Incorporating intraspecific trait variation into functional diversity: Impacts of selective logging on birds in Borneo

1. As conservation increasingly recognises the importance of species’ functional roles in ecosystem processes, studies are shifting away from measuring species richness towards measures that account for the functional differences between species in a community. These functional diversity (FD) indices have received much recent attention and refinement, but their greatest limitation remains their inability to incorporate information about intraspecific trait variation (ITV). 2. We use an individual-based model to account for ITV when calculating the functional diversity of two avian communities in Borneo; one in primary (unlogged) forest and one in selectively logged forest. We deal with the scarcity of trait data for individual species by developing a simulation approach, taking data from the literature where necessary. Using a bootstrapping procedure, we produce a range of ecologically feasible FD values taking account of ITV for five commonly-used FD indices, and we quantify the confidence that can be placed in these values using a newly-developed bootstrapping method: btFD. 3. We found that incorporating ITV significantly altered the FD values of all indices used in our models. The rank order of FD for the two communities, indicating whether diversity was higher in primary or selectively logged forest, was largely unchanged by the inclusion of ITV. However, by accounting for ITV, we were able to reveal previously unrecognized impacts of selective logging on avian functional diversity through a narrower dispersion of individuals in functional trait space in logged forest. 4. Our results highlight the importance of incorporating ITV into measures of functional diversity, whilst our simulation approach addresses the frequently encountered difficulty of working with sparse trait data and quantifies the confidence that should be placed in such findings

CASPER: Compiler-Assisted Securing of Programs at Runtime

Ensuring the security and integrity of computer systems deployed on the Internet is growing harder. This is especially true in the case of server systems based on open source projects like Linux, Apache, Sendmail, etc. since it is easier for a hacker to get access to the binary format of deployed applications if the source code to the software is publicly accessible. Often, having a binary copy of an application program is enough to help locate security vulnerabilities in the program. In the case of legacy systems where the source code is not available, advanced reverse-engineering and decompilation techniques can be used to construct attacks. This paper focuses on measures that reduce the effectiveness of hackers at conducting large-scale, distributed attacks. The first line of defense involves additional runtime checks that are able to counteract the majority of hacking attacks. Introducing diversity in deployed systems to severely diminish the probability of propagation to other systems helps to prevent effective attacks like the DDOS attack against the DNS root servers in October 21, 2002

Tropical land-use change alters trait-based community assembly rules for dung beetles and birds

Tropical rainforest disturbance and conversion are critical drivers of biodiversity loss. A key knowledge gap is understanding the impacts of habitat modification on mechanisms of community assembly, which are predicted to respond differently between taxa and across spatial scales. We use a null model approach to detect trait assembly of species at local- and landscape-scales, and then subdivide communities with different habitat associations and foraging guilds to investigate whether the detection of assembly mechanisms varies between groups. We focus on two indicator taxa, dung beetles and birds, across a disturbance gradient of primary rainforest, selectively logged rainforest, and oil palm plantations in Borneo, Southeast Asia. Random community assembly was predominant for dung beetles across habitats, whereas trait convergence, indicative of environmental filtering, occurred across the disturbance gradient for birds. Assembly patterns at the two spatial scales were similar. Subdividing for habitat association and foraging guild revealed patterns hidden when focusing on the overall community. Dung beetle forest specialists and habitat generalists showed opposing assembly mechanisms in primary forest, community assembly of habitat generalists for both taxa differed with disturbance intensity, and insectivorous birds strongly influenced overall community assembly relative to other guilds. Our study reveals the sensitivity of community assembly mechanisms to anthropogenic disturbance via a shift in the relative contribution of stochastic and deterministic processes. This highlights the need for greater understanding of how habitat modification alters species interactions and the importance of incorporating species’ traits within assessments

Rapid bidirectional reorganization of cortical microcircuits.

Mature neocortex adapts to altered sensory input by changing neural activity in cortical circuits. The underlying cellular mechanisms remain unclear. We used blood oxygen level-dependent (BOLD) functional magnetic resonance imaging (fMRI) to show reorganization in somatosensory cortex elicited by altered whisker sensory input. We found that there was rapid expansion followed by retraction of whisker cortical maps. The cellular basis for the reorganization in primary somatosensory cortex was investigated with paired electrophysiological recordings in the periphery of the expanded whisker representation. During map expansion, the chance of finding a monosynaptic connection between pairs of pyramidal neurons increased 3-fold. Despite the rapid increase in local excitatory connectivity, the average strength and synaptic dynamics did not change, which suggests that new excitatory connections rapidly acquire the properties of established excitatory connections. During map retraction, entire excitatory connections between pyramidal neurons were lost. In contrast, connectivity between pyramidal neurons and fast spiking interneurons was unchanged. Hence, the changes in local excitatory connectivity did not occur in all circuits involving pyramidal neurons. Our data show that pyramidal neurons are recruited to and eliminated from local excitatory networks over days. These findings suggest that the local excitatory connectome is dynamic in mature neocortex

Selective-logging and oil palm: Multitaxon impacts, biodiversity indicators, and trade-offs for conservation planning

Strong global demand for tropical timber and agricultural products has driven large-scale logging and subsequent conversion of tropical forests. Given that the majority of tropical landscapes have been or will likely be logged, the protection of biodiversity within tropical forests thus depends on whether species can persist in these economically exploited lands, and if species cannot persist, whether we can protect enough primary forest from logging and conversion. However, our knowledge of the impact of logging and conversion on biodiversity is limited to a few taxa, often sampled in different locations with complex land-use histories, hampering attempts to plan cost-effective conservation strategies and to draw conclusions across taxa. Spanning a land-use gradient of primary forest, once- and twice-logged forests, and oil palm plantations, we used traditional sampling and DNA metabarcoding to compile an extensive data set in Sabah, Malaysian Borneo for nine vertebrate and invertebrate taxa to quantify the biological impacts of logging and oil palm, develop cost-effective methods of protecting biodiversity, and examine whether there is congruence in response among taxa. Logged forests retained high species richness, including, on average, 70% of species found in primary forest. In contrast, conversion to oil palm dramatically reduces species richness, with significantly fewer primary-forest species than found on logged forest transects for seven taxa.Using a systematic conservation planning analysis, we show that efficient protection of primary-forest species is achieved with land portfolios that include a large proportion of logged-forest plots. Protecting logged forests is thus a cost-effective method of protecting an ecologically and taxonomically diverse range of species, particularly when conservation budgets are limited. Six indicator groups (birds, leaf-litter ants, beetles, aerial hymenopterans, flies, and true bugs) proved to be consistently good predictors of the response of the other taxa to logging and oil palm. Our results confidently establish the high conservation value of logged forests and the low value of oil palm. Cross-taxon congruence in responses to disturbance also suggests that the practice of focusing on key indicator taxa yields important information of general biodiversity in studies of logging and oil palm

Quantifying habitual levels of physical activity according to impact in older people: accelerometry protocol for the VIBE study

Physical activity (PA) may need to produce high impacts to be osteogenic. The aim of this study was to identify threshold(s) for defining high impact PA for future analyses in the VIBE (Vertical Impact and Bone in the Elderly) study, based on home recordings with triaxial accelerometers. Recordings were obtained from 19 Master Athlete Cohort (MAC; mean 67.6 years) and 15 Hertfordshire Cohort Study (HCS; mean 77.7 years) participants. Data cleaning protocols were developed to exclude artifacts. Accelerations expressed in g units were categorized into three bands selected from the distribution of positive Y-axis peak accelerations. Data were available for 6.6 and 4.4 days from MAC and HCS participants respectively, with approximately 14 hr recording daily. Three-fold more 0.5–1.0g impacts were observed in MAC versus HCS, 20-fold more 1.0–1.5g impacts, and 140-fold more impacts ≥ 1.5g. Our analysis protocol successfully distinguishes PA levels in active and sedentary older individuals

Tumour-derived alkaline phosphatase regulates tumour growth, epithelial plasticity and disease-free survival in metastatic prostate cancer

BACKGROUND: Recent evidence suggests that bone-related parameters are the main prognostic factors for overall survival in advanced prostate cancer (PCa), with elevated circulating levels of alkaline phosphatase (ALP) thought to reflect the dysregulated bone formation accompanying distant metastases. We have identified that PCa cells express ALPL, the gene that encodes for tissue nonspecific ALP, and hypothesised that tumour-derived ALPL may contribute to disease progression. METHODS: Functional effects of ALPL inhibition were investigated in metastatic PCa cell lines. ALPL gene expression was analysed from published PCa data sets, and correlated with disease-free survival and metastasis. RESULTS: ALPL expression was increased in PCa cells from metastatic sites. A reduction in tumour-derived ALPL expression or ALP activity increased cell death, mesenchymal-to-epithelial transition and reduced migration. Alkaline phosphatase activity was decreased by the EMT repressor Snail. In men with PCa, tumour-derived ALPL correlated with EMT markers, and high ALPL expression was associated with a significant reduction in disease-free survival. CONCLUSIONS: Our studies reveal the function of tumour-derived ALPL in regulating cell death and epithelial plasticity, and demonstrate a strong association between ALPL expression in PCa cells and metastasis or disease-free survival, thus identifying tumour-derived ALPL as a major contributor to the pathogenesis of PCa progression.British Journal of Cancer advance online publication, 22 December 2016; doi:10.1038/bjc.2016.402 www.bjcancer.com

Discussing life expectancy with surgical patients: Do patients want to know and how should this information be delivered?

<p>Abstract</p> <p>Background</p> <p>Predicted patient life expectancy (LE) and survival probability (SP), based on a patient's medical history, are important components of surgical decision-making and informed consent. The objective of this study was to assess patients' interpretation of and desire to know information relating to LE, in addition to establishing the most effective format for discussion.</p> <p>Methods</p> <p>A cross sectional survey of 120 patients (mean age = 68.7 years, range 50–90 years), recruited from general urological and surgical outpatient clinics in one District General and one Teaching hospital in Southwest England (UK) was conducted. Patients were included irrespective of their current diagnosis or associated comorbidity. Hypothetical patient case scenarios were used to assess patients' desire to know LE and SP, in addition to their preferred presentation format.</p> <p>Results</p> <p>58% of patients expressed a desire to know their LE and SP, if it were possible to calculate, with 36% not wishing to know either. Patients preferred a combination of numerical and pictorial formats in discussing LE and SP, with numerical, verbal and pictorial formats alone least preferred. 71% patients ranked the survival curve as either their first or second most preferred graph, with 76% rating facial figures their least preferred. No statistically significant difference was noted between sexes or educational backgrounds.</p> <p>Conclusion</p> <p>A proportion of patients seem unwilling to discuss their LE and SP. This may relate to their current diagnosis, level of associated comorbidity or degree of understanding. However it is feasible that by providing this information in a range of presentation formats, greater engagement in the shared decision-making process can be encouraged.</p

Muscle fiber conduction velocity is more affected after eccentric than concentric exercise

It has been shown that mean muscle fiber conduction velocity (CV) can be acutely impaired after eccentric exercise. However, it is not known whether this applies to other exercise modes. Therefore, the purpose of this experiment was to compare the effects of eccentric and concentric exercises on CV, and amplitude and frequency content of surface electromyography (sEMG) signals up to 24 h post-exercise. Multichannel sEMG signals were recorded from biceps brachii muscle of the exercised arm during isometric maximal voluntary contraction (MVC) and electrically evoked contractions induced by motor-point stimulation before, immediately after and 2 h after maximal eccentric (ECC group, N = 12) and concentric (CON group, N = 12) elbow flexor exercises. Isometric MVC decreased in CON by 21.7 ± 12.0% (± SD, p < 0.01) and by 30.0 ± 17.7% (p < 0.001) in ECC immediately post-exercise when compared to baseline. At 2 h post-exercise, ECC showed a reduction in isometric MVC by 24.7 ± 13.7% (p < 0.01) when compared to baseline, while no significant reduction (by 8.0 ± 17.0%, ns) was observed in CON. Similarly, reduction in CV was observed only in ECC both during the isometric MVC (from baseline of 4.16 ± 0.3 to 3.43 ± 0.4 m/s, p < 0.001) and the electrically evoked contractions (from baseline of 4.33 ± 0.4 to 3.82 ± 0.3 m/s, p < 0.001). In conclusion, eccentric exercise can induce a greater and more prolonged reduction in muscle force production capability and CV than concentric exercis

Theory of differential inclusions and its application in mechanics

The following chapter deals with systems of differential equations with discontinuous right-hand sides. The key question is how to define the solutions of such systems. The most adequate approach is to treat discontinuous systems as systems with multivalued right-hand sides (differential inclusions). In this work three well-known definitions of solution of discontinuous system are considered. We will demonstrate the difference between these definitions and their application to different mechanical problems. Mathematical models of drilling systems with discontinuous friction torque characteristics are considered. Here, opposite to classical Coulomb symmetric friction law, the friction torque characteristic is asymmetrical. Problem of sudden load change is studied. Analytical methods of investigation of systems with such asymmetrical friction based on the use of Lyapunov functions are demonstrated. The Watt governor and Chua system are considered to show different aspects of computer modeling of discontinuous systems