bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic eigenvector maps: a framework to model and predict species traits
Authors: Guénard Guillaume , Legendre Pierre , Peres‐Neto Pedro 
Published: September 2013

Summary

Phylogenetic signals are the legacy related to evolutionary processes shaping trait variation among species. Biologists can use these signals to tackle questions related to the evolutionary processes underlying trait evolution, estimate the ancestral state of a trait and predict unknown trait values from those of related species (i.e. ‘phylogenetic modelling’). Approaches to model phylogenetic signals rely on quantitative descriptors of the structures representing the consequences of evolution on trait differences among species.

Here, we propose a novel framework to model phylogenetic signals: Phylogenetic Eigenvectors Maps (PEM). PEM are a set of eigenfunctions obtained from the structure of a phylogenetic graph, which can be a standard phylogenetic tree or a phylogenetic tree with added reticulations. These eigenfunctions depict a set of potential patterns of phenotype variation among species from the structure of the phylogenetic graph. A subset of eigenfunctions from a PEM is selected for the purpose of predicting the phenotypic values of traits for species that are represented in a tree, but for which trait data are otherwise lacking. This paper introduces a comprehensive view and the computational details of the PEM framework (with calculation examples), a simulation study to demonstrate the ability of PEM to predict trait values and four real data examples of the use of the framework.

Simulation results show that PEM are robust in representing phylogenetic signal and in estimating trait values.

The method also performed well when applied to the real‐world data: prediction coefficients were high (0·76–0·88), and no notable model biases were found.

Phylogenetic modelling using PEM is shown to be a useful methodological asset to disciplines such as ecology, ecophysiology, ecotoxicology, pharmaceutical botany, among others, which can benefit from estimating trait values that are laborious and often expensive to obtain.
Is pregnancy a trigger for recovery from an eating disorder?
Authors: Coker Elise L. , Mitchell‐Wong Lisa A. , Abraham Suzanne F. 
Published: September 2013

AbstractObjectivePregnancy produces significant changes in a woman's body weight and shape. This study examines changes in body mass index (BMI) and quality of life related to eating disorders (QOLED) prior to, during and after pregnancy in both women with and without eating disorders.DesignProspective study.SettingRoyal North Shore Hospital, Northshore Private and Northside Clinic, Sydney.SampleThe study comprised 178 pregnant women.MethodsWomen completed the QOLED questionnaire retrospectively before pregnancy, prospectively for each trimester of pregnancy and at 3, 6 and 12 months postpartum. The QOLED is a validated questionnaire used to assess quality of life related to eating disorders, including physical health, social function and psychological state. Changes in current BMI and QOLED were examined across the stages of pregnancy.ResultsThe women with eating disorders (n = 19) had significantly lower BMIs before, during and after pregnancy. Both women with and without eating disorders had significant weight gain in the second and third trimesters compared with pre‐pregnancy. There were significant interactions between stage of pregnancy and eating disorder status on global QOLED scores. These scores improved significantly during second and third trimesters compared with pre‐pregnancy but varied after pregnancy, particularly among women with eating disorders. The QOLED scores for women with eating disorders remained within the eating disorder range throughout the study.ConclusionsPregnancy is not associated with recovery from eating disorders. Women with eating disorders need support during pregnancy and the postnatal year, and should not be told that their eating disorder will improve during this time.
Valsalva manoeuver, intra‐ocular pressure, cerebrospinal fluid pressure, optic disc topography: Beijing intracranial and intra‐ocular pressure study
Authors: Zhang Zheng , Wang Xiaolei , Jonas Jost B. , Wang Huaizhou , Zhang Xiaojun , Peng Xiaoxia , Ritch Robert , Tian Guohong , Yang Diya , Li Lei , Li Junfa , Wang Ningli 
Published: September 2013

AbstractPurposeTo assess whether a Valsalva manoeuver influences intra‐ocular pressure (IOP), cerebrospinal fluid pressure (CSF‐P) and, by a change in the trans‐laminar cribrosa pressure difference, optic nerve head morphology.MethodsIn the first part of the study, 20 neurological patients (study group ‘A’) underwent measurement of IOP and lumbar CSF‐P measurement in a lying position before and during a Valsalva manoeuver. In the second study part, 20 healthy subjects (study group ‘B’) underwent ocular tonometry and confocal scanning laser tomography of the optic nerve head before and during a Valsalva manoeuver.ResultsDuring the Valsalva manoeuver in study group ‘A’, the increase in CSF‐P by 10.5 ± 2.7 mmHg was significantly (p < 0.001) higher than the increase in IOP by 1.9 ± 2.4 mmHg. The change in CSF‐P was not significantly (p = 0.61) correlated with the change in IOP. During the Valsalva manoeuver in study group ‘B’, IOP increased by 4.5 ± 4.2 mmHg and optic cup volume (p < 0.001), cup/disc area ratio (p = 0.02), cup/disc diameter ratio (p = 0.03) and maximum optic cup depth (p = 0.01) significantly decreased, while neuroretinal rim volume (p = 0.005) and mean retinal nerve fibre layer thickness (p = 0.02) significantly increased.ConclusionsThe Valsalva manoeuver‐associated short‐term increase in CSF‐P was significantly larger than a simultaneous short‐term increase in IOP. It led to a Valsalva manoeuver‐associated decrease or reversal of the trans‐laminar cribrosa pressure difference, which was associated with a change in the three‐dimensional optic nerve head morphology: optic cup‐related parameters decreased and neuroretinal rim‐related parameters enlarged. These findings may be of interest for the pathogenesis of glaucomatous optic neuropathy.
Intravitreal low‐dosage bevacizumab for retinopathy of prematurity
Authors: Harder Björn C. , von Baltz Stefan , Jonas Jost B. , Schlichtenbrede Frank C. 
Published: September 2013

AbstractPurposeTo report on the therapeutic effect of intravitreal low‐dose bevacizumab for treatment for retinopathy of prematurity (ROP).MethodsThe single‐centre retrospective, non‐comparative case series study included all infants who consecutively underwent intravitreal injection of 0.375 mg bevacizumab (0.03 ml) under light sedation in topical anaesthesia as therapy of ROP in zone I or zone II.ResultsThe clinical charts of 29 patients (57 eyes) with a median birth weight of 630 g (range: 290–1390 g) and median gestational age of 25 + 1 weeks (range: 23 + 1–30 weeks) were reviewed. Six children (12 eyes) were graded as ROP with zone I retinopathy and plus disease. The 23 remaining infants had extraretinal neovascularizations in zone II or partly zone I. The intravitreal bevacizumab injection was injected at a median age of 12 + 1 weeks (range: 7 + 4–21 + 4), the median follow‐up was 4.2 months (range: from 3 days to 45.1 months). In all eyes treated, a regression of plus disease occurred within two to six days, retinal neovascularizations regressed within 2–3 weeks and pupillary rigidity improved. None except one child in exceptionally bad general health conditions needed a second intravitreal bevacizumab injection. In none of the infants, any ophthalmologic side‐effects of the bevacizumab application were detected during the follow‐up period.ConclusionsThe intravitreal injection of a low dose of 0.375 mg bevacizumab showed a high efficacy as treatment for ROP. The question arises whether the low dosage of bevacizumab as compared to the dosage of 0.625 mg bevacizumab may be preferred.
Immunohistochemical analysis of extracellular matrix bleb capsules of functioning and non‐functioning glaucoma drainage implants
Authors: Välimäki Juha , Uusitalo Hannu 
Published: September 2013

AbstractPurposeTo detect by immunohistochemical means the changes in bleb capsules at the cellular level between functioning and non‐functioning glaucoma drainage implants (GDIs).MethodsThree samples each of functioning (1 Baerveldt and 2 Molteno implants) and non‐functioning filtration blebs (1 Molteno and 2 Ahmed implants) were studied. A non‐functioning bleb was defined as an intra‐ocular pressure (IOP) >21 mmHg or a <20% reduction in IOP from baseline on three consecutive follow‐up visits with maximal tolerated medication. The capsules were obtained between 6 and 108 months after GDI insertion for medical reasons only. Primary antibodies were used to stain fibronectin, tenascin, laminin, collagen IV and smooth muscle actin (SMA). The samples were graded on the basis of the intensity and quantity of immunohistochemical staining into four categories as follows: no staining or a mild, moderate or marked staining.ResultsThe non‐functioning blebs expressed more fibronectin, tenascin and SMA through the whole capsule wall than the functioning blebs. In the functioning blebs, tenascin was found mainly in the inner layer of the capsule. More type IV collagen and laminin were also found in the non‐functioning bleb capsules than in the functioning blebs. No difference was found between the bleb capsules irrespective of whether they had been perfused with aqueous humour immediately after surgery (Ahmed) or after a delay (Molteno, Baerveldt).ConclusionAccumulation of extracellular matrix components and activated fibroblasts in the bleb capsules of non‐functioning GDI indicates the presence of an active wound healing process, suggesting a possible reduction in filtration through the bleb wall.
Change in retinal blood flow and retinal arterial diameter after intraocular pressure reduction in glaucomatous eyes
Authors: Kurvinen Leena , Kytö Janne P. , Summanen Paula , Vesti Eija , Harju Mika 
Published: September 2013

AbstractPurposeTo study retinal blood flow and vessel diameter after intra‐ocular pressure (IOP) reduction in high‐ and low‐pressure glaucomas, that is, exfoliation glaucoma (ExG) and normal‐tension glaucoma (NTG).MethodsThe study included 17 eyes with ExG and 20 with NTG. A minimum of 25% IOP reduction was achieved by deep sclerectomy. Blood flow in the temporal peripapillary retina was measured with scanning laser Doppler flowmetry (Heidelberg Retina Flowmeter, HRF), and retinal vessel diameters were evaluated with the retinal vessel analyser (RVA). Examinations were carried out before and 3 months after the operation.ResultsPre‐operative IOP was significantly higher in ExG than in NTG (median 26 mmHg, range 20–33 mmHg versus 15 mmHg, 12–20; p < 0.001). Surgery reduced IOP significantly both in ExG eyes (postoperative IOP 13 mmHg, 5–17; p < 0.001) and NTG eyes (9 mmHg, 3–13; p < 0.001). After the operation, systolic retinal flow was significantly reduced in ExG eyes, whereas in NTG, HRF parameters remained unchanged. Pre‐operatively, the central retinal artery equivalent (CRAE) and arteriovenous ratio (AVR) were higher in ExG than in NTG eyes. After IOP reduction, both CRAE and AVR were reduced in ExG eyes, but remained unchanged in NTG.ConclusionThe study showed that before IOP reduction, arterial diameter was larger in ExG eyes than in NTG eyes. IOP reduction resulted in vasoconstriction and reduction of flow in ExG, whereas in NTG, both vessel diameter and retinal flow remained unchanged.
Measuring stone volume – three‐dimensional software reconstruction or an ellipsoid algebra formula?
Authors: Finch William , Johnston Richard , Shaida Nadeem , Winterbottom Andrew , Wiseman Oliver 
Published: September 2013

Objectives
To determine the optimal method for assessing stone volume, and thus stone burden, by comparing the accuracy of scalene, oblate, and prolate ellipsoid volume equations with three‐dimensional (3D)‐reconstructed stone volume.
Kidney stone volume may be helpful in predicting treatment outcome for renal stones. While the precise measurement of stone volume by 3D reconstruction can be accomplished using modern computer tomography (CT) scanning software, this technique is not available in all hospitals or with routine acute colic scanning protocols. Therefore, maximum diameters as measured by either X‐ray or CT are used in the calculation of stone volume based on a scalene ellipsoid formula, as recommended by the European Association of Urology.
Methods
In all, 100 stones with both X‐ray and CT (1–2‐mm slices) were reviewed. Complete and partial staghorn stones were excluded.
Stone volume was calculated using software designed to measure tissue density of a certain range within a specified region of interest.
Correlation coefficients among all measured outcomes were compared. Stone volumes were analysed to determine the average ‘shape’ of the stones.
Results
The maximum stone diameter on X‐ray was 3–25 mm and on CT was 3–36 mm, with a reasonable correlation (r = 0.77).
Smaller stones (<9 mm) trended towards prolate ellipsoids (‘rugby‐ball’ shaped), stones of 9–15 mm towards oblate ellipsoids (disc shaped), and stones >15 mm towards scalene ellipsoids.
There was no difference in stone shape by location within the kidney.
Conclusions
As the average shape of renal stones changes with diameter, no single equation for estimating stone volume can be recommended.
As the maximum diameter increases, calculated stone volume becomes less accurate, suggesting that larger stones have more asymmetric shapes.
We recommend that research looking at stone clearance rates should use 3D‐reconstructed stone volumes when available, followed by prolate, oblate, or scalene ellipsoid formulas depending on the maximum stone diameter.
Towards a better cannabis drug
Authors: Mechoulam Raphael , Parker Linda 
Published: September 2013

This commentary discusses the importance of a new study entitled ‘Cannabidiol attenuates deficits of visuo‐spatial associative memory induced by Δ9‐tetrahydrocannabinol’ by Wright et al. from the Scripps Institute in La Jolla, California. The results in this study show that the non‐psychoactive cannabis constituent cannabidiol opposes some, but not all, forms of behavioural and memory disruption caused by Δ9‐tetrahydrocannabinol in male rhesus monkeys.Linked ArticleThis article is a commentary on the research paper by Wright et al., pp 1365–1373 of this issue. To view this paper visit http://dx.doi.org/10.1111/bph.12199
Pancreatic cancer
Authors: Güngör C , Hofmann B T , Wolters‐Eisfeld G , Bockhorn M 
Published: September 2013

In recent years, it has become clear that the current standard therapeutic options for pancreatic cancer are not adequate and still do not meet the criteria to cure patients suffering from this lethal disease. Although research over the past decade has shown very interesting and promising new therapeutic options for these patients, only minor clinical success was achieved. Therefore, there is still an urgent need for new approaches that deal with early detection and new therapeutic options in pancreatic cancer. To provide optimal care for patients with pancreatic cancer, we need to understand better its complex molecular biology and thus to identify new target molecules that promote the proliferation and resistance to chemotherapy of pancreatic cancer cells. In spite of significant progress in curing cancers with chemotherapy, pancreatic cancer remains one of the most resistant solid tumour cancers and many studies suggest that drug‐resistant cancer cells are the most aggressive with the highest relapse and metastatic rates. In this context, activated Notch signalling is strongly linked with chemoresistance and therefore reflects a rational new target to circumvent resistance to chemotherapy in pancreatic cancer. Here, we have focused our discussion on the latest research, current therapy options and recently identified target molecules such as Notch‐2 and the heparin‐binding growth factor midkine, which exhibit a wide range of cancer‐relevant functions and therefore provide attractive new therapeutic target molecules, in terms of pancreatic cancer and other cancers also.Linked ArticlesThis article is part of a themed section on Midkine. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue‐4
Elevated CD8 T cell responses in type 1 diabetes patients to a 13 amino acid coeliac-active peptide from α-gliadin
Authors: Barbeau W E , Hontecillas R , Horne W , Carbo A , Koch M H , Bassaganya-Riera J 
Published: September 2013

Summary
Some type 1 diabetes (T1D) patients have been reported to exhibit T cell reactivity to wheat gluten. We tested the hypothesis that this T cell reactivity could be abolished by using prolyl-endopeptidase (PEP), an enzyme that cleaves peptide bonds after proline. Peripheral blood mononuclear cells (PBMCs) were isolated from T1D patients and healthy controls. PBMCs were stimulated with a peptic–tryptic digest of wheat gluten; a peptic–tryptic-PEP digest of wheat gluten; and a 13 amino acid peptide from wheat gluten. Fluorescent-labelled antibodies to CD3, CD4 and CD8 cell marker proteins were utilized to determine proliferative responses of CD3, CD4 and CD8 T cells. There were no significant differences in proliferative responses of CD3 or CD4 T cells to the wheat gluten antigens. A significantly higher proportion of CD8+ T cells from T1D patients proliferated in the presence of the 13 amino acid peptide than when challenged with the peptic–tryptic or the peptic–tryptic–PEP digests of wheat gluten. PEP treatment had no significant effect on CD8 T cell reactivity to the peptic–trytic digest of wheat gluten. Our results suggest that wheat gluten-derived peptides, containing ≤ 13 amino acids, may evoke T cell responses in T1D patients.
Risk assessment and domestic violence – how do child welfare workers in three countries assess and substantiate the risk level of a 5‐year‐old girl?
Authors: Skivenes Marit , Stenberg Hanne 
Published: September 2013

AbstractThis paper examine how a sample of 301 child welfare workers in Norway, England and California, USA assess risk in cases of domestic violence. Decisions in child welfare cases are made under a high degree of uncertainty, and by using the vignette method, we explore whether child welfare systems and risk assessment approaches result in different assessment of risk level and substantiations. We find both cross‐country differences and similarities: Norwegian workers consider the risk level to be significantly higher than their peers in England and USA. However, workers' justifications for and identification of decisive factors in the case are strikingly similar across countries. These similarities are observed for both high‐risk and low‐risk assessors, and they may exist due to widespread knowledge about domestic violence and its negative consequences. We argue that the international differences in risk level assessments are due to system differences in the countries studied.
Histological Evaluation of Bone Formation Adjacent to Dental Implants with a Novel Apical Chamber Design: Preliminary Data in the Rabbit Model
Authors: Meirelles Luiz , Brånemark Per‐Ingvar , Albrektsson Tomas , Feng Changyong , Johansson Carina 
Published: September 2013

AbstractBackgroundWound healing events after implant placement will vary according to the extent of the necrotic zone.PurposeThe goal of the present study was to evaluate bone healing around titanium implants with a novel apical chamber design.Materials and MethodsTitanium implants grade 4 were turned with different apex design. Control implants had a self tapping design with centric cutting grooves. Test implants exhibited eccentric cutting grooves interconnected by a hollow chamber. A total of 60 implants were installed in the femur/tibia of 10 rabbits for histological analysis.ResultsAfter 1 week, immature bone formation started at the cortical level of the test implants associated to scalloped contours indicative of bone resorption. Control implants failed to show new bone formation, and the space within the threads was filled mainly by red blood cells and surgical debris. Bone contact values showed no difference after 1 week, and significant higher values for test implants showed likewise after 4 weeks compared with control implants in the tibia.ConclusionThis experimental study verifies the beneficial effect of bone formation in the chamber at the apical part of the fixture coupled to a faster bone healing to implants placed in dense bone.
Technical Accuracy of Printed Surgical Templates for Guided Implant Surgery with the coDiagnostiXTM Software
Authors: Kühl Sebastian , Payer Michael , Zitzmann Nicola Ursula , Lambrecht Jörg Thomas , Filippi Andreas 
Published: September 2013

AbstractBackgroundPrinting of templates for guided surgery represents an alternative to laboratory manufactured templates.PurposeTo determine the technical accuracy of a virtually designed and printed surgical template for guided implant surgery based on a surface scan of a cast model using the coDiagnostiXTM software.Materials and MethodsCast models and the virtual planning data of nine patients receiving guided implant surgery with the coDiagnostiX software were analyzed. The original cast models were equipped with three titanium pins and scanned with a three‐dimensional scanner. The scans were uploaded in the coDiagnostiX software and the virtual surgical templates were designed including the sleeves at their original positions. After printing the surgical templates, the sleeve positions were determined by optical scanning, and deviations were calculated and compared with the virtual positions of the sleeves.ResultsThe sleeves showed a mean three‐dimensional deviation of 0.22 mm (range: 0.07–0.38 mm) in the center of the sleeve top, 0.24 mm (range: 0.08–0.36 mm) in the center of the sleeve bases and a mean angular deviation of 1.5° (range: 0.4°–3.3°) compared with the virtual positions.ConclusionsA high accuracy can be achieved using printed templates for guided implant surgery, by taking into account all sources of inaccuracies.