Can treadmill walking be used to assess propulsion generation?

Instrumented treadmills offer significant advantages for analysis of human locomotion, including recording consecutive steady-state gait cycles, precisely controlling walking speed, and avoiding force plate targeting. However, some studies of hemiparetic walking on a treadmill have suggested that the moving treadmill belt may fundamentally alter propulsion mechanics. Any differences in propulsion mechanics during treadmill walking would be problematic since recent studies assessing propulsion have provided fundamental insight into hemiparetic walking. The purpose of this study was to test the hypothesis that there would be no difference in the generation of anterior/posterior (A/P) propulsion by performing a carefully controlled comparison of the A/P ground reaction forces (GRFs) and impulses in healthy adults during treadmill and overground walking. Gait data were collected from eight subjects walking overground and on a treadmill with speed and cadence controlled. Peak negative and positive horizontal GRFs in early and late stance, respectively, were reduced by less than 5% of body weight (p<0.05) during treadmill walking compared to overground walking. The magnitude of the braking impulse was similarly lower (p<0.05) during treadmill walking, but no significant difference was found between propulsion impulses. While there were some subtle differences in A/P GRFs between overground and treadmill walking, these results suggest there is no fundamental difference in propulsion mechanics. We conclude that treadmill walking can be used to investigate propulsion generation in healthy and by implication clinical populations.     

High resolution imaging to assess oilseed species?? root hair responses to soil water stress

An imaging method was developed to evaluate crop species differences in root hair morphology using high resolution scanners, and to determine if the method could also detect root hair responses to soil water availability. High resolution (1890 picture elements (pixels) cm^?1) desktop scanners were buried in containers filled with soil to characterize root hair development under two water availability levels (?63 and ?188?kPa) for canola (Brassica napus L. cv Clearwater), camelina (Camelina sativa L. Crantz cv Cheyenne), flax (Linum usitatissimum L. cv CDC Bethune), and lentil (Lens culinaris Medik. cv Brewer). There was notable effect of available moisture on root hair geometry (RHG). At ?188?kPa, length from the root tip to the root hair initiation zone decreased and root hair length (RHL) became more variable near the root hair initiation zone as compared to ?63?kPa. For the response of primary axial RHL, significant main effects were present for both water availability (P?<?0.05) and species (P?<?0.0001); lateral RHL showed a significant main effect for both water availability (P?<?0.05) and species (P?<?0.01) as well. For both primary axial and lateral root hair density (RHD), there was a significant effect of species (P?<?0.0001), but no significant response to water availability. No water availability x species interaction was present in any case. Low available water reduced RHL in both primary axial and lateral roots. The change in RHL due to water availability was most evident in canola and camelina. Additionally, those with greater RHL $ \left( {\text{canola} = \text{camelina} > \text{flax} = \text{lentil}} \right) $ had lower RHD $ \left( {\text{canola} = \text{camelina} < \text{flax} < \text{lentil}} \right) $ in primary axial roots and a similar trend was found in lateral RHL. Both water and species had a significant effect on primary axial root surface area (RSA) (P?<?0.05) but no significant effect was found for lateral RSA. For primary axial RSA the longest and most dense root hair had the greatest RSA. This novel approach to in situ rhizosphere imaging allowed observation of species differences in root hair development in response to water availability and should be useful in future studies of rhizosphere interactions and crop water and nutrient management.     

Are there adequate data to assess how well theories of rarity apply to marine invertebrates?

Understanding the biology of rare species is a very important part of conservation biology. Most of our current understanding of rarity has, however, come from studies of terrestrial plants, birds, mammals and some insects. Freshwater and marine habitats are underrepresented in published studies of rare species or conservation biology. We therefore have little knowledge about how well our understanding of what makes particular species rare and how rare species persist applies to marine invertebrates which form a major component of coastal biodiversity. In this review, I examine some theories about rarity with respect to intertidal and shallow subtidal invertebrates to identify whether there are adequate data to apply these theories to marine invertebrates and how well such theories apply. The general conclusions are that the lack of quantitative data on abundances, ranges, habitat-requirements, dispersal and connectedness among populations for marine invertebrates means that their status as rare species cannot really be assessed appropriately. It is also unlikely that, without extensive sampling programmes and considerable expense, adequate data could be obtained for these small, cryptic animals, which typically have very patchy, variable and unpredictable patterns of distribution and abundance. Intertidal and subtidal assemblages are diverse, including species with many different life-histories from many phyla, occupying the same suite of habitats. It is therefore suggested that future research on rare organisms in marine habitats should build upon the long and successful history of experimental marine studies to test specific hypotheses about processes influencing rarity in the field. Such studies would not only add a new dimension to our current understanding of rarity, but would also provide badly-needed data on the status of rare marine invertebrates. abundances, invertebrates, marine, range, rarity     

Using 2′, 7′-dichlorodihydrofluorescein-diacetate to assess polysaccharides as immunomodulating agents

Neutrophils play a key role in the defense against microbial infections. One of their primary weapons to destroy microbes is the production of reactive oxygen species (ROS). This paper shows how 2′, 7′-dichlorodihydrofluorescein-diacetate (DCFH-DA) was used to measure the effects of polysaccharides on the production of ROS by polymorphonuclear leukocytes (PMNs). The DCFH-DA method has been designed to provide a highly sensitive, quantifiable, real-time assessment of ROS production by PMNs.     

Network analysis to assess landscape connectivity trends: Application to European forests (1990–2000)

Landscape networks and ecosystems worldwide are undergoing changes that may impact in different ways relevant ecological processes such as gene flow, pollination, or wildlife dispersal. A myriad of indices have been developed to characterize landscape patterns, but not all of them are equally suited to evaluate temporal changes in landscape connectivity as is increasingly needed for biodiversity monitoring and operational indicator delivery. Relevant advancements in this direction have been recently proposed based on graph theoretical methods to analyze landscape network connectivity and on the measurement of habitat availability at the landscape scale. Building from these developments, we modify a recent index and present the equivalent connected area (ECA) index, defined as the size of a single patch (maximally connected) that would provide the same probability of connectivity than the actual habitat pattern in the landscape. The temporal changes in ECA can be directly compared with the changes in total habitat area. This allows for additional and straightforward insights on the degree to which the gains or losses in habitat amount can be beneficial or deleterious by affecting landscape elements that uphold connectivity in a wider landscape context. We provide a demonstrative example of application and interpretation of this index and approach to monitor changes in functional landscape connectivity. We focus on the trends in European forests at the province level in the period 1990–2000 from Corine land cover data, considering both changes in the forest spatial pattern and in the average permeability of the landscape matrix. The degree of connectivity was rather stable over most of the study area, with a slight overall increase in forest connectivity in Europe. However, a few countries and regions concentrated remarkably high changes in the analyzed period, particularly those with a low forest cover. The species traits also affected the responses to landscape pattern changes, which were more prominent for those species with limited dispersal abilities. We conclude discussing the potential of this approach for consistent indicator delivery, as well as the limitations and possibilities of application to a variety of situations, for which the required quantitative tools are freely available as open source projects.     

Chemo-somatosensory evoked potentials: A sensitive tool to assess conditioned pain modulation?

Background: Chemo-somatosensory evoked potentials (CSSEPs) elicited by chemical stimulation (CO₂ gas) of the nasal mucosa have been shown to be sensitive enough to pick up even weak analgesic effects. With the present study we wanted to investigate whether CSSEPs are also a sensitive tool to capture endogenous pain inhibitory mechanisms elicited by conditioned pain modulation (CPM; where a first conditioning stimulus reduces the sensitivity for a second test stimulus) with a conditioning stimulus of rather low noxious load.

Methods: Seventeen healthy participants were tested for CPM effects (conditioning stimulus: tonic heat pain with intensities around the pain threshold induced via a thermode; test stimulus: chemonasal stimulation (73% and 78% CO₂)) on CSSEPs and on self-report ratings.

Results: We found significant CPM effects in the CSSEPS, with reduced amplitudes and prolonged latencies at several electroencephalogram (EEG) recording positions when using the lower CO₂ concentration (73% CO₂). In contrast to the visible inhibitory effects on the CSSEPs, subjective ratings of the test stimulus did not reflect CPM action.

Discussion: The experimental pain model using CO₂ stimuli to elicit CSSEPs proved to be sensitive enough to capture weak CPM effects elicited by a conditioning stimulus of rather low noxious load. The usage of such mild noxious conditioning stimuli—in contrast to stimuli of higher noxious load (e.g., cold pressor test)—has the advantage that the activation of other types of pain inhibitory mechanisms in parallel (like attentional distraction, stress-induced analgesia) can be avoided.     

Is photometry an accurate and reliable method to assess boar semen concentration?

Sperm concentration assessment is a key point to insure appropriate sperm number per dose in species subjected to artificial insemination (AI). The aim of the present study was to evaluate the accuracy and reliability of two commercially available photometers, AccuCell™ and AccuRead™ pre-calibrated for boar semen in comparison to UltiMate™ boar version 12.3D, NucleoCounter SP100 and Thoma hemacytometer. For each type of instrument, concentration was measured on 34 boar semen samples in quadruplicate and agreement between measurements and instruments were evaluated. Accuracy for both photometers was illustrated by mean of percentage differences to the general mean. It was −0.6% and 0.5% for Accucell™ and Accuread™ respectively, no significant differences were found between instrument and mean of measurement among all equipment. Repeatability for both photometers was 1.8% and 3.2% for AccuCell™ and AccuRead™ respectively. Low differences were observed between instruments (confidence interval 3%) except when hemacytometer was used as a reference. Even though hemacytometer is considered worldwide as the gold standard, it is the more variable instrument (confidence interval 7.1%).The conclusion is that routine photometry measures of raw semen concentration are reliable, accurate and precise using AccuRead™ or AccuCell™. There are multiple steps in semen processing that can induce sperm loss and therefore increase differences between theoretical and real sperm numbers in doses. Potential biases that depend on the workflow but not on the initial photometric measure of semen concentration are discussed.     

Sample coherence – a field study approach to assess similarity of macroinvertebrate samples

The EU-funded STAR-project provided an opportunity to analyse 1418 macroinvertebrate samples from 310 sampling sites throughout Europe. At most of the sites, samples were taken in two seasons using both national protocols and the project’s STAR-AQEM protocol. At a subset of sites (86), two replicate samples were taken by each method in each of the two seasons. The resulting taxalists were analysed in terms of community similarity using the Bray–Curtis Index, Jaccard, and Renkonen Indices. A new concept of sample ‘coherence’ is used to measure the relative strength of within-site, within-season and within-method similarity and to determine their importance on variability in community composition. Site-coherence (i.e., highest similarity to another sample from the same site) was much higher where replicate samples were available. Season-coherence of samples was nearly 100% even if different methods were compared. Season appeared to be one of the major determinants of in-stream fauna. The STAR-AQEM method is most comparable to the Nordic, Portuguese and Czech (PERLA) national methods and less comparable to the Italian (IBE) and Latvian methods. Samples collected by these latter methods had higher similarities to other sites sampled with the same methods than to samples of the same site using the STAR-AQEM method, thus there was low site-coherence. In three stream types from Italy, Latvia and Greece 28–38% of the samples were most similar to a sample from a different site than to a replicate sample from the same site. This fact could have serious consequences for follow up bioassessments or impact assessments by cluster analysis based on similarity measures. Replicate samples are less coherent within site, season or method if the taxonomic resolution is family rather than species. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Which fields under a coverslip should one assess to estimate sperm motility?

Under field conditions the motility of bull semen often has to be estimated under a coverslip on a microscope slide. This study was aimed at determining which combination of fields under coverslips provides measurements of sperm motility that best represent the motility in semen specimens as measured in a specially designed chamber for use in a computer-assisted sperm analyzer (CASA). We measured the motility (percentages motile, progressively motile, and aberrantly motile spermatozoa) in each of four straws of frozen-thawed semen from each of 10 bulls five times, ranging from 5 to 120 minutes after thawing with each bull by straw by time combination yielding one semen specimen. Motility was measured in duplicate in a Hamilton, Thorne IVOS CASA; once in each of 12 fields equally spaced along the equatorial radius of a coverslip (Field 0 at the edge and Field 11 at the center) and once in each of eight equally spaced fields along the equator of a Leja 4 chamber designed for use in a CASA. We used the weighted average motility of all fields in a chamber as gold standard and compared it to the average motility of each the following combinations of fields under the coverslip: all 12 fields, Fields 2 to 4, Fields 2 and four, Field 3 and the center three fields. The concordance correlation coefficient (CCC) was determined between the motility in each combination of fields under coverslips and the chambers as a reproducibility index, which evaluates the agreement between the readings under the coverslips and the gold standard readings in the chambers (n = 187 for each CCC). We performed pairwise comparisons of the CCCs (P < 0.005 for each comparison) and established that the average motility under all 12 fields better reproduced the motility in the chamber than the center three fields or Field 3. The averages of Fields 2 to 4 and Fields 2 and 4 reproduced chamber motility as well as the average of all 12 fields, except for the percentage motile sperm, where the average of all 12 fields was better. Using the average motility of Fields 2 and 4, 50% of estimates fell within 6%, 4% and 3% above or below the percentages motile, progressively motile and aberrantly motile spermatozoa in the Leja 4 chamber, 80% of estimates fell within 12%, 8% and 7% thereof and 95% fell within 23%, 13% and 12% thereof. In conclusion, for the method of spreading semen under a coverslip and the range in motility values used, this study shows that the average of the motility over the 12 fields along the equatorial radius under a coverslip provides the best estimate of the motility of a semen specimen, while the average of Fields 2 and 4 is also suitable for the subjective estimation of motility under field conditions, although the estimated motility is expected to fall within 6% above or below the motility of the specimen in only 50% of semen specimens.     

How to assess the pathogenicity of mutations in Charcot-Marie-Tooth disease and other diseases?

Knowledge whether a certain DNA variant is a pathogenic mutation or a harmless polymorphism is a critical issue in medical genetics, in which results of a molecular analysis may serve as a basis for diagnosis and genetic counseling. Due to its genetic heterogeneity expressed at the levels of loci, genes and mutations, Charcot-Marie-Tooth (CMT) disease can serve as a model group of clinically homogenous diseases for studying the pathogenicity of mutations. Close to a 17p11.2-p12 duplication occurring in 70% of patients with the demyelinating form of CMT disease, numerous mutations have been identified in poorly characterized genes coding for proteins of an unknown function. Functional analyses, segregation analyses of large pedigrees, and inclusion of large control groups are required to assess the potential pathogenicity of CMT mutations. Hence, the pathogenicity of numerous CMT mutations remains unclear. Some variants detected in the CMT genes and originally described as pathogenic mutations have been shown to have a polymorphic character. In contrast, polymorphisms initially considered harmless were later reclassified as pathogenic mutations. However, the process of assessing the pathogenicity of mutations, as presented in this study for CMT disorders, is a more general issue concerning all disorders with a genetic background. Since the number of DNA variants is still growing, in the near future geneticists will increasingly have to cope with the problem of pathogenicity of identified genetic variants.     

How effective are non-destructive sampling methods to assess aquatic invertebrate diversity in bromeliads?

With the growing interest in small aquatic water bodies, especially as naturally replicated model systems for ecological research, aquatic invertebrate communities in phytotelmata are increasingly receiving attention these days. The recognition of the substantial contribution to the regional species pool of specialised species draws further attention to these small and often temporary habitats. The methods currently used for studying communities in some types of phytotelma, such as bromeliads, tend to be destructive, typically involving complete dissection of the plant. The expected increase in sampling intensity associated with the increasing interest in phytotelmata may result in a negative impact on plant populations in some areas, decreasing numbers in an unsustainable way, especially in locations with ongoing, intensive research. We therefore aimed to investigate whether less-destructive sampling methods can achieve sufficient data quality to allow their use as alternatives to complete plant dissection. We tested the effectiveness of three such methods in measuring the aquatic invertebrate communities in tank bromeliads (Tillandsia guatemalensis) in Cusuco National Park, Honduras. The three methods were pipetting the water out of the bromeliad, turning the bromeliad upside down and dissecting only the outer part of the plant (the oldest, often deteriorating leaves). Overall, we found that these methods were poor predictors of richness and abundance of the organisms in communities. However, we found big differences between taxonomic groups, depending in part on the ecology of the organisms, and we suggest that some less-destructive alternative methods may be appropriate for studying some specific groups (e.g. Culicidae). Based on these results and a rapid survey of the abundance of bromeliads in the national park, we question whether intensive, ongoing research into aquatic invertebrate communities in similar phytotelma populations is sustainable. From the point of view of conservation, alternative model systems need to be found.     

Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

Summary The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.To whom correspondence should be addressed.     

How will climate novelty influence ecological forecasts? Using the Quaternary to assess future reliability

Future climates are projected to be highly novel relative to recent climates. Climate novelty challenges models that correlate ecological patterns to climate variables and then use these relationships to forecast ecological responses to future climate change. Here, we quantify the magnitude and ecological significance of future climate novelty by comparing it to novel climates over the past 21,000 years in North America. We then use relationships between model performance and climate novelty derived from the fossil pollen record from eastern North America to estimate the expected decrease in predictive skill of ecological forecasting models as future climate novelty increases. We show that, in the high emissions scenario (RCP 8.5) and by late 21st century, future climate novelty is similar to or higher than peak levels of climate novelty over the last 21,000 years. The accuracy of ecological forecasting models is projected to decline steadily over the coming decades in response to increasing climate novelty, although models that incorporate co‐occurrences among species may retain somewhat higher predictive skill. In addition to quantifying future climate novelty in the context of late Quaternary climate change, this work underscores the challenges of making reliable forecasts to an increasingly novel future, while highlighting the need to assess potential avenues for improvement, such as increased reliance on geological analogs for future novel climates and improving existing models by pooling data through time and incorporating assemblage‐level information.     

Strategy to select and assess antagonistic bacteria for biological control of Rhizoctonia solani Kühn

A screening strategy was developed to assess the potential of plant-associated bacteria to control diseases caused by Rhizoctonia solani Kühn. About 434 already characterized antagonistic bacterial strains isolated from diverse plant species and microenvironments were evaluated for biocontrol and plant growth promotion by a hierarchical combination of assays. Analyzing in vitro antagonism towards different Rhizoctonia isolates resulted in a selection of 20 potential biocontrol agents. The strains were characterized by their antagonistic mechanisms in vitro as well as their production of the plant growth hormone indole-3-acetic acid. The plant growth promoting effect by antagonistic bacteria was determined using a microtiter plate assay on the basis of lettuce seedlings. Lettuce and sugar beet as host plant were included in the biocontrol experiments in which the antagonistic effect of 17 bacterial isolates could be confirmed in vivo. Sequencing of the 16S rDNA gene and (or) fatty acid methyl ester gas chromatography was used to identify the antagonistic isolates. Molecular fingerprints of isolates obtained by BOX-polymerase chain reaction were compared to avoid further investigation with genetically very similar strains and to obtain unique molecular fingerprints for quality control and patent licensing. According to our strategy, an assessment scheme was developed and four interesting biological control agents, Pseudomonas reactans B3, Pseudomonas fluorescens B1, Serratia plymuthica B4, and Serratia odorifera B6, were found. While S. plymuthica B4 was the best candidate to biologically control Rhizoctonia in lettuce, P. reactans B3 was the best candidate to suppress the pathogen in sugar beet.     

Activation of interspecies-hybrid Rubisco enzymes to assess different models for the Rubisco–Rubisco activase interaction

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is prone to inactivation from non-productive binding of sugar-phosphates. Reactivation of Rubisco requires conformational remodeling by a specific chaperone, Rubisco activase. Rubisco activase from tobacco and other plants in the family Solanaceae is an inefficient activator of Rubisco from non-Solanaceae plants and from the green alga Chlamydomonas reinhardtii. To determine if the Rubisco small subunit plays a role in the interaction with Rubisco activase, a hybrid Rubisco (SSNT) composed of tobacco small subunits and Chlamydomonas large subunits was constructed. The SSNT hybrid, like other hybrid Rubiscos containing plant small subunits, supported photoautotrophic growth in Chlamydomonas, but growth in air was much slower than for cells containing wild-type Rubisco. The kinetic properties of the SSNT hybrid Rubisco were similar to the wild-type enzyme, indicating that the poor growth in air was probably caused by disruption of pyrenoid formation and the consequent impairment of the CO₂concentrating mechanism. Recombinant Rubisco activase from Arabidopsis activated the SSNT hybrid Rubisco and hybrid Rubiscos containing spinach and Arabidopsis small subunits at rates similar to the rates with wild-type Rubisco. However, none of the hybrid Rubiscos was activated by tobacco Rubisco activase. That replacement of Chlamydomonas small subunits with plant small subunits does not affect the species-specific interaction between Rubisco and Rubisco activase suggests that the association is not dominated by the small subunits that surround the Rubisco central solvent channel. Therefore, the geometry of a side-on binding mode is more consistent with the data than a top-on or ring-stacking binding mode.     

Why species composition is not a good indicator to assess restoration success? Counter‐response to Reid (2015)

The absence of species composition among the indicators of restoration success, recommended for the Brazilian Atlantic Forest by Suganuma and Durigan, was criticized by Reid. In his critic, Reid argues that species composition can be (1) predictable from site history and restoration technique and (2) a surrogate for poor ecosystem functioning and lack of resilience. We disagree on the deterministic view behind the first argument, and the latter is still controversial. Even though, we recommended richness as a good indicator of ecosystem functioning instead of composition—which depends on the exhaustive labor of botanical identification.     

A novel and high-throughput approach to assess photosynthetic thermal tolerance of kelp using chlorophyll α fluorometry

Foundation seaweed species are experiencing widespread declines and localized extinctions due to increased instability of sea surface temperature. Characterizing temperature thresholds are useful for predicting patterns of change and identifying species most vulnerable to extremes. Existing methods for characterizing seaweed thermal tolerance produce diverse metrics and are often time-consuming, making comparisons between species and techniques difficult, hindering insight into global patterns of change. Using three kelp species, we adapted a high-throughput method – previously used in terrestrial plant thermal biology – for use on kelps. This method employs temperature-dependent fluorescence (T–F₀) curves under heating or cooling regimes to determine the critical temperature (T_crit) of photosystem II (PSII), i.e., the breakpoint between slow and fast rise fluorescence response to changing temperature, enabling rapid assays of photosynthetic thermal tolerance using a standardized metric. This method enables characterization of T_crit for up to 48 samples per two-hour assay, demonstrating the capacity of T–F₀ curves for high-throughput assays of thermal tolerance. Temperature-dependent fluorescence curves and their derived metric, T_crit, may offer a timely and powerful new method for the field of phycology, enabling characterization and comparison of photosynthetic thermal tolerance of seaweeds across many populations, species, and biomes.