bluuebunny/crossref_metadata_2025 huggingface dataset:
Bacteria associated to human saliva are major microbial components of Ecuadorian indigenous beers (chicha)
Authors: Freire Ana L. , Zapata Sonia , Mosquera Juan , Trueba Gabriel
Published: January 2018

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers relay probably on microorganisms from: fermenting substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota) where among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers) could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.
Emergent properties of a computational model of tumour growth
Authors: Pantziarka Pan
Published: January 2018

While there have been enormous advances in our understanding of the genetic drivers and molecular pathways involved in cancer in recent decades, there also remain key areas of dispute with respect to fundamental theories of cancer. The accumulation of vast new datasets from genomics and other fields, in addition to detailed descriptions of molecular pathways, cloud the issues and lead to ever greater complexity. One strategy in dealing with such complexity is to develop models to replicate salient features of the system and therefore to generate hypotheses which reflect on the real system. A simple tumour growth model is outlined which displays emergent behaviours that correspond to a number of clinically relevant phenomena including tumour growth, intra-tumour heterogeneity, growth arrest and accelerated repopulation following cytotoxic insult. Analysis of model data suggests that the processes of cell competition and apoptosis are key drivers of these emergent behaviours. Questions are raised as to the role of cell competition and cell death in physical cancer growth and the relevance that these have to cancer research in general is discussed.
Post-graduate scholars can create Literature-Guides on the Web using Compending-Forum Software to build Knowledge-Step Compendia
Authors: Jewett Don L
Published: January 2018

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of many activities, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is not adequate for a Web-based world!

In 2006, an estimated 3,700 peer-reviewed articles were published per day (Bjork2009)! As will become apparent, the methods and features described here are needed now, and will be absolutely necessary in the future, when even more articles are published.

A New Knowledge-Tool is proposed that is in addition to those already available. The new Knowledge-Tool is a new Literature-Guide called a "Knowledge-Step Compendium". This Compendium will be on a very-narrow topic, will be organized in a new MultiLevel-Format, and will be created in a Compending-Forum on the Internet.

This New Knowledge-Tool will, in turn, be the basis for a change in academic careers, of the timing of when a scholar "Compends" Knowledge. A "Knowledge-Compendor" need not be a senior faculty member (as is presently the case in traditional literature-reviews), but can be a Post-Graduate Student new to a field. Because a Knowledge-Step Compendium is based on a very-narrow topic and created with the aid of an Internet Forum, for a Graduate Student Compendor this activity will be a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.
Post-graduate scholars can publish Compended-Guides to the literature of their field using Knowledge-Step-Forums
Authors: Jewett Don L
Published: January 2018

"Publication forms the core structure supporting the development and transmission of scientific knowledge" (Galbraith2015). Yet, with the WorldWideWeb a dominant part of current scientific publication and information-dissemination, internet "publication" is still paper-based in its style and methods, even when it uses a digital medium. Such a paper-based publishing "model" is not adequate for a Web-based world.

In 2006, an estimated 3,700 peer-reviewed scientific articles were published per day (Bjork2009)! This totals about 1.35 million articles per year. A similar estimate for 2011 was 1.8 million (Outsell2013), which is almost 5,000 per day. The total number of English-language scholarly documents accessible on the Web was estimated in 2014 to be at least 114 million (Khabsa2014). The methods and features described here are clearly needed now, and will be absolutely necessary in the future, when even more articles are published and available.

In this context of an overload of information from scientific articles, described here is the idea of Knowledge-Step Forums as the basis for creating new peer-reviewed, compended "Literature-Guides", each on a very narrow topic and in a MultiLevel Format (Knowledge-Step Compendia). A multitude of Forum-Compendors, who need not be a senior faculty member (as is the case in traditional literature-reviews), but can be pre-docs, post-docs, and senior medical/surgical residents, will be aided by their mentors and online experts to create these Knowledge-Step Compendia. All participants (students and faculty) will be motivated by their own self-interest and thus each gains from the activity, it being a means to self-organize groups of like-minded scholars that can be the basis for reviews of new data, discovering new ideas, and finding jobs.

The Software for Knowledge-Step Forums will also be useful to speed publication on the Web because it will easily support Publication Preprints with online peer-review.
Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates
Authors: Marjanović David , Laurin Michel
Published: January 2018

The largest published data matrix for phylogenetic analysis of Paleozoic limbed vertebrates (Ruta M, Coates MI. 2007. Journal of Systematic Palaeontology 5:69–122) supported variously controversial hypotheses; e.g., it recovered Seymouriamorpha, Diadectomorpha and (in some trees) Caudata as paraphyletic and found the “temnospondyl hypothesis” on the origin of Lissamphibia (TH) to be more parsimonious than the “lepospondyl hypothesis” (LH) – though only, as we show, by one step.

We report thousands of suboptimal scores due to typographic and similar errors and to questionable coding decisions: logically linked (redundant) characters, others with only one described state, even characters for which most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded.

After these issues are improved – we document and justify all changes to the matrix –, but no characters are removed or added, we find (Analysis R1) much longer trees with e.g. monophyletic Caudata, Diadectomorpha and (in some trees) Seymouriamorpha; Ichthyostega rootward of Acanthostega; Anthracosauria rootward of Temnospondyli which includes Caerorhachis; the LH is 9 steps shorter than the TH (R2; constrained) and 12 steps shorter the “polyphyly hypothesis” (PH – R3; constrained).

We then added 48 OTUs to the original 102. This destabilizes some parts of the tree, e.g. the positions of Anthracosauria, Temnospondyli and Caerorhachis. Yet, many added taxa have well-resolved positions, ranging from the well known Chroniosaurus (Chroniosuchia), which lies just crownward of Temnospondyli and Gephyrostegidae, to isolated lower jaws. Even though Gerobatrachus, Micropholis and Tungussogyrinus and the extremely peramorphic salamander Chelotriton are added, the difference between LH (R4) and TH (R5) rises to 12 steps, that between LH and PH (R6) to 17 steps; the TH also requires several more regains of lost bones than the LH. Brachydectes (Lysorophia) is not found next to Lissamphibia.

We duplicated all analyses after coding losses of bones as irreversible. The impact on the results is modest. Anthracosauria is always rootward of Temnospondyli. With 102 OTUs, the LH (R7) is 10 steps shorter than the TH (R8) and 11 steps shorter than the PH (R9); with 150, the LH (R10) is 14 steps shorter than the TH (R12) – and 13 steps shorter than the PH (R11).

Bootstrap values are mostly low, and plummet when taxa are added. Statistically, the TH (R2, R5, R8, R12) is not distinguishable from the LH or the PH, but the LH (R1, R4, R7, 53 R10) and the PH (R3, R6, R9, R11) may be distinguishable from each other under both taxon samples and both reversibility settings. A reliable test is not available.

We discuss the relationships of certain taxa, approaches to coding, some character complexes, and prospects for further improvement of this matrix.
Potential contribution of fish restocking to the recovery of deteriorated coral reefs: an alternative restoration method?
Authors: Obolski Uri , Hadany Lilach , Abelson Avigdor
Published: January 2018

Counteracting the worldwide trend of coral reef degeneration is a major challenge for the scientific community. A crucial management approach to minimizing stress effects on healthy reefs and helping the recovery of disturbed reefs is reef protection. However, the current rapid decline of the world's reefs suggests that protection might be insufficient as a viable stand-alone management approach for some reefs. We thus suggest that the ecological restoration of coral reefs (CRR) should be considered as a valid component of coral reef management, in addition to protection, if the applied method is economically applicable and scalable. This theoretical study examines the potential applicability and outcomes of restocking grazers as a restoration tool for coral reef recovery – a tool that has not been applied so far in reef restoration projects. We studied the effect of restocking grazing fish as a restoration method using a mathematical model of degrading reefs, and analyzed the financial outcomes of the restocking intervention. The results suggest that applying this restoration method, in addition to protection, can facilitate reef recovery. Moreover, our analysis suggests that the restocking approach almost always becomes profitable within several years. Considering the relatively low cost of this restoration approach and the feasibility of mass production of herbivorous fish, we suggest that this approach should be considered and examined as an additional viable restoration tool for coral reefs.
A computational analysis of Salt Overly Sensitive 1 homologs in halophytes and glycophytes
Authors: Kim Cherin , Bressan Ray
Published: January 2018

Soil salinity is one of the most serious impediments to global agricultural productivity. Although most terrestrial plants are glycophytes which cannot tolerate high salt concentrations, a small fraction of species are halophytes. Exactly what allows these extremophile plants to survive in saline conditions is not yet well understood. Several studies have established the Salt Overly Sensitive (SOS) pathway as the canonical model for the mechanism responsible for salt tolerance. The SOS pathway involves interplay among Na+-H+ antiporters for transporting sodium, and the activation of the kinase that phosphorylates the transporter. Among them, SOS1, a plasma membrane Na+-H+ antiporter, has been shown to be a critical component for maintaining salt homeostasis by pumping sodium out of cells upon activation. Therefore, it is of great interest to evaluate any differences of SOS1 in halophytes as compared to glycophytes. Here we report a computational analysis of the primary and secondary structures of eight halophytes and seven glycophytes. ClustalW alignment of the protein sequences as a whole reveals no regions conserved specifically in only halophytes or in only glycophytes. In addition, the key regulatory residues at the C-terminus of SOS1, S1136 and S1138, which were shown to be the phosphorylation sites by the kinase SOS2, were completely conserved in all 15 halophytes and glycophytes. The four amino acids, G136, R365, G777, and G784, in which alterations affect the function of SOS1, are mostly conserved in the 15 species. The 14-3-3 binding site in the C-terminus which is important in the phosphorylation step of SOS1 in the SOS signal transduction cascade is also well conserved. Furthermore, the number of transmembrane helices for each species is between 9 and 12 and there is no significant difference between halophytes and glycophytes. If halophytes present any special feature of SOS1, it likely involves the presence (halophytes) or absence (glycophytes) of a SOS1-interacting component.
Effect of the Blowflies (Diptera: Calliphoridae) on the size and weight of Mango (Mangifera indica L.)
Authors: Saeed Shafqat , Naqqash Muhammad Nadir , Jaleel Waqar , Saeed Qamar , Ghouri Fozia
Published: January 2018

Background: Pollination has a great effect on the yield of fruit trees. Blowflies are considered as an effective pollinator compared to hand pollination in fruit orchards. Therefore, this study was designed to evaluate the effect of different pollination methods in mango orchards. Methodology: The impact of pollination on quantity and quality of mango yield by blowflies was estimated by using three treatments, i.e., open pollinated trees, trees were covered by a net in the presence of blowflies for pollination, and trees were covered with a net but without insects. Results: The maximum number of flowers was recorded in irregular type of inflorescence, i.e., 434.80flowers/inflorescence. Fruit setting (bud) was higher in open pollinated mango tree (i.e. 37.00/inflorescence) than enclosed pollination by blowflies (i.e. 22.34/inflorescence). The size of the mango fruit was the highest (5.06mm) in open pollinated tree than the pollinated by blowflies (3.93mm) and followed by without any pollinator (3.18mm) at marble stage. We found maximum weight of mango fruit (201.19g) in open pollinated trees. Discussion: The results demonstrated that blowflies can be used as effective mango pollinators along with other bees. The blowflies have shown a positive impact on the quality and quantity of mango. This study will be helpful in future and also applicable at farm level to use blow flies as pollinators that are cheap and easy to rear.
Biological and biosimilar medicinal products: safety and efficacy
Authors: Brodniewicz Teresa
Published: January 2018

Biological medicinal products are one of most innovative and promising methods of pharmacotherapy. During the last 20 years several original biological medicinal products have been registered and marketed. Their safety and efficacy have been investigated thoroughly at the level of pre-clinical and clinical studies. These are large, complex protein structures obtained through methods used in genetic engineering, or they are isolated from biological sources. Basically there are two types of biological products: 1) Those naturally present in the body like: Insulin, human growth factor, Factor VIII, erythropoietin; 2) Substances influencing certain mechanisms being the cause of the disease: anti-TNF; anti-IL 17; Anti-CD-20. These biological medicinal products can be divided into Blood and blood components, Vaccines, Allergen extracts, Proteins, Human tissues, Cell and gene therapy, Monoclonal antibodies. The size of biological products may vary between 4 500 D (enoxaparin) and 150 000 (monoclonal antibody) and more, while aspirin size is only 150 D. While biological products are attractive, most patients cannot afford their high cost (roughly estimated 550 US$ a day). However, biosimilar products are much cheaper while offering a good therapeutical alternative with the same safety and efficacy features as the former. Currently, 200 companies worldwide have about 700 of biosimilars under the development. Consequently biosimilar products are having more success in the market and thus are more accessible to patients.
Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish
Authors: Singer Matthew L , Oreschak Kris , Rhinehart Zachariah , Robison Barrie D
Published: January 2018

Zebrafish (Danio rerio) have emerged as a popular model for studying the pharmacology and behavior of anxiety. While there have been numerous studies documenting the anxiolytic and anxiogenic effects of common drugs in zebrafish, many do not report or test for behavioral differences between the sexes. Previous studies have indicated that males and females differ in their baseline level of anxiety. In this study, we test for a sex interaction with fluoxetine and nicotine. We exposed fish to system water (control), 10 mg/L fluoxetine, or 1 mg/L nicotine for three minutes prior to being subjected to four minutes in an open-field drop test. Video recordings were tracked using ProAnalyst. Fish from both drug treatments reduced swimming speed, increased vertical position, and increased use of the top half of the open field when compared with the control, though fluoxetine had a larger effect on depth related behaviors while nicotine mostly affected swimming speed. a significant sex effect was observed where females swam at a slower and more constant speed than males, however neither drug produced a sex-dependent response.
Gender differences and bias in open source: Pull request acceptance of women versus men
Authors: Terrell Josh , Kofink Andrew , Middleton Justin , Rainear Clarissa , Murphy-Hill Emerson , Parnin Chris , Stallings Jon
Published: January 2018

Biases against women in the workplace have been documented in a variety of studies. This paper presents the largest study to date on gender bias, where we compare acceptance rates of contributions from men versus women in an open source software community. Surprisingly, our results show that women's contributions tend to be accepted more often than men's. However, women's acceptance rates are higher only when they are not identifiable as women. Our results suggest that although women on GitHub may be more competent overall, bias against them exists nonetheless.
Aging and serum MCP-1 are associated with gut microbiome composition in a murine model
Authors: Conley Melissa N. , Wong Carmen P. , Duyck Kyle M. , Hord Norman , Ho Emily , Sharpton Thomas J.
Published: January 2018

Introduction Age is the primary risk factor for major human chronic diseases, including cardiovascular disorders, cancer, type 2 diabetes, and neurodegenerative diseases. Chronic, low-grade, systemic inflammation is associated with aging and the progression of immunosenescence. Immunosenescence may play an important role in the development of age-related chronic disease and the widely observed phenomenon of increased production of inflammatory mediators that accompany this process, referred to as “inflammaging”. While it has been demonstrated that the gut microbiome and immune system interact, the relationship between the gut microbiome and age remains to be clearly defined, particularly in the context of inflammation. The aim of the study was to clarify the associations between age, the gut microbiome, and pro-inflammatory marker serum MCP-1 in a C57BL/6 murine model. Results We used 16S rRNA gene sequencing to profile the composition of fecal microbiota associated with young and aged mice. Our analysis identified an association between microbiome structure and mouse age, and revealed specific groups of taxa whose abundances stratify young and aged mice. This includes the Ruminococcaceae, Clostridiaceae, and Enterobacteriaceae. We also profiled pro-inflammatory serum MCP-1 levels of each mouse and found that aged mice exhibited elevated serum MCP-1, a phenotype consistent with inflammaging. Robust correlation tests identified several taxa whose abundance in the microbiome associates with serum MCP-1 status, indicating that they may interact with the mouse immune system. We find that taxonomically similar organisms can exhibit differing, even opposite, patterns of association with the host immune system. We also find that many of the OTUs that associate with serum MCP-1 also stratify individuals by age. Discussion Our results demonstrate that gut microbiome composition is associated with age and the pro-inflammatory marker, serum MCP-1. The correlation between age, relative abundance of specific taxa in the gut microbiome, and serum MCP-1 status in mice indicates that the gut microbiome may play a modulating role in age-related inflammatory processes. These findings warrant further investigation of taxa associated with the inflammaging phenotype and the role of gut microbiome in the health status and immune function of aged individuals.
Zika virus: A newly emergent vector-borne public health threat in the Americas
Authors: Pujhari Sujit , Rasgon Jason L.
Published: January 2018

Zika virus is a newly emergent mosquito-borne flavivirus. Once almost ignored epidemiologically, recent major outbreaks and links to neurological birth defects have focused attention on this neglected pathogen. We review the discovery, biology and symptomatology of Zika virus, what is known and not known about the mosquitoes that transmit the virus, conspiracy theories currently hampering control efforts, and potential avenues of Zika control. It is likely that Zika virus is here to stay in the Americas, so a thorough understanding of the complete epidemiological transmission cycle and potential effects on the human population will be critical for managing this new disease in the coming years.
Evidence of model based transmission bias in captive chimpanzees: initial tool choice matches proficient groupmate
Authors: Wood Lara A , Kendal Rachel L , Hopper Lydia M , Lambeth Susan P , Schapiro Steven J , Flynn Emma G
Published: January 2018

Social learning theories predict biased transmission dictating what and whom is copied. We presented a novel tool-use task to six groups of captive chimpanzees (Pan troglodytes) to investigate a model proficiency bias. The study included six groups totalling 54 chimpanzees (24 males) housed in six social groups at the KCCMR, University of Texas, U.S.A. Subjects were aged 12- to 43-years-old (M = 24.5 years, SD = 7). In each of four groups (N = 33, Males = 18), two models were trained to use one of two visually and functionally different ‘hook’ and ‘spoon’ tools to obtain baskets containing food that were otherwise out-of-reach. Once trained, the models demonstrated their tool-use in the presence of the group. The two models differed in their novel-task-solving proficiency as ascertained by prior interactions with novel tasks (also observed by group members) and caregiver ratings of each chimpanzee’s general proficiency. Two groups of ‘control’ chimpanzees (N = 21) had no prior information regarding the task and saw no conspecific demonstrations. Within the experimental groups, significantly more chimpanzees touched the tool used by the ‘high proficiency’ model than the one used by the ‘low proficiency’ model (p < 0.001), demonstrating some degree of model-based social learning bias. The tool used in observing chimpanzees’ first attempts and first successes, however, did not differ as a function of which model used the tool. This was likely because the task could be easily learned asocially. We propose that the chimpanzees’ tool-use behaviour was guided by biased stimulus enhancement alongside asocial learning. As with humans, chimpanzees demonstrate an ability to discern the most proficient model but also show the flexibility to asocially acquire multiple successful methods. Thus, chimpanzees and humans both demonstrate adaptive social learning strategies dictating when and whom they copy.
Foundations of cumulative culture in apes: improved foraging efficiency through relinquishing and combining witnessed behaviors in chimpanzees (Pan troglodytes)
Authors: Davis Sarah J , Vale Gillian L , Schapiro Steven J , Lambeth Susan P , Whiten Andrew
Published: January 2018

Evidence for culture in non-human species continues to grow, yet there are few candidate examples of cumulative culture outside of humans’ distinctively complex achievements. Prerequisites for cumulative culture include not only the ability to build on established behaviors but also to relinquish old ones and flexibly switch to more productive or efficient alternatives. Here, we established an inefficient solution to a foraging task in five groups of captive adult chimpanzees (N=19 - 4 male, 15 female; average group size of 8 individuals) living at the Michale E. Keeling Center for Comparative Medicine and Research. Three groups were subsequently seeded with a conspecific model who demonstrated an alternative, more efficient, solution to the same task. When participants could still successfully forage with their previously established behaviors, the majority of individuals did not switch to this more efficient solution; however, when their foraging method eventually became highly inefficient relative to that of the available alternative, nine chimpanzees with socially-acquired information (four of whom were exposed to additional human demonstrations) relinquished their old behaviors in favor of the more efficient one. In contrast, only one individual in a control group that did not witness a knowledgeable model was seen to do this (One-tailed Fisher’s exact test, p<.01). Individuals who switched were later able to combine behavioral components of these two techniques to produce a more efficient solution than their extensively used original extractive method (One-tailed Wilcoxon signed-rank test: Z = -2.410, N = 10, p < .01, r = -0.54). This suggests that the ability to combine independent behaviors to produce a superior compound technique, thought to be a major driving force of cultural evolution in hominin history, may have been inherited from an ancient ancestor shared with chimpanzees.
Socio-behavioral convergence in female affiliative behaviors in Pan and Ateles
Authors: Rodrigues Michelle A , Boeving Emily R
Published: January 2018

Pan and Ateles converge in many aspects of their social organization. Both are characterized by a high degree of fission-fusion dynamics, in which species exhibit high variation in party size, composition, and spatial cohesion. Within this framework, chimpanzees (Pan troglodytes) and spider monkeys (Ateles sp.) exhibit the most similarity in subgrouping patterns and social relationships. Specifically, significant overlap is found in the context of female social relationships and patterns of male-female aggression. Here, we examine how affiliative behaviors mediate female social relationships in captive spider monkeys, chimpanzees, and bonobos. Focal data were collected from five female Ateles geoffroyi at Brookfield Zoo (mean age=13.2, range: 7-21), five female bonobos at Columbus Zoo (mean age=22.0, range: 7-31), and five chimpanzees at North Carolina Zoo (mean age=20.4, range: 15-43). Female dyads did not differ in their rates of total or directional grooming, but spider monkeys engaged in significantly less mutual grooming (Kruskal-Wallis H= 8.917, N=30, p=0.012). All three species exhibited grooming reciprocity. There were no significant differences in the overall use of tension-reduction behaviors. However, there were significant differences in the types of tension-reduction behaviors, with spider monkeys using embraces (H=14.306, p=0.001), bonobos using socio-sexual behaviors (H=14.269, p=0.001), and chimpanzees using kisses (H=11.50, p=0.003). Furthermore, bonobos used tension-reduction behaviors significantly more often in feeding contexts (ANOVA F=14.357, N=15, p=0.001). We suggest that each species use tension-reduction behaviors that are species-typical, but serve as functional equivalents. However, bonobos may experience increased tension in feeding contexts, which suggests differing social and ecological pressures may necessitate an increase in tension-reduction behaviors.
On causality of extreme events
Authors: Zanin Massimiliano
Published: January 2018

Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect both linear and non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task.
Mechano-adaptation of bone: Are all strains equal?
Authors: Rittweger Jörn
Published: January 2018

Bone research has been re-directed in the 1990s by three revolutions: firstly the recognition that bones respond to changes in their mechanical environment in a dose-dependent way; secondly by the idea that these changes in bone size can be understood as self-adaptation to variant forces by a servo-control mechanism (mechanostat theory); and thirdly by the proposition that muscles ‘enslave’ bone’s mechan-adaptation. It has been an inherent assumption in most of these bone studies that bone deformations mostly result from bending and compression, and little to no attention was paid to torsional loading. Notably, axial strains dominate in axial loading, whilst torsional loading is associated with relatively large shear strains. To better understand the mechanical interplay between regional muscle contractions and bone deformations, my team performed the MUST-study: bone pins were inserted into the human tibia, and non-collinear retro-reflective marker clusters were affixed to these pins in order to assess translational and rotational tibia deformations. Results from that study revealed that torsion is a prevailing deformation type within the human tibia, and that tibia torsion is causally linked to calf muscle contractions. Simultaneously, a series of in-silico experiments in our lab with a mechanostat model were undertaken. They revealed that torsion (i) is the most effective mode of bone deformation, and (ii) that it can explain the so-called flexure neutralization of miss-aligned fractures, which is inexplicable on grounds of compression and bending alone. Moreover, recent data also suggest that torsion, rather than impact may the bone-effective agent in the side-differences encountered in tennis players and baseball pitchers. Thus, I am currently following the idea of torsion as an effective deformation mode to elicit bone-anabolic responses. This is in contradiction to the main stream in bone research, which still regards impact loading as the most efficient way. Understanding and settling this question will be important in order to provide optimized exercise prescriptions that will maximize the benefits for bone, and minimize adverse events, such as joint sprains, cartilage damage, and tendon problems.
To transmit genes without becoming mother: An evolutionary conflict behind denial of pregnancy
Authors: Sandoz Patrick
Published: January 2018

Aim: The etiology of pregnancy denial remains poorly understood. Neither necessary nor sufficient conditions can be synthesized from the risk factors identified from psychological analyses. In accordance with clinical observations, we aim to explain denial of pregnancy from an evolutionary conflict perspective.

Methods: Authors investigate evolutionary biology aspects and emphasize on the transition from solitary animal species to social species. The possibility of conflicts between primitive species-perpetuation forces and subjective social-identity forces are explored.

Results: As members of a social species, human beings have a dual, contradictory character of independent organisms but interdependent people. This results in evolutionary inherited conflicts that, with respect to women's reproduction, distinguish between primitive and social-identity issues: i) to transmit genes by giving birth and ii) to become mother. Authors explain denial of pregnancy as a standby-in-tension response to a conflicting attempt to transmit genes without becoming mother. It may thus be considered as temporarily adaptive response by postponing conflict resolution. This model, based on subjective internal appraisals, is compatible with a huge diversity of causative events as expected from the specificity of each woman's life course.

Conclusions: The proposed etiology is consistent with clinical observations and brings prior models into agreement. From a clinical practice perspective, the ability to explain denial of pregnancy rationally may favor understanding and acceptation by concerned women. Health professionals' information may also be facilitated and psychotherapeutic follow up may gain in efficiency with reduced recidivism.

More generally, this evolutionary conflict approach provides a supplementary perspective to explore psychosomatic dysfunctions.
Detection of a Yersinia pestis gene homologue in rodent samples
Authors: Giles Timothy A , Greenwood Alex D , Tsangaras Kyriakos , Barrow Paul A , Hannant Duncan , Abu-Median Abu-Bakr , Yon Lisa
Published: January 2018

A homologue to a widely used genetic marker, pla, for Yersinia pestis has been identified in tissue samples of two species of rat (Rattus rattus and Rattus norvegicus) and of mice (Mus musculus and Apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. Samples were from urban locations in the UK (Liverpool) and Canada (Vancouver). The results indicate the presence of an unknown bacterium that shares a homologue with Yersinia pestis.
Carotenoid biotransformation pathways and oxidative stress in a bird: an experimental approach and its implications for color signaling
Authors: García-de Blas Esther , Mateo Rafael , Alonso-Alvarez Carlos
Published: January 2018

Colorful ornaments have been the focus of sexual selection studies since the work of Darwin. Yellow to red coloration is often produced by carotenoid pigments. Different hypotheses have been formulated to explain the evolution of these traits as signals of individual quality. Many of these hypotheses involve the existence of a signal production cost. The carotenoids necessary for signaling can only be obtained from food. In this line, carotenoid-based signals could reveal an individual's capacity to find sufficient dietary pigments. However, the ingested carotenoids are often yellow and became transformed by the organism to produce pigments of more intense color (red ketocarotenoids). Biotransformation often involves oxidation reactions. We tested the hypothesis that biotransformation could be costly because a certain level of oxidative stress is required. Thus, the carotenoid-based signals could reveal the efficiency of the owner in successfully managing this challenge. In a bird with ketocarotenoid-based ornaments (the red-legged partridge; Alectoris rufa), the availability of different carotenoids in the diet and oxidative stress were manipulated. We found that color and pigment levels in the ornaments depended on the relative quantity in the food of those carotenoids used as substrates in biotransformation (i.e. zeaxanthin and lutein). Moreover, we found that birds exposed to certain levels of a free radical generator (diquat) developed redder bills and deposited higher amounts of ketocarotenoids (astaxanthin) in ornaments, thus supporting the hypothesis. However, the effect also depended on the relative abundance of substrate carotenoids in the diet. This last result suggests the involvement of a resource allocation trade-off, which would support, to some extent, a signaling cost linked to carotenoid acquisition.
Similarities between decapod and insect neuropeptidomes
Authors: Veenstra Jan A
Published: January 2018

Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified, elongated PDH (pigment dispersing hormone), a variation on PDH that has a two amino acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides that have been deorphanized in insects. This includes the androgenic insulin like peptide that seems to be homologous to drosophila insulin-like peptide 8.
An empirical study on principles and practices of continuous delivery and deployment
Authors: Schermann Gerald , Cito Jürgen , Leitner Philipp , Zdun Uwe , Gall Harald
Published: January 2018

Despite substantial recent research activity related to continuous delivery and deployment (CD), there has not yet been a systematic, empirical study on how the practices often associated with continuous deployment have found their way into the broader software industry. This raises the question to what extent our knowledge of the area is dominated by the peculiarities of a small number of industrial leaders, such as Facebook. To address this issue, we conducted a mixed-method empirical study, consisting of a pre-study on literature, qualitative interviews with 20 software developers or release engineers with heterogeneous backgrounds, and a Web-based quantitative survey that attracted 187 complete responses. A major trend in the results of our study is that architectural issues are currently one of the main barriers for CD adoption. Further, feature toggles as an implementation technique for partial rollouts lead to unwanted complexity, and require research on better abstractions and modelling techniques for runtime variability. Finally, we conclude that practitioners are in need for more principled approaches to release decision making, e.g., which features to conduct A/B tests on, or which metrics to evaluate.
Preliminary study of water sources for maintenance and water utilization strategies of Haloxylon ammodendron in the arid desert area of northwestern China
Authors: Liu Guojun , Lv Jinling , Zhang Ximing
Published: January 2018

Natural vegetation in arid desert areas has been severely affected by uneven spatial-temporal precipitation and underground water distribution. Therefore, it is quite necessary to reserve maintenance water sources and water utilization strategies of natural vegetation. In our experiment, the Haloxylon ammodendron was selected to learn about the maintenance water sources and water utilization strategies. The results displayed that H. ammodendron could utilize various water sources, in which groundwater (30%) and shallow soil water (average 35%) accounted for very huge proportion to be the most important maintenance water sources H. ammodendron does not directly absorb from snowfall, but the application of shallow soil water was stemed from melt snow. The utilization percentage of groundwater is relatively higher in winter (80%) and summer (30%). The utilization percentages of different water sources change with the actual situations of these water sources; Precipitation is also one of main water sources of H. ammodendron (respond quickly but not influential). The mainly water of H. ammodendron in the study area are as follows: groundwater, shallow soil water formed by snowmelt, medium and large precipitation. Therefore, H. ammodendron can make efficient use of water sources in arid desert areas, and transform water sources reasonably under the tremendous variations in water conditions to meet the water requirements.
Green synthesis of silver nanoparticles in aloe vera plant extract prepared by a hydrothermal method and their synergistic antibacterial activity
Authors: Tippayawat Patcharaporn , Phromviyo Nutthakritta , Boueroy Parichart , Chompoosor Apiwat
Published: January 2018

Background: There is worldwide interest in silver nanoparticles (AgNPs) synthesized by various chemical reactions for use in applications exploiting their antibacterial activity, even though these processes exhibit a broad range of toxicity in vertebrates and invertebrates alike. To avoid the chemical toxicity, biosynthesis (green synthesis) of metal nanoparticles is proposed as a cost-effective and environmental friendly alternative. Aloe vera leaf extract is a medicinal agent with multiple properties including an antibacterial effect. Moreover the constituents of aloe vera leaves include lignin, hemicellulose, and pectins which can be used in the reduction of silver ions to produce as AgNPs@aloe vera (AgNPs@AV) with antibacterial activity. Methods: AgNPs were prepared by an eco-friendly hydrothermal method using an aloe vera plant extract solution as both a reducing and stabilizing agent. AgNPs@AV were characterized using XRD and SEM. Additionally, an agar well diffusion method was used to screen for antimicrobial activity. MIC and MBC were used to correlate the concentration of AgNPs@AV its bactericidal effect. SEM was used to investigate bacterial inactivation. Then the toxicity with human cells was investigated using an MTT assay. Results: The synthesized AgNPs were crystalline with sizes of 70.70 ± 22-192.02 ± 53 nm as revealed using XRD and SEM. The sizes of AgNPs can be varied through alteration of times and temperatures used in their synthesis. These AgNPs were investigated for potential use as an antibacterial agent to inhibit pathogenic bacteria. Their antibacterial activity was tested on S. epidermidis and P. aeruginosa. The results showed that AgNPs had a high antibacterial which depended on their synthesis conditions, particularly when processed at 100 oC for 6 h and 200 oC for 12 h. The cytotoxicity of AgNPs was determined using human PBMCs revealing no obvious cytotoxicity. These results indicated that AgNPs@AV can be effectively utilized in pharmaceutical, biotechnological and biomedical applications. Discussion: Aloe vera extract was processed using a green and facile method. This was a hydrothermal method to reduce silver nitrate to AgNPs@AV. Varying the hydrothermal temperature provided the fine spherical shaped nanoparticles. The size of the nanomaterial was affected by its thermal preparation. The particle size of AgNPs could be tuned by varying both time and temperature. A process using a pure AG phase could go to completion in 6h at 200 oC, whereas reactions at lower temperatures required longer times. Moreover, the antibacterial effect of this hybrid nanomaterial was sufficient that it could be used to inhibit pathogenic bacteria since silver release was dependent upon its particle size. The high activity of the largest AgNPs might have resulted from a high concentration of aloe vera compounds incorporated into the AgNPs during hydrothermal synthesis.
Analyzing test driven development based on GitHub evidence
Authors: Borle Neil C , Feghhi Meysam , Stroulia Eleni , Greiner Russ , Hindle Abram
Published: January 2018

Testing is an integral part of the software development lifecycle, approached with varying degrees of rigor by different process models. Agile process models advocate Test Driven Development (TDD) as one among their key practices for reducing costs and improving code quality. In this paper we comparatively analyze GitHub repositories that adopt TDD against repositories that do not, in order to determine how TDD affects a number of variables related to productivity and developer satisfaction, two aspects that should be considered in a cost-benefit analysis of the paradigm. In this study, we searched through GitHub and found that a relatively small subset of Java-based repositories can be seen to adopt TDD, and an even smaller subset can be confidently identified as rigorously adhering to TDD. For comparison purposes, we created two same-size control sets of repositories. We then compared the repositories in these two sets in terms of number of test files, average commit velocity, number of commits that reference bugs, number of issues recorded, whether they use continuous integration, and the sentiment of their developers’ commits. We found some interesting and significant differences between the two sets, including higher commit velocity and increased likelihood of continuous integration for TDD repositories.
Do chimpanzees and orangutans use communication in a cooperative task?
Authors: de las Heras Africa , Sperber Dan , Call Josep
Published: January 2018

Previous experimental studies show that captive chimpanzees (Pan troglodytes) and orangutans (Pongo abelii) cooperate with conspecifics but communication does not seem to play a crucial role. We presented a coordination task in which pairs of conspecifics had to communicate to succeed. Participants faced each other from opposite sides of an apparatus playing either a communicator or an operator role. At the beginning of each trial, the communicator was provided with a tool that could only be used from the operator’s side. If the operator inserted the tool into the baited tube the apparatus delivered food for both apes. Successful cooperation required that the communicator pass the tool to the operator and indicate the location of the baited tube so that the operator could insert it into the baited tube. In the experimental condition, only the communicator could see which one of four tubes was baited, while in the control condition both individuals had visual access to the baited tube. Data collection is currently ongoing. Participants are chimpanzees (1 male, 5 females; mean age= 22 years) and orangutans (2 males, 5 females; mean age= 18 years) housed at the Wolfgang Köhler Primate Research Center in Leipzig (Germany). So far, four dyads of chimpanzees have cooperated to solve the task. Preliminary results indicate that the communicator typically transfers the tool near the location of the food. In the experimental condition, success rate varies from 25% to 81% (compared to 94-100% in the control condition). Communicators pass the tool, touch or point at the food location, whereas operators request the tool, and both use attention getters aimed at their partners. We are currently analyzing whether these behaviors are independent of the operator’s visual access to the baited location.