Discriminative learning for protein conformation sampling

Protein structure prediction without using templates (i.e., ab initio folding) is one of the most challenging problems in structural biology. In particular, conformation sampling poses as a major bottleneck of ab initio folding. This article presents CRFSampler, an extensible protein conformation sampler, built on a probabilistic graphical model Conditional Random Fields (CRFs). Using a discriminative learning method, CRFSampler can automatically learn more than ten thousand parameters quantifying the relationship among primary sequence, secondary structure, and (pseudo) backbone angles. Using only compactness and self-avoiding constraints, CRFSampler can efficiently generate protein-like conformations from primary sequence and predicted secondary structure. CRFSampler is also very flexible in that a variety of model topologies and feature sets can be defined to model the sequence-structure relationship without worrying about parameter estimation. Our experimental results demonstrate that using a simple set of features, CRFSampler can generate decoys with much higher quality than the most recent HMM model.     

Methods of evaluating human exposure to electromagnetic fields radiated from operating base stations in Korea

This article presents measurement methods used to determine the human exposure to electromagnetic fields radiated from operating base stations. In Korea, when evaluating the human exposure to electromagnetic fields from operating base stations, the measurement procedure is different between the following cases: in situ measurement and electromagnetic environment measurement. When performing an in situ measurement, compliance with human exposure limits is determined by the spatially averaged field value obtained within the space occupied by humans at one arbitrary position, but when performing an electromagnetic environment measurement, it is determined by the maximum value at the highest field position selected from several places.     

Pulsed electric field reduces the permeability of potato cell wall

The effect of the application of pulsed electric fields to potato tissue on the diffusion of the fluorescent dye FM1-43 through the cell wall was studied. Potato tissue was subjected to field strengths ranging from 30 to 500 V/cm, with one 1 ms rectangular pulse, before application of FM1-43 and microscopic examination. Our results show a slower diffusion of FM1-43 in the electropulsed tissue when compared with that in the non-pulsed tissue, suggesting that the electric field decreased the cell wall permeability. This is a fast response that is already detected within 30 s after the delivery of the electric field. This response was mimicked by exogenous H2O2 and blocked by sodium azide, an inhibitor of the production of H2O2 by peroxidases.     

Recent advances in research relevant to electric and magnetic field exposure guidelines

Limits on exposures to extremely low-frequency electric fields, magnetic fields and contact currents, designated as voluntary guidelines or standards by several organizations worldwide, are specified so as to minimize the possibility of neural stimulation. The limits, which we refer to as guidelines, derive from "basic restrictions" either on electric fields or current density within tissue, or on avoidance of annoying or startling interactions that may be experienced with spark discharge or contact current. Further, the guidelines specify more conservative permissible doses and exposure levels for the general public than for exposures in controlled environments, which most typically involve occupational settings. In 2001 we published an update on guideline science. This paper covers more recent developments that are relevant to the formulation and implementation of the next generation of guidelines. The paper deals with neurostimulation thresholds and the relevance of magnetophosphenes to setting guideline levels; dosimetry associated with contact current benchmarked against basic restrictions; tissue and cellular dosimetry from spark discharge; assessment of exposures to high electric fields in realistic situations (e.g., line worker in a transmission tower); a simplified approach to magnetic field assessment in non-uniform magnetic fields; and a quantitative approach to sampling workplace exposure for assessing compliance.     

Statistical analysis of personal radiofrequency electromagnetic field measurements with nondetects

Exposimeters are increasingly applied in bioelectromagnetic research to determine personal radiofrequency electromagnetic field (RF‐EMF) exposure. The main advantages of exposimeter measurements are their convenient handling for study participants and the large amount of personal exposure data, which can be obtained for several RF‐EMF sources. However, the large proportion of measurements below the detection limit is a challenge for data analysis. With the robust ROS (regression on order statistics) method, summary statistics can be calculated by fitting an assumed distribution to the observed data. We used a preliminary sample of 109 weekly exposimeter measurements from the QUALIFEX study to compare summary statistics computed by robust ROS with a naïve approach, where values below the detection limit were replaced by the value of the detection limit. For the total RF‐EMF exposure, differences between the naïve approach and the robust ROS were moderate for the 90th percentile and the arithmetic mean. However, exposure contributions from minor RF‐EMF sources were considerably overestimated with the naïve approach. This results in an underestimation of the exposure range in the population, which may bias the evaluation of potential exposure‐response associations. We conclude from our analyses that summary statistics of exposimeter data calculated by robust ROS are more reliable and more informative than estimates based on a naïve approach. Nevertheless, estimates of source‐specific medians or even lower percentiles depend on the assumed data distribution and should be considered with caution. Bioelectromagnetics. Bioelectromagnetics 29:471–478, 2008. © 2008 Wiley‐Liss, Inc.     

Perception of the electromagnetic field emitted by a mobile phone

Electromagnetic sensibility refers to the ability to perceive the electromagnetic field (EMF) without necessarily developing health symptoms attributed to EMF exposure. A large sample of young healthy adults (n = 84) performed two forced‐choice tasks on the perception of the GSM mobile phone EMF (902 MHz pulsed at 217 Hz), “Was the field on?” and “Did the field change?” (3 conditions × 100 trials for each task, n = 600 trials in total). A monetary prize was announced for good performance (correct response rate ≥75%, n = 600 trials). The performance was no better than expected by chance, and thus none of the participants won the prize. Two participants showed extraordinary performance in one of the task conditions (“Was the field on?”, n = 100 trials), with correct response rates of 97% (P = 1.28 × 10^?25) and 94% (P = 9.40 × 10^?22), but they failed to replicate the result in the retest of six blocks of the same condition 1 month later. Six participants had reported being able to perceive the mobile phone EMF in the preliminary inquiry, but they performed no better than the others. This study provides empirical evidence against the existence of electromagnetic sensibility to the mobile phone EMF, demonstrating the necessity for replication in EMF studies. Bioelectromagnetics 29:154–159, 2008. © 2007 Wiley‐Liss, Inc.     

Influence of information about specific absorption rate (SAR) upon customers' purchase decisions and safety evaluation of mobile phones

This study investigated whether the SAR value is a purchase-relevant characteristic of mobile phones for laypersons and what effect the disclosure of a precautionary SAR value has on laypersons' risk perception. The study consisted of two parts: Study part 1 used a conjoint analysis design to explore the relevance of the SAR value and other features of mobile phones for an intended buying decision. Study part 2 used an experimental, repeated measures design to examine the effect of the magnitude of SAR values and the disclosure of a precautionary SAR value on risk perception. In addition, the study included an analysis of prior concerns of the study participants with regard to mobile phone risks. Part 1 indicates that the SAR value has a high relevance for laypersons' purchase intentions. In the experimental purchase setting it ranks even before price and equipment features. The results of study part 2 show that providing information of a precautionary limit value does not influence risk perception. This result suggests that laypersons' underlying subjective "safety model" for mobile phones resembles more a "margin of safety" concept than a threshold concept. The latter observation holds true no matter how concerned the participants are.     

Physiological indicators of stress in African forest elephants (Loxodonta africana cyclotis) in relation to petroleum operations in Gabon,Central Africa

Aim Human activities are major determinants of forest elephant (Loxodonta africana cyclotis) distribution in Gabon, but the types and intensity of disturbance that elephants can tolerate are not known. We conducted dung surveys within the Gamba Complex of Protected Areas in SW Gabon to examine (1) the feasibility of noninvasive faecal analyses for monitoring stress physiology, and (2) the influence of petroleum operations on stress levels in forest elephants. Location Gabon, Central Africa. Methods We identified multiple dung piles from the same individual by matching their eight‐locus microsatellite genotypes, and measured faecal concentrations of glucocorticoid metabolites as an indicator of stress in areas subject to different levels of disturbance: (1) Loango National Park (2) an ‘industrial corridor’ dominated by oil fields, and (3) a nearby area of human settlements. Results We obtained unique microsatellite genotypes and faecal glucocorticoid metabolite (FGM) concentrations for 150 forest elephant individuals, which is the largest hormonal data set for wild African forest elephants to date. Adults exhibited higher mean FGM concentrations than juveniles, and in contradiction of our expectations of chronic stress around oil fields, elephants in Loango National Park exhibited significantly higher FGM concentrations than elephants in the industrial corridor. Main conclusions We argue that forest elephants in the industrial corridor of the Gamba Complex have become acclimated to oil fields, resulting in part from oil company regulations that minimize stressful interactions between elephants and petroleum operations. Our findings for a flagship species with substantial ecological requirements bode well for other taxa, but additional studies are needed to determine whether oil operations are compatible over their life span with rain forest ecosystems in Central Africa.     

The response of herbaceous-layer vegetation to anthropogenic disturbance in intermittent stream bottomland forests of southern Indiana,USA

Between 1993 and 1995 we sampled herbaceous layer vegetation on 84 plots in Platanus/Asarum Wet-Mesic Bottomland forests to determine how these forests have responded to human disturbance. Four different disturbance types were sampled (abandoned agricultural are as, clearcuts, group-selection openings, and single-tree selection openings), and uncut 80–100 year-old reference stands were sampled for comparison. Detrended Correspondence Analysis (DCA), distance analyses (chord distance and normalized Euclidean distance) and similarity analysis (Bray-Curtis similarity coefficient) suggest that agricultural use has shifted herbaceous-layer vegetation composition away from that typical of the reference forests, but that clearcutting, group-selection harvest, and single-tree selection harvest have not greatly shifted herbaceous composition. This shift in vegetation on abandoned agricultural land resulted from a loss of indicator species, such as Cardamine concatenata (Michx.) Sw., Stellaria pubera Michx., and Laportea canadensis (L.) Weddell and an influx of disturbance, exotic, and nonforest species (e.g., Lycopodium complanatum L., Lonicera japonica Thunb. and Senecio aureus L.). However, only two species found in reference stands, Erigenia bulbosa (Michx.) Nutt. and Sphenopholis obtusata (Michx.) Scribn., were missing from clearcuts, group-selection openings, and single-tree selection openings. The species richness values of abandoned agriculture, clearcut, and group-selection plots were generally greater than those of single-tree selection and reference plots. Abandoned agricultural areas had much greater total species richness because of the influx of dry-site, exotic, disturbance, and non-forest species.     

Ontogenetic shifts in competitive interactions and intra-guild predation between two wolf spider species

Abstract. 1. The wolf spiders (Araneae: Lycosidae) Hogna helluo (Walckenaer) and Pardosa milvina Hentz co-occur in soybean fields of south-west Ohio, U.S.A. As adults, Hogna is the larger species and has the competitive advantage in most interactions; due to differing phenologies, however, their size-classes frequently overlap and as such there is potential for shifts in competitive ability and intra-guild predation. The hypothesis that competitive interactions and intra-guild predation will favour Pardosa when Pardosa is similar-sized, or has a size advantage over Hogna , was tested in laboratory and field experiments.
2. Studies in laboratory arenas, pairing similar-sized individuals of these species and Hogna spiderlings with larger spiders of both species, revealed that intra-guild predation seldom occurs with similar-sized Hogna and Pardosa , however Pardosa will consume small Hogna individuals in laboratory arenas.
3. Field experiments involved stocking high densities (50 m^{– 2} ) of Pardosa and Hogna in enclosures placed in soybean fields. In experiments with spiders of similar size, no interspecific effects were uncovered, but an intraspecific effect was found for Pardosa as its survival and weight gain were lower in the presence of more conspecifics. Large Hogna or Pardosa had no effect on the survival or weight gain of Hogna spiderlings.
4. Although Hogna is a better competitor as an adult, it has no advantage over Pardosa when their size-classes overlap, and Pardosa effects on Hogna may be inconsequential under field conditions. Therefore, the co-existence of these species is fostered by the fact that there are few negative interspecific interactions during their ontogeny.