bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species distribution models predict rare species occurrences despite significant effects of landscape context
Authors: McCune J. L. 
Published: June 2016

Summary

The true status of many endangered plants is uncertain because the locations of all extant populations are not known. Species distribution models (SDMs) can direct searches for additional populations, but habitat fragmentation may influence the distribution of rare species more than climatic or edaphic factors in human‐dominated landscapes. In this study, I test the ability of SDMs to predict rare plant occurrences in a fragmented landscape and the importance of predicted habitat suitability versus landscape context.

I built SDMs for eight rare woodland plants and assessed them using an independent data set including plant community surveys of 51 sites. I used community data to determine whether SDMs predict the right habitat type even when the target rare species was absent. I then modelled rare species presence based on predicted habitat suitability, distance to the nearest known population and the amount of forest habitat within 500 m of the site.

SDMs were effective for seven of the eight species, with the degree of predicted habitat suitability positively related to species' occurrence. I found new populations of four of the eight species. However, the amount of forest habitat available in the vicinity of a plot was also a positive predictor of rare plant occurrences. Among sites predicted to be suitable, the distance to the nearest known population was the strongest predictor of rare plant occurrence.

Synthesis and applications. Species distribution models (SDMs) can effectively target searches for populations of rare species even in human‐dominated landscapes. Surveying the plant community at sites predicted to be suitable can help to improve the SDM. SDMs used in conjunction with data on landscape context can maximize the efficiency of searches for rare species and show which species are restricted by dispersal limitation and habitat fragmentation in addition to edaphic and climatic factors.
Patient‐Centered Medical Home Recognition and Clinical Performance in U.S. Community Health Centers
Authors: Shi Leiyu , Lee De‐Chih , Chung Michelle , Liang Hailun , Lock Diana , Sripipatana Alek 
Published: June 2016

IntroductionAmerica's community health centers (HCs) are uniquely poised to implement the patient‐centered medical home (PCMH) model, as they are effective in providing comprehensive, accessible, and continuous primary care. This study aims to evaluate the relationship between PCMH recognition in HCs and clinical performance.MethodsData for this study came from the 2012 Uniform Data System (UDS) as well as a survey of HCs' PCMH recognition achievement. The dependent variables included all 16 measures of clinical performance collected through UDS. Control measures included HC patient, provider, and practice characteristics. Bivariate analyses and multiple logistic regressions were conducted to compare clinical performance between HCs with and without PCMH recognition.FindingsHealth centers that receive PCMH recognition generally performed better on clinical measures than HCs without PCMH recognition. After controlling for HC patient, provider, and practice characteristics, HCs with PCMH recognition reported significantly better performance on asthma‐related pharmacologic therapy, diabetes control, pap testing, prenatal care, and tobacco cessation intervention.ConclusionThis study establishes a positive association between PCMH recognition and clinical performance in HCs. If borne out in future longitudinal studies, policy makers and practices should advance the PCMH model as a strategy to further enhance the quality of primary care.
The Great Lakes Hydrography Dataset: Consistent, Binational Watersheds for the Laurentian Great Lakes Basin
Authors: Forsyth Danielle K. , Riseng Catherine M. , Wehrly Kevin E. , Mason Lacey A. , Gaiot John , Hollenhorst Tom , Johnston Craig M. , Wyrzykowski Conrad , Annis Gust , Castiglione Chris , Todd Kent , Robertson Mike , Infante Dana M. , Wang Lizhu , McKenna James E. , Whelan Gary 
Published: June 2016

AbstractEcosystem‐based management of the Laurentian Great Lakes, which spans both the United States and Canada, is hampered by the lack of consistent binational watersheds for the entire Basin. Using comparable data sources and consistent methods, we developed spatially equivalent watershed boundaries for the binational extent of the Basin to create the Great Lakes Hydrography Dataset (GLHD). TheGLHDconsists of 5,589 watersheds for the entire Basin, covering a total area of approximately 547,967 km2, or about twice the 247,003 km2surface water area of the Great Lakes. TheGLHDimproves upon existing watershed efforts by delineating watersheds for the entire Basin using consistent methods; enhancing the precision of watershed delineation using recently developed flow direction grids that have been hydrologically enforced and vetted by provincial and federal water resource agencies; and increasing the accuracy of watershed boundaries by enforcing embayments, delineating watersheds on islands, and delineating watersheds for all tributaries draining to connecting channels. In addition, theGLHDis packaged in a publically available geodatabase that includes synthetic stream networks, reach catchments, watershed boundaries, a broad set of attribute data for each tributary, and metadata documenting methodology. TheGLHDprovides a common set of watersheds and associated hydrography data for the Basin that will enhance binational efforts to protect and restore the Great Lakes.
megasat: automated inference of microsatellite genotypes from sequence data
Authors: Zhan Luyao , Paterson Ian G. , Fraser Bonnie A. , Watson Beth , Bradbury Ian R. , Nadukkalam Ravindran Praveen , Reznick David , Beiko Robert G. , Bentzen Paul 
Published: June 2016

Abstractmegasat is software that enables genotyping of microsatellite loci using next‐generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length–frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0–1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.
The commercial use of digital media to market alcohol products: a narrative review
Authors: Lobstein Tim , Landon Jane , Thornton Nicole , Jernigan David 
Published: June 2016

AbstractBackground and aimsThe rising use of digital media in the last decade, including social networking media and downloadable applications, has created new opportunities for marketing a wide range of goods and services, including alcohol products. This paper aims to review the evidence in order to answer a series of policy‐relevant questions: does alcohol marketing through digital media influence drinking behaviour or increases consumption; what methods of promotional marketing are used, and to what extent; and what is the evidence of marketing code violations and especially of marketing to children?Method and findingsA search of scientific, medical and social journals and authoritative grey literature identified 47 relevant papers (including 14 grey literature documents). The evidence indicated (i) that exposure to marketing through digital media was associated with higher levels of drinking behaviour; (ii) that the marketing activities make use of materials and approaches that are attractive to young people and encourage interactive engagement with branded messaging; and (iii) there is evidence that current alcohol marketing codes are being undermined by alcohol producers using digital media.ConclusionsThere is evidence to support public health interventions to restrict the commercial promotion of alcohol in digital media, especially measures to protect children and youth.
Sublingual misoprostol for management of empty sac or missed miscarriage: The first two years’ experience at a metropolitan Australian hospital
Authors: Mcgee Therese M. , Diplock Hayley , Lucewicz Ania 
Published: June 2016

BackgroundMisoprostol management of miscarriage is only now becoming widely used in Australia.AimsTo review the efficacy, safety and the popularity of outpatient sublingual misoprostol in empty sac/missed miscarriage management over its first two years of availability in a metropolitan Australian hospital.Materials and methodsA retrospective cohort review was undertaken of women choosing sublingual misoprostol 600 μg (three tablets) × three doses for miscarriage management. Principal outcomes assessed were miscarriage resolution without the need for curettage and complications. Additionally, the relative popularity of misoprostol versus surgery by place of birth and over time, and the return of pregnancy tissue for histology were analysed.ResultsBetween 1 December 2012 and 30 November 2014, 279 women chose sublingual misoprostol for nonurgent miscarriage management, while 420 chose surgery (40 and 60%, respectively). Of the misoprostol cohort, 269 had complete data; 239 of 269 (88.8%) had resolution without curettage, nine (3.3%) had acute curettage, 21 (7.8%) had nonacute curettage, 30 (11.15%) had unplanned emergency department presentation, 11 (4.1%) had unplanned admission, three (1.1%) had blood transfusion and one (0.4%) had an infection requiring admission. Misoprostol was as popular with Australian‐born as overseas‐born women; 53.5% of patients returned histopathology specimens; one (0.7%) demonstrated partial hydatidiform mole.ConclusionsOutpatient management of missed/empty gestational sac miscarriage using sublingual misoprostol is associated with a high rate of avoiding curettage and the low rate of complication. It is equally popular with Australian‐born and overseas‐born women. Just over 50% returned pregnancy tissue for analysis.
The cnidome and internal morphology of Lophelia pertusa (Linnaeus, 1758) (Cnidaria, Anthozoa)
Authors: Strömberg Susanna M. , Östman Carina 
Published: June 2016

AbstractThe cnidome of the scleractinian cold‐water coral Lophelia pertusa (Linnaeus, 1758, syn. Lophohelia prolifera) was described by Carlgren in 1940. Due to a renewed interest in the cnidae of L. pertusa, specifically comparisons of adult and larval cnidae and their functions, we now redescribe the cnidome from material collected at the Tisler reef in Norway, close to Carlgren's collection site at Saekken (Sweden). Cnidae from column, tentacles, actinopharynx, mesenterial filaments and acontia were investigated. Fresh tissue preparations were compared to histological preparations of decalcified polyps to verify the presence of cnidocysts and secretory cells, and their composition and organization within tissues. The cnidome included microbasic b‐mastigophores, microbasic and mesobasic p‐mastigophores, holotrichous isorhizas and spirocysts. The nematocyst type cnidae (b‐, p‐mastigophores, isorhizas) appeared in different size classes with different distributions within the tissue. Spirocysts were highly variable in shape and size, without distinct size classes. In addition, developing stages of cnidae were documented, with new observations on the succession of p‐mastigophore shaft development. The present observations were in general congruent with the cnidocyst descriptions from L. prolifera made by Carlgren; however, a tiny cnida, possibly of isorhiza type, has been added. Finally, the use of the term acontia is discussed.
Population PK–PD analyses of CD25 occupancy, CD56bright NK cell expansion, and regulatory T cell reduction by daclizumab HYP in subjects with multiple sclerosis
Authors: Diao Lei , Hang Yaming , Othman Ahmed A. , Mehta Devangi , Amaravadi Lakshmi , Nestorov Ivan , Tran Jonathan Q. 
Published: June 2016

AimDaclizumab high yield process (HYP) is a humanized IgG1 monoclonal antibody that binds to the α‐subunit of the interleukin‐2 receptor and is being developed for treatment of multiple sclerosis (MS). This manuscript characterized the pharmacokinetic–pharmacodynamic (PK–PD) relationships of daclizumab HYP in subjects with MS.MethodsApproximately 1400 subjects and 7000 PD measurements for each of three biomarkers [CD25 occupancy, CD56bright natural killer (NK) cell count, regulatory T cell (Treg) count] from four clinical trials were analyzed using non‐linear mixed effects modelling. Evaluated regimens included 150 or 300 mg subcutaneous (s.c.) every 4 weeks.ResultsCD25 occupancy was characterized using a sigmoidal maximum response (Emax) model. Upon daclizumab HYP treatment, CD25 saturation was rapid with complete saturation occurring after approximately 7 h and maintained when daclizumab HYP serum concentration was ≥5 mg l‐1. After the last 150 mg s.c. dose, unoccupied CD25 returned to baseline levels in approximately 24 weeks, with daclizumab HYP serum concentration approximately ≤1 mgl‐11L. CD56bright NK cell expansion was characterized using an indirect response model. Following daclizumab HYP 150 mg s.c. every 4 weeks, expansion plateaus approximately at week 36, at which the average maximum expansion ratio is 5.2. After the last dose, CD56bright NK cells gradually declined to baseline levels within 24 weeks. Treg reduction was characterized by a sigmoidal Emax model. Average maximum reduction of 60% occurred approximately 4 days post 150 mg s.c. dose. After the last dose, Tregs were projected to return to baseline levels in approximately 20 weeks.ConclusionsRobust PK–PD models of CD25 occupancy, CD56bright NK cell expansion and Treg reduction by daclizumab HYP were developed to characterize its key pharmacodynamic effects in the target patient population.
Learning and assessment with images: A view of cognitive load through the lens of cerebral blood flow
Authors: Loftus Jay J. , Jacobsen Michele , Wilson Timothy D. 
Published: June 2016

AbstractUnderstanding the relationship between cognitive processing and learner performance on tasks using digital media has become increasingly important as the transition towards online learning programs increases. Determining the impact of implementation of instructional resources is often limited to performance outcomes and comparisons to the status quo. This study measured changes in cerebral blood velocity (CBV) of the right middle cerebral artery during visual learning tasks using static images. Transcranial Doppler ultrasonography was used to compare the changes in CBV during learning of individuals with high and low spatial ability. Our results show that there is a slight increase from baseline values of CBV in individuals with high spatial ability during the learning task for the present study. In contrast, individuals with low spatial ability experience a decrement from baseline during the learning task. These results suggest spatial ability mitigates cognitive load and potentially has an impact on learner performance on visual learning tasks.
Cerebral Hypoperfusion and the Energy Deficit in Alzheimer's Disease
Authors: Love Seth , Miners J.Scott 
Published: June 2016

AbstractThere is a perfusion deficit in Alzheimer's disease (AD), commencing in the precuneus and spreading to other parts of the cerebral cortex. The deficit anticipates the development of dementia, contributes to brain damage, and is caused by both functional and structural abnormalities of the cerebral vasculature. Most of the abnormalities are probably secondary to the accumulation of Aβ but the consequent hypoperfusion may, in turn, increase Aβ production. In the early stages of disease, abnormalities that cause vasoconstriction predominate. These include cholinergic vascular denervation, inhibition of endothelial nitric oxide synthase, increased production of endothelin‐1 production and possibly also of angiotensin II. Patients with AD also have an increased prevalence of structural disease of cerebral microvessels, particularly CAA and capillary damage, and particularly in the later stages of disease these are likely to make an important contribution to the cerebral hypoperfusion. The metabolic abnormalities that cause early vascular dysfunction offer several targets for therapeutic intervention. However, for intervention to be effective it probably needs to be early. Prolonged cerebral hypoperfusion may induce compensatory circulatory changes that are themselves damaging, including hypertension and small vessel disease. This has implications for the use of antihypertensive drugs once there is accumulation of Aβ within the brain.
Alzheimer's Disease: From Mitochondrial Perturbations to Mitochondrial Medicine
Authors: Cardoso Susana , Carvalho Cristina , Correia Sónia C. , Seiça Raquel M. , Moreira Paula I. 
Published: June 2016

AbstractAge‐related neurodegenerative diseases such as Alzheimer's disease (AD) are distressing conditions causing countless levels of suffering for which treatment is often insufficient or inexistent. Considered to be the most common cause of dementia and an incurable, progressive neurodegenerative disorder, the intricate pathogenic mechanisms of AD continue to be revealed and, consequently, an effective treatment needs to be developed. Among the diverse hypothesis that have been proposed to explain AD pathogenesis, the one concerning mitochondrial dysfunction has raised as one of the most discussed with an actual acceptance in the field. It posits that manipulating mitochondrial function and understanding the deficits that result in mitochondrial injury may help to control and/or limit the development of AD. To achieve such goal, the concept of mitochondrial medicine places itself as a promising gathering of strategies to directly manage the major insidious disturbances of mitochondrial homeostasis as well as attempts to directly or indirectly manage its consequences in the context of AD. The aim of this review is to summarize the evolution that occurred from the establishment of mitochondrial homeostasis perturbation as masterpieces in AD pathogenesis up until the development of mitochondrial medicine. Following a brief glimpse in the past and current hypothesis regarding the triad of aging, mitochondria and AD, this manuscript will address the major mechanisms currently believed to participate in above mentioned events. Both pharmacological and lifestyle interventions will also be reviewed as AD‐related mitochondrial therapeutics.
Design, synthesis, biological evaluation, NMR and DFT studies of structurally simplified trimethoxy benzamides as selective P‐glycoprotein inhibitors: the role of molecular flatness
Authors: Stefanachi Angela , Mangiatordi Giuseppe Felice , Tardia Piero , Alberga Domenico , Leonetti Francesco , Niso Mauro , Colabufo Nicola Antonio , Adamo Carlo , Nicolotti Orazio , Cellamare Saverio 
Published: June 2016

In a recent investigation carried out on a panel of trimethoxybenzanilides, we showed that the formation of an intramolecular hydrogen bond is a key element for tuning P‐gp inhibitory activity. In this study, we designed new structurally simplified trimethoxy benzamides (5–17, Table ) with the aim to uncover the minimal molecular requirements needed for P‐gp inhibition. The new prepared smaller‐sized compounds exhibited IC50 in the low micromolar range. The combined use of NMR and DFT studies suggested that molecular flatness is causatively related to the P‐gp inhibition. Our results clearly pointed out that concerted theoretical and experimental approaches herein presented might be very helpful in addressing the design of structurally simplified and highly efficient compounds biasing P‐gp protein.
Role of podoplanin in the high interleukin-17A secretion resulting from interactions between activated lymphocytes and psoriatic skin-derived mesenchymal cells
Authors: Noack M , Ndongo-Thiam N'D , Miossec P 
Published: June 2016

Summary
In the context of psoriasis, T helper type 17 (Th17) cells infiltrate the inflammatory site and interact with local mesenchymal cells, including skin fibroblasts. The aim of this work was to study the interactions of skin-derived fibroblasts with peripheral blood mononuclear cells (PBMC) with a focus on the Th17 pathway and to identify a mechanism which leads to a high interleukin (IL)−17 secretion. A co-culture system between PBMC and skin fibroblasts was developed. Healthy and patient PBMC were added to non-lesional or lesional skin fibroblasts at a 5:1 ratio for 48 h in the presence or not of activation with phytohaemagglutinin (PHA). Monocytes were removed or not by adherence before the co-culture. An anti-podoplanin antibody was also used during the co-culture. Cytokine production (IL-8, IL-6, IL-1β and IL-17) was measured by enzyme-linked immunosorbent assay (ELISA) and cell staining (CD3, CD4, IL-17 and podoplanin) by flow cytometry. Without T cell receptor (TCR) activation, IL-8, IL-6 and IL-1β production increased in PBMC-fibroblast co-culture compared to PBMC alone. No additional effect was observed with TCR activation, with no difference in the Th17 cell percentage in activated-PBMC alone or co-cultured. Conversely, IL-17 production was increased highly only in co-cultures between control and patient activated-PBMC and skin fibroblasts. Removal of monocytes decreased cytokine production, notably that of IL-17. Addition of an anti-podoplanin antibody decreased IL-17 secretion by 60%. Interactions between resting PBMC and fibroblasts induce the IL-8, IL-6 and IL-1β production. PBMC activation and cell interactions are critical for a high IL-17 secretion. Podoplanin contributes largely to this massive IL-17 secretion.