bluuebunny/crossref_metadata_2025 huggingface dataset:
The earth is flat (p>0.05): Significance thresholds and the crisis of unreplicable research
Authors: Amrhein Valentin , Korner-Nievergelt Fränzi , Roth Tobias
Published: January 2018

The widespread use of 'statistical significance' as a license for making a claim of a scientific finding leads to considerable distortion of the scientific process (according to the American Statistical Association). We review why degrading p-values into 'significant' and 'nonsignificant' contributes to making studies irreproducible, or to making them seem irreproducible. A major problem is that we tend to take small p-values at face value, but mistrust results with larger p-values. In either case, p-values tell little about reliability of research, because they are hardly replicable even if an alternative hypothesis is true. Also significance (p≤0.05) is hardly replicable: at a good statistical power of 80%, two studies will be 'conflicting', meaning that one is significant and the other is not, in one third of the cases if there is a true effect. A replication can therefore not be interpreted as having failed only because it is nonsignificant. Many apparent replication failures may thus reflect faulty judgment based on significance thresholds rather than a crisis of unreplicable research. Reliable conclusions on replicability and practical importance of a finding can only be drawn using cumulative evidence from multiple independent studies. However, applying significance thresholds makes cumulative knowledge unreliable. One reason is that with anything but ideal statistical power, significant effect sizes will be biased upwards. Interpreting inflated significant results while ignoring nonsignificant results will thus lead to wrong conclusions. But current incentives to hunt for significance lead to selective reporting and to publication bias against nonsignificant findings. Data dredging, p-hacking, and publication bias should be addressed by removing fixed significance thresholds. Consistent with the recommendations of the late Ronald Fisher, p-values should be interpreted as graded measures of the strength of evidence against the null hypothesis. Also larger p-values offer some evidence against the null hypothesis, and they cannot be interpreted as supporting the null hypothesis, falsely concluding that 'there is no effect'. Information on possible true effect sizes that are compatible with the data must be obtained from the point estimate, e.g., from a sample average, and from the interval estimate, such as a confidence interval. We review how confusion about interpretation of larger p-values can be traced back to historical disputes among the founders of modern statistics. We further discuss potential arguments against removing significance thresholds, for example that decision rules should rather be more stringent, that sample sizes could decrease, or that p-values should better be completely abandoned. We conclude that whatever method of statistical inference we use, dichotomous threshold thinking must give way to non-automated informed judgment.
Morphology of an Early Oligocene beaver Propalaeocastor irtyshensis and the status of the genus Propalaeocastor
Authors: Li Lüzhou , Li Qiang , Lu Xiaoyu , Ni Xijun
Published: January 2018

The Early to Late Oligocene Propalaeocastor is the earliest known beaver genus from Eurasia. Although many species of this genus have been described, these species are defined based on very fragmentary specimens. Propalaeocastor irtyshensis from the Early Oligocene Irtysh River Formation in northwestern Xinjiang, China is one of the earliest-known members of Propalaeocastor. This species is defined on a single maxillary fragment. We revise the diagnosis of P. irtyshensis and the genus Propalaeocastor, based on newly discovered specimens from the Irtysh River Formation. The dental morphology of P. irtyshensis is very similar to other early castorids. The caudal palatine foramen of P. irtyshensis is situated in the maxillary-palatine suture. This is a feature generally accept as diagnostic character for the castorids. On the other hand, P. irtyshensis has two upper premolars, a rudimentarily developed sciuromorph-like zygomatic plate, and a relatively large protrogomorph-like infraorbital foramen. Some previous researchers suggested that Propalaeocastor is a junior synonym of Steneofiber, while other took it as a valid genus. Our morphological comparison and phylogenetic analysis suggest that Propalaeocastor differs from Steneofiber and is a valid genus. We also suggest that Agnotocastor aubekerovi, A. coloradensis, A. galushai, A. readingi, Oligotheriomys primus, and “Steneofiber aff. dehmi” should be referred to Propalaeocastor. Propalaeocastor is the earliest and most basal beaver. The origin place of Propalaeocastor and castorids is uncertain. The Early Oligocene radiation of castorids probably is propelled by the global climate change during the Eocene-Oligocene transition.
Characterisation of false-positive observations in botanical surveys
Authors: Groom Quentin J , Whild Sarah J.
Published: January 2018

Errors in botanical surveying are a common problem. The presence of a species is easily overlooked, leading to false-absences; while misidentifications and other mistakes lead to false-positive observations. While it is common knowledge that these errors occur, there are few data that can be used to quantify and describe these errors. Here we characterise false-positive errors for a controlled set of surveys conducted as part of a field identification test of botanical skill. Surveys were conducted at sites with a verified list of vascular plant species. The candidates were asked to list all the species they could identify in a defined botanically rich area. They were told beforehand that their final score would be the sum of the correct species they listed, but false-positive errors counted against their overall grade. The number of errors varied considerably between people, some people create a high proportion of false-positive errors, but these are scattered across all skill levels. Therefore, a person’s ability to correctly identify a large number of species is not a safeguard against the generation of false-positive errors. There was no phylogenetic pattern to falsely observed species, however, rare species are more likely to be false-positive as are species from species rich genera. Raising the threshold for the acceptance of an observation reduced false-positive observations dramatically, but at the expense of more false negative errors. False-positive errors are higher in field surveying of plants than many people may appreciate. Greater stringency is required before accepting species as present at a site, particularly for rare species. Combining multiple surveys resolves the problem, but requires a considerable increase in effort to achieve the same sensitivity as a single survey. Therefore, other methods should be used to raise the threshold for the acceptance of a species. For example, digital data input systems that can verify, feedback and inform the user are likely to reduce false-positive errors significantly.
Effects of long-term preservation on amphibian body conditions: Implications for historical morphological research
Authors: Shu Guocheng , Gong Yuzhou , Xie Feng , Wu Nicholas C. , Li Cheng
Published: January 2018

Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens do not affect their analyses. We compared the body length and body mass of 14 live and preserved (up to 10 years) amphibian species and found that the body length and body mass of preserved specimens significantly decreased by 7.1% and 26.7%, respectively, compared to those measurements of their live counterparts. Additionally, there was greater body length (3.6%) and body mass (6.6%) shrinkage in the order Urodela than in the order Anura, but there were no significant differences in body length and body mass shrinkage between males and females. Furthermore, preservation apparently distorted the magnitude of the intersexual and interspecific differences in body length observed in the fresh specimens. When species were compared, we found that the shrinkage was proportionately greater in longer species, while the body mass of heavier individuals shrank proportionately less than that of lighter individuals. Due to the effects of preservation on amphibian morphology, we propose parsimonious conversion equations to back-calculate the original body length and body mass of study animals for researchers working with historical data because morphological data from preserved specimens may lead to incorrect biological interpretations. Therefore, researchers must correct for errors due to preservation effects that may lead to the misinterpretation of results.
An updated understanding of Texas bumble bee (Hymenoptera: Apidae) species presence and potential distributions in Texas, USA
Authors: Beckham Jessica L , Atkinson Samuel
Published: January 2018

Texas is the second largest state in the United States of America, and the largest state in the contiguous USA at nearly 700,000 sq. km. Several Texas bumble bee species have shown evidence of declines in portions of their continental ranges, and conservation initiatives targeting these species will be most effective if species distributions are well established. To date, statewide bumble bee distributions for Texas have been inferred primarily from specimen records housed in natural history collections. To improve upon these maps, and help inform conservation decisions, this research aimed to (1) update existing Texas bumble bee presence databases to include recent (2007-2016) data from citizen science repositories and targeted field studies, (2) model statewide species distributions of the most common bumble bee species in Texas using MaxEnt, and (3) identify conservation target areas for the state that are most likely to contain habitat suitable for multiple declining species. The resulting Texas bumble bee database is comprised of 3,580 records, to include previously compiled museum records dating from 1897, recent field survey data, and vetted records from citizen science repositories. These data yielded an updated state species list that includes 11 species, as well as species distribution models (SDMs) for the most common Texas bumble bee species, including two that have shown evidence of range-wide declines: B. fraternus (Smith, 1854) and B. pensylvanicus (DeGeer, 1773). Based on analyses of these models, we have identified conservation priority areas within the Texas Cross Timbers, Texas Blackland Prairies, and East Central Texas Plains ecoregions where suitable habitat for both B. fraternus and B. pensylvanicus are highly likely to co-occur.
The South-American distribution and southernmost record of Biomphalaria peregrina - a potential intermediate host of schistosomiasis
Authors: Rumi Alejandra , Vogler Roberto Eugenio , Beltramino Ariel Anibal
Published: January 2018

Schistosomiasis remains a major parasitic disease, endemic in large parts of South America. Five neotropical species of Biomphalaria have been found to act as intermediate hosts of Schistosoma mansoni in natural populations, while others have been shown to be susceptible in experimental infections, although not found infected in the field. Among these potential intermediate hosts, Biomphalaria peregrina represents the most widespread species in South America, with confirmed occurrence records from Venezuela to northern Patagonia. In this study, we report the southernmost record for the species at the Pinturas River, in southern Patagonia, which finding implies a southward reassessment of the limit for the known species of this genus. The identities of the individuals from this population were confirmed through morphological examination, and by means of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16S-rRNA. With both markers, phylogenetic analyses were conducted in order to compare the genetic background of individuals from the Pinturas River with previously genetically characterized strains of B. peregrina from various South American locations. In addition, we produced a potential distribution model of B. peregrina in South America and identified the environmental variables that best predict that distribution. The model was estimated through a maximum entropy algorithm and run with occurrence points obtained from several sources, including the scientific literature and international databases, along with climatic and hydrographic variables. Different phylogenetic analyses with either the COI or 16S-rRNA sequences did not conflict, but rather gave very similar topological organizations. Two major groups were identified, with sequences from the Pinturas River grouping together with haplotypes from subtropical and temperate regions. The model developed had a satisfactory performance for the study area. We observed that the areas with higher habitat suitability were found to be mainly linked to subtropical and temperate regions of South America between 15° and 45° south latitude, with different moderate- and low-suitability areas outside this range. We also identified the coldest temperatures as the main predictors of the potential distribution of this snail. Susceptibility surveys would be required to evaluate if southern populations of B. peregrina still retain their potential as intermediate hosts of S. mansoni.
Use of necrophagous insects as evidence of cadaver relocation: myth or reality?
Authors: Charabidze Damien , Gosselin Matthias , Hedouin Valéry
Published: January 2018

The use of insects as indicators of postmortem displacement is discussed in many text, courses and TV shows, and several studies addressing this issue have been published. However, the concept is widely cited but poorly understood, and only a few forensic cases have successfully applied such a method. Surprisingly, this question has never be taken into account entirely as a cross-disciplinary theme. The use of necrophagous insects as evidence of cadaver relocation actually involves a wide range of data on their biology: distribution areas, microhabitats, phenology, behavioral ecology and molecular analysis are among the research areas linked to this problem. This article reviews for the first time the current knowledge on these questions and analysze the possibilities/limitations of each method to evaluate their feasibility. This analysis reveals numerous weaknesses and mistaken beliefs but also many concrete possibilities and research opportunities.
Exploring the occurrence of and explanations for nighttime spikes in dissolved oxygen across coral reef environments
Authors: Calhoun Sandi K. , Haas Andreas F. , Takeshita Yui , Johnson Maggie D. , Fox Michael D. , Kelly Emily L. A. , Mueller Benjamin , Vermeij Mark J. A. , Kelly Linda W. , Nelson Craig E. , Price Nichole N. , Roach Ty N. F. , Rohwer Forest L. , Smith Jennifer E.
Published: January 2018

Primary production due to photosynthesis results in daytime oxygen production across marine and freshwater ecosystems. However, a prevalent, globally-occurring nighttime spike in dissolved oxygen (DO) challenges our traditional assumption that oxygen production is limited to daylight hours, particularly in tropical coral reefs. When considered in the context of ecosystem oxygen budget estimates, these nocturnal spikes in DO could account for up to 24 percent of the daytime oxygen production. Here we show, 1) the widespread nature of this phenomenon, 2) the reproducibility across tropical marine ecosystems, 3) the lack of a consistent abiotic mechanism across all datasets we examined, and 4) the observation of nighttime DO spikes in vitro from incubations of coral reef benthic samples. Our study suggests that in addition to physical forcing, biological processes may be responsible for the production of oxygen at night, a finding that demands additional research.
Parallel and in-process compilation of individuals for genetic programming on GPU
Authors: Ayral Hakan , Albayrak Songül
Published: January 2018

Three approaches to implement genetic programming on GPU hardware are compilation, interpretation and direct generation of machine code. The compiled approach is known to have a prohibitive overhead compared to other two.

This paper investigates methods to accelerate compilation of individuals for genetic programming on GPU hardware. We apply in-process compilation to minimize the compilation overhead at each generation; and we investigate ways to parallelize in-process compilation. In-process compilation doesn’t lend itself to trivial parallelization with threads; we propose a multiprocess parallelization using memory sharing and operating systems interprocess communication primitives. With parallelized compilation we achieve further reductions on compilation overhead. Another contribution of this work is the code framework we built in C# for the experiments. The framework makes it possible to build arbitrary grammatical genetic programming experiments that run on GPU with minimal extra coding effort, and is available as open source.
The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata)
Authors: Wolcott Hayley L , Barbosa Miguel , Ojanguren Alfredo F
Published: January 2018

Predation is the main driver of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers anti predator benefits. Less, however, is known about how predator evasion is affected by social experience during early stages. In this study we test the hypothesis that familiarization acquired during early life stages improves anti predator escape responses. Using the Trinidadian guppy we examine the effect of different early social conditions in the three main components of predator evasion. Using high-speed motion analysis we compared the responsiveness, reactive distance and magnitude of the response (maximum speed, maximum acceleration and distance) of the response to a visual stimulus in groups composed either of familiar or non-familiar individuals. Surprisingly, groups composed by familiar individuals were less responsive than groups of unfamiliar individuals. It is plausible that familiarity equips individuals with better skills to accurately assess the threat avoiding false alarms. Reactive distance and magnitude of response were more dependent on individual size than on familiarity. Larger individuals reached higher maximum speeds and total distances in their escape response. Our approach allowed us to tease apart which aspects of an escape response are more likely to be influenced by early social conditions.
A clinical assessment of external beam focal therapy for localized prostate cancer measured by Gafchromic film
Authors: Van Delinder Kurt W
Published: January 2018

Background: Traditionally, EBRT prostate treatments have been administered using three different techniques: three-dimensional conformal radiation therapy (3D-CRT), intensity modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT). These radiation therapy treatment techniques are often combined with additional options focusing on treating systemic disease and the entire volume of the prostate. A novel approach to EBRT is currently in development, a localized treatment administered to only the primary disease within the prostate volume termed ‘Focal Therapy’.

Methods/Design: The proposed research study is aimed to simulate 10 random EBRT prostate focal therapy treatments replicated within two treatment planning software; Monaco treatment planning system and Eclipse treatment planning system. All ten plans will be contoured simulations of focal therapy imaging sets replicated from authentic mpMRI anatomical images of focal therapy eligible prostate cancer patients. Following the completion of the 10 clinical plans, QA plans will be generated and administered via each products current commercial linacs; the TrueBeam and the Versa. All QA plans will have their radiation doses measured with Gafchromic EBT3 radiochromic film and analyzed using the gamma analysis index (γ).

Discussion: To examine the uncertainties and limitations of an EBRT focal therapy prostate cancer treatment, it’s imperative that a large study replicating many clinical cases under varying conditions should be conducted. This allows the ability for the clinician to investigate errors and uncertainties at each stage of the treatment process prior to committing to a clinical study. The experimental results can also be used as a reference for the creation of a standard guideline for the administration of focal therapy as a curative treatment for prostate cancer.
A standalone software platform for the interactive management and pre-processing of ATAC-seq samples
Authors: Ahmed Zeeshan , Ucar Duygu
Published: January 2018

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncover how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation, but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross platform, user-friendly desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (e.g., FASTQC for quality checking) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+ T cells. I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists.
Penetrance of symbiont-mediated parthenogenesis is driven by reproductive rate in a parasitoid wasp
Authors: Lindsey Amelia R.I. , Stouthamer Richard
Published: January 2018

Trichogramma wasps are tiny parasitoids of lepidopteran eggs, used extensively for biological control. They are often infected with the bacterial symbiont Wolbachia, which converts Trichogramma to an asexual mode of reproduction, whereby females develop from unfertilized eggs. However, this Wolbachia-induced parthenogenesis is not always complete, and previous studies have noted that infected females will produce occasional males. The conditions that reduce penetrance of the parthenogenesis phenotype are not well understood. We hypothesize that more ecologically relevant conditions of limited host access will sustain female-biased sex ratios. By restricting access to host eggs, we see a strong relationship between reproductive rate and sex ratio. We show that reproductive output in the first 24 hours is critical to the total sex ratio of the entire brood, and limiting oviposition in that period results in near-complete parthenogenesis that can be sustained for long periods, without any significant impact on total fecundity. Our data suggest that this phenomenon may be due to the depletion of Wolbachia when oviposition occurs relatively constantly, and that Wolbachia titers may recover when offspring production is limited. In addition to the potential to improve mass rearing of Trichogramma for biological control, findings from this study help elucidate the context dependent nature of a pervasive symbiotic relationship.
Genetic effects on life-history traits in the Glanville fritillary butterfly
Authors: Duplouy Anne , Wong Swee C , Corander Jukka , Lehtonen Rainer , Hanski Ilkka
Published: January 2018

Background. Adaptation to local habitat conditions may lead to the natural divergence of populations in life-history traits such as body size, time of reproduction, mate signaling or dispersal capacity. Given enough time and strong enough selection pressures, populations may experience local genetic differentiation. The genetic basis of many life-history traits, and their evolution according to different environmental conditions remain however poorly understood.

Methods. We conducted an association study on the Glanville fritillary butterfly, using material from five populations along a latitudinal gradient within the Baltic Sea region, which show different degrees of habitat fragmentation. We investigated variation in ten principal components, cofounding in total 21 life-history traits, according to two environmental types, and 33 genetic SNP markers from 15 candidate genes.

Results. We found that nine SNPs from five genes showed strong trend for trait associations (p-values under 0.001 before correction). These associations, yet non-significant after multiple test corrections, with a total number of 1086 tests, were consistent across the study populations. Additionally, these nine genes also showed an allele frequency difference between the populations from the northern fragmented versus the southern continuous landscape.

Discussion. Our study provides further support for previously described trait associations within the Glanville fritillary butterfly species across different spatial scales. Although our results alone are inconclusive, they are concordant with previous studies that identified these associations to be related to climatic changes or habitat fragmentation within the Åland population.
Trichoplax adhaerens reveals an endocrine-like network sensitive to 9-cis-retinoic acid at the base of metazoan evolution
Authors: Novotný Jan Philipp , Chughtai Ahmed Ali , Kostrouchová Markéta , Kostrouchová Veronika , Kostrouch David , Kaššák Filip , Kaňa Radek , Schierwater Bernd , Kostrouchová Marta , Kostrouch Zdenek
Published: January 2018

Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely homologues of RXR (NR2B), HNF4 (NR2A), COUP (NR2F) and ERR (NR3B) that show a high degree of similarity with human homologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70 % in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens homologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has profound effect on T. adhaerens growth and appearance. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution.
Defending scientific integrity in conservation policy processes: lessons from Canada, Australia, and the United States
Authors: Carroll Carlos , Hartl Brett , Goldman Gretchen T , Rohlf Daniel J , Treves Adrain , Kerr Jeremy T , Ritchie Euan G , Kingsford Richard T , Gibbs Katherine E , Maron Martine , Watson James E M
Published: January 2018

Government agencies faced with politically controversial decisions often discount or ignore scientific information, whether from agency staff or non-governmental scientists. Recent developments in scientific integrity (the ability to perform, use, communicate and publish science free from censorship or political interference) in Canada, Australia and the United States demonstrate a similar trajectory: a perceived increase in scientific integrity abuses is followed by concerted pressure by the scientific community, leading to efforts to improve scientific integrity protections under a new administration. However, protections are often inconsistently applied, and are at risk of reversal under administrations that are publicly hostile to evidence-based policy. We compare recent challenges to scientific integrity to determine what aspects of scientific input into conservation policy are most at risk of political distortion and what can be done to strengthen safeguards against such abuses. To ensure the integrity of outbound communication from government scientists to public, we suggest that governments strengthen scientific integrity policies, include scientists’ right to speak freely in collective bargaining agreements, guarantee public access to scientific information, and strengthen agency culture supporting scientific integrity. To ensure the transparency and integrity with which information from non-governmental scientists (e.g., submitted comments or formal policy reviews) informs the policy process, we suggest that governments broaden the scope of independent reviews, ensure greater diversity of expert input with transparency regarding conflicts of interest, require substantive response to input from agencies, and engage proactively with scientific societies. For their part, scientists and scientific societies have a civic responsibility to engage with the wider public to affirm that science is a crucial resource for developing evidence-based policy and regulations that are in the public interest.
Differential effect of Platelet Endothelial Cell Adhesion Molecule-1 (PECAM-1) on leukocyte infiltration during contact hypersensitivity responses
Authors: Early Merideth , Schroeder William G , Unnithan Ranajana , Gilchrist John M , Muller William A , Schenkel Alan
Published: January 2018

BACKGROUND: 2’-4’ Dinitrofluorobenzene (DNFB) induced contact hypersensitivity is an established model of contact sensitivity and leukocyte migration. Platelet Endothelial Cell Adhesion Molecule-1 (PECAM-1) deficient mice were used to examine the role of PECAM-1 in the migration capacity of several different leukocyte populations after primary and secondary application. RESULTS: γδ T lymphocytes, granulocytes, and Natural Killer cells were most affected by PECAM-1 deficiency at the primary site of application. γδ T lymphocytes, granulocytes, DX5+ Natural Killer cells, and, interestingly, effector CD4+ T lymphocytes were most affected by the loss of PECAM-1 at the secondary site of application. CONCLUSIONS: PECAM-1 is used by many leukocyte populations for migration, but there are clearly differential effects on the usage by each subset. Further, the overall kinetics of each population varied between primary and secondary application, with large relative increases in γδ T lymphocytes during the secondary response.
From boss to mentor to partner : transitioning in medical education
Authors: Rossinot Helene , Brunoni Andre , Filipce Venko , Kalejs Martins , Liyanapathirana Veranja , Senkubuge Flavia , Toldi Gergely , Toth Csongor , Boufford Jo Ivey
Published: January 2018

The relationship between the teacher and the student is changing as information becomes more readily available, and the science of education is evolving in parallel.

The question then is: what is expected from the modern teacher in medicine? As young physician professionals from all regions of the world, we asked ourselves: how should this question be answered? This paper was motivated by the shared concerns and recommendations that we, as a team of Young Physician Leaders (footnote on the program) presented at the Global Health Summit held in Berlin in October, 2015 and by our subsequent discussions.
Germination ecophysiology for three peri-urban ephemeral weeds
Authors: Martínez D. Nayeli , de la Barrera Erick
Published: January 2018

We determined the environmental requirements leading to germination by three common species found during the summer rainy season in a peri-urban site where construction of a university campus was underway. In particular, we evaluated laboratory responses to low-temperature stratification, day/night air temperature, and water potential for the native Onagraceae Lopezia racemosa and Ludwigia octovalvis, and the exotic Polygonaceae Rumex crispus. Low-temperature stratification had no effect on germination by L. racemosa, for which maximum germination averaging 88% was optimal at 25/15 and 30/20 ºC. Germination at 21 d was halved at –0.5 MPa and completely inhibited at –1.0 MPa. The seeds of L. octovalvis were also insensitive to low temperature stratification and their germination never exceeded 70%, with the two highest temperatures of 30/20 and 35/25 ºC being the optimum. For this species germination was maximal at 0.0 MPa, decreasing significantly under every treatment with a minimum germination of 21% for seeds incubated at –0.1 MPa. Germination for the exotic R. crispus was delayed by low-temperature stratification, although all of its seeds germinated regardless of the temperature or water potential treatment. While the environmental requirements for germination of ephemeral species often match the typical climate of their growing season, the differential responses found for the species considered in the present study provide some insight into the mechanisms leading to changes in species composition for communities from disturbed environments, including the displacement of native species and the proliferation of exotic, potentially invasive, plants.
The appropriation of GitHub for curation
Authors: Wu Yu , Wang Na , Kropczynski Jessica , Carroll John M
Published: January 2018

Github is a key online collaborative software development environment. In this paper we describe a new category of Github project: Curation projects collect, evaluate, and preserve resources for software developers. We investigated 1) what motivates software developers to engaged in curation; 2) how software developers benefit from curation activities; and 3) how well GitHub supports/fails to support curation practices. We conducted in-depth interviews with 16 software developers each of whom host curation projects on GitHub. Our results suggest that software developers’ motivations for curation on GitHub are similar to their participation in open source projects. Convenient tools (e.g. Markdown syntax and Git version control system) and the opportunity to address professional needs of interests of large numbers of peers attract developers to engage in curation projects. Software developers benefit from curation projects through learning opportunities, support for development work, and professional interaction. However, curation is limited by GitHub’s document structure & format and also its lack of key features, such as search. We discuss design possibilities to encourage and improve curation appropriations of GitHub.
Biases in genome reconstruction from metagenomic data
Authors: Nelson William C , Mobberley Jennifer M
Published: January 2018

Background: Technological advances in sequencing, assembly and segregation of resulting contigs into species-specific bins has enabled the reconstruction of individual genomes from environmental metagenomic data sets. Though a powerful technique, it is shadowed by an inability to truly determine whether assembly and binning techniques are accurate, specific, and sensitive due to a lack of complete reference genome sequences against which to check the data. Errors in genome reconstruction, such as missing or mis-attributed activities, can have a detrimental effect on downstream metabolic and ecological modeling, and thus it is important to assess the accuracy of the process.

Methods: We compared genomes reconstructed from metagenomic data to complete genome sequences of 10 organisms isolated from the same community to identify regions not captured by typical binning techniques. The nucleotide content, as %G+C and tetranucleotide frequencies, and sequence redundancy within both the genome and across the metagenome were determined for both the captured and uncaptured regions. This direct comparison allowed us to evaluate the efficacy of nucleotide composition and coverage profiles as elements of binning protocols and look for biases in sequence characteristics and gene content in regions missing from the reconstructions.

Results: We found that repeated sequences were frequently missed in the reconstruction process as were short sequences with variant nucleotide composition. Genes encoded on the missing regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function.

Conclusions: Our observation of increased mis-binning of short regions, especially those with variant nucleotide content, and repeated regions implies that factors which affect assembly efficiency also impact binning accuracy. To a large extent, mis-binned regions appear to derive from mobile elements. Our results support genome reconstruction as a robust process, and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function.
Catch-per-unit effort of exploited finfishes and crustaceans in Ilog River Estuary, Negros Occidental, Philippines
Authors: Bucol Abner A , Galon Floredel D. , Alcala Angel C.
Published: January 2018

This paper reports the catch-per-unit effort (CPUE) of the finfish and crustacean fishery in Ilog River Estuary in Negros Occidental. We monitored catch data of fishing gears, mainly trawl (small type), beach seine and mud crab pot from April, May, September, October, December 2013 and January 2014.We estimated at least 37.82 metric tonnes of annual fishery yield (fishes and crustaceans combined) for the entire Malabong estuarine area. Two gears (liftnet and fish corrals) were used by the local fishers since the 1980s. Based on the baseline annual yield of 21 tonnes, the annual yield for these gears (at present ~7.5 tonnes) combined has declined by 13.5 tonnes (~65%) since the early 1980s (~30 years). This decline might be due to habitat degradation (including conversion of original mangrove forests into fish ponds and nipa plantations), over-exploitation, and organic pollution (resulting to recurring fish kill events) in the area.
Can we predict ecosystem functioning using tightly linked functional gene diversity?
Authors: Roger Fabian , Alsterberg Christian , Wittorf Lea , Sundbäck Kristina , Hulth Stefan , Hallin Sara , Gamfeldt Lars
Published: January 2018

Biodiversity generally affects ecosystem processes, but to what extent detailed knowledge about specific aspects of biodiversity helps us understand and predict specific ecosystem functions is not well-known. We hypothesised that information about functional gene abundance and diversity would provide a better way of predicting a particular function catalysed by that gene product, than would a more generic descriptor of species diversity. For our purposes, we used marine benthic nitrogen-fixing bacteria as a model system. We first used published observational data to relate nitrogen fixation to the abundance of the gene nifH, which encodes enzymes involved in the fixation of atmospheric nitrogen gas. We then used the fitted model, which explained 37% of the variance, to predict nitrogen fixation in other sediment samples for which nitrogen fixation and nifH abundance was determined. The model provided no predictive power for benthic nitrogen fixation on independent data. Additional information on the diversity of the general bacterial community, and the nitrogen fixing community in particular did not improve predictions. It was also not possible to predict nitrogen fixation based on the abundance of particular gene variants or bacterial taxa. Our results demonstrate that process rates can be intrinsically difficult to predict based on community metrics even when the community data and the process are tightly coupled.
AFCMHeatMap: A shiny web tool for HeatMap generation of genetic expression datasets using R packages
Authors: Tarek Mohammad , Shafei Ayman S , Ali Mahmoud A
Published: January 2018

Generating heatmaps of genes datasets have been known to be a graphical representation of data where the individual values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction genomics data and results from microarrays or RNA-Seq to highlight expression levels of various genetic datasets with a .CSV input file. The application also facilitates downloading heatmaps as a supplementary material for user's publications. Written in R using Shiny framework, it is a user-friendly framework for integrative genetic analyses that can be easily deployed across various operating systems distributions.
Predict protein-protein interactions from protein primary sequences: using wavelet transform combined with stacking algorithm
Authors: Xu Pin-San , Luo Jun , Dou Tong-Yi
Published: January 2018

Most biological processes within a cell are carried out by protein-protein interaction (PPI) networks, or so called interactomics. Therefore, identification of PPIs is crucial to elucidating protein functions and further understanding of various cellular biological processes. Currently, a series of high-throughput experimental technologies for detect PPIs have been presented. However, the time-consuming and labor-driven characteristics of these methods forced people to turn to virtual technology for PPIs prediction. Herein, we developed a new predictor which uses stacking algorithm with information extraction by wavelet transform. When applied on the Saccharomyces cerevisiae PPI dataset, the proposed method got a prediction accuracy of 83.35% with sensitivity of 92.95% at the specificity of 65.41%. An independent data set of 2726 Helicobacter pylori PPIs was also used to evaluate this prediction model, and the prediction accuracy is 80.39%, which is better than that of most existing methods.
Multi-scale and multi-site resampling of study area in spatial genetics: implications for flying insect species
Authors: Haran Julien M , Rossi Jean-Pierre , Pajares Juan , Bonifacio Luis , Naves Pedro , Roques Alain , Roux Géraldine
Published: January 2018

The use of multiple sampling areas in landscape genetic analysis has been recognized as a useful way to generalize the patterns of environmental effects on gene flow. It allows reducing the variability of inference, accounting for multiple scales and locations of study areas. Although several reviews have stressed the importance of this point, few studies have considered multiple sampling areas in analysis and formally tested their effects on inference. In this study, we present a method for resampling of study areas at multiple scales and multiple locations (sliding windows) to track the variation of inference in spatial genetics. We explored the effects of environmental features on gene flow of a flying long-horned beetle (Monochamus galloprovincialis) in 3*104 study areas ranging in scale from 220 to 1000 km and spread over 132 locations among the Iberian Peninsula. We show that there were no general or recurrent effects of environmental features detected among scales and locations, independent of variation in environmental features. Detection of environmental features on gene flow generally increased with an increasing scale of study, and was variable between locations. The resampling method presented here provides the opportunity to explore the effects of environmental features on gene flow of organisms in their whole extent and to conclude about general landscape effects on the dispersal of organisms, while keeping sampling effort to a reasonable level.
Indicators for the use of robotic labs in basic biomedical research
Authors: Groth Paul , Cox Jessica
Published: January 2018

Robotic Labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs are applicable in current experimental practice. We do this by text mining 1628 papers for occurrences of methods that are supported by commercial robotic labs. We find that 62% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments.
Norwegian honey bees surviving Varroa destructor miteinfestations by means of natural selection
Authors: Oddie Melissa AY , Dahle Bjørn , Neumann Peter
Published: January 2018

Background: Managed, feral and wild populations of European honey bee subspecies, Apis mellifera, are currently facing severe colony losses globally. There is consensus that the ectoparasite mite Varroa destructor, that switched hosts from the Eastern honey bee Apis cerana to the Western honey bee A. mellifera, is a key factor driving these losses. For >20 years, breeding efforts have not achieved that European honey bee colonies survive infestations without the need for mite control. However, at least three populations of European honey bees have developed this by means of natural selection and have been surviving for >10 years without mite treatments. Reduced mite reproductive success has been suggested as a key factor explaining this natural survival. Here, we report a managed A. mellifera population in Norway, that has been naturally surviving consistent V. destructor infestations for >17 years. Methods: Surviving colonies and local susceptible controls were evaluated for mite infestation levels, mite reproductive success and twopotential mechanisms explaining colony survival: grooming of adult worker bees and Varroa Sensitive Hygiene (VSH): adult workers specifically detecting and removing mite-infested brood. Results: Mite infestation levels were significantly lower in surviving colonies and mite reproductive success was reduced by ~30% compared to the controls. No significant differences were found between surviving and control colonies for either grooming or VSH. Discussion: Our data confirm that reduced mite reproductive success seems to be a key factor for natural survival of infested A. mellifera colonies. However, neither grooming nor VSH seem to explain colony survival. Instead, other behaviors of the adult bees seem to be sufficient to hinder mite reproductive success, because brood for this experiment was taken from susceptible donor colonies only. To mitigate the global impact of V. destructor, we suggest learning more from nature, i.e. identifying the obviously efficient mechanisms favored by natural selection.