bluuebunny/crossref_metadata_2025_split huggingface dataset:
How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China?
Authors: Hou Lin , Hou Sijia 
Published: January 2018

Background. Restoration of degraded forest ecosystem is crucial for regional sustainable development. To protect the country’s fragile and fragmented environment, the Chinese government has initiated an ecological engineering, the Natural Forest Protection Program in seventeen provinces in China since 1998. Fully hillside-closed forest protection (vegetation restoration naturally without any artificial disturbance) was one of vital measures of the Natural Forest Protection Program applied national wide. Whether plant diversity, biomass and age structure of dominant tree species and soil nutrients in protected stands may become better with increase of protected period are still open problems.
Methods. We investigated community diversity, biomass of dominant tree species, age structures, and analyzed soil chemical properties of a Pinus tabulaeformis population at protected sites representing different protected ages at Huanglongshan Forest Bureau on the Loess Plateau, Shaanxi, China.
Results. Plant species richness of Pinus tabulaeformis community was significantly affected (p<0.05) by forest protection and the effect attenuated with protection age.Shannon evenness index of plant species generally increased with protection age. Stands protected for 45 years had the highest tree biomass and considerable natural regeneration capacity. Contents of organic carbon, available phosphorus and available potassium in top soil increased in protected stands less than 45 years, however decreased significantly thereafter. Long-term forest protection also decreased content of mineral nitrogen in top soil.
Discussion. We found that richness of shrubs and herbs was significantly affected by forest protection, and evenness indices of tree, shrub and herb increased inconsistently with protected ages. Forest protection created more complex age structures and tree densities with increasing age of protection. Content of soil mineral nitrogen at 0-20 cm soil depth showed a decreasing trend in stands of up to 30 years. Soil available phosphorus and potassium contents were higher in stands with greater proportions of big and middle trees. Long-term protection (> 45 years) of Pinus tabulaeformisstand in southeast Loess Plateau, China, may be associated with decreasing plant species richness, proportion of medium to large trees, dominant biomass of Pinus tabulaeformis and soil nutrients.
Effect of light on aggregational behavior of planarian Dugesia tigrina
Authors: Lee Jaemin 
Published: January 2018

Introduction. Planarians are renowned for their regenerative ability due to pluripotent stem cells, as well as their peculiar photophobic response. However, few facts are known about their aggregational behavior. This study aims to reveal the effect of light on aggregational behavior. Reynierse (1966) suggested that light has a negative effect on the formation of aggregations. However, one of his objectives for aggregational behavior was inappropriate. This study reevaluated the effect of existence of light on aggregational behavior, as well as ascertained the effect of wavelength on the formation of aggregations.
Methods. In this study, the ratio of individuals participating in aggregations was measured as a criterion to determine aggregational behavior. Aggregational behavior was measured after two hours from the initial exposure to different light sources. The behaviors under white LED light and under shade were compared, as well as the behaviors under five different light sources: infrared lamp, red, green, blue LED, and ultraviolet lamp.
Results. The existence of light interfered the formation of aggregations (t-test, p < 0.0001), which supports the former study of Reynierse. Also, aggregational behavior differed under different wavelengths (ANOVA, p < 0.0001). Except for the infrared light which emitted a wide range of wavelengths, the behavior showed hierarchy: decreasing aggregational behavior in accordance with decreasing wavelength. UV light has the most significant negative effect on the formation of aggregations.
Discussion. Exposure to light caused negative effects on performing aggregational behavior. Participation in aggregations appears to be influenced by photophobic response, especially under lights of short wavelength. Disintegrating aggregations under exposure to lights can potentially bring evolutionary benefit. This behavior possibly makes the aggregating planarians altogether exposed to a higher risk or predation, considering that they lack defense mechanisms. Planarians can lower the risk and continue the populations by disintegrating the aggregational behavior under the existence of UV and lights of higher wavelength, which are indicatives of daytime. Understanding aggregational behavior of animals of a lower order would give better insight on general herding behavior, and potentially help interpreting more complex behaviors of higher animals.
Fertilization and stocking of unmanaged ponds through temporal plankton community structure map (PCSM): A nascent concept in aquaculture planning
Authors: Roy Koushik 
Published: January 2018

Background: This paper deals with a non-conventional approach called PCSM model. It was developed to aid in horizontal expansion of aquaculture through utilization of unmanaged ponds for modified extensive aquaculture. This model applies to small lentic water bodies like ponds (<10 ha area) where plankton count and limnological parameters are naturally within permissible range for fish culture or survival. It can only help in – ‘modified extensive aquaculture’ by increasing the abundance of plankton groups that are most preferred. This is only applicable for culturing planktophagus fishes.
Methods: PCSM incorporates annual plankton community dynamics (data) of some representative ‘unmanaged’ ponds of the region. Only the dynamics of top two highly palatable and highly preferable Phytoplankton (Chlorophyceae and Bacillariophyceae) and Zooplankton (Rotifera and Copepoda) groups for Indian Major Carps were focused upon. The monthly composition of each plankton group in each pond of the region was averaged and plotted into a graphical model called Multiple Spline Curve with 5% padding using SigmaPlot.
Results: The model here has been developed in reference to pond based polyculture of 3 Indian Major Carps (Catla catla, Labeo rohita and Cirrhinus mrigala), which is still a dominant practice in the unmanaged freshwater ponds in India. The model can help in deciding two things – Fertilization timing (PCSM: Fertilization Module) and Stocking time (PCSM: Stocking Module). It is region specific and presently developed for Raipur district of Chhattisgarh, India.
Discussions: Through PCSM, effective pond fertilization period is 7 months out of 12 (April, June, August, September, October, December and February). Moreover, year round multiple stocking multiple harvesting based fish culture can be ensured in unmanaged pond through PCSM guided stocking schedule (June, August, November and December).
On the connection between supersaturation in the upper airways and «humid-rainy» and «cold-dry» seasonal patterns of influenza
Authors: Ishmatov Aleksandr N 
Published: January 2018

We have originally shown for the first time the two different climatic patterns of seasonality of influenza and common colds have an only one common “link”. It is the effect of supersaturation and condensational growth in the upper airways which occurs under specific environmental conditions when flu seasons take place in the tropical/subtropical and temperate regions.
We have found that under climatic conditions which are peculiar to the seasonal patterns of influenza and common colds (“humid-rainy” and “cold-dry”) the effect of supersaturation and condensational growth may be additional factor/reason leading to the next:
- dramatic rise of deposition rate of infectious agents from inhaled air in the upper airways;
- additional acidification of epithelial lining fluid in the local areas of the respiratory tract, and, as a result, may lead to destructive impacts on host cells and weakening of the defense mechanisms of the airways;
- additional affecting on the critical local cooling and reducing (as a consequence) the antiviral immune response of the airway epithelial cells.
Thus, the effect of supersaturation and condensational growth in the upper airways can act as a common trigger for influenza, common colds and other respiratory infection in both mid-latitudes and in the tropics/subtropics.
Probability that p-value provides misleading evidence cannot be controlled by sample size
Authors: Grendar Marian , Judge George G 
Published: January 2018

A measure of statistical evidence should permit the sample size determination so that the probability M of obtaining (strong) misleading evidence can be held as low as desired. On this desideratum the p-value fails completely, as it leads either to an arbitrary sample size if M >= 0.01 or no sample size at all, if M < 0.01.
Unlike the p-value, the ratio of likelihoods, the ratio of posteriors, as well as the Bayes Factor, permit controlling the probability of misleading evidence by the sample size.
Factors influencing healthcare provider respondent fatigue answering a globally administered in-app survey
Authors: O'Reilly-Shah Vikas N 
Published: January 2018

Background: Respondent fatigue, also known as survey fatigue, is a common problem in the collection of survey data. Factors that are known to influence respondent fatigue include survey length, survey topic, question complexity, and open-ended question type. There is a great deal of interest in understanding the drivers of physician survey responsiveness due to the value of information received from these practitioners. With the recent explosion of mobile smartphone technology 7, it has been possible to obtain survey data from users of mobile applications (apps) on a question-by-question basis. We obtained basic demographic survey data as well as survey data related to an anesthesiology-specific drug called sugammadex and leveraged nonresponse rates to examine factors that influenced respondent fatigue.
Methods: Primary data were collected between December 2015 and February 2017. Surveys and in-app analytics were collected from global users of a mobile anesthesia calculator app. Key independent variables were user country, healthcare provider role, rating of importance of the app to personal practice, length of time in practice, and frequency of app use. Key dependent variable was the metric of respondent fatigue.
Results: Provider role and World Bank country income level were predictive of the rate of respondent fatigue for this in-app survey. Importance of the app to the provider and length of time in practice were moderately associated with fatigue. Frequency of app use was not associated. This study focused on a survey with a topic closely related to the subject area of the app. Respondent fatigue rates will likely change dramatically if the topic does not align closely,
Discussion: Although apps may serve as powerful platforms for data collection, responses rates to in-app surveys may differ on the basis of important respondent characteristics. Studies should be carefully designed to mitigate fatigue as well as powered with the understanding of the respondent characteristics that may have higher rates of respondent fatigue.
Cross-institutional evaluation of a mastoidectomy assessment instrument
Authors: Kerwin Thomas , Hittle Brad , Stredney Don , De Boeck Paul , Wiet Gregory 
Published: January 2018

Objective: The objective of this work is to obtain validity evidence for an evaluation instrument used to assess the performance level of a mastoidectomy. The instrument has been previously described and had been formulated by a multi-institutional consortium.
Design: Mastoidectomies were performed on a virtual temporal bone system and then rated by experts using a previously described 15 element task-based checklist. Based on the results, a second, similar checklist was created and a second round of rating was performed.
Setting: Twelve otolaryngological surgical training programs in the United States.
Participants: 65 mastoidectomy performances were evaluated coming from 37 individuals with a variety of temporal bone dissection experience, from medical students to attending physicians. Raters were attending surgeons from 12 different institutions.
Results: Intraclass correlation (ICC) scores varied greatly between items in the checklist with some being low and some being high. Percentage agreement scores were similar to previous rating instruments. There is strong evidence that a high score on the task-based checklist is necessary for a rater to consider a mastoidectomy to be performed at the level of an expert but a high score is not a sufficient condition.
Conclusions: Rewording of the instrument items to focus on safety does not result in increased reliability of the instrument. The strong result of the Necessary Condition Analysis suggests that going beyond simple correlation measures can give extra insight into grading results. Additionally, we suggest using a multiple point scale instead of a binary pass/fail question combined with descriptive mastery levels.
Upper Karoo vertebrate assemblages (Late Triassic/Early Jurassic) of the Lake Kariba region, Zimbabwe
Authors: Barrett Paul M , Broderick Tim , Chapelle Kimberley , Choiniere Jonah , Edwards Steve , Munyikwa Darlington , Viglietti Pia , Zondo Michel 
Published: January 2018

Southern Africa provides critical information on Late Triassic–Early Jurassic terrestrial tetrapod faunas. Most of the localities in this region are in South Africa and Lesotho, but preliminary work in Zimbabwe has revealed significant potential. Early Jurassic Zimbabwean localities have yielded the basal sauropodomorph Massospondylus, the early sauropod Vulcanodon and theropod material. Late Triassic localities are also known, but have yielded only fragmentary specimens thus far.
In early 2017, a joint South African-Zimbabwean-UK team conducted fieldwork in the upper Karoo-aged deposits along the shores of Lake Kariba, northern Zimbabwe (Mid-Zambesi Basin). We relocated the Vulcanodon type locality on Island 126/127 and found that, contrary to previous reports suggesting a Toarcian age, the quarry was in a horizon pre-dating the onset of Drakensburg volcanism (= Batoka Basalts). It is situated instead within the earlier Lower Jurassic Forest Sandstone. This indicates that Vulcanodon is 10–15 million years older than thought previously, recalibrating several nodes within Sauropoda and indicating extensive overlap between true sauropods and 'prosauropods'.
Other new vertebrate localities show that sauropodomorphs are present in the Forest Sandstone and upper Tashinga (Late Triassic) formations, but a grey mudstone facies within the Pebbly Arkose Member of the latter unit yields a more aquatic fauna, including lungfish and phytosaurs, but lacking sauropodomorphs. The phytosaur occurrence is the first in Africa south of the Sahara. Faunal and sedimentological evidence indicates that the Late Triassic and Early Jurassic sites in this region were deposited under more mesic environments than their lateral equivalents in South Africa.
DeepBlueR: Large-scale epigenomic analysis in R
Authors: List Markus , Albrecht Felipe , Bock Christoph , Lengauer Thomas 
Published: January 2018

Epigenetic research focuses on understanding non-inheritable factors influencing gene regulation and covers various cellular mechanisms such as DNA methylation, histone modification, miRNA function and transcription factor binding sites. Recent advances in high-throughput profiling technologies allow for systematically collecting data on each of these mechanisms in large-scale experiments. These efforts are fostered and concerted by international collaborations, such as the International Human Epigenome Consortium (IHEC) and its members. As a result of these collaborations, researchers can exploit massive amounts of publicly available epigenomic data on dozens of cell types, cell lines and tissues. Access to these data is streamlined by existing data portals and, in principle, allows for answering important biomedical questions.
However, working with such data requires a suitable computational infrastructure not accessible ubiquitously. This creates a serious bottleneck in research and, as a result, data from these costly experiments are currently underused. To address this issue, we developed a new web resource, the DeepBlue Epigenomic Data Server to provide access to more than 40,000 experimental files from four major epigenome projects: ENCODE, ROADMAP, BLUEPRINT, the German Epigenome Program DEEP, the Canadian CEEHRC, and the Japanese CREST.
A common challenge with this resources is that researchers are typically interested in a small fraction of the available epigenomic data to answer specific biomedical questions. Using a typical data repository to solve this task would require the user to download several files amounting to gigabytes of data that subsequently need to be filtered locally. In addition, it is often important to perform memory- and cpu-intensive operations to transform or aggregate these data, while the necessary computational resources are not accessible to every user. Therefore, the DeepBlue Data Server offers features beyond those of a centralized epigenomic data repository. It has a comprehensive programmatic interface (API) to enable users to perform complex data operations, such as searching, selecting, filtering, summarizing, and downloading of epigenomic data of interest. These operations can be combined into custom workflows, thus offering nearly the same degree of flexibility as a local programming environment.
Here, we present DeepBlueR, a new R/Bioconductor package that enables users to engage with the DeepBlue server in a seamless fashion from within the R environment. DeepBlueR mirrors all DeepBlue data operations as R commands and provides additional features for compressing, downloading and transforming aggregated epigenomic data into suitable R data structures. A mechanism for local caching guarantees that complex scripts can be executed without the need to download previously requested data from the server.
GenHap: A novel computational method based on genetic algorithms for haplotype assembly
Authors: Tangherloni Andrea , Spolaor Simone , Rundo Leonardo , Nobile Marco S , Merelli Ivan , Cazzaniga Paolo , Besozzi Daniela , Mauri Giancarlo , Liò Pietro 
Published: January 2018

The process of inferring a full haplotype of a cell is known as haplotyping, which consists in assigning all heterozygous Single Nucleotide Polymorphisms (SNPs) to exactly one of the two chromosomes. In this work, we propose a novel computational method for haplotype assembly based on Genetic Algorithms (GAs), named GenHap. Our approach could efficiently solve large instances of the weighted Minimum Error Correction (wMEC) problem, yielding optimal solutions by means of a global search process. wMEC consists in computing the two haplotypes that partition the sequencing reads into two unambiguous sets with the least number of corrections to the SNP values. Since wMEC was proven to be an NP-hard problem, we tackle this problem exploiting GAs, a population-based optimization strategy that mimics Darwinian processes. In GAs, a population composed of randomly generated individuals undergoes a selection mechanism and is modified by genetic operators. Based on a quality measure (i.e., the fitness value), inspired by Darwin’s “survival of the fittest” laws, each individual is involved in a selection process.
Our preliminary experimental results show that GenHap is able to achieve correct solutions in short running times. Moreover, this approach can be used to compute haplotypes in organisms with different ploidity. The proposed evolutionary technique has the advantage that it could be formulated and extended using a multi-objective fitness function taking into account additional insights, such as the methylation patterns of the different chromosomes or the gene proximity in maps achieved through Chromosome Conformation Capture (3C) experiments.
Developmental effects of environmental light on male nuptial coloration in Lake Victoria cichlid fish
Authors: Wright Daniel S. , Rietveld Emma , Maan Martine E. 
Published: January 2018

Background. Efficient communication requires that signals are well transmitted and perceived in a given environment. Natural selection therefore drives the evolution of different signals in different environments. In addition, environmental heterogeneity at small spatial or temporal scales may favour phenotypic plasticity in signaling traits, as plasticity may allow rapid adjustment of signal expression to optimize transmission. In this study, we explore signal plasticity in the nuptial coloration of Lake Victoria cichlids, Pundamilia pundamilia and Pundamilia nyererei. These two species differ in male coloration, which mediates species-assortative mating. They occur in adjacent depth ranges with different light environments. Given the close proximity of their habitats, overlapping at some locations, plasticity in male coloration could contribute to male reproductive success but interfere with reproductive isolation.
Methods. We reared P. pundamilia, P. nyererei, and their hybrids under light conditions mimicking the two depth ranges in Lake Victoria. From photographs, we quantified the nuptial coloration of males, spanning the entire visible spectrum. In experiment 1, we examined developmental colour plasticity by comparing sibling males reared in each light condition. In experiment 2, we assessed colour plasticity in adulthood, by switching adult males between conditions and tracking coloration for 100 days.
Results. We found that nuptial colour in Pundamilia did respond plastically to our light manipulations, but only in a limited hue range. Fish that were reared in light conditions mimicking the deeper habitat were significantly greener than those in conditions mimicking shallow waters. The species-specific nuptial colours (blue and red) did not change. When moved to the opposing light condition as adults, males did not change colour.
Discussion. Our results show that species-specific nuptial colours, which are subject to strong divergent selection by female choice, are not plastic. We do find plasticity in green coloration, a response that may contribute to visual conspicuousness in darker, red-shifted light environments. These results suggest that light-environment-induced plasticity in male nuptial coloration in P. pundamilia and P. nyererei is limited and does not interfere with reproductive isolation.