Machine learning algorithms accurately identify free-living marine nematode species

Background

Identifying species, particularly small metazoans, remains a daunting challenge and the phylum Nematoda is no exception. Typically, nematode species are differentiated based on morphometry and the presence or absence of certain characters. However, recent advances in artificial intelligence, particularly machine learning (ML) algorithms, offer promising solutions for automating species identification, mostly in taxonomically complex groups. By training ML models with extensive datasets of accurately identified specimens, the models can learn to recognize patterns in nematodes' morphological and morphometric features. This enables them to make precise identifications of newly encountered individuals. Implementing ML algorithms can improve the speed and accuracy of species identification and allow researchers to efficiently process vast amounts of data. Furthermore, it empowers non-taxonomists to make reliable identifications. The objective of this study is to evaluate the performance of ML algorithms in identifying species of free-living marine nematodes, focusing on two well-known genera: Acantholaimus Allgén, 1933 and Sabatieria Rouville, 1903.

Methods

A total of 40 species of Acantholaimus and 60 species of Sabatieria were considered. The measurements and identifications were obtained from the original publications of species for both genera, this compilation included information regarding the presence or absence of specific characters, as well as morphometric data. To assess the performance of the species identification four ML algorithms were employed: Random Forest (RF), Stochastic Gradient Boosting (SGBoost), Support Vector Machine (SVM) with both linear and radial kernels, and K-nearest neighbor (KNN) algorithms.

Results

For both genera, the random forest (RF) algorithm demonstrated the highest accuracy in correctly classifying specimens into their respective species, achieving an accuracy rate of 93% for Acantholaimus and 100% for Sabatieria, only a single individual from Acantholaimus of the test data was misclassified.

Conclusion

These results highlight the overall effectiveness of ML algorithms in species identification. Moreover, it demonstrates that the identification of marine nematodes can be automated, optimizing biodiversity and ecological studies, as well as turning species identification more accessible, efficient, and scalable. Ultimately it will contribute to our understanding and conservation of biodiversity.

UBC Neck C4-C5: An Anatomically and Biomechanically Accurate Surrogate C4-C5 Functional Spinal Unit

Millions of people worldwide suffer from spinal cord injuries (SCIs) and traumatic brain injuries (TBIs) annually. Safety devices meant to protect against SCIs and TBIs, such as helmets, airbags, seat belts, and compliant floors are often evaluated with the use of anthropometric test devices (ATD s); however, there are currently no neck surrogates appropriate for the multiplane loading that often occurs in real-world scenarios leading to injury. As such, our objective in this study was to design and create an anatomically correct functional spinal unit (FSU) that produces a repeatable and biofidelic response to lateral bending, axial rotation, and quasistatic flexion-extension motion. This is a critical step in developing a biofidelic omnidirectional surrogate that can be used in future evaluations of safety devices in transportation, occupational, and sports settings. To create a biofidelic C4-C5 FSU, anatomically accurate C4 and C5 vertebrae were designed and manufactured using a 3D printer using geometry derived from the CT scans of a healthy 31-year-old male. Potential intervertebral disc and ligament surrogate materials were tested in compression and tension, respectively, to select representative materials for the surrogate intervertebral disc and cervical ligaments. The C4-C5 FSU was assembled and tested repeatedly in quasistatic flexion-extension, axial rotation, and lateral bending. Kinematic results were captured and compared to previously published cadaver data. The surrogate disc showed excellent Biofidelity (ISO/TR 9790) in compression, and the surrogate ligaments were within 25 N/mm of linear cadaveric stiffness ranges. The assembled FSU named UBC Neck C4-C5 showed good biofidelity under quasistatic axial rotation, lateral bending, flexion-extension, and coupled motion (ISO/TR 9790). However, the instantaneous centre of rotation was not similar to ex vivo or in vivo published studies. The UBC Neck C4-C5 FSU resulted in good biofidelity ratings and will inform future construction of a full surrogate neck to be used in the testing of head and neck safety equipment.

Two new species of Cyatholaimidae (Nematoda: Chromadorida) from the Southeastern Brazilian coast with emphasis on the pore complex and lateral pore-like structures

Cyatholaimidae is a common and diverse family of mainly marine nematodes, potentially, with a large number of species to be discovered. The taxonomy of the group is marked by a lack of information about the evolutionary history of the characters and of detailed descriptions of morphological structures that may be taxonomically relevant. Two new species of the family are described from a sublittoral region in Southeastern Brazil, emphasizing the importance of the distribution and morphology of pore complex and pore-like structures present on the cuticle. The taxonomic importance of the cuticle ornamentation and spicule shape for the Biarmifer species, as well as the precloacal supplements structures of Pomponema species, are discussed. Biarmifer nesiotes sp. nov. differs from other species of the genus by the presence of eight longitudinal rows of pore complex on the cuticle and by the shape of the copulatory structure. Pomponema longispiculum sp. nov. differs from the most similar species, P. stomachor Wieser, 1954, by the smaller number of turns of the amphidial fovea, the shorter tail and the beginning of the cuticle lateral differentiation (3/4 of the pharynx length vs. end of the pharynx, respectively). We also obtained the SSU rDNA sequence from Pomponema longispiculum sp. nov., which is closely related to Pomponema sp. (MN250093) by about 91%. Updated tabular keys to species identification of each genus (Biarmifer and Pomponema) are included, containing morphometric data, characters related to cuticle ornamentation, and copulatory structures.

Pomalidomide, dexamethasone, and daratumumab immediately after lenalidomide-based treatment in patients with multiple myeloma: updated efficacy, safety, and health-related quality of life results from the phase 2 MM-014 trial

Patients with relapsed/refractory multiple myeloma (RRMM) need proven subsequent therapies after early-line lenalidomide treatment failure. The phase 2 MM-014 trial (NCT01946477) investigated pomalidomide, dexamethasone, and daratumumab after 1 to 2 prior treatment lines (62.5%, 1 prior line) in patients with RRMM and prior lenalidomide (75.0%, lenalidomide refractory). With a median follow-up of 28.4 months, overall response rate was 77.7% (52.7% achieved very good partial response or better) and median progression-free survival was 30.8 months. For patients with lenalidomide-refractory disease, these outcomes were 76.2%, 47.6%, and 23.7 months, respectively. No new safety signals were observed; 64.3% experienced grade 3/4 neutropenia. Health-related quality of life was preserved or trended toward improvement through 12 treatment cycles. Pomalidomide, dexamethasone, and daratumumab given immediately after early-line lenalidomide-based treatment continues to demonstrate safety and efficacy, supporting pomalidomide-dexamethasone as a foundation of combination therapy in RRMM and providing evidence that the immunomodulatory agent class delivers benefit after lenalidomide treatment failure.

M-Triad: An improvement of the sediment quality triad

The traditional sediment quality triad generally uses three lines of evidence (LOE) in the assessment, integrating environmental chemistry, ecology and ecotoxicology. However the assessment is performed without considering the multivariate structure within LOE. In order to improve the sediment quality assessment, the M-Triad is proposed. Instead of averaging the values within a LOE, the new approach is based on the Euclidean distance between each sampling station and the reference station (s) for each LOE. These distances are then plotted in a radar-chart to obtain the area of the triangle and the quality assessment is subsequently obtained from the difference between the triangle areas of the impacted and the reference station. Three studies were selected to test the applicability of the M-Triad. In two cases, the M-Triad returned a more realistic ranking of the stations as observed in the principal component analysis (PCA) from each LOE By including the Euclidean distance, the use of M-Triad is advantageous when multiple variables with negative or uncorrelated patterns within a LOE are analyzed simultaneously. The combination of the M-Triad and the results of the PCA allows one to identify multiple contamination gradients and how biota and bioassays respond to each of these gradients. In comparison to the traditional method, the M-Triad reduces the uncertainty of the final analysis, permitting a more comprehensive ecological assessment.

Kinematic and Clinical Outcomes to Evaluate the Efficacy of a Multidisciplinary Intervention on Functional Mobility in Parkinson's Disease

Introduction: Functional mobility (FM) is a concept that incorporates the capacity of a person to move independently and safely to accomplish tasks. It has been proposed as a Parkinson's disease (PD) functional and global health outcome. In this study, we aimed to identify which kinematic and clinical outcomes changes better predict FM changes when PD patients are submitted to a specialized multidisciplinary program. Methods: PD patients engaged in a pre-defined specialized multidisciplinary program were assessed at admission and discharge. Change from baseline was calculated for all kinematic and clinical outcomes, and Timed Up and Go (TUG) was defined as the primary outcome for FM. A stepwise multivariate linear regression was performed to identify which outcome measures better predict TUG changes. Results: Twenty-four patients were included in the study. The changes in TUG Cognitive test, supervised step length, and free-living (FL) step time asymmetry were identified as the best predictors of TUG changes. The supervised step length and FL step time asymmetry were able to detect a small to moderate effect of the intervention (d values ranging from -0.26 to 0.42). Conclusions: Our results support the use of kinematic outcome measures to evaluate the efficacy of multidisciplinary interventions on PD FM. The TUG Cognitive, step length, and FL step time asymmetry were identified as having the ability to predict TUG changes. More studies are needed to identify the minimal clinically important difference for step length and FL step time asymmetry in response to a multidisciplinary intervention for PD FM.

Umbralisib, a Dual PI3Kδ/CK1ε Inhibitor in Patients With Relapsed or Refractory Indolent Lymphoma

PURPOSE

Phosphatidylinositol-3-kinase (PI3K) inhibitors have shown activity in relapsed or refractory (R/R) indolent non-Hodgkin lymphoma (iNHL). PI3K inhibitors have been hampered by poor long-term tolerability and toxicity, which interfere with continuous use. Umbralisib, a dual inhibitor of PI3Kδ/casein kinase-1ε, exhibits improved selectivity for PI3Kδ compared with other PI3K inhibitors. This phase IIb trial was designed to evaluate the efficacy and safety of umbralisib in patients with R/R iNHL.

PATIENTS AND METHODS

In this multicohort, open-label, phase IIb study, 208 patients with R/R marginal zone, follicular, or small lymphocytic lymphoma (MZL, FL, or SLL) unresponsive to prior treatments (≥ 1 MZL; ≥ 2 FL/SLL), including ≥ 1 anti-CD20-based therapy, were administered umbralisib 800 mg orally once daily until disease progression, unacceptable toxicity, or study withdrawal. Primary end point is overall response rate; secondary end points include time to response, duration of response, progression-free survival, and safety.

RESULTS

The median follow-up is 27.7 months (efficacy) and 21.4 months (safety). The overall response rate was 47.1%, and tumor reduction occurred in 86.4% of patients. The median time to response was 2.7-4.6 months. The median duration of response was not reached for MZL, 11.1 months for FL, and 18.3 months for SLL. Median progression-free survival was not reached for MZL, 10.6 months for FL, and 20.9 months for SLL. At least one grade ≥ 3 treatment-emergent adverse event (TEAE) was reported in 53.4% of patients. TEAEs led to umbralisib discontinuation in 32 patients (15.4%). A total of 31 patients (14.9%) discontinued because of a treatment-related adverse event. Grade ≥ 3 TEAEs reported in ≥ 10% of patients: neutropenia (11.5%) and diarrhea (10.1%). Increased ALT/AST (grade ≥ 3) occurred in 6.7%/7.2% of patients.

CONCLUSION

Umbralisib achieved meaningful clinical activity in heavily pretreated patients with iNHL. The safety profile was manageable, with a relatively low incidence of immune-mediated toxicities and adverse event-related discontinuations.

The relative contribution of non-selection and selection processes in marine benthic assemblages

We tested the hypothesis that the ubiquity of marine meiofaunal nematodes and their indiscriminate passive dispersal create assemblages that are less limited by its environment; whereas the relatively smaller population sizes of macrofauna, associated with their ability to track environmental conditions before settlement, renders their distribution more environmentally-restricted. We compared the empirical distribution of macrofauna and nematode species with that of communities simulated under different assumptions of selection (e.g. environmental filtering) and non-selection (e.g. dispersal limitation) processes. Selection processes were the prime driver of both meio- and macrofauna assemblages, with rare species strongly contributing to this component. The total number of species explained by non-selection processes was 27% higher in nematodes than in macrofauna. Our results underline the importance of a species-level approach to determine the contribution of selection and non-selection assembly processes. Moreover, they highlight the important yet overlooked role of dispersal and stochastic processes in determining species dynamics.

Food-triad: An index for sustainable consumption

This study proposes an index for food labeling in order to promote sustainable consumption. The index is calculated by ranking multiple features from the environmental, health and nutritional dimensions of the target product in relation to a pre-set reference value; the obtained scores from each dimension are plotted in a radar chart resulting in a triangular area. An increase in area represents a greater impact. As examples, tuna and the potato-based foods at three different processing levels (in natura or minimally processed, processed and ultra-processed) were analyzed. For both cases, the index increases according to the processing grades and has proved to be capable of expressing in numbers and graphically a wide range of environmental, nutritional and health issues.

Response of life-history traits of estuarine nematodes to the surfactant sodium dodecyl sulfate

Species responses to stress are expected to be dependent on their life-history strategy. In this study, we compare the responses of two free-living marine nematodes, Litoditis marina and Diplolaimella dievengatensis, both considered opportunistic, fast-growing, and stress-tolerant species, to the exposure to sublethal concentrations of sodium dodecyl sulfate (SDS) surfactant. Specifically, we evaluated the growth and reproduction rates, as well as the survival of individuals exposed from eggs and/or juveniles (J1) onwards. Exposure to SDS significantly affected the growth and reproduction rates of both species. However, whereas growth and reproduction rates of D. dievengatensis were significantly enhanced at low and intermediate concentrations of SDS (0.001% and 0.003%), for L. marina both parameters were significantly reduced by all SDS concentrations tested (0.001%, 0.003% and 0.006%). Exposure to SDS did not affect the survival of adult nematodes of D. dievengatensis, while for L. marina, survival of males exposed to 0.006% SDS was significantly reduced compared to the control. Responses of the life-history traits growth, fecundity and survival did not exhibit clear trade-offs. The contrasting responses of D. dievengatensis and L. marina indicate that biologically and ecologically similar species can have remarkably distinct tolerances to stress, and that, in agreement with recent studies, rhabditid nematodes cannot a priori be considered very stress tolerant. Consequently, single species traits and phylogenetic relatedness are poor predictors of nematode responses to toxic stress posed by anthropogenic activities.

Parental Knowledge about Healthy Sleep Hygiene practices in Children under 6 Year Old: an Exploratory Study

Introduction Children aged 5 to 12 years old needs, at least, 10-11 hours of sleep. Nowadays, children under 6 years old become more interested in TV, computers and in Internet which can lead to difficulty falling asleep. Parent knowledge about child sleep hygiene can influence parent capacity to promote healthy sleep habits, and should be supported by accurate information.

Objectives To analyse parents knowledge of children sleep practices.

Methodology A convenience sample of parents (n = 201) of children from three schools in a northern city of Portugal completed the "Sleep Ideas" Parent Survey on child sleep habits and parental basic sleep knowledge, beliefs and attitudes regarding sleep as a health behaviour.

Results Of the 201 analysed surveys (response rate 67 %), 33.8 % are from parents of children aged under 3 years old, 19.4 % of children with 3 years older, 24.4 % of children with 4 years old, 16.4 % of children with 5 years old and 6.0 % of children with 6 years old. In general, the percentage of correct answers was 84.8 %. Regarding children age, the percentage of correct answers ranged between 77.9 to 86.2 %, being the parents of children with 6 years old those who had the highest percentage of incorrect answers (22.1 %) and, on the other hand, the parents of children with 3 years old those who had the lowest percentage of incorrect answers (13.8 %). The answer with the highest percentage of incorrect answers, in all parents, was “Making a physical effort before going to sleep makes falling asleep easier” (46.8 %).

Conclusion In this study, parents revealed a very reasonable knowledge about sleep, which suggests a good capability to influence positively children’s habits. Parents with high sleep knowledge are more able to promote healthy sleep hygiene habits. Further studies are warranted to promote a better understanding of all the determinant dimensions for good sleeping habits.

Implementation of a Sleep Hygiene Program in 4 - 6 Year Old Portuguese Children: the “It is Time to Sleep” Project First Results

Introduction Sleep, as one of the most determining and present factors in our life, is fundamental for humans, and especially during childhood: it is indispensable for good cognitive, physical and emotional development.

Objectives Designed in the scope of the Portuguese National School Health Program, the objectives of this project were to promote adequate sleep routines, raise awareness of children’s sleep deprivation and to the consequences of an abusive contact with technologies. At the end of this activity, children should be able to recognize the importance of these dimensions.

Methodology The formative activity, performed by 2 school nurses, was applied to 104 children (from 3 different schools from a northern city of Portugal), with 4 (41.3 %), 5 (44.2 %) and 6 years old (14.4 %), and lasted 45 minutes. The project comprises 4 stages: the first one relates to nurses and project theme presentation; the second one is the implementation of a theatre where major issues of the project are presented, namely the importance of sleep and nap, sleep hygiene rules, consequences of sleep deprivation and the influence of technologies on sleep; the third one is the discussion of the main ideas using the song "Sleep Hour"; at the end, a questionnaire was applied to assess children knowledge about sleep hygiene habits divided into six questions with two images each, in which one corresponds to a healthy practice and the other does not.

Results The percentage of correct answers ranged between 96.6 to 98.3 %, suggesting that the formative activity had a positive impact on children’s knowledge about healthy sleep hygiene habits. The 2 questions on which the rate of incorrect answers was higher relate to the fact that sleeping with parents is better than sleeping alone (6.3 %) and that watching TV before going to sleep is a better option than reading a story (4.4 %).

Conclusion This intervention has given children important knowledge about healthy sleep hygiene habits, resulting in its understanding through an approach tailored to their age.

Invasive Lobular Breast Carcinoma Can Be a Challenging Diagnosis Without the Use of Tumor Markers

Invasive lobular carcinoma is often challenging to diagnose due to the lack of physical examination findings and macrocalcifications on mammography. The cells of invasive lobular carcinoma form a distinct single file pattern that can be identified on histology slides. Often, when patients present, there is metastasis to the bones, lymph nodes, and gastrointestinal tract. Tumor markers are a valuable tool in identification, especially the loss of E-cadherin protein. However, if E-cadherin protein is not available, epidermal membrane antigen, which inhibits E-cadherin, can prove to be a significant diagnostic tool. Epidermal membrane antigen was the key tumor marker in our patient case. Other tumor markers and histology stains can drive treatment plans and help predict prognosis.

Pomalidomide, dexamethasone, and daratumumab in relapsed refractory multiple myeloma after lenalidomide treatment

Patients with multiple myeloma who have relapsed after or become refractory to lenalidomide in early treatment lines represent a clinically important population in need of effective therapies. The safety and efficacy of pomalidomide, low-dose dexamethasone, and daratumumab was evaluated in lenalidomide-pretreated patients with relapsed or refractory multiple myeloma (RRMM) after one to two prior treatment lines in the phase 2 MM-014 study. Patients received pomalidomide 4 mg daily from days 1-21 and dexamethasone 40 mg weekly (28-day cycles). Daratumumab 16 mg/kg was administered per label. Primary endpoint was overall response rate (ORR); secondary endpoints included progression-free survival (PFS) and safety. Per protocol, all patients (N = 112) had received lenalidomide in their most recent prior regimen (75.0% lenalidomide refractory). ORR was 77.7% (76.2% in lenalidomide-refractory patients); median follow-up was 17.2 months. Median PFS was not reached (1-year PFS rate 75.1%). The most common hematologic grade 3/4 treatment-emergent adverse event was neutropenia (62.5%). Grade 3/4 infections were reported in 31.3% of patients, including 13.4% with grade 3/4 pneumonia. These results demonstrate the safety and efficacy of pomalidomide-based therapy as early as second line in patients with RRMM, even immediately after lenalidomide failure, indicating that switching from the immunomodulatory agent class is not necessary.

Future ocean climate homogenizes communities across habitats through diversity loss and rise of generalist species

Predictions of the effects of global change on ecological communities are largely based on single habitats. Yet in nature, habitats are interconnected through the exchange of energy and organisms, and the responses of local communities may not extend to emerging community networks (i.e., metacommunities). Using large mesocosms and meiofauna communities as a model system, we investigated the interactive effects of ocean warming and acidification on the structure of marine metacommunities from three shallow-water habitats: sandy soft-bottoms, marine vegetation, and rocky reef substrates. Primary producers and detritus-key food sources for meiofauna-increased in biomass under the combined effect of temperature and acidification. The enhanced bottom-up forcing boosted nematode densities but impoverished the functional and trophic diversity of nematode metacommunities. The combined climate stressors further homogenized meiofauna communities across habitats. Under present-day conditions metacommunities were structured by habitat type, but under future conditions they showed an unstructured random pattern with fast-growing generalist species dominating the communities of all habitats. Homogenization was likely driven by local species extinctions, reducing interspecific competition that otherwise could have prevented single species from dominating multiple niches. Our findings reveal that climate change may simplify metacommunity structure and prompt biodiversity loss, which may affect the biological organization and resilience of marine communities.

The state of the art of Chromadoridae (Nematoda, Chromadorida): a historical review, diagnoses and comments about valid and dubious genera and a list of valid species

Chromadoridae is a widespread family of mostly free-living marine nematodes. This systematic review provides for each genus: a historical background, an updated diagnosis and a list of species. Our review recognizes 37 valid genera, 395 valid species, 57 descriptions without enough morphological information for accurate identification (species inquirenda) and 10 species incerta sedis. We also recognize 21 species as nomena nuda. Additionally, polytomous keys were constructed for the subfamilies and for the genera of the three major subfamilies (Chromadorinae, Euchromadorinae and Hypodontolaiminae) using the most important diagnostic characters. A phylogenetic analysis based on rDNA sequences of species available in the GenBank was also conducted. Phylogenetic trees based on the 18S and 28S rDNA confirmed the classification into three subfamilies (Spilipherinae, Hypodontolaiminae and Chromadorinae), despite the absence of defined synapomorphies. Phylogenetic relationships at lower taxonomic level are problematic given the large number of sequences not identified to species level.

The use of metabarcoding for meiofauna ecological patterns assessment

Marine meiofauna comprises up to 22 phyla. Its morphological identification requires time and taxonomists' expertise, and molecular tools can make this task faster. We aim to disentangle meiofaunal diversity patterns at Araçá Bay by applying a model selection approach and estimating the effectiveness of metabarcoding (18S rDNA) and morphological methods for estimating the response of meiofauna diversity in small-scale interactions with environmental variables. A rarefaction curve indicated that ten samples were sufficient for estimating the total number of meiofauna OTUs in a tidal flat. In both approaches, richness was predicted by mean sand percentage, sediment sorting, and bacteria concentration. Nematode genera composition differed significantly between approaches, the result of taxonomic mismatch in the genetic database. The similarity between the model selected for diversity descriptors, the richness of nematode genera and meiofauna composition emphasized the utility of predictive models for metabarcoding estimates to detect small-scale interactions of these organisms.

Inhibition of the Platelet Reaction by a High Molecular Weight Phosphoglycoprotein Isolated from Human Platelet Plasma Membranes

The effect of a phospho-glycoprotein (HMW-GP), obtained from human platelet plasma membranes, on the aggregation and secretion of human platelets was studied. Incubation of PRP with 4 to 16 μg/ml of HMW-GP results in inhibition of ADP-, Epinephrine-, Collagen-, and Thrombin-induced platelet aggregation. The effect is mainly reflected on the secondary wave of aggregation. The inhibitory effect is partially overcome by higher concentration of the inducers, however, even under these conditions, a clear tendency towards disaggregation is observed. 5HT release (Col-induced) is strongly decreased from 50% to 4.5. The inhibitory effect on Thrombin-induced aggregation is markedly dependent on external calcium, being maximal at 5 mM calcium. The HMW-GP does not bind ADP or Thrombin. Membrane conformation is markedly affected, as evidenced by the effect of HMW-GP on the iodination of surface polypeptides of intact platelets. It is suggested that interaction of HMW-GP with the platelet membrane blocks the signal(s) transmission that links stimulus to activation. The inhibition observed might just represent an experimental amplification of the endogenous modulatory function that has been proposed for this high molecular weight phosphoglycoprotein.

Large-scale distribution patterns of mangrove nematodes: A global meta-analysis

Mangroves harbor diverse invertebrate communities, suggesting that macroecological distribution patterns of habitat-forming foundation species drive the associated faunal distribution. Whether these are driven by mangrove biogeography is still ambiguous. For small-bodied taxa, local factors and landscape metrics might be as important as macroecology. We performed a meta-analysis to address the following questions: (1) can richness of mangrove trees explain macroecological patterns of nematode richness? and (2) do local landscape attributes have equal or higher importance than biogeography in structuring nematode richness? Mangrove areas of Caribbean-Southwest Atlantic, Western Indian, Central Indo-Pacific, and Southwest Pacific biogeographic regions. We used random-effects meta-analyses based on natural logarithm of the response ratio (lnRR) to assess the importance of macroecology (i.e., biogeographic regions, latitude, longitude), local factors (i.e., aboveground mangrove biomass and tree richness), and landscape metrics (forest area and shape) in structuring nematode richness from 34 mangroves sites around the world. Latitude, mangrove forest area, and forest shape index explained 19% of the heterogeneity across studies. Richness was higher at low latitudes, closer to the equator. At local scales, richness increased slightly with landscape complexity and decreased with forest shape index. Our results contrast with biogeographic diversity patterns of mangrove-associated taxa. Global-scale nematode diversity may have evolved independently of mangrove tree richness, and diversity of small-bodied metazoans is probably more closely driven by latitude and associated climates, rather than local, landscape, or global biogeographic patterns.

Regime shifts in coastal lagoons: Evidence from free-living marine nematodes

We test the validity of using the regime shift theory to account for differences in environmental state of coastal lagoons as a response to variation in connectivity with the sea, using free-living nematodes as a surrogate. The study is based on sediment samples from the inner and outer portions of 15 coastal lagoons (5 open to the sea, 5 intermittently open/closed, and 5 permanently closed lakes) along the southern coast of Brazil. Environmental data suggested that there are two contrasting environmental conditions, with coastal lakes being significantly different from open and intermittent lagoons. Marine nematode assemblages corroborate these two mutually exclusive alternative stable states (open vs. closed systems), but assemblages from the intermittently open/closed lagoons showed a gradual change in species composition between both systems independently of the environmental conditions. The gradient in the structural connectivity among lagoons and the sea, due to their regime shifts, changes the movement of resources and consumers and the internal physico-chemical gradients, directly affecting regional species diversity. Whereas openness to the sea increased similarity in nematode assemblage composition among connected lagoons, isolation increased dissimilarity among closed lagoons. Our results from a large-scale sampling program indicated that as lagoons lose connectivity with the sea, shifting the environmental state, local processes within individual intermittently open/closed lagoons and particularly within coastal lakes become increasingly more important in structuring these communities. The main implication of these findings is that depending on the local stable state we may end up with alternative regional patterns of biodiversity.

The importance of vertical and horizontal dimensions of the sediment matrix in structuring nematodes across spatial scales

Intensive surveys have been conducted to unravel spatial patterns of benthic infauna communities. Although it has been recognized that benthic organisms are spatially structured along the horizontal and vertical dimensions of the sediment, little is known on how these two dimensions interact with each other. In this study we investigated the interdependence between the vertical and horizontal dimensions in structuring marine nematodes assemblages. We tested whether the similarity in nematode species composition along the horizontal dimension was dependent on the vertical layer of the sediment. To test this hypothesis, three-cm interval sediment samples (15 cm depth) were taken independently from two bedforms in three estuaries. Results indicated that assemblages living in the top layers are more abundant, species rich and less variable, in terms of species presence/absence and relative abundances, than assemblages living in the deeper layers. Results showed that redox potential explained the greatest amount (12%) of variability in species composition, more than depth or particle size. The fauna inhabiting the more oxygenated layers were more homogeneous across the horizontal scales than those from the reduced layers. In contrast to previous studies, which suggested that reduced layers are characterized by a specific set of tolerant species, the present study showed that species assemblages in the deeper layers are more causal (characterized mainly by vagrant species). The proposed mechanism is that at the superficial oxygenated layers, species have higher chances of being resuspended and displaced over longer distances by passive transport, while at the deeper anoxic layers they are restricted to active dispersal from the above and nearby sediments. Such restriction in the dispersal potential together with the unfavorable environmental conditions leads to randomness in the presence of species resulting in the high variability between assemblages along the horizontal dimension.

Effects of drill cuttings discharge on meiofauna communities of a shelf break site in the southwest Atlantic

The present study investigates the effects of drill cutting discharges on the structure of meiofauna communities in an area of the shelf break at Campos Basin, Southeast Brazil. Drilling activities were operated, in a first phase, with water-based fluid and, in a second phase, with synthetic fluid paraffin-based (NAF-III). A total of 135 samples taken at a pre-drilling situation (MS1) and two post-drilling moments (MS2 and MS3-3 and 22 months post-drilling, respectively) were analyzed. Effects on meiofauna were dependent on two main factors: 1-the impact received during drilling operation, if water-based or synthetic/water-based drilling fluid and 2-the background state, if it already presented signs of previous drilling activities or not. Based on univariate and multivariate analysis, there were evidences that the most affected area after drilling was those under the influence of synthetic-based fluid and that already had signs of previous drillings activities. The region impacted only by water-based fluid was less affected and the only one that completely recovered after 22 months. Nematodes and copepods had different responses to the impact. While copepods flourish in the impacted area and recovered 22 months after drilling, nematodes were adversely affected shortly after drilling and the community structure only recovered where hydrocarbons had been depleted.

Diversity of free-living marine nematodes (Enoplida) from Baja California assessed by integrative taxonomy

We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.

Comprehensive exercise training improves ventilatory muscle function and reduces dyspnea perception in patients with COPD

BACKGROUND

Comprehensive exercise training (CET) is an efficient strategy to decrease dyspnea perception in chronic obstructive pulmonary disease (COPD) and may result in significant improvement in ventilatory muscles function. Our aim was to evaluate the effects of general exercise training on dyspnea perception and on respiratory muscles strength in COPD patients.

METHODS

Consecutive COPD patients were enrolled to complete a CET programme. The patients underwent a routine that included a global warm up, upper and lower limbs endurance exercise as well as stretching and relaxation. Before and after the CET programme, patients completed maximal inspiratory (PImax) and expiratory (PEmax) pressures measurements, maximal incremental test, endurance test, and 6-min walk distance (6MWD).

RESULTS

71 patients (52 male). Mean age 67.6 +/- 8.6 years, FEV1 (%) 44.2 +/- 16.2 and Mahler dyspnea scale 6.4 +/- 1.8. The results before and after the exercise programme were: PImax 64.7 +/- 22.9 vs. 75.5 +/- 23.7 cmH2O (p=0.001), PEmax 110.8 +/- 28.1 vs. 120.4 +/- 28.1 cmH2O (p=0.004), 6MWD 510.6 +/- 90.3 vs. 528.2 +/- 99.7 metres (p=0.88), time of incremental test 672 +/- 135 vs. 856 +/- 226 sec (p<0.0001). Compared with the pre exercise programme, we observed a significant reduction on Borg dyspnea scale (6.1 +/- 2.8 to 3.6 +/- 2.3, p<0.0001) as well as a longer test time (504 +/- 218 to 1.038 +/- 841, p<0.0001) at the end of the endurance test after CET programme. Improvement of PImax correlated negatively with dyspnea perception at iso-time during the endurance test (r = -0.33, p=0.03).

CONCLUSIONS

Our results confirm that CET is associated with significant improvement in PImax, PEmax and provide evidence demonstrating that CET reduces dyspnea perception in patients with COPD.