bluuebunny/crossref_metadata_2025 huggingface dataset:
Mammal camera trapping success in a fragmented suburban landscape
Authors: Cove Michael , Jones Brandon , Bossert Aaron , Jackson Victoria
Published: January 2018

Camera traps are commonly used for mammal surveys and many recent studies have published variable trap success rates. All published reports have focused survey efforts in protected areas or large contiguous forests, but we used camera traps in a highly altered suburban landscape. We selected 22 camera trap sites in Warrensburg and Lee’s Summit, Missouri and surveyed for a total of 308 trapnights (TN) of effort. Procyon lotor (raccoon) had the highest trap success (38.96/100 TN), followed by: Didelphis virginiana (Virginia opossum, 37.34/100 TN); Odocoileus virginianus (white tailed deer, 27.92/100 TN); Sciurus niger and S. carolinensis (fox and gray squirrel, 19.48/100 TN); Vulpes vulpes (red fox, 8.77/100 TN); Canis latrans (coyote, 7.79/100 TN); Sylvilagus floridanus (cottontail rabbit, 3.90/100 TN); Urocyon cinereoargenteus (gray fox, 2.92/100 TN); Lynx rufus (bobcat, 1.95/100 TN); and Mephitis mephitis (striped skunk, 1.62/100 TN). These results are higher than any other published findings. We used 1-3 kg of deer meat as bait at each camera station and we believe this increased our trap success of mesopredators (Cove et al., 2012) versus studies that used no bait. However, our trap success for deer, squirrels, and rabbits were also higher than those published and these species were not attracted to bait. We hypothesize that the increased trap success in our study reflects (1) a true state of increased mesopredator abundance due to increased human-derived resources in the suburbs, and (2) concentrated activity of mammals in small fragmented forest patches versus the expansive forest tracts in other studies.
An intergenerational conflict model of age at first birth in humans
Authors: Moya Cristina , Sear Rebecca
Published: January 2018

Background. Parental absences in childhood are often associated with accelerated reproductive maturity in humans. These results are counterintuitive for evolutionary social scientists because reductions in parental investment should be detrimental for offspring, but earlier reproduction is generally associated with higher fitness. In this paper we discuss a neglected hypothesis that early reproduction is often associated with parental absence because it decreases the average relatedness of a developing child to her future siblings. Method. We illustrate this “intergenerational conflict hypothesis”with a formal game-theoretic model. Results. We show that parents will generally win reproductive conflicts with children when parents and children share limited household or kin resources, thus prioritizing their own reproduction and delaying offspring reproductive maturity. This is due to the asymmetric relatedness between grandparents and grandchildren (r=.25), compared to siblings (r=0.5) However, if a parent loses or replaces their partner, the conflict between the parent and offspring becomes symmetric since half siblings are as related to one another as grandparents are to grandchildren. This means that the offspring stand to gain more from earlier reproduction when their remaining parent would produce half, rather than full, siblings. We further show that if parents senesce in a way that decreases the quality of their infant relative to their offspring’s infant, the intergenerational conflict can shift to favor the younger generation, suggesting that it is primarily younger parents who should delay their offspring’s reproduction. Discuss. We use insights from this model to discuss the father absence literature and develop predictions about how the effects of parental absences should vary cross-culturally.
Meta Products towards a “gait/running style app”
Authors: Daumer Martin , Schneider Andreas N. , Mrowca Damian , Ding Rui , Gao Han , Christian Lederer
Published: January 2018

Background: The individual running style has an impact on the running performance as well as the running injury risk. In order to increase the performance and lower the injury risk, runners should be educated towards a healthy running style. But before advices can be made it is crucial to distinguish running styles from each other.Aim: The stretch goal is to build a running style app, which is able to track and display the user’s current running style by using accelerometry data, based on which advice can be given for a healthy and efficient running style with the help of gaming tools. To validate the approach, a gold standard with outdoor running acceleration data has to be created.Methods: The accelerometry data used by the smartphone app is gathered from the “actibelt”, an accelerometer included in a belt buckle. This sensor collects data close to the body COM in all three dimensions which is transferred to a smartphone via Bluetooth in real-time. The focus of this work is the validation of an acceleration based detection of different running styles, namely heel strikes, midfoot strikes and forefoot strikes. Features, which are able to clearly distinguish different running styles, have to be extracted out of the accelerometry data with machine learning techniques (SVM). Laboratory experiments have been conducted to analyze the actibelt data of three test persons performing heel, midfoot and forefoot strikes on a pressure sensitive treadmill with video control. As running apps are mainly used outdoors, the results had to be reproduced with outdoor running data. In an extreme ends approach four test persons with different running experience ranging from professional to occasional runners were asked to successively run on their heels, midfoot and forefoot, while accelerometry data was recorded and synchronized with mobile high speed video. The different running styles were performed on different substrates, with different shoes and speeds. Discussion/Conclusion: While significant differences in the accelerometry data of the running styles have been observed in the laboratory, those differences couldn’t be reproduced in outdoor environments. Characteristic peak patterns (Lieberman, nature 463, 531-535) could be reproduced in the laboratory but disappeared in outdoor running. The most distorting aspects are the harder and less comfortable surface and an irregular speed compared to treadmill running. Hence, for a reliable detection of the running style, the actibelt data may be complemented by further sensors, e.g. placed in the socks. A promising idea is to influence the stride frequency of runners at given speeds to improve the individual running style.
Protein structure determination using chemical shifts
Authors: Christensen Anders S
Published: January 2018

In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure is determined using only chemical shifts recorded and assigned through automated processes. The CA-RMSD to the experimental X-ray for this structure is 1.1 Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100 residues. For Rhodopsin (225 residues) a structure is found at 2.5 Å CA-RMSD from the experimental X-ray structure, and a structure is determined for the Savinase protein (269 residues) with 2.9 Å CA-RMSD from the experimental X-ray structure.
Human Hearing Loss
Authors: Ware Stacy Lee
Published: January 2018

Hearing loss affects as much as 5% of the global human population and its negative consequences, often exacerbated by cultural bias or distributive injustice, include delayed cognitive and language development, learning deficits and poor academic performance, chronic unemployment and dependency, poverty, elevated risk of harm and poor health. This paper is based on a review of the academic literature as well as other credible published resources to identify the principal causes of hearing loss; its consequences for individuals, communities, and states; and potential interventions most appropriate for developing and low-resource countries where hearing loss is currently most prevalent and its burdens most egregious.
Practical interpretation of ecological meta-analyses
Authors: Lortie Christopher J. , Stewart Gavin , Rothstein Hannah , Lau Joseph
Published: January 2018

Meta-analysis offers ecologists a powerful tool for knowledge synthesis. There is however obvious and subtle issues to consider specific to ecology with respect to the appropriate interpretation of meta-analyses once the statistics are completed. Meta-analysts in any field must clearly define a priori the scope of inference and the purpose of the meta-analysis, but ecological meta-analysis often faces issues particular to this field. For example, the primary studies being combined, even for tests of the same hypothesis, in ecology are generally conducted at different study sites or have difference ecological contexts (i.e. often few studies are not conducted in a laboratory) and use very different methods to test a single hypothesis. General objectives of the meta-analysis could include assessment of confidence limits of the treatment or ecological process of interest, detection of differences in treatments from no effect, identification of research gaps, and differences between groups such as different populations or communities. Meta-analyses can also be used in ecology to assess whether the scope of tests of a hypothesis are adequate. Reporting more than one summary statistic such as different effect size metrics is an excellent means to enhance synthetic potential for ecologists. Magnitude and sign of effect sizes can also be interpreted in novel ways for ecology given the broad scope of forms of hypotheses explored in this discipline. Ecology is now poised to take advantage of the synthesis developments common in other disciplines and this brief conceptual methods review provides the appropriate framing for this endeavor.
Forgotten treasures: the fate of data in animal behavior studies
Authors: Caetano Daniel S , Aisenberg Anita
Published: January 2018

Published discussions on data stewardship often focus on standardized datasets whose reuse patterns are known. Improvements in stewardship of animal behavior data are virtually absent and lag behind other disciplines such as molecular biology and systematics. In this essay, we discuss best practices of three key aspects related to the collection and archival of behavioral data: data supporting published results; data collected from field observations; and the potential of museum specimens as source of data to animal behavior and ecology. To quantify how much data is shared in publications we reviewed selected journals in animal behavior and behavioral ecology. We found that only an extremely small proportion of the articles published in 2013 made even part of their data available. We discuss about the benefits of making data available, review resources available for data archiving and provide practical guidance for ethologists. We discuss and provide examples of the amount of ethological and ecological data that can be recorded during field observations. To investigate the potential of museum specimens as source of data, we surveyed researchers working in areas related to ecology, animal behavior, and systematics. Both ethologists and systematists agreed that natural history information stored in collections would be a valuable source of data. We make recommendations to enhance data collection and stewardship from the point of view of researchers in animal behavior sciences, considering the special characteristics of the discipline and the type of data that is often produced. We suggest that there is a large amount of crucial data about natural history, ecology and behavior that investigators could glean from collections. Although it is difficult to appreciate the relevance of data for future studies at the time of publication, such data may inspire fruitful opportunities that we cannot afford to lose.
A couple’s marital disharmony and its psychological effects on their children during the HIV disclosure process in Kenya
Authors: Gachanja Grace
Published: January 2018

HIV-positive parents are challenged with disclosure to their children. Limited published data exists on how HIV-positive parents perform disclosure to all their children in the household. To start addressing this gap, data is presented on a couple’s HIV disclosure experiences to all their children. The couple participated in a larger study conducted to understand the lived experiences of HIV-positive parents and their children during the disclosure process in Kenya. Each underwent an individualized in-depth semi-structured interview. Their interviews were transcribed and transferred into NVivo 8 for analysis using the Van Kaam method. Three themes emerged including HIV testing, full disclosure delivery accompanied by marital disharmony, and post-disclosure psychological effects on the family. The couple’s narration of their diagnoses, and disclosure experiences to their children differed significantly. Ongoing poor paternal health caused persistent inquisitive questions from children. A poor paternal-children relationship, accompanied with his avoidance and non-involvement in disclosure matters caused the mother to fully disclose both parents’ illnesses to the four oldest children. These children were affected by disclosure and held animosity towards their father. One had an emotional outburst directed at the father, while another still displayed anger and withdrawal years later. Therefore, the couple was hesitant to fully disclose their illnesses to their youngest son and differed in how they wanted to disclose to him. HIV-positive parents with poor relationships among family members before HIV testing and/or disclosure should be provided with intense counseling aimed at increasing family cohesion. Extra support before, during, and after disclosure may be required for these families to increase positive outcomes.
What’s for dinner?: Undescribed species of porcini in a commercial packet
Authors: Dentinger Bryn TM , Suz Laura M
Published: January 2018

Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.
Preface of Proceedings of GNOME 2014 — Festschrift for Gaston Gonnet
Authors: Anisimova Maria , Dessimoz Christophe
Published: January 2018

It is an immense pleasure to present this Festschrift on the occasion of Professor Gaston H. Gonnet’s retirement. This volume accompanies the associated symposium Gonnet is Not Only about Molecular Evolution (GNOME) on the 4th of July 2014 at ETH Zurich. Born in Uruguay, Gaston completed his undergraduate studies in Montevideo before going to Waterloo, Canada, where he completed his Master’s and, just less than two years later, his PhD degree under the supervision of J. Alan George.
On the processes generating latitudinal richness gradients: identifying diagnostic patterns and predictions
Authors: Hurlbert Allen H , Stegen James C
Published: January 2018

Many processes have been put forward to explain the latitudinal gradient in species richness. Here, we use a simulation model to examine four of the most common hypotheses and identify patterns that might be diagnostic of those four hypotheses. The hypotheses examined include (1) tropical niche conservatism, or the idea that the tropics are more diverse because a tropical clade origin has allowed more time for diversification in the tropics and has resulted in few species adapted to extra-tropical climates. (2) The productivity, or energetic constraints, hypothesis suggests that species richness is limited by the amount of biologically available energy in a region. (3) The tropical stability hypothesis argues that major climatic fluctuations and glacial cycles in extratropical regions have led to greater extinction rates and less opportunity for specialization relative to the tropics. (4) Finally, the speciation rates hypothesis suggests that the latitudinal richness gradient arises from a parallel gradient in rates of speciation. We found that tropical niche conservatism can be distinguished from the other three scenarios by phylogenies which are more balanced than expected, no relationship between mean root distance and richness across regions, and a homogeneous rate of speciation across clades and through time. The energy gradient, speciation gradient, and disturbance gradient scenarios all exhibited phylogenies which were more imbalanced than expected, showed a negative relationship between mean root distance and richness, and diversity-dependence of speciation rate estimates through time. Using Bayesian Analysis of Macroevolutionary Mixtures on the simulated phylogenies, we found that the relationship between speciation rates and latitude could distinguish among these three scenarios. We emphasize the importance of considering multiple hypotheses and focusing on diagnostic predictions instead of predictions that are consistent with more than one hypothesis.
Low effect on open-farmland birds of young afforestations in heterogeneous Mediterranean croplands
Authors: Sánchez-Oliver Juan S. , Rey Benayas José M. , Carrascal Luis M. L.M.
Published: January 2018

Afforestation programs such as the one promoted by the EU Common Agricultural Policy have spread tree plantations on former cropland. These afforestations attract generalist forest and ubiquitous species but may cause severe damage to open habitat species, especially birds of high conservation value. We investigated the effects of young (< 20 yr) tree plantations dominated by pine P. halepensis on bird communities inhabiting the adjacent open farmland habitat in central Spain. We hypothesize that pine plantations with larger surface, and areas at shorter distances from plantations, would result in lower bird species richness and conservation value of open farmland birds. Regression models controlling for the influence of land use types around plantations revealed significant positive effects of distance to pine plantation edge on community species richness in winter, and negative effects on an index of conservation concern (SPEC) during the breeding season. However, plantation area did not have any effect on species richness or community conservation value. Our results indicate that pine afforestation of Mediterranean cropland in heterogeneous agricultural landscapes has an overall low detrimental effect on bird species that are characteristic of open farmland habitat.
Removal of organics and metal ion nanoparticles from synthetic wastewater by activated sludge process (ASP)
Authors: Singh Tarunveer , Jain Shubhanshu
Published: January 2018

Adsorption technique is widely used for removal of toxic organic contaminants from aqueous streams. Owing to the hazardous or otherwise undesirable characteristics of phenolic compounds in particular, their presence in wastewater from municipal and industrial discharge is one of the most important environmental issue. The discharge of poor quality effluents by the chemical-based laboratories and refineries in India is posing a serious threat to water sources and wastewater treatment installations alike. Our study was set up in the Indo - French Unit for Water & Wastewater Technologies (IFUWWT), IIT Delhi. The main objective of this study was to assess the efficiency of a laboratory-scale activated sludge treatment process in producing a final effluent conforming to regulatory standards of Central Pollution Control Board, India (CPCB norms) with regards to COD and metal ion loads. The study was conducted in three principal stages: characterization of wastewater containing nanoparticles; treatability studies of laboratory generated discards and investigations of heavy metal ions before and after treatment. The various raw effluent parameters analyzed were COD, BOD, F/M ratio, Sludge Value Index, Total Solids and concentrations of Cu, Ag and Zn. Studies were conducted using two aerobic sequencing batch reactors (SBR). MLSS of the aeration basin was calculated to be 7180±261.3 mg/L while the F/M ratio was kept down to 0.1560±.0149; besides, an SVI of 107.24 mL/g complied with the state of bioreactor’s sludge. These set of values suggested to set an extended aeration processes for the reactors. Accordingly, the detention time in aeration basin was 24 hours. The results showed over 98% influent COD reduction and nearly 100% removal of metal ions. The sample used was operated on sludge collected from Vasant Kunj Wastewater Treatment plant. Based on the results from waste characterization and treatability studies, it was decided that the mixed liquor discharged in the activation tank should have glucose solution and laboratory discarded sample in 1:1 ratio. The reactor was operated on a glucose fed batch basis for 30 days. For the sake of metal analysis, the digested water samples were analyzed for the presence of copper, silver and zinc using the ElementAS AAS4141 Atomic Absorption Spectrophotometer (by Electronics Corporation of India Ltd). The biosorption capacities were found to be over 95% in all the cases with the minimum correlation coefficient for calibration curve being 0.9811. Such a high sludge yield is suggestive of the fact that heavy metals are in very low concentrations in the considered carboy sample. Because of these insignificant values, the amount of metal ions introduced to the system gets adsorbed almost completely, hence leaving behind no metal ion within the supernatant. Well-treated wastewater has enormous potential as a source of water for crops, households and industry.
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Authors: Polka Jessica , Silver Pamela A
Published: January 2018

Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism which typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases cell length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a genetically tractable chassis for engineering compression sensitive organisms in the future. Second, the sensitivity of colony morphology to media compression in Bacillus is a physical rather than biological phenomenon dependent on a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
Psychosocial determinants of antenatal anxiety and depression in Pakistan: Is social support a mediator?
Authors: Waqas Ahmed , Raza Nahal , Wajid Lodhi Haneen , Muhammad Zerwah , Jamal Mehak , Suleman Abdul Rehman
Published: January 2018

Introduction: Pregnancy is generally viewed as a time of fulfillment and joy; however, for many women it can be a stressful event. In South Asia it is associated with cultural stigmas revolving around gender discrimination, abnormal births and genetic abnormalities. It is also associated with several psychiatric problems in women, most notably depression and anxiety.

Methodology: This cross-sectional study was done at four teaching hospitals in Lahore from February, 2014 to June, 2014. A total of 500 pregnant women seen at hospital obstetrics and gynecology departments were interviewed with a questionnaire consisting of three sections: demographics, the Hospital Anxiety and Depression Scale (HADS) and the Social Provisions Scale (SPS). All data were analyzed with SPSS v. 20. Descriptive statistics were analyzed for demographic variables. Pearson’s chi-squared test, bivariate correlations and multiple linear regression were used to analyze associations between the independent variables and scores on the HADS and SPS.

Results: Mean age among the 500 respondents was 27.41 years (5.65). Anxiety levels in participants were categorized as normal (145 women, 29%), borderline (110, 22%) or anxious (245, 49%). Depression levels were categorized as normal (218 women, 43.6%), borderline (123, 24.6%) or depressed (159, 31.8%). Inferential analysis revealed that higher HADS scores were significantly associated with lower scores on the SPS, rural background, history of harassment, abortion, cesarean delivery and unplanned pregnancies (P < .05). Social support (SPS score) mediated the relationship between the total number of children, gender of previous children and HADS score. Women with more daughters were significantly more likely to score higher on the HADS and lower on the SPS, whereas higher numbers of sons were associated with the opposite trends in the scores (P < .05)

Conclusion: Because of the predominantly patriarchal sociocultural context in Pakistan, the predictors of antenatal anxiety and depression may differ from those in developed countries. Rural women and working women had higher levels of antenatal anxiety and depression, which contradicts earlier findings in western countries. Our study found that higher numbers of daughters were associated with higher levels of depression and anxiety, whereas sons had a protective influence. We therefore suggest that interventions designed and implemented to reduce antenatal anxiety and depression should take into account these unique factors operating in developing countries and patriarchal societies.
Quality of life of Syrian refugees living in camps in the Kurdistan Region of Iraq
Authors: Aziz Izaddin A , Hutchinson Claire V , Maltby John
Published: January 2018

The current study explores the perceived quality of life of Syrian refugees who have entered the Kurdistan Region of Iraq. Two hundred and seventy participants residing in refugee camps in the Erbil region in Kurdistan completed the WHOQOL-BREF, which measures quality of life (QoL) within four domains; physical, psychological, social relationships and environment. Syrian refugees in Kurdistan scored significantly lower for general population norms on physical health, psychological and environment QoL, and score significantly lower for physical health and psychological QOL for refugees in the Gaza strip. However, respondents in the current sample scored significantly higher on environment QoL to refugees in the Gaza strip, and significantly higher on all the QoL domains than those reported for refugees in West Africa. Finally, Syrian refugees in Kurdistan scored significantly higher than general population norms for environment-related QoL. The current findings provide the first report of QoL domain scores among Syrian refugees, and position the QoL scores among this sample, for the most part, within the range mean scores for QoL domains of other samples, and may, for environment-related QoL, be higher than for other refugee samples.
Stiffness without mineral: material properties and biochemical components of jaws and chondrocrania in the Elasmobranchii (sharks, skates, and rays)
Authors: Porter Marianne E , Beltran Jennie L , Kajiura Stephen M , Koob Thomas J , Summers Adam P
Published: January 2018

Chondrichthyians (sharks, ratfish, and rays) can function at extremes (growing big, swimming fast, and eating hard-prey) suggesting their skeletons are experiencing loading regimes equal to or greater than those of other fishes. In most vertebrates, cartilage is a soft connective tissue serving two purposes; a low-friction bearing surface and contour filler; however, cartilaginous fishes maintain a skeleton made of cartilage throughout life. We examined material properties and biochemical components of cartilage from the jaws and/or chondrocranium of seven species of shark. For each species cylindrical plugs were drilled from the specimen, mineralized tesserae were removed, and plugs tested in compression to ten percent of initial thickness (ε=0.10) at 2mm/sec. Stiffness and strength varied significantly among species and in both cases the chondrocranial properties were greater than those of the jaws. After materials testing, cartilage plugs were lyophilized to obtain water content; then collagen and proteoglycan was measured with hydroxyproline and DMMB assays, respectively. Water content was greatest in the chondrocranial cartilage while collagen content was consistent between the jaws and chondrocrania. However, proteoglycan content was greater in the jaw cartilage. The average values for water and proteoglycan content were consistent with mammalian cartilage, while collagen content was much lower than mammalian cartilage. Material properties and biochemical components were also similar to the mineralized cartilage found in elasmobranch vertebral cartilage.
Prior mating success can affect allocation towards future sexual signaling in crickets
Authors: Chiswell Rachel , Girard Madeline , Fricke Claudia , Kasumovic Michael
Published: January 2018

Fitness is often correlated with the expression level of a sexually selected trait. However, sexually selected traits are costly to express such that investment in their expression should be optimised to maximize their overall fitness gains. Social interactions, in the form of successful and unsuccessful matings, may offer males one type of feedback allowing them to gauge how to allocate their resources towards sexual signalling. Here we tested whether adult male black field crickets (Teleogryllus commodus) modify the extent of their calling effort (the sexually selected trait) in response to successful and unsuccessful matings with females. To examine the effect that mating interactions with females have on investment into sexual signalling, we monitored male calling effort after maturation and then provided males with a female at two points within their life, manipulating whether or not males were able to successfully mate each time. Our results demonstrate that males alter their investment towards sexual signalling in response to successful matings, but only if the experience occurs early their life. Males that mated early in their life decreased their calling effort sooner than males that were denied a mating. Our results demonstrate that social feedback in the form of successful and unsuccessful matings has the potential to alter the effort a male places in sexual signalling.
Placental vascular pathology and increased thrombin generation as mechanisms of disease in obstetrical syndromes
Authors: Mastrolia Salvatore Andrea , Mazor Moshe , Loverro Giuseppe , Klaitman Vered , Erez Offer
Published: January 2018

Obstetrical complications including preeclampsia, fetal growth restriction, preterm labor, preterm prelabor rupture of membranes and fetal demise are all the clinical endpoint of several underlying mechanisms (i.e. infection inflammation, thrombosis, endocrine disorder, immunologic rejection, genetic, and environmental), therefore, they may be regarded as syndromes. Placental vascular pathology and increased thrombin generation were reported in all of these obstetrical syndromes. Moreover, elevated concentrations of thrombin-anti-thrombin III complexes and changes in the coagulation as well as anticoagulation factors can be detected in the maternal circulation prior to the clinical development of the disease in some of these syndromes. In this review, we will assess the changes in the hemostatic system during normal and complicated pregnancy in maternal blood, maternal-fetal interface and amniotic fluid, and describe the contribution of thrombosis and vascular pathology to the development of the great obstetrical syndromes.
Transferability and scaling of soil total carbon prediction models in Florida
Authors: Grunwald Sabine , Yu Congrong , Xiong Xiong
Published: January 2018

The applicability, transfer, and scalability of visible/near-infrared (VNIR)-derived soil models are still poorly understood. The objectives of this study in Florida, U.S. were to: (i) compare three methods to predict soil total carbon (TC) using five fields (local scale) and a pooled (regional scale) VNIR spectral dataset, (ii) assess the model’s transferability among fields, and (iii) evaluate the up- and down-scaling behavior of TC prediction models. A total of 560 TC-spectral sets were modeled by Partial Least Square Regression (PLSR), Support Vector Machine (SVM), and Random Forest. The transferability and up- and down-scaling of models were limited by the following factors: (i) the spectral data domain, (ii) soil attribute domain, (iii) methods that describe the internal model structure of VNIR-TC relationships, and (iv) environmental domain space of attributes that control soil carbon dynamics. All soil logTC models showed excellent performance based on all three methods with R2 > 0.86, bias < 0.01%, root mean square prediction error (RMSE) = 0.09%, residual predication deviation (RPD) > 2.70% , and ratio of prediction error to inter-quartile range (RPIQ) > 4.54. PLSR performed substantially better than SVM to scale and transfer models. Upscaled soil TC models performed somewhat better in terms of model fit (R2), RPD, and RPIQ, whereas downscaled models showed less bias and smaller RMSE based on PLSR. Given the many factors that can impinge on empirically derived soil spectral prediction models, as demonstrated by this study, more focus on the applicability and scaling of them is needed.
Different running in shod vs. minimal footwear/barefoot runners - adaptions for prevention of injuries
Authors: Daumer Martin , Subkowski Paul , Trost Michael , Stolle Christoph , Kleinmond Christine , Fasching Matthias , Walther Markus , Lederer Christian
Published: January 2018

In the last years the number of long distance runners who wear minimal footwear or run completely barefoot increased considerably. There is an ongoing debate about the benefits and risks of running in minimal footwear/barefoot instead of running in conventional running shoes. The objectives were to investigate the effect of different types of shoes as well as of different running techniques on acceleration of centre of gravity and to explore a potential link to injuries (subjects are described in table 1). We assessed data with a mobile accelerometry device (actibelt ®, http://www.actibelt.com) during competition. Three runners were additionally investigated during a treadmill test using a high speed camera system simultaneously coupled to a wireless stream of acceleration data. Acceleration raw data was analysed with standardized algorithm packages using R software environment.
SUPERSMART: ecology and evolution in the era of big data
Authors: Antonelli Alexandre , Condamine Fabien L. , Hettling Hannes , Nilsson Karin , Nilsson R Henrik , Oxelman Bengt , Sanderson Michael J , Sauquet Hervé , Scharn Ruud , Silvestro Daniele , Töpel Mats , Vos Rutger A
Published: January 2018

Rapidly growing biological data volumes – including molecular sequences, species traits, geographic occurrences, specimen collections, and fossil records – hold an unprecedented, yet largely unexplored potential to reveal how ecological and evolutionary processes generate and maintain biodiversity. Most biodiversity studies integrating ecological data and evolutionary history use an idiosyncratic step-by-step approach for the reconstruction of time-calibrated phylogenies in light of ecological and evolutionary scenarios. Here we introduce a conceptual framework, termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of biodiversity research. This framework reconstructs dated phylogenies based on the assembly of molecular datasets and collects pertinent data on ecology, distribution, and fossils of the focal clade. The data handled for each step are continuously updated as databases accumulate new records. We exemplify the practice of our method by presenting comprehensive phylogenetic and dating analyses for the orders Primates and the Gentianales. We believe that this emerging framework will provide an invaluable tool for a wide range of hypothesis-driven research questions in ecology and evolution.
The design of Maple's sum-of-products and POLY data structures for representing mathematical objects
Authors: Monagan Michael M
Published: January 2018

The principal data structure in Maple used to represent polynomials and general mathematical expressions involving functions like sqrt(x), sin x, exp(2x), y'(x) etc., is known to the Maple developers as the sum-of-products data structure. Gaston Gonnet, as the primary author of the Maple kernel, designed and implemented this data structure in the early 80s. As part of the process of simplifying a mathematical formula, he represented every Maple object and every sub-object uniquely in memory. This makes testing for equality, which is used in many operations, very fast. In this article, on occasion of Gaston's retirement, we present details of his design, its pros and cons, and changes we have made to it over the years. One of the cons is the sum-of-products data structure is not nearly as efficient for multiplying multivariate polynomials as other special purpose computer algebra systems. We describe the new data structure called POLY which we added to Maple 17 (released 2013) to improve performance for polynomials in Maple, and recent work done for Maple 18 (released 2014).
Associating disease-related genetic variants in intergenic regions to the genes they impact
Authors: Macintyre Geoff , Jimeno Yepes Antonio , Ong Cheng Soon , Verspoor Karin
Published: January 2018

We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus.
The electronic McPhail trap
Authors: Potamitis Ilyas , Rigakis Iraklis
Published: January 2018

Certain insects affect cultivations in a detrimental way. A notable case is the Olive fruit ﬂy Bactrocera oleae (Diptera: Tephritidae) that in Europe alone causes billions of euros crop loss per year. Pests can be controlled with aerial and ground bait pesticide sprays, the efficiency of which depends on knowing the time and location of insect infestations as early as possible. The inspection of traps is currently carried out manually. Automatic monitoring traps can enhance efficient monitoring of flying pests by identifying and counting targeted pests as they enter the trap. This work deals with the hardware setup of an insect trap with an embedded opto-electronic sensor that automatically records insects as they fly in the trap. The sensors responsible for detecting the insect is an array of phototransistors receiving light from an infrared LED. The wing-beat recording is based on the interruption of the emitted light due to the partial occlusion from insect’s wings. We show that the recording are of high quality paving the way for automatic recognition and transmission of insect detections from the field to a smartphone. This work emphasizes the hardware implementation of the core sensor giving all necessary implementation details needed to construct it.
Intragenomic polymorphisms among high-copy loci: A genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)
Authors: Weitemier Kevin , Straub Shannon C. K. , Fishbein Mark , Liston Aaron
Published: January 2018

Despite knowledge that concerted evolution of high-copy loci is often imperfect, few studies investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual's consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).
Traverse the landscape of the mind by walking: an exploration of a new brainstorming practice
Authors: Wang Xiaofeng , Graziotin Daniel , Rikkilä Juha , Abrahamsson Pekka
Published: January 2018

Group brainstorming is a well-known idea generation technique, which plays a key role in software development processes. Despite this, the relevant literature has had little to offer in advancing our understanding of the effectiveness of group brainstorming sessions. In this paper we present a research-in-progress on brainstorming while walking, which is a practice built upon the relationship between thinking and walking. The objective is to better understand how to conduct group brainstorming effectively. We compared two brainstorming sessions, one performed during a mountain walk, the other traditionally in a room. Three preliminary findings are obtained: walking can lead to an effective idea generation session; brainstorming while walking can encourage team members to participate in and contribute to the session in an equal manner; and it can help a team to maintain sustainable mental energy. Our study opens up an avenue for future exploration of effective group brainstorming practices.
The role of macrobiota in structuring microbial communities along rocky shores
Authors: Pfister Catherine A , Gilbert Jack A , Gibbons Sean M
Published: January 2018

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.