bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flask culture system: Part 2
Authors: Ng Wenfa , Ting Yen-Peng
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, at the outset, a comprehensive medium with all necessary nutrients for conversion into biomass and, also serves as a repository for secreted metabolites - some of which are detrimental for cell growth. Thus, designing medium for high cell density cultivation in shake-flask is an optimization process aiming 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 flask. 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 maximal 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 on glucose at 37 oC. Following 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 along 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.
A proposed solution to the problem posed by reduction(s) in osmolyte infusion interval: A theory on the origins of 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: Effects of Osmolyte Infusion Interval Reductions on the Aggregate Measure of Systemic Failure: for a unicellular system. 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, and by so doing, initiate the required functional response(s) against their [stimuli] effects. By stating anticipatory roles in biological systems, we are suggesting a possible origin for the stimulus-response pairing noted in these systems.
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 and sintered zirconia 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 .
A test of ecological and ethnolinguistic determinants of maize diversity in southern Mexico
Authors: Orozco-Ramírez Quetzalcóatl , Santacruz-Varela Amalio , Ross-Ibarra Jeffrey , Brush Stephen B
Published: January 2018

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and mid elevations in two adjacent municipalities of differing ethnicity: Mixtec or Chatino. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with municipality explaining a larger proportion of the differentiation than altitude. Consistent with an important role of social origin in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnically distinct municipalities, but underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale.
Temporal stability of an endemic Mexican treefrog
Authors: Cruz-Ruiz Griselda , Venegas-Barrera Crystian S. , Sanchez-Sanchez Hermilo , Manjarrez Javier
Published: January 2018

The demographic characteristics of an amphibian population fluctuate independently over time, mainly in response to the temporal variation of environmental factors, especially precipitation and temperature. These temporal fluctuations may contribute to the effective size of an amphibian population and could be used to inform the current conservation status of a species. During a five year (2004-2008) period, we studied the relative abundance, sex ratio, and size-age structure of a population of metamorphosed individuals of the endemic treefrog Hyla eximia in Central Mexico. We also studied the species’ relationship with climatic variables such as temperatura and precipitation. We found an interannual constant abundance during the study period. However, interannual differences were observed in the population structure by age-sex category (males, females, or juveniles), with increased abundance of juveniles during the rainy months (August-November). The annual abundance of H. eximia was positively correlated with rainfall, but negatively with monthly temperature. We found the sex ratio was male-biased (2:1) except for year 2008. Also, differences in snout-vent length (SVL) were found between years, suggesting changes in recruitment of new individuals. We conclude that variations in abundance, and frequencies by age-sex category, of H. eximia are related to seasonal variations in temperature and precipitation characteristics of temperate zones. However, this temporal stability may suggest that anurans have an unusual capacity to persist even in the face of human-induced habitat change.
The four pillars of scholarly publishing: The future and a foundation
Authors: Byrnes Jarrett E.K. , Baskerville Edward , Caron Bruce , Neylon Cameron , Tenopir Carol , Schildhauer Mark , Budden Amber , Aarssen Lonnie , Lortie Christopher J
Published: January 2018

With the rise of electronic publishing and the inherent paradigm shifts for so many other scientific endeavours, it is time to consider a change in the practices of scholarly publication in Ecology and Evolutionary Biology. To facilitate the speed and quality of science, the future of scholarly communication will rest on four pillars - an ecosystem of scholarly products, immediate and open access, open peer review, and full recognition for participating in the process. These four pillars enable us to build better tools to facilitate the discovery of new relevant work for individual scientists, one of the greatest challenges of our time as we cope with the current deluge of scientific information. By incorporating these principles into future publication platforms, we argue that science and society will be better served than by remaining locked into a publication formula that arose in the 1600s. It has served its purpose admirably and well, but it is time to move forward. With the rise of the Internet, scholarly publishing has embraced electronic distribution. But the tools afforded by the Internet and other advancing technologies have profound implications for scholarly communication beyond just distribution. We argue that, to best serve science, the process of scholarly communication must embrace these advances and evolve. Here we consider the current state of the process in ecology and evolutionary biology and propose directions for change. We identify four pillars for the future of scientific communication: (1) an ecosystem of scholarly products; (2) immediate and open access; (3) open peer review; and (4) full recognition for participating in the process. These four pillars will guide the development of better tools and practices for discovering and sharing scientific knowledge in a modern networked world. Things were far different when the existing system arose in the 1600s, and though it has served its purpose admirably and well, it is time to move forward.
The effect of achievement motive on social participation, ikigai, and role expectations in community-dwelling elderly people by using cross-sectional research
Authors: Sano Nobuyuki , Kyougoku Makoto
Published: January 2018

Background: Achievement motive is defined as the intention to achieve one's goals. It is an important consideration in rehabilitation. However, previous studies have not demonstrated the causal relationship between achievement motive and a more enhanced quality of life such as the concept of ikigai and role expectation. Purpose: The purpose of this study is to identify the effect of achievement motive on ikigai, social participation, and role expectations of community-dwelling elderly people. Method: Participants were community-dwelling elderly people in day-service centers. A total of 281 participants (male: 127, female: 154) answered the self-administered questionnaire in cross-sectional research. The questionnaire comprised demographic data and scales that evaluated achievement motive, social participation, ikigai, and role expectation. We studied the causal relationship established on our hypothesized model by a structural equation modeling approach. Results: We checked the standardized path coefficients and the modification indices, and the modified model were good fit statistics: CFI = .984, TLI = .983, RMSEA = .050, 90% CI [.044, 055]. Achievement motive had a significant direct effect on ikigai (direct effect = .455, p value = .000), a significant indirect effect on ikigai via social participation or role expectation (indirect effect = .170, p value = .000) and a total effect on ikigai (total effect = .615). Discussion: This result suggested that enhancing the intention to achieve one's goals enables participants to feel a spirit of challenge with a purpose and a sense of fulfillment in daily living. At the same time, engaging in important activities for oneself as well as recognizing one's role in society enables participants to experience a willingness to help others. We recommend that rehabilitation therapists collaborate with their clients to form new goals based on the client's achievement motive.
Overt prosody and plausibility as cues to relative-clause attachment in English spoken sentences
Authors: Zahn Daniela , Scheepers Christoph
Published: January 2018

We investigated the interplay between overt prosodic cues and semantic cues on the structural interpretation of spoken sentences that permit either high- or low-attachment of a final relative clause. Prosodic cues were manipulated via the presence or absence of a strong prosodic boundary before the relative clause, and semantic cues were induced via plausibility restrictions (e.g., the servant of the actress who was {serving tea / very famous}). In the first two experiments, each type of cue was studied in isolation while keeping influences of the relevant other cue constant. Experiment 1 employed a standard off-line comprehension task and suggested that prosodic cues were not as effective as semantic cues in biasing participants’ attachment preferences. However, using a more implicit (and less biased) structural priming task, Experiment 2 showed that our overt prosody manipulation was actually no less effective than plausibility in biasing relative-clause attachments. Experiment 3 was, again, based on structural priming; here, the two factors were fully crossed to investigate the interaction between overt prosody and plausibility. This experiment showed that the two types of cues interact in a complex way, suggesting that (a) the amount of surprisal associated with cueing a generally dispreferred structure and (b) the type of revision necessary to resolve the ambiguity both play a major role in determining relative clause attachments.
Improving Brill's tagger lexical and transformation rule for Afaan Oromo language
Authors: Ayana Abraham G
Published: January 2018

Natural Language Processing (NLP) refers to Human-like language processing which reveals that it is a discipline within the field of Artificial Intelligence (AI). However, the ultimate goal of research on Natural Language Processing is to parse and understand language, which is not fully achieved yet. For this reason, much research in NLP has focused on intermediate tasks that make sense of some of the structure inherent in language without requiring complete understanding. One such task is part-of-speech tagging, or simply tagging. Lack of standard part of speech tagger for Afaan Oromo will be the main obstacle for researchers in the area of machine translation, spell checkers, dictionary compilation and automatic sentence parsing and constructions. Even though several works have been done in POS tagging for Afaan Oromo, the performance of the tagger is not sufficiently improved yet. Hence,the aim of this thesis is to improve Brill’s tagger lexical and transformation rule for Afaan Oromo POS tagging with sufficiently large training corpus. Accordingly, Afaan Oromo literatures on grammar and morphology are reviewed to understand nature of the language and also to identify possible tagsets. As a result, 26 broad tagsets were identified and 17,473 words from around 1100 sentences containing 6750 distinct words were tagged for training and testing purpose. From which 258 sentences are taken from the previous work. Since there is only a few ready made standard corpuses, the manual tagging process to prepare corpus for this work was challenging and hence, it is recommended that a standard corpus is prepared. Transformation-based Error driven learning are adapted for Afaan Oromo part of speech tagging. Different experiments are conducted for the rule based approach taking 20% of the whole data for testing. A comparison with the previously adapted Brill’s Tagger made. The previously adapted Brill’s Tagger shows an accuracy of 80.08% whereas the improved Brill’s Tagger result shows an accuracy of 95.6% which has an improvement of 15.52%. Hence, it is found that the size of the training corpus, the rule generating system in the lexical rule learner, and moreover, using Afaan Oromo HMM tagger as initial state tagger have a significant effect on the improvement of the tagger.
Rapid loss of phosphorus during early pedogenesis along a glacier retreat choronosequence, Gongga Mountain (SW China)
Authors: Wu Yanhong , Zhou Jun , Bing Haijian , Sun Hongyang , Wang Jipeng
Published: January 2018

The loss of phosphorus (P) during the early pedogenesis stage is important at the ecosystem level, and it also plays an important role in the global P cycle. The seasonal variation of total P (Pt) and its fractions along a young soil chronosequence (Hailuogou chronosequence) on the eastern slope of Gongga Mountain, SW China, was investigated based on the modified Hedley fractionation technique to understand P loss during the early pedogenesis stage. The results showed that the mineral P (mainly apatite) was the dominant fraction of Pt in the C horizon of the soil, and the seasonal difference in Pt and its fractions was insignificant. In the A horizon, Pt concentrations decreased markedly compared with those in the C horizon, and as the age of the soil increased, the inorganic P (Pi) significantly decreased and the organic P (Po) prominently increased. Seasonally, the P fractions exhibited various distributions in the A horizon. The variation of Pt and its fractions revealed that the P loss was rapid along the 120-year soil chronosequence. The concentrations of Pt in the original minerals decreased more than 50% in the 52 years since the glacier retreated, and the depletion reached almost 80% at the 120-year pedogenesis. The loss of P from the soil of the Hailuogou chronosequence was mainly attributed to weathering, plant uptake, and transport by runoff. The data obtained indicated that the glacier retreat chronosequence could be used to elucidate the fast rate of P loss during the early pedogenesis stage.
Effects of in situ climate warming on monarch caterpillar (Danaus plexippus) development
Authors: Lemoine Nathan P , Capdevielle Jillian N , Parker John D
Published: January 2018

Climate warming will fundamentally alter basic life history strategies of many ectothermic insects. In the lab, rising temperatures increase growth rates of lepidopteran larvae, but also reduce final pupal mass and increase mortality. Using in situ field warming experiments on their natural host plants, we assessed the impact of climate warming on development of monarch (Danaus plexippus) larvae. Monarchs were reared on Asclepias tuberosa grown under ‘Ambient’ and ‘Warmed’ conditions. We quantified time to pupation, final pupal mass, and survivorship. Warming significantly decreased time to pupation, such that an increase of 1˚ C corresponded to a 0.5 day decrease in pupation time. In contrast, survivorship and pupal mass were not affected by warming. Our results indicate that climate warming will speed the developmental rate of monarchs, influencing their ecological and evolutionary dynamics. However, the effects of climate warming on larval development in other monarch populations and at different times of year should be investigated.
Is Acropora palmata really coming back? an analysis from Los Roques, Venezuela
Authors: Croquer Aldo , Cavada-Blanco Francoise , Zubillaga Ainhoa L. , Agudo-Adriani Esteban
Published: January 2018

Ten years ago, we studied the distribution and status of Acropora palmata at archipelago Los Roques because the actual status of this species at Los Roques was unclear in this archipelago after its regional collapse. In that opportunity we aimed to produce a baseline study for this species in Los Roques combining population genetics with demographic data. At that time, our results suggested that this species had the potential to come back at least in 6 out of 10 surveyed sites. This conclusion was based upon high abundance, low disease prevalence, high genetic diversity and a dominance of sexual reproduction in these populations. However, we recognized that the potential of recovery could be hindered depending on local and regional threats. In 2014, the status of this species was re-evaluated by increasing the number of sites from 12 to 106 and by identifying and targeting local and global threats that may affect population recovery. The results from this new survey showed that A. palmata had a restricted distribution being only present in 15% of the surveyed sites. Large stands of old dead colonies were common throughout the archipelago; which demonstrates that this species has lost almost 50% of its original distribution over the past decades. In most cases live colonies were large adults (̴ 2m height); however, partial mortality and degradation of living tissues were found in 45% of the colonies. Moreover 44.78% of them were located on degraded reefs. In the past 8 years, two massive bleaching events occurred in Los Roques, the last one was known to decrease coral cover to unprecedented levels in the the archipelago. These events might have produced significant mortality for this species for signs of recent mortality was also common across sites. In addition, a growing local tourism industry, which has become massive and the concomitant increase of pressure on ecosystems goods and services are both becoming a problem of serious concern. Our results suggest that increasing use conflicts within the MPA and global threats such as ocean warming could prevent the recovery of this endangered species in Los Roques.
Unraveling mysteries of personal performance style; biomechanics of left-hand position changes (shifting) in violin performance
Authors: Visentin Peter , Li Shiming , Tardif Guillaume , Shan Gongbing
Published: January 2018

Instrumental music performance ranks among the most complex of learned human behaviors, requiring development of highly nuanced powers of sensory and neural discrimination, intricate motor skills, and adaptive abilities in a temporal activity. Teaching, learning and performing on the violin generally occur within musico-cultural parameters most often transmitted through aural traditions that include both verbal instruction and performance modeling. In most parts of the world, violin is taught in a manner virtually indistinguishable from that used 200 years ago. The current study uses methods from movement science to examine the “how” and “what” of left-hand position changes (shifting), a movement skill essential during violin performance. In doing so, it begins a discussion of artistic individualization in terms of anthropometry, the performer-instrument interface, and the strategic use of motor behaviors. Results based on 540 shifting samples, a case series of 6 professional-level violinists, showed that some elements of the skill were individualized in surprising ways while others were explainable by anthropometry, ergonomics and entrainment. Remarkably, results demonstrated each violinist to have developed an individualized pacing for shifts, a feature that should influence timing effects and prove foundational to aesthetic outcomes during performance. Such results underpin the potential for scientific methodologies to unravel mysteries of performance that are associated with a performer’s personal artistic style.
Cancer as a script and possible implications on workings of genome
Authors: Khan Muhummadh
Published: January 2018

There is a need for a genomic theoretical framework which would explain the increasingly vast and discreet genomic data in the context of phenomena observed in cell. The search for a genomic explanation to functional networks of cancer metasignature genes lead to the concept of the genomic script which extends its influence over the workings of genome in general. This framework explains multiple phenomenon like the development of an embryo, differentiation of cells, and genomic workings of cancer. It also shines light on the evolution of unicellular and multicellular organisms. Yet it remains a simple construct; a perennial loop with its adaptor loops constituting the genomic script.
A template model for agent-based simulations
Authors: Fachada Nuno , Lopes Vitor V , Martins Rui C , Rosa Agostinho C
Published: January 2018

Agent-based modeling (ABM) is a bottom-up modeling approach, where each entity of the system being modeled is uniquely represented as an independent decision-making agent. ABMs are very sensitive to implementation details. Thus, it is very easy to inadvertently introduce changes which modify model dynamics. Such problems usually arise due to the lack of transparency in model descriptions, which constrains how models are assessed, implemented and replicated. In this paper, we present a template ABM which aims to serve as a basis for a series of investigations, including, but not limited to, conceptual model specification, statistical analysis of simulation output, model comparison and model parallelization. This paper focuses on the first two aspects (conceptual model specification and statistical analysis of simulation output), also providing a canonical implementation of the template ABM, such that it serves as a complete reference to the presented model. Additionally, this study is presented in a tutorial fashion, and can be used as a road map for simulation practitioners who wish to improve the way they communicate their ABMs.
Agriculture-independent, sustainable, fail-safe and efficient food production by autotrophic single-cell protein
Authors: Bogdahn Ingvar
Published: January 2018

Industrial agriculture is destructive to the environment, pollutes large amounts of water, fosters climate change and cannot guarantee food security for the 21st century. Single-cell protein (SCP) represents a safe alternative with minimal carbon and water footprints, but does not truly improve sustainability or food security when grown on waste products of industrial agriculture. This hypothesis paper proposes autotrophic SCP bioprocess designs which enable sustainable, fail-safe and efficient production of edible biomass from CO2 and N2 or NH3. They can be driven by H2, CO, HCOOH from several sustainable sources and provide versatile options of biowaste upgrading. Most promising designs consist of 2-stages. In the 1st stage, homoacetogenic bacteria fix CO2 and secrete it as acetate with unrivaled yields. In the 2nd stage, selected microbes transform the acetate to edible biomass. Bacteria have various unique features including O2-tolerant hydrogenases, N2-fixation and H2S tolerance. Eukaryotic microalgae are approved as food and exhibit oxygenic photosynthesis which partly replaces solar-panels, seawater desalination and H2O- electrolyzers. Photoheterotrophic growth on acetate allows to decouple the efficient light-reaction from inefficient CO2 fixation. Slow gas mass-transfer, poor light distribution and expensive cell harvest are major challenges arising from the cultivation in liquid media. To cope with this, microbes grow as hydrated biofilms, exposed directly to substrate gases and light. Two suitable bioreactors are presented and adaptations for 2-stage designs are proposed. Since provision with substrates is expensive, two strategies are proposed for the safe extraction of substrates from food-grade as well as non-food-grade biowastes via partial anaerobic digestion. Additionally, alkalic pH and hydroxides formed at the cathode during electrolysis may be used to precipitate CO2 from the air as carbonates. In two use cases, 2-stage designs with solar-powered H2-generation from seawater were estimated to exceed productivity of wheat 20-200 fold. Since for that particular bioprocess design electricity is the dominant cost driver, overall product cost can be estimated to 0,5-1 € per kg dry SCP. When direct and indirect subsidies are taken into account, autotrophic SCP likely outperforms industrial agriculture not only in ecological but also in economical aspects.
Luminophonics experiment: A user study on visual sensory substitution device
Authors: Tan Shern Shiou , Maul Tomas , Mennie Neil
Published: January 2018

Loss of vision is a severe impairment to the dominant sensory system. It often has a catastrophic effect upon the sufferer, with knock-on effects to their standard of living, their ability to support themselves, and their care-givers lives. Research into visual impairments is multi-faceted, focusing on the causes of these debilitating conditions as well as attempting to alleviate the daily lives of affected individuals. One of the methods is through the usage of sensory substitution device. Our proposed system, Luminophonics, focuses on visual to auditory cross modalities information conversions. A visual to audio sensory substitution device a type of system that obtains a continual stream visual inputs which it converts into corresponding auditory soundscape. Ultimately, this device allows the visually impaired to visualize the surrounding environment by only listening to the generated soundscape. Even though there is a huge potential for this kind of devices, public usage is still minimal (Loomis, 2010). In order to promote the adoption from the visually impaired, the overall performance of these devices need to be improved in terms of soundscape interpretability, information preservation and listening comfort amongst other factors. Luminophonics has developed 3 type of prototypes, which we have used to explore different ideas pertaining to visual to audio sensory substitution. In addition to these, one of the prototypes has been converted to include depth information using time of flight camera. Previously, an automated measurement method is used to evaluate the performance of the 3 prototypes (Tan, 2013). The results of the measurement cover the effectiveness in terms of interpretability and information preservation. The main purpose of the experiment reported herein, was to test the prototypes on human subjects in order to gain greater insight on how they perform in real-life situations.
From raw ion mobility measurements to disease classification: a comparison of analysis processes
Authors: Horsch Salome , Kopczynski Dominik , Baumbach Jörg Ingo , Rahnenführer Jörg , Rahmann Sven
Published: January 2018

Ion mobility spectrometry (IMS) is a technology for the detection of volatile compounds in the air of exhaled breath that is increasingly used in medical applications. One major goal is to classify patients into disease groups, for example diseased versus healthy, from simple breath samples. Raw IMS measurements are data matrices in which peak regions representing the compounds have to be identified and quantified. A typical analysis process consists of pre-processing and peak detection in single experiments, peak clustering to obtain consensus peaks across several experiments, and classification of samples based on the resulting multivariate peak intensities. Recently several automated algorithms for peak detection and peak clustering have been introduced, in order to overcome the current need for human-based analysis that is slow, subjective and sometimes not reproducible. We present an unbiased comparison of a multitude of combinations of peak processing and multivariate classification algorithms on a disease dataset. The specific combination of the algorithms for the different analysis steps determines the classification accuracy, with the encouraging result that certain fully-automated combinations perform even better than current manual approaches.
Cluster analysis and visualization techniques for large datasets in complexome profiling
Authors: Giese Heiko , Ackermann Jörg , Brandt Ulrich , Wittig Ilka , Koch Ina
Published: January 2018

Dysfunctional protein complexes are often associated with diseases. To develop effective treatments it is essential to understand the composition, formation and functionality of protein complexes. Novel techniques like complexome profiling give an overview of possible protein-protein interactions in an entire sample. In this approach intact protein complexes are separated using blue-native electrophoresis. The migration patterns of thousands of proteins are then uncovered using quantitative mass spectrometry and compared to find co-migrating proteins. Here, we present the concepts of our visualization approach for large complexome profiling datasets using our software NOVA. In agreement with recent literature we show that the protein NDUFA4, a previously known subunit of complex I of the mitochondrial respiratory chain, is instead a subunit of complex IV.
Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
Authors: Kimball Rebecca T , Braun Edward L
Published: January 2018

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. Some of the key findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.
Codes of conduct for Nursing students: bioethical commitment to higher education in Spain
Authors: Cambil-Martin Jacobo
Published: January 2018

Background: As a profession, Nursing has its own code of ethics and codes of conduct which establish personal and professional behavior expected on Nursing professionals and students to be competent in their practice, learning and development. The Nursing and Midwifery Council has a Code of Professional Conduct for students of Nursing and Midwife. Considering that the diversity of values is a fact in the university community, it is necessary to explore the validity and meaning to implement Codes of Professional Conduct for Nursing students in the teaching and learning process. Objective: To identify and assess codes of conduct aimed at Nursing students to understand the commitment to Bioethics training of higher education in Spain. Methods: A literature review was conducted. Main elements of ethical codes and the dimensions of the attitudinal assessment template for Nursing students in clinical practice with the code of conduct of the English Council were compared. Results: The literature review brings two articles in Spanish language and according to the selection criteria. The journal “Etica de los cuidados” -indexed in “Cuiden” database- collects these studies reporting that both professionals and students know the Spanish Code of Ethics for Nursing and there is a need to establish a new teaching and learning framework in Bioethics; however, no specific articles provide knowledge about codes of conduct for Nursing students in Spain. Conclusion: In general, the standards of conduct for students of the Nursing and Midwifery Council are already implicit in the ethical rules, rights and duties of the Spanish code of professional ethics. So it is still necessary to consider the Code of Conduct of the Spanish Nursing Council and the White Paper of the Nursing Degree to understand the commitment to Bioethics training on Nursing.
Assessing Indonesian manta and devil ray populations through historical landings and fishing community interviews
Authors: Lewis Sarah A , Setiasih Naneng , Fahmi  , Dharmadi Dharmadi , O'Malley Mary P , Campbell Stuart J , Yusuf Muhammad , Sianipar Abraham B
Published: January 2018

International concern is growing with regard to the sustainability of manta and devil ray (collectively mobulids) fisheries as demand for mobulid products has increased in international markets over the last decade. While Indonesia has been reported to be one of the worlds’ top three catchers of mobulid rays, detailed information on these fisheries and the status of Indonesian mobulid populations are lacking. Through collection of historical and recent mobuild fisheries data from published and unpublished sources, this study aimed to identify trends in abundance of Indonesian manta and devil rays and explore socio-economic factors and incentives associated with mobulid fisheries. Comparison of catches from 2001-5 to the most recent data from 2013-14 revealed dramatic declines in mobulid landings over the study period of 64% at Cilacap, 75% at Lamakera, and 94% at Tanjung Luar. The largest declines were observed for Manta spp. and the two large devil rays, Mobula tarapacana and Mobula japanica. Anecdotal reports indicated that catches had declined substantially at three additional sites and local extirpations are strongly suspected to have occurred at three locations. A lack of data on the population ecology of Indonesia’s mobulids makes it difficult to determine whether natural fluctuations may be playing a part in the declining catch rates. However, mobulid life history traits, including low reproductive rates and late age of sexual maturation, indicate that fishing pressure is likely the primary driver in these declines. Interviews in Lamakera, a community which depends on income from its targeted mobulid fishery, suggest that programs focused on education, training and infrastructure development to enable shifts to sustainable livelihood alternatives are likely to offer the most successful path to long-term conservation and management of manta and devil rays, while simultaneously yielding economic and social benefits to fishing communities.
The first dromaeosaurid (Dinosauria: Theropoda) from the Early Cretaceous Bayan Gobi Formation of Nei Mongol, China
Authors: Pittman Michael , Pei Rui , Xu Xing
Published: January 2018

The first dromaeosaurid theropod from the Early Cretaceous Bayan Gobi Formation is identified based on an incompletely preserved partially-articulated left leg, increasing the known diversity of its understudied ecosystem. The leg belongs to specimen IVPP V22530 and includes a typical deinonychosaurian pedal phalanx II-2 with a distinct constriction between the enlarged proximal end and the distal condyle as well as a typical deinonychosaurian enlarged pedal phalanx II-3. It possesses a symmetric metatarsus and a slender and long MT V that together suggest it is a dromaeosaurid. Two anatomical traits suggest the leg is microraptorine-like, but a more precise taxonomic referral was not possible: metatarsals II, III and IV are closely appressed distally and the ventral margin of the medial ligament pit of phalanx II-2 is close to the centre of the rounded distal condyle. This taxonomic status invites future efforts to discover additional specimens at the study locality because - whether it is a microraptorine or a close relative - this animal is expected to make important contributions to our understanding of dromaeosaurid evolution and biology. IVPP V22530 also comprises of an isolated manual ungual, a proximal portion of a right dorsal rib and an indeterminate bone mass that includes a collection of ribs. However, these specimens cannot be confidently referred to Dromaeosauridae, although they may very well belong to the same individual from whom the left leg belongs.
Study of gallbladder cancer in the light of proteomics
Authors: Pradhan Arpit , Saha Soham , Ghosh Shyamasree
Published: January 2018

Gallbladder carcinoma (GBC) is a chronic malignancy of the gall bladder and intrahepatic and extrahepatic common bile ducts with a high mortality rate and forms the fifth common cancer of gastrointestinal tract globally. Women remain at higher risk than men and recent studies have reported the highest rate of incidence in women from Delhi, India. GBC treatment suffers from the disadvantage of lack of suitable biomarkers for early diagnosis of the disease. Different proteomic approaches including (i) 2D gel electrophoresis (ii) Mass spectroscopic studies (iii) Isobaric tags for relative and absolute quantization (iTRAQ) -based quantitativeproteomicsstudies are being employed for detection of biomarkers in order to undertake early diagnosis of the disease. In this review we focus on (i) risk factors in GBC, (ii) diagnosis and treatment, (iii) molecular markers, and (iv) proteomic studies in GBC. The future scope of this review lies in the identifying biomarkers of GBC, and may provide directions to unraveling future implications in disease treatment.
Evaluation of a drug & alcohol primary health care team
Authors: Patton Robert
Published: January 2018

As part of an ongoing assessment of the physical health needs of injecting drug users during 2005, all 167 general practices in the Lambeth, Southwark & Lewisham (LSL) area were sent a questionnaire. The results indicate that the majority of IDUs visited the surgery because of DVT, pregnancy, chest infections or skin ulceration, and the GPs themselves opportunistically identified more serious problems such as BBV’s and Liver problems. Interestingly we found significant variation in the rate of opportunistic detection between PCTs. Many practices indicated that health promotion activity would benefit their IDU clients, in particular issues related to smoking and drinking, as well as dental health, diet and exercise needed to be addressed. In general it was felt that a nurse led resource integrated into existing services, such as that offered by the Drug and Alcohol Health Care Team, would be of greatest benefit to IDU clients.
A generalized computer vision approach to mapping crop fields in heterogeneous agricultural landscapes
Authors: Debats Stephanie , Luo Dee , Estes Lyndon , Fuchs Thomas J , Caylor Kelly K
Published: January 2018

Smallholder farms dominate in many parts of the world, particularly Sub-Saharan Africa. These systems are characterized by small, heterogeneous, and often indistinct field patterns, requiring a specialized methodology to map agricultural land cover. Using a variety of sites in South Africa, we present a new approach to mapping agricultural fields, based on efficient extraction of a vast set of simple, highly correlated, and interdependent features, followed by a random forest classifier. We achieved similar high performance across agricultural types, including the spectrally indistinct smallholder fields as well as the more easily distinguishable commercial fields, and demonstrated the ability to generalize performance across large geographic areas. In sensitivity analyses, we determined multi-temporal information provided greater gains in accuracy than multi-spectral information.
Assessing conservation status of resident and migrant birds on Hispaniola with constant-effort mist-netting
Authors: Lloyd John D , Rimmer Chris C , McFarland Kent P
Published: January 2018

We analyzed temporal trends in mist-net capture rates of resident (n = 8) and overwintering Nearctic-Neotropical migrant (n = 3) bird species at two sites in montane broadleaf forest of the Sierra de Bahoruco, Dominican Republic, with the goal of providing quantitative information on population trends that could inform conservation assessments. We conducted sampling at least once annually during the winter months of January – March from 1997 – 2010. We found evidence of steep declines in capture rates for three resident species, including one species endemic to Hispaniola. Capture rate of Rufous-throated Solitaire (Myadestes genibarbis) declined by 3.9% per year (95% CL = 0%, 7.3%), Green-tailed Ground-Tanager (Microlegia palustris) by 6.8% (95% CL = 3.9%, 8.8%), and Greater Antillean Bullfinch (Loxigilla violacea) by 4.9% (95% CL = 0.9%, 9.2%). Two rare and threatened endemics, Hispaniolan Highland-Tanager (Xenolegia montana) and Western Chat-Tanager (Calyptophilus tertius), showed statistically significant declines, but we have low confidence in these findings because trends were driven by exceptionally high capture rates in 1997 and varied between sites. Analyses that excluded data from 1997 revealed no trend in capture rate over the course of the study. We found no evidence of temporal trends in capture rates for any other residents or Nearctic-Neotropical migrants. We do not know the causes of the observed declines, nor can we conclude that these declines are not a purely local phenomenon. However, our findings, along with other recent reports of declines in these same species, suggest that a closer examination of their conservation status is warranted. Given the difficulty in obtaining spatially extensive, long-term estimates of population change for Hispaniolan birds, we suggest focusing on other metrics of vulnerability that are more easily quantified yet remain poorly described, such as extent of occurrence.
Transgenerational effects enhance specific immune response in a wild passerine
Authors: Broggi Juli , Soriguer Ramon C. , Figuerola Jordi
Published: January 2018

Vertebrate mothers transfer diverse compounds to developing embryos that can affect their development and final phenotype (i.e. maternal effects). However, the way such effects modulate offspring phenotype, in particular their immunity remains unclear. To test the impact of maternal effects on offspring development we treated with Newcastle disease virus (NDV) vaccine wild breeding house sparrow (Passer domesticus) females in Sevilla, SE Spain. Female parents were vaccinated when caring first broods, and their offspring from their following brood were evaluated for their immune response to the same vaccine and to the PHA inflammatory test. Vaccinated chicks from vaccinated mothers developed a stronger specific response that was related to maternal NDV antibody concentration. Chick’s carotenoid concentration and total antioxidant capacity in blood were negatively related to NDV antibody concentration, whereas no relation with PHA response was found. Specific NDV antibodies could not be detected on 10 day old control chicks from vaccinated mothers, implying that maternally transmitted antibodies promote offspring specific immunity through a priming effect, while other immunity components remain unaffected. Maternally transmitted antibodies are short-lived, depend on maternal circulation levels and may be adaptive when chicks are frequently exposed to the same pathogens as their mothers.