bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control study of short-term after effect in diving exposure related pulmonary ventilation function
Authors: Cheng Hua 
Published: January 2018

Objective: Ventilation attenuation often happened in professional divers due to long-term cumulative effects in diving exercises. By case-control experiments, we observed the immediate effects of pulmonary ventilation before and after the exposure of 12m-depth underwater for 20 min to discuss the relationships between the short-term and long-time effects caused by diving environment.
Methods: Participants were randomly assigned into the Experimental Group (EG) who stayed for 20 min under 12-m water environment or the Control Group (CG) who stayed in hyperbaric chamber under the pressure of 2.2ATA. Pulmonary ventilation function parameters including VC, FVC, MVV and MV were detected respectively before and after hyperbaric exposure by the Spirometer. Immediate effects of pulmonary ventilation before and after diving were compared by paired t test to reveal the different influence caused by environmental pressure.
Results: The value of VC appears to rise while the MV, MVV were detected decreased after the exposure of 2.2ATA of environment pressure for 20min in the two groups. VC increased more significantly in the CG (t=-1.26, p=0.23) after hyperbaric exposure, that leads to the FEV1.0%t (=FEV1.0/VC %) increase in EG (t=-0.73, p=0.48) while decrease in CG (t=0.42, p=0.17). The same trend in VC, MV and MVV after high pressure exposure in the two groups mainly due to the effect of common factors –the pressure. In addition to the impact of the pressure itself, EG members also face diving related immersion effect, influence of diving equipment load and water under low temperature. The FVC is detected decreased in EG (t=1.21, P =0.25) while it increased in CG (t=-0.42, P =0.68)，but the differences are not significant and couldn’t affect the measured FEV1.0% (=FEV1.0/FVC %) values showed both increasing in EG(t=-1.48, P =0.16) and in CG(t=-0.23, P =0.82). The expiratory flow rate including PEF, FEF25-75, MEF75, MEF50 increased in EG (t are -0.72, -0.69, -0.87 and -0.36 respectively with P all greater than 0.05) while decreased in CG (t are 1.67, 0.50, 1.53 and 0.71 respectively with P all greater than 0.05). MEF25 is the expiratory flow index of not affected by respiratory muscle force and the measured values of MEF25 increased in the EG (t=-0.68, P =0.51) and in the CG (t=-0.36, P =0.72).
Conclusion: Water immersion and water temperature during diving exposure could cause and accelerate hemodynamic changes in pulmonary circulation induced pulmonary interstitial edema and led to the increase of external respiratory work. Instant effects of diving exposure in the study are quite consistent with the long-term cumulative effect of professional divers in previous research, which is FVC reduced because small airway become narrower. The results illustrate even the small depth of short-range diving exercise have definite influences on pulmonary ventilation, which mainly comes from the environmental factor but not the pressure increases.
De novo gene evolution: How do we transition from non-coding to coding?
Authors: Ruiz-Orera Jorge , Villanueva-Cañas José Luis , Blevins William , Albà M.Mar 
Published: January 2018

Recent years have witnessed the discovery of protein–coding genes which appear to have evolved de novo from previously non-coding sequences. This has changed the long-standing view that coding sequences can only evolve from other coding sequences. However, there are still many open questions regarding how new protein-coding sequences can arise from non-genic DNA.
Two prerequisites for the birth of a new functional protein-coding gene are that the corresponding DNA fragment is transcribed and that it is also translated. Transcription is known to be pervasive in the genome, producing a large number of transcripts that do not correspond to conserved protein-coding genes, and which are usually annotated as long non-coding RNAs (lncRNA). Recently, sequencing of ribosome protected fragments (Ribo-Seq) has provided evidence that many of these transcripts actually translate small proteins. We have used mouse non-synonymous and synonymous variation data to estimate the strength of purifying selection acting on the translated open reading frames (ORFs). Whereas a subset of the lncRNAs are likely to actually be true protein-coding genes (and thus previously misclassified), the bulk of lncRNAs code for proteins which show variation patterns consistent with neutral evolution. We also show that the ORFs that have a more favorable, coding-like, sequence composition are more likely to be translated than other ORFs in lncRNAs. This study provides strong evidence that there is a large and ever-changing reservoir of lowly abundant proteins; some of these peptides may become useful and act as seeds for de novo gene evolution.
Maxent-directed field surveys identify new populations of narrowly endemic habitat specialists
Authors: Rhoden Cody M , Peterman William E , Taylor Christopher A 
Published: January 2018

Background. Rare or narrowly endemic organisms are difficult to monitor and conserve when their total distribution and habitat preferences are incompletely known. One method employed in determining distributions of these organisms is species distribution modeling (SDM).
Methods. Using two species of narrowly endemic burrowing crayfish species as our study organisms, we sought to ground validate Maxent, a commonly used program to conduct SDMs. We used fine scale (30 m) resolution rasters of pertinent habitat variables collected from historical museum records in 2014. We then ground validated the Maxent model in 2015 by randomly and equally sampling the output from the model.
Results. The Maxent models for both species of crayfish showed positive relationships between predicted relative occurrence rate and crayfish burrow abundance in both a Receiver Operating Characteristic and generalized linear model approach. The ground validation of Maxent led us to new populations and range extensions of both species of crayfish.
Discussion. We conclude that Maxent is a suitable tool for the discovery of new populations of narrowly endemic, rare habitat specialists and our technique may be used for other rare, endemic organisms.
Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing
Authors: Csizmár Nikolett , Mihók Sándor , Jávor András , Kusza Szilvia 
Published: January 2018

Background. Hungarian draft is a horse breed with a recent mixed ancestry. The interest in their conservation and characterization has increased over the last few years. It was developed in the 1920s by crossing local mares with draught horses imported from France and Belgium. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks.
Methods. To genetically characterize the breed and to set up the basis for a conservation programme, in this present study a hypervariable region of the mithocrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed.
Results. One hundred and sixty-four haplotypes were revealed. Thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd=0.954±0.004; π=0.028±0.0004) were identified in Hungarian populations, although they were higher within than among the total number of breeds (Hd =0.972±0.002; π=0.03097±0.002). Fourteen of the previously observed seventeen haplogroups were detected.
Discussion. Our samples showed a large intra- and interbreed variation. There were no clear clustering on the median joining tree. The overall information given in this work led us to consider that the genetic scenario of this breed is more likely to be due to ‘ancestrally’ different genetic backrounds. This study could contribute to the development of a detailed breeding plan of Hungarian draft horse and help to formulate its genetic conservation plan, with the aim of increasing the population size, but avoiding inbreeding while, on the other hand, also facilitating genetic exchange among the populations.
Positive association of supersaturation effects in the human airways with influenza activity in subtropical climate: influenza seasons in Okinawa (2007-2012) – New method for analyzing and forecasting (first preliminary results)
Authors: Ishmatov Aleksandr N 
Published: January 2018

There are many theories of the seasonality of influenza for different climatic zones. But none of the known theories provides a clear explanation, especially for the tropical and subtropical climate.
Here we have originally analyzed the association/connection of activity of seasonal influenza in Okinawa (subtropical zone) with the probability of occurring of supersaturation in the human airways when inhaling environmental air under specific weather conditions.
We have shown for the first time that the effects of supersaturation in the human airways may be associated with main representative peaks of intensity/activity of influenza in Okinawa in the period of observation from Jan 2007 until Dec 2012 including 2009 pandemic.
Our observation is the first one which clearly shows in the practice that the effect of supersaturation in the airways can be used for understanding and forecast the influenza activity in subtropical and tropical zones. Because the effect of supersaturation may lead to an additional risk of acidification of epithelial lining fluid in the local areas of the respiratory tract and to additional risk of deposition of infectious agents from inhaled air in the upper airways.
Upper Karoo vertebrate assemblages (Late Triassic/Early Jurassic) of the Late 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.
Human-Borg dynamics during a cybernetic alien invasion
Authors: Pabico Jaderick P 
Published: January 2018

We propose a series of ODE systems to model the various dynamics of human-Borg interaction during a Borg invasion. These models, progressively developed one after the other, could provide humanity and other peace-loving intergalactic species the necessary mathematical tools to develop survival strategies in the event of future alien invasion. The Borg is a race of technologically-advanced cybernetic aliens and acts as a very powerful antagonist against the peace-loving human species in various Star Trek sci-fi story lines. Cybernetics, also called cyborgs, are organic individuals implanted with intelligent electromechanical devices for the purpose of increasing the individuals' efficiency by several degrees (e.g., strength, speed, and intelligence) but in the expense of procreation. Thus, the "parasitic" Borg needs to assimilate other species in an epidemiological manner for the survival of their own race.
In these models, humans can be transformed into one of six types depending on their reaction on or resistance to Borg assimilation. These are Susceptible (\(S\)), Captured (\(C\)), Assimilated (\(A\)), Rescued (\(R\)), Educated (or Rehabilitated, \(E\)), and Defiant (\(D\)). {\em Susceptible} humans can be captured and then assimilated into being a Borg drone. The remaining humans can rescue those who were captured or assimilated. Once rescued, they will undergo rehabilitation after which they either end up (again) susceptible to or strongly defiant from being captured and assimilated.
We start by describing the SCA model which has the same (analytical and/or numerical) solution to the Susceptible-Exposed-Infected model in epidemiology. Then we move on to the SCAR model which incorporates the tendency of humans to fight back by rescuing the captured or assimilated. SCARE further models the propensity of humans to educate (or rehabilitate) those whom they have rescued. Finally, we present the SCARED model which describes the natural inclinations of humans to either "relapse" to being susceptible to or grow being defiant against assimilation after undergoing rehabilitation. The numerical solutions to all these models will be presented using a popular yet simple computer software.
The SCA, SCAR, and SCARE models are reduction from the SCARED model when all the respective coefficients of the quantities not present in the reduced model are zero. In other words, SCA reduces from SCAR; SCA and SCAR both reduce from SCARE; and SCA, SCAR, and SCARE all reduce from SCARED. The bottomline is SCA \(\subset\) SCAR \(\subset\) SCARE \(\subset\) SCARED. The dynamics in the general SCARED model is governed by the system of ODEs shown (as a teaser) in the attached addendum.
Self-efficacy, relationship satisfaction, and social support: The quality of life of maternal caregivers of children with type 1 diabetes
Authors: Thorsteinsson Einar B , Loi Natasha M , Rayner Kylie 
Published: January 2018

Objectives. To examine maternal functioning and wellbeing as important aspects of a family’s adaptation to chronic paediatric conditions, in particular, children with diabetes.
Method. This cross-sectional study investigated the difference between the perceived quality of life of mothers of children with diabetes (n=63) and mothers of children without diabetes (n=114). The study also examined the role of self-efficacy, relationship satisfaction, number of social support providers, and satisfaction with social support in predicting quality of life.
Results. Mothers who had a child with diabetes had lower quality of life measured by general health, vitality, social functioning, role-emotional, and mental health than mothers that did not have a child with diabetes. Self-efficacy, relationship satisfaction, and social support were significant predictors of quality of life (mental health domain).
Conclusion. In order to enhance their psychological wellbeing, mothers of children with diabetes require adequate psychosocial support. Other implications for research and potential interventions are discussed.
Bored bones from the terrestrial middle Cretaceous Kem-Kem beds of southeast Morocco
Authors: Shears-Ozeki Christina 
Published: January 2018

During the last two decades, bioerosion of bone has become more widely investigated, with the earliest identified coming from mid-Triassic strata. Bioerosion has even been identified in bone fragments from a Jurassic theropod coprolite. Although the effects of this destructive process can lead to a loss of important information form the fossil record, understanding of bone bioerosion may be useful for identifying palaeoclimatic conditions in a variety of ancient fluvial settings.
Recent examination of bones of terrestrial fauna (mostly dinosaurs) form the middle Cretaceous Kem-Kem beds (?Albian-late Cenomanian) of southeast Morocco identified several distinctive bioerosional traces (surface scratches, bite marks [up to 10cm long] and borings in the form of channels and oval shaped chambers ~5mm diameter) from indeterminate producers. One heavily bored specimen suggests successive infestation during prolonged subaerial exposure.
Silicon moulding, thin sections and SEM analysis enabled investigation of the bones to determine the producers responsible, and evaluate their role in the taphonomy of ancient fluvial systems.
The bite marks can be attributed to macro predators/ scavengers, whereas the borings and surface scratches, are comparable to traces produced by recent insects including isopterans and the larvae of coleopterans. Scratches (approximately 1-2mm long) within the chambers and channels were also identified and considered fodinichnia and domichnia in the form of feeding trails and pupation chambers.
Agricultural constraints on microbial resource use and niche breadth in drainage ditches
Authors: Hunting Ellard R , Barmentlo Henrik , Schrama Maarten , van Bodegom Peter , Zhai Yujia , Vijver Martina 
Published: January 2018

Background. Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in organic matter (OM) degradation in natural systems remains poorly understood.
Methods. Here we evaluated effects of differences in organic matter (OM) related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed 1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and 2) how changes in community resource niche breadth translates to the degradation of natural OM.
Results. A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality.
Discussion. Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.
In-silico prediction and modeling of ApxA exotoxins of Actinobacillus pleuropneumoniae: ApxIA, -IIA, -IIIA and -IVA
Authors: Oh Myung Whan , Yoo Han Sang 
Published: January 2018

Background. Actinobacillus pleuropneumonia is a gram-negative bacterium that serves as the major etiological agent for porcine pleuropneumonia, one of critical diseases causing substantial socio-economic losses in swine rearing industry world-wide. Apx exotoxins are the members of RTX-toxin family secreted by gram-negative bacteria that facilitates Type-I Secretion System (T1SS), reported as the major virulence factor in the pathogenesis. This study was conducted to demonstrate successful pre-experimental approach by predicting the tertiary structures of ApxA exotoxins and further characterizing their structural and functional annotations via application of appropriate in silico methods.
Methods. The sequences of ApxA exotoxins were retrieved from the National Centre for Biotechnology Information database (NCBI) for bioinformatics analyses in this study. ApxA exotoxins were subjected to several computational analyses to characterize in different aspects. I-TASSER and Phyre2 servers were used to predict 3-D structures of ApxA toxins which were further validated by ProSA and SAVES servers. Antigenic epitopes of each ApxA exotoxin were predicted using the BepiPred 2.0 program.
Results. Based on predictions on secondary structure compositions, hydropathicity, domain boundaries, tertiary structures and their structural analogs, ApxIA, -IIA and –IIIA shared remarkable resemblance in structural and functional aspects while ApxIVA exhibited distinct and complex characteristics.
Discussion. 3-D modeling of ApxA exotoxins were executed to best interpret the proteins in their structure and functions to gain novel insights of their pathogenesis. The domain-wise interpretation of the proteins indicates the likely roles of each toxin with conjectured antigenic epitopes. The structural and functional annotations suggested in this study via in silico predictive approach may provide insights to prevent and control A. pleuropneumoniae by development of diagnostic methods and vaccine candidates.
Molecular phylogeny of genus Horaglanis (Indian blind catfishes) within Family Clariidae
Authors: Pavan-Kumar Annam 
Published: January 2018

Background: India is one of the mega biodiverse countries with a large number of endemic freshwater fishes. Recently, species of genus Horaglanis (family: Clariidae) have been reported from the southern part of India. Due to their unique morphological adaptations, these enigmatic species have been subjected to phylogenetic studies to understand the evolution of adaptive traits. Further, the taxonomic status of these species has not been verified using molecular data.
Methods: In the present study, secondary data i.e. reported sequences of mitochondrial cytochrome c oxidase subunit I gene was used to estimate the genetic divergence values for 14 species of the family Clariidae. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian Inference methods.
Results: The average genetic divergence value among genera Clarias-Clariallabes-Platyallabes-Dolichallabes-Gymnallabes-Tanganikallabes-Channallabes was 0.082 ± 0.01. However, these genera showed an average divergence value of 0.296±0.02 with genus Horaglanis. In all tree topologies, species of the genus Horaglanis formed a basal group to all other clariids.
Discussion : The higher genetic divergence value between genus Horaglanis and other genera of Clariidae family suggested that genus Horaglanis may belong to a separate sub family. Based on phylogenetic trees, it is evident that species of Horaglanis might have originated early in the evolution of Clariids than other species.