bluuebunny/crossref_metadata_2025 huggingface dataset:
The nonavian theropod quadrate I: standardized terminology and overview of the anatomy, function and ontogeny
Authors: Hendrickx Christophe , Araújo Ricardo , Mateus Octávio
Published: January 2018

By allowing the articulation of the mandible with the cranium, the quadrate of diapsids and most other tetrapods plays an important role morphofunctionally. In Theropoda, its morphology is particularly complex and varies importantly among different clades of nonavian theropods so that the quadrate possesses a strong taxonomic potential. Inconsistencies in the notation and terminology used in discussions of the theropod quadrate anatomy have been noticed, a number of no less than height different terms being sometimes given to a same structure. A standardization list of terms and notation for each quadrate anatomical entity is here proposed, with the goal of facilitating future descriptions of this important cranial bone. An overview of the quadrate function, pneumaticity and ontogeny in nonavian theropods is also given. The quadrate of the large majority of nonavian theropod is akinetic and the diagonally oriented sulcus of the mandibular articulation allowed both rami of the mandible to move laterally when opening the mouth in many of them. Pneumaticity of the quadrate is also present in most of tetanuran clades and the pneumatic chamber, invaded by the quadrate diverticulum of the mandibular arch pneumatic system, was connected to one or several pneumatopores on the medial, lateral, posterior, anterior or ventral sides of the quadrate. Absence of a quadrate foramen in allosauroid embryos and a poor delimitation of mandibular condyles in both embryonic and juveniles tetanurans seems to be ontogenetic features of some theropods. Finally, the numerous morphological differences existing in the quadrates of the two specimens of Shuvuuia deserti, interpreted by some as juvenile and adult individuals, are considered as ontogenetic, taphonomic, and perhaps also taxonomic variations.
Groups, groupoids, and information sources: models of mitochondrial deterioration and aging
Authors: Wallace Rodrick
Published: January 2018

Using mitochondrial free energy delivery rate as a temperature analog, we examine the 'spontaneous symmetry breaking' of the group associated with the error minimization coding scheme related to protein folding, and characterize the phase transition that drives the collapse of normal folding to pathological amyloid production. Similarly, groupoids prove central to the study of analogous, often highly punctuated, 'ground state' failures in far more complex biological processes, adopting Maturana's perspective on the central role of cognition throughout the living state.
Equilibrium switching in nonlinear biological interaction networks with concurrent antagonism
Authors: Rabajante Jomar , Talaue Cherryl O.
Published: January 2018

Concurrent decision-making model (CDM) of interaction networks involving more than two antagonistic components can represent various biological systems, such as gene interaction, species competition and mental perception. The model assumes sigmoid kinetics where every component stimulates itself but concurrently represses the others. Here we prove general dynamical properties of the CDM (e.g., location and stability of steady states) for any dimension of the state space even if the reciprocal antagonism between two components is asymmetric. Significant modifications in parameter values serve as biological regulators for inducing steady state switching by leading a temporal state to escape an undesired equilibrium. Increasing the maximal growth rate and decreasing the decay rate expand the basin of attraction of a steady state with the desired dominant component. Perpetually adding an external stimulus can shut down multi-stability of the system that increases the robustness of the system against stochastic noise. We further show that asymmetric interaction that forms a repressilator-type network generates oscillatory behavior.
Spiraldynamik - intelligent movement
Authors: Wippert Jens
Published: January 2018

Spiraldynamik ® is an anatomically based movement and therapy concept. It was founded by the physiotherapist Yolanda Deswarte, and Dr. med. Christian Larsen. During the time that he was professionally active as a pediatrician, Christian Larsen repeatedly wondered: “is the universal principle of organization, the spiral, also embodied in man?” Observing the babies and toddlers that he worked with inspired him to research further into movement sequences. International interdisciplinary research communities in medicine, physiotherapy, pedagogy, yoga, fitness,sports and dance have been working together researching this question since 1981. Their main preoccupations have been the connections between anatomy, the three-dimensional system and the laws of nature (i.e. gravity), using the spiral as a basic building block. Spatially, the spiral structure dominates as a place saving and stable structure. The temporal dimension of motion is defined by wave movement and rhythm. Time and space are united in the spiral and in dynamism. Coordinated movements are three-dimensional, using the anatomically given corporal structures. Only the three-dimensional joining of the spiral structures throughout our body makes harmonious movement possible. The form of the body’s joints and bones and the arrangement of the ligaments and muscles, indicate the body’s preferred movement and rotation directions. Since a spiral has basically two directions of rotation, it is a matter of turning in the direction set forth by the given structure of the body. This anatomical understanding trains precise three-dimensional movement coordination and permits an unexpected variety of movement to emerge.
Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas
Authors: Timmins-Schiffman Emma , Coffey William D , Hua Wilber , Nunn Brook L , Dickinson Gary H , Roberts Steven B
Published: January 2018

Background. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wide-ranging effects on many aquatic organisms, however the exact mechanisms of the impacts of ocean acidification on many of these animals remains to be characterized.

Methods. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different pCO2 levels for four weeks: 400 µatm (pH 8.0), 800 µatm (pH 7.7), 1000 µatm (pH 7.6), or 2800 µatm (pH 7.3). At the end of 4 weeks a variety of physiological parameters were measured to assess the impacts of ocean acidification: tissue glycogen content and fatty acid profile, shell micromechanical properties, and response to acute heat shock. To determine the effects of ocean acidification on the underlying molecular physiology of oysters and their stress response, some of the oysters from 400 µatm and 2800 µatm were exposed to an additional mechanical stress and shotgun proteomics were done on oysters from high and low pCO2 and from with and without mechanical stress.

Results. At the end of the four week exposure period, oysters in all four pCO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated pCO2. Elevated pCO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with pCO2, with numerous processes significantly affected by mechanical stimulation at high versus low pCO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835).

Discussion. Oyster physiology is significantly altered by exposure to elevated pCO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of pCO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.
Stress, Pain & Sport
Authors: Wippert Pia
Published: January 2018

Stressors in everyday life can entail, along with emotional and behavioral reactions, a whole series of physiological reactions at different systematic levels (endocrinological, metabolic, immunological). This is also a cause for the development of stress-associated illnesses such as cardiovascular disease, cognitive impairment, fatigue syndrome, delayed healing of injuries, and pain syndromes. Current research has focused increasing attention on pain syndromes due to the significant economic harm caused by chronic pain patients. Sports, and especially endurance sports, are well-suited for the psychophysiological reduction of stress. Extreme sports, however, can actually induce stress and result in symptoms related to being overstressed. A good balance between exertion and recovery is therefore very important for elite athletes. The presentation gives an overview about this different topics and measurement methods of stress.
Spatial analysis of United States ethanol production infrastructure vulnerability to flooding
Authors: Chen Yingying , Cuba Nicholas
Published: January 2018

Early-growing season, long duration floods are harmful to the cultivation of maize, the source of 80% of the US bioethanol fuel. Due to the centrality of this industry to US government efforts to bolster domestic energy production, Midwest flooding has implications for US energy production. This paper uses spatial statistics to characterize the spatial distribution of ethanol plants relative to maize production in twelve Midwestern US states which account for approximately 90% of US corn production. County-based territories are delineated for each of the 176 plants in these states, and the total maize production and average annual production are summed for each plant. Multi-decadal flooding data from the Dartmouth Flood Observatory (1982-2007) are used in conjunction with data from the US Department of Agriculture National Agricultural Statistical Service to derive flood risk levels for each plant, and for total production capacity in the region.
Setting the record straight on invasive lionfish control: Culling works
Authors: Côté Isabelle M , Akins Lad , Underwood Elizabeth , Curtis-Quick Jocelyn , Green Stephanie J
Published: January 2018

Indo-Pacific lionfish have invaded large parts of the western Atlantic, Caribbean and Gulf of Mexico, and have already caused measurable declines in native Atlantic reef fauna. Culling efforts are occurring across the region, particularly on coral reefs, to reduce local lionfish abundances. Frequent culling has recently been shown to cause a shift towards more wary and reclusive behaviour by lionfish, which has prompted calls for halting culls. However, the effectiveness of culling per se is not in question. Culling successfully lowers lionfish numbers and has been shown to stabilise or even reverse declines in native prey fish. In fact, partial culling is often as effective as complete local eradication, yet requires significantly less time and effort. Abandoning culling altogether would therefore be seriously misguided and a hindrance to conservation. We offer suggestions for how to design removal programs that minimize behavioural changes and maximize culling success.
GroopM: An automated tool for the recovery of population genomes from related metagenomes
Authors: Imelfort Michael , Parks Donovan , Woodcroft Ben J , Dennis Paul , Hugenholtz Philip , Tyson Gene W
Published: January 2018

Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.
Consistent, comprehensive and computationally efficient OTU definitions
Authors: Rideout Jai Ram , He Yan , Navas-Molina Jose Antonio , Walters William A , Ursell Luke K , Gibbons Sean M , Chase John H , McDonald Daniel , Gonzalez Antonio , Robbins-Pianka Adam , Clemente Jose C , Gilbert Jack , Huse Susan M , Zhou Hong-Wei , Knight Rob , Caporaso J Gregory
Published: January 2018

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to “classic” open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, “classic” open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of “classic” open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by “classic” open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME’s uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME’s OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.
Analysis of Protein Kinase Domain and Tyrosine Kinase or Serine/Threonine Kinase signatures Involved In Lung Cancer
Authors: Barik Manas  Ranjan , Bagga Tripti Kaur , Bhattacharya Anupam , Palaka Bhagath Kumar , Kotapati Kasi Viswanath , Ampasala Dinakara Rao
Published: January 2018

Lung cancer results when normal check and balance system of cell division is disrupted and ultimately the cells divide and proliferate in an uncontrollable manner forming a mass of cells in our body, known as tumor. Frequent mutations in Protein Kinase Domain alter the process of phosphorylation which results in abnormality in regulations of cell apoptosis and differentiation. Tyrosine Protein kinases and Serine/Threonine Protein Kinases are the two broad classes of protein kinases in accordance to their substrate specificity. The study of Tyrosine protein kinase and serine Kinase coding regions have the importance of sequence and structure determinants of cancer-causing mutations from mutation-dependent activation process. In the present study, we analyzed huge amounts of data extracted from various biological databases and NCBI. Out of the 534 proteins that may play a role in lung cancer, 71 proteins were selected that are likely to be actively involved in lung cancer. These proteins were evaluated by employing Multiple Sequence Alignment and a Phylogenetic tree was constructed using Neighbor-Joining Algorithm. From the constructed phylogenetic tree, protein kinase domain and motif study was performed. The results of this study revealed that the presence of Protein Kinase Domain and Tyrosine or Serine/Threonine Kinase signatures in some of the proteins are mutated, which play a dominant role in the pathogenesis of Lung Cancer and these may be addressed with the help of inhibitors to develop an efficient anticancer drugs. Furthermore, the present study contributes to the possibility that genetic components are more important in Lung Cancer as compared to environmental and smoking(carcinogens) factors.
The exhaustive genome comparison effort. A quarter-century later
Authors: Benner Steven A. , Bradley Kevin M. , Chamberlain Stephan G.
Published: January 2018

A quarter century after the Benner and Gonnet groups began their collaboration in evolutionary bioinformatics, evolution-based functional genomics is a field with considerable scope. Even with the remarkable advances in computing power over this period, the explosion of data derived from genomic and protein sources have required more and more sophisticated approaches be developed and utilized. We describe here new software combined with data organization techniques and illustrate how we are harnessing these to place physiological function of protein sequence data using natural history.
The second axillary in Hymenoptera
Authors: Mikó István , Deans Andy R
Published: January 2018

The wing base of basal hymenopterans (Insecta) have never been properly described perhaps due to the difficulties of its visualization and understanding the 3D relationships between wing base components. Novel 3D visualization techniques such as microCT and Confocal Laser Scanning Microscopy (CLSM) allow us to provide easily digestible morphological data. The wing base of four basal Hymenoptera and 10 apocritan species have been imaged with CLSM and dissected under a stereomicroscope. The second axillary is composed of two sclerites (on on the dorsal wing membrane and one on the ventral in Macroxyela, Xyela and Athalia whereas it is represented by a single sclerite traversing the wing in other Hymenoptera. Consequences related to this observation as well are drawn and future directions in Hymenoptera wing base studies are provided.
Mitochondrial cytochrome b sequence data are not an improvement for species identification in Scleractinian corals
Authors: Wares John
Published: January 2018

There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of all available Scleractinian CYB sequence data indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
The effects of improvisational theatre (improv) vs. group television watching on cognitive ability and mood in people with age-related memory complaints
Authors: Harris Dustin , Koh Justin , Lai Andrew C , Fernandez Josue
Published: January 2018

As people age, there is a high chance their cognitive abilities will decline. The Baby Boomer population will soon reach an age where this is a major problem. As cognitive ability declines, so does quality of life. Everyday, 10,000 baby boomers turn 65 and this trend will continue for the next 15 years. With potential millions in need of a solution, cost is a major issue as well. Different forms of stimulation, like music and puzzles, have been shown to improve cognitive ability. Improvisational theatre is a form of stimulation that has not been thoroughly researched in older adults. This is a randomized control pilot study for utility and preliminary efficacy of improvisational theatre on cognitive ability and mood in older adults with age-related memory complaints. 11 elderly participants with age-related memory complaints from an assisted living center were randomized into an improv class (n=5) or a television watching control group (n=6). The improv group participated in an improv class once a week, for 8 weeks, lasting one hour per session. The passive stimulation group watched television or a movie for one hour a week at the same time as the improv class, for 8 weeks. The participants were given the following surveys one week prior to the start of the study and again the day of the last session: Montreal Cognitive Assessment, Verbal Fluency Test, Letter-Number Sequencing Test, Geriatric Depression Scale, Memory Functioning Questionnaire and the Functional Activities Questionnaire. The improv group demonstrated an average improvement in executive function, memory self-appraisal, phonemic cognition, and a decrease in mild cognitive impairment. The verbal fluency test, which measures phonemic cognition showed significant improvement with a p-value of 0.037. In the television watching group, there was an average improvement in executive function, phonemic cognition and some aspects of memory self-appraisal. None of which were significant. No adverse events occurred during the study. This study shows that improv has the potential to improve phonemic cognition because there was a significant increase in the study. Though the other areas that were tested (depression, executive function, working memory, memory self-appraisal or mild cognitive impairment) did not improve significantly, all either improved more than the control group or regressed less than the control group. Since this was the first study of its kind, more researchers should explore the effects of improv on cognition in elderly persons. Subjectively, the improv participants improved greatly in their ability to follow and remain active during the various games.
Sperm specific expression of temperature-sensitive ion channel TRPM8 correlates with vertebrate evolution
Authors: Kumar Majhi Rakesh , Saha Somdatta , Kumar Ashutosh , Swain Nirlipta , Goswami Luna , Mohapatra Pratyush , Maity Apratim A , Kumar Sahoo Vivek , Kumar Abhishek , Goswami Chandan
Published: January 2018

Transient Receptor Potential subfamily Melastatin member 8 (TRPM8) is involved in detection of cold temperature and different noxious compounds, execute thermo- as well as chemo-sensitive responses at cellular levels. Here we explored the molecular evolution of TRPM8 by analyzing sequences from different species. We elucidate that different regions of TRPM8 had different levels of selection pressure and the 4-5th transmembrane regions remain highly conserved. Synteny analysis suggests that since vertebrate origin, TRPM8 gene is linked with SPP2, a bone morphogen. We found 16656 TRPM8 variants in 1092 human genomes with top variations are SNPs, insertions and deletions. 692 missense mutations are also mapped to human TRPM8 protein. TRPM8 expresses endogenously in sperm cells of different vertebrates ranging from fish to human. We conclude that TRPM8 has emerged during vertebrate evolution (ca 450 MYA) and sperm-specific expression has guided its molecular evolution. These understandings may have medical importance as well.
Approaches to describing inter-rater reliability of the overall clinical appearance of febrile infants and toddlers in the Emergency Department.
Authors: Walsh Paul , Thornton Justin M. , Walker Nicholas , McCoy John Gary , Baal Joe , Baal Jed , Mendoza Nanse , Banimahd MD Faried , Asato Julie
Published: January 2018

Objectives To measure inter-rater agreement of overall clinical appearance of febrile children aged less than 24 months and to compare methods for doing so.

Study Design and setting We performed an observational study of inter-rater reliability of the assessment of febrile children in a county hospital emergency department serving a mixed urban and rural population. Two emergency medicine healthcare providers independently evaluated the overall clinical appearance of children less than 24 months of age who had presented for fever. They recorded the initial ‘gestalt’ assessment of whether or not the child was ill appearing or if they were unsure. They then repeated this assessment after examining the child. Each rater was blinded to the other’s assessment. Our primary analysis was graphical. We also calculated Cohen’s κ, Gwet’s agreement coefficient and other measures of agreement and weighted variants of these. We examined the effect of time between exams and patient and provider characteristics on inter-rater agreement.

Results We analyzed 159 of the 173 patients enrolled. Median age was 9.5 months (lower and upper quartiles 4.9-14.6), 99/159 (62%) were boys and 22/159 (14%) were admitted. Overall 118/159 (74%) and 119/159 (75%) were classified as well appearing on initial ‘gestalt’ impression by both examiners. Summary statistics varied from 0.223 for weighted κ to 0.635 for Gwet’s AC2. Inter rater agreement was affected by the time interval between the evaluations and the age of the child but not by the experience levels of the rater pairs. Classifications of ‘not ill appearing’ were more reliable than others.

Conclusion The inter-rater reliability of emergency providers' assessment of overall clinical appearance was adequate when described graphically and by Gwet’s AC. Different summary statistics yield different results for the same dataset.
Swabs to genomes: a comprehensive workflow
Authors: Dunitz Madison I , Lang Jenna M , Jospin Guillaume , Darling Aaron E , Eisen Jonathan A , Coil David A
Published: January 2018

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
Ancient pheromone blend as an alternative for copulation in internally fertilizing salamanders
Authors: Van Bocxlaer Ines , Treer Dag , Maex Margo , Vandebergh Wim , Janssenswillen Sunita , Stegen Gwij , Kok Philippe J. R. , Willaert Bert , Matthijs Severine , Martens Erik , Mortier Anneleen , De Greve Henri , Proost Paul , Bossuyt Franky
Published: January 2018

Throughout the animal kingdom, internal fertilization - the merging of sperm and egg inside the female body - nearly invariably relies on the use of a copulatory organ. In contrast, males of advanced salamanders (Salamandroidea) attain internal fertilization by depositing a spermatophore on the substrate in the environment, which females subsequently take up with their cloaca. The aquatically reproducing modern Eurasian newts (Salamandridae) have taken this to extremes, since the majority does not display physical contact between the sexes and largely rely on females following the male track at spermatophore deposition. Although the use of pheromones has been widely assumed during their courtship, molecules able to induce the female following behaviour that culminates in insemination have not been identified. Here we show that uncleaved glycosylated SPF protein pheromones, secreted during courtship, are sufficient to elicit such behaviour in palmate newts (Lissotriton h. helveticus), indicating that these molecules obviate the need for copulation in these salamanders. Surprisingly, our finding of side-by-side secretion of Late Palaeozoic diverged proteins in a single species suggests that these molecules already had a courtship function in stem salamanders about 300 million years ago, rendering them one of the oldest vertebrate pheromone systems.
Tracheostomy in children with congenital heart disease: a national analysis of the Kids' Inpatient Database.
Authors: Maxwell Bryan G , Nelson McMillan Kristen
Published: January 2018

Background: While single-institution studies reported the indications and outcomes of tracheostomy in children with congenital heart disease (CHD), no national analyses have been performed. We sought to examine the indications, performance, outcomes, and resource utilization of tracheostomy in children with CHD using a nationally representative database.

Methods: We identified all children undergoing tracheostomy in the Kids’ Inpatient Database 1997 through 2009, and we compared children with CHD to children without CHD. Within the CHD group, we compared children whose tracheostomy occurred in the same hospital admissions as a cardiac operation to those whose tracheostomy occurred without a cardiac operation in the same admission.

Results: Tracheostomy was performed in n=2,495 children with CHD, which represents 9.6% of all tracheostomies performed in children (n=25,928), and 3.5% of all admissions for children with CHD (n=355,460). Over the study period, there was an increasing trend in the proportion of all tracheostomies that were done in children with CHD (p<0.0001) and an increasing trend in the proportion of admissions for children with CHD that involved a tracheostomy (p<0.0001). The population of children with CHD undergoing tracheostomy differed markedly in baseline characteristics, outcomes, and resource utilization. Similarly, the subgroup of children whose tracheostomy was performed in the same admission as a cardiac operation differed significantly from those whose tracheostomy was not.

Conclusions: Tracheostomy is an increasingly common procedure in children with CHD despite being associated with significantly greater resource utilization and in-hospital mortality. The population of children with CHD who undergo tracheostomy differs markedly from that of children without CHD who undergo tracheostomy, and important differences are observed between children who undergo tracheostomy in the same admission as a cardiac surgical procedure and those who undergo tracheostomy in a nonsurgical admission, as well as between children with single-ventricle physiology and children with two-ventricle physiology.
Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: A cross-sectional study
Authors: Flølo Tone Nygaard , Andersen John Roger , Nielsen Hans Jørgen , Nativig Gerd Karin
Published: January 2018

Background: Researchers have emphasized a need to identify predictors that can explain the variability in weight management after bariatric surgery. Eating self-efficacy has demonstrated predictive impact on patients’ adherence to recommended eating habits following multidisciplinary treatment programs, but has to a limited extent been subject for research after bariatric surgery. Recently an American short form version (WEL-SF) of the commonly used Weight Efficacy Lifestyle Questionnaire (WEL) was available for research and clinical purposes.

Objectives: We intended to translate and culturally adapt the WEL-SF to Norwegian conditions, and to evaluate the new versions’ psychometrical properties in a Norwegian population of morbidly obese patients eligible for bariatric surgery.

Design: Cross-sectional

Methods: A total of 225 outpatients selected for Laparoscopic sleeve gastrectomy (LSG) were recruited; 114 non-operated and 111 operated patients, respectively. The questionnaire was translated through forward and backward procedures. Structural properties were assessed performing principal component analysis (PCA), correlation and regression analysis were conducted to evaluate convergent validity and sensitivity, respectively. Data was assessed by mean, median, item response, missing values, floor- and ceiling effect, Cronbach`s alpha and alpha if item deleted.

Results: The PCA resulted in one factor with eigenvalue>1, explaining 63.0% of the variability. The WEL-SF sum scores were positively correlated with the Self-efficacy and quality of life instruments (p<0.001). The WEL-SF was associated with body mass index (BMI) (p<0.001) and changes in BMI (p=0.026). A very high item response was obtained with only one missing value (0.4%). The ceiling effect was in average 0.9 and 17.1% in the non-operated and operated sample, respectively. Strong internal consistency (r =0.92) was obtained, and Cronbach’s alpha remained high (0.86-0.92) if single items were deleted.

Conclusion: The Norwegian version of WEL-SF appears to be a valid questionnaire on eating self-efficacy, with acceptable psychometrical properties in a population of morbidly obese patients
MicroRNAs expression profile in CCR6+ regulatory T cells
Authors: Zhao Juanjuan , Li Yongju , Hu Yan , Chen Chao , Zhou Ya , Tao Yijin , Guo Mengmeng , Qin Nalin , Xu Lin
Published: January 2018

Backgroud: CCR6+ CD4+ regulatory T cells (CCR6+Tregs), a distinct Tregs subset, played an important role in various immune diseases. Recent evidence showed that microRNAs (miRNAs) are vital regulators in the function of immune cells. However, the potential role of miRNAs in the function of CCR6+Tregs remains largely unknown. In this study, we detected the expression profile of miRNAs in CCR6+ Tregs. Materials and Methods: The expression profile of miRNAs as well as genes in CCR6+Tregs or CCR6-Tregs from Balb/c mice were detected by microarray. The signaling pathways were analyzed using Keggs pathway library. Results: We found that there were 58 miRNAs significantly upregulated and 62 downregulated up to 2 fold in CCR6+Tregs compared with CCR6-Tregs. Moreover, 1391 genes were observed with 3 fold change and 20 signaling pathways were enriched using Keggs pathway library. Conclusion: The present data firstly showed CCR6+Tregs expressed specific miRNAs pattern, which provide an insight into the role of miRNAs in the biological function of distinct Tregs subsets.
Effects of mobile phone radiation on heart rate: a radiation-detector controlled pilot study
Authors: Roggeveen Suzanne , van Os Jim , Gielissen Johan , Mengelers Ron , Golombeck Klaus , Lousberg Richel
Published: January 2018

Objectives: To investigate to what degree radiofrequency electromagnetic radiation, induced by a mobile phone placed on the chest, impacts cardiac rhythm. Design: n=1, single blinded pilot study Setting: Academic hospital, Maastricht, the Netherlands Participants: One healthy female 24 years old participant. Interventions: The participant underwent four experimental sessions, spread over four days. A session consisted of four consecutive 15 minute conditions, three with a sham phone and one with a dialling mobile phone. The participant was blind for the condition. During each condition, per-millisecond electrocardiac activity (lead V4) and radiofrequency radiation was recorded jointly. Primary outcome measure: Heart rate. The association with radiation was analysed at two levels, (i) at macrolevel, based on averaged condition effects, and (ii) at microlevel, focusing on radiation peak-related effects within the exposure condition. Results: The macrolevel analysis clearly indicated that heart rate was lowered during the radiation exposure condition. The heart rate during the preceding and subsequent sham phone condition was respectively 1.014 beats/minute (p < 0.001) and 1.009 beats/minute (p < 0.001) higher compared to the radiation exposure condition. In order to conduct radiation-detector controlled microlevel analyses, 142 critical segments were identified, in which a radiation-free period was followed by a radiation peak. The heart rate during the radiation-free period showed a mean increase, whereas the radiation peak period was associated with a mean decrease in heart rate (time*period interaction: p=0.001). Thus, the macrolevel finding was confirmed at microlevel. Conclusions: Mobile phone radiation may impact heart rate, suggesting urgent further study to assess physiological safety parameters.
Development and testing of a new type of „barefoot running shoe“: The freeheel runningpad
Authors: Daumer Martin , Trost Michael , Subkowski Paul , Lederer Christian
Published: January 2018

Common barefoot running shoes or minimal footwear have one or several of the following properties/deficiencies, depending on the type and brand and personal taste: - Coverage of a considerable fraction of the foot’s surface with textile/plastic leading to sub-optimal foot climate - Considerable weight for a true “barefoot shoe” - Toe pockets that do not fit with non-standard feet - Considerable size and thickness, in particular in the heel section of the protective sole for a true “barefoot shoe” - Positive drop and therefore a change in the biomechanics compared to barefoot running. We wanted to design a new type of shoe that would be as close as possible to “real” barefoot running” and thereby overcome one or several of these perceived deficiencies. Whether this would lead to a reduction or increase in running related injuries and how to best train with the new shoes is not within the scope of this article.
A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 Influenza Hemagglutinin
Authors: Dalby Andrew R , Iqbal Munir
Published: January 2018

A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species.

The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment.

The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.
Stigma of mental illnesses in Pakistani university students: A cross sectional survey
Authors: Waqas Ahmed , Zubair Muhammad , Ghulam Hamzah , Wajih Ullah Muhammad , Zubair Tariq Majeed Muhammad
Published: January 2018

Background: The objectives of the study were to explore the knowledge and attitudes of Pakistani university students toward mental illnesses. People with mental illnesses are challenged not only by their symptoms but also by the prejudices associated with their illness. Acknowledging the stigma of mental illness should be the first essential step toward devising an appropriate treatment plan. Methods: A cross-sectional survey was conducted at the University of Punjab, Lahore, CMH Lahore Medical and Dental College, Lahore, and University of Sargodha, Sub-campus Lahore, from February to May, 2014. The self-administered questionnaire consisted of three sections: demographics, general knowledge of psychiatric illnesses, and Community Attitudes towards Mental Illnesses (CAMI) Scale. The questionnaire was distributed to 650 participants enrolled in different disciplines (Social Sciences, Medicine and Formal Sciences). Results: Response rate was 81% (527/650 respondents). Mean age was 20.98 years. Most of the students (331, 62.8%) had an urban background and studied Social Sciences (238, 45.2%). 418 (79.3%) considered religion very important and most respondents considered psychiatrists (334, 63.4%) and spiritual leaders (72, 13.7%) to be best able to treat mental illnesses. 169 (32.1%) considered black magic to be a cause of mental illness. Only 215 (41%) had ever read an article on mental illnesses. Multiple regression analysis revealed study discipline, exposure, perceived causes of mental illnesses and superstitions to be significantly associated with attitudes towards mental illnesses (p < .05). Conclusion: Although low awareness and exposure were found in this sample of Pakistani university students, their attitude towards mental illnesses was generally positive. Most respondents gave supernatural explanations for mental illnesses but only a few believed that spiritual leaders can play a role in treatment.
The story of invasive algae, arginine, and turtle tumors does not make sense
Authors: Work Thierry M , Ackermann Mathias , Casey James W , Chaloupka Milani , Herbst Lawrence , Lynch Jennifer M , Stacy Brian A
Published: January 2018

We are presenting a rebuttal letter to the following article that appeared recently on PeerJ: Van Houtan KS, Smith CM, Dailer ML, and Kawachi M. 2014. Eutrophication and the dietary promotion of sea turtle tumors. PeerJ 2:e602. This article is available at the following URL: https://peerj.com/articles/602/. We argue that the article lacks an inferential framework to answer the complex question regarding the drivers of the turtle tumor disease fibropapillomatosis in Hawaii. The article also contains procedural flaws and does not provide any compelling evidence of a link between algae, arginine, and turtle tumors.
A systematic review of the use of statistics in studies of restoration ecology of arid areas
Authors: Noble Taylor
Published: January 2018

Restoration ecology is the study of restoration or restoration practices in degraded areas. It is of particular importance in arid environments due to the heavy impact humans have had in these areas. Some studies of restoration may require different statistics due to the unique challenges faced when examining degraded areas. A systematic review was conducted to assess the use of statistics in the field. It was determined that the field and influence of restoration ecology had increased dramatically since its development. Statistics are widely used in the study of restoration of arid areas. Major tests are similar to those found in other ecological studies such as ANOVAs and linear regressions. There were a few less common tests used in some of the studies. These include tests such as the Mantel test which may be useful to restoration ecology and should be explored further. Finally it was determined that the description of how statistics were used in the study was particularly important. The description should be detailed to help other researchers understand the findings of the paper. This will help to advance the field and the restoration of arid environments.
A systematic review of the statistical scope of restoration ecology of invaded grassland ecosystems
Authors: Liczner Amanda R
Published: January 2018

Restoration ecology is a rapidly growing field of research. The statistical analyses and experimental designs used in this field have likely also expanded. In this review, the statistical scope of the restoration ecology of invaded grasslands will be investigated. A systematic review was conducted on 103 articles to examine the types of statistical tests used and how they changed over time, if assumptions are tested, and how the number of statistical tests and the experimental design influence both the citation rate of articles and the impact factor of journals where these articles are published. ANOVAs have consistently been the dominant test. Statistical test diversity has increased since the year 2000. Most articles did test the assumptions of statistical analyses. The number of tests, and sample size of experiments are both positively correlated with the average citation rate of articles and the impact factor of the journal while the number of factors was negatively correlated. GLMs are recommended as a statistical test to be used more frequently in the future over ANOVAs. There is room for improvement in terms of reporting statistics accurately, including testing assumptions. When possible, sample sizes should be increased to both increase the quality of data, and the citation rate and the journal impact where articles are published. When possible and appropriate, sample sizes and the number of statistical tests should be increased. Adding factors in experimental designs should only be done so without compromising sample size as it has been shown to hinder the citation rate and journal impact.
Brainstem projections to molecular layer heterotopia of the cerebellar vermis: Evidence from the Allen Mouse Brain Connectivity Database
Authors: Ramos Raddy L
Published: January 2018

Molecular layer heterotopia of the cerebellar vermis are a characteristic feature of C57BL/6 mice. Heterotopia consist of neurons and glia in the molecular layers between folia VIII and IX in regions lacking pia. Previously, we described the cellular composition of heterotopia which includes granule cells, Purkinje cells, Golgi cells, etc. However, the axonal constituents and afferent connections of these malformations remain poorly understood. In the present report axonal projections to heterotopia are documented from diverse brainstem nuclei such as the spinal vestibular nucleus, dorsal cochlear nucleus, and nucleus prepositus. These findings are relevant toward understanding the mechanisms of normal and abnormal cerebellar development and the establishment of cerebellar circuits.