Extent of the selectivity filter conferred by the sixth transmembrane region in the CFTR chloride channel pore

Point mutations within the pore region of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl^? channel have previously been shown to alter the selectivity of the channel between different anions, suggesting that part of the pore may form an anion 'selectivity filter'. However, the full extent of this selectivity filter region and the location of anion binding sites in the pore are currently unclear. As a result, comparisons between CFTR and other classes of Cl^? channel of known structure are difficult. We compare here the effects of point mutations at each of eight consecutive amino acid residues (arginine 334-serine 341) in the crucial sixth transmembrane region (TM6) of CFTR. Anion selectivity was determined using patch-clamp recording from inside-out membrane patches excised from transiently transfected mammalian cell lines. The results suggest that selectivity is predominantly controlled by a single site involving adjacent residues phenylalanine 337 and threonine 338, and that the selectivity conferred by this 'filter' region is modified by anion binding to flanking sites involving the more extracellular arginine 334 and the more intracellular serine 341. Other residues within this part of the pore play only minor roles in controlling anion permeability and conductance. Our results support a model in which specific TM6 residues make important contributions to a single, localized anion selectivity filter in the CFTR pore, and also contribute to multiple anion binding sites both within and on either side of the filter region.     

Characterization of measurement errors using structure‐from‐motion and photogrammetry to measure marine habitat structural complexity

Habitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure‐from‐motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time. This study evaluated the accuracy, precision, and bias in measurements of marine habitat structural complexity derived from structure‐from‐motion and photogrammetric measurements using repeated surveys of artificial reefs (with known structure) as well as natural coral reefs. We quantified measurement errors as a function of survey image coverage, actual surface rugosity, and the morphological community composition of the habitat‐forming organisms (reef corals). Our results indicated that measurements could be biased by up to 7.5% of the total observed ranges of structural complexity based on the environmental conditions present during any particular survey. Positive relationships were found between measurement errors and actual complexity, and the strength of these relationships was increased when coral morphology and abundance were also used as predictors. The numerous advantages of structure‐from‐motion and photogrammetry techniques for quantifying and investigating marine habitats will mean that they are likely to replace traditional measurement techniques (e.g., chain‐and‐tape). To this end, our results have important implications for data collection and the interpretation of measurements when examining changes in habitat complexity using structure‐from‐motion and photogrammetry.     

Estimation and validation of spatio-temporal parameters for sprint running using a radio-based tracking system

Spatio-temporal parameters like step length, step frequency and ground contact time are directly related to sprinting performance. There is still a lack of knowledge, however, on how these parameters interact.Recently, various algorithms for the automatic detection of step parameters during sprint running have been presented which have been based on data from motion capture systems, video cameras, opto-electronic systems or Inertial measurement units. However, all of these methods suffer from at least one of the following shortcomings: they are (a) not applicable for more than one sprinter simultaneously, (b) only capable of capturing a small volume or (c) do not provide accurate spatial parameters. To circumvent these issues, the radio-based local position measurement system RedFIR could be used to obtain spatio-temporal information during sprinting based on lightweight transmitters attached to the athletes. To assess and optimize the accuracy of these parameters 19 100 m sprints of twelve young elite athletes (age: 16.5 ± 2.3 years) were recorded by a radio-based tracking system and a opto-electronic reference instrument. Optimal filter parameters for the step detection algorithm were obtained based on RMSE differences between estimates and reference values on an unseen test set. Attaching a transmitter above the ankle showed the best results.Bland-Altman analysis yielded 95% limits of agreement of [−14.65 cm, 15.05 cm] for step length [−0.016 s, 0.016 s] for step time and [−0.020 s, 0.028 s] for ground contact time, respectively. RMS errors smaller than 2% for step length and step time show the applicability of radio-based tracking systems to provide spatio-temporal parameters. This creates new opportunities for performance analysis that can be applied for any running discipline taking place within a stadium. Since analysis for multiple athletes is available in real-time this allows immediate feedback to coaches, athletes and media.     

Testing random effects in linear mixed‐effects models with serially correlated errors

In linear mixed‐effects models, random effects are used to capture the heterogeneity and variability between individuals due to unmeasured covariates or unknown biological differences. Testing for the need of random effects is a nonstandard problem because it requires testing on the boundary of parameter space where the asymptotic chi‐squared distribution of the classical tests such as likelihood ratio and score tests is incorrect. In the literature several tests have been proposed to overcome this difficulty, however all of these tests rely on the restrictive assumption of i.i.d. measurement errors. The presence of correlated errors, which often happens in practice, makes testing random effects much more difficult. In this paper, we propose a permutation test for random effects in the presence of serially correlated errors. The proposed test not only avoids issues with the boundary of parameter space, but also can be used for testing multiple random effects and any subset of them. Our permutation procedure includes the permutation procedure in Drikvandi, Verbeke, Khodadadi, and Partovi Nia (2013) as a special case when errors are i.i.d., though the test statistics are different. We use simulations and a real data analysis to evaluate the performance of the proposed permutation test. We have found that random slopes for linear and quadratic time effects may not be significant when measurement errors are serially correlated.     

Dynamic accuracy of inertial measurement units during simple pendulum motion

A motion measurement system based on inertial measurement units (IMUs) has been suggested as an alternative to contemporary video motion capture. This paper reports an investigation into the accuracy of IMUs in estimating 3D orientation during simple pendulum motion. The IMU vendor's (XSens Technologies) accuracy claim of 3° root mean squared (RMS) error is tested. IMUs are integrated electronic devices that contain accelerometers, magnetometers and gyroscopes. The motion of a pendulum swing was measured using both IMUs and video motion capture as a reference. The IMU raw data were processed by the Kalman filter algorithm supplied by the vendor and a custom fusion algorithm developed by the authors. The IMU measurement of pendulum motion using the vendor's Kalman filter algorithm did not compare well with the video motion capture with a RMS error of between 8.5° and 11.7° depending on the length and type of pendulum swing. The maximum orientation error was greater than 30°, occurring approximately eight seconds into the motion. The custom fusion algorithm estimation of orientation compared well with the video motion capture with a RMS error of between 0.8° and 1.3°. Future research should concentrate on developing a general purpose fusion algorithm and vendors of IMUs should provide details about the errors to be expected in different measurement situations, not just those in a ‘best case’ scenario.     

The consequences of using indirect signs that decay to determine species' occupancy

Statistical models of species' distributions rely on data on species' occupancy, or use, of sites across space and/or time. For rare or cryptic species, indirect signs, such as dung, may be the only realistic means of determining their occupancy status across broad spatial extents. However, the consequences of sign decay for errors in estimates of occupancy have not previously been considered. If signs decay very rapidly, then false‐negative errors may occur because signs at an occupied site have decayed by the time it is surveyed. On the other hand, if signs decay very slowly, false‐positive errors may occur because signs remain present at sites that are no longer occupied. We addressed this issue by quantifying, as functions of sign decay and accumulation rates: 1) the false‐negative error rate due to sign decay and, 2) the expected time interval prior to a survey within which signs indicate the species was present; as this time interval increases, false‐positives become more likely. We then applied this to the specific example of koala Phascolarctos cinereus occupancy derived from faecal pellet surveys using data on faecal pellet decay rates. We show that there is a clear trade‐off between false‐negative error rates and the potential for false‐positive errors. For the koala case study, false‐negative errors were low on average and the expected time interval prior to surveys that detected pellets indicate the species was present within less than 2–3 yr. However, these quantities showed quite substantial spatial variation that could lead to biased parameter estimates for distribution models based on faecal pellet surveys. This highlights the importance of observation errors arising from sign decay and we suggest some modifications to existing methods to deal with this issue.     

Relative strengths of competition for space and food in a sessile filter feeder

Previous workers have demonstrated that sessile filter feeders compete for food and space, but little is known about the relative strengths of these two processes. To determine this, the density and position of barnacles (Balanus improvisus) in a unidirectional current were manipulated to alter the amount of competition for space and food, respectively. Results indicated that competition for space significantly reduced growth, and marginally reduced survivorship. Competition for food was also detected, but only among uncrowded individuals; thus, it appears to be the weaker of the two interactions. However, under crowded conditions, downstream individuals actually grew more than those upstream. The most likely explanation for this result is that downstream individuals fed more efficiently because they were not exposed to the full force of the current. The results also suggest that since natural densities started high but continually decreased throughout the study, barnacles undergo an ontogenetic shift in the relative importance of these processes.     

Making sense of ultrahigh‐resolution movement data: A new algorithm for inferring sites of interest

Decomposing the life track of an animal into behavioral segments is a fundamental challenge for movement ecology. The proliferation of high‐resolution data, often collected many times per second, offers much opportunity for understanding animal movement. However, the sheer size of modern data sets means there is an increasing need for rapid, novel computational techniques to make sense of these data. Most existing methods were designed with smaller data sets in mind and can thus be prohibitively slow. Here, we introduce a method for segmenting high‐resolution movement trajectories into sites of interest and transitions between these sites. This builds on a previous algorithm of Benhamou and Riotte‐Lambert (2012). Adapting it for use with high‐resolution data. The data’s resolution removed the need to interpolate between successive locations, allowing us to increase the algorithm’s speed by approximately two orders of magnitude with essentially no drop in accuracy. Furthermore, we incorporate a color scheme for testing the level of confidence in the algorithm's inference (high = green, medium = amber, low = red). We demonstrate the speed and accuracy of our algorithm with application to both simulated and real data (Alpine cattle at 1 Hz resolution). On simulated data, our algorithm correctly identified the sites of interest for 99% of “high confidence” paths. For the cattle data, the algorithm identified the two known sites of interest: a watering hole and a milking station. It also identified several other sites which can be related to hypothesized environmental drivers (e.g., food). Our algorithm gives an efficient method for turning a long, high‐resolution movement path into a schematic representation of broadscale decisions, allowing a direct link to existing point‐to‐point analysis techniques such as optimal foraging theory. It is encoded into an R package called SitesInterest , so should serve as a valuable tool for making sense of these increasingly large data streams.     

A smart device inertial-sensing method for gait analysis

The purpose of this study was to establish and cross-validate a method for analyzing gait patterns determined by the center of mass (COM) through inertial sensors embedded in smart devices. The method employed an extended Kalman filter in conjunction with a quaternion rotation matrix approach to transform accelerations from the object onto the global frame. Derived by double integration, peak-to-trough changes in vertical COM position captured by a motion capture system, inertial measurement unit, and smart device were compared in terms of averaged and individual steps. The inter-rater reliability and levels of agreement for systems were discerned through intraclass correlation coefficients (ICC) and Bland–Altman plots. ICCs corresponding to inter-rater reliability were good-to-excellent for position data (ICCs,.80–.95) and acceleration data (ICCs,.54–.81). Levels of agreements were moderate for position data (LOA, 3.1–19.3%) and poor for acceleration data (LOA, 6.8%–17.8%). The Bland–Altman plots, however, revealed a small systematic error, in which peak-to-trough changes in vertical COM position were underestimated by 2.2 mm; the Kalman filter?s accuracy requires further investigation to minimize this oversight. More importantly, however, the study?s preliminary results indicate that the smart device allows for reliable COM measurements, opening up a cost-effective, user-friendly, and popular solution for remotely monitoring movement. The long-term impact of the smart device method on patient rehabilitation and therapy cannot be underestimated: not only could healthcare expenditures be curbed (smart devices being more affordable than today‘s motion sensors), but a more refined grasp of individual functioning, activity, and participation within everyday life could be attained.     

Time‐to‐kill: measuring attack rates in a heterogenous landscape with multiple prey types

Although spatial heterogeneity of prey and landscapes are known to contribute to variation around predator‐prey functional response models, few studies have quantified these effects. We illustrate a new approach using data from winter movement paths of GPS‐collared wolves in the Rocky Mountains of Canada and time‐to‐event models with competing risks for measuring the effect of prey and landscape characteristics on the time‐to‐kill, which is the reciprocal of attack rate (aN) in a Holling's functional response. We evaluated 13 a priori models representing hypothesized mechanisms influencing attack rates in a heterogeneous landscape with two prey types. Models ranged from variants on Holling's disc equation, including search rate and prey density, to a full model including prey density and patchiness, search rates, satiation, and landscape features, which were measured along the wolf's movement path. Movement rates of wolves while searching explained more of the variation in time‐to‐kill than prey densities. Wolves did not compensate for low prey density by increasing movement rates and there was little evidence that spatial aggregation of prey influenced attack rates in this multi‐prey system. The top model for predicting time‐to‐kill included only search rate and landscape features. Wolves killed prey more quickly in flat terrain, likely due to increased vulnerability from accumulated snow, whereas attack rates were lower when wolves hunted near human‐made features presumably due to human disturbance. Understanding the sources of variation in attack rates provides refinements to functional response models that can lead to more effective predator–prey management in human‐dominated landscapes.     

Maintaining the accuracy of a computer practice register: household index

In this practice, with a family practitioner committee list of 9726 patients, we use a computer register for recall, screening, morbidity data, audit, and repeat prescribing. The computing techniques used to achieve accuracy in maintaining the register are described. After one year of full use the register was validated by using the computer to select a random sample of 200 patients from patients'' computer records that had not been updated recently. Two patients were untraceable, and in only 11 records were errors of information found, none of which was important. We think that it is feasible and valuable to have a household index.     

Multiple Comparisons for a Large Number of Parameters

When there are many parameters of interest (finitely large or infinite), standard multiple comparison procedures for a finite number of parameters (called discrete‐domain approaches) may lead to a simultaneous confidence region (SCR) too conservative to be useful. Such cases often arise in locating disease genes, detecting changes in image data and examining shapes and patterns in growth curves; or generally, in quantifying uncertainty in an estimate of a regression function (as one entity). In these cases, procedures designed for a continuous domain must be used. Scheffe's method is a classical example of continuous‐domain approaches. It provides an SCR for a regression function when errors are iid Gaussian and the predictor space is unconstrained, i.e. the domain of interest is the q dimensional Euclidean space. In practice, however, functions defined on finite intervals or other constrained domains are often of interest and data may not be Gaussian. Thus, Scheffe's SCR becomes either too conservative or inadequate. In this paper, we introduce and survey a modern‐type continuous‐domain approach, and explore a connection between some discrete‐ and continuous‐domain multiple comparison procedures. We show that, in some cases, even for a small number of parameters, it is still better to use a continuous‐domain multiple comparison procedure. The main ideas behind the continuous‐domain procedures are shown. A new procedure for comparing a finite number of contrasts about k regression curves is developed. Relevant software is provided.     

Understanding the Role of Cesium and Rubidium Additives in Perovskite Solar Cells: Trap States,Charge Transport,and Recombination

Adding cesium (Cs) and rubidium (Rb) cations to FA_0.83MA_0.17Pb(I_0.83Br_0.17)₃ hybrid lead halide perovskites results in a remarkable improvement in solar cell performance, but the origin of the enhancement has not been fully understood yet. In this work, time‐of‐flight, time‐resolved microwave conductivity, and thermally stimulated current measurements are performed to elucidate the impact of the inorganic cation additives on the trap landscape and charge transport properties within perovskite solar cells. These complementary techniques allow for the assessment of both local features within the perovskite crystals and macroscopic properties of films and full devices. Strikingly, Cs‐incorporation is shown to reduce the trap density and charge recombination rates in the perovskite layer. This is consistent with the significant improvements in the open‐circuit voltage and fill factor of Cs‐containing devices. By comparison, Rb‐addition results in an increased charge carrier mobility, which is accompanied by a minor increase in device efficiency and reduced current–voltage hysteresis. By mixing Cs and Rb in quadruple cation (Cs‐Rb‐FA‐MA) perovskites, the advantages of both inorganic cations can be combined. This study provides valuable insights into the role of these additives in multiple‐cation perovskite solar cells, which are essential for the design of high‐performance devices.     

Divide to conquer: a complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest

The identification of northern and southern components in different vertebrate species led researchers to accept a two‐component hypothesis for the Brazilian Atlantic forest (BAF). Nevertheless, neither a formal proposal nor a meta‐analysis to confirm this coincidence was ever made. Our main objective here was therefore to systematically test in how many vertebrate components the BAF could be divided by analysing existing empirical data. We used two approaches: (1) mapping and comparing the proposed areas of vertebrate endemism in the BAF and (2) analysing studies mentioning spatial subdivisions in distinct forest‐dependent vertebrates within the biome, by the use of panbiogeography. The four large‐scale endemism area components together with the six small‐scale panbiogeographical ones allowed the definition of three BAF greater regions, subdivided into nine vertebrate components, latitudinally and longitudinally organized. Empirical time estimates of the diversification events within the BAF were also reviewed. Diversification of these vertebrates occurred not only in the Pleistocene but also throughout the Miocene. Our results confirm the BAF's complex history, both in space and time. We propose that future research should be small‐scale and focused in the vertebrate components identified herein. Given the BAF's heterogeneity, studying via sections will be much more useful in identifying the BAF's historical biogeography. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Long-term Behavioral Tracking of Freely Swimming Weakly Electric Fish

Long-term behavioral tracking can capture and quantify natural animal behaviors, including those occurring infrequently. Behaviors such as exploration and social interactions can be best studied by observing unrestrained, freely behaving animals. Weakly electric fish (WEF) display readily observable exploratory and social behaviors by emitting electric organ discharge (EOD). Here, we describe three effective techniques to synchronously measure the EOD, body position, and posture of a free-swimming WEF for an extended period of time. First, we describe the construction of an experimental tank inside of an isolation chamber designed to block external sources of sensory stimuli such as light, sound, and vibration. The aquarium was partitioned to accommodate four test specimens, and automated gates remotely control the animals'' access to the central arena. Second, we describe a precise and reliable real-time EOD timing measurement method from freely swimming WEF. Signal distortions caused by the animal''s body movements are corrected by spatial averaging and temporal processing stages. Third, we describe an underwater near-infrared imaging setup to observe unperturbed nocturnal animal behaviors. Infrared light pulses were used to synchronize the timing between the video and the physiological signal over a long recording duration. Our automated tracking software measures the animal''s body position and posture reliably in an aquatic scene. In combination, these techniques enable long term observation of spontaneous behavior of freely swimming weakly electric fish in a reliable and precise manner. We believe our method can be similarly applied to the study of other aquatic animals by relating their physiological signals with exploratory or social behaviors.     

Differences in seasonal survival suggest species‐specific reactions to climate change in two sympatric bat species

Long‐lived animals with a low annual reproductive output need a long time to recover from population crashes and are, thus, likely to face high extinction risk, if the current global environmental change will increase mortality rates. To aid conservation of those species, knowledge on the variability of mortality rates is essential. Unfortunately, however, individual‐based multiyear data sets that are required for that have only rarely been collected for free‐ranging long‐lived mammals. Here, we used a five‐year data set comprising activity data of 1,445 RFID‐tagged individuals of two long‐lived temperate zone bat species, Natterer's bats (Myotis nattereri) and Daubenton's bats (Myotis daubentonii), at their joint hibernaculum. Both species are listed as being of high conservation interest by the European Habitats Directive. Applying mixed‐effects logistic regression, we explored seasonal survival differences in these two species which differ in foraging strategy and phenology. In both species, survival over the first winter of an individual's life was much lower than survival over subsequent winters. Focussing on adults only, seasonal survival patterns were largely consistent with higher winter and lower summer survival but varied in its level across years in both species. Our analyses, furthermore, highlight the importance of species‐specific time periods for survival. Daubenton's bats showed a much stronger difference in survival between the two seasons than Natterer's bats. In one exceptional winter, the population of Natterer's bats crashed, while the survival of Daubenton's bats declined only moderately. While our results confirm the general seasonal survival pattern typical for hibernating mammals with higher winter than summer survival, they also show that this pattern can be reversed under particular conditions. Overall, our study points toward a high importance of specific time periods for population dynamics and suggests species‐, population‐, and age class‐specific responses to global climate change.     

Examining deep litter as environmental enrichment for a family group of wolf's guenons,Cercopithecus wolfi

Manipulable substrates promote species‐typical behavior and decrease abnormal behavior in a variety of primate species. However, the effects of providing litter to arboreal primates are not as well studied, and there is little information specifically concerning enrichment for guenons. To inform the captive management of an under‐studied species, we evaluated deep litter substrate as environmental enrichment for a family group of Wolf's guenons, Cercopithecus wolfi. We expected it to promote species‐typical behavior and to act as an intervention by reducing aggressive behaviors targeted toward a juvenile group member by his parents. We compared the guenons' behavior during baseline periods in which normal husbandry routines were followed to periods when the entire floor of their enclosure was covered with 30 cm of straw or wood wool. We then evaluated the group's preference between litters by comparing their relative use. The guenons spent more time feeding and were more active during both litter conditions, but relative to their respective baselines, they spent more time examining straw and less time examining wood wool. Straw, but not wood wool, promoted some affiliative behavior as well as greater tolerance of the juvenile's social proximity to others. However, the addition of deep litter did not ameliorate patterns of agonistic behavior among our subjects. Our results suggest that straw conferred greater behavioral benefits than wood wool as a deep litter substrate for this guenon group and may constitute a form of environmental enrichment for this species. Zoo Biol 29:626–632, 2010. © 2009 Wiley‐Liss, Inc.     

Micro‐CT evaluation of murine fetal skeletal development yields greater morphometric precision over traditional clear‐staining methods

Traditional techniques for quantification of murine fetal skeletal development (gross measurements, clear‐staining) are severely limited by specimen processing, soft tissue presence, diffuse staining, and unclear landmarks between which to make measurements. Nondestructive microcomputed tomography (micro‐CT) imaging is a versatile, well‐documented tool traditionally used to generate high‐resolution 3‐D images and quantify microarchitectural parameters of trabecular bone. Although previously described as a tool for phenotyping fetal murine specimens, micro‐CT has not previously been used to directly measure individual fetal skeletal structures. Imaging murine fetal skeletons using micro‐CT enables the researcher to nondestructively quantify fetal skeletal development parameters including limb length, total bone volume, and average bone mineral density, as well as identify skeletal malformations. Micro‐CT measurement of fetal limb lengths correlates well with traditional clear‐staining methods (83.98% agreement), decreases variability in measurements (average standard errors: 6.28% for micro‐CT and 10.82% for clear‐staining), decreases data acquisition time by eliminating the need for tissue processing, and preserves the intact fixed fetus for further analysis. Use of the rigorous micro‐CT technique to generate 3‐D images for digital measurement enables isolation of skeletal structures based on degree of mineralization (local radiodensity), eliminating the complications of blurred stain boundaries and soft tissue inclusion that accompany clear‐staining and gross measurement techniques. Microcomputed tomography provides a facile, accurate, and nondestructive method for determining the developmental state of the fetal skeleton using not only limb lengths and identification of malformations, but total skeletal bone volume and average skeletal mineral density as well. Birth Defects Res (Part B) 2008. © 2008 Wiley‐Liss, Inc.     

Packing of large‐scale chromatography columns with irregularly shaped glass based resins using a stop‐flow method

Rigid chromatography resins, such as controlled pore glass based adsorbents, offer the advantage of high permeability and a linear pressure‐flow relationship irrespective of column diameter which improves process time and maximizes productivity. However, the rigidity and irregularly shaped nature of these resins often present challenges in achieving consistent and uniform packed beds as formation of bridges between resin particles can hinder bed consolidation. The standard flow‐pack method when applied to irregularly shaped particles does not yield well‐consolidated packed beds, resulting in formation of a head space and increased band broadening during operation. Vibration packing methods requiring the use of pneumatically driven vibrators are recommended to achieve full packed bed consolidation but limitations in manufacturing facilities and equipment may prevent the implementation of such devices. The stop‐flow packing method was developed as an improvement over the flow‐pack method to overcome these limitations and to improve bed consolidation without the use of vibrating devices. Transition analysis of large‐scale columns packed using the stop‐flow method over multiple cycles has shown a two‐ to three‐fold reduction of change in bed integrity values as compared to a flow‐packed bed demonstrating an improvement in packed bed stability in terms of the height equivalent to a theoretical plate (HETP) and peak asymmetry (A_s). © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1319–1325, 2014