invasion. Korea would most likely be reached by S. frugiperda from northern Zhejiang, Jiangsu, Anhui and Shandong in 1 June–15 July and later. Our results indicated a very high risk that S. frugiperda would annually invade Japan and the Korean Peninsula and cause a possible significant decrease in agricultural productivity. [ABSTRACT FROM AUTHOR]

Tumor‐infiltrating myeloid cells are the most abundant leukocyte population within tumors. Molecular cues from the tumor microenvironment promote the differentiation of immature myeloid cells toward an immunosuppressive phenotype. However, the in situ dynamics of the transcriptional reprogramming underlying this process are poorly understood. Therefore, we applied single cell RNA‐seq (scRNA‐seq) to computationally investigate the cellular composition and transcriptional dynamics of tumor and adjacent normal tissues from 4 early‐stage non‐small cell lung cancer (NSCLC) patients. Our scRNA‐seq analyses identified 11 485 cells that varied in identity and gene expression traits between normal and tumor tissues. Among these, myeloid cell populations exhibited the most diverse changes between tumor and normal tissues, consistent with tumor‐mediated reprogramming. Through trajectory analysis, we identified a differentiation path from CD14+ monocytes to M2 macrophages (monocyte‐to‐M2). This differentiation path was reproducible across patients, accompanied by increased expression of genes (eg, MRC1/CD206, MSR1/CD204, PPARG, TREM2) with significantly enriched functions (Oxidative phosphorylation and P53 pathway) and decreased expression of genes (eg, CXCL2, IL1B) with significantly enriched functions (TNF‐α signaling via NF‐κB and inflammatory response). Our analysis further identified a co‐regulatory network implicating upstream transcription factors (JUN, NFKBIA) in monocyte‐to‐M2 differentiation, and activated ligand‐receptor interactions (eg, SFTPA1‐TLR2, ICAM1‐ITGAM) suggesting intratumoral mechanisms whereby epithelial cells stimulate monocyte‐to‐M2 differentiation. Overall, our study identified the prevalent monocyte‐to‐M2 differentiation in NSCLC, accompanied by an intricate transcriptional reprogramming mediated by specific transcriptional activators and intercellular crosstalk involving ligand‐receptor interactions. [ABSTRACT FROM AUTHOR]

Although Japan has maintained the state of eradication of the oriental fruit fly, Bactrocera dorsalis Hendel complex (Diptera: Tephritidae) since 1986, B. dorsalis complex are occasionally trapped within a limited area and short time period on Japan's small south‐western islands. Trapping events occurred on Amamioshima Island, Kagoshima Prefecture, in 2015, and male adults were also caught in surveillance traps on neighbouring Tokunoshima (south of Amamioshima) and Yakushima (north of Amamioshima) islands as well as on several islands in Okinawa Prefecture (south of Amamioshima). To investigate possible domestic dispersal of the pest from Amamioshima Island, a trajectory analysis was performed to reveal the timing and flight distance of possible dispersal. Surveillance data indicated that the first trappings on Tokunoshima and Yakushima islands occurred in November, which was after the number of trapped male adults on Amamioshima Island peaked in late October. Backward trajectories from Tokunoshima Island beginning 14 days prior to the first trapping passed over Amamioshima Island, which suggested possible dispersal between the islands. Several backward trajectories from the islands in Okinawa Prefecture also passed Amamioshima Island. Moreover, forward trajectories from Amamioshima Island beginning during peak occurrence, from mid‐October to early November, arrived over Tokunoshima, Iheya and Okinawa islands where the flies were caught. Such circumstantial evidence suggests that domestic dispersal of B. dorsalis complex occurred on Amamioshima Island. A situation similar to that on Tokunoshima Island also occurred on Yakushima Island. However, since the number of traps has been limited until the first capture, it was not clear when and from where the immigrants arrived on the island. [ABSTRACT FROM AUTHOR]

Objectives: To identify and characterize distinct trajectories of change in young women's sexual functioning over the first 5 years following breast cancer diagnosis.Methods: Group-based trajectory modeling was applied to the sexual functioning of 896 women diagnosed with stage I-IV breast cancer at age 40 or younger. The Cancer Rehabilitation Evaluation System was used to evaluate women's symptoms of sexual dysfunction annually for 5 years.Results: Five distinct trajectories of sexual functioning were identified: one asymptomatic, one minimally symptomatic, two moderately symptomatic, and one severely symptomatic trajectory. Twelve percent of women were asymptomatic throughout follow-up. The plurality of women experienced stable mild symptoms (42%). Among those with moderate symptoms, some experienced improvement over time (22%) while others experienced deterioration (13%); 11% experienced stable severe symptoms that did not remit over time. Independent predictors of experiencing a symptomatic rather than asymptomatic trajectory (P < 0.05, two-sided) included diagnosis with stage 2 versus 1 disease, ER positive disease treated with oophorectomy or ovarian suppression, being partnered, having anxiety, poorer body image, and greater musculoskeletal pain.Conclusions: We identified distinct trajectories that describe the reported sexual symptoms in this cohort of young breast cancer survivors. The majority of women reported various degrees of sexual dysfunction that remained stable over the study period. There is, however, potential for improvement of moderate and severe symptoms of sexual dysfunction in early survivorship. [ABSTRACT FROM AUTHOR]

Abstract: Sometimes, extreme weather is vital for the population survival of migratory insects by causing sudden population collapse or outbreak. Several studies have shown that rice planthopper migration was significantly influenced by typhoons in eastern Asia. Most typhoons occur in the summer, especially in August. In August, brown planthopper Nilaparvata lugens (Stål) migrates northward or southward depending on wind direction, and thus typhoons can potentially influence its migration process and population distribution. However, this has not yet been studied. This paper reported a case study on the effects of Typhoon Soudelor on the summer migration of N. lugens in eastern China in 2015. The migration pathways of N. lugens were reconstructed for the period under the influence of a typhoon by calculating the trajectories and migration events in eight counties of the Yangtze River Valley region with ancillary information. Trajectory modelling showed that most migrants took short distance migrations (less than 200 km) under the influence of the Typhoon Soudelor. Numerous N. lugens migrants were concentrated and deposited at the rear of the typhoon during the last 5 days of Typhoon Soudelor on August 9–13 due to horizontal convergence, and this led to an outbreak population. These results indicated that the N. lugens population was redistributed by the typhoon in the summer and that the population dynamics at the rear of a typhoon should be kept under close surveillance. This study provided insight into migratory organisms adapting to atmospheric features. [ABSTRACT FROM AUTHOR]

Advances in biomolecular simulation methods and access to large scale computer resources have led to a massive increase in the amount of data generated. The key enablers have been optimization and parallelization of the simulation codes. However, much of the software used to analyze trajectory data from these simulations is still run in serial, or in some cases many threads via shared memory. Here, we describe the addition of multiple levels of parallel trajectory processing to the molecular dynamics simulation analysis software CPPTRAJ. In addition to the existing OpenMP shared‐memory parallelism, CPPTRAJ now has two additional levels of message passing (MPI) parallelism involving both across‐trajectory processing and across‐ensemble processing. All three levels of parallelism can be simultaneously active, leading to significant speed ups in data analysis of large datasets on the NCSA Blue Waters supercomputer by better leveraging the many available nodes and its parallel file system. © 2018 Wiley Periodicals, Inc. Advances in MD simulation speed has enabled the generation of terabytes of data. This article describes how the MD simulation data analysis tool CPPTRAJ has been parallelized to take advantage of modern HPC hardware to accelerate data analysis. [ABSTRACT FROM AUTHOR]

Abstract: Observational records of the stratospheric mean age of air (AoA), the average transit time of an air parcel since entering the stratosphere, must reflect changes in the in‐mixing from the extratropical lower stratosphere to the tropical tropopause layer (TTL). Focusing on the mixing fraction of tropospheric and stratospheric air masses in the upper TTL, the impact of mixing processes that occur prior to air masses entering the stratosphere separately from those that occur within the stratosphere is investigated. Using trajectory analysis, the mixing fraction during 1980–2016 is evaluated, and AoA and water vapor mixing ratios in the upper TTL are reconstructed. The interannual variation in the reconstructed water vapor shows good agreement with observations in the tropics. Furthermore, the reconstructed AoA exhibits long‐term variation with a positive trend between 1980 and 1999. To compare the reconstructed AoA with the observed AoA in the midlatitude stratosphere, the transit time spectra are estimated for the 1989–2016 period, and the AoA in the midlatitude stratosphere is estimated by integration of the spectrum together with the AoA in the upper TTL. As a result, although the explicitly calculated transit time shows a clear underestimation compared with previous studies, it is suggested that the “aging” effects are 3.1–4.2 years for transit time in the stratosphere, 0.2–0.7 years for in‐mixing prior to entering the stratosphere, 0.1 years for transit time from the troposphere to upper TTL, and 0.0–1.6 years for subgrid‐scale mixing in the stratosphere. [ABSTRACT FROM AUTHOR]

Abstract: The quantity of GPS trajectories on the movement of individuals has far outstripped our ability to analyse them. Segmentation, a first step in trajectory analysis, is fundamental to imputing behaviour from patterns of movement. Behaviour occurs at multiple scales that are captured at different temporal frequencies. To identify behaviour from a complex trajectory it is essential to use a segmentation procedure that captures different frequency ranges. A limitation of existing segmentation algorithms is that they require training and parameterisation that can lead to special use segmentations that are not generalisable. This paper presents a new approach to the automated segmentation of movement trajectories at multiple scales. It has two distinguishing characteristics: it can capture movement patterns at multiple temporal frequencies through its recursive application; and requires no training or thresholding. The methodology is tested on two sets of simulated data and GPS tracking data of two species, the Turkey Vulture (Cathartes aura) and the Galapagos Albatross (Phoebastria irrorata). For the Turkey Vulture dataset, segments and transition points are evaluated using behavioural segmentations delineated by domain experts, and results are also compared with an existing approach. For the Albatross dataset, the segmentation results are evaluated using the geographic context of the movement tracks through visualisation. An Albatross trajectory is used to illustrate the application of recursive segmentation for extracting movement patterns at multiple temporal scales. The evaluation suggests that the segmentation technique is capable of extracting the right number of segments and in estimating transition points for most of the evaluated datasets. The proposed methodology has the potential to automate the segmentation process by enabling researchers to analyse a broad range of heterogeneous datasets without training. It will enable them to segment datasets recursively to derive multiple scales of movement patterns in a trajectory that may relate to different scales of behaviour. [ABSTRACT FROM AUTHOR]

We seek to identify heterogeneous trajectories of marital conflict during the early childhood period, identify predictors associated with these trajectories, and examine associations between trajectory group membership and children's disruptive behavior. Participants were 469 families examined 4 times when the children were 2 to 54 months of age. Maternal reports of marital conflict, adverse childhood experiences, depressive symptoms, and sociodemographic characteristics were collected, and averaged maternal and paternal reports of child disruptive problems were used. Using growth mixture modeling, 3 trajectories of marital conflict were identified: high increasing (21.8%), high decreasing (7%), and low stable (71.2%). Maternal adverse childhood experiences predicted increased risk of belonging in the high-increasing group, whereas depressive symptoms predicted increased risk of belonging in the high-decreasing group. Importantly, children of mothers in the high-increasing group exhibited higher levels of disruptive behavior at 54 months when compared with children of mothers in the high-decreasing and low-stable groups. [ABSTRACT FROM AUTHOR]

A major challenge in the modern educational research is the large amount of time-dependent data, which requires suitable methods to provide an efficient decision making. The fields of visual analytics and interactive visualization can help to cope with the related issues by involving the analyst in the exploration process. The time is an important variable that needs to be modeled in visual analytics. Methods like motion charts show the changes over time by presenting animations in the two-dimensional space and by changing the element appearances. In this paper, we present a novel web-based visual analytics framework, which is primarily designed for exploratory analysis of academic analytics and employs a combination of improved motion charts methods, trajectory-based visualizations, and automated analytic methods for the purpose of analyzing data elements based on their relations with the time dimension and examining data dynamics. We evaluate the usefulness and the general applicability of the framework with a controlled experiment to assess the efficacy of the methods. To interpret the experiment results, we utilize one-way repeated measures analysis of variance. Also, a questionnaire survey with experts was conducted to evaluate the usability of the methods. [ABSTRACT FROM AUTHOR]

ABSTRACT The actin capping protein (CP) binds to actin filaments to block further elongation. The capping activity is inhibited by proteins V-1 and CARMIL interacting with CP via steric and allosteric mechanisms, respectively. The crystal structures of free CP, CP/V-1, and CP/CARMIL complexes suggest that the binding of CARMIL alters the flexibility of CP rather than the overall structure of CP, and this is an allosteric inhibition mechanism. Here, we performed molecular dynamics (MD) simulations of CP in the free form, and in complex with CARMIL or V-1. The resulting trajectories were analyzed exhaustively using Motion Tree, which identifies various rigid-body motions ranging from small local motions to large domain motions. After enumerating all the motions, CP flexibilities with different ligands were characterized by a list of frequencies for 20 dominant rigid-body motions, some of which were not identified in previous studies. The comparative analysis highlights the influence of the binding of the CARMIL peptide to CP flexibility. In free CP and the CP/V-1 complex, domain motions around a large crevice between the N-stalk and the CP-S domain occur frequently. The CARMIL peptide binds the crevice and suppresses the motions effectively. In addition, the binding of the CARMIL peptide enhances and alters local motions around the pocket that participates in V-1 binding. These newly identified motions are likely to suppress the binding of V-1 to CP. The observed changes in CP motion provide insights that describe the mechanism of allosteric regulation by CARMIL through modulating CP flexibility. Proteins 2016; 84:948-956. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from . © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Aims To estimate physical activity trajectories for people who quit smoking, and compare them to what would have been expected had smoking continued. Design, Setting and Participants A total of 5115 participants in the Coronary Artery Risk Development in Young Adults Study ( CARDIA) study, a population-based study of African American and European American people recruited at age 18-30 years in 1985/6 and followed over 25 years. Measurements Physical activity was self-reported during clinical examinations at baseline (1985/6) and at years 2, 5, 7, 10, 15, 20 and 25 (2010/11); smoking status was reported each year (at examinations or by telephone, and imputed where missing). We used mixed linear models to estimate trajectories of physical activity under varying smoking conditions, with adjustment for participant characteristics and secular trends. Findings We found significant interactions by race/sex ( P = 0.02 for the interaction with cumulative years of smoking), hence we investigated the subgroups separately. Increasing years of smoking were associated with a decline in physical activity in black and white women and black men [e.g. coefficient for 10 years of smoking: −0.14; 95% confidence interval ( CI) = −0.20 to −0.07, P < 0.001 for white women]. An increase in physical activity was associated with years since smoking cessation in white men (coefficient 0.06; 95% CI = 0 to 0.13, P = 0.05). The physical activity trajectory for people who quit diverged progressively towards higher physical activity from the expected trajectory had smoking continued. For example, physical activity was 34% higher (95% CI = 18 to 52%; P < 0.001) for white women 10 years after stopping compared with continuing smoking for those 10 years ( P = 0.21 for race/sex differences). Conclusions Smokers who quit have progressively higher levels of physical activity in the years after quitting compared with continuing smokers. [ABSTRACT FROM AUTHOR]

Reachability analysis and viability theory play an important role in control synthesis and trajectory analysis of constrained dynamical systems, many methods are known for computing them in low‐dimensional non‐linear systems, but these well‐known methods rely on gridding the state space and hence suffer from the curse of dimensionality. In this study, for systems whose dynamics are described by polynomials, a method based on semi‐definite programming is proposed to estimate an invariance kernel with target as large as possible by iteratively searching for Lyapunov‐like functions. The proposed methodology is scalable, since the size of the semi‐definite programming problem to be solved grows linearly with the system dimension. We test the method on two interesting examples and compare them with some existing methods, the results show that our method is more efficient. [ABSTRACT FROM AUTHOR]

Objective Heightened psychological distress after cancer is common but likely highly heterogeneous. This raises potential challenges in how and when to target services; however, data describing longitudinal patterns of distress are limited. This study describes the long term psychological outcomes for colorectal cancer (CRC) survivors and trajectories of adjustment over time. Methods A prospective survey of a population-based sample of 1966 CRC survivors assessed sociodemographic variables, perceived social support and psychological distress, including distress subtypes of anxiety, depression and somatization, at six time points from 5 months to 5 years post-diagnosis. Results Over the 5-year trajectory, the prevalence of high overall distress ranged between 44% and 32% but was greater for men compared with women ( p < 0.001). Four distress trajectory styles within clusters were identified for overall distress and for each distress subtype with a constant low distress group providing the basis for comparison. Higher distress trajectories varied for overall distress and distress subtypes but were generally differentiated by gender, younger age, lower education, poor socioeconomic advantage, late disease stage and poor social support. Conclusions For global distress, by comparison with women, men with CRC are vulnerable to distress, with men who are younger and with low education and poor social support being a priority for targeted intervention. While distress screening early in the cancer experience will identify those with a constant high distress trajectory, others with late emerging distress or caseness may be missed. On this basis, distress screening through the illness trajectory into long term survivorship seems warranted. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Developing objective tools for tracking progress of restored sites is of general concern. Here, we present an innovative approach based on principal response curves (PRC) and species classification according to their preferential habitats to monitor changes in community composition. Following large-scale restoration of a cut-over peatland, vegetation was surveyed biannually over 8 years. We evaluated whether the establishing plant communities fell within the range of natural variation. We used both general diversity curves and PRC applied on plant species grouped by preferred habitat to compare restored sites and unrestored sites to a reference ecosystem. After 8 years, diversity and richness differed between the sites, with Forest and Ruderal species more prominent in unrestored sites, and Peatland, Forest, and Wetland species dominant in restored sites. The PRC revealed that the restored site became rapidly dominated by typical peatland plants, the main drivers of temporal changes being Sphagnum rubellum, Pohlia nutans, and Mylia anomala. Some differences remained between the restored and the undisturbed species pools: the former had more herbaceous species associated with wetlands such as Calamagrostis canadensis and Typha latifolia and the latter had more forested species like Kalmia angustifolia throughout the study. PRC revealed to be an efficient tool identifying species driving changes at the community level after restoration. In our case study, examining PRC scores after classifying species according to their preferred habitat allowed to illustrate objectively how restoration promotes target species (associated to peatlands) and how lack of intervention benefits ruderal species. [ABSTRACT FROM AUTHOR]

Most of existing software for analysis of molecular dynamics (MD) simulation results is based on command-line, script-guided processes that require the researchers to have an idea about programming language constructions used, often applied to the one and only product. Here, we describe an open-source cross-platform program, MD Trajectory Reader and Analyzer (MDTRA), that performs a large number of MD analysis tasks assisted with a graphical user interface. The program has been developed to facilitate the process of search and visualization of results. MDTRA can handle trajectories as sets of protein data bank files and presents tools and guidelines to convert some other trajectory formats into such sets. The parameters analyzed by MDTRA include interatomic distances, angles, dihedral angles, angles between planes, one-dimensional and two-dimensional root-mean-square deviation, solvent-accessible area, and so on. As an example of using the program, we describe the application of MDTRA to analyze the MD of formamidopyrimidine-DNA glycosylase, a DNA repair enzyme from Escherichia coli. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from . © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We report on a python interface to the GROMACS molecular simulation package,GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C.To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls. GromPy can be used for extending the current GROMACS simulation and analysis modes. In this work, we demonstrate that the interface enables hybrid Monte-Carlo/molecular dynamics (MD) simulations in the grand-canonical ensemble, a simulation mode that is currently not implemented in GROMACS. For this application, the interplay between GromPy and GROMACS requires only minor modifications of the GROMACS source code, not affecting the operation, efficiency, and performance of the GROMACS applications. We validate the grand-canonical application against MD in the canonical ensemble by comparison of equations of state. The results of the grand-canonical simulations are in complete agreement with MD in the canonical ensemble. The python overhead of the grand-canonical scheme is only minimal. [ABSTRACT FROM AUTHOR]