bluuebunny/crossref_metadata_2025 huggingface dataset:
Best beach front real estate: microhabitat segregation of sympatric species of geckos on Mo'orea, French Polynesia
Authors: Zughaiyir Ferris Eric-Hisham
Published: January 2018

Background

Understanding how interspecific interactions affect a species and its access to resources is of great importance in a changing environment with limited resources. Investigating the effects of interspecific interactions of sympatric gecko species in Moorea provided insight into gecko community dynamics. The aim of this study is to understand the preference of diurnal shelter as a means of effectively managing available resources in a manner that allows for the coexistence of four sympatric species of nocturnal geckos. Microhabitat preference of four species of nocturnal geckos who coexist within an overlapping niche were examined by addressing the following questions: Will different species of geckos prefer to choose different diurnal shelters when in the presence of heterospecifics? Will shelter choice by the native geckos differ in different biomes? Out of the three most common species of geckos studied, which species will have a higher prevalence of taking refuge in horizontal microhabitats as opposed to vertical microhabitats?

Methods

To quantify patterns of microhabitat selection of sympatric gekkonids, a field survey categorized into three zones that ranged from high, intermediate, and low human disturbance was conducted. In field study observed shelter preferences was categorized into either ground, plant, or vertical shelters. In addition, interaction experiments with individuals of three gecko species were conducted.

Results

The results suggested interspecific interactions may in fact have an impact on the preference of diurnal sleeping shelter choice by geckos. Comparing conspecific with heterospecific trials of G. oceanica and H. frenatus, results suggested interspecific interactions playing a significant role in shelter preference. This same comparison for L. lugubris revealed interspecific interactions not playing an important role in their preference for shelter. Results from field survey yielded significant trends of each of the four species preferring certain shelter types from three categories. Shelter preference of vertical shelters by G. oceanica was reflected both in experimental and field studies. This trend of similar shelter preference when both field and experimental studies were compared did not hold true for H. frenatus and L. lugubris. Furthermore, human disturbance did not seem to play a significant role in influencing diurnal shelter preference of gecko species.

Discussion

Using this investigative approach, gecko shelter preferences was revealed. The results from this study suggested that although in some cases certain species held strong shelter preferences, these preferences change due to interspecific interactions. Understanding more about the severity of these interactions can help bridge the gap of understanding pertaining to the factors that shape the distributions and abundances of different gecko species who live in communities where resources are very limited.
Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs
Authors: Al Kait , Sarr Ousseynou , Dunlop Kristyn , Gloor Gregory B , Reid Gregor , Burton Jeremy , Regnault Timothy RH
Published: January 2018

Background: The gastrointestinal tract (GIT) microbiota is essential to metabolic health, and the prevalence of the Western diet (WD) high in fat and sugar is increasing, with evidence highlighting a negative interaction between the GIT and WD resulting in liver dysfunction. Additionally, an adverse in utero environment such as placental insufficiency resulting in low birth weight (LBW) offspring, contributes to an increased risk of metabolic diseases such as fatty liver infiltration and liver dysfunction in later life. We sought to understand the potential interactive effects of exposure to a WD upon growing LBW offspring. We postulated that LBW offspring when challenged with a poor postnatal diet, would display an altered microbiota and more severe liver metabolic dysfunction.

Methods: The fecal microbiota of normal birth weight (NBW) and LBW young guinea pig offspring, weaned onto either a control diet (CD) or WD was determined with 16S rRNA gene next generation sequencing and liver blood chemistry at young adulthood following the early rapid growth phase after weaning. A liver blood chemistry profile was also performed.

Results: The life-long consumption of WD following weaning into young adulthood resulted in increased total cholesterol, triglycerides and alanine aminotransferase levels in association with an altered GIT microbiota when compared to offspring consuming CD. Neither birth weight nor sex were associated with any significant changes in microbiota alpha diversity, by measuring the Shannon’s diversity index. One hundred forty-eight operational taxonomic units were statistically distinct between the diet groups, independent of birth weight. In the WD group, significant decreases were detected in Barnesiella, Methanobrevibacter smithii and relatives of Oscillospira guillermondii, while Butyricimonas and Bacteroides spp. were increased.

Discussion: These results describe the GIT microbiota in a guinea pig model of LBW and WD associated metabolic syndrome and highlight several WD specific GIT alterations associated with human metabolic disease.
An investigation of visual cryptography and its applications in secure communications
Authors: Shahab Elham , Abdolrahimpour Hadi
Published: January 2018

Secret sharing approach and in particular Visual Cryptography (VC) try to address the security issues in dealing with images. In fact, VC is a powerful technique that combines the notions of perfect ciphers and secret sharing in cryptography. VC takes an image (secret) as an input and encrypts (divide) into two or more pieces (shares) that each of them can not reveal any information about the main input. The decryption way in this scenario is done through superimposing shares on top of each other to receive the input image. No computer participation is required, thus showing one of the distinguishing features of VC. It is claimed that VC is a unique technique in the sense that the encrypted message can be decrypted directly by the human visual system.
A comprehensive investigation of visual cryptography and its role in secure communications
Authors: Shahab Elham , Abdolrahimpour Hadi
Published: January 2018

Secret sharing approach and in particular Visual Cryptography (VC) try to address the security issues in dealing with images. In fact, VC is a powerful technique that combines the notions of perfect ciphers and secret sharing in cryptography. VC takes an image (secret) as an input and encrypts (divide) into two or more pieces (shares) that each of them can not reveal any information about the main input. The decryption way in this scenario is done through superimposing shares on top of each other to receive the input image. No computer participation is required, thus showing one of the distinguishing features of VC. It is claimed that VC is a unique technique in the sense that the encrypted message can be decrypted directly by the human visual system.
Possible variation in microbiota community structure and composition in same species bred in zoos and a wildlife refuge, and its implications on reproductive success
Authors: Ng Wenfa
Published: January 2018

Considering the difficulty of breeding endangered species in captivity relative to those in the wild, specific environmental factors such as availability of roaming space and nutrition may be important reasons contributing to the relative lack of procreation capability in animals housed in zoos. Like humans, animals acquire their microbiota from the immediate environment they reside as well as from food. Specifically, the environs in which an animal grows and matures as well as nutrition play important roles in modulating the types and relative abundances of different microbes present on different parts of the animal body. Thus, differential microbiota may exist on animals in captivity and in the wild (e.g., a wildlife refuge or a national park), and this may impact on reproductive success. Hence, one research direction that could lay the foundation for understanding the microbiological underpinnings impacting on breeding success of animals in zoos may be the profiling of the gut and skin microbiota of endangered species such as pandas in zoos and in wildlife refuges. In particular, while most panda breeding programs around the world try to recapitulate the conditions and nutrient sources available in the native environment, significant differences remain such as the influence of human contact with pandas on the transfer of microbial species, as well as the amount and type of spaces available for roaming. By using a tracking and periodic sampling approach for understanding the microbial populations in the gut and skin of wild and zoo pandas, knowledge could be progressively accumulated on the microbiological evolution of animals throughout their lives in captivity or in the wild, and correlated with their relative success in procreation. Doing so would help unlock mysteries on fundamental questions of how does human contact and breeding programs change microbiome structure and function in zoo animals relative to wild pandas, and, more importantly, the roles of differential microbiota in health and disease of the animals, which directly impact on reproduction fitness. Taken together, success of breeding programs hinge on multitude of factors ranging from human influence on social behavior of pandas, nutrition, artificial recreated habitat, and microbiological environment of enclosure, but given the important roles of microbial species (alone and in aggregate) on animal physiology and neurobiology, profiling the possible differentiated microbiota of animals in captivity and the wild may be the first incision point for unveiling deeper mysteries of how microbes influence higher order animal function and decision making. Interested researchers can expand on the ideas presented herein.
Assessing value of biomedical digital repositories
Authors: Hsu Chun-Nan , Bandrowski Anita , Grethe Jeffrey S. , Martone Maryann E.
Published: January 2018

Digital repositories bring direct impact and influence on the research community and society but measuring their value using formal metrics remains challenging. their value. It is challenging to define a single perfect metric that covers all quality aspects. Here, we distinguish here between impact and influence and discuss measures and mentions as the basis of quality metrics of a digital repository. We argue that these challenges may potentially be overcome through the introduction of standard resource identification and data citation practices. We briefly summarize our research and experience in the Neuroscience Information Framework, the BD2K BioCaddie project on data citation, and the Resource Identification Initiative. Full implementation of these standards will depend on cooperation from all stakeholders --- digital repositories, authors, publishers, and funding agencies, but both resource and data citation have been gaining support with researchers and publishers.
An artificial immune system approach to automated program verification: Towards a theory of undecidability in biological computing
Authors: Banerjee Soumya
Published: January 2018

An immune system inspired Artificial Immune System (AIS) algorithm is presented, and is used for the purposes of automated program verification. Relevant immunological concepts are discussed and the field of AIS is briefly reviewed. It is proposed to use this AIS algorithm for a specific automated program verification task: that of predicting shape of program invariants. It is shown that the algorithm correctly predicts program invariant shape for a variety of benchmarked programs. Program invariants encapsulate the computability of a particular program, e.g. whether it performs a particular function correctly and whether it terminates or not. This work also lays the foundation for applying concepts of theoretical incomputability and undecidability to biological systems like the immune system that perform robust computation to eliminate pathogens.
Which method is more accurate? or errors have error bars
Authors: Jensen Jan H
Published: January 2018

This document is my attempt at distilling some of the information in two papers published by Anthony Nicholls (J. Comput. Aided Mol. Des. 2014, 28, 887; ibid 2016, 30, 103). Anthony also very kindly provided some new equations, not found in the papers, in response to my questions. The paper describes how one determines whether the difference in accuracy of two methods in predicting some properties for the same data set is statistically significant using root-mean-square errors, mean absolute errors, mean errors, and Pearsons r values.
Poleward and vertical migration of animals under climate change highlights possible environmental effects on social behaviour
Authors: Ng Wenfa
Published: January 2018

Temperature rise from climate change may completely change geological landscapes and environmental conditions at habitats previously conducive for specific animal species. Together with increasing difficulty in coping with greater fluctuations in temperature between seasons as well as reduced or enhanced precipitations in areas normally accustomed to consistent patterns of rainfall, variation in nutrient availability is another significant factor impacting on the survivability of animals in a specific area, particularly those in the mid-latitudes and on mountain slopes. Thus, prompted by the lack of nutrients or availability of water arising from climatic changes, many warm and cold-blooded species may migrate towards polar regions as well as higher altitudes of mountains in search of more habitable conditions. Such migrations open up myriad research opportunities into understanding how predators and prey adapt to changes in environmental factors and nutrient availability under climate change, which is accelerating in the polar regions. Specifically, predators and prey may differentially move to different locales with predators having to adapt to new food sources or change their foraging patterns, which, in turn, may impact on their social behaviours on parenting and hunting habits. An example would be lack of food sources prompting predators high in the food chain to adapt by having fewer offsprings, switching to available but less nutritious food, as well as changing foraging patterns. On the other hand, prey may use changes in geological formations between habitats to adapt their breeding patterns as well as foraging activities; for example, using camouflage available in the new environment to better protect their young from new and old predators. Similarly, species on the vertical transect of mountains would also move to higher altitudes to adapt to heat from global warming, or execute a poleward movement in search of more conducive habitats. Altogether, many interesting research directions are awaiting exploration as animal species move towards the poles or higher altitudes on mountains, prompted by rising temperatures that changed environmental conditions and nutrient availability. Mass migrations such as these may potentially unsettle entire ecosystems as species able to adapt to higher temperatures benefit from reduced competition, while those choosing the migratory path face an uncertain future in finding a habitable niche similar to the abandoned one, as well as ability to adapt to the new locale in foraging behaviour, breeding patterns and social behaviour. Possible changes in social behaviour is one significant area for understanding how climate change induced migration exert a selection pressure on animal behaviour and neural development. Interested researchers can expand on the ideas presented in this abstract preprint.
Water (or the lack thereof), management, and conservation of an endangered desert wetland obligate, Lilaeopsis schaffneriana var. recurva
Authors: Malcom Jacob W , Malcom Anna C , Radke William R
Published: January 2018

Huachuca water umbel, Lilaeopsis schaffneriana var. recurva, is a federally endangered desert wetland plant restricted to southeastern Arizona, USA, and adjacent portions of Mexico. Very little is known about the factors that influence the species presence, absence, and abundance, including the effects of wetland drying caused by drought or water withdrawals. We conducted three lines of research to address the lack of information about the species’ ecology using observational field research and controlled experiments. First, we examined ecological correlates of the species presence and absence along a perennial stream in Southeast Arizona where the species has been established for over a decade. Next, we used a full-factorial experiment to examine the species’ drought resistance and drought resilience. Last, we monitored transplanting efforts of the species along the upper Rio Yaqui. We found that distance to the nearest water umbel patch centroid—a measure of historical factors—and distance to surface water were the best predictors of the species’ presence and leaf density. The drought experiments demonstrated that leaf density is an important factor influencing both resistance and resilience: low leaf-density was associated with replicates reaching critical conditions approximately one full day before high leaf-density plants, and high leaf-density plants rebounded at nearly twice the rate of low-density plants when water became available. Transplants appeared to be most successful in areas where water levels remained relatively constant, herbaceous-layer competitors were rare, and water velocity was low. These results indicate that protecting existing populations by ensuring stable water sources is the most important action for conserving the species in current locations and future transplant locations.
Dual roles of tear lipocalins as ‘chemical signalling’ and ‘toxic waste disposal’ systems of the house mouse
Authors: Stopka Pavel , Klempt Petr , Kuntova Barbora , Stopkova Romana
Published: January 2018

Mammalian tears are produced by lacrimal glands to protect eyes and to function in chemical communication and immunity. However, excess tears flow through nasolacrimal ductsto nasal tissues, and via the nasopharyngeal duct to the oral cavity where digestion starts. Tears contain soluble proteins that attack pathogens, as well as proteins from the lipocalin family that – with their capacity to transport volatile organic compounds (VOCs) in their eight-stranded beta barrel – are involved in sexual signalling and may also transport toxic VOCs towards digestion. Therefore, we generated the tear proteome of the wild-living house mouse (Mus musculus musculus) and detected a total of 719 proteins in tears with 20% being sexually dimorphic. Those proteins that showed the most elevated sexual dimorphisms are VOC transporters from the recently discovered odorant binding protein (OBP), and major urinary protein (MUP) families, thus demonstrating that tears have the potential to elicit sex-specific signals in combination with different lipocalins. Moreover, some tear lipocalins are non-dimorphic – with MUP20/Darcin, LCN11, and LCN13 being good examples – thus suggesting that they are involved in other biological processes besides sexual signalling.
Porpitids (Cnidaria: Hydrozoa) from the early Cambrian (Series 2: Stage 4) of Nevada, U.S.A.
Authors: Lieberman Bruce S , Kurkewicz Richard , Shinogle Heather
Published: January 2018

The morphology and affinities of newly discovered soft-bodied fossils from the early Cambrian (Series 2: Stage 4, Dyeran) Carrara Formation that resemble modern and fossil porpitids are discussed. These specimens show substantial similarity to the Ordovician porpitid Discophyllum peltatum Hall, 1847. The status of various Proterozoic and Phanerozoic taxa previously referred to porpitids is also briefly considered. To verify that the specimens were not dubio- or pseudofossils, elemental mapping using energy dispersive X-ray spectroscopy (EDS) was conducted. This indicated that the fossils were not hematite, iron sulfide, pyrolusite, or other abiologic mineral precipitates. Instead, their status as biologic structures and thus actual fossils is supported. Enrichment in the element carbon, and also possibly to some extent the elements magnesium and iron, seems to be playing some role in the preservation process.
Inhibition of Nf-ҝb prevents trauma-induced heterotopic ossification in rat model
Authors: Ju Jinyong , Yu Du , Xue Feng , Zhao Yong , Shi Weizhe , Pan Mingmang , Tang Guo , Xiao Haijun
Published: January 2018

Background. To find a better prophylactic regimen, the pathogenesis of acquired heterotopic ossification (AHO) must be more understood. To date, AHO formation is largely thought to be related to inflammation, which is activated by trauma, resulting in AHO by up-regulation of pro-osteogenic genes. Methods. Brain-traumatic/burn/tenotomy model is firstly used in experiment. At first, 44 rats were randomly divided into two groups: E group and C group. Two rats in every group were euthanized during second, third, fourth, sixth, eighth, tenth weeks for collecting tendon. The remaining rats survived until tenth week for X-Ray radiation examination to confirm the size of AHO.Then, 124 rats were randomly divided into four group: P group, L group, M group, H group. The three rats of every group were euthanized during every week of the first seven weeks for collecting tendon to detect P65 protein. The remaining rats survived until tenth week for X-Ray examination to confirm the size of AHO. Results. The success rate of Brain-traumatic/Burn/Tenotomy model is 100%. Difference of P65 expression in E group and in C group are statistically significant,and that in E group is higher.Pharmacologic inhibition of Nf-ҝb signaling pathway limits AHO formation, and that The bone formation content of M group is decreased. Conclusion. Brain-traumatic/Burn/Tenotomy model is highly reliable.Results indicate that the Nf-ҝb /p65 signaling response occurs in the forming process of AHO. PDTC limits formation of AHO. The most effective concentration is 6mg/ml for local injection.
Notes on the distribution of Gastrotheca testudinea (Jiménez de la Espada, 1870) in Ecuador
Authors: Urgilés Verónica L. , Sánchez-Nivicela Juan Carlos , Cisneros-Heredia Diego F
Published: January 2018

We present new information on the distribution of the marsupial frog Gastrotheca testudinea (Jiménez de la Espada, 1870) in Ecuador. We provide the first record from the province of Cañar, and the country’s southernmost locality (which also corresponds to the third known report from the province of Zamora-Chinchipe). In addition, we discuss the validity of the locality of Loreto for this species. Based on this discussion, we review the elevation range of the species and propose to change the lowest elevation limit of Gastrotheca testudinea from 1100 to 700 m.
Imagining the ‘open’ university: Sharing scholarship to improve research and education
Authors: McKiernan Erin C
Published: January 2018

Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education, as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar. I describe some of the challenges inherent to practicing open scholarship, and some of the tensions created by incompatibilities between institutional policies and personal practice. To address this, I propose several concrete actions universities could take to support open scholarship, and outline ways in which such initiatives could benefit the public as well as institutions. Importantly, I do not think most of these actions would require new funding, but rather a redistribution of existing funds and a rewriting of internal policies to better align with university’s stated missions of dissemination of knowledge and societal impact.
Species-specific audio detection: A comparison of three template-based classification algorithms using random forests
Authors: Corrada Bravo Carlos J , Álvarez Berríos Rafael , Aide T. Mitchell
Published: January 2018

We developed a web-based cloud-hosted system that allow users to archive, listen, visualize, and annotate recordings. The system also provides tools to convert these annotations into datasets that can be used to train a computer to detect the presence or absence of a species. The algorithm used by the system was selected after comparing the accuracy and efficiency of three variants of a template-based classification. The algorithm computes a similarity vector by comparing a template of a species call with time increments across the spectrogram. Statistical features are extracted from this vector and used as input for a Random Forest classifier that predicts presence or absence of the species in the recording. The fastest algorithm variant had the highest average accuracy and specificity; therefore, it was implemented in the ARBIMON web-based system.
Photoperiodic regime influences onset of lens opacities in a non-human primate
Authors: Dubicanac Marko , Strueve Julia , Mestre-Frances Nadine , Verdier Jean-Michel , Zimmermann Elke , Joly Marine
Published: January 2018

Background. Opacities of the lens are typical age related phenomena which have high influence on photoreception and consequently circadian rhythm. In mouse lemurs, a small bodied non-human primate, a high incidence (more than 50% when > 7 years) of cataract has been previously described during aging. Previous studies showed that photoperiodical induced accelerated annual rhythms alter some of mouse lemurs’ life history traits. Whether a modification of photoperiod also affects the onset of age dependent lens opacities has not been investigated so far. The aim of this study was therefore to characterize the type of opacity and the mouse lemurs’ age at its onset in two colonies with different photoperiodic regimen. Methods. Two of the largest mouse lemur colonies in Europe have been investigated; Colony 1 with a natural annual photoperiodic regime and Colony 2 with an induced accelerated annual cycle. A Slit-lamp was used to determine opacities in the lens and a subset of all animals which showed no opacities in the lens nucleus in the first examination but developed first changes in the following examination were further used to estimate the age at onset of opacities. In total 387 animals were examined and 57 represent the subset for age at onset estimation. Results. The first and most common observable opacity in the lens was nuclear sclerosis. Mouse lemurs from Colony 1 showed a delayed onset of nuclear sclerosis compared to mouse lemurs of Colony 2 (4.35 ± 1.50 years vs. 2.75 ± 0.99 years). For colony 1, the chronological age was equivalent to the number of seasonal cycles experienced by the mouse lemurs. For colony 2, in which seasonal cycles are accelerated by factor 1.5, mouse lemurs had experienced 4.13 ± 1.50 seasonal cycles in 2.75 ± 0.99 chronological years. Discussion. Our study showed clear differences in the age at the onset of nuclear sclerosis formation between lemurs kept under different photoperiodic regimes. Instead of measuring the chronological age, the number of seasonal cycles (N = 4) experienced by a mouse lemur can be used as an estimation for risk of beginning NS formation. Ophthalmological investigations should be taken into account when animals older than 5 - 6 seasonal cycles are used for experiments in which unrestricted visual ability has to be ensured. This study is the first to assess and demonstrate the influence of annual photoperiod regime on the incidence of lens opacities in a non-human primate.
Exploring biomedical ontology mappings with graph theory methods
Authors: Kocbek Simon , Kim Jin-Dong
Published: January 2018

Background

In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies.

Methods

We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature.

Results

With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.
Safe and sensible baseline correction of pupil-size data
Authors: Mathôt Sebastiaan , Fabius Jasper , van Heusden Elle , Van der Stigchel Stefan
Published: January 2018

Measurement of pupil size (pupillometry) has recently gained renewed interest from psychologists, but there is little agreement on how pupil-size data is best analyzed. Here we focus on one aspect of pupillometric analyses: baseline correction, that is, analyzing changes in pupil size relative to a baseline period. Baseline correction is useful in experiments that investigate the effect of some experimental manipulation on pupil size. In such experiments, baseline correction improves statistical power by taking into account random fluctuations in pupil size over time. However, we show that baseline correction can also distort data if unrealistically small pupil sizes are recorded during the baseline period, which can easily occur due to eye blinks, data loss, or other distortions. Divisive baseline correction (corrected pupil size = pupil size / baseline) is affected more strongly by such distortions than subtractive baseline correction (corrected pupil size = pupil size - baseline). We make four recommendations for safe and sensible baseline correction of pupil-size data: 1) use subtractive baseline correction; 2) visually compare your corrected and uncorrected data; 3) be wary of pupil-size effects that emerge faster than the latency of the pupillary response allows (within ±220 ms after the manipulation that induces the effect); and 4) remove trials on which baseline pupil size is unrealistically small (indicative of blinks and other distortions).
­Glial and stem cell expression of Fibroblast Growth Factor Receptor 1 in the embryonic and perinatal nervous system
Authors: Collette Jantzen C , Choubey Lisha , Smith Karen Muller
Published: January 2018

Background. Fibroblast growth factors (FGFs) and their receptors (FGFRs) are involved in the development and function of multiple organs and organ systems, including the central nervous system (CNS). FGF signaling via FGFR1, one of the three FGFRs expressed in the CNS, stimulates proliferation of stem cells during prenatal and postnatal neurogenesis and participates in regulating cell-type ratios in many developing regions of the brain. Anomalies in FGFR1 signaling have been implicated in certain neuropsychiatric disorders. Fgfr1 expression has been shown, via in situ hybridization, to vary spatially and temporally throughout embryonic and postnatal development of the brain. However, in situ hybridization lacks sufficient resolution to identify which cell-types directly participate in FGF signaling. Furthermore, because antibodies raised against FGFR1 commonly cross-react with other members of the FGFR family, immunocytochemistry is not alone sufficient to accurately document Fgfr1 expression. Here, we elucidate the identity of Fgfr1 expressing cells in both the embryonic and perinatal mouse brain.

Methods. To do this, we utilized a tgFGFR1-EGFPGP338Gsat BAC line (tgFgfr1-EGFP+) obtained from the GENSAT project. The tgFgfr1-EGFP+ line expresses EGFP under the control of a Fgfr1 promoter, thereby causing cells endogenously expressing Fgfr1 to also present a positive GFP signal. Through simple immunostaining using GFP antibodies and cell-type specific antibodies, we were able to accurately determine the cell-type of Fgfr1 expressing cells.

Results. This technique revealed Fgfr1 expression in proliferative zones containing BLBP+ radial glial stem cells, such as the cortical and hippocampal ventricular zones, and cerebellar anlage of E14.5 mice, in addition to DCX+ neuroblasts. Furthermore, our data reveal Fgfr1 expression in proliferative zones containing BLBP+ cells of the anterior midline, hippocampus, cortex, hypothalamus, and cerebellum of P0.5 mice, in addition to the early-formed GFAP+ astrocytes of the anterior midline.

Discussion. Understanding when during development and where Fgfr1 is expressed is critical to improving our understanding of its function during neurodevelopment as well as in the mature CNS. This information may one day provide an avenue of discovery towards understanding the involvement of aberrant FGF signaling in neuropsychiatric disorders.
Differential gene expression analysis by RNA-seq reveals the importance of actin cytoskeletal proteins in leukemia cells
Authors: Fernández-Calleja Vanessa , Hernández Pablo , Schvartzman Jorge B , Krimer Dora B
Published: January 2018

Development of drug resistance limits the effectiveness of anticancer treatments. Understanding the molecular mechanisms triggering this event in tumor cells may lead to improved therapeutic strategies. Here we used RNA-seq to compare the transcriptomes of an erythroleukemia progenitor cell line (MEL-DS19) and a derived cell line with induced resistance to differentiation (MEL-R). RNA-seq analysis identified a total of 596 genes that were differentially expressed by more than two-fold, of which 486 genes were up-regulated in MEL-DS19 cells and 110 up-regulated in MEL-R cells. These observations revealed that the number of genes expressed in the parental cell line decreased as the cells acquired the resistant phenotype. Clustering analysis of a group of genes showing the highest differential expression allowed identification of a sub-group among genes up-regulated in MEL cells. These genes are related with the organization of the actin cytoskeleton network. Moreover, the majority of these genes are preferentially expressed in the hematopoietic lineage and at least three of them, Was (Wiskott Aldrich syndrome), Btk (Bruton tyrosine kinase) and Rac2, when mutated in humans, give rise to severe hematopoietic deficiencies. Among the group of genes that were up-regulated in MEL-R cells, a significant percentage (16%) corresponded to genes coding for histone proteins, both canonical and variants. A potential implication of these results on the blockade of differentiation in resistant cells is discussed.
A Monte Carlo simulation for bioprospecting the endemic New Zealand terrestrial flora for antibiotic drug leads
Authors: Buenz Eric J
Published: January 2018

Natural product libraries are important tools for drug discovery. However, until now, there has not been a system to allow projections of the potential number of hits from creating these libraries. The objective of this study was to develop a stochastic model system that predicts the number of hits from creating a natural product library. A Monte Carlo simulation was developed with data from the peer-reviewed literature. Using types of endemic New Zealand terrestrial flora as examples, the number of antibacterial hits expected from creating natural product libraries were calculated. The model predicts the following bounds for the 90% range of validated antibiotic leads for the categories of the terrestrial endemic flora of New Zealand with a right skewed distribution: [grasses: 1.43-6.50; liverworts: 2.75-12.5; fungi: 45.2-207; mosses: 0.98-4.48; vascular plants: 21.4-97.8]. Furthermore, per full-time equivalent (FTE) person employed on the project, a mean of 1.31 hits (90% range 0.48-2.42) is expected. This model system allows the number of expected hits to be calculated when developing a natural product library for a therapeutic target. There is an opportunity to create a natural product library from New Zealand endemic terrestrial flora. This model is scalable to other geographic areas as well as to other therapeutic targets and screening systems.
Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
Authors: Dang Yalong , Waxman Susannah , Wang Chao , Jensen Adrianna , Loewen Ralitsa T , Bilonick Richard A , Loewen Nils A
Published: January 2018

Objective: Trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might represent a novel therapeutic breakthrough. Various decellularized TM scaffolds were developed by ablating existing cells with suicide gene therapy or saponin, but always with incomplete cell removal or dissolve the extracellular matrix. We hypothesized that a chemical-free, freeze-thaw method would be able to produce a fully decellularized TM scaffold for cell transplantation.

Materials and Methods: We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion and pressure transduction system within two hours of sacrifice. After they stabilized for 72 hours, eight eyes each were assigned to freeze-thaw (F) ablation (-80°C×2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The trabecular meshwork was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture medium for 180 hours. We assessed histological changes by hematoxylin and eosin staining. TM cell viability was evaluated with a calcein AM/propidium iodide (PI) assay. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with 5 degrees of freedom.

Results: F and S experienced a similar IOP reduction by 30% from baseline (P=0.64). IOP reduction of about 30% occurred in F within 24 hours and in S within 48 hours. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calcein staining in F in contrast to numerous PI-labeled dead TM cells and calcein-labeled viable TM cells in S.

Conclusion: We developed a rapid TM ablation method that uses cyclic freezing that is free of biological or chemical agents and able to produce a decellularized TM scaffold with preserved TM excellular matrix in an organotypic perfusion culture.
How developers debug
Authors: Beller Moritz , Spruit Niels , Zaidman Andy
Published: January 2018

Debugging software is an inevitable chore, often difficult and more time-consuming than expected, giving it the nickname the “ dirty little secret of computer science.” Surprisingly, we have little knowledge on how software engineers debug software problems in the real world, whether they use dedicated debugging tools, and how knowledgeable they are about debugging. This study aims to shed light on these aspects by following a mixed-methods research approach. We conduct an online survey capturing how 176 developers reflect on debugging. We augment this subjective survey data with objective observations from how 458 developers use the debugger included in their Integrated Development Environments (IDEs) by instrumenting the popular ECLIPSE and INTELLIJ IDEs with our purpose-built plugin WATCHDOG 2.0. To better explain the insights and controversies obtained from the previous steps, we followed up by conducting interviews with debugging experts and regular debugging users. Our results indicate that the the IDE-provided debugger is not used as often as expected, since “printf debugging” remains a feasible choice for many programmers. Furthermore, both knowledge and use of advanced debugging features are low. Our results call to strengthen hands-on debugging experience in Computer Science curricula and can and have already influenced the design of modern IDE debuggers.
Rapid learning curve assessment in an ex vivo training system for microincisional glaucoma surgery
Authors: Dang Yalong , Waxman Susannah , Wang Chao , Parikh Hardik A , Bussel Igor I , Loewen Ralitsa T , Xia Xiaobo , Lathrop Kira L , Bilonick Rick , Loewen Nils A
Published: January 2018

Purpose: Microincisional glaucoma surgeons operate in a highly confined space, making it difficult to learn by observation or assistance alone. We hypothesized that an ex vivo model would allow for better refinement of technique, quantification of progress, and computation of a learning curve.

Methods: Seven trainees without angle surgery experience performed nine ab interno trabeculectomies in pig eyes (n=63) after preparing with training slides and videos. Trainees placed the eyes on a tiltable mannequin head, visualized the trabecular meshwork gonioscopically through an ophthalmic microscope, and removed it by trabectome-mediated ablation. An expert surgeon observed, guided, and rated the procedure using an Operating Room Score (ORS). The extent of accessed outflow beds was estimated with canalograms using fluorescent microspheres. Data was fit using mixed effect models.

Results: ORS reached a half-maximum on an asymptote after only 2.5 eyes. Surgical time decreased by 0.9 minutes per eye in linear fashion. The ablation arc followed an asymptotic function with a half-maximum inflection point after 5.3 eyes. The mean ablation arc improved from 73 to 135 degrees. Canalograms revealed that this progress did not correlate well with improvement in outflow instead suggesting that about 30 eyes are needed for true mastery.

Conclusion: This inexpensive pig eye model provides a safe and effective training model for ab interno trabeculectomy and allows for quantification of outcomes. Trainees without prior angle surgery experience improved quickly. Actual outflow improvements progressed at a slower rate, which serves as a reminder to remain humbly committed to training.
The first reported ceratopsid dinosaur from eastern North America (Owl Creek Formation, Upper Cretaceous, Mississippi, USA)
Authors: Farke Andrew A. , Phillips George E.
Published: January 2018

Ceratopsids (“horned dinosaurs”) are known from western North America and Asia, a distribution reflecting an inferred subaerial link between the two landmasses during the Late Cretaceous. However, this clade was previously unknown from eastern North America, presumably due to limited outcrop of the appropriate age and depositional environment as well as the separation of eastern and western North America by the Western Interior Seaway during much of the Late Cretaceous. A dentary tooth from the Owl Creek Formation (late Maastrichtian) of Union County, Mississippi, represents the first reported occurrence of Ceratopsidae from eastern North America. This tooth shows a combination of features typical of Ceratopsidae, including a double root and a prominent, blade-like carina. Based on the age of the fossil, we hypothesize that it is consistent with a dispersal of ceratopsids into eastern North America during the very latest Cretaceous, presumably after the two halves of North America were reunited following the retreat of the Western Interior Seaway.
Statistical heartburn: An attempt to digest four pizza publications from the Cornell Food and Brand Lab
Authors: van der Zee Tim , Anaya Jordan , Brown Nicholas J L
Published: January 2018

We present the initial results of a reanalysis of four articles from the Cornell Food and Brand Lab based on data collected from diners at an Italian restaurant buffet. On a ﬁrst glance at these articles, we immediately noticed a number of apparent inconsistencies in the summary statistics. A thorough reading of the articles and careful reanalysis of the results revealed additional problems. The sample sizes for the number of diners in each condition are incongruous both within and between the four articles. In some cases, the degrees of freedom of between-participant test statistics are larger than the sample size, which is impossible. Many of the computed F and t statistics are inconsistent with the reported means and standard deviations. In some cases, the number of possible inconsistencies for a single statistic was such that we were unable to determine which of the components of that statistic were incorrect. We contacted the authors of the four articles, but they have thus far not agreed to share their data. The attached Appendix reports approximately 150 inconsistencies in these four articles, which we were able to identify from the reported statistics alone. We hope that our analysis will encourage readers, using and extending the simple methods that we describe, to undertake their own efforts to verify published results, and that such initiatives will improve the accuracy and reproducibility of the scientiﬁc literature.
Collaborative research: about licensing, waiving, and ownership
Authors: Willighagen Egon
Published: January 2018

Research collaborations are hampered by copyright law. While these laws are aimed at solving sustainability of writing and later other creative processes, and nowadays knowledge too, the make it harder in a time where research is funded with on temporary projects. This article discusses some of the aspects involved, though the legal foundations are only minimally brought up. One critical aspect is the role of consortium agreements. It also outlines how open licenses can simplify international research, particularly when multiple research projects are involved and when projects have ended.