Insights into Blue Whale (Balaenoptera musculus L.) Population Movements in the Galapagos Archipelago and Southeast Pacific.

The Galapagos Marine Reserve is vital for cetaceans, serving as both a stopover and residency site. However, blue whales, occasionally sighted here, exhibit poorly understood migratory behavior within the Galapagos and the broader Eastern Tropical Pacific. This study, the first to satellite tag blue whales in the Galapagos (16 tagged between 2021 and 2023), explored their behavior in relation to environmental variables like chlorophyll-a concentration, sea surface temperature (SST), and productivity. Key findings show a strong correlation between foraging behavior, high chlorophyll-a levels, productivity, and lower SSTs, indicating a preference for food-rich areas. Additionally, there is a notable association with geomorphic features like ridges, which potentially enhance food abundance. Most tagged whales stayed near the Galapagos archipelago, with higher concentrations observed around Isabela Island, which is increasingly frequented by tourist vessels, posing heightened ship strike risks. Some whales ventured into Ecuador's exclusive economic zone, while one migrated southward to Peru. The strong 2023 El Niño-Southern Oscillation event led to SST and primary production changes, likely impacting whale resource availability. Our study provides crucial insights into blue whale habitat utilization, informing adaptive management strategies to mitigate ship strike risks and address altered migration routes due to climate-driven environmental shifts.

Effects of stance control via hidden Markov model-based gait phase detection on healthy users of an active hip-knee exoskeleton.

Introduction: In the past years, robotic lower-limb exoskeletons have become a powerful tool to help clinicians improve the rehabilitation process of patients who have suffered from neurological disorders, such as stroke, by applying intensive and repetitive training. However, active subject participation is considered to be an important feature to promote neuroplasticity during gait training. To this end, the present study presents the performance assessment of the AGoRA exoskeleton, a stance-controlled wearable device designed to assist overground walking by unilaterally actuating the knee and hip joints. Methods: The exoskeleton's control approach relies on an admittance controller, that varies the system impedance according to the gait phase detected through an adaptive method based on a hidden Markov model. This strategy seeks to comply with the assistance-as-needed rationale, i.e., an assistive device should only intervene when the patient is in need by applying Human-Robot interaction (HRI). As a proof of concept of such a control strategy, a pilot study comparing three experimental conditions (i.e., unassisted, transparent mode, and stance control mode) was carried out to evaluate the exoskeleton's short-term effects on the overground gait pattern of healthy subjects. Gait spatiotemporal parameters and lower-limb kinematics were captured using a 3D-motion analysis system Vicon during the walking trials. Results and Discussion: By having found only significant differences between the actuated conditions and the unassisted condition in terms of gait velocity (ρ = 0.048) and knee flexion (ρ ≤ 0.001), the performance of the AGoRA exoskeleton seems to be comparable to those identified in previous studies found in the literature. This outcome also suggests that future efforts should focus on the improvement of the fastening system in pursuit of kinematic compatibility and enhanced compliance.

Packet Loss Characterization Using Cross Layer Information and HMM for Wi-Fi Networks.

Packet loss is a major problem for wireless networks and has significant effects on the perceived quality of many internet services. Packet loss models are used to understand the behavior of packet losses caused by several reasons, e.g., interferences, coexistence, fading, collisions, and insufficient/excessive memory buffers. Among these, the Gilbert-Elliot (GE) model, based on a two-state Markov chain, is the most used model in communication networks. However, research has proven that the GE model is inadequate to represent the real behavior of packet losses in Wi-Fi networks. In this last category, variables of a single network layer are used, usually the physical one. In this article, we propose a new packet loss model for Wi-Fi that simultaneously considers the temporal behavior of losses and the variables that describe the state of the network. In addition, the model uses two important variables, the signal-to-noise ratio and the network occupation, which none of the packet loss models available for Wi-Fi networks simultaneously take into account. The proposed model uses the well-known Hidden Markov Model (HMM), which facilitates training and forecasting. At each state of HMM, the burst-length of losses is characterized using probability distributions. The model was evaluated by comparing computer simulation and real data samples for validation, and using the log-log complementary distribution of burst-length. We compared the proposed model with competing models through the analysis of mean square error (MSE) using a validation sample collected from a real network. Results demonstrated that the proposed model outperforms the currently available models for packet loss in Wi-Fi networks.

Tracking and Classification of Head Movement for Augmentative and Alternative Communication Systems.

The use of assistive technologies can mitigate or reduce the challenges faced by individuals with motor disabilities to use computer systems. However, those who feature severe involuntary movements often have fewer options at hand. This work describes an application that can recognize the user's head using a conventional webcam, track its motion, model the desired functional movement, and recognize it to enable the use of a virtual keyboard. The proposed classifier features a flexible structure and may be personalized for different user need. Experimental results obtained with participants with no neurological disorders have shown that classifiers based on Hidden Markov Models provided similar or better performance than a classifier based on position threshold. However, motion segmentation and interpretation modules were sensitive to involuntary movements featured by participants with cerebral palsy that took part in the study.

Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus-Host Interaction Signatures.

Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5' base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host.

Growth Rate and Acceleration Analysis of the COVID-19 Pandemic Reveals the Effect of Public Health Measures in Real Time.

Background: Ending the COVID-19 pandemic is arguably one of the most prominent challenges in recent human history. Following closely the growth dynamics of the disease is one of the pillars toward achieving that goal. Objective: We aimed at developing a simple framework to facilitate the analysis of the growth rate (cases/day) and growth acceleration (cases/day2) of COVID-19 cases in real-time. Methods: The framework was built using the Moving Regression (MR) technique and a Hidden Markov Model (HMM). The dynamics of the pandemic was initially modeled via combinations of four different growth stages: lagging (beginning of the outbreak), exponential (rapid growth), deceleration (growth decay), and stationary (near zero growth). A fifth growth behavior, namely linear growth (constant growth above zero), was further introduced to add more flexibility to the framework. An R Shiny application was developed, which can be accessed at https://theguarani.com.br/ or downloaded from https://github.com/adamtaiti/SARS-CoV-2. The framework was applied to data from the European Center for Disease Prevention and Control (ECDC), which comprised 3,722,128 cases reported worldwide as of May 8th 2020. Results: We found that the impact of public health measures on the prevalence of COVID-19 could be perceived in seemingly real-time by monitoring growth acceleration curves. Restriction to human mobility produced detectable decline in growth acceleration within 1 week, deceleration within ~2 weeks and near-stationary growth within ~6 weeks. Countries exhibiting different permutations of the five growth stages indicated that the evolution of COVID-19 prevalence is more complex and dynamic than previously appreciated. Conclusions: These results corroborate that mass social isolation is a highly effective measure against the dissemination of SARS-CoV-2, as previously suggested. Apart from the analysis of prevalence partitioned by country, the proposed framework is easily applicable to city, state, region and arbitrary territory data, serving as an asset to monitor the local behavior of COVID-19 cases.

A New Method to Reconstruct Quantitative Food Webs and Nutrient Flows from Isotope Tracer Addition Experiments.

Understanding how nutrients flow through food webs is central in ecosystem ecology. Tracer addition experiments are powerful tools to reconstruct nutrient flows by adding an isotopically enriched element into an ecosystem and tracking its fate through time. Historically, the design and analysis of tracer studies have varied widely, ranging from descriptive studies to modeling approaches of varying complexity. Increasingly, isotope tracer data are being used to compare ecosystems and analyze experimental manipulations. Currently, a formal statistical framework for analyzing such experiments is lacking, making it impossible to calculate the estimation errors associated with the model fit, the interdependence of compartments, and the uncertainty in the diet of consumers. In this article we develop a method based on Bayesian hidden Markov models and apply it to the analysis of N15-NH4+ tracer additions in two Trinidadian streams in which light was experimentally manipulated. Through this case study, we illustrate how to estimate N fluxes between ecosystem compartments, turnover rates of N within those compartments, and the associated uncertainty. We also show how the method can be used to compare alternative models of food web structure, calculate the error around derived parameters, and make statistical comparisons between sites or treatments.

Gait Phase Detection for Lower-Limb Exoskeletons using Foot Motion Data from a Single Inertial Measurement Unit in Hemiparetic Individuals.

Due to the recent rise in the use of lower-limb exoskeletons as an alternative for gait rehabilitation, gait phase detection has become an increasingly important feature in the control of these devices. In addition, highly functional, low-cost recovery devices are needed in developing countries, since limited budgets are allocated specifically for biomedical advances. To achieve this goal, this paper presents two gait phase partitioning algorithms that use motion data from a single inertial measurement unit (IMU) placed on the foot instep. For these data, sagittal angular velocity and linear acceleration signals were extracted from nine healthy subjects and nine pathological subjects. Pressure patterns from force sensitive resistors (FSR) instrumented on a custom insole were used as reference values. The performance of a threshold-based (TB) algorithm and a hidden Markov model (HMM) based algorithm, trained by means of subject-specific and standardized parameters approaches, were compared during treadmill walking tasks in terms of timing errors and the goodness index. The findings indicate that HMM outperforms TB for this hardware configuration. In addition, the HMM-based classifier trained by an intra-subject approach showed excellent reliability for the evaluation of mean time, i.e., its intra-class correlation coefficient (ICC) was greater than 0 . 75 . In conclusion, the HMM-based method proposed here can be implemented for gait phase recognition, such as to evaluate gait variability in patients and to control robotic orthoses for lower-limb rehabilitation.

Bioinformatic Identification of Functionally and Structurally Relevant Residues and Motifs in Protein S-Acyltransferases.

DHHC palmitoyltransferases (DHHC-PATs) are very peculiar in that, outside the DHHC domain, they are very divergent even across orthologs from closely related species. This represents a challenge for the bioinformatic analyses of these proteins. Sequence-based analyses and predictions require a valid sequence alignment, which for this family of proteins requires extensive manual curation and this is difficult to attain for the nonspecialist. Here we present a simple method for the in silico analysis of the sequence of a particular PAT, that would allow for the identification of important structural features and functional residues in a PAT or PAT family.

Open population maximum likelihood spatial capture-recapture.

Open population capture-recapture models are widely used to estimate population demographics and abundance over time. Bayesian methods exist to incorporate open population modeling with spatial capture-recapture (SCR), allowing for estimation of the effective area sampled and population density. Here, open population SCR is formulated as a hidden Markov model (HMM), allowing inference by maximum likelihood for both Cormack-Jolly-Seber and Jolly-Seber models, with and without activity center movement. The method is applied to a 12-year survey of male jaguars (Panthera onca) in the Cockscomb Basin Wildlife Sanctuary, Belize, to estimate survival probability and population abundance over time. For this application, inference is shown to be biased when assuming activity centers are fixed over time, while including a model for activity center movement provides negligible bias and nominal confidence interval coverage, as demonstrated by a simulation study. The HMM approach is compared with Bayesian data augmentation and closed population models for this application. The method is substantially more computationally efficient than the Bayesian approach and provides a lower root-mean-square error in predicting population density compared to closed population models.

Smart Web-Based Platform to Support Physical Rehabilitation.

The enhancement of ubiquitous and pervasive computing brings new perspectives in medical rehabilitation. In that sense, the present study proposes a smart, web-based platform to promote the reeducation of patients after hip replacement surgery. This project focuses on two fundamental aspects in the development of a suitable tele-rehabilitation application, which are: (i) being based on an affordable technology, and (ii) providing the patients with a real-time assessment of the correctness of their movements. A probabilistic approach based on the development and training of ten Hidden Markov Models (HMMs) is used to discriminate in real time the main faults in the execution of the therapeutic exercises. Two experiments are designed to evaluate the precision of the algorithm for classifying movements performed in the laboratory and clinical settings, respectively. A comparative analysis of the data shows that the models are as reliable as the physiotherapists to discriminate and identify the motion errors. The results are discussed in terms of the required setup for a successful application in the field and further implementations to improve the accuracy and usability of the system.

Distribution and Classification of Serine ß-Lactamases in Brazilian Hospital Sewage and Other Environmental Metagenomes Deposited in Public Databases.

ß-lactam is the most used antibiotic class in the clinical area and it acts on blocking the bacteria cell wall synthesis, causing cell death. However, some bacteria have evolved resistance to these antibiotics mainly due the production of enzymes known as ß-lactamases. Hospital sewage is an important source of dispersion of multidrug-resistant bacteria in rivers and oceans. In this work, we used next-generation DNA sequencing to explore the diversity and dissemination of serine ß-lactamases in two hospital sewage from Rio de Janeiro, Brazil (South Zone, SZ and North Zone, NZ), presenting different profiles, and to compare them with public environmental data available. Also, we propose a Hidden-Markov-Model approach to screen potential serine ß-lactamases genes (in public environments samples and generated hospital sewage data), exploring its evolutionary relationships. Due to the high variability in ß-lactamases, we used a position-specific scoring matrix search method (RPS-BLAST) against conserved domain database profiles (CDD, Pfam, and COG) followed by visual inspection to detect conserved motifs, to increase the reliability of the results and remove possible false positives. We were able to identify novel ß-lactamases from Brazilian hospital sewage and to estimate relative abundance of its types. The highest relative abundance found in SZ was the Class A (50%), while Class D is predominant in NZ (55%). CfxA (65%) and ACC (47%) types were the most abundant genes detected in SZ, while in NZ the most frequent were OXA-10 (32%), CfxA (28%), ACC (21%), CEPA (20%), and FOX (19%). Phylogenetic analysis revealed ß-lactamases from Brazilian hospital sewage grouped in the same clade and close to sequences belonging to Firmicutes and Bacteroidetes groups, but distant from potential ß-lactamases screened from public environmental data, that grouped closer to ß-lactamases of Proteobacteria. Our results demonstrated that HMM-based approach identified homologs of serine ß-lactamases, indicating the specificity and high sensitivity of this approach in large datasets, contributing for the identification and classification of a large number of homologous genes, comprising possible new ones. Phylogenetic analysis revealed the potential reservoir of ß-lactam resistance genes in the environment, contributing to understanding the evolution and dissemination of these genes.

Non-linear Parameter Estimates from Non-stationary MEG Data.

We demonstrate a method to estimate key electrophysiological parameters from resting state data. In this paper, we focus on the estimation of head-position parameters. The recovery of these parameters is especially challenging as they are non-linearly related to the measured field. In order to do this we use an empirical Bayesian scheme to estimate the cortical current distribution due to a range of laterally shifted head-models. We compare different methods of approaching this problem from the division of M/EEG data into stationary sections and performing separate source inversions, to explaining all of the M/EEG data with a single inversion. We demonstrate this through estimation of head position in both simulated and empirical resting state MEG data collected using a head-cast.

Modeling the Complex Dynamics and Changing Correlations of Epileptic Events.

Patients with epilepsy can manifest short, sub-clinical epileptic "bursts" in addition to full-blown clinical seizures. We believe the relationship between these two classes of events-something not previously studied quantitatively-could yield important insights into the nature and intrinsic dynamics of seizures. A goal of our work is to parse these complex epileptic events into distinct dynamic regimes. A challenge posed by the intracranial EEG (iEEG) data we study is the fact that the number and placement of electrodes can vary between patients. We develop a Bayesian nonparametric Markov switching process that allows for (i) shared dynamic regimes between a variable number of channels, (ii) asynchronous regime-switching, and (iii) an unknown dictionary of dynamic regimes. We encode a sparse and changing set of dependencies between the channels using a Markov-switching Gaussian graphical model for the innovations process driving the channel dynamics and demonstrate the importance of this model in parsing and out-of-sample predictions of iEEG data. We show that our model produces intuitive state assignments that can help automate clinical analysis of seizures and enable the comparison of sub-clinical bursts and full clinical seizures.

Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo.

In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-ß superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica.