Length-based Approach Research Articles

LBFextract: Unveiling transcription factor dynamics from liquid biopsy data

MotivationThe analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation, but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns. ResultsWe introduce Liquid Biopsy Feature extract (LBFextract), a comprehensive package designed to streamline feature extraction from cfDNA sequencing data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies. LBFextract facilitates the integration of preprocessing and postprocessing steps through alignment fragment tags and a hook mechanism. It incorporates various methods, including coverage-based and fragment length-based approaches, alongside two novel feature extraction methods: an entropy-based method to infer TF activity from fragmentomics data and a technique to amplify signals from nucleosome dyads. Additionally, it implements a method to extract condition-specific differentially active TFs based on these features for biomarker discovery. We demonstrate the use of LBFextract for the subtype classification of advanced prostate cancer patients using coverage signals at transcription factor binding sites from cfDNA. We show that LBFextract can generate robust and interpretable features that can discriminate between different clinical groups. LBFextract is a versatile and user-friendly package that can facilitate the analysis and interpretation of liquid biopsy data. Data and Code Availability and ImplementationLBFextract is freely accessible at https://github.com/Isy89/LBF. It is implemented in Python and compatible with Linux and Mac operating systems. Code and data to reproduce these analyses have been uploaded to 10.5281/zenodo.10964406.

Evaluating stock status of shortfin mako (Isurus oxyrinchus) in southern Java and West Nusa Tenggara, Indonesia, using length-based approach

Evaluating stock status of shortfin mako (Isurus oxyrinchus) in southern Java and West Nusa Tenggara, Indonesia, using length-based approach

Stock Assessment of Exploited Populations of Shovel-Nosed Lobster Thenus unimaculatus (Scyllaridae, Burton and Davie, 2007) Along the Indian Coast Using Length-Based Approaches

Stock Assessment of Exploited Populations of Shovel-Nosed Lobster Thenus unimaculatus (Scyllaridae, Burton and Davie, 2007) Along the Indian Coast Using Length-Based Approaches

Tensile behavior of polycarbonate: Key aspects for accurate constitutive modelling and simulation

Polycarbonate (PC) is a thermoplastic polymer used in many engineering applications such as safety devices and aerospace components. However, the unique behavior of PC under tensile load and its effects on the estimation of its constitutive curve are often overlooked in the literature, neglecting to consider crucial aspects of the characterization process. This work carries out a comprehensive analysis of the mechanical behavior of PC to understand the key points for accurate constitutive modeling and simulation of its static tensile performance, including its unconventional deformation mechanisms. The work starts from the accurate analysis of a representative experimental static tensile test on a rectangular section PC specimen and the evaluation of its true stress-strain curve. This analysis, carried out considering the classic length-based approach and the more accurate area-based approach, makes it possible to evaluate in detail the peculiar tensile behavior of this material. The mathematical form of the PC true stress-strain curve is then justified and the coincidence of the obtained length-based and area-based estimates of the same is demonstrated. Then, based on the in-depth understanding of the dynamics underlying the mechanical behavior of PC and making use of FEM simulations, the key points for obtaining its constitutive curve are defined. It is demonstrated that the constitutive curve is able to completely determine the behavior of PC, including its peculiar deformation mechanism. It is also highlighted which specific characteristics of the constitutive curve are critical in affecting various aspects of the material's behavior. The final constitutive curve of PC at hand is then obtained with an inverse approach, capable of accurately simulating all aspects of its tensile behavior. The validity of the proposed modelling key points is then confirmed, effectively explaining the underlying phenomena controlling the tensile behavior of PC and massively reducing uncertainty in the estimation of its constitutive curve starting from its area-based true curve.

Length-based stock assessment for Malabar blood snapper in Makassar Strait-Indonesia: Status and recommendation for sustainability

Snapper is one of the important groups of fish in demersal-reef fisheries in Indonesia. Malabar blood snapper Lutjanus malabaricus is the main and dominant species in snapper fisheries, making it the major target of fishing activities in Indonesia, including in Makassar Strait. Current management is still limited based on aggregate stocks (i.e., TAC for demersal-reef fish, snapper is included in this group), to reduce uncertainty, focused management is needed on specific fish stocks. The length-based approach for stock assessment was conducted under a data-limited situation. This study revealed the character of L.malabaricus in the Makassar Strait based on life history parameters as the categories of slow growth, late maturity and long-lived species. The condition of L.malabaricus has indicated a decrease in stocks based on several length models (LBSPR, LBB and LBI). A simulation of determining reference points for setting length size as a management intervention has been carried out with the scenarios: BaU (Lc=33.5 cm), Limit (Lc=Lm50=47.2 cm), and Target (Lc=Lc-opt =57 cm), but F is constant (F=0.5, as the current F). The BaU scenario performed it is difficult for L.malabaricus to achieve sustainability. In the limit scenario, MSY could be achieved by maintaining F=0.5 and SPR at 30% with Lc=Lm50. In the target scenario, there is no sustainability risk with FFSPR40%=0.5 and Lc=Lc-opt. It can be said that the limit reference point is determined at SPR 30% with Lc=Lm50, while the target reference point is at SPR 40% with Lc=Lc-opt.

Population Status of Sardinella longiceps of the Sultanate of Oman: Perspectives of Length-based Approach

Population Status of Sardinella longiceps of the Sultanate of Oman: Perspectives of Length-based Approach

KONDISI STOK IKAN KARANG DI KAWASAN KONSERVASI PERAIRAN TWP GITA NADA, PROVINSI NUSA TENGGARA BARAT

TWP Gita Nada is one of the water conservation areas in NTB Province whose reef fish resources are used by fishers around the area, especially in zones that are permitted for fishing activities. However, there are indications that the use of the area by fishers causes a decrease in the abundance and biomass of reef fish in TWP Gita Nada. Therefore, it is necessary to research the condition of reef fish stocks in TWP Gita Nada to know for certain about the availability of reef fish resources in the area. This study collected data at 11 fish landing sites around TWP Gita Nada from March 2017 to December 2021. Data were collected using a sampling technique on 35% of the total fish landing activity in TWP Gita Nada. Data consisted of fishing units, fishing operations, fishing areas, catches, fish species, and fish length. Data analysis in this study used a length-based stock assessment approach to identify the condition of reef fish stocks and their utilization status. The results indicated that 271 species of reef fish landed in the TWP Gita Nada waters conservation area were identified from 31 family groups dominated by fish of the species Lutjanus gibbus, Lethrinus ornatus, Acanthurus mata, Naso thynnoides, and Lethrinus rubrioperculatus. Among those four dominant reef fish species, Lutjanus gibbus is in fully exploited utilization status with an SPR value of 0.26 or 26%. Meanwhile, the other three types of reef fish are under-exploited with SPR values above 0.3 or 30%.
 
 Keywords: fishing, Lc, length-based approach, Lm, SPR.

Gaussian mixture model with local consistency: a hierarchical minimum message length-based approach

Gaussian mixture model with local consistency: a hierarchical minimum message length-based approach

Assessment of the stock status of blackfin tuna Thunnus atlanticus in the Southwest Atlantic Ocean: a length-based approach

This is the first assessment of blackfin tuna Thunnus atlanticus stock status. The aim of the present study was to estimate the status of its Southwestern stock using length-based models. A total of 1929 individuals was gathered in four years of length data (1998–2019). Two length-based models were applied, Length-Based Spawning Potential Ratio (LBSPR) and Stock Synthesis Data-limited tool (SS-DL) and five scenarios combining a set of growth parameters (asymptotic length-L∞, and growth constant-K) were built to accommodate different life histories available in the literature. The natural mortality (M) was estimated through four empirical methods. Given that the fishery only selects mature fish, length at selectivity were larger than the length at first maturity and high relative fishing mortality were found at most scenarios, even with high spawning potential ratio (SPR) values. The LBSPR estimated higher values of SPR, it presented a steeper decline than SS-DL between 1998 and 2019. In addition, growth parameters influence the estimation of the virginal stock, and intermediate M/K values seems to represent better the estimated length composition, given the low historical catch of the species. A declining pattern in SPR was observed over time with a reduction of 12% according to LBSPR and 7% decrease based on SS-DL methods. However, the overall evaluation of the Southwestern Atlantic stock of blackfin tuna in 2019 revealed an SPR range of 0.41 to 0.63, suggesting sustainable exploitation. Even with the limited data, we could have a proxy of stock status estimation by using length-based models which highlights the importance of such data. However, due to the high uncertainty of the results, better collection of catch, effort and length data should be considered. Additionally, SS-DL seems to estimate better SPR values when variability of growth parameters are placed for a given species.

Comparative assessment of the impacts of artisanal trolling and industrial longlining on yellowfin tuna exploited off the Kenyan coast

The Indian Ocean yellowfin tuna stock has been classified as overfished and remains subject to overfishing by industrial and artisanal fleets despite the implementation of catch reduction measures to rebuild the stocks. This study assessed the impacts of artisanal trolling and industrial pelagic longlining on the population structure of yellowfin tuna exploited in Kenyan waters. Catch data including fork length, sex and gonad maturity was examined for the two fisheries between April 2019 and April 2021. Selection patterns were then compared using eight length-based indicators and a suite of indicator ratios. Results showed that artisanal trolling caught smaller individuals ranging from 32−177 cm with a mean of 76 ± 0.5 cm and a mode of 71 cm. The industrial fishery caught significantly larger individuals (p > 0.05) ranging from 52 – 204 cm with a mean of 137 ± 0.7 cm and a mode of 160 cm. Length at first capture (Lc) for artisanal trolling was estimated at 36 cm and 80 cm for the industrial fishery. Statistical tests further revealed significant differences in length distribution and selectivity curves. It was clear that the fisheries consistently captured distinct components of the yellowfin tuna population structure. The industrial fishery was dominated by mature individuals above length at 50 % maturity (>100 cm, L50) constituting 90 % of the sampled catch of which 56 % were large mega-spawners above the optimum length (> Lopt + 10%). On the other hand, 92 % the artisanal trolling fishery constituted small individuals below L50 and no mega-spawners. Overall, the average monthly sex ratio was skewed to males (F:M ratio = 1: 1.14). Deviations from the expected 1:1 sex-ratio were not significant; however, industrial longline catches were skewed towards large males, and artisanal trolling catches towards small females. The study illustrates application of widely used lengthbased approaches to derive insights on fishery interactions in data limited scenarios.

Assessing Low Value Crustacean Bycatch Species Using Length Based Bayesian Biomass (LBB) Method, a Tool for Data Poor Fish Stock Assessment

The majority of tropical fish stocks lack sufficient data for conventional fish stock assessment, making them data-poor fisheries. The status of stock assessment is even more dismal for the low value fishes or crustaceans landed by the trawlers in a significant quantity. Crustaceans like non-edible small crabs (Charybdis spp) and stomatopods form a significant component of the low-value bycatch landed along the northwest coast. Despite the high ecological importance of these groups and the recent declining trend in catches (2007-19), no attempts so far have been made to evaluate the stock status of these groups from the study region. As reliable time series catch and effort data for the individual species are not available, a recently developed length-based approach, LBB (Length Based Bayesian Biomass) estimation method is adopted for the present study. Two of the evaluated stocks, Charybdis hoplites and Miyakella nepa were found abundant (B/BMSY>1.1), whereas Oratosquillina interrupta (B/BMSY=0.94) was found slightly overfished. The sufficient number of larger individuals were found lacking in all three species (L95th/L∞<<1.0). A higher incidence of juveniles in catches was estimated for C. hoplites and O. interrupta (Lmean/Lopt<<1.0).

Assessment of Coilia mystus and C. nasus in the Yangtze River Estuary, China, Using a Length-Based Approach

An assessment of the stock status and historical changes in abundance of Coilia mystus and C. nasus in the Yangtze River Estuary, China, was carried out based on field surveys conducted in 2019–2020 and published length-frequency (L/F) data from earlier periods. These two species’ current and past relative biomasses (B/BMSY) were estimated using a length-based Bayesian biomass estimation method (LBB). The LLB method also estimated their asymptotic lengths (Linf), current and optimum mean lengths at first capture (Lc; Lopt_c), and their ratios of natural and fishing mortality to growth (M/K; F/K). In response to increasing fishing pressure, both species’ maximum lengths declined, along with their B/BMSY ratio, which declined for C. mystus from 1.7 in 1982 to 0.47 in 2020 and for C. nasus from 1.7 in 2006 (or earlier) to 0.17 in 2020. These assessments show that both of the two Coilia species are overfished, with C. nasus impacted more severely than C. mystus. The prospect for the recovery of these two species is briefly discussed. This contribution will help toward the management of the population of these two Coilia species and provides a basis for evaluating the effect of the 10-year fishing ban in the Yangtze River.

Length-based approaches to estimating natural mortality using tagging and fisheries data: The example of the eastern Aleutian Islands, Alaska golden king crab (Lithodes aequispinus)

We evaluated natural mortality (M yr−1) estimation reliability for eastern Aleutian Islands male golden king crab (Lithodes aequispinus), an exploited stock, by comparing an integrated length-based assessment model approach and a likelihood method using tag release-recapture data. We used 1997, 2003, and 2006 tag release-recapture data to estimate the size transition matrix, M, fishing mortality, total selectivity, and retained selectivity and compared M likelihood profiles between both methods. Furthermore, we conducted simulations with varying initial survival and tag reporting rates to show that M estimation reliability declines as these rates decline. Restricted time-at-large, full initial survival, and complete reporting assumptions produce an M estimate closer to that of the integrated length-based assessment method. Because the reliability of the M estimate is sensitive to changes in these assumptions, future efforts should focus on maximizing the number of tagged crab (and hence recaptures), evaluating initial tag-induced mortality, and optimizing tagged crab recapture reporting rates. The reliance of fishery-dependent data and high tag reporting rates highlights the importance for maintaining a positive cooperation with fishers for efforts towards sustainable management.

Relatively low tooth replacement rate in a sauropod dinosaur from the Early Cretaceous Ruyang Basin of central China.

Tooth replacement rate is an important feature related to feeding mechanics and food choices for dinosaurs. However, only a few data points are available for sauropod dinosaurs, partially due to rarity of relevant fossil material. Four somphospondylan sauropod species have been recovered from the Lower Cretaceous Aptian–Albian Haoling Formation in the Ruyang Basin, Henan Province of central China, but no cranial material has been reported except for a single crown. Here we report the discovery of the rostral portion of a left dentary with replacement teeth in its first five alveoli. Comparative anatomical study shows the partial dentary can be assigned to a member of early diverging somphospondylans. The non-destructive tooth length-based approach to estimating tooth formation time and replacement rate is adopted here. The estimated tooth replacement rate is 76 days, faster than that of Brachiosaurus (83 days) and much lower than typical late diverging lithostrotian titanosaurians (20 days). Thus, this discovery adds an intermediate tooth replacement rate in the evolution of titanosauriform sauropods and supports the idea that evolution of tooth replacement rate is clade-specific. This discovery also provides more information to understand the Ruyang sauropod assemblage, which includes one of the most giant dinosaurs to have walked our Earth (Ruyangosaurus giganteus).

Sustainability status of the grouper fishery in the Azores archipelago: A length-based approach

Small-scale fisheries, demersal, in particular, are a main fishery component in the Azores archipelago, catching a high diversity of species, including “groupers” (Serranidae family) that have high commercial value and demand in the market. Blacktail comber (Serranus atricauda) and Dusky grouper (Epinephelus marginatus) dominate grouper landings, but their fishery status in the Azores is generally unknown. This study applied a length-based approach (Length-Structured Growth-Type-Group Model) to assess the status of grouper fisheries in the Azores, using length-composition data from the commercial fishery and covering distinct gear selectivity and spatial (islands) patterns. Blacktail comber is in worse condition than dusky grouper, with spawning potential ratio (SPR) estimates below 30%, which indicates that this species is fished currently at unsustainable levels in the Azores; SPR for dusky grouper, well above 30%, suggests that this species is fished at sustainable levels. Given the low SPR estimates for São Miguel Island, we propose to, urgently, develop, and implement management measures to ensure the recovery and sustainability of blacktail comber. Our findings support the development of management measures that take into account different selectivity by fleet (gear) and the distinct fishing strategies by island (spatial patterns). This study, the first attempt to assess the sustainability status of serranids in the Azores, highlighted limitations of the sampling coverage that deserve urgent fix, as well as other areas where improvements are critical to ensure the sustainability of these resources in the Azores.

Gastric Tract Disease Recognition Using Optimized Deep Learning Features

Artificial intelligence aids for healthcare have received a great deal of attention. Approximately one million patients with gastrointestinal diseases have been diagnosed via wireless capsule endoscopy (WCE). Early diagnosis facilitates appropriate treatment and saves lives. Deep learning-based techniques have been used to identify gastrointestinal ulcers, bleeding sites, and polyps. However, small lesions may be misclassified. We developed a deep learning-based best-feature method to classify various stomach diseases evident in WCE images. Initially, we use hybrid contrast enhancement to distinguish diseased from normal regions. Then, a pretrained model is fine-tuned, and further training is done via transfer learning. Deep features are extracted from the last two layers and fused using a vector length-based approach. We improve the genetic algorithm using a fitness function and kurtosis to select optimal features that are graded by a classifier. We evaluate a database containing 24,000 WCE images of ulcers, bleeding sites, polyps, and healthy tissue. The cubic support vector machine classifier was optimal; the average accuracy was 99%.

A Comparison of the Effectiveness in Management of Threatened Preterm Labor Between Cervical Length-based Approach and Conventional Approach: A Randomized Control Trial

A Comparison of the Effectiveness in Management of Threatened Preterm Labor Between Cervical Length-based Approach and Conventional Approach: A Randomized Control Trial

POPULATION DYNAMIC AND SPAWNING POTENTIAL RATIO OF SHORT MACKEREL (Rastrelliger brachysoma Bleeker, 1851) IN THE NORTHERN COAST OF JAVA

Short mackerel fish (Rastrelliger brachysoma) is one of small pelagic fish mostly exploited by mini purse seine fishing gear. Exploitation of short mackerel by mini purse seine has an increasing trend every year and suspected to have negative impacts. One of the negative impact is the decrease of fish abundance, so it is necessary to carry out population dynamics and Spawning Potential Ratio (SPR) studies through length-based approach to provide exploitation indicator as biology reference point. The result of length-weight relationship analysis shows that the growth pattern (b = 2.3483) is negative allometry. The estimated length at first capture and its first sexual maturity analysis shows that the value of length at first capture (Lc = 15.4 cm FL) is greater than the length at first sexual maturity (Lm = 15.21 cm FL). The estimated maximum length (L∞) is 21.05 cm FL with growth rates (K) is 1.01 year-1 and t0 at -0.177 years. The estimated total mortality (Z) was 5.48 year-1, natural mortality (M) was 2.02 year-1 and fishing mortality (F) was 3.46 year-1. The predicted exploitation rate (E) is 0.63 which higher than the optimum value (E = 0.5). The estimated length-based SPR (LB-SPR) of 30% (SPR > 20% or above limit) means that short mackerel fishing activity has full exploitation.

Assessment of the stock status of small-scale and multi-gear fisheries resources in the tropical Eastern Pacific region

Small-scale multi-gear fisheries contribute half of global fisheries landings but are generally data-poor, hindering their assessment and management. Aiming to overcome various existing challenges, we used two complementary length-based approaches to assess the status of three main target species in the small-scale fisheries of Eastern Pacific countries: Spotted rose snapper Lutjanus guttatus, Pacific sierra Scomberomorus sierra, and Pacific bearded Brotula clarkae, using length-frequency catch data (LFCD) from the Colombian Pacific coast. Two data sources – official governmental data and community-based monitoring from a non-government organization – were used to estimate two sets of stock indicators: one based on the derivation of growth and mortality parameters from modal progression, catch curve analysis and a yield-per-recruit model using TropFishR; and the second based on the relative contribution of fish sizes with regard to proposed reference values for healthy stocks. Growth estimates differed between data sources and exhibited large confidence intervals, indicating an overall high uncertainty underlying the LFCD revealed through a novel bootstrapped approach. Estimated values of stock indicators, exploitation rate, fishing mortality and size-proportions converged in suggesting a state of heavy to over-exploitation for the three assessed species, although differences were observed among data sources that we attribute mainly to fisheries selectivity and sampling design. In order to improve future assessments of stocks in multi-gear and data-poor contexts, estimations of fleet-specific selectivity should be used to reconstruct LFCD prior to analyses. Additionally, sampling design should be based on fishing effort distribution among gears and areas and, when feasible, fishery-independent data on stock conditions should be included.

Length-based risk analysis for assessing sustainability of data-limited tropical reef fisheries

AbstractThis study extended a “data-limited” length-based stock assessment approach to a risk analysis context. The estimation-simulation method used length frequencies as the principal data in lieu of catch and effort. Key developments were to: (i) incorporate probabilistic mortality and growth dynamics into a numerical cohort model; (ii) employ a precautionary approach for setting sustainability reference points for fishing mortality (FREF) and stock reproductive biomass (BREF); (iii) define sustainability risks in terms of probability distributions; and, (iv) evaluate exploitation status in terms of expected length frequencies, the main “observable” population metric. This refined length-based approach was applied to six principal exploited reef fish species in the Florida Keys region, consisting of three groupers (black grouper, red grouper, and coney), two snappers (mutton snapper and yellowtail snapper), and one wrasse (hogfish). The estimated sustainability risks for coney were low (<35%) in terms of benchmarks for fishing mortality rate and stock reproductive biomass. The other five species had estimated sustainability risks of greater than 95% for both benchmarks. The data-limited risk analysis methodology allowed for a fairly comprehensive probabilistic evaluation of sustainability status from species and community perspectives, and also a frame of reference for exploring management options balancing sustainability risks and fishery production.