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https://www.readbyqxmd.com/read/28097076/a-critical-issue-in-model-based-inference-for-studying-trait-based-community-assembly-and-a-solution
#1
Cajo J F Ter Braak, Pedro Peres-Neto, Stéphane Dray
Statistical testing of trait-environment association from data is a challenge as there is no common unit of observation: the trait is observed on species, the environment on sites and the mediating abundance on species-site combinations. A number of correlation-based methods, such as the community weighted trait means method (CWM), the fourth-corner correlation method and the multivariate method RLQ, have been proposed to estimate such trait-environment associations. In these methods, valid statistical testing proceeds by performing two separate resampling tests, one site-based and the other species-based and by assessing significance by the largest of the two p-values (the pmax test)...
2017: PeerJ
https://www.readbyqxmd.com/read/28097075/effects-of-an-8-week-yoga-program-on-sustained-attention-and-discrimination-function-in-children-with-attention-deficit-hyperactivity-disorder
#2
Chien-Chih Chou, Chung-Ju Huang
This study investigated whether a yoga exercise intervention influenced the sustained attention and discrimination function in children with ADHD. Forty-nine participants (mean age = 10.50 years) were assigned to either a yoga exercise or a control group. Participants were given the Visual Pursuit Test and Determination Test prior to and after an eight-week exercise intervention (twice per week, 40 min per session) or a control intervention. Significant improvements in accuracy rate and reaction time of the two tests were observed over time in the exercise group compared with the control group...
2017: PeerJ
https://www.readbyqxmd.com/read/28097074/resources-available-for-autism-research-in-the-big-data-era-a-systematic-review
#3
Reem Al-Jawahiri, Elizabeth Milne
Recently, there has been a move encouraged by many stakeholders towards generating big, open data in many areas of research. One area where big, open data is particularly valuable is in research relating to complex heterogeneous disorders such as Autism Spectrum Disorder (ASD). The inconsistencies of findings and the great heterogeneity of ASD necessitate the use of big and open data to tackle important challenges such as understanding and defining the heterogeneity and potential subtypes of ASD. To this end, a number of initiatives have been established that aim to develop big and/or open data resources for autism research...
2017: PeerJ
https://www.readbyqxmd.com/read/28097073/handling-stress-may-confound-murine-gut-microbiota-studies
#4
Cary R Allen-Blevins, Xiaomeng You, Katie Hinde, David A Sela
BACKGROUND: Accumulating evidence indicates interactions between human milk composition, particularly sugars (human milk oligosaccharides or HMO), the gut microbiota of human infants, and behavioral effects. Some HMO secreted in human milk are unable to be endogenously digested by the human infant but are able to be metabolized by certain species of gut microbiota, including Bifidobacterium longum subsp. infantis (B. infantis), a species sensitive to host stress (Bailey & Coe, 2004). Exposure to gut bacteria like B...
2017: PeerJ
https://www.readbyqxmd.com/read/28097072/aggregations-and-parental-care-in-the-early-triassic-basal-cynodonts-galesaurus-planiceps-and-thrinaxodon-liorhinus
#5
Sandra C Jasinoski, Fernando Abdala
Non-mammaliaform cynodonts gave rise to mammals but the reproductive biology of this extinct group is still poorly known. Two exceptional fossils of Galesaurus planiceps and Thrinaxodon liorhinus, consisting of juveniles closely associated with an adult, were briefly described more than 50 years ago as examples of parental care in non-mammaliaform cynodonts. However, these two Early Triassic fossils have largely been excluded from recent discussions of parental care in the fossil record. Here we re-analyse these fossils in the context of an extensive survey of other aggregations found in these two basal cynodont taxa...
2017: PeerJ
https://www.readbyqxmd.com/read/28097071/the-fishing-and-natural-mortality-of-large-piscivorous-bull-trout-and-rainbow-trout-in-kootenay-lake-british-columbia-2008-2013
#6
Joseph L Thorley, Greg F Andrusak
BACKGROUND: Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout. METHODS: Between 2008 and 2013, 88 large (≥500 mm) Bull Trout and 149 large (≥500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake...
2017: PeerJ
https://www.readbyqxmd.com/read/28097070/sponge-exhalent-seawater-contains-a-unique-chemical-profile-of-dissolved-organic-matter
#7
Cara L Fiore, Christopher J Freeman, Elizabeth B Kujawinski
Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater)...
2017: PeerJ
https://www.readbyqxmd.com/read/28097069/italian-and-swedish-adolescents-differences-and-associations-in-subjective-well-being-and-psychological-well-being
#8
Danilo Garcia, Elisabetta Sagone, Maria Elvira De Caroli, Ali Al Nima
BACKGROUND: One important aspect of subjective judgments about one's well-being (i.e., subjective well-being: life satisfaction, positive affect, and negative affect) is that cultural features, such as, nationality seem to shape cognitive judgments about the "the ideal life." In this comparative study we examined differences in subjective well-being and psychological well-being between Italian and Swedish adolescents and tested if the relationship between the three constructs of subjective well-being (i...
2017: PeerJ
https://www.readbyqxmd.com/read/28097068/hepatic-fibrosis-and-factors-associated-with-liver-stiffness-in-hiv-mono-infected-individuals
#9
Mihály Sulyok, Tamás Ferenci, Mihály Makara, Gábor Horváth, János Szlávik, Zsófia Rupnik, Luca Kormos, Zsuzsanna Gerlei, Zita Sulyok, István Vályi-Nagy
BACKGROUND: Liver disease has become an important cause of morbidity and mortality even in those HIV-infected individuals who are devoid of hepatitis virus co-infection. The aim of this study was to evaluate the degree of hepatic fibrosis and the role of associated factors using liver stiffness measurement in HIV mono-infected patients without significant alcohol intake. METHODS: We performed a cross-sectional study of 101 HIV mono-infected patients recruited prospectively from March 1, 2014 to October 30, 2014 at the Center for HIV, St István and St László Hospital, Budapest, Hungary...
2017: PeerJ
https://www.readbyqxmd.com/read/28097067/anatomical-mechanism-of-spontaneous-recovery-in-regions-caudal-to-thoracic-spinal-cord-injury-lesions-in-rats
#10
Lu-Sheng Li, Hao Yu, Raynald Raynald, Xiao-Dong Wang, Guang-Hui Dai, Hong-Bin Cheng, Xue-Bin Liu, Yi-Hua An
BACKGROUND: The nerve fibre circuits around a lesion play a major role in the spontaneous recovery process after spinal cord hemisection in rats. The aim of the present study was to answer the following question: in the re-control process, do all spinal cord nerves below the lesion site participate, or do the spinal cord nerves of only one vertebral segment have a role in repair? METHODS: First we made a T7 spinal cord hemisection in 50 rats. Eight weeks later, they were divided into three groups based on distinct second operations at T7: ipsilateral hemisection operation, contralateral hemisection, or transection...
2017: PeerJ
https://www.readbyqxmd.com/read/28097066/henricia-djakonovi-sp-nov-echinodermata-echinasteridae-a-new-sea-star-species-from-the-sea-of-japan
#11
Anton Chichvarkhin
A new sea star species, H. djakonovi sp.n., was discovered in Rudnaya Bay in the Sea of Japan. This is a sympatric species of the well-known and common species Henricia pseudoleviuscula Djakonov, 1958. Both species are similar in body size and proportions, shape of skeletal plates, and life coloration, which distinguishes them from the other Henricia species inhabiting the Sea of Japan. Nevertheless, these species can be distinguished by their abactinal spines: in both species, they are short and barrel-like, but the new species is the only Henricia species in Russian waters of the Pacific that possesses such spines with a massive, smooth, bullet-like tip...
2017: PeerJ
https://www.readbyqxmd.com/read/28097065/upregulation-of-noxa-by-10-hydroxycamptothecin-plays-a-key-role-in-inducing-fibroblasts-apoptosis-and-reducing-epidural-fibrosis
#12
Jihang Dai, Yu Sun, Lianqi Yan, Jingcheng Wang, Xiaolei Li, Jun He
The fibrosis that develops following laminectomy or discectomy often causes serious complications, and the proliferation of fibroblasts is thought to be the major cause of epidural fibrosis. 10-Hydroxycamptothecin (HCPT) has been proven to be efficient in preventing epidural fibrosis, but the exact mechanism is still unclear. NOXA is a significant regulator of cell apoptosis, which has been reported to be beneficial in the treatment of fibrosis. We performed a series of experiments, both in vitro and in vivo, to explore the intrinsic mechanism of HCPT that underlies the induction of apoptosis in fibroblasts, and also to investigate whether HCPT has positive effects on epidural fibrosis following laminectomy in rats...
2017: PeerJ
https://www.readbyqxmd.com/read/28097064/phalangeal-joints-kinematics-during-ostrich-struthio-camelus-locomotion
#13
Rui Zhang, Qiaoli Ji, Gang Luo, Shuliang Xue, Songsong Ma, Jianqiao Li, Lei Ren
The ostrich is a highly cursorial bipedal land animal with a permanently elevated metatarsophalangeal joint supported by only two toes. Although locomotor kinematics in walking and running ostriches have been examined, these studies have been largely limited to above the metatarsophalangeal joint. In this study, kinematic data of all major toe joints were collected from gaits with double support (slow walking) to running during stance period in a semi-natural setup with two selected cooperative ostriches. Statistical analyses were conducted to investigate the effect of locomotor gait on toe joint kinematics...
2017: PeerJ
https://www.readbyqxmd.com/read/28097063/interferon-%C3%AE-responses-to-plasmodium-falciparum-vaccine-candidate-antigens-decrease-in-the-absence-of-malaria-transmission
#14
Cyrus Ayieko, Bilha S Ogola, Lyticia Ochola, Gideon A M Ngwena, George Ayodo, James S Hodges, Gregory S Noland, Chandy C John
BACKGROUND: Malaria elimination campaigns are planned or active in many countries. The effects of malaria elimination on immune responses such as antigen-specific IFN- γ responses are not well characterized. METHODS: IFN- γ responses to the P. falciparum antigens circumsporozoite protein, liver stage antigen-1, thrombospondin-related adhesive protein, apical membrane antigen-1, MB2, and merozoite surface protein-1 were tested by ELISA in 243 individuals in highland Kenya in April 2008, October 2008, and April 2009, after a one-year period of interrupted malaria transmission from April 2007 to March 2008...
2017: PeerJ
https://www.readbyqxmd.com/read/28097062/diversity-and-distribution-of-the-caddisflies-insecta-trichoptera-of-ecuador
#15
Blanca Ríos-Touma, Ralph W Holzenthal, Jolanda Huisman, Robin Thomson, Ernesto Rázuri-Gonzales
BACKGROUND: Aquatic insects and other freshwater animals are some of the most threatened forms of life on Earth. Caddisflies (Trichoptera) are highly biodiverse in the Neotropics and occupy a wide variety of freshwater habitats. In Andean countries, including Ecuador, knowledge of the aquatic biota is limited, and there is a great need for baseline data on the species found in these countries. Here we present the first list of Trichoptera known from Ecuador, a country that harbors two global biodiversity "hotspots...
2017: PeerJ
https://www.readbyqxmd.com/read/28097061/contrasting-molecular-and-morphological-evidence-for-the-identification-of-an-anomalous-buteo-a-cautionary-tale-for-hybrid-diagnosis
#16
William S Clark, Spencer C Galen, Joshua M Hull, Megan A Mayo, Christopher C Witt
An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus;). It is now a specimen in the Museum of Wildlife and Fisheries Biology (WFB 4816) at the University of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus) and Red-shouldered Hawk (ssp elegans), leading us to hypothesize that the bird was a hybrid...
2017: PeerJ
https://www.readbyqxmd.com/read/28097060/why-choose-random-forest-to-predict-rare-species-distribution-with-few-samples-in-large-undersampled-areas-three-asian-crane-species-models-provide-supporting-evidence
#17
Chunrong Mi, Falk Huettmann, Yumin Guo, Xuesong Han, Lijia Wen
Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models)...
2017: PeerJ
https://www.readbyqxmd.com/read/28097059/the-complete-chloroplast-genome-sequence-of-an-endemic-monotypic-genus-hagenia-rosaceae-structural-comparative-analysis-gene-content-and-microsatellite-detection
#18
Andrew W Gichira, Zhizhong Li, Josphat K Saina, Zhicheng Long, Guangwan Hu, Robert W Gituru, Qingfeng Wang, Jinming Chen
Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H...
2017: PeerJ
https://www.readbyqxmd.com/read/28097058/determining-virus-host-interactions-and-glycerol-metabolism-profiles-in-geographically-diverse-solar-salterns-with-metagenomics
#19
Abraham G Moller, Chun Liang
Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics...
2017: PeerJ
https://www.readbyqxmd.com/read/28097057/a-gene-expression-study-of-dorso-ventrally-restricted-pigment-pattern-in-adult-fins-of-neolamprologus-meeli-an-african-cichlid-species
#20
Ehsan Pashay Ahi, Kristina M Sefc
Fish color patterns are among the most diverse phenotypic traits found in the animal kingdom. Understanding the molecular and cellular mechanisms that control in chromatophore distribution and pigmentation underlying this diversity is a major goal in developmental and evolutionary biology, which has predominantly been pursued in the zebrafish model system. Here, we apply results from zebrafish work to study a naturally occurring color pattern phenotype in the fins of an African cichlid species from Lake Tanganyika...
2017: PeerJ
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