bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad‐leaved forests
Authors: Xiang Xiao‐Guo , Mi Xiang‐Cheng , Zhou Hai‐Lang , Li Jian‐Wu , Chung Shih‐Wen , Li De‐Zhu , Huang Wei‐Chang , Jin Wei‐Tao , Li Zhen‐Yu , Huang Lu‐Qi , Jin Xiao‐Hua 
Published: February 2016

AbstractAimEvergreen broad‐leaved forests (EBLFs) occupy most tropical and subtropical regions of mainland Asia and exhibit high species diversity, productivity and richness. Understanding the historical dynamics of EBLFs is important for biodiversity conservation and regional carbon storage and cycling under global climate change. However, little is known about the historical dynamics of EBLFs in mainland Asia. Dendrobium, an epiphytic orchid genus found in EBLFs, was used to gain new insights of the historical establishment and extension of EBLFs in mainland Asia.LocationMainland Asia.MethodsWe sampled c. 80% of the currently recognized species of Dendrobium found in mainland Asia. A phylogeny was generated using maximum parsimony, maximum likelihood and Bayesian inference methods. A calibrated chronogram was obtained using a Bayesian relaxed‐clock model approach. Biogeographical scenarios were investigated using the statistical dispersal–vicariance analysis and dispersal–extinction–cladogenesis methods. Ancestral states were constructed by mesquite and bayestraits, and diversification of Dendrobium was investigated by APE and LASER packages.ResultsOur results indicate that Asian Dendrobium was present on mainland Asia since the Oligocene, after which this genus diversified in this region and dispersed into higher elevations. The ancestral habit of Dendrobium was epiphytic and terrestrial and lithophytic habits each have multiple, recently independent origins.Main conclusionsOur results support the hypothesis that EBLFs have been established in mainland Asia at least since the Oligocene and further suggest that the EBLFs of mainland Asia expanded into higher elevations prior to the late Cenozoic. The diversification of Asian Dendrobium coincided with a warmer climate during the late Oligocene and middle Miocene and the expansion of key groups (including Fagaceae, Lauraceae, Magnoliaceae and Theaceae) of EBLFs during the early Cenozoic.
Quantifying the similarity between genes and geography across Alaska's alpine small mammals
Authors: Knowles L. Lacey , Massatti Rob , He Qixin , Olson Link E. , Lanier Hayley C. 
Published: February 2016

AbstractAimQuantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species‐specific or shared manner.LocationAlaska and adjacent north‐western Canada.MethodsFor each taxon we generated 3500–7500 single‐nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between principal components analysis maps of genetic variation and geographical maps of sample locations. We generate stability maps using projected distributions from ecological niche models of the Last Glacial Maximum and the present.ResultsSignificant similarity between genes and geography exists across taxa. However, the extent to which geography is predictive of patterns of genetic variation not only differs among taxa, but the correspondence between genes and geography varies over space. Geographical areas where genetic structure aligns poorly with the geographical coordinates are of particular interest because they indicate regions where processes other than isolation by distance (IBD) have influenced genetic variation. The clustering of individuals according to their sample location does not support suppositions of admixture, despite the presumed high vagility of some species (e.g. arctic ground squirrels).Main conclusionsGenomic data indicate a more nuanced biogeographical history for the taxa than suggested by previous studies based on mtDNA alone. These include departures from IBD that are shared among taxa, which suggest some shared processes structuring genetic variation, including new potential ancestral source populations. In addition, some regions fit expectations of IBD where incremental migration and gene flow play a strong role in population structure, despite any ecological difference among taxa. Differences in dispersal capabilities do not result in different species‐specific local patterns of population structure, at least at the sampling scale examined here. We highlight how the general fit to, as well as departures from, expectations for patterns of genetic variation based on the Procrustes analyses can be used to generate hypotheses about the underlying processes.
Ecological, evolutionary and human‐mediated determinants of poeciliid species richness on Caribbean islands
Authors: Furness Andrew I. , Reznick David N. , Avise John C. 
Published: February 2016

AbstractAimThe theory of island biogeography provides a predictive framework relating species richness to island size and distance from the mainland. However, the theory as originally formulated does not necessarily scale to large islands and continental landmasses that are capable of generating species through in situ speciation (rather than entirely by colonization), nor does it necessarily account for how human introduction of species alters traditional biogeographical patterns. Here, we examine the ecological (colonization and extinction), evolutionary (in situ speciation) and human‐mediated (deliberate introductions) determinants of species richness in a taxonomic group that has undergone a radiation on Caribbean islands: live‐bearing fishes of the family Poeciliidae.LocationThe Caribbean.MethodsWe created a database of both native and introduced poeciliid species occurrence on Caribbean islands through literature review, and estimated the number of colonizations versus speciation events on each island using a molecular phylogeny. Linear regression and other statistical tests were used to explore species–area and species–isolation relationships.ResultsSpecies richness on small islands results entirely from colonization and does not significantly increase with island area, whereas on larger islands species richness increases dramatically as a function of area due primarily to in situ speciation. Poeciliid fishes have been introduced widely, both as a by‐product of their popularity in the aquarium hobby and as a means of mosquito control. We show that such establishments have occurred disproportionately on islands depauperate in native species, and that introduced species richness is positively correlated with economic interconnectedness (shipping traffic) and human population size.Main conclusionsOn large Caribbean islands in situ speciation has elevated the number of poeciliid species beyond that predicted from ecological processes alone. Introduced species significantly alter biogeographical patterns.
Factors driving structure of natural and anthropogenic forest edges from temperate to boreal ecosystems
Authors: Esseen Per‐Anders , Hedström Ringvall Anna , Harper Karen Amanda , Christensen Pernilla , Svensson Johan 
Published: February 2016

AbstractQuestionsWhat factors control broad‐scale variation in edge length and three‐dimensional boundary structure for a large region extending across two biomes? What is the difference in structure between natural and anthropogenic edges?LocationTemperate and boreal forests across all of Sweden, spanning latitudes 55–69° N.MethodsWe sampled more than 2000 forest edges using line intersect sampling in a monitoring programme (National Inventory of Landscapes in Sweden). We compared edge length, ecosystem attributes (width of adjacent ecosystem, canopy cover, canopy height, patch contrast in canopy height, forest type) and boundary attributes (profile, abruptness, shape) of natural edges (lakeshore, wetland) with anthropogenic edges (clear‐cut, agricultural, linear disturbance) in five regions.ResultsAnthropogenic edges were nearly twice as abundant as natural edges. Length of anthropogenic edges was largest in southern regions, while the abundance of natural edges increased towards the north. Edge types displayed unique spectrums of boundary structures, but abrupt edges dominated, constituting 72% of edge length. Anthropogenic edges were more abrupt than natural edges; wetland edges had the most gradual and sinuous boundaries. Canopy cover, canopy height, patch contrast and forest type depended on region, whereas overall boundary abruptness and shape showed no regional pattern. Patch contrast was related to temperature sum (degree days ≥ 5 °C), suggesting that regional variability can be predicted from climate‐controlled forest productivity. Boundary abruptness was coupled with the underlying environmental gradient, land use and forest type, with higher variability in deciduous than in conifer forest.ConclusionsEdge origin, land use, climate and tree species are main drivers of broad‐scale variability in forest edge structure. Our findings have important implications for developing ecological theory that can explain and predict how different factors affect forest edge structure, and help to understand how land use and climate change affect biodiversity at forest edges.
Woody species composition in an African savanna: determined by centuries of termite activity but modulated by 50 years of ungulate herbivory
Authors: Seymour Colleen L. , Joseph Grant S. , Makumbe Milton , Cumming Graeme S. , Mahlangu Zacheus , Cumming David H.M. 
Published: February 2016

AbstractQuestionsUngulate herbivory and formation of large termite mounds occur over different time scales, but both can affect plant community composition in savannas. Human‐managed savanna systems are increasingly dominated by domesticated grazing herbivores. These have replaced a mix of indigenous browsers and grazers, leading to changes in plant communities such as increased bush encroachment. We compared the relative impacts of five decades of different types of ungulate herbivory (cattle grazing, browsing and grazing by wild herbivores, and exclusion of all larger herbivores) on woody plant assemblages in two habitats, namely, large termite mounds, which may be thousands of years old, and the surrounding matrix.LocationMiombo woodland savanna, Zimbabwe.MethodsTo determine the influence of termite mounds and herbivory on spatial distribution and composition of woody assemblages, we compared 40 paired mound–matrix plots from the three herbivory treatments using PERMANOVA. We assessed whether mound plots were more similar to each other than matrix plots were to each other, and whether herbivory influenced similarity. We used SIMPER analysis to identify changes in abundance of indicator species for each habitat (i.e. mound or matrix).ResultsSpecies composition differed significantly between mound and matrix and also between herbivory treatments. Woody plant assemblages on mounds were more similar to each other than woody plant assemblages in matrix plots were to each other, regardless of type of herbivory, but herbivory reduced the mound/matrix contrast. Sample location (i.e. on mound or in matrix) explained 23% of the variation in woody species composition, compared to 12% explained by herbivory. Woody plant abundance was lowest where there were both grazers and browsers.ConclusionsThe influence of large termite mounds on plant assemblages was roughly double that of herbivory, which has occurred over five decades. Type of herbivory emerged as relatively influential on woody plant species composition, given that the time periods involved were short by comparison to the slow formation of termite mounds. Type of herbivory also influenced species composition and vegetation structure, with a diversity of herbivores necessary to reduce encroachment by woody species.
The Category of the Supernatural: A Valid Anthropological Term?
Authors: Dein Simon 
Published: February 2016

AbstractThis paper is a survey of the anthropological literature pertaining to the term ‘supernatural’. It considers a number of questions: Is the distinction between natural and supernatural universal? Can the distinction be applied to non‐western cultures? What does the term mean as a cultural construction and as a response to reality? Finally, it examines the use of the term supernatural in the contemporary cognitive science of religion. The inspiration for the paper arose from the way that anthropologists often fail to problematise the uses and cross‐cultural applicability of the term supernatural.
Injury, inflammation and the emergence of human‐specific genes
Authors: Baird Andrew , Costantini Todd , Coimbra Raul , Eliceiri Brian P. 
Published: February 2016

AbstractIn light of the central role of inflammation in normal wound repair and regeneration, we hypothesize that the preponderance of human‐specific genes expressed in human inflammatory cells is commensurate with the genetic versatility of inflammatory response and the emergence of injuries associated with uniquely hominid behaviors, like a bipedal posture and the use of tools, weapons and fire. The hypothesis underscores the need to study human‐specific signaling pathways in experimental models of injury and infers that a selection of human‐specific genes, driven in part by the response to injury, may have facilitated the emergence of multifunctional genes expressed in other tissues.
Response of human macrophages to wound matrices in vitro
Authors: Witherel Claire E. , Graney Pamela L. , Freytes Donald O. , Weingarten Michael S. , Spiller Kara L. 
Published: February 2016

AbstractChronic wounds remain a major burden to the global healthcare system. Myriad wound matrices are commercially available but their mechanisms of action are poorly understood. Recent studies have shown that macrophages are highly influenced by their microenvironment, but it is not known how different biomaterials affect this interaction. Here, it was hypothesized that human macrophages respond differently to changes in biomaterial properties in vitro with respect to phenotype, including pro‐inflammatory M1, anti‐inflammatory M2a, known for facilitating extracellular matrix deposition and proliferation, and M2c, which has recently been associated with tissue remodeling. Using multiple donors, it was found that collagen scaffolds cross‐linked with 1‐ethyl‐3‐(3‐dimethylaminopropyl) carbodiimide and N‐hydroxysuccinimide (EDC/NHS) promoted the least inflammatory phenotype in primary human macrophages compared with scaffolds cross‐linked with formaldehyde or glutaraldehyde. Importantly, gene expression analysis trends were largely conserved between donors, especially TNFa (M1), CCL22 (M2a), and MRC1 (M2a). Then the response of primary and THP1 monocyte‐derived macrophages to four commercially available wound matrices were compared—Integra Dermal Regeneration Template (Integra), PriMatrix Dermal Repair Scaffold (PriMatrix), AlloMend Acellular Dermal Matrix (AlloMend), and Oasis Wound Matrix (Oasis). Gene expression trends were different between primary and THP1 monocyte‐derived macrophages for all six genes analyzed in this study. Finally, the behavior of primary macrophages cultured onto the wound matrices over time was analyzed. Integra and Oasis caused down‐regulation of M2a markers CCL22 and TIMP3. PriMatrix caused up‐regulation of TNFa (M1) and CD163 (M2c) and down‐regulation of CCL22 and TIMP3 (both M2a). AlloMend caused up‐regulation in CD163 (M2c). Lastly, Oasis promoted the largest increase in the combinatorial M1/M2 score, defined as the sum of M1 genes divided by the sum of M2 genes. This preliminary study suggested that biomaterials influenced the wound microenvironment to affect macrophage phenotype.
Clinical expression of facioscapulohumeral muscular dystrophy in carriers of 1–3 D4Z4 reduced alleles: experience of the FSHD Italian National Registry
Authors: Nikolic Ana , Ricci Giulia , Sera Francesco , Bucci Elisabetta , Govi Monica , Mele Fabiano , Rossi Marta , Ruggiero Lucia , Vercelli Liliana , Ravaglia Sabrina , Brisca Giacomo , Fiorillo Chiara , Villa Luisa , Maggi Lorenzo , Cao Michelangelo , D'Amico Maria Chiara , Siciliano Gabriele , Antonini Giovanni , Santoro Lucio , Mongini Tiziana , Moggio Maurizio , Morandi Lucia , Pegoraro Elena , Angelini Corrado , Di Muzio Antonio , Rodolico Carmelo , Tomelleri Giuliano , Grazia D'Angelo Maria , Bruno Claudio , Berardinelli Angela , Tupler Rossella 
Published: February 2016

ObjectivesFacioscapulohumeral muscular dystrophy type 1 (FSHD1) has been genetically linked to reduced numbers (≤8) of D4Z4 repeats at 4q35. Particularly severe FSHD cases, characterised by an infantile onset and presence of additional extra-muscular features, have been associated with the shortest D4Z4 reduced alleles with 1–3 repeats (1–3 DRA). We searched for signs of perinatal onset and evaluated disease outcome through the systematic collection of clinical and anamnestic records of de novo and familial index cases and their relatives, carrying 1–3 DRA.SettingItaly.Participants66 index cases and 33 relatives carrying 1–3 DRA.OutcomesThe clinical examination was performed using the standardised FSHD evaluation form with validated inter-rater reliability. To investigate the earliest signs of disease, we designed the Infantile Anamnestic Questionnaire (IAQ). Comparison of age at onset was performed using the non-parametric Wilcoxon rank-sum or Kruskal-Wallis test. Comparison of the FSHD score was performed using a general linear model and Wald test. Kaplan-Meier survival analysis was used to estimate the age-specific cumulative motor impairment risk.ResultsNo patients had perinatal onset. Among index cases, 36 (54.5%) showed the first signs by 10 years of age. The large majority of patients with early disease onset (26 out of 36, 72.2%) were de novo; whereas the majority of patients with disease onset after 10 years of age were familial (16, 53.3%). Comparison of the disease severity outcome between index cases with age at onset before and over 10 years of age, failed to detect statistical significance (Wald test p value=0.064). Of 61 index cases, only 17 (27.9%) presented extra-muscular conditions. Relatives carrying 1–3 DRA showed a large clinical variability ranging from healthy subjects, to patients with severe motor impairment.ConclusionsThe size of the D4Z4 allele is not always predictive of severe clinical outcome. The high degree of clinical variability suggests that additional factors contribute to the phenotype complexity.
The efficacy and safety of complete pericardial drainage by means of intrapericardial fibrinolysis for the prevention of complications of pericardial effusion: a systematic review protocol
Authors: Kakia Aloysious , Wiysonge Charles S , Ochodo Eleanor A , Awotedu Abolade A , Ristic Arsen D , Mayosi Bongani M 
Published: February 2016

IntroductionIntrapericardial fibrinolysis has been proposed as a means of preventing complications of pericardial effusion such as cardiac tamponade, persistent and recurrent pericardial effusion, and pericardial constriction. There is a need to understand the efficacy and safety of this procedure because it shows promise.Methods and analysisWe aim to assess the effects of intrapericardial fibrinolysis in the treatment of pericardial effusion. We will search PubMed, the Cochrane Library, African Journals online, Cumulative Index to Nursing and Allied Health Literature, Trip database, Clinical trials.gov and the WHO International Clinical Trials Registry Platform for studies that evaluate the efficacy and/or safety of complete pericardial fluid drainage by intrapericardial fibrinolysis irrespective of study design, geographical location, language, age of participants, aetiology of pericarditis or types of fibrinolytics. Two authors will do the search independently, screen the search outputs for potentially eligible studies and assess whether the studies meet the inclusion criteria. Discrepancies between the two authors will be resolved through discussion and arbitration by a third author. Data from the selected studies shall be extracted using a standardised data collection form which will be piloted before use. The methodological quality of studies will be assessed using the Cochrane Collaboration's tools for assessing risk of bias for experimental studies and non-randomised studies, respectively. The primary meta-analysis will use random effects models due to expected interstudy heterogeneity. Dichotomous data will be analysed using relative risk and continuous with data mean differences, both with 95% CIs.Ethics and disseminationApproval by an ethics committee is not required for this study as it is a protocol for a systematic review of published studies. The results will be disseminated through a conference presentation and peer-reviewed publication.Review registration numberPROSPERO, CRD42014015238.
Acupuncture point injection treatment of primary dysmenorrhoea: a randomised, double blind, controlled study
Authors: Wade C , Wang L , Zhao W J , Cardini F , Kronenberg F , Gui S Q , Ying Z , Zhao N Q , Chao M T , Yu J 
Published: February 2016

ObjectiveTo determine if injection of vitamin K3 in an acupuncture point is optimal for the treatment of primary dysmenorrhoea, when compared with 2 other injection treatments.SettingA Menstrual Disorder Centre at a public hospital in Shanghai, China.ParticipantsChinese women aged 14–25 years with severe primary dysmenorrhoea for at least 6 months not relieved by any other treatment were recruited. Exclusion criteria were the use of oral contraceptives, intrauterine devices or anticoagulant drugs, pregnancy, history of abdominal surgery, participation in other therapies for pain and diagnosis of secondary dysmenorrhoea. Eighty patients with primary dysmenorrhoea, as defined on a 4-grade scale, completed the study. Two patients withdrew after randomisation.InterventionsA double-blind, double-dummy, randomised controlled trial compared vitamin K3 acupuncture point injection to saline acupuncture point injection and vitamin K3 deep muscle injection. Patients in each group received 3 injections at a single treatment visit.Primary and secondary outcome measuresThe primary outcome was the difference in subjective perception of pain as measured by an 11 unit Numeric Rating Scale (NRS). Secondary measurements were Cox Pain Intensity and Duration scales and the consumption of analgesic tablets before and after treatment and during 6 following cycles.ResultsPatients in all 3 groups experienced pain relief from the injection treatments. Differences in NRS measured mean pain scores between the 2 active control groups were less than 1 unit (−0.71, CI −1.37 to −0.05) and not significant, but the differences in average scores between the treatment hypothesised to be optimal and both active control groups (1.11, CI 0.45 to 1.78) and (1.82, CI 1.45 to 2.49) were statistically significant in adjusted mixed-effects models. Menstrual distress and use of analgesics were diminished for 6 months post-treatment.ConclusionsAcupuncture point injection of vitamin K3 relieves menstrual pain rapidly and is a useful treatment in an urban outpatient clinic.Trial registration numberNCT00104546; Results.