bluuebunny/crossref_metadata_2025 huggingface dataset:
Shades of yellow: interactive effects of visual and odour cues in a pest beetle
Authors: Arnold Sarah EJ , Stevenson Philip C , Belmain Steven R
Published: January 2018

Background. The visual ecology of pest insects is poorly studied compared to the role of odour cues in determining their behaviour. Furthermore, the combined effects of both odour and vision on insect orientation are frequently ignored, but could impact behavioural responses.

Methods. A locomotion compensator was used to evaluate use of different visual stimuli by a major coleopteran pest of stored grains ( Sitophilus zeamais ), with and without the presence of host odours (known to be attractive to this species), in an open-loop setup.

Results. Some visual stimuli – in particular, one shade of yellow, solid black and high contrast black-against-white stimuli – elicited positive orientation behaviour from the beetles in the absence of odour stimuli. When host odours were also present, at 90° to the source of the visual stimulus, the beetles presented with yellow and vertical black-on-white grating patterns changed their walking course and typically adopted a path intermediate between the two stimuli. The beetles presented with a solid black-on-white target continued to orient more strongly towards the visual than the odour stimulus.

Discussion. Visual stimuli can strongly influence orientation behaviour, even in species where use of visual cues is sometimes assumed to be unimportant, while the outcomes from exposure to multimodal stimuli are unpredictable and need to be determined under differing conditions. The importance of the two modalities of stimulus (visual and olfactory) in food location is likely to depend upon relative stimulus intensity and motivational state of the insect.
An exploration of the influence of diagonal dissociation and moderate changes in speed on locomotor parameters in trotting horses
Authors: Hobbs Sarah Jane , Bertram John E A , Clayton Hilary M
Published: January 2018

Background. Although the trot is described as a diagonal gait, contacts of the diagonal pairs of hooves are not usually perfectly synchronized. Although subtle, the timing dissociation between contacts of each diagonal pair could have consequences on gait dynamics and provide insight into the functional strategies employed. This study explores the mechanical effects of different diagonal dissociation patterns when speed was matched between individuals and how these effects link to moderate, natural changes in trotting speed. We anticipate that hind-first diagonal dissociation at contact increases with speed, diagonal dissociation at contact can reduce collision-based energy losses and predominant dissociation patterns will be evident within individuals.

Methods. The study was performed in two parts: in the first 17 horses performed speed-matched trotting trials and in the second, 5 horses each performed 10 trotting trials that represented a range of individually preferred speeds. Standard motion capture provided kinematic data that were synchronized with ground reaction force (GRF) data from a series of force plates. The data were analyzed further to determine temporal, speed, GRF, postural, mass distribution, moment, and collision dynamics parameters.

Results. Fore-first, synchronous, and hind-first dissociations were found in horses trotting at (3.3 m/s ± 10%). In these speed-matched trials, mean centre of pressure (COP) cranio-caudal location differed significantly between the three dissociation categories. The COP moved systematically and significantly (P=.001) from being more caudally located in hind-first dissociation (mean location = 0.41±0.04) through synchronous (0.36±0.02) to a more cranial location in fore-first dissociation (0.32±0.02). Dissociation patterns were found to influence function, posture, and balance parameters. Over a moderate speed range, peak vertical forelimb GRF had a strong relationship with dissociation time (R=.594; P<.01) and speed (R=.789; P<.01), but peak vertical hindlimb GRF did not have a significant relationship with dissociation time (R=.085; P>.05) or speed (R=.223; P=.023).

Discussion. The results indicate that at moderate speeds individual horses use dissociation patterns that allow them to maintain trunk pitch stability through management of the cranio-caudal location of the COP. During the hoof-ground collisions, reduced mechanical energy losses were found in hind-first dissociations compared to fully synchronous contacts. As speed increased, only forelimb vertical peak force increased so dissociations tended towards hind-first, which shifted the net COP caudally and balanced trunk pitching moments.
Characterization of lactic acid bacterium Pediococcus pentosaceus 4I1 from fresh water fish Zacco koreanus and its antibacterial mode of action
Authors: Bajpai Vivek K. , Han Jeong-Ho , Rather Irfan A. , Majumder Rajib , Nam Gyeong-Jun , ChanSeo Park , Lim Jeongheui , Paek Woon Kee , Park Yong-Ha
Published: January 2018

The present study aimed to characterize a lactic acid bacterium Pediococcus pentosaceus 4I1, isolated from the intestine of fresh water fish sample Zacco koreanus. Biochemical analysis using the API 50 CHL kit and molecular characterization of 4I1 revealed its identity as a lactic acid bacterium Pediococcus pentosaceus 4I1. Further, cell free supernatant (CFS) of P. pentosaceus 4I1 exhibited significant (p<0.05) antibacterial effect as diameters of inhibition zones (16.5–20.4 mm) against the tested foodborne pathogenic bacteria with minimum inhibitory (MIC) and minimum bactericidal (MBC) concentration values found in the range of 250-500 and 500-1,000 µg/mL, respectively. Further, to confirm the efficacy of 4I1 on membrane permeability against foodborne pathogens, antibacterial mode of action of CFS of P. pentosaceus 4I1 against two selected bacteria Staphylococcus aureus KCTC-1621 (gram-positive) and Escherichia coli O157:H7 (gram-negative) was determined by measuring cell viable count, release of 260-nm absorbing materials, leakage of potassium ions and measurement of relative electrical conductivity of the bacterial cells treated at MIC concentration. The CFS of P. pentosaceus 4I1 revealed its mode of action on membrane integrity as confirmed by reduction in viable cell count, increased release of potassium ions (900 and 800 mM/L), loss of 260-nm absorbing materials (3.99 and 3.77 OD), and increase in relative electrical conductivity (9.9 and 9.7%) against the tested bacteria S. aureus KCTC-1621 and E. coli O157:H7, respectively. The above findings hypothesize that P. pentosaceus 4I1 compromised its mode of action on membrane integrity, suggesting its enormous potential in food and pharma industries.
Thermal treatment and leaching biochar alleviates plant growth inhibition from mobile organic compounds
Authors: Gale Nigel V , Sackett Tara E , Thomas Sean C
Published: January 2018

Recent meta-analyses of plant responses to biochar boast positive average effects of between 10 and 40 %. Plant responses, however, vary greatly across systems, and null or negative biochar effects are increasingly reported. The mechanisms responsible for such responses remain unclear. In a glasshouse experiment we tested the effects of three forestry residue wood biochars, applied at five dosages (0, 5, 10, 20, 50 t/ha) to a temperate forest drystic cambisol as direct surface applications and as complete soil mixes on the herbaceous pioneers Lolium multiflorum and Trifolium repens. Null and negative effects of biochar on growth were found in most cases. One potential cause for null and negative plant responses to biochar is plant exposure to mobile compounds produced during pyrolysis that leach or evolve following additions of biochars to soil. In a second glasshouse experiment we examined the effects of simple leaching and heating techniques to ameliorate potentially phytotoxic effects of volatile and leachable compounds released from biochar. We used Solid Phase Microextraction (SPME) – gas chromatography – mass spectrometry (GC-MS) to qualitatively describe organic compounds in both biochar (through headspace extraction), and in the water leachates (through direct injection). Convection heating and water leaching of biochar prior to application alleviated growth inhibition. Additionally, growth was inhibited when filtrate from water-leached biochar was applied following germination. SPME-GC-MS detected primarily short-chained carboxylic acids and phenolics in both the leachates and solid chars, with relatively high concentrations of several known phytotoxic compounds including acetic acid, butyric acid, bisphenol and benzonoic acid. We speculate that variable plant responses to phytotoxic organic compounds leached from biochars may largely explain negative plant growth responses and also account for strongly species-specific patterns plant responses to biochar amendments in short-term experiments.
Can head louse repellents really work? Field studies of piperonal 2% spray
Authors: Burgess Ian F , Brown Christine M , Burgess Nazma A , Kaufman Judith
Published: January 2018

Background: Many families find regular checking of children’s heads for head louse infestation too onerous and would prefer to be able to prevent infestation by use of a topical application that deters lice from infesting the head. Identification in the laboratory of a repellent activity for piperonal provided the basis for developing a spray product to repel lice.

Methods: A proof of principle field study in Dhaka, Bangladesh, compared the effect of using 2% piperonal spray with that of a placebo in 105 children and adults from three communities with infestation levels close to 100%. All participants were treated for infestation and subsequent incidence of reinfestation monitored daily by investigators. A second randomised, controlled, double blind, study in North London, UK, evaluated the effect of the product in normal use. One hundred and sixty-three children from schools with a high level (20-25%) of infestation were treated and confirmed louse free and randomly divided between 2% piperonal, a placebo spray, and a control group for up to 22 weeks. Parents applied the spray and monitored for infestation. Regular investigator visits confirmed the parental monitoring and replenished supplies of spray.

Results: In Dhaka, over 18 days there were only 4 infestations in the piperonal group and 8 in the placebo group. This difference was not significant (p = 0.312). In North London, there were 41 cases of infestation over the course of the study. Analysis of time to first infestation showed a non-significant (p = 0.4368) trend in favour of piperonal.

Conclusion: Routine use of 2% piperonal spray in communities with a high prevalence of head louse infestation may provide some protection from infestation. However, the difference between use of the product and no active intervention was sufficiently small that regular checking for presence of lice is likely to be a more practical and cost effective approach to prevention of infestation.
Application of zero-inflated negative binomial mixed model to human microbiota sequence data
Authors: Fang Rui , Wagner Brandie , Harris J. Kirk , Fillon Sophie A
Published: January 2018

Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. Zero-inflated models are useful for analyzing such data. Moreover, the non-zero observations may be over-dispersed in relation to the Poisson distribution, biasing parameter estimates and underestimating standard errors. In such a circumstance, a zero-inflated negative binomial (ZINB) model better accounts for these characteristics compared to a zero-inflated Poisson (ZIP). In addition, complex study designs are possible with repeated measurements or multiple samples collected from the same subject, thus random effects are introduced to account for the within subject variation. A zero-inflated negative binomial mixed model contains components to model the probability of excess zero values and the negative binomial parameters, allowing for repeated measures using independent random effects between these two components. The objective of this study is to examine the application of a zero-inflated negative binomial mixed model to human microbiota sequence data.
Embodied cognition, embodied regulation, and the Data Rate Theorem
Authors: Wallace Rodrick
Published: January 2018

The Data Rate Theorem that establishes a formal linkage between linear control theory and information theory carries deep implications for the design of biologically inspired cognitive architectures (BICA), and for the more general study of embodied cognition. For example, modest extensions of the theorem provide a spectrum of necessary conditions dynamic statistical models that will be useful in empirical studies. A large deviations argument, however, suggests that the stabilization of such systems is itself an interpenetrating dynamic process necessarily convoluted with embodied cognition. As our experience with mental disorders and chronic disease implies, evolutionary process has had only modest success in the regulation and control of cognitive biological phenomena. For humans, the central role of culture has long been known. Although a ground-state collapse analogous to generalized anxiety appears ubiquitous to such systems, lack of cultural modulation for real-time automatons or distributed cognition man-machine `cockpits' makes them particularly subject to a canonical pathology under which `all possible targets are enemies'. More general dysfunctions of large-scale topology and connectivity analogous to autism spectrum and schizophenoform disorders also appear likely. A kind of machine psychiatry may become a central engineering discipline as the number of computation cores in real-time critical systems increases exponentially over the next few decades.
Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
Authors: Bombarely Aureliano , Coate Jeremy E , Doyle Jeff J
Published: January 2018

Allopolyploidy combines two progenitor genomes in the same nucleus, and is a common mechanism for producing new species, especially in plants. Deciphering the origins of polyploid species is a complex problem, due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. In this work,

we studied three allopolyploid species in the genus Glycine, which includes the cultivated soybean (G. max). Previous work based on two nuclear sequences showed that these allopolyploids combine the genomes of extant diploid species in the G. tomentella complex. We use several phylogenetic and population genomics approaches to clarify the origin of these species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that each of the three polyploid species are fixed hybrids combining the homoeologous genomes of its two putative parents. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also indicates multiple origins for G. tomentella polyploid species, and suggest that origins occurred within the last several hundred thousands years.
Effects of repeated head trauma causing mental health problems including chronic traumatic encephalopathy (CTE) in athletes
Authors: Briles Mason W
Published: January 2018

This paper focuses on the effects of repeated head trauma in athletes and how these repetitive blows to the head are causing a range of mental health problems. The primary focus, in terms of problems addressed, is chronic traumatic encephalopathy (often referred to as CTE) in the population of athletes, especially those participating in contact and combat sports. The disorders covered are caused by the cumulative effects of both concussive and sub-concussive blows to the head over a period of time.
Swedish high-school pupils’ attitudes towards drugs in relation to drug usage, impulsiveness and other risk factors
Authors: Mousavi Fariba , Garcia Danilo , Jimmefors Alexander , Archer Trevor , Ewalds-Kvist Béatrice M
Published: January 2018

Background: Illicit drug use influences people’s lives and elicits unwanted here is an increase in young people’s drug use in Sweden. This study aimed to investigate Swedish high-school pupils’ attitudes, impulsiveness and gender differences linked to drug use. Also risk and protective factors relative to drug use were a focus of interest.

Method: High school pupils (n = 146) aged 17- 21 years, responded to the Adolescent Health and Development Inventory, Barratt Impulsiveness Scale and Knowledge, and the Attitudes and Beliefs. Direct logistic, multiple regression analyses, and Multivariate Analysis of Variance were used to analyse the data.

Results: Positive Attitudes towards drugs was predicted by risk factors (odds ratio = 37.31) and gender (odds ratio = .32). Risk factors (odds ratio = 46.89), positive attitudes towards drugs (odds ratio = 4.63), and impulsiveness (odds ratio = 1.11) predicted drug usage. Risk factors dimensions Family, Friends and Individual Characteristic were positively related to impulsiveness among drug users. Moreover, although males reported using drugs to a greater extent, but female expressed more positive attitude towards drugs and even reported more impulsiveness than male students.

Conclusion: This study reinforces the idea that research must focus on gender differences relative to pro-drug attitudes along with testing for differences in the predictors of girls’ and boys’ delinquency and impulsiveness. Positive attitudes towards drugs among adolescents seem to be part of a vicious circle including risk factors, such as friendly drug environments (e.g., friends who use drugs) and unsupportive family environments, individual characteristics, and impulsiveness.
Mapping the self-association domains of ataxin-1: Identification of novel non overlapping motifs
Authors: Menon Rajesh , Soong Daniel , de Chiara Cesira , Holt Mark , McCormick John , Anilkumar N. , Pastore Annalisa
Published: January 2018

The neurodegenerative spinocerebellar ataxia type 1 (SCA1) is caused by aggregation and misfolding of the ataxin-1 protein. While the pathology correlates with mutations that lead to expansion of a polyglutamine tract in the protein, other regions contribute to the aggregation process as also non-expanded ataxin-1 is intrinsically aggregation-prone and forms nuclear foci in cell. Here, we have used a combined approach based on FRET analysis, confocal microscopy and in vitro techniques to map aggregation-prone regions other than polyglutamine and to establish the importance of dimerization in self-association/foci formation. Identification of aggregation-prone regions other than polyglutamine could greatly help the development of SCA1 treatment more specific than that based on targeting the low complexity polyglutamine region.
Multi-gene analysis of the symbiotic and free-living dinoflagellate genus Symbiodinium
Authors: Pochon Xavier , Putnam Hollie M , Gates Ruth D
Published: January 2018

Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.
Formation of intracellular glutamine synthetase bodies depends strongly upon cellular age and glucose availability
Authors: O'Connell Jeremy , Tsechansky Mark , West-Driga Marguerite , Marcotte Edward M
Published: January 2018

The enzyme glutamine synthetase serves key roles in central nitrogen metabolism, catalyzing the biosynthesis of glutamine, as well as regulating ammonia assimilation and integrating metabolic signals to balance nitrogen use. The budding yeast enzyme was recently found to form intracellular bodies (GS bodies) composed of glutamine synthetase and Hsp90 chaperones following various types of nutrient depletion or chemical stress. In order to better quantify and characterize the in vivo formation of GS bodies, we developed an assay for their formation in single yeast cells using imaging flow cytometry, which enables the quantitative measurement of rates of GS body formation and their population penetrance. Either reduction of supplied glucose, or addition of the competitive inhibitor of glycolysis, 2-deoxyglucose, markedly enhanced the formation of GS bodies. The occurrence of GS bodies increased with increasing cell size, a proxy for cell age, while treatment with rapamycin antagonized their formation. Direct measurement of GS body formation as a function of replicative age showed that mother cells exhibited a significantly higher incidence of GS bodies than daughter cells, and the frequency of GS body formation increased with increasing replicative cell age. Thus, we find that yeast glutamine synthetase bodies form in a manner strongly dependent on available glucose and increase markedly with cell age.
Increasing the precision of orthology-based complex prediction through network alignment
Authors: Pache Roland , Aloy Patrick
Published: January 2018

Macromolecular assemblies play an important role in almost all cellular processes. However, despite several large-scale studies, our current knowledge about protein complexes is still quite limited, thus advocating the use of in silico predictions to gather information on complex composition in model organisms. Since protein-protein interactions present certain constraints on the functional divergence of macromolecular assemblies during evolution, it is possible to predict complexes based on orthology data. Here, we show that incorporating interaction information through network alignment significantly increases the precision of orthology-based complex prediction. Moreover, we performed a large-scale in silico screen for protein complexes in human, yeast and fly, through the alignment of hundreds of known complexes to whole organism interactomes. Systematic comparison of the resulting network alignments to all complexes currently known in those species revealed many conserved complexes, as well as several novel complex components. In addition to validating our predictions using orthogonal data, we were able to assign specific functional roles to the predicted complexes. In several cases, the incorporation of interaction data through network alignment allowed to distinguish real complex components from other orthologous proteins. Our analyses indicate that current knowledge of yeast protein complexes exceeds that in other organisms and that predicting complexes in fly based on human and yeast data is complementary rather than redundant. Lastly, assessing the conservation of protein complexes of the human pathogen Mycoplasma pneumoniae, we discovered that its complexes repertoire is different from that of eukaryotes, suggesting new points of therapeutic intervention, whereas targeting the pathogen’s Restriction enzyme complex might lead to adverse effects due to its similarity to ATP-dependent metalloproteases in the human host.
Human Motion Project - The importance of patient compliance
Authors: Porter Miriam
Published: January 2018

For a patient to be compliant in wearing a device it is necessary to consider many factors as early on as at the time of device conception. These factors are divided up into outside influences and patient behavior. Outside influences can come from the treating physician’s attitude about the device or the patient’s own family. Any device affecting or altering patient’s behavior/lifestyle will have a major impact on compliance. It is necessary to invest time and money in order to identify these factors to understand which type of patient populations will be compliant.
Disjoint combinations profiling (DCP): a new method for the prediction of antibody CDR conformation from sequence
Authors: Nikoloudis Dimitris , Pitts Jim E. , Saldanha José W.
Published: January 2018

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in antibody variable regions. It relies on canonical templates which detail allowed residues at key positions in the variable region framework or in the CDR itself for 5 of the 6 CDRs. While no templates have as yet been defined for the hypervariable CDR-H3, instead, reliable sequence rules have been devised for predicting the base of the CDR-H3 loop. Here a new method termed Disjoint Combinations Profiling (DCP) is presented, which contributes a considerable advance in the prediction of CDR conformations. This novel method is explained and compared with canonical templates and sequence rules in a 3-way blind prediction. DCP achieved 93% accuracy over 951 blind predictions and showed an improvement in cumulative accuracy compared to predictions with canonical templates or sequence-rules. In addition to its overall improvement in prediction accuracy, it is suggested that DCP is open to better implementations in the future and that it can improve as more antibody structures are deposited in the databank. In contrast, it is argued that canonical templates and sequence rules may have reached their peak.
HIV-positive parents, HIV-positive children, and HIV-negative children’s perspectives on disclosure of a parent’s and child’s illness in Kenya
Authors: Gachanja Grace , Burkholder Gary J , Ferraro Aimee
Published: January 2018

HIV disclosure from parent to child is complex and challenging to HIV-positive parents and healthcare professionals. The purpose of the study was to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. Sixteen HIV-positive parents, seven HIV-positive children, and five HIV-negative children completed semistructured, in-depth interviews. Data were analyzed using the Van Kaam method; NVivo 8 software was used to assist data analysis. We present data on the process of disclosure based on how participants recommended full disclosure be approached to HIV-positive and negative children. Participants recommended disclosure as a process starting at fiveyears with full disclosure delivered at 10 years when the child was capable of understanding the illness, or by 14 years when the child was mature enough to receive the news if full disclosure had not been conducted earlier. Important considerations at the time of full disclosure included the parent’s and/or child’s health statuses, number of infected family members’ illnesses to be disclosed to the child, child’s maturity and understanding level, and the person best suited to deliver full disclosure to the child. The results also revealed it was important to address important life events such as taking a national school examination during disclosure planning and delivery. Recommendations are made for inclusion into HIV disclosure guidelines, manuals, and programs in resource-poor nations with high HIV prevalence.
Integrating ecology and epidemiology using individual-based multi-species networks
Authors: Pilosof Shai , Morand Serge , Krasnov Boris R , Nunn Charles L
Published: January 2018

Parasite transmission in host communities is a function of ecological factors that influence interspecific contacts and contact patterns within species. These two levels are studied with different kinds of networks – ecological networks and individual contact networks – and the integration of these levels is essential for effective understanding of parasite transmission. We combined these approaches by creating epidemiological networks based on parasite sharing from individual-based ecological host-parasite networks. We compared multi- to single-species networks to investigate the drivers of helminth infection in wild individual rodents of South-east Asia. Network modularity was higher in the multi-species than in the single-species networks. Phylogeny affected affiliation of individuals to modules. The importance of individuals differed between multi- and single-species networks, with species identity and individual traits influencing their position in the networks. Simulations revealed that a novel parasite spreads more slowly in multi- than in single-species networks and that this depended on network structure. Although the relative contribution of within- vs. between-species transmission rates to disease dynamics is important, using multi-host epidemiological networks improves our understanding of parasite dynamics as it further considers interaction structure between individuals.
Potential parasite transmission in multi-host networks based on parasite sharing
Authors: Pilosof Shai , Morand Serge , Krasnov Boris R , Nunn Charles L
Published: January 2018

Epidemiological networks are commonly used to explore dynamics of parasite transmission among individuals in a population of a given host species. However, many parasites infect multiple host species, and thus multi-host networks may offer a better framework for investigating parasite dynamics. We investigated the factors that influence parasite sharing – and thus potential transmission pathways – among rodent hosts in Southeast Asia. We focused on differences between networks of a single host species and networks that involve multiple host species. In host-parasite networks, modularity (the extent to which the network is divided to subgroups composed of individuals that interact more among themselves than with individuals outside the subgroup) was higher in the multi-species than in the single-species networks. This suggests that phylogeny affects patterns of parasite sharing, which was confirmed in analyses showing that it predicted affiliation of individuals to modules. We then constructed “potential transmission networks” based on the host-parasite networks, in which edges depict the number of parasites shared between a pair of individuals. The centrality of individuals in these networks differed between multi- and single-species networks, with species identity and individual characteristics influencing their position in the networks. Simulations further revealed that parasite dynamics differed between multi- and single-species networks. We conclude that multi-host networks based on parasite sharing can provide new insights into the potential for transmission among hosts in an ecological community. In addition, the factors that determine the nature of parasite sharing (i.e. structure of the host-parasite network) may impact transmission patterns.
Objective classification of North Atlantic right whale (Eubalaena glacialis) vocalizations to improve passive acoustic detection
Authors: Urazghildiiev Ildar R , Parks Susan E.
Published: January 2018

Passive acoustic monitoring is playing an increasing role in the detection of endangered North Atlantic right whales (NARW). Previous acoustic monitoring has relied on a single stereotyped vocalization, the upcall. Here the entire repertoire produced by NARW during the winter and early spring in Cape Cod Bay, Massachusetts is described. An objective sound classification scheme and automatic classification algorithm were developed. Nine days of acoustic recordings were used for the data analysis and a total of 9,611 right whale sounds were identified. The objective classification scheme of right whale sounds allowed for rapid identification of a diversity of right whale sounds. These sounds were assigned to 6 classes of narrowband upcalls, downsweep, complex and high frequency calls, wideband gunshot sounds and complex sounds. Results indicate that the prevalence of upcalls varied from 28% of detected calls in January to 80% in April. Other classes of signals were also well represented in the repertoire including the narrowband complex(10-36%) and high frequency calls (1-26%), wideband gunshot sounds (4-25%) and wideband complex sounds (0 – 25%). The prevalence of non-upcall signals suggests that including more signals classes may improve rates of detection for right whales in the Cape Cod Bay habitat.
Adeno-associated virus Type 2 Rep proteins mediate integration of lentiviral vectors
Authors: McAlister Victor J , Craig Anthony T , Owens Roland A
Published: January 2018

Aims: Adeno-associated virus type 2 (AAV2) is a naturally defective human parvovirus that is being developed as a gene therapy vector. In dividing cells, AAV2 DNA persists by integration into the host chromosomes. AAV2 is unique among mammalian viruses in its ability to integrate preferentially into a particular locus within human chromosome 19, designated AAVS1(also known as Mbs 85). The AAV2 Rep68 and Rep78 proteins mediate this integration. Recent data suggest that Rep68 and Rep78 can mediate integration of non-AAV2 DNA with free ends. To test this hypothesis, we targeted insertion of different lentiviral vectors to AAVS1. Methods: Cells were co-infected with wild-type AAV2, and integrase-proficient or integrase-deficient lentivirus vectors. A highly specific PCR-based assay was used to detect lentivirus integration at AAVS1. Similar experiments were performed using lentiviral vectors containing the AAV2 rep gene. Results: All lentiviral vectors tested integrated at AAVS1, if the rep gene was present either within the lentiviral vector or supplied in trans. All that was required for integration at AAVS1 was the amino acid sequence shared between Rep68 and Rep78. The results were similar with integrase-proficient or integrase-deficient lentiviral vectors. Conclusions: The inclusion of the rep gene with lentiviral vectors may produce more predictable integration patterns.
Beyond birth-weight: Improved ascertainment of early growth predicts blood pressure in Peruvian adolescents
Authors: Sterling Robie , Checkley William , Gilman Robert H , Cabrera Lilia , Sterling Charles R , Bern Caryn , Miranda J. Jaime
Published: January 2018

Background: Longitudinal investigations into the origins of adult essential hypertension have found elevated blood pressure in children to accurately track into adulthood, however the direct causes of essential hypertension in adolescence and adulthood remains unclear.

Methods: Cohort study, we revisited 152 Peruvian adolescents from a birth cohort evaluated with monthly anthropometric measurements between 1995 and 1998, and obtained anthropometric and blood pressure measurements 11 to 14 years later. We used multivariable regression models to study the effects of infantile and childhood growth trends on blood pressure and central obesity in early adolescence.

Results: In regression models adjusted for childhood growth, each 0.1 SD increase in weight for length from 0 to 5 months of age, and 1 SD increase from 6 to 30 months of age, predicted decreased adolescent systolic blood pressure by 1.3 mm Hg (95% CI -2.4 to -0.1) and 2.5 mm Hg (95% CI -4.9 to 0.0), and decreased waist circumference by 0.6 (95% CI -1.1 to 0.0) and 1.2 cm (95% CI -2.3 to -0.1) respectively. Growth in infancy and early childhood was not a significant predictor of adolescent waist-to-hip ratio.

Conclusions: Rapid compensatory growth in early life has been posited to increase the risk of long-term cardiovascular morbidities such that nutritional interventions may do more harm than good. However, we found increased weight growth during infancy and early childhood to predict decreases in adolescent systolic blood pressure and central adiposity.
Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition
Authors: Silva Pedro J , Bernardo Carlos E. P.
Published: January 2018

The binding of several rubromycin-based ligands to HIV1-reverse transcriptase was analyzed using molecular docking and molecular dynamics simulations. MM-PBSA analysis and examination of the trajectories allowed the identification of several promising compounds with predicted high affinity towards reverse transcriptase mutants which have proven resistant to current drugs. Important insights on the complex interplay of factors determining the ability of ligands to selectively target each mutant have been obtained.
Functional enhancement of platelet activation and aggregation by erythrocytes: role of red cells in thrombosis
Authors: Brown Gabrielle E , Ritter Leslie S. , McDonagh Paul F. , Cohen Zoe
Published: January 2018

Platelets expose phosphatidylserine (PS), a component of the prothrombinase complex, on the outer surface of the plasma membrane when activated. [ref 1] The prothrombinase complex catalyzes the conversion of prothrombin to thrombin, and it has been demonstrated that an increase in PS exposure is correlated with an increase in thrombin generation by platelets. [refs 2,3] Similarly, erythrocyte (RBC) activation, or eryptosis, is also characterized by PS exposure on the plasma membrane. [ref 4] Although PS exposure on RBCs is considered a signal for splenic macrophage destruction, eryptosis may allow RBCs to contribute to thrombosis.[ref 4] The aims of this study were to determine whether the addition of RBCs to platelets increased functional platelet aggregation and coagulation properties. A ratio of 4 RBCs to 1 platelet (4:1) was evaluated for aggregation and coagulation compared to platelet control. Platelet aggregation and coagulation properties were evaluated with impedance aggregometry and thromboelastography, respectively. The 4:1 experimental group had significant increases in aggregation and coagulation relative to the platelet control. These results indicate that RBCs increase platelet aggregation and coagulation properties. This suggests that RBCs play a role in diseases traditionally thought of as associated solely via dysregulated platelet activation.
Foundations of computational psychiatry: a mathematical treatment of embodied cognition and its disorders
Authors: Wallace Rodrick
Published: January 2018

The Data Rate Theorem that establishes a formal linkage between real-time linear control theory and information theory carries deep implications for the study of embodied cognition and its dysfunctions across human, machine, and composite man-machine cockpit entities. The stabilization of such cognition is a dynamic process deeply intertwined with it, constituting, in a sense, the riverbanks directing the flow of a stream of generalized consciousness. The fundamental role of culture in human life has long been understood. Here we argue that, not only is culture, in the words of the evolutionary anthropologist Robert Boyd, 'as much a part of human biology as the enamel on our teeth', but that it is an important part of the disorders of embodied cognition that different communities socially construct as mental illness. A shift in perspective on such illness is badly needed, from naive geneticism and a simplistic 'biomarker' focus to a broad cognitive theory that recognizes the central roles of culture, socioeconomic structure, their histories and their dynamics, in human development. Unfortunately, stabilizing analogs to cultural influence are unavailable to high-order real-time machine and cockpit systems that, increasingly, will be tasked with control of critical enterprises ranging from communication, power, and travel networks to nuclear and chemical reactors, organized deadly force, and so on.
Shifting thresholds: rapid evolution of migratory life histories in steelhead/rainbow trout, Oncorhynchus mykiss
Authors: Phillis Corey , Moore Jonathan W , Buoro Mathieu , Hayes Sean , Garza Carlos , Pearse Devon
Published: January 2018

Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or extirpation. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g. growth rate) or the state (e.g. size threshold) at which an individual switches between conditional strategies. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier waterfall in 1910, we evaluate how the conditional strategy to migrate evolves in response to selection against migration. Common garden-raised offspring of parents from the above-barrier population were 11% smaller and 31% lighter than offspring of parents from the below-barrier source population. Using a novel analytical approach we estimate that the mean size at which above-barrier fish switch between the resident and migrant strategy is 43% larger than below-barrier fish. As a result, above-barrier fish were 30% less likely to express the migratory strategy. Our results demonstrate how rapid and opposing changes in growth rate and threshold size contribute to the contemporary evolution of a conditional strategy and indicate that migratory barriers may elicit rapid evolution towards the resident life-history on timescales relevant for conservation and management of conditionally migratory species.
Futures of tropical forests (sensu lato)
Authors: Putz Francis E , Romero Claudia
Published: January 2018

When net deforestation declines in the tropics, attention will be drawn to the composition and structure of the retained, restored, invaded, and created forests. At that point the seemingly inexorable trends towards increased intensities of exploitation and management will be recognized as having taken their tolls of biodiversity and other forest values. Celebrations when a country passes the “forest transition” (i.e., suffers no net deforestation) will then be tempered by realization that what has been accepted as “forest” spans the gamut from short-rotation mono-clonal stands of genetically engineered trees to fully protected old growth natural forest. With management intensification, climate change, species introductions, landscape fragmentation, fire, and shifts in economics and governance, forests will vary along gradients of biodiversity, novelty of composition, stature, permanence, and the relative roles of natural and anthropogenic forces. Management intensity will increase with the increased availability of financial capital associated with economic globalization, scarcity of wood and other forest products, demand for biofuels, improved governance (e.g., security of property rights), improved accessibility, and technological innovations that lead to new markets for forest products. In a few places the trend towards land-use intensification will be counterbalanced by recognition of the many benefits of natural and semi-natural forests, especially where forest-fate determiners are compensated for revenues foregone from not intensifying management. Land-use practices informed by research will help minimize the tradeoffs between the financial profits from forest management and the benefits of retention of biodiversity and the full range of environmental services.
Effect of mutualist partner identity on plant demography
Authors: Bruna Emilio M , Izzo Thiago J , Inouye Brian D , Vasconcelos Heraldo L
Published: January 2018

Mutualisms play a central role in the origin and maintenance of biodiversity. Because many mutualisms have strong demographic effects, interspecific variation in partner quality could have important consequences for population dynamics. Nevertheless, few studies have quantified how a mutualist partner influences population growth rates, and still fewer have compared the demographic impacts of multiple partner species. We used integral projection models parameterized with three years of census data to compare the demographic effects of two ant species – Crematogaster laevis and Pheidole minutula – on populations of the Amazonian ant-plant Maieta guianensis. Estimated population growth rates were positive (i.e., λ>1) for all ant-plant combinations. However, populations with only Pheidole minutula had the highest asymptotic growth rate (λ=1.23), followed by those colonized by Crematogaster laevis (λ=1.16), and in which the partner ant alternated between C. laevis and P. minutula at least once during our study (λ=1.15). Our results indicate that the short-term superiority of a mutualist partner – in this system P. minutula is a better defender of plants against herbivores than C. laevis – can have long-term demographic consequences. Furthermore, the demographic effects of switching among alternative partners appear to be context-dependent, with no benefits to plants hosting C. laevis but a major cost of switching to plants hosting P. minutula. Our results underscore the importance of expanding the study of mutualisms beyond the study of pair-wise interactions to consider the demographic costs and benefits of interacting with different, and multiple, potential partners.
Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management
Authors: Cho Alyssa , Johnson Shelly A , Schuman Carrie , Adler Jennifer , Gonzalez Oscar , Graves Sarah J , Huebner Jana , Marchant D Blaine , Rifai Sami , Skinner Irina , Bruna Emilio M
Published: January 2018

Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership (i.e., Associate Editors and Editors-in-Chief) from 1985-2013. We found that during this time period only 16% of editorial board members were women, with more pronounced disparities in positions of editorial leadership. Although the trend was towards improvement over time, there was surprising variation between journals, including those with similar disciplinary foci. While demographic changes in academia may reduce these disparities over time, we argue journals should proactively strive for gender parity on their editorial boards. This will both increase the number of women afforded the opportunities and benefits that accompany board membership and increase the number of role models and potential mentors for early-career scientists and students.