Mixed Model Research Articles

Abstract 7418: LongFuse: Detecting gene fusion transcripts from high throughput long-read single cell RNA sequencing data

Abstract Gene fusion resulted from genomic translocation plays important oncogenic roles including but not limited to gene activation and changing protein coding sequences. Historically, fusion gene analysis has been limited to bulk levels resulting in mixed oncogene activation models. Single cell Nanopore RNA sequencing (scNanoRNAseq) has the unique strength in detecting full-length chimeric transcripts in thousands of single cells in parallel. However, robust computational tools for detecting fusion genes in single cells from scNanoRNAseq data are missing. Here, we developed LongFuse, a fast and accurate tool, to detect fusion genes and their splicing isoforms in single cells from scNanoRNAseq data. LongFuse implements an XOR logic gate algorithm to speed up fusion candidate searching and stringent criteria to eliminate false discoveries due to trans-splicing events and randomly ligated chimeras. We applied LongFUSE onto scNanoRNAseq data of both human prostate cancer cell line, VCaP, and tumor tissues with known TMPRSS2-ERG fusion. Our results showed that both cancer cell line and prostate tumors harbored a mixture of fusion positive and fusion negative tumor cells. Gene expression analysis revealed transcriptional differences between fusion positive and negative cells including genes involved in cancer cell proliferation and invasion programs such as ELL2, ZBTB16, IGF1R, ANK3, MYPOP and PLPP1 genes. LongFUSE also calculates the splicing isoforms of fusion gene transcripts, allowing prediction of protein sequences of fusion gene transcripts. Taken together, our data demonstrated that LongFUSE is a robust computational tool for detecting gene fusions and their splicing isoforms at single cell level from scNanoRNAseq data. Citation Format: Cheng-Kai Shiau, Yueying He, Hsiao-Yun Lin, Lina Lu, Xiao-Dong Lu, Jindan Yu, Ruli Gao. LongFuse: Detecting gene fusion transcripts from high throughput long-read single cell RNA sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7418.

Abstract 1377: The role of TIM3 and PD1 blockades in head and neck cancer

Abstract Background: Our group has recently developed and validated a novel prognostic score for human papillomavirus (HPV+) oropharyngeal cancer called UWO3, which stratifies patients into low risk (immune rich), intermediate risk (immune mixed), and high risk (immune desert) groups. The high-risk immune desert group had a paucity of immune cells, however, that population of lymphocytes expressed high levels of the checkpoint molecule TIM3. To follow up on this, we assessed the therapeutic effect of anti-TIM3 mAb alone and in combination with anti-PD-1 in a syngenic murine HPV+ head and neck cancer model using the mERR. T-cell immunoglobulin mucin 3 (TIM3) and Programmed death 1 (PD-1) are negative immune checkpoint receptors that are expressed on tumor-infiltrating lymphocytes (TIL), play a crucial role in tumor-induced immune suppression. Given the critical role that the tumour microenvironment (TME) has on the prognosis of head and neck squamous cell carcinoma (HNSCC), immune checkpoint inhibitor immunotherapy approaches, specifically anti-PD1 and/or anti-TIM3 antibody therapy, may be very effective treatment strategies and may offer improved survival outcomes. Methods:Immunocompetent C57BL/6 mice were injected in one flank with the syngeneic mouse HPV+ cell line, mEERL (106 cells), for tumour generation. Mice were then treated with either IgG2a isotype control, anti-PD1 (200μg), anti-TIM3 (200 μg) antibodies or a combination of anti-PD-1 and anti-TIM3 were administered via intraperitoneal injection 3 times per week following tumour establishement for 6 weeks (n = 7 mice per arm, total of 28 mice). Tumour volumes were measured every 2 days. Three representative tumors from each treatment group were collected for bulk RNA sequencing, scRNA-seq, and flow cytometry to characterise immune cell populations and transcriptional changes and monitor their impact on the TME of HNSCC. Results:Anti-PD1 and anti-TIM3 both restricted tumour growth by size and weight relative to the IgG2a control (p<0.01, linear mixed model [lmm]). The combination of anti-PD1 and anti-TIM3 was more effective than either monotherapy alone (p<0.05, lmm). RNA sequencing analysis revealed differential abundance in CCL6, CCL9, CFD, and MAP3K5 transcripts relative to control for anti-PD1, anti-TIM3, and combination checkpoint inhibition. Conclusion:Targeting both PD-1 and TIM3 enhanced the anti-tumor immune response in HPV+ head and neck tumours, providing further support for dual targeting of these molecules for more effective cancer immunotherapy. Our results suggest that immune checkpoint inhibitor therapy (PD1 and TIM3 blockades) could be a promising treatment strategy for HPV+ HNSCC, and the expression of these immune checkpoint molecules could serve as a predictive biomarker of patient outcome in HPV+ HNSCC. Citation Format: Mushfiq Shaikh, Amir Karimi, Peter Zeng, Harrison Pan, John Barrett, Anthony Nichols. The role of TIM3 and PD1 blockades in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1377.

Cancer-related cognitive impairment and wellbeing in patients with newly diagnosed aggressive lymphoma compared to population norms and healthy controls: an exploratory study

PurposeThere has been little dedicated research on cancer-related cognitive impairment in patients with aggressive lymphoma. We describe and compare patients’ cognitive function with that of healthy controls and patients’ wellbeing and distress with general population values. We also explore associations between patients’ neuropsychological test performance and self-reported cognitive function and distress.MethodsSecondary analysis of data from a feasibility study of 30 patients with newly diagnosed aggressive lymphoma and 72 healthy controls. Patients completed neuropsychological tests and self-report measures before and 6–8 weeks after chemotherapy. Healthy controls completed neuropsychological tests and the FACT-Cog at enrolment and 6 months later. Mixed models were used to analyze neuropsychological test and FACT-Cog scores. One-sample t-tests were used to compare patients’ self-reported wellbeing and distress with population norms. Associations were explored with Kendall’s Tau b.ResultsPatients and healthy controls were well matched on socio-demographics. Differences between neuropsychological test scores were mostly large-sized; on average, patients’ scores on measures of information processing speed, executive function, and learning and memory were worse both before and after chemotherapy (all p ≤ 0.003). The same pattern was observed for impact of perceived cognitive impairment on quality-of-life (both p < 0.001). Patients’ physical and emotional wellbeing scores were lower than population norms both before and after chemotherapy (all p ≤ 0.018). Associations between neuropsychological performance and other measures were mostly trivial (all p > 0.10).ConclusionFor many patients with aggressive lymphoma, impaired neuropsychological test performance and impact of perceived impairments on quality-of-life precede chemotherapy and are sustained after chemotherapy. Findings support the need for large-scale longitudinal studies with this population to better understand targets for interventions to address cognitive impairments.

One-year effectiveness of high-load compared with low-load strengthening exercise on self-reported function in patients with hypermobile shoulders: a secondary analysis from a randomised controlled trial

ObjectivesTo investigate the long-term effectiveness of high-load versus low-load strengthening exercise on self-reported function in patients with hypermobility spectrum disorder (HSD) and shoulder symptoms.MethodsA secondary analysis of a superiority, parallel-group,...

A spectral approach using fractional Jaiswal functions to solve the mixed time-fractional Black-Scholes European option pricing model with error analysis

A spectral approach using fractional Jaiswal functions to solve the mixed time-fractional Black-Scholes European option pricing model with error analysis

Stability of parallel evolution in shell traits between the littoral and sublittoral ecotypes of the Antarctic limpet Nacella concinna along a 17-year time series

Abstract Ecotypes constitute valuable markers for understanding the phenotypic responses influenced by evolutionary forces and environmental variations. Assessing the role of these processes in establishing and maintaining ecotype divergence is essential for anticipating evolutionary responses to future climate shifts. We studied the evolutionary dynamics of phenotypic population structure between Nacella concinna ecotypes through a morphometric and temporal analysis (2004–2021) in Antarctica. This approach enables the assessment of contemporary evolutionary dynamics in the presence of biotic and abiotic factors, facilitating the inference of interactions between the acting forces. Using generalized Procrustes analysis, ecotypes were successfully discriminated by their lateral shell traits consistently persisting over the analysed period. Multivariate linear and univariate mixed models revealed a significant temporal effect on shell phenotypic variation, surpassing the effect of inter-ecotype differences. However, according to phenotypic trajectory analysis, this temporal effect did not alter the direction of the phenotypic trajectory of ecotype shell shape, which evolved in parallel during the time series. Despite the environmental variation, the evidence of parallel evolution might indicate the incidence of natural selection in ecotype divergence rather than relying solely on phenotypic plasticity. This work enhances our understanding of ecotype temporal changes and microevolution, underscoring the importance of long-term phenotypic monitoring.

Dietary inflammatory potential and arterial stiffness in a French cohort: Insights from the STANISLAS study

Background and aimsChronic inflammation plays a key role in arterial stiffness pathogenesis. Dietary components can display anti- or pro-inflammatory properties. Nonetheless, the association between the diet's overall inflammatory potential and arterial stiffness is unclear. This study aimed to assess the association between the diet's overall inflammatory potential and arterial stiffness assessed by carotid-femoral pulse wave velocity (cfPWV). Methods and resultsThis cross-sectional study included 1307 participants from the STANISLAS family cohort study. Dietary data were collected using a validated food frequency questionnaire. The adapted dietary inflammatory index (ADII) score was calculated to assess the inflammatory potential of the participants’ diet. The association of ADII score quartile with cfPWV was assessed using IPW-weighted linear mixed models with random family effect.The median (Q1-Q3) ADII score was 0.45 (-1.57, 2.04). Participants exhibiting higher ADII scores demonstrated elevated energy intake, dietary saturated fat, and ultra-processed foods. Conversely, individuals with lower ADII scores exhibited higher vitamins and omega intakes, and a higher diet quality, as assessed by the DASH score. Despite these observations from the descriptive analyses, ADII score quartiles were not significantly associated with cfPWV (β(95% CI) were 0.01 (-0.02,0.04) for Q2, 0.02 (-0.01,0.05) for Q3, and 0.02 (-0.01,0.05) for Q4 compared to Q1). ConclusionIn this cross-sectional study, participants had a relatively modest consumption of pro-inflammatory foods, no substantial associations were observed between the diet inflammatory potential and arterial stiffness. Further longitudinal studies in larger cohorts are needed to better understand the link between inflammatory diet and arterial stiffness.

An error components mixed logit with heterogeneity in means and variance for fixed object occupant severity outcomes

This paper presents an error components mixed logit with heterogeneity in means and variance to capture the heterogeneous effects of contributing factors on fixed object occupant severity. One year (2021) of crash data on fixed object related crashes in Lubbock County, Texas was analyzed with fixed object details extracted from crash narratives and classified into 11 groupings. Crash data included any fixed object collision occurring at any point in the sequence of crash events (not exclusive to the first harmful event). The random parameters were identified as indicators for occupant involvement in the first harmful crash sequence event, with that event being collision with a fixed object, for possible injury and injury severity outcomes. Heterogeneity in the means of these random parameters was found with respect to six different indicator variables. Additionally, heterogeneity in the variance of the injury random parameter was found with respect to two different indicator variables. Inclusion of two error component nests improved prediction accuracy at the observation level for higher severity outcomes. The findings in this study suggest that fixed object classification types should be explored further in relation to heterogeneous effects on occupant severity outcomes. Furthermore, the findings also highlight the applicability of an error components mixed logit model for severity analysis.

Differential Cognitive Effects of Unilateral Subthalamic Nucleus Deep Brain Stimulation for Parkinson's Disease.

The aim of this study was to investigate the cognitive effects of unilateral directional versus ring subthalamic nucleus deep brain stimulation (STN DBS) in patients with advanced Parkinson's disease. We examined 31 participants who underwent unilateral STN DBS (left n = 17; right n = 14) as part of an National Institutes of Health (NIH)-sponsored randomized, double-blind, crossover study contrasting directional versus ring stimulation. All participants received unilateral DBS implants in the hemisphere more severely affected by motor parkinsonism. Measures of cognition included verbal fluency, auditory-verbal memory, and response inhibition. We used mixed linear models to contrast the effects of directional versus ring stimulation and implant hemisphere on longitudinal cognitive function. Crossover analyses showed no evidence for group-level changes in cognitive performance related to directional versus ring stimulation. Implant hemisphere, however, impacted cognition in several ways. Left STN participants had lower baseline verbal fluency than patients with right implants (t [20.66 = -2.50, p = 0.02]). Verbal fluency declined after left (p = 0.013) but increased after right STN DBS (p < 0.001), and response inhibition was faster following right STN DBS (p = 0.031). Regardless of hemisphere, delayed recall declined modestly over time versus baseline (p = 0.001), and immediate recall was unchanged. Directional versus ring STN DBS did not differentially affect cognition. Similar to prior bilateral DBS studies, unilateral left stimulation worsened verbal fluency performance. In contrast, unilateral right STN surgery increased performance on verbal fluency and response inhibition tasks. Our findings raise the hypothesis that unilateral right STN DBS in selected patients with predominant right brain motor parkinsonism could mitigate declines in verbal fluency associated with the bilateral intervention. ANN NEUROL 2024;95:1205-1219.

Word-object and action-object learning in a unimodal context during early childhood

Abstract Word-object and action-object learning in children aged 30 to 48 months appears to develop at a similar time scale and adheres to similar attentional constraints. However, children below 36 months show different patterns of learning word-object and action-object associations when this information is presented in a bimodal context (Eiteljoerge et al., 2019b). Here, we investigated 12- and 24-month-olds’ word-object and action-object learning when this information is presented in a unimodal context. Forty 12- and 24-month-olds were presented with two novel objects that were either first associated with a novel label (word learning task) and then later with a novel action (action learning task) or vice versa. In subsequent yoked test phases, children either heard one of the novel labels or saw a hand performing one of the actions presented with the two objects on screen while we measured their target looking. Generalized linear mixed models indicate that 12-month-olds learned action-object associations but not word-object associations and 24-month-olds learned neither word- nor action-object associations. These results extend previous findings (Eiteljoerge et al., 2019b) and, together, suggest that children appear to learn action-object associations early in development while struggling with learning word-object associations in certain contexts until 2 years of age.

Social Activity and Cognitive Decline in Older Residents of Long-Term Care Facilities: A Cohort Study.

Cognitive decline is a major reason for dependence and resource use in long-term care. We explored whether social activities may prevent cognitive decline of older residents of long-term care facilities. In a routine care cohort, 3,603 residents of long-term care facilities were assessed on average 4.4 times using the interRAI-Long-Term-Care-Facilities instrument which includes frequency of participation in social activities of long standing interest over the last 30 days and the Cognitive Performance Scale. Linear mixed models repeated measures analyses were performed corrected for age, sex, physical activity, Activities of Daily Living, mood, and health indicators. Social activity was associated with cognitive preservation over time. This association was stronger in those with no or mild cognitive impairment at baseline, relative to those with moderate to severe impairment. Participation in specific social activities such as conversing and helping others showed a similar positive association. The relation between social activity and cognitive impairment appeared to be bi-directional. The protective effects of social activity offer a window of opportunity to preserve cognitive functioning in long-term care residents.

Generalized functional additive mixed models with (functional) compositional covariates for areal Covid-19 incidence curves

Abstract We extend the generalized functional additive mixed model to include compositional and functional compositional (density) covariates carrying relative information of a whole. Relying on the isometric isomorphism of the Bayes Hilbert space of probability densities with a sub-space of the L2, we include functional compositions as transformed functional covariates with constrained yet interpretable effect function. The extended model allows for the estimation of linear, non-linear, and time-varying effects of scalar and functional covariates, as well as (correlated) functional random effects, in addition to the compositional effects. We use the model to estimate the effect of the age, sex, and smoking (functional) composition of the population on regional Covid-19 incidence data for Spain, while accounting for climatological and socio-demographic covariate effects and spatial correlation.

First trimester maternal tryptophan metabolism and embryonic and fetal growth: the Rotterdam Periconceptional Cohort (Predict Study).

What is the association between first trimester maternal tryptophan (TRP) metabolites and embryonic and fetal growth? Higher 5-hydroxytryptophan (5-HTP) concentrations are associated with reduced embryonic growth and fetal growth and with an increased risk of small-for-gestational age (SGA), while higher kynurenine (KYN) concentrations are associated with a reduced risk of SGA. The maternal TRP metabolism is involved in many critical processes for embryonic and fetal growth, including immune modulation and regulation of vascular tone. Disturbances in TRP metabolism are associated with adverse maternal and fetal outcomes. This study was embedded within the Rotterdam Periconceptional Cohort (Predict Study), an ongoing prospective observational cohort conducted at a tertiary hospital from November 2010 onwards. A total of 1115 women were included before 11 weeks of gestation between November 2010 and December 2020. Maternal serum samples were collected between 7 and 11 weeks of gestation, and TRP metabolites (TRP, KYN, 5-HTP, 5-hydroxytryptamine, and 5-hydroxyindoleacetic acid) were determined using a validated liquid chromatography (tandem) mass spectrometry method. Serial 3D ultrasound scans were performed at 7, 9, and 11 weeks of gestation to accurately assess features of embryonic growth, including crown-rump length (CRL) and embryonic volume (EV) offline using virtual reality systems. Fetal growth parameters were retrieved from medical records and standardized according to Dutch reference curves. Mixed models were used to assess associations between maternal TRP metabolites and CRL and EV trajectories. Linear and logistic regression models were utilized to investigate associations with estimated fetal weight (EFW) and birthweight, and with SGA, respectively. All analyses were adjusted for potential confounders. Maternal 5-HTP concentrations and the maternal 5-HTP/TRP ratio were inversely associated with embryonic growth (5-HTP, √CRL: β = -0.015, 95% CI = -0.028 to -0.001; 5-HTP 3√EV: β = -0.009, 95% CI = -0.016 to -0.003). An increased maternal 5-HTP/TRP ratio was also associated with lower EFW and birthweight, and with an increased risk of SGA (odds ratio (OR) = 1.006, 95% CI = 1.00-1.013). In contrast, higher maternal KYN concentrations were associated with a reduced risk of SGA in the unadjusted models (OR = 0.548, 95% CI = 0.320-0.921). Residual confounding cannot be ruled out because of the observational design of this study. Moreover, this study was conducted in a single tertiary hospital, which assures high internal validity but may limit external validity. The novel finding that maternal 5-HTP concentrations are associated with a smaller embryo and fetus implies that disturbances of the maternal serotonin pathway in the first trimester of pregnancy are potentially involved in the pathophysiology of fetal growth restriction. The association between higher maternal KYN concentrations and a reduced risk of SGA substantiate the evidence that the KYN pathway has an important role in fetal growth. More research is needed to delve deeper into the potential role of the maternal TRP metabolism during the periconception period and pregnancy outcome for mother and offspring. This study was funded by the Department of Obstetrics and Gynecology and the Department of Clinical Chemistry of the Erasmus MC, University Medical Center, Rotterdam, the Netherlands. The authors have no competing interests to disclose. N/A.

Community Preferences for the Care of Older People at the End of Life: How Important is the Disease Context?

Population preferences for care at the end of life can inform palliative care policy and direction. Research investigating preferences for care at the end of life has focused predominantly on the context of advanced cancer, with relatively little attention to other life-limiting illnesses that are common causes of death. We aimed to investigate preferences for the care of older people at the end of life in three different disease contexts. The purpose was to understand if population preferences for care in the last 3 weeks of life would differ for patients dying from cancer, heart failure or dementia. Three discrete choice experiments were conducted in Australia with a general population sample using similar methods but different end-of-life disease contexts. Some attributes were common across the three experiments and others differed to accommodate the specific disease context. Each survey was completed by a different panel sample aged ≥45years (cancer, n=1548; dementia, n=1549; heart failure, n=1003). Analysis was by separate mixed logit models. The most important attributes across all three surveys were costs to the patient and family, patient symptoms and informal carer stress. The probability of choosing an alternative was lowest (0.18-0.29) when any one of these attributes was at the least favourable level, holding other attributes constant across alternatives. The cancer survey explored symptoms more specifically and found patient anxiety with a higher relative importance score than the symptom attribute of pain. Dementia was the only context where most respondents preferred to not have a medical intervention to prolong life; the probability of choosing an alternative with a feeding tube was 0.40 (95% confidence interval 0.36-0.43). This study suggests a need for affordable services that focus on improving patient and carer well-being irrespective of the location of care, and this message is consistent across different disease contexts, including cancer, heart failure and dementia. It also suggests some different considerations in the context of people dying from dementia where medical intervention to prolong life was less desirable.

Major Depressive Disorder as a Driver of Dual Systems Model Development During Adolescence and Emerging Adulthood Among Justice-Involved Youth: Is Salience Age-Graded?

The dual systems model is a psychological framework centered on differential development of sensation-seeking and impulse control during adolescence and emerging adulthood with implications for understanding antisocial behavior. However, there is a dearth of research which has examined mental illness as a driver of differential development of these constructs. This study examined major depressive disorder as a risk factor for elevated sensation-seeking and diminished impulse control and tested to determine whether the salience differed by age. The Pathways to Desistance data were analyzed. Mixed effects models examined the direct effect of major depressive disorder on dual systems outcomes and test for moderation by age. Findings indicated that major depressive disorder at baseline was associated with increased sensation-seeking and diminished impulse control. Relationships did not differ in salience based on age. Results suggest that treatment effective for addressing depression may have relevance for mitigating the impact of the disorder on cognition.

Lifetime seismic fragility analysis of long-span spatial structures considering the wind-induced fatigue effect

Long-span spatial structures are susceptible to cumulative fatigue damage over their lifespan due to prolonged exposure to wind loads. The degradation in material properties resulting from fatigue can impact the structure's performance to resist earthquakes. However, previous studies and current design specifications do not address the issue of wind-induced fatigue in long-span spatial structures, making it difficult to evaluate the multihazard risk of the facilities under the combined action of fatigue and earthquakes. In this study, an assessment framework for the lifetime multihazard fragility of long-span spatial structures subjected to fatigue and earthquakes is developed to address this issue. The innovation of the proposed wind-induced fatigue analysis is that the influence of wind direction can be considered. Multihazard fragility surfaces are established with a mixed exponential model to assess the seismic fragility of the structure with different service times. The proposed method is applied to the seismic analysis of a typical single-layer Kiewitt-8 reticulated dome (SK8RD) to verify its feasibility. The results demonstrate that after 47 years of service, the ultimate bearing capacity of SK8RD decreases by 45.5% due to the wind-induced fatigue, while its collapse probability increases by 25.3% under the seismic action. Neglecting wind direction randomness and focusing solely on a single direction can lead to an overestimation of wind fatigue damage by more than twofold. Utilizing the probabilistic multihazard demand model based on the mixed exponential function enhances the regression accuracy by 12.9%, facilitating a more precise assessment of multihazard fragility for the SK8RD subjected to seismic and long-term wind fatigue. The proposed framework offers a valuable tool for evaluating multihazard risk considering the wind-induced fatigue for in-service long-span spatial structures.

Exploring the depths of on‐water training in highly‐trained rowing athletes

AbstractThis investigation examined the association between on‐water rowing stroke‐rate (SR), velocity and heart‐rate (HR) in highly trained rowers (n = 8 male; n = 8 female and 19.3 ± 1.1 year) over a 4‐month real‐world (i.e., variable environment and boat class) training period. On‐water SR, prognostic velocity (percent of world's best velocity) and HR were captured for 1453 sessions via smart‐watch and chest‐strap HR monitor. Data was filtered and smoothed with individual HR training zones identified (T1–T5). Linear mixed modeling and an overlapping index () were used to assess differences in SR and prognostic velocity between HR zones. Correlation coefficient (r) was used to assess the SR and prognostic velocity relationship and progression of prognostic velocity at a SR of 20spm over time. There were significant differences in SR and prognostic velocity between HR zones (T1&gt;T2&gt;T3&gt;T4&gt;T5, p &lt; 0.001); however, data overlap between adjacent zones was substantial for both variables ( = 0.69–0.85; prognostic velocity: = 0.46–0.86). A significant, positive correlation (r = 0.50 and p &lt; 0.001) between SR and prognostic velocity was found. Progression of prognostic velocity at SR 20spm over the study duration was trivial (r = −0.01 and p = 0.71). Variables commonly used to prescribe and describe on‐water rowing training showed large variability in a real‐world training environment impacting the ability to accurately monitor training performance and progression.

Into the wild: coupling otolith and archival tag records to test assumptions underpinning otolith chemistry applications in wild fish

Chronological records of elemental concentrations in fish otoliths are a widely used tool to infer the environmental conditions experienced by individual fish. To interpret elemental signals within the otolith, it is important to understand how both external and internal factors impact ion uptake, transport and incorporation. In this study, we have combined chronological records from otoliths and archival data storage tags to quantify the influence of internal (sex, size, age, growth) and external (temperature, depth, salinity) conditions on otolith elemental chemistry of cod (Gadus morhua) in natural settings of the Baltic Sea. This study focused on elements primarily under physiological control: Phosphorus (P), magnesium (Mg) and zinc (Zn); and elements under environmental control: Strontium (Sr), barium (Ba) and manganese (Mn). Based on known spatial and temporal patterns in environmental conditions and fish size, growth, and maturity, we posed a series of hypotheses of expected otolith element patterns. Partial effects of internal and external drivers on element concentration were analyzed using a Linear Mixed Model approach with random variables (fish and year). Predicted effects of otolith concentrations of all elements under physiological control (P, Mg, Zn) showed similar trends, with distinct seasonal patterns (lowest concentration in late spring, highest concentrations in winter), and a positive correlation with water temperature, in addition to higher Zn and lower P in spawning individuals. Predicted effects of otolith concentrations of elements expected to be predominantly under environmental control showed the predicted geographic and depth-related trends based on ambient salinity (Ba) and coastal hypoxia (Mn). However, contrary to expectation, Sr was unrelated to salinity. Predicted otolith Ba, Sr and Mn concentrations also exhibited pronounced seasonal patterns that were out of phase with each other but appeared to be partly explained by spawning/feeding migrations. While performing laboratory validation studies for adult fish is typically not possible, these results highlight the importance of assessing local water chemistry and freshwater endmembers in one’s study system before otolith elemental chemistry can be reliably used to reconstruct fish habitat use and environmental histories.

Analysis of the Swordfish Xiphias gladius Linnaeus, 1758 Catches by the Pelagic Longline Fleets in the Eastern Pacific Ocean

During the last 50 years, the increase in the efforts of the longline fleet in the Eastern Pacific Ocean (EPO) resulted in an increase in the capture of the swordfish Xiphias gladius. We analyzed a historical database of swordfish catches (1980–2020) reported by the industrial longline fleet to the Inter-American Tuna Tropical Commission (IATTC), which contains catch and effort data aggregated in monthly quadrants of 5° × 5° in the EPO. The swordfish catch reported by the international longline fleets was analyzed to evaluate the spatiotemporal variation of the catch and the different phases through which this important fishery has gone through. Different statistical models such as the Generalized Additive Mixed Model (GAMM) and the breaks for additive season and trend BFAST algorithm were used for the decomposition of the time series. Results indicated that the effort directed towards the swordfish increased in recent years and that the highest catches occurred by Peru. The adjusted GAMM explained 80% of the total temporal variation of the swordfish catch per unit effort CPUE and had a 90% prediction efficiency. The BFAST algorithm found three break points in the time series of the standardized CPUE, points associated with abrupt changes, thus defining four distinct periods, all of them statistically significant. According to the BFAST model, the current trend of swordfish CPUE is upward. It is recommended to take this finding with caution to obtain the sustainable exploitation of the swordfish fishery resource.

In vitro evaluation of the inhibitory capacity of three Trichoderma isolates on Ralstonia solanacearum

Bacterial wilt in bananas, caused by Ralstonia solanacearum or Moko, limits crop production and threatens Ecuador. This study evaluated Trichoderma isolates in laboratory conditions as an innovative alternative to ensure sustainability in banana production. The four R. solanacearum. isolates were obtained from banana plants exhibiting disease symptoms and were characterized through morphological and biochemical tests. Four treatments were evaluated: three isolates of fungi from the genus Trichoderma (Trichoderma viride, T. harzianum, T. asperellum) and one consisting of a combination of the three isolates above. The inhibitory capacity of the Trichoderma isolates on R. solanacearum colonies was measured. A completely randomized design with three replicates was used, and general linear and mixed models were employed, with qq-plot graphs for normality and residual plots for variance homogeneity. Furthermore, a Fisher's LSD test was conducted at a significance level of α = 0.05. In the biochemical tests, the bacterial isolates exhibited specific characteristics of R. solanacearum in two bacterial isolates. In the inhibition tests, treatment four and treatment one (consortium of the three Trichoderma isolates and Trichoderma viride) showed the highest inhibitory potential, with 76.07% and 61.19%, respectively. The consortium of Trichoderma isolates demonstrated the highest inhibitory potential against R. solanacearum, with day 10 being the time with the highest percentage of inhibition (72.61%). Keywords: Bacterial wilt, Ralstonia solanacearum, Trichoderma, inhibition