bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling animal movement using the Argos satellite telemetry location error ellipse
Authors: McClintock Brett T. , London Joshua M. , Cameron Michael F. , Boveng Peter L. 
Published: November 2014

Summary

The Argos satellite telemetry system is popular for studying the movement and space use of marine animals. The life histories of marine mammals, in particular, result in a relatively large proportion of inaccurate locations, thus making analysis methods that do not account for location measurement error inappropriate for these data. Using a new Kalman filtering algorithm, Argos now provides locations and estimated error ellipses associated with each satellite fix, but to our knowledge, the location error ellipse has yet to be incorporated into analyses of animal movement or space use.

We first present an observation model utilizing the Argos error ellipse and then demonstrate how this observation model can be combined with a simple three‐dimensional movement model in a state‐space formulation to infer activity budgets and movement characteristics from location and dive data of two species of seal, the bearded seal (Erignathus barbatus) and the Hawaiian monk seal (Monachus schauinslandi). These example data sets are of variable quality and represent species that differ in both space use and latitudinal range relative to the polar orbits of Argos satellites. We also compare the results from our error ellipse model with those from an approximate (isotropic) error circle model.

We found the error circle to be a crude approximation of the actual anisotropic error ellipse for the higher quality bearded seal data, but inferences from the lower quality Hawaiian monk seal data were more robust to the choice of observation model. In both examples, we found the theoretical bivariate normal distribution corresponding to the error ellipse often failed to adequately explain the most extreme location outliers.

In practice, we suspect the inferential consequences of using traditional isotropic location quality classes or other crude approximations in lieu of the error ellipse will be largely case‐dependent. We support the Argos recommendation that practitioners wishing to more properly account for location measurement error utilize the error ellipse in analyses. However, the continued presence of outliers using the new algorithm suggests practitioners should consider using a fat‐tailed distribution derived from the error ellipse (e.g. bivariate t‐distribution) or filtering extreme outliers during data pre‐processing.
Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution
Authors: Altermatt Florian , Fronhofer Emanuel A. , Garnier Aurélie , Giometto Andrea , Hammes Frederik , Klecka Jan , Legrand Delphine , Mächler Elvira , Massie Thomas M. , Pennekamp Frank , Plebani Marco , Pontarp Mikael , Schtickzelle Nicolas , Thuillier Virginie , Petchey Owen L. 
Published: November 2014

SummaryLaboratory microcosm experiments using protists as model organisms have a long tradition and are widely used to investigate general concepts in population biology, community ecology and evolutionary biology. Many variables of interest are measured in order to study processes and patterns at different spatiotemporal scales and across all levels of biological organization. This includes measurements of body size, mobility or abundance, in order to understand population dynamics, dispersal behaviour and ecosystem processes. Also, a variety of manipulations are employed, such as temperature changes or varying connectivity in spatial microcosm networks.Past studies, however, have used varying methods for maintenance, measurement, and manipulation, which hinders across‐study comparisons and meta‐analyses, and the added value they bring. Furthermore, application of techniques such as flow cytometry, image and video analyses, andin situenvironmental probes provide novel and improved opportunities to quantify variables of interest at unprecedented precision and temporal resolution.Here, we take the first step towards a standardization of well‐established and novel methods and techniques within the field of protist microcosm experiments. We provide a comprehensive overview of maintenance, measurement and manipulation methods. An extensive supplement contains detailed protocols of all methods, and these protocols also exist in a community updateable online repository.We envision that such a synthesis and standardization of methods will overcome shortcomings and challenges faced by past studies and also promote activities such as meta‐analyses and distributed experiments conducted simultaneously across many different laboratories at a global scale.
Impact of corneal cross‐linking on topical drug penetration in humans
Authors: Tappeiner Christoph , Tschopp Markus , Schuerch Kaspar , Frueh Beatrice E. 
Published: November 2014

AbstractPurposeTo analyse the influence of corneal cross‐linking (CXL) with ultraviolet‐A (UV‐A) and riboflavin on drug permeability in human subjects.MethodsKeratoconus patients (n = 23; mean age 26.9 ± 5.8 years) undergoing a standard CXL procedure with UV‐A (5.4 J/cm2, 30 min) and riboflavin in one eye were included in the study. The pupillary diameter, measured before and every 3 min for 30 min after the topical application of one drop of 2% pilocarpine, was used as an indirect measure of the corneal permeability. The pupillary diameter was measured with an infrared pupillometer device before (baseline) and 4 months after CXL.ResultsPrior to pilocarpine application, no significant difference in the pupillary diameter was detected before CXL and 4 months later. The mean decrease in the pupillary diameter after the application of pilocarpine was similar at baseline and the 4‐month follow‐up visit: mean decreases of 3.9 and 3.7 mm were observed 30 min after pilocarpine application, respectively (p > 0.05).ConclusionsNo significant influence of CXL on the corneal penetration of topically applied pilocarpine was observed in this clinical study.
High expression of metadherin correlates with malignant pathological features and poor prognostic significance in papillary thyroid carcinoma
Authors: Li Wen‐Fang , Wang Gen , Zhao Zong‐Bin , Liu Chang‐An 
Published: November 2014

SummaryBackgroundMetadherin (MTDH) protein, also called astrocyte elevated gene‐1 (AEG‐1) is over expressed in a variety of malignant tumours, and is closely related to tumour invasion and the poor prognosis.ObjectiveThis study tries to explore the clinical pathological significance of MTDH expression in a large cohort of patients with PTC.Design and patientsImmunohistochemistry was used to detect MTDH expression in 156 cases of PTC, 6 cases of anaplastic thyroid carcinoma (ATC), 10 cases of multinodular goitre (MNG) and 10 cases of thyroid adenoma tissues who received a thyroid operation between June 2003 and July 2008.MeasurementsClinical pathological data of 156 cases of PTC were analysed according to MTDH expression. The Kaplan–Meier method was used to plot survival curves and log‐rank test to compare the postoperative survival results. The prognostic meaning of MTDH expression in PTC was evaluated by Cox regression analysis.ResultsThe positive expression rates of MTDH in PTC and ATC tissues were 37·2% (58/156) and 50% (3/6), respectively, and MTDH positive expression rates were both 10% (1/10) in MNG and thyroid adenoma tissues. High MTDH expression in PTC was associated with larger tumour size (P = 0·030), high rates of lymph node (P = 0·041) and distant metastasis (P = 0·028), but no relation with the patient age, gender, tumour multicenter, extrathyroid invasion and tumour grade. High MTDH expression was associated with recurrence‐free survival (RFS) and disease‐specific survival rate (DSS) (P = 0·014, P = 0·001, respectively). Cox regression analysis showed that high MTDH expression was independent prognostic indicators for RFS and DSS in patients with PTC (P = 0·023 and P = 0·035, respectively).ConclusionHigh MTDH expression in PTC might play an important role in tumour growth and metastasis, and targeting MTDH treatment might have potential therapeutic value for patients with PTC.
Dopamine receptor subtype 2 expression profile in nonfunctioning pituitary adenomas and in vivo response to cabergoline therapy
Authors: Vieira Neto Leonardo , Wildemberg Luiz Eduardo , Moraes Aline B. , Colli Leandro M. , Kasuki Leandro , Marques Nelma Verônica , Gasparetto Emerson L. , de Castro Margaret , Takiya Christina Maeda , Gadelha Mônica R. 
Published: November 2014

SummaryObjectivesTo determine the dopamine receptor subtype 2 (DR2) mRNA levels and protein expression and to evaluate the effect of adjuvant cabergoline therapy on tumour volume (TV) in patients with postoperative residual nonfunctioning pituitary adenoma (NFPA).MethodsThe mRNA expression was quantified by real‐time RT‐PCR (TaqMan®), and protein expression was evaluated by immunohistochemistry. Tumours were classified according to the percentage of immunostained cells for DR2 as scores 1 (<50% of stained cells) or 2 (≥50%). Cabergoline was started at least 6 months after surgery in nine patients with residual tumours (3 mg/week). The cabergoline effect was prospectively evaluated by magnetic resonance imaging using three‐dimensional volume calculation. TV reduction >25% was considered significant.ResultsThe DR2 mRNA expression was variable but was observed in 100% of the samples (N = 20). DR2 protein expression was also observed in all the tumours (N = 34). Twenty‐nine tumours (85%) were classified as score 2. The median DR2 mRNA expression was higher in the tumours classified as score 2 compared with score 1 (P = 0·007). TV reduction with cabergoline therapy was observed in 67% of the patients (6/9). The median TV before and after 6 months of treatment was 1·90 cm3 (0·61–8·74) and 1·69 cm3 (0·36–4·20) [P = 0·02], respectively.ConclusionIn conclusion, DR2 is expressed in all adenomas and the majority of the patients in this study displayed tumour shrinkage on cabergoline (CAB) therapy. Thus, CAB might be useful in adjuvant therapy in NFPA patients with residual tumours after surgery.
Bone resorption in different parts of the mandible in patients restored with an implant overdenture. A retrospective radiographic analysis
Authors: Kremer Urs , Schindler Sven , Enkling Norbert , Worni Andreas , Katsoulis Joannis , Mericske‐Stern Regina 
Published: November 2014

AbstractAimThis study investigated the pattern of resorption of the mandibular ridge under implant‐supported overdentures.Material and methodsFiles of 60 patients were available for analysis (45 women and 15 men, mean age at the time of the follow‐up 76.5 ± 8.5 years, 54 patients restored with bars, 6 with ball anchors). A baseline was defined by different stable landmarks and quartered. Linear measurements from this baseline at different clinical relevant sites approximately at: (i) the area close to the mental foramen/close to the implant, (ii) the chewing center, and (iii) the distal edge of the denture flange were carried out on rotational tomograms (OPTs). The OPTs were taken after prosthetic restoration and at an individual follow‐up time (mean 11 ± 4.75 years). The known implant length served to scale each measurement to avoid any distortion errors.ResultsThe resorption rate showed a high individual variation, but among the three sites, the difference was highly significant. Median values of site (i) left = −0.07 mm/right = +0.05 mm, site (ii) left = −0.60 mm/right = −0.55 mm, and site (iii) left = −1.58 mm/right = −2.01 mm.ConclusionsThe load of the distal flange of a mandibular implant overdenture increases bone resorption as a local factor, whereas implants may help to prevent resorption in the neighboring bone. An individual‐adapted follow‐up protocol should be established for each patient restored with an implant overdenture.
Activating Cannabinoid Receptor 2 Alleviates Pathogenesis of Experimental Autoimmune Encephalomyelitis Via Activation of Autophagy and Inhibiting NLRP3 Inflammasome
Authors: Shao Bo‐Zong , Wei Wei , Ke Ping , Xu Zhe‐Qi , Zhou Jv‐Xiang , Liu Chong 
Published: November 2014

SummaryAimsActivation of cannabinoid receptor 2 (CB2R) has been reported to ameliorate the pathogenesis of experimental autoimmune encephalomyelitis (EAE). In this study, we examined whether autophagy is involved in the beneficial effect of CB2R on EAE and explored the mechanism with a focus on inflammasome activation.MethodsEAE severity was analyzed with clinical score and histological score stained by hematoxylin and eosin or luxol fast blue in spinal cord. Immunoblot analysis was conducted to detect proteins of NOD‐like receptor family, pyrin domain containing 3 (NLRP3) inflammasome‐related caspase‐1 (Casp‐1) and the maturation of interleukin (IL)‐1β as well as autophagy‐related light chain 3 (LC3), and Beciln 1 both in vivo and in vitro. Reverse transcription and real‐time PCR were used to detect mRNA of NLRP3, IL‐1β and Casp‐1. Autophagy‐related gene 5 (ATG5)‐specific siRNA was transiently transfected in BV2 microglia, and immunofluorescence staining was carried out to detect the expression of NLRP3, caspase recruitment domain (ASC), and pro‐caspase‐1.ResultsThe current data indicated that deleting CB2R decreased the expression of LC3‐II/LC3‐I ratio, Beclin 1 and increased caspase‐1 activation and IL‐1β production in the spinal cord of EAE mice, whereas activation of CB2R with a specific agonist HU‐308 induced inverse effects. Further study indicated that HU‐308 could promote autophagy and inhibit expression and activation of NLRP3 inflammasome in BV2 microglia. Blocking autophagy by ATG5‐specific siRNA dismissed the effort of CB2R in mediating NLRP3 inflammasome in vitro.ConclusionCollectively, our results demonstrated for the first time that CB2R plays a protective role in EAE through promoting autophagy and inhibiting NLRP3 inflammasome activation.
The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China
Authors: Liu Juan , Yan Hai‐Fei , Newmaster Steven G. , Pei Nancai , Ragupathy Subramanyam , Ge Xue‐Jun 
Published: November 2014

AbstractAimRapid and accurate species identification is the foundation for biodiversity assessment. DNA barcoding has been shown to be an effective tool to overcome the taxonomic impediment to facilitate biodiversity conservation in temperate forests. However, this tool has rarely been considered for use in tropical forests. This study aims to investigate the utility and species resolution of DNA barcoding in a subtropical region.LocationThe Dinghushan National Nature Reserve (DNNR) in China.MethodsA DNA barcoding database was constructed for 531 trees present in the DNNR. We used a phylogenetic method (neighbour‐joining trees) and sequence similarity (all‐to‐all BLASTn searches) to evaluate the utility and species resolution of five DNA barcode regions (rbcL, matK, ITS, ITS2 and trnH‐psbA), both singly and in combinations of two or three region.ResultsThe combination of rbcL + matK + ITS had the highest species resolution (94.19%). However, when considering the difficulty of sequence recoverability, rbcL + ITS2 performed best (64.64%). Species resolution for large genera containing more than two species was substantially lower than that for small genera with one and two species per genus. Local small spatial scales (1‐ha quadrats) resulted in moderately improved species resolution (70.82% for rbcL + ITS2) compared to larger spatial scales (20 and 1133 ha). We document incongruent signals between nuclear and cpDNA regions and the challenges associated with barcoding large genera inherent to subtropical floras.Main conclusionsThis study considerably expands the global DNA barcode database for subtropical trees. Based on cost‐effectiveness and the trade‐off between sequence recovery and species resolution, we suggest that the rbcL + ITS2 barcode combination is an effective tool for documenting plant diversity in the DNNR. This study also sheds some light on the limitations and challenges for the application of barcoding to conservation biogeography in subtropical forests.
Representing taxonomic, phylogenetic and functional diversity: new challenges forMediterranean marine‐protected areas
Authors: Guilhaumon François , Albouy Camille , Claudet Joachim , Velez Laure , Ben Rais Lasram Frida , Tomasini Jean‐Antoine , Douzery Emmanuel J. P. , Meynard Christine N. , Mouquet Nicolas , Troussellier Marc , Araújo Miguel B. , Mouillot David 
Published: November 2014

AbstractAimTo assess gaps in the representation of taxonomic, phylogenetic and functional diversity among coastal fishes inMediterranean marine‐protected areas (MPAs).LocationMediterraneanSea.MethodsWe first assessed gaps in the taxonomic representation of the 340 coastal fish species inMediterraneanMPAs, with representation targets (the species range proportion to be covered byMPAs) set to be inversely proportional to species' range sizes. We then asked whetherMPAs favoured representation of phylogenetically and functionally more distinct species or whether there was a tendency to favour less distinctive ones. We finally evaluated the overall conservation effectiveness of theMPAs using a metric that integrates species' phylogenetic and functional relationships and targets achievement. The effectiveness of theMPAsystem at protecting biodiversity was assessed by comparison of its achievements against a null model obtained by siting currentMPAs at random over the study area.ResultsAmong the coastal fish species analysed, 16 species were not covered by anyMPA. All the remaining species only partially achieved the pre‐defined representation target. The currentMPAsystem missed fewer species than expected from sitingMPAs at random. However,c. 70% of the species did not achieve better protection in the currentMPAs than expected from sitingMPAs at random. Functional and evolutionary distinctiveness were weakly correlated with target achievement. The observed coverage of taxonomic, phylogenetic and functional diversity was not different or lower than expected from sitingMPAs at random.Main conclusionsTheMediterraneanMPAsystem falls short in meeting conservation targets for coastal fish taxonomic diversity, phylogenetic diversity and functional diversity.MediterraneanMPAs do not encompass more biodiversity than expected by chance. This study reveals multiple ongoing challenges and calls for regional collaboration for the extension of theMediterranean system ofMPAs to meet international commitments and reduce the ongoing loss of marine biodiversity.
Jet Length/Velocity Ratio: A New Index for Echocardiographic Evaluation of Chronic Aortic Regurgitation
Authors: Güvenç Tolga Sinan , Karaçimen Denizhan , Erer Hatice Betül , İlhan Erkan , Sayar Nurten , Karakuş Gültekin , Çekirdekçi Elif , Eren Mehmet 
Published: November 2014

BackgroundManagement of aortic regurgitation depends on the assessment for severity. Echocardiography remains as the most widely available tool for evaluation of aortic regurgitation. In this manuscript, we describe a novel parameter, jet length/velocity ratio, for the diagnosis of severe aortic regurgitation.Methods and ResultsA total of 30 patients with aortic regurgitation were included to this study. Severity of aortic regurgitation was assessed with an aortic regurgitation index incorporating five echocardiographic parameters. Jet length/velocity ratio is calculated as the ratio of maximum jet penetrance to mean velocity of regurgitant flow. Jet length/velocity ratio was significantly higher in patients with severe aortic regurgitation (2.03 ± 0.53) compared to patients with less than severe aortic regurgitation (1.24 ± 0.32, P < 0.001). Correlation of jet length/velocity ratio with aortic regurgitation index was very good (r2 = 0.86) and correlation coefficient was higher for jet length/velocity ratio compared to vena contracta, jet width/LVOT ratio and pressure half time. For a cutoff value of 1.61, jet length/velocity ratio had a sensitivity of 92% and specificity of 88%, with an AUC value of 0.955.ConclusionsJet length/velocity ratio is a novel parameter that can be used to assess severity of chronic aortic regurgitation. Main limitation for usage of this novel parameter is jet impringement to left ventricular wall.
Relation of Epicardial Fat Thickness to the Severity of Heart Failure in Patients with Nonischemic Dilated Cardiomyopathy
Authors: Tabakci Mehmet Mustafa , Durmuş Halil İbrahim , Avci Anil , Toprak Cuneyt , Demir Serdar , Arslantaş Uğur , Cerşit Sinan , Fidan Serdar , Kulahçioğlu Şeyhmus , Batgerel Ulaankhuu , Kargin Ramazan 
Published: November 2014

BackgroundThe aim of this study was to assess whether epicardial fat thickness (EFT) is associated with the severity of heart failure in patients with nonischemic dilated cardiomyopathy (NICMP).MethodsThe study group was composed of 93 patients with NICMP and38 age‐ and sex‐matched healty individuals as the control group. The EFT was identified during end‐systole at the point on the free wall of the right ventricle.ResultsPatients with NICMP had significantly lower mean EFT than those in the control group (4.1 ± 0.8 vs. 6.1 ± 1.8 mm, P < 0.001). EFT was thinnest in patients with New York Heart Association (NYHA) functional class III or IV (3.5 ± 0.5, P < 0.001). There was a significant correlation between EFT, left ventricle EF (r = 0.540 P < 0.001), and B‐type natriuretic peptide (BNP) (r = −0.695, P < 0.001) values in patients with NICMP. In addition, when EFT was corrected for BMI, EFT/BMI was lower in patients with NYHA functional class III–IV than patients with NYHA class I–II and control group (0.13 ± 0.01, 0.16 ± 0.02, 0.23 ± 0.04, respectively; P < 0.001). There was a significant correlation between EFT/BMI, left ventricle EF (r = 0.489, P < 0.001), and BNP (r = −0.549, P < 0.001) in patients with NICMP. In multivariate regression analysis, EFT (P = 0.009), BNP (P = 0.039), and left atrium volume index (P = 0.039) were independently associated with impaired functional status.ConclusionEchocardiographic EFT is an inexpensive, simple, and readily available marker that may be used to asses the severity of chronic heart failure in patients with NICMP.