Generalized Additive Mixed Models Research Articles

The acoustic profiles of vocal emotions in Japanese: A corpus study with generalized additive mixed modeling

This study investigated the vocal emotions in Japanese by analyzing acoustic features from emotional utterances in the Online Gaming Voice Chat Corpus with Emotional Label (Arimoto and Kawatsu, 2013). The corpus contains the recorded sentences produced in 8 emotions by four native Japanese speakers who are professional actors. For acoustic feature extraction, Praat script ProsodyPro was used. Principle component analysis (PCA) was conducted to evaluate the contribution of each acoustic feature. In addition, a linear discriminant classifier (LDA) was trained with the extracted acoustic features to predict the emotion category and intensity. A generalized additive mixed model (GAMM) was performed to examine the effect of gender, emotional category, and emotional intensity on the time-normalized f0 values. The GAMM’s results suggested the effects of gender, emotion, and emotional intensity on the time-normalized f0 values of vocal emotions in Japanese. The recognition accuracy of the LDA classifier reached about 60%, suggesting that although pitch-related measures are important to differentiate vocal emotions, bio-informational features (e.g., jitter, shimmer, and harmonicity) are also informative. In addition, our correlation analysis suggested that vocal emotions could be conveyed by a set of features rather than some individual features alone.

Vowel trajectories of African Americans in Georgia, USA

Within the United States, dialectal variation is often characterized by vowel shifts: systematic differences in vowels' relative qualities and vowel-inherent dynamics. The African American Vowel Shift (AAVS), in particular, includes raising and fronting of front lax /ɪ ɛ æ/, among other features. The more recent pan-regional Low Back Merger Shift (LBMS), by contrast, includes lowering and backing of the same vowels. We evaluate these two shifts in an audio corpus of over 40 Black speakers from the Southern state of Georgia. Speakers, born between the 1930s and 2000, represent five demographic generations. Normalized formant values (F1,F2) from five temporal points per token are input to Generalized Additive Mixed Models (GAMMs). We test for significant changes in vowels' trajectories across time by fitting Year of Birth as a continuous smooth term. Additionally, we use linear mixed-effects modeling to test for raising versus lowering on the (F2–F1) front-vowel diagonal, across generations. Evidence from GAMMs and linear modeling indicates raised positions of /ɪ ɛ æ/ among older generations (1950s–1980s), followed by significant retraction from 1990–2000. These acoustic results are consistent with strengthening of the AAVS in the third quarter of the 20th Century, followed by a rapid transition to the pan-regional LBMS.

Modelling the spatial population structure and distribution of the queen conch, Aliger gigas, on the Pedro Bank, Jamaica

The estimation of reliable indices of abundance for sedentary stocks requires the incorporation of the underlying spatial population structure, including issues arising from the sampling design and zero inflation. We applied seven spatial interpolation techniques [ordinary kriging (OK), kriging with external drift (KED), a negative binomial generalized additive model (NBGAM), NBGAM plus OK (NBGAM+OK), a general additive mixed model (GAMM), GAMM plus OK (GAMM+OK) and a zero-inflated negative binomial model (ZINB) ] to three survey datasets to estimate biomass for the gastropod Aliger gigas on the Pedro Bank Jamaica. The models were evaluated using 10-fold cross-validation diagnostics criteria for choosing the best model. We also compared the best model estimations against two common design methods to assess the consequences of ignoring the spatial structure of the species distribution. GAMM and ZINB were overall the best models but were strongly affected by the sampling design, sample size, the coefficient of variation of the sample and the quality of the available covariates used to model the distribution (geographic location, depth and habitat). More reliable abundance indices can help to improve stock assessments and the development of spatial management using an ecosystem approach.

The Effect Of Sex On The Mechanical Cost And Work Of Breathing During Exercise

Sex differences in pulmonary system structure and function lead to differences in respiratory mechanics during exercise. Specifically, women incur a greater power of breathing (Pb) during exercise than men. However, women typically display a more rapid breathing pattern at a given minute ventilation during exercise and, as such, it remains unclear whether previously reported sex differences in Pb are due to higher respiratory frequencies (i.e., more breaths per minute), or if the work of breathing (Wb) is indeed greater per breath in women compared with men. Moreover, it remains unclear whether differences exist between sexes when the Wb during exercise is converted to a mechanical cost of breathing (i.e., J·L-1). PURPOSE: To examine differences in the Wb (J·breath-1) and the mechanical cost of breathing (J·L-1) between men and women during incremental cycling. METHODS: Forty-two healthy participants (29 ± 15 yrs) completed a graded exercise test on a cycle ergometer. During the test, participants were instrumented with an esophageal balloon catheter to measure esophageal pressure as a surrogate of pleural pressure. Chest wall compliance was measured at rest before exercise via the two-point method. The Wb was determined via the modified Campbell diagram. The mechanical cost was computed as Wb divided by tidal volume. To compare the Wb (and components) and the mechanical cost between sexes we used a generalized additive mixed model (GAMM) approach. Values are reported as the mean and 95% confidence interval. RESULTS: The total Wb was greater in men than women at ventilations >140 L·min-1 (men = 12.9 J·breath-1 [11.8, 14.1]; women = 11.4 J·breath-1 [10.2, 12.5]; p < 0.05). The mechanical cost of breathing was greater in women at ventilations >95 L·min-1 (men = 2.7 J·L-1 [2.3, 3.2]; women = 3.4 J·L-1 [2.9, 3.8]; p < 0.05). CONCLUSIONS: Wb (J·breath-1) is effectively no different between sexes across all ventilations attained by the women in our study (up to 120 L·min-1). Even when tidal volume is taken into consideration, the mechanical cost of breathing is not greater in women until high ventilations suggesting that differences in the Pb are due to sex differences in breathing pattern rather than differences in the mechanical cost of breathing.

Therapies for lysosomal storage diseases: Principles, practice, and prospects for refinements based on evolving science.

Infantile nephropathic cystinosis, due to impaired transport of cystine out of lysosomes, occurs with an incidence of 1 in 100–200,000 live births. It is characterized by renal Fanconi syndrome in the first year of life and glomerular dysfunction progression to end-stage kidney disease by approximately 10 years of age. Treatment with oral cysteamine therapy helps preserve glomerular function, but affected individuals eventually require kidney replacement therapy. This is because glomerular damage had already occurred by the time a child is diagnosed with cystinosis, typically in the second year of life. We performed a retrospective multicenter study to investigate the impact of initiating cysteamine treatment within the first 2 months of life in some infants and comparing two different levels of adherence in patients diagnosed at the typical age. We collected 3983 data points from 55 patients born between 1997 and 2020; 52 patients with 1592 data points could be further evaluated. These data were first analyzed by dividing the patient cohort into three groups: (i) standard treatment start with good adherence, (ii) standard treatment start with less good adherence, and (iii) early treatment start. At every age, mean estimated glomerular filtration rate (eGFR) was higher in early-treated patients than in later-treated patients. Second, a generalized additive mixed model (GAMM) was applied showing that patients with initiation of treatment before 2 months of age are expected to have a 34 ml/min/1.73 m2 higher eGFR than patients with later treatment start while controlling for adherence and patients' age. These data strongly suggest that oral cysteamine treatment initiated within 2 months of birth preserves kidney function in infantile nephropathic cystinosis and provide evidence of the utility of newborn screening for this disease.

Benthic studies adjacent to Sakhalin Island, Russia 2015 III: benthic energy density spatial models in the nearshore gray whale feeding area

Energy densities of six dominant benthic groups (Actinopterygii, Amphipoda, Bivalvia, Cumacea, Isopoda, and Polychaeta) and total prey energy were modeled for the nearshore western gray whale feeding area, Sakhalin Island, Russia, as part of a multi-disciplinary research program in the summer of 2015. Energy was modeled using generalized additive mixed models (GAMM) with accommodations for zero-inflation (logistic regression and hurdle models) and regression predictions combined with kriging to interpolate energy densities across the nearshore feeding area. Amphipoda energy density was the highest nearshore and in the south whereas Bivalvia energy density was the highest offshore and in the northern portion of the study area. Total energy was the highest in mid-range distances from shore and in the north. Amphipoda energy density was higher than minimum energy estimates defining gray whale feeding habitats (312–442 kJ/m2) in 13% of the nearshore feeding area whereas total prey energy density was higher than the minimum energy requirement in 49% of the habitat. Inverse distance-weighted interpolations of Amphipoda energy provided a broader scale representation of the data whereas kriging estimates were spatially limited but more representative of higher density in the southern portion of the study area. Both methods represented the general trend of higher Amphipoda energy density nearshore but with significant differences that highlight the value of using multiple methods to model patterns in highly complex environments.

O5-5 Neighbourhood Walkability and Physical Activity: Moderating Role of a Physical Activity Interventions in Overweight and Obese Older Adults with Metabolic Syndrome

BackgroundWhile urban built environments might promote active ageing, an infrequently studied question is how the neighbourhood walkability modulates physical activity changes during a physical activity intervention program in older adults. We assessed the influence of objectively assessed neighbourhood walkability on the change in physical activity during the intervention program used in the ongoing PREvención con DIeta MEDiterránea (PREDIMED)-Plus trial. PREDIMED-Plus is a parallel-group, randomized trial which tested the effect of an intensive lifestyle intervention on cardiovascular disease prevention, in overweight and obese participants with the metabolic syndrome.MethodThe present study involved 228 PREDIMED-Plus senior participants aged between 55 to 75, recruited in Palma de Mallorca (Spain). Overweight/obese older adults with metabolic syndrome were randomized to an intensive weight-loss lifestyle intervention or a control group (106 intervention group and 122 control group). A home neighborhood environment walkability index (residential density, land use mix, intersections density) was calculated using geographic information systems (1km sausage-network buffer). Physical activity was assessed using accelerometer for seven days, and a REGICOR validated physical activity questionnaire, at baseline and 2 follow-up visits (six-months and one-year later). Generalized Additive Mixed Models (GAMMs) were fitted to estimate the association between the neighbourhood walkability index and changes in physical activity during follow-up.ResultsHigher neighbourhood walkability (1 z-score increment) was associated with moderate-to-vigorous accelerometer assessed physical activity duration, (ß = 3,44; 95% CI = 0.52;6.36 minutes per day). When analyses were stratified by intervention arm, the association was only observed in the intervention group (ß = 6.357; 95% CI = 2.07;10.64 minutes per day) (p for interaction = 0.055). There were no statistically significant associations between neighbourhood walkability and self-reported physical activity nor brisk walking duration.ConclusionsThe results indicate that the walkability of the neighbourhood could support a physical activity intervention, helping to maintain or increase older adults' objectively measured physical activity. This research may modify evidence on whether environmental factors modify habits acquisition during physical activity intervention programs.

State-dependent tDCS modulation of the somatomotor network: A MEG study

ObjectiveTranscranial direct current stimulation (tDCS) is a non-invasive technique widely used to investigate brain excitability and activity. However, the variability in both brain and behavioral responses to tDCS limits its application for clinical purposes.This study aims to shed light on state-dependency, a phenomenon that contributes to the variability of tDCS. MethodsTo this aim, we investigated changes in spectral activity and functional connectivity in somatomotor regions after Real and Sham tDCS using generalized additive mixed models (GAMMs), which allowed us to investigate how modulation depends on the initial state of the brain. ResultsResults showed that changes in spectral activity, but not connectivity, in the somatomotor regions depend on the initial state of the brain, confirming state-dependent effects. Specifically, we found a non-linear interaction between stimulation conditions (Real vs Sham) and initial state: a reduction of alpha and beta power was observed only in participants that had higher alpha and beta power before Real tDCS. ConclusionsThis study highlights the importance of considering state-dependency to tDCS and shows how it can be taken into account with appropriate statistical models. SignificanceOur findings bear insight into tDCS mechanisms, potentially leading to discriminate between tDCS responders and non-responders.

Forecasting seasonal peaks in roadkill patterns for improving road management

For several species, roadkill is not spatially aggregated on hotspots, having instead a more diffuse pattern along the roads. For such species, management measures such as road passages may be insufficient for effective mitigation, since a large part of the road crossings is likely to occur outside the influence of those structures. One complementary approach could be to implement temporary mitigation actions, such as traffic calming. This requires understanding when roadkill peaks may occur. We tested the feasibility of predicting seasonal peaks of roadkill using data from a 3-year systematic monitoring (78 surveys over ca. 960 km of roads) from eight non-flying vertebrate species from Mato Grosso do Sul, Brazil, with different body size and life history traits (ca. 6400 records from focal species). We modelled the time-series of the roadkill of these species at large scale (state level) using generalized additive mixed models (GAMMs). We used the data of the first 2 years as training datasets, and the information from the third year of surveys as testing datasets to evaluate the prediction performance of models. Overall, the models of species feed with a higher number of records were able to follow reasonably well the variations of roadkill over time, although they were not able to correctly predict the number of collisions. For species with fewer observations, the models presented a poorer goodness-of-fit and prediction ability. Our results suggest that, at least for those species with higher roadkill rates, it can be possible to forecast periods of higher probability of occurring hot-moments of mortality. Such models can provide valuable information to implement seasonal management actions.

Global spatiotemporal trends of cardiovascular diseases due to temperature in different climates and socio-demographic index regions from 1990 to 2019.

With the rapidly changing climate, assessing the global trends of cardiovascular diseases (CVDs) attributed to high and low temperatures in different climate zones and under varying socio-demographic levels is crucial for regulations, preparation, intervention, and clinical practice for CVD. Our study included 204 countries with global CVD data ranging from 1990 to 2019. We obtained the age-standardized mortality rate (ASMR); disability-adjusted life rate of CVD attributed to high, low, and non-optimal temperatures; and socio-demographic index (SDI) data from the Global Health Data Exchange. We also downloaded the temperature data from the Climatic Research Unit. These 204 countries were divided into five climate zones and five SDI levels according to the annual average temperature data and SDI in 2019. The temporal trends of CVD burden attributed to high, low, and non-optimal temperatures were estimated by using the cubic regression spline and the generalized additive mixed model (GAMM). The total burden of temperature-related CVD has been declining in the last 30years. However, the burden of CVD attributed to high temperature showed an increasing trend. Among different climate regions, the ASMRs of CVD attributed to high temperature were the highest in the tropical regions, followed by subtropical regions, and the lowest in the boreal regions. In the past 30years, the burden of CVD attributed to high temperatures has shown a significant increasing trend, while declining trends are observed for non-optimal and low temperatures. The CVD burden attributed to high temperatures is particularly pronounced in warmer and low-SDI regions with an increasing trend of CVD burden due to high temperature.

Dorsal harmony in Squliq Atayal: An Acoustic and Ultrasound Study

Dorsal harmony, understood as a process of changing from /*k/ into /q/ when followed by a uvular /q/ or a pharyngeal /ħ/, has been reported as a historical sound change in Atayal dialects, such as Squliq and Skikun. However, it is unattested if the observed dorsal harmony also occurs in those Atayal dialects as a synchronic morpho-phonological process. In the present study, we examined dorsal harmony in Squliq Atayal through ultrasonography and acoustic measurement (onset F3 – F2). Generalized additive mixed models (GAMMs), principal component analysis (PCA) and linear discriminant analysis (LDA) were applied to fit the tongue contours and compare the similarities of tongue images across different conditions. One participant showed that all variants of [k] were deviated from Baseline [k], and the linear discriminant (LD) values of all variants of [k] fell between Baseline [k] and [q]. The other participant exhibited consistent tongue postures in Short distance [k] and Cross-boundary [q]-[k]. The observed results suggest that dorsal harmony occurs in Squliq Atayal as a morpho-phonological process. Moreover, dorsal harmony is physiologically driven and best accounted for by coarticulatory aggressiveness, though with some individual variations. These variations nevertheless may support a coarticulatory path to sound change.

Global habitat loss of a highly migratory predator, the blue marlin (Makaira nigricans)

AbstractAimClimate change is driving the redistribution of species throughout the oceans. However, the speed and magnitude of species responses, including shifts in their distribution, are variable and species specific. Quantifying the effect of environmental conditions on species distributions is crucial to informing management and conservation efforts. Blue marlin (Makaira nigricans) is a wide‐ranging top predator occurring circumglobally in tropical and subtropical waters and is heavily impacted by international longline fisheries. This study aimed to predict the global distribution of blue marlin and characterize the effects of climate variability thereon.LocationGlobal.MethodsTo conduct this study, pop‐up satellite archival tags (n = 144) deployed by recreational anglers through a global citizen science programme were used to generate a large tracking data set (14,928 days, 210,983 km from deployment to pop‐up locations) of blue marlin movement across three ocean basins. State‐space modelled tracking position estimates were used to create a species distribution model to represent global habitat suitability for blue marlin. Habitat suitability was determined by fitting a generalized additive mixed model (GAMM) as a function of environmental covariates which was used to predict monthly global blue marlin habitat from 2000 to 2016.ResultsBlue marlin habitat preference had the strongest association with sea surface temperature. Seasonal variation in blue marlin habitat occurs primarily at the latitudinal edges of the distribution range. Over the duration of the study, 96% of core habitat declined in suitability, with a concurrent poleward increase in suitability of marginal habitat.Main ConclusionsThis study highlights the successful application of citizen‐based science to develop a long‐term global telemetry dataset. The present‐day loss of highly suitable habitat suggests ocean warming may be making equatorial waters less suitable even to highly mobile species. Blue marlin is likely to respond by following preferred habitat as it shifts poleward.

Relationship between age at initiation of cysteamine treatment, adherence with therapy, and glomerular kidney function in infantile nephropathic cystinosis.

Infantile nephropathic cystinosis, due to impaired transport of cystine out of lysosomes, occurs with an incidence of 1 in 100-200,000 live births. It is characterized by renal Fanconi syndrome in the first year of life and glomerular dysfunction progression to end-stage kidney disease by approximately 10 years of age. Treatment with oral cysteamine therapy helps preserve glomerular function, but affected individuals eventually require kidney replacement therapy. This is because glomerular damage had already occurred by the time a child is diagnosed with cystinosis, typically in the second year of life. We performed a retrospective multicenter study to investigate the impact of initiating cysteamine treatment within the first 2 months of life in some infants and comparing two different levels of adherence in patients diagnosed at the typical age. We collected 3983 data points from 55 patients born between 1997 and 2020; 52 patients with 1592 data points could be further evaluated. These data were first analyzed by dividing the patient cohort into three groups: (i) standard treatment start with good adherence, (ii) standard treatment start with less good adherence, and (iii) early treatment start. At every age, mean estimated glomerular filtration rate (eGFR) was higher in early-treated patients than in later-treated patients. Second, a generalized additive mixed model (GAMM) was applied showing that patients with initiation of treatment before 2 months of age are expected to have a 34 ml/min/1.73 m2 higher eGFR than patients with later treatment start while controlling for adherence and patients' age. These data strongly suggest that oral cysteamine treatment initiated within 2 months of birth preserves kidney function in infantile nephropathic cystinosis and provide evidence of the utility of newborn screening for this disease.

Longitudinal trajectories of cortical development in 22q11.2 copy number variants and typically developing controls

Probing naturally-occurring, reciprocal genomic copy number variations (CNVs) may help us understand mechanisms that underlie deviations from typical brain development. Cross-sectional studies have identified prominent reductions in cortical surface area (SA) and increased cortical thickness (CT) in 22q11.2 deletion carriers (22qDel), with the opposite pattern in duplication carriers (22qDup), but the longitudinal trajectories of these anomalies—and their relationship to clinical symptomatology—are unknown. Here, we examined neuroanatomic changes within a longitudinal cohort of 261 22q11.2 CNV carriers and demographically-matched typically developing (TD) controls (84 22qDel, 34 22qDup, and 143 TD; mean age 18.35, ±10.67 years; 50.47% female). A total of 431 magnetic resonance imaging scans (164 22qDel, 59 22qDup, and 208 TD control scans; mean interscan interval = 20.27 months) were examined. Longitudinal FreeSurfer analysis pipelines were used to parcellate the cortex and calculate average CT and SA for each region. First, general additive mixed models (GAMMs) were used to identify regions with between-group differences in developmental trajectories. Secondly, we investigated whether these trajectories were associated with clinical outcomes. Developmental trajectories of CT were more protracted in 22qDel relative to TD and 22qDup. 22qDup failed to show normative age-related SA decreases. 22qDel individuals with psychosis spectrum symptoms showed two distinct periods of altered CT trajectories relative to 22qDel without psychotic symptoms. In contrast, 22q11.2 CNV carriers with autism spectrum diagnoses showed early alterations in SA trajectories. Collectively, these results provide new insights into altered neurodevelopment in 22q11.2 CNV carriers, which may shed light on neural mechanisms underlying distinct clinical outcomes.

Influence of Rising Water Temperature on the Temperate Seagrass Species Eelgrass (Zostera marina L.) in the Northeast USA

Sea surface temperature (SST) has increased worldwide since the beginning of the 20th century, a trend which is expected to continue. Changes in SST can have significant impacts on marine biota, including population-level shifts and alterations in community structure and diversity, and changes in the timing of ecosystem events. Seagrasses are a group of foundation species that grow in shallow coastal and estuarine systems, where they provide many ecosystem services. Eelgrass, Zostera marina L., is the dominant seagrass species in the Northeast United States of America (USA). Multiple factors have been cited for losses in this region, including light reduction, eutrophication, and physical disturbance. Warming has the potential to exacerbate seagrass loss. Here, we investigate regional changes in eelgrass presence and abundance in relation to local water temperature using monitoring data from eight sites in the Northeastern USA (New Hampshire to Maryland) where a consistent monitoring protocol, SeagrassNet, has been applied. We use a hurdle model consisting of a generalized additive mixed model (GAMM) with binomial and beta response distributions for modeling eelgrass presence and abundance, respectively, in relation to the local summer average water temperature. We show that summer water temperature one year prior to monitoring is a significant predictor of eelgrass presence, but not abundance, on a regional scale. Above average summer temperatures correspond to a decrease in probability of eelgrass presence (and increased probability of eelgrass absence) the following year. Cooler than average temperatures in the preceding year, down to approximately 0.5°C below the site average, are associated with the highest predicted probability of eelgrass presence. Our findings suggest vulnerability in eelgrass meadows of the Northeast USA and emphasize the value of unified approaches to seagrass monitoring, conservation and management at the seascape scale.

Variation by default: cesarean section discharge opioid prescription patterns and outcomes in Military Health System hospitals: a retrospective longitudinal cohort study

BackgroundTo examine factors associated with post-Cesarean section analgesic prescription variation at hospital discharge in patients who are opioid naïve; and examine relationships between pre-Cesarean section patient and care-level factors and discharge morphine equivalent dose (MED) on outcomes (e.g., probability of opioid refill within 30 days) across a large healthcare system.MethodsThe Walter Reed Institutional Review Board provided an exempt determination, waiver of consent, and waiver of HIPAA authorization for research use in the present retrospective longitudinal cohort study. Patient records were included in analyses if: sex assigned in the medical record was “female,” age was 18 years of age or older, the Cesarean section occurred between January 2016 to December 2019 in the Military Health System, the listed TRICARE sponsor was an active duty service member, hospitalization began no more than three days prior to the Cesarean section, and the patient was discharged to home < 4 days after the Cesarean section.ResultsAcross 57 facilities, 32,757 adult patients had a single documented Cesarean section procedure in the study period; 24,538 met inclusion criteria and were used in analyses. Post-Cesarean section discharge MED varied by facility, with a median MED of 225 mg and median 5-day supply. Age, active duty status, hospitalization duration, mental health diagnosis, pain diagnosis, substance use disorder, alcohol use disorder, gestational diabetes, discharge opioid type (combined vs. opioid-only medication), concurrent tubal ligation procedure, single (vs. multiple) births, and discharge morphine equivalent dose were associated with the probability of an opioid prescription refill in bivariate analyses, and therefore were included as covariates in a generalized additive mixed model (GAMM). Generalized additive mixed model results indicated that non-active duty beneficiaries, those with mental health and pain conditions, those who received an opioid/non-opioid combination medication, those with multiple births, and older patients were more likely to obtain an opioid refill, relative to their counterparts.ConclusionSignificant variation in discharge pain medication prescriptions, as well as the lack of association between discharge opioid MED and probability of refill, indicates that efforts are needed to optimize opioid prescribing and reduce unnecessary healthcare variation.

Integrating data types to estimate spatial patterns of avian migration across the Western Hemisphere.

For many avian species, spatial migration patterns remain largely undescribed, especially across hemispheric extents. Recent advancements in tracking technologies and high-resolution species distribution models (i.e., eBird Status and Trends products) provide new insights into migratory bird movements and offer a promising opportunity for integrating independent data sources to describe avian migration. Here, we present a three-stage modeling framework for estimating spatial patterns of avian migration. First, we integrate tracking and band re-encounter data to quantify migratory connectivity, defined as the relative proportions of individuals migrating between breeding and nonbreeding regions. Next, we use estimated connectivity proportions along with eBird occurrence probabilities to produce probabilistic least-cost path (LCP) indices. In a final step, we use generalized additive mixed models (GAMMs) both to evaluate the ability of LCP indices to accurately predict (i.e., as a covariate) observed locations derived from tracking and band re-encounter data sets versus pseudo-absence locations during migratory periods and to create a fully integrated (i.e., eBird occurrence, LCP, and tracking/band re-encounter data) spatial prediction index for mapping species-specific seasonal migrations. To illustrate this approach, we apply this framework to describe seasonal migrations of 12 bird species across the Western Hemisphere during pre- and postbreeding migratory periods (i.e., spring and fall, respectively). We found that including LCP indices with eBird occurrence in GAMMs generally improved the ability to accurately predict observed migratory locations compared to models with eBird occurrence alone. Using three performance metrics, the eBird + LCP model demonstrated equivalent or superior fit relative to the eBird-only model for 22 of 24 species-season GAMMs. In particular, the integrated index filled in spatial gaps for species with over-water movements and those that migrated over land where there were few eBird sightings and, thus, low predictive ability of eBird occurrence probabilities (e.g., Amazonian rainforest in South America). This methodology of combining individual-based seasonal movement data with temporally dynamic species distribution models provides a comprehensive approach to integrating multiple data types to describe broad-scale spatial patterns of animal movement. Further development and customization of this approach will continue to advance knowledge about the full annual cycle and conservation of migratory birds.

Site quality and intensive early stand management practices affect growth dominance, structural complexity, and tree growth in ponderosa pine plantations

During stand initiation, the influences of silvicultural practices such as competing vegetation control and fertilization have been primarily examined in terms of stand-level growth rather than structural complexity. Understanding how intensive silvicultural treatments alter the long-term trajectory of stand development may be critical to meeting management objectives, such as habitat restoration, minimizing ladder fuels, or carbon sequestration. Previous studies have found mixed evidence for an effect of vegetation control and fertilization on structural complexity. Investigating how early pulse treatments drive tree size differentiation in young stands, as indicated by growth dominance (GD), could potentially allow managers to anticipate or design treatments to alter the development of structural complexity later in stand development. We reanalyzed data from the Garden of Eden experiment, a full-factorial study investigating how competing vegetation and nutrients impact ponderosa pine growth and yield over a gradient of site quality in northern California, USA. Our goals were to determine whether these silvicultural practices alter GD and structural complexity, and whether GD and structural complexity created potential feedbacks to alter stand productivity. We examined data for the first 20 years of stand development across 6 study sites. For each site and observation period, we calculated the growth dominance coefficient of total cubic volume to represent GD and the Gini coefficient of inequality in basal area distribution (GC) to represent structural complexity. We created a series of competing generalized additive mixed models (GAMMs) to disentangle the roles of site, stand age, and treatment on GD and GC. We created a set of competing individual-tree GAMMs at age 20 to isolate the influences of GC and GD on volume increment, controlling for the effects of competition, tree size, site, and treatment influences. In agreement with previous research, we found that GD deviated little from size-symmetry (tree growth being roughly proportional to tree size) and did not vary consistently with treatment. Competing vegetation control and higher site quality promoted lower GC, indicative of lower structural complexity. Fertilization increased structural complexity relative to other treatments on two sites in particular, which may reflect unintentional increases in drought stress from fertilization on sites with metasedimentary soils. While GD had limited influence on individual-tree growth, GC interacted with tree size such that small-medium sized trees grew more rapidly on structurally simple plots. Our results have implications for balancing objectives such as fire risk, carbon sequestration, and habitat during reforestation projects.

Space-time modeling of intensive binary time series eye-tracking data using a generalized additive logistic regression model.

Eye-tracking has emerged as a popular method for empirical studies of cognitive processes across multiple substantive research areas. Eye-tracking systems are capable of automatically generating fixation-location data over time at high temporal resolution. Often, the researcher obtains a binary measure of whether or not, at each point in time, the participant is fixating on a critical interest area or object in the real world or in a computerized display. Eye-tracking data are characterized by spatial-temporal correlations and random variability, driven by multiple fine-grained observations taken over small time intervals (e.g., every 10 ms). Ignoring these data complexities leads to biased inferences for the covariates of interest such as experimental condition effects. This article presents a novel application of a generalized additive logistic regression model for intensive binary time series eye-tracking data from a between- and within-subjects experimental design. The model is formulated as a generalized additive mixed model (GAMM) and implemented in the mgcv R package. The generalized additive logistic regression model was illustrated using an empirical data set aimed at understanding the accommodation of regional accents in spoken language processing. Accuracy of parameter estimates and the importance of modeling the spatial-temporal correlations in detecting the experimental condition effects were shown in conditions similar to our empirical data set via a simulation study. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Historical analysis of an imperiled fish species: environmental variables modeling, biotic interactions, extirpation, and current restricted-range.

Analyses of spatial and temporal patterns and interactions are important for determining the abiotic factors limiting populations and the impact from other species and different anthropogenic stressors that promote the extirpation of species. The fish Hubbsina turneri de Buen (1940) was studied as a model species in a historical context at varying locations. Originally distributed only in the Lerma-Chapala basin, the main lake complex in Mexico, this species has not been collected from Lake Cuitzeo (LC) and now is restricted to Lake Zacapu (LZ). At present, the Highland splitfin is classified as critically endangered. Historical information of LC and historical and current information from LZ were explored by applying cluster analysis and generalized additive mixed model (GAMM) to describe the biotic interactions among fish species and the relationship between density and environmental variables, respectively. The two lakes' contrasting abiotic/biotic characteristics provided elements to describe some species distribution limits in chemical ion gradients. Extirpation calendar dates were estimated using an optimal linear estimation method. Finally, a bibliographic review was conducted on the causes that promoted the extirpation and restriction of H. turneri and the prognosis for its reestablishment and conservation. Clusters showed the fishes relationship according to their distribution along the lakes. GAMM indicated that high H. turneri density is related to low hardness/fecal coliforms, medium depth/suspended solids, and high oxygen concentration. Estimated extirpation dates were between the years 2013 and 2018. The extirpation was linked to an abrupt drop in the LC volume, water quality degradation, increased biotic interactions within macrophytes habitats with native and introduced species, and fisheries bycatches. The current restricted range of H. turneri resulted from the draining of the larger lake, forcing the remaining populations to small spring-fed remnants. Recent samplings in LZ resulted in a low number of individuals. The integration of ecological interactions derived from statistical models, extirpation dates from nonparametric tests, and the exhaustive analysis of historical information can be applied to define the current situation of imperiled, ecologically relevant species, in different aquatic ecosystems. We are confident that this general framework is important for determining (1) the requirements and limitations of populations regarding abiotic variables, (2) biotic interactions (trophic and spatial) with native and introduced species, and (3) different anthropogenic stressors within and around the ecosystem. This knowledge will also allow understanding those aspects that contribute to the extirpation of populations and could help the restoration of the habitat and the reintroduction of extirpated species.