bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring the value of the social network: analysis, quantitative approach, and application
Authors: Jindal Sujata , Sindhu Ritu
Published: January 2018

Social networks are growing day by day. Users of the social networks are generating values for these networks. All the users can’t be considered equal as they have different social network impact value. In this paper we analyze the social impact of a user and propose a method to estimate an individual’s worth to a social network in terms of impact. The mathematical evaluations show the effectiveness of our method. Based on the proposed method many applications can be built taking into consideration the impact any individual’s social profile has. We have tried to make various social data attributes more valuable and meaningful.
Unexpectedly high precision of consumer-grade GPS units for small-scale animal movement studies
Authors: Breed Greg A , Severns Paul M
Published: January 2018

Consumer-grade GPS units are a staple of modern field ecology, but the relatively large error radii reported by manufacturers (up to 10 meters) ostensibly precludes their utility in measuring fine-scale movement of small animals such as insects. Here we demonstrate that for data collected at fine spatio-temporal scales, these devices can produce exceptionally precise data on step-length and movement patterns of small animals. With an understanding of the properties of GPS error and how it arises, it is possible, using a simple field protocol, to use consumer grade GPS units to collect step-length data for the movement of small animals that introduces a median of 11 cm of error. Such small errors make these inexpensive units useful for measuring insect and other small animal movements on small to intermediate scales on budgets that are orders of magnitude lower than the survey-grade units used in past studies. As an additional advantage, these units are much simpler to operate and insect or other small animal trackways can be collected more quickly than either survey-grade units or more traditional ruler / gird approaches.
Smart learning: A search-based approach to rank change and defect prone classes
Authors: Alexandru Carol V , Panichella Annibale , Panichella Sebastiano , Bacchelli Alberto , Gall Harald C
Published: January 2018

Research has yielded approaches for predicting future changes and defects in software artifacts, based on historical information, helping developers in effectively allocating their (limited) resources. Developers are unlikely able to focus on all predicted software artifacts, hence the ordering of predictions is important for choosing the right artifacts to concentrate on. We propose using a Genetic Algorithm (GA) for tailoring prediction models to prioritize classes with more changes/defects. We evaluate the approach on two models, regression tree and linear regression, predicting changes/defects between multiple releases of eight open source projects. Our results show that regression models calibrated by GA significantly outperform their traditional counterparts, improving the ranking of classes with more changes/defects by up to 48%. In many cases the top 10% of predicted classes can contain up to twice as many changes or defects.
Maternal and paternal psychopathological risk in children with Non Organic Failure to Thrive
Authors: Cerniglia Luca , Cimino Silvia
Published: January 2018

Recent researches have underlined that maternal psychopathology can be considered as a crucial risk factor for the development and maintaining of several emotional behavioural problems in children. While several researches have dealt prominently with maternal psychopathological risk and with their outcomes on NOFTT, limited attention has been given in literature to fathers’ involvement in caregiving and to their psychological profiles, while this issue may represent a significant risk and/or protective factor. The present longitudinal study is aimed to further elaborate on the impact of the maternal psychological functioning on the adaptation of the child between the first and second childhood, focusing also on the paternal involvement in caregiving.
Non-native species in the vascular flora of highlands and mountains of Iceland
Authors: Wasowicz Pawel
Published: January 2018

Highlands and mountains of Iceland (defined here as areas located above 400 m a.s.l) are considered to be the largest remaining wilderness areas in Europe. The present study provides first comprehensive and up-to-date data on non-native plant species from this area. The study was aimed to provide a checklist of alien plant species recorded from highland and mountain areas of Iceland, assess their naturalisation status, define spatial patterns and hotspots of their distribution and analyse temporal trends in the data. The presence of 18 non-native vascular plant species was evidenced including 13 casuals and 5 naturalised taxa (1 invasive). The results showed that the central highland is most vulnerable to alien plant colonisation, while mountain and highland areas in other parts of the country are much less impacted by non-native plant taxa. Clear hotspots of occurrence of alien flora can be defined and their geographic location corresponds to places of touristic interest such as hot springs, geothermal areas, mountain huts and shelters as well as main roads and tracks. Temporal trends characterizing non-native plant colonization show clearly that the process is still in its initial phase. The research suggests that human-mediated dispersal is the major force contributing to increased invasion risk within the investigated area.
Non-native species in the vascular flora of highlands and mountains of Iceland
Authors: Wasowicz Pawel
Published: January 2018

The highlands and mountains of Iceland, defined here as areas located above 400 m above sea level (m.a.s.l.) are one of the largest remaining wilderness areas in Europe. The present study was aimed to provide the first comprehensive and up-to-date data on non-native plant species from this region. The study was aimed to answer the following questions: (1) How many non-native vascular plant species inhabit highland and mountainous environments in Iceland? (2) Do temporal trends in alien species immigration to Iceland and highland areas differ? (3) Do human disturbed and undisturbed areas within Icelandic highlands differ in terms of alien species occurrence? (4) Is spread within the highland areas a second step in alien plant colonization? and (5) Can we point out hot-spots in the distribution of non native taxa within highlands? Overall, 16 non-native vascular plant species were detected, including 11 casuals and 5 naturalized taxa (1 invasive). Results showed that temporal trends in alien species immigration to Iceland and to highland areas are similar, but it is clear that the process of colonization of highland areas is still in its initial phase. It was evidenced that non-native plants tend to occur close to man-made infrastructure and buildings including huts, shelters, road network etc. Analysis of spatio-temporal patterns showed that the spread within highland areas is a second step in non-native plant colonization in Iceland. Several statically significant hot spots of alien plant occurrences were be identified using Getis-Ord Gi* statistic and linked to human disturbance. This research suggests that human-mediated dispersal is the main driving force increasing the risk of invasion in Icelandic highlands and mountain areas.
Putative long distance gene flow of the Crown-of-Thorns Starfish in the Pacific Ocean
Authors: Tusso Sergio , Morcinek Kerstin , Vogler Catherine , Schupp Peter J , Caballes Ciemon F , Vargas Sergio , Woerheide Gert
Published: January 2018

Population outbreaks of the corallivorous crown-of-thorns starfish (COTS), Acanthaster ‘planci’ L., are considered among the most important biological disturbances of tropical coral reefs. A local COTS outbreak, a “primary outbreak”, can lead to so-called “secondary outbreaks” in adjacent coral reefs due to increased larval release and subsequent dispersion. Previous analyses have shown that in the Pacific Ocean, this dispersion may be geographically restricted to certain regions. Guam, an island in the western Pacific region, suffered from several severe COTS outbreaks in the last 50 years, and in this study we tested whether Guam is genetically connected with surrounding long distant regions. We used microsatellites to measure gene flow and genetic structure among 14 localities in the Pacific Ocean. Our results show substantial genetic structure between geographical regions. There was, however, a lack of significant genetic differentiation between localities separated by large geographic distances (e.g., Guam, Kingman Reef and Johnston Atoll) – a finding consistent with the existence of contemporary long distance larval dispersion and the gradual erasing of ancestral signatures of divergence. Our findings highlight the importance of addressing likely triggers of both primary and secondary outbreaks in conservation efforts using highly variable markers that provide enough variance to infer contemporary patterns of gene-flow and allow to implement programs that strive to control the growth and spread of A. ‘planci’ in the Pacific Ocean.
When one code = 2,300 species: Expanding our understanding of the trade in aquatic marine wildlife
Authors: Rhyne Andrew L , Tlusty Michael F , Szczebak Joseph , Holmberg Robert J
Published: January 2018

The trade of marine ornamental animals for home and public aquariums has grown into a major global industry. Since the 1990s, the aquarium hobby has shifted focus from fish to miniature reef ecosystems. Millions of marine fish and invertebrates are removed from coral reefs and associated habitats each year, and the majority are imported into the United States, with the remainder imported by Europe, Japan, and a handful of other countries. This shift in aquarium complexity demands increases in not only the volume but also the diversity of species harvested by collectors, who now must supply the trade with species sought for both aesthetics as well as ecosystem services (e.g., species that benefit the life support services of aquariums). Despite the recent growth and diversification of the aquarium trade, to date, data collection is not mandatory, and hence comprehensive information on species volume or diversity is wanting. The lack of this information makes it impossible to study trade pathways. Without species-specific volume and diversity data, it is unclear how importing and exporting governments can oversee this industry effectively. It is also unclear how sustainability should be encouraged given the paucity of data. To expand our knowledge and understanding of this trade, and to be able to effectively communicate this new understanding, we introduce the Marine Aquarium Biodiversity and Trade Flow online database (https://www.aquariumtradedata.org/). This tool was created as a means to assess the volume and diversity of marine fishes and/or invertebrates imported into the US over four years (2005, 2008, 2009, and 2011) and one month of additional data in 2000. It is available online for perusal by the public which will help communicate this new understanding in the trade of aquatic wildlife. To create this online tool, invoices pertaining to shipments of live marine fish and invertebrates were scanned and analyzed for species name, quantity, country of origin, and city of import destination. The results for October 2000 as well as the year between June 2004 and May 2005 have been published (Rhyne et al. 2012, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035808; Balboa 2003). Here we focus on the later three years of data and also produce an estimate of fish to create complete calendar years for 2000, 2004, and 2005. The three-year aggregate totals indicate that just under 2,300 fish and 725 invertebrate species were imported into the US, even though each year, just shy of 1,800 fish and 550 invertebrate species were traded. Overall, the total number of live marine animals decreased between 2008 and 2011. In 2008, 2009, and 2011, the total number of individual fish (8.2, 7.3, and 6.9 million) and invertebrates (4.2, 3.7, and 3.6 million) assessed by analyzing the invoice data are roughly 60% of the total volumes recorded through the LEMIS dataset.
Giving increased value to invertebrates conservation through entotourism activity in current and planned ecotourism activity. Tourist attitudes preliminary study in Sabah, Borneo of Malaysia
Authors: Ak Matusin Ak Mohd Rafiq , Saikim Fiffy Hanisdah , Mohd Suki Norazah , M. Dawood Mahadi Menakbar
Published: January 2018

Tabin Wildlife Resort in Tabin Wildlife Reserve, Lahad Datu, Sabah is a popular tourist spot in Malaysia for being the largest wildlife reserve by mainly focusing on endangered mammals and birds. Thus, in this research, it is proposed to include invertebrates’ information in the current ecotourism activities in Tabin Wildlife Reserve. Implicitly, it could increase a sustainable invertebrates’ conservation. Invertebrates possess large benefits to humankind, namely waste recycling whereby, they cycle the minerals and organic minerals for plants and animals. Thus, this investigation aimed to study the tourists’ perception on including invertebrates’ information in current Tabin Wildlife Resort ecotourism activity. Hence, to collect data from tourists, pre-visit and post-visit questionnaire surveys were adopted as the methodological approach during preliminary entotourism activity. Two different conceptual framework sets (pre-visit and post-visit) were posited in this investigation. The collected data were analysed via Statistical Package for Social Sciences (SPSS) and Analysis of Moment Structure (AMOS) software program by adopting Structural Equation Modelling (SEM). SEM analyses revealed that both pre-visit and post-visit surveys have significant variance towards the ecotourism. This implied a good potential in including invertebrates in ecotourism activities especially in Sabah. The findings of this study are important to contribute to the literature of invertebrates’ species conservation awareness in Sabah, since very limited researches are conducted specifically on entotourism field.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks: Part 2
Authors: Ng Wenfa
Published: January 2018

The characteristics of the culture vessel determine, to a large extent, the type of growth medium suitable for use. For example, most growth media for high cell density cultivation are designed for expensive bioreactors operating either in continuous or fed-batch mode, where provision of additional nutrients and/or removal of metabolic waste products from the basal medium (comprising salts, buffer components and small amount of carbon and nitrogen sources) help increase biomass yield by maintaining culture conditions within the range conducive for growth. The inexpensive and ubiquitous shake flask, in contrast, is usually operated in batch mode and contains a comprehensive medium with all necessary nutrients for converting cells into biomass, and as a repository for secreted metabolites, some of which detrimental for cell growth. Thus, designing medium for high cell density cultivation in shake flask is an optimization process with the aim to increase biomass formation while reducing toxic metabolite secretion. This preprint reports improvements to a previously reported semi-defined medium for high cell density aerobic cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. Specifically, by reducing the concentrations of glucose (from 6.0 to 4.0 g/L) and ammonium chloride (from 1.5 to 1.0 g/L), the following improvements were obtained: a shorter diauxic lag phase (3 versus 5 hours); a higher maximum optical density (12.0 versus 11.0) in a shorter total culture period (27 versus 48 hours), and smaller pH variation during cultivation (6.0 to 7.6 versus 5.5 to 7.8). Similar to the earlier study, glucose and yeast extract served as principal carbon sources in separate growth phases for E. coli in the improved formulated medium (FMimproved). Specifically, an OD600nm of 6.6 was attained after 9 hours of growth at 37 oC. After a lag phase of 3 hours, growth resumed on yeast extract and the OD600nm reached 12.0 after 27 hours. The broth’s pH decreased from 7.1 to 6.0 during the first growth phase, whereupon it gradually rose to 7.6 at the end of culture. A smaller pH decrease together with higher biomass yield in the first growth phase suggested that the lower glucose concentration in FMimproved might have prevented overflow metabolism (and associated negative effects on growth); thus, resulting in a shorter diauxic lag phase and total culture period. Collectively, increase in cell yield, as well as decrease in total culture time and a shorter diauxic lag phase arise from a small reduction in glucose concentration, which suggested that an optimum exist, beyond which occurrence of overflow metabolism would reduce cell yield and biomass formation. Part 1 of this work can be found at: https://peerj.com/preprints/115/
Interactions between donor Agreeableness and recipient characteristics in predicting charitable donation and positive social evaluation
Authors: Yarkoni Tal , Ashar Yoni K , Wager Tor D
Published: January 2018

Agreeable people are more likely to display prosocial attitudes and helpful behavior in a broad range of situations. Here we show that this tendency interacts with the personal characteristics of interaction partners. In an online study (n = 284), participants were given the opportunity to report attitudes toward and make monetary donations to needy individuals who were described in dynamically generated biographies. Using a machine learning and multilevel modeling framework, we tested three potential explanations for the facilitatory influence of Agreeableness on charitable behavior. We find that Agreeableness preferentially increased donations and prosocial attitudes toward targets normatively rated as being more deserving, but not to targets considered less deserving. Our results advance understanding of person-by-situation interactions in the context of charitable behavior and prosocial attitudes.
Predicting programmers' personality via interaction behaviour with keyboard and mouse
Authors: Khan Iftikhar A , Khalid Osman , Jadoon Waqas , Shan Rafi Us. , Nasir Abdul Nasir
Published: January 2018

This exploratory research was conducted to study the relationship between Big Five personality measurement scale and the interaction behaviour of the programmers with keyboard and mouse to examine the possibility of creating a computer based objective personality measurement scale. A field study with two analyses (N = 20), (N = 12) and a lab study (N = 15) were conducted where N is the number of participants who participated in the research. In the field study, interaction data were collected during normal PC use over several days. In the laboratory study, participants worked on a programming task while their interaction with keyboard and mouse was being recorded in background. All of the participants rated their personality online and uploaded the data for analysis. Results found inconsistent behaviour of all of the personality traits except ‘activity level’ in all studies and thus suggested that a programmer’s ‘activity level’ can be predicted from his/her interaction behaviour with keyboard and mouse. This prediction will help in differentiating good programmers from not so good programmers objectively.
Low serum albumin and total lymphocyte count as predictors of 30 day hospital readmission in patients 65 years of age or older
Authors: Robinson Robert
Published: January 2018

Introduction: Hospital readmission within 30 days of discharge is a target for health care cost savings through the medicare Value Based Purchasing initiative. Because of this focus, hospitals and health systems are investing considerable resources into the identification of patients at risk of hospital readmission and designing interventions to reduce the rate of hospital readmission. Malnutrition is a known risk factor for hospital readmission.

Materials and Methods: All medical patients 65 years of age or older discharged from Memorial Medical Center from January 1, 2012 to March 31, 2012 who had a determination of serum albumin level and total lymphocyte count on hospital admission were studied retrospectively. Admission serum albumin levels and total lymphocyte counts were used to classify the nutritional status of all patients in the study. Patients with a serum albumin less than 3.5 grams/dL and/or a TLC less than 1,500 cells per mm3 were classified as having protein energy malnutrition. The primary outcome investigated in this study was hospital readmission for any reason within 30 days of discharge.

Results: The study population included 1,683 hospital discharges with an average age of 79 years. The majority of the patients were female (55.9%) and had a DRG weight of 1.22 (0.68). 219 patients (13%) were readmitted within 30 days of hospital discharge. Protein energy malnutrition was common in this population. Low albumin was found in 973 (58%) patients and a low TLC was found in 1,152 (68%) patients. Low albumin and low TLC was found in 709 (42%) of patients. Kaplan-Meier analysis shows any laboratory evidence of PEM is a significant (p < 0.001) predictor of hospital readmission. Low serum albumin (p < 0.001) and TLC (p = 0.018) show similar trends. Cox proportional-hazards regression analysis showed low serum albumin (Hazard Ratio 3.27, 95% CI: 2.30-4.63) and higher DRG weight (Hazard Ratio 1.19, 95% CI: 1.03-1.38) to be significant independent predictors of hospital readmission within 30 days.

Discussion: This study investigated the relationship of PEM to the rate of hospital readmission within 30 days of discharge in patients 65 years of age or older. These results indicate that laboratory markers of PEM can identify patients at risk of hospital readmission within 30 days of discharge. This risk determination is simple and identifies a potentially modifiable risk factor for readmission: protein energy malnutrition.
A proposed solution to the problem posed by reduction(s) in osmolyte infusion interval: A theory on the origins of non-natural stimulus-functional response pairs in biological systems
Authors: Jeff-Eke Imadol V
Published: January 2018

This work follows as a response to a problem posed in a previous work (Jeff-Eke, 2015b). Here we propose and explore a probable solution to the posed problem of how well a cellular system can tolerate random changes to the frequency of osmolytes infused into an intracellular space of interest. The proposed solution involves the ability of biological systems to anticipate occurrences of imminent challenge stimuli, with such means involving alignment of moments of initiation of the required functional response mechanism(s) to stimuli, in relation to moments of initiation of occurrences of these stimuli. The resultant outcome is reduction of the lag interval for the functional response mechanism. We also present propositions on the means by which these anticipatory relationships may be formed, and some consequences for biological systems. By stating anticipatory roles in biological systems, we are suggesting a possible origin for non-natural stimulus-functional response pairing.
Resin and osteoblastic adhesion on zirconia and titanium implant materials blasted with various grits
Authors: Cornelius Timothius Celine Joyce , Lung Christie YK , Seneviratne Chaminda Jayampath , Tsoi James KH , Matinlinna Jukka P
Published: January 2018

Objective: The aim of this study was to evaluate the resin and initial osteoblastic adhesion of zirconia and titanium implant surfaces grit-blasted with four different sands, namely silica-coated alumina, alumina, silicon carbide and boron carbide. Materials and methods: Titanium (Permascand, Ljungaverk, Sweden) of size 20 mm × 40 mm × 1 mm and sintered zirconia (3M ESPE, Lava™ Frame, St. Paul, MN, USA) of size 9 mm × 12 mm × 3 mm specimens were polished and grit-blasted with one of the following grits: silica-coated alumina, alumina, silicon carbide and boron carbide. Two study groups were prepared. For the first group, a silane coupling agent and a resin was applied on grit-blasted sample surfaces (n=8), and adhesive strengths of the dental resins to these specimens were evaluated under shear mode in three storage conditions: dry, 24h water aging and thermo-cycled for 6000 cycles. The results were analyzed by using two-way ANOVA test with 0.05 significance level. For the second group, the specimens were immersed in a cell line medium (MC3T3-E1) and the attachment was observed under a confocal microscope after 24 hours. The attached cells were fixed and viewed under an SEM to observe the cell morphology. Results: Surface topography and chemical composition of zirconia and titanium were changed after grit-blasting with four different grits. The specimens grit-blasted with silica-coated alumina or alumina exhibited a significantly higher mean resin adhesive strengths (p<0.05) than other two grits. In addition, SEM and confocal microscopy confirmed the specimens grit-blasted with alumina powder showed the maximum osteoblastic attachment, and revealed the cell morphology. Conclusion: With the limitation of the laboratory study, alumina deemed to be the best grit-blasting material to achieve satisfactory osteoblastic cell and resin adhesions for both titanium and zirconia implant materials .
Isolated instrument transcription using a deep belief network
Authors: Burlet Gregory , Hindle Abram
Published: January 2018

Automatic music transcription is a difficult task that has provoked extensive research on transcription systems that are predominantly general purpose, processing any number or type of instruments sounding simultaneously. This paper presents a polyphonic transcription system that is constrained to processing the output of a single instrument with an upper bound on polyphony. For example, a guitar has six strings and is limited to producing six notes simultaneously. The transcription system consists of a novel pitch estimation algorithm that uses a deep belief network and multi-label learning techniques to generate multiple pitch estimates for each audio analysis frame, such that the polyphony does not exceed that of the instrument. The implemented transcription system is evaluated on a compiled dataset of synthesized guitar recordings. Comparing these results to a prior single-instrument polyphonic transcription system that received exceptional results, this paper demonstrates the effectiveness of deep, multi-label learning for the task of polyphonic transcription.
Diet and kwashiorkor: a prospective study from rural DR Congo
Authors: Kismul Hallgeir , Van den Broeck Jan , Lunde Torleif Markussen
Published: January 2018

The etiology of kwashiorkor remains enigmatic and longitudinal studies examining potential causes of kwashiorkor are scarce. Using historical, longitudinal study data from the rural area of Bwamanda, Democratic Republic of Congo, we investigated the potential causal association between diet and the development of kwashiorkor in 5 657 preschool children followed 3-monthly during 15 months.We compared dietary risk factors for kwashiorkor with those of marasmus. Kwashiorkor was diagnosed as pitting oedema of the ankles; marasmus as abnormal visibility of skeletal structures and palpable wasting of the gluteus muscle. A food frequency questionnaire was administered 3-monthly to record the consumption of the 41 locally most frequent food items. We specified Hanley-Miettinen smooth-in-time risk models containing potential causal factors, including food items, specialmeals prepared for the child, breastfeeding, disease status, nutritional status, birth rank, age, season and number of meals. Bayesian Information Criteria identified the most plausible causal model of why some children developed kwashiorkor.In a descriptive analysis of the diet at the last dietary assessment prior to development of kwashiorkor, the diet of children who developed kwashiorkor was characterized by a low intake of sweet potatoes, papaya and “other vegetables” [0.0% , 2.3% (95%CI: 0.4, 12.1) and 2.3% (95%CI: 0.4, 12.1)] in comparison with children who did not develop kwashiorkor [6.8% (95%CI: 6.4, 7.2), 15.5% (95%CI: 15, 16.1) and 15.1% (95%CI: 14.6, 15.7)] or children who developed marasmus [4.5% (95%CI 2.6, 7.5) 11.8% (95%CI: 8.5, 16.0) and 17.6% (95%CI: 13.7, 22.5)]. Sweet potatoes and papaya have high β-Carotene content and so may some of “the other vegetables”. We found that a risk model containing an age function, length/height-for age Z-score, consumption of sweet potatoes, papaya or other vegetables , duration of this consumption and its interaction term, was the most plausible model. Among children aged aged 10-42 months, the risk of developing kwashiorkor increased with longer non-consumption of theses foods.The analysis was repeated with only children who developed marasmus as the reference series, yielding similar results. Our study supports that β-Carotene may play an important role in the protection against kwashiorkor development.
Conceptual and methodological issues in comparative neuroscience and psychology: a reassessment
Authors: Willemet Romain
Published: January 2018

By analysing species differences in brain and behaviour, comparative neuroscience & psychology can help to understand the nature and mechanisms of behaviour. The task is enormously complex due to the number of dimensions onto which species can differ. In addition, it is shown here that the approaches, methods and concepts used in these fields contain numerous issues. Many of these issues result from the persistence of misconceptions on the evolution of brain and behaviour; despite increasing evidence that more complex approaches and concepts should be considered. Most of the issues discussed here have been presented in a previous publication (Willemet, 2013, doi: 10.3389/fpsyg.2013.00396) but have not been addressed by recent literature. They are restated here in detail, using as a reference a recent paper resulting from the cooperative work of many researchers in the field (Maclean et al. 2014, doi: 10.1073/pnas.1323533111). The factors responsible for the evolution of brain structure size are reviewed, with particular emphasis on the adjustment effect recently introduced (Willemet, 2015, doi: 10.3389/fnana.2015.00084:). The traditional interpretation of the concept of allometry is critically evaluated, and an alternative is discussed. It is also argued that the lack of consideration towards emotional, motivational and attentional factors constitutes a major obstacle to understanding the evolution of behaviour. A dataset on the neuroecology of repertoire size in songbirds is analyzed using the framework discussed here. It is concluded that until the issues detailed here are addressed, progress in our understanding of the evolution of brain and behaviour will be undermined.
The iterated Data Rate Theorem for unstable biological dynamics
Authors: Wallace Rodrick
Published: January 2018

Counterintuitively, unstable control systems can allow extremely rapid responses that may be strongly selected by evolutionary process. Application of an information bottleneck iteration to the Data Rate Theorem -- taking the minimum necessary rate of control information as a distortion measure -- leads to a diffusion dynamic for onset of sudden failure in such systems via the necessary convexity of the Rate Distortion Function. Imposition of maintenance mechanisms seems a necessary consequence, but those too are subject to deterioration by aging or pathological exposures. In sum, a fairly simple control theory model that iterates the Data Rate Theorem provides deep insight across a wide sweep of diseases and the chronic dysfunctions of senescence.
Modeling C. elegans as a thermodynamic stable system
Authors: Elkington Joshua
Published: January 2018

The nematode, C. elegans is a useful organism to study aging due to its relatively short lifespan and genetic tractability. The lifespan of a population of worms can be easily determined. Under normal conditions worms can live up to 2 weeks, and if they are under heat shock, most worms die within 2 days. In order to investigate the effects of drug concentration and temperature on an organism ability to survive, a model based on Gibbs Free Energy was used to determine under what conditions is survival rate increased or decreased. Furthermore, along with wildtype, N2, worms, a small RNA mutant, eri-6 (mg379), was studied to try to understand the role of small RNA pathways in aging and stress response. The ultimate goal of the model is to prove that the types of chemical reactions within an organism depend on temperature and substrate concentration. Worm lifespan was used as a marker for chemical reactions within an organism. Differences in aging may be a result of different types of chemistry occurring in an organism. For example a long-lived species may used redox reactions more than a short-lived species.
Co-evolution hints at soil microbial biomass as the entity of soil fertility
Authors: Oda Masato , Hosen Yasukazu , Sukchan Uchada
Published: January 2018

Nitrogen (N) and Carbon (C) are popular indicators of soil fertility; however, they are not soil fertility itself. In fact, they may be seen as just two aspects of the one entity. Soil microbial biomass (SMB) is also one of soil fertility indicators; furthermore, recent study of co-evolution between plants and microorganisms raises an idea that SMB might be the entity of fertility. The correlation between SMB and crop yield has been found in some studies but not in others. Those studies were conducted from the standpoint of N stock balance; therefore, the correlation between soil properties before planting and plant yields were analyzed. Here, we show—in our analysis of harvest-time soil properties and crop yields—that SMB correlates more strongly than inorganic N, total N, or total C with average crop yield under a wide range of cultivation conditions. From the viewpoint of co-evolution, plant biomass is a part of the plant and soil microorganism system; therefore, increasing SMB will balance by increasing plant biomass. In addition, the SMB could increase independently from the plant growth by artificial organic matter input. This concept will break through the yield limitation of conventional farming.
On the impact of sampling frequency on software energy measurements
Authors: Saborido Rubén , Arnaoudova Venera , Beltrame Giovanni , Khomh Foutse , Antoniol Giuliano
Published: January 2018

Energy consumption is a major concern when developing and evolving mobile applications and researchers are investigating ways to reduce energy consumption. We conjecture that these studies are at the border between hardware and software and we must be careful on how the energy consumption is measured. To the best of our knowledge, no previous work investigates how much energy and power consumption is due to high frequency events missed when sampling at low frequencies such as 10 kHz and verified the error at the precision of method level. In this paper, we propose an approach for accurate measurements of the energy consumption of mobile applications. We apply the proposed approach to assess the energy consumption of 21 mobile, closed source, applications and four open source Android applications. We show that by sampling at 10 kHz one may expect a median error of 8%, however, such error may be as high as 50%.
Report on open access publishing at the College of Education, Health and Human Development, University of Canterbury, New Zealand
Authors: Basu Arindam
Published: January 2018

Open access publications are those where following the publication itself, the publishers allow anyone to access the article or publication to read, or download without any restriction. It is believed that publishing in open access journals can increase the visibility of the publication, although uncertainties prevail. In a bid to improve the PBRF ratings, the College research committee in its monthly meeting agreed to organise an Open Access Seminar in the college. The seminar was organised on 4th of June, 2015, Thursday. Four speakers were identified. They were: Peter Lund and Anton Angelo from the University of Canterbury Central Library and Researcn Unit, Peter Binfield from PeerJ, and Viriginia Barbour from Australian Open Access Support Group. The topics of the seminar included a brief introduction to open access publishing and the state of the scenario in NZ and Australia and exploration of the issues around green and gold open access, and future directions as to what can be done to increase participation in open access. The seminar was also designed to be an open to all, and free flowing discussion. This seminar followed a format of webinar and on the spot presentations, questions and answers. A web based page was set up using the openly accessible Adobe Connect "room" where participants could connect even if they were not able to attend in person. Dr Binfield and Barbour were overseas speakers and they connected using the webinar (Adobe Connect). Mr Lund and Angelo were local speakers and they came to the meeting hall directly and spoke. A resource website was set up and the event was recorded for later viewing. The event was publicised across the university and through online channels. About 30 individuals attended the meeting in person, and ten participants joined online. Mr Lund introduced the concept of open access at the University of Canterbury, and introduced the concepts of gold and green open access; Mr Angelo introduced the concepts of creative commons, and Drs Binfield and Barbour discussed models of open access and the situation in Australia. The floor was open for questions, and clarifications and discussions from the audience participation. Key takeaway lessons from the seminar included: at the University of Canterbury, scholars are active in publishing in Open Access channels; green open access is popular in Australia and in New Zealand; newer channels and novel publishing models uitlising the Open Access formats are emerging and becoming popular; while some reservations about quality in open access exist, quality of peer review in OA journals were at par.
Promoting active learning out-of-class via online “study questions” leads to higher than expected exam scores in General Biology
Authors: Gibson Susan I
Published: January 2018

A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of a form of out-of-class active learning on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated, with feedback provided for 73% of the questions. Students in seven course sections (with an average of approximately 265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of approximately 1,323 questions (94.5 questions per lecture) covering material from the half of the semester for which the questions were available. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five (average of 2.3) exams administered to students in course sections that had access to the online study questions and on three to 77 (average of 24.8) exams administered to students in sections that lacked access to the online study questions. Data from over 1,800 students in sections with access to the online study questions show that those students scored a statistically significant average of 6.6 percentage points higher on the exam questions analyzed than students in sections without access to the study questions. This difference was greater than the average amount necessary to raise students’ exam grades by one grade (e.g. from a “B-“ to a “B”). In addition, there was a higher correlation between number of questions answered and success on exam questions on material related to the study questions than between number of questions answered and success on exam questions on material unrelated to the study questions. The online study question system analyzed in this work required substantial effort to set up in the first year, but required minimal effort to maintain in subsequent years and was effective in significantly raising average exam scores for even very large course sections.
2,4-dinitrophenol downregulates genes for diabetes and fatty liver in obese mice
Authors: Gao Qian , He Jiang , Liao Tao , Zeng Qing-Ping
Published: January 2018

Whether obesity is a disease or a risk factor of chronic diseases including diabetes and fatty liver remains debating. We report here that a high-fat diet (HFD) alone or HFD and intramuscular injection of mice with a high dose (1.2 mg/kg) of lipopolysaccharide (LPS) induces the peripheral noninflammatory obesity. In contrast, HFD and intraperitoneal injection of mice with a low dose (0.25 mg/kg) of LPS induces the visceral low-grade inflammatory obesity. While the noninsulin dependent diabetes mellitus (NIDDM)- and nonalcoholic fatty liver disease (NAFLD)-related genes are globally upregulated in HFD+low-dose LPS mice, NIDDM and NAFLD genes are not extensively upregulated in HFD+high-dose LPS mice. The mitochondrial uncoupler 2,4-dinitrophenol (DNP) was found to exert a weight-reducing effect in obese mice by downregulating NF-κB-primed inflammatory response accompanying with NIDDM and NAFLD genes, thereby abrogating inflammatory hepatic injury. In conclusion, visceral low-grade inflammatory obesity that predisposes NIDDM and NAFLD can be ameliorated by DNP via anti-inflammation.
A transcriptome resource for the coral, Orbicella faveolata (Scleractinia-Meruliniidae) – an emerging model of coral innate immunity
Authors: Anderson David A , Walz Marcus E , Weil Ernesto , Tonellato Peter , Smith Matthew C
Published: January 2018

Research on climate change-driven coral disease outbreaks has greatly advanced our understanding of the coral innate immune system, and coral genomics has provided insight into the evolution of metazoan immune systems. However, only recently has next generation sequencing (NGS) technology been used to investigate coral immune responses to environmental stress and disease. In the present investigation, tissue of the threatened Caribbean reef-building coral, Orbicella faveolata¸ was collected during a warm water thermal anomaly and coral disease outbreak in 2010 in Puerto Rico. Multiplex sequencing of messenger RNA that was extracted from tissue samples of diseased, bleached and apparently healthy coral colonies was conducted on the Illumina GAIIx platform, and total reads were pooled accordingly for de novo assembly into contigs by Trinity software. From 70,745,177 raw short-sequence reads, 32,463 contigs were assembled in silico and taxonomically identified as O. faveolata in origin. The resulting reference transcriptome was annotated with gene ontologies, and sequences were mapped to KEGG pathways. The reference transcriptome presented here expands upon the genetic data currently available for O. faveolata. By sampling coral colonies affected by infectious disease and thermal stress in situ, it was possible to enrich the data set for genes that are expressed under natural conditions as part of the coral innate immune response. The results of the present investigation advance our understanding of the coral immune system and expand upon bioinformatic data available for O. faveolata – a threatened coral species that is widely studied as a model for immune responses to climate-driven stress and disease.
N-Acyl homoserine lactone-mediated quorum sensing in pathogenic Aeromonas veronii biovar sobria strain 159: Identification of LuxIR homologs
Authors: Chan Xin Yue , How Kah Yan , Yin Wai Fong , Chan Kok Gan
Published: January 2018

Quorum sensing (QS) is a mechanism that plays important roles in gene expression in response to an expanding bacterial population. In many Gram-negative bacteria, N-acyl homoserine lactone is mainly secreted as the diffusible signalling molecules. This QS system has been shown to control diverse array of virulence and secondary metabolism. Recently, whole genome sequencing of Aeromonas veronii biovar sobria strain 159 was performed. Genome comparison with closely-related Aeromonas species showed that A. veronii strain 159 shares a high degree of genome synteny with A. hydrophila ATCC 7966. A detailed genome analysis and gene annotation led us to the findings that A. veronii strain 159 harbors QS system which relies on its signal generator, AveI and the transcriptional regulator, AveR. This Aeromonas strain was found to secrete N-butanoylacyl homoserine lactone (C4-HSL). Its LuxIR homologs are similar to proteins of LuxIR famililies among Aeromonas species. This study aims to gain further insights into AveIR system and to compare with AhyIR from A. hydrophila ATCC 7966 and AsaIR from A. salmonicida.
Angiosperm Phylogeny Group (APG) in jeopardy – Where have the flowers gone?
Authors: Cole Theodor C. H.
Published: January 2018

The Angiosperm Phylogeny Group (APG) is a loose assemblage of systematic botanists aiming to establish a stable, modern classification system of flowering plants strongly based on molecular phylogenetics. The group published three seminal papers starting in 1998. An update to be entitled "APG IV" is in preparation and due shortly. A survey was conducted among systematic botanists in the forefront of this project, the results of which were recently published. The author of this Opinion Piece comments on the concept, evaluation, and results of this survey, and on the advice provided by the initiators, in particular regarding the order Boraginales. Expert opinion should be favored over a general majority vote on suggestive questions of an uncoordinated survey conducted by a single "authority". Science is based on knowledge and on scholarly expertise, and should not be made a matter of popular votes and majority preferences.
Superchords: decoding EEG signals in the millisecond range
Authors: Normand Rogerio , Ferreira Hugo Alexandre
Published: January 2018

Electroencephalography (EEG) signals’ interpretation is based on waveform analysis, where meaningful information should emerge from a plethora of data. Nonetheless, the continuous increase in computational power and the development of new data processing algorithms in the recent years have put into reach the possibility of analyzing raw EEG signals. Bearing that motivation, the authors propose a new approach using raw data EEG signals and deep learning neural networks, for the classification of motor activities (executed and imagery). The hypothesis to be presented here is: each instantaneous measurement of the raw signal of all EEG channels (superchord) is unique per motor activity regardless the moment of measurement. This study has confirmed the hypothesis (results with accuracy over 80%, mean for 109 subjects), reinforcing the need of further research for the understanding of mental processes.