bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin
Authors: Douillard François P. , Kant Ravi , Ritari Jarmo , Paulin Lars , Palva Airi , de Vos Willem M.
Published: July 2013

The members of the Lactobacillus genus are widely used in the food and feed industry and show a remarkable ecological adaptability. Several Lactobacillus strains have been marketed as probiotics as they possess health‐promoting properties for the host. In the present study, we used two complementary next‐generation sequencing technologies to deduce the genome sequences of two Lactobacillus casei strains LcA and LcY, which were isolated from the products Actimel and Yakult, commercialized as probiotics. The LcA and LcY draft genomes have, respectively, an estimated size of 3067 and 3082 Mb and a G+C content of 46.3%. Both strains are close to identical to each other and differ by no more than minor chromosomal re‐arrangements, substitutions, insertions and deletions, as evident from the verified presence of one insertion‐deletion (InDel) and only 29 single‐nucleotide polymorphisms (SNPs). In terms of coding capacity, LcA and LcY are predicted to encode a comparable exoproteome, indicating that LcA and LcY are likely to establish similar interactions with human intestinal cells. Moreover, both L. casei LcA and LcY harboured a 59.6 kb plasmid that shared high similarities with plasmids found in other L. casei strains, such as W56 and BD‐II. Further analysis revealed that the L. casei plasmids constitute a good evolution marker within the L. casei species. The plasmids of the LcA and LcY strains are almost identical, as testified by the presence of only three verified SNPs, and share a 3.5 kb region encoding a remnant of a lactose PTS system that is absent from the plasmids of W56 and BD‐II but conserved in another smaller L. casei plasmid (pLC2W). Our observations imply that the results obtained in animal and human experiments performed with the Actimel and Yakult strains can be compared with each other as these strains share a very recent common ancestor.
Liver diseases and aging: friends or foes?
Authors: Sheedfar Fareeba , Biase Stefano Di , Koonen Debby , Vinciguerra Manlio
Published: July 2013

The liver is the only internal human organ capable of natural regeneration of lost tissue, as little as 25% of a liver can regenerate into a whole liver. The process of aging predisposes to hepatic functional and structural impairment and metabolic risk. Therefore, understanding how aging could affect the molecular pathology of liver diseases is particularly important, and few studies to date have tackled this complex process. The most common liver disease, affecting one‐third of the overall population, is nonalcoholic fatty liver disease (NAFLD), characterized by an intrahepatic accumulation of lipids. NAFLD can evolve into nonalcoholic steatohepatitis (NASH) in the presence of oxidative stress and inflammation. NASH is a serious risk factor for disabling and deadly liver diseases such as cirrhosis and hepatocellular carcinoma (HCC). Old age seems to favor NAFLD, NASH, and ultimately HCC, in agreement with the inflamm‐aging theory, according to which aging accrues inflammation. However, the incidence of HCC drops significantly in the very elderly (individuals aged more than 70) and the relationship between the progression of NAFLD/NASH/HCC and very old age is obscure. In this review, we discuss the literature and we argue that there might be an age window in which the liver becomes resistant to the development of injury; this needs to be studied to understand fully the interaction between age and liver diseases from a therapeutic perspective.
The Caenorhabditis elegans LET‐418/Mi2 plays a conserved role in lifespan regulation
Authors: De Vaux Véronique , Pfefferli Catherine , Passannante Myriam , Belhaj Khaoula , von Essen Alina , Sprecher Simon G. , Müller Fritz , Wicky Chantal
Published: July 2013

The evolutionarily conserved nucleosome‐remodeling protein Mi2 is involved in transcriptional repression during development in various model systems, plays a role in embryonic patterning and germ line development, and participates in DNA repair and cell cycle progression. It is the catalytic subunit of the nucleosome remodeling and histone deacetylase (NuRD) complex, a key determinant of differentiation in mammalian embryonic stem cells. In addition, the Drosophila and C. elegans Mi2 homologs participate in another complex, the MEC complex, which also plays an important developmental role in these organisms. Here we show a new and unexpected feature of the C. elegans Mi2 homolog, LET‐418/Mi2. Lack of LET‐418/Mi2 results in longevity and enhanced stress resistance, a feature that we found to be conserved in Drosophila and in Arabidopsis. The fact that depletion of other components of the NuRD and the MEC complexes did not result in longevity suggests that LET‐418 may regulate lifespan in a different molecular context. Genetic interaction studies suggest that let‐418 could act in the germ‐cell‐loss pathway, downstream of kri‐1 and tcer‐1. On the basis of our data and on previous findings showing a role for let‐418 during development, we propose that LET‐418/Mi2 could be part of a system that drives development and reproduction with concomitant life‐reducing effects later in life.
Time‐series econometric analyses of biofuel‐related price volatility
Authors: Serra Teresa
Published: July 2013

Time‐series econometrics studies have analyzed volatility interactions between biofuel and food and fossil fuel markets. We review data, modeling techniques and the main findings in the literature, and present our latest contributions. We identify areas for further research.
Robot‐assisted laparoscopic vs open radical cystectomy: comparison of complications and perioperative oncological outcomes in 200 patients
Authors: Kader A. Karim , Richards Kyle A. , Krane L. Spencer , Pettus Joseph A. , Smith John J. , Hemal Ashok K.
Published: July 2013

Objective

To compare perioperative morbidity and oncological outcomes of robot‐assisted laparoscopic radical cystectomy (RARC) to openRC(ORC) at a single institution.

Patients and Methods

A retrospective analysis was performed on a consecutive series of patients undergoingRC(100RARCand 100ORC) atWakeForestUniversity with curative intent from 2006 until 2010.

Complication data using theClavien system were collected for 90 days postoperatively.

Complications and other perioperative outcomes were compared between patient groups.

Results

Patients in both groups had comparable preoperative characteristics.

The overall and major complication (Clavien ≥3) rates were lower forRARCpatients at 35 vs 57% (P= 0.001) and 10 vs 22% (P= 0.019), respectively.

There were no significant differences between groups for pathological outcomes, including stage, number of nodes harvested or positive margin rates.

Conclusion

Our data suggest that patients undergoingRARChave perioperative oncological outcomes comparable withORC, with fewer overall or major complications.

Definitive claims about comparative outcomes withRARCrequire results from larger, randomised controlled trials.
Can the Leibovich score for clear cell renal cell carcinoma (ccRCC) be accurately reported by a general pathologist?
Authors: Vasdev Nikhil , Altal Yaman , Mafeld Sebastian , Wong Kevin , Chadwick David , Gowda Basavaraj D.R. , Mutton Adrienne , Nagarajan Srikantiah , Bhatti Aftab
Published: July 2013

Objectives

To evaluate the accuracy of reporting of the Leibovich score (LS) by general pathologists at our centre by comparing the LS in their initial reports with the LS in subsequent review reports by our specialist urological pathologists.

We also assessed whether a revision in the LS subsequently altered the risk group.

Patients and Methods

In all, 54 consecutive patients had had their initial histology after nephrectomy reported by a general pathologist between August 2008 and March 2012.

The histological slides were subsequently re‐reviewed by the two specialist urological pathologists and revised LS were given if appropriate. The cases were then discussed at the Uro‐oncology Multi disciplinary meeting (MDT) and the reason for the revised LS was discussed with the participating panel and reviewed by the uropathologist.

Results

The general pathologists allocated the 54 patients into low‐ (13 patients), intermediate‐ (25) and high‐risk (16) categories.

After a review of the slides by the specialist urological pathologists and discussion at the MDT meeting the LS was revised in 23 patients (42.6%).

The 23 patients who had their LS revised were divided into two groups for the purpose of the present study. On revision of the LS a total of eight patients (14.8%) changed their prognostic group.

The change in the prognostic group in the eight patients was increased from intermediate‐ to high‐risk in four patients.

There was a reduction in the LS in four patients, which was from high‐ to intermediate‐risk category in one patient and intermediate‐ to low‐risk in three patients.

Conclusion

In the present study, histopathology review by a specialist urological pathologist led to a change in LS in 42.6% of cases leading a change in risk grouping in 14.8% of cases. This level of discrepancy is not insignificant. However, the few cases evaluated in the present study does limit robust conclusions and further studies are needed to investigate this issue, so that recommendations can be made to enhance diagnostic accuracy and reproducibility.
On the limitations of fixed‐step‐size adaptive methods with response confidence
Authors: Hsu Yung‐Fong , Chin Ching‐Lan
Published: July 2013

The family of (non‐parametric, fixed‐step‐size) adaptive methods, also known as ‘up–down’ or ‘staircase’ methods, has been used extensively in psychophysical studies for threshold estimation. Extensions of adaptive methods to non‐binary responses have also been proposed. An example is the three‐category weighted up–down (WUD) method (Kaernbach, 2001) and its four‐category extension (Klein, 2001). Such an extension, however, is somewhat restricted, and in this paper we discuss its limitations. To facilitate the discussion, we characterize the extension of WUD by an algorithm that incorporates response confidence into a family of adaptive methods. This algorithm can also be applied to two other adaptive methods, namely Derman's up–down method and the biased‐coin design, which are suitable for estimating any threshold quantiles. We then discuss via simulations of the above three methods the limitations of the algorithm. To illustrate, we conduct a small scale of experiment using the extended WUD under different response confidence formats to evaluate the consistency of threshold estimation.
Progressive High‐Quality Response Surfaces for Visually Guided Sensitivity Analysis
Authors: Demir I. , Westermann R.
Published: July 2013

In this paper we present a technique which allows us to perform high quality and progressive response surface prediction from multidimensional input samples in an efficient manner. We utilize kriging interpolation to estimate a response surface which minimizes the expectation value and variance of the prediction error. High computational efficiency is achieved by employing parallel matrix and vector operations on the GPU. Our approach differs from previous kriging approaches in that it uses a novel progressive updating scheme for new samples based on blockwise matrix inversion. In this way we can handle very large sample sets to which new samples are continually added. Furthermore, we can monitor the incremental evolution of the surface, providing a means to early terminate the computation when no significant changes have occurred. When the generation of input samples is fast enough, our technique enables steering this generation process interactively to find relevant dependency relations.
Nonparametric Models for Uncertainty Visualization
Authors: Pöthkow Kai , Hege Hans‐Christian
Published: July 2013

An uncertain (scalar, vector, tensor) field is usually perceived as a discrete random field with a priori unknown probability distributions. To compute derived probabilities, e.g. for the occurrence of certain features, an appropriate probabilistic model has to be selected. The majority of previous approaches in uncertainty visualization were restricted to Gaussian fields. In this paper we extend these approaches to nonparametric models, which are much more flexible, as they can represent various types of distributions, including multimodal and skewed ones. We present three examples of nonparametric representations: (a) empirical distributions, (b) histograms and (c) kernel density estimates (KDE). While the first is a direct representation of the ensemble data, the latter two use reconstructed probability density functions of continuous random variables. For KDE we propose an approach to compute valid consistent marginal distributions and to efficiently capture correlations using a principal component transformation. Furthermore, we use automatic bandwidth selection, obtaining a model for probabilistic local feature extraction. The methods are demonstrated by computing probabilities of level crossings, critical points and vortex cores in simulated biofluid dynamics and climate data.
Mass‐Dependent Integral Curves in Unsteady Vector Fields
Authors: Günther Tobias , Kuhn Alexander , Kutz Benjamin , Theisel Holger
Published: July 2013

Recent research in flow visualization is focusing on the analysis of time‐dependent, but mass‐less particles. However, in many application scenarios, the mass of particles – and their resulting inertia – is essential in understanding fluid mechanics. This includes critical processes, such as dust particles interacting with aircraft (e.g., brown‐or white‐out effects) and particle separation based on density variation. In this paper, we contribute a generalized description of mass‐dependent particle trajectories and apply existing unsteady flow visualization methods to the mass‐dependent case. This comprises the extension of common concepts, i.e., path lines, streak lines, and time lines. Furthermore, we introduce a new class of integral curves, called mass lines that effectively visualizes mass separation and captures mass‐related features in unsteady flow fields that are inaccessible using traditional methods. We demonstrate the applicability of our method, using a number of real‐world and artificial data sets, in which mass is a crucial parameter. In particular, we focus on the analysis of brown‐out conditions, introduced by a helicopter in forward flight close to the ground.
Vessel Visualization using Curvicircular Feature Aggregation
Authors: Mistelbauer G. , Morar A. , Varchola A. , Schernthaner R. , Baclija I. , Köchl A. , Kanitsar A. , Bruckner S. , Gröller E.
Published: July 2013

Radiological investigations are common medical practice for the diagnosis of peripheral vascular diseases. Existing visualization methods such as Curved Planar Reformation (CPR) depict calcifications on vessel walls to determine if blood is still able to flow. While it is possible with conventional CPR methods to examine the whole vessel lumen by rotating around the centerline of a vessel, we propose Curvicircular Feature Aggregation (CFA), which aggregates these rotated images into a single view. By eliminating the need for rotation, vessels can be investigated by inspecting only one image. This method can be used as a guidance and visual analysis tool for treatment planning. We present applications of this technique in the medical domain and give feedback from radiologists.
AmniVis – A System for Qualitative Exploration of Near‐Wall Hemodynamics in Cerebral Aneurysms
Authors: Neugebauer M. , Lawonn K. , Beuing O. , Berg P. , Janiga G. , Preim B.
Published: July 2013

The qualitative exploration of near‐wall hemodynamics in cerebral aneurysms provides important insights for risk assessment. For instance, a direct relation between complex flow patterns and aneurysm formation could be observed. Due to the high complexity of the underlying time‐dependent flow data, the exploration is challenging, in particular for medical researchers not familiar with such data. We present the AmniVis‐Explorer, a system that is designed for the preparation of a qualitative medical study. The provided features were developed in close collaboration with medical researchers involved in the study. This comprises methods for a purposeful selection of surface regions of interest and a novel approach to provide a 2D overview of flow patterns that are represented by streamlines at these regions. Furthermore, we present a specialized interface that supports binary classification of patterns and temporal exploration as well as methods for selection, highlighting and automatic 3D navigation to particular patterns. Based on eight representative datasets, we conducted informal interviews with two bord‐certified radiologists and a flow expert to evaluate the system. It was confirmed that the AmniVis‐Explorer allows for an easy selection, qualitative exploration and classification of near‐wall flow patterns that are represented by streamlines.
AOI Rivers for Visualizing Dynamic Eye Gaze Frequencies
Authors: Burch Michael , Kull Andreas , Weiskopf Daniel
Published: July 2013

It is difficult to explore and analyze eye gaze trajectories for commonly applied visual task solution strategies because such data shows complex spatio‐temporal structure. In particular, the traditional eye gaze plots of scan paths fail for a large number of study participants since these plots lead to much visual clutter. To address this problem we introduce the AOI Rivers technique as a novel interactive visualization method for investigating time‐varying fixation frequencies, transitions between areas of interest (AOIs), and the sequential order of gaze visits to AOIs in a visual stimulus of an eye tracking experiment. To this end, we extend the ThemeRiver technique by influents, effluents, and transitions similar to the concept of Sankey diagrams. The AOI Rivers visualization is complemented by linked spatial views of the data in the form of heatmaps, gaze plots, or display of the visual stimulus. The usefulness of our technique is demonstrated for gaze trajectory data recorded in a previously conducted eye tracking experiment.
Visualizing Motional Correlations in Molecular Dynamics using Geometric Deformations
Authors: Fioravante M. , Shook A. , Thorpe I. , Rheingans P.
Published: July 2013

In macromolecules, an allosteric effect is said to occur when a change at one site of a molecule affects a distant site. Understanding these allosteric effects can be important for understanding how the functions of complex molecules such as proteins are regulated. One potential application of this knowledge is the development of small molecules that alter the function of proteins involved in diseases. Studying motional correlation can help researchers to discover how a change at a source site affects the target site and thus how allosteric ligands that could serve as drugs are able to exert their therapeutic effects. By improving our ability to analyze these correlated relationships, it may be possible to develop new medications to combat deadly diseases such as Hepatitis C. We present four visual techniques which represent motional correlation on rendered three‐dimensional molecular models, providing new ways to view clusters of correlated residues and paths of allosteric interactions. These techniques give us a new way of investigating the presence of motional correlations in complex molecules. We compare each of these techniques to determine which are the most useful for representing motional correlations.
dPSO‐Vis: Topology‐based Visualization of Discrete Particle Swarm Optimization
Authors: Volke S. , Middendorf M. , Hlawitschka M. , Kasten J. , Zeckzer D. , Scheuermann G.
Published: July 2013

Particle swarm optimization (PSO) is a metaheuristic that has been applied successfully to many continuous and combinatorial optimization problems, e.g., in the fields of economics, engineering, and natural sciences. In PSO, a swarm of particles moves within a search space in order to find an optimal solution. Unfortunately, it is hard to understand in detail why and how changes in the design of PSO algorithms affect the optimization behavior. Visualizing the particle states could provide substantially better insight into PSO algorithms. Though in case of combinatorial optimization problems, it often raises the problem of illustrating the states within the discrete search space that cannot be embedded spatially. We propose a visualization approach to depict the optimization problem topologically using a landscape metaphor. This visualization is augmented by an illustration of the time‐dependent states of the particles. Thus, the user of dPSO‐Vis is able to analyze the swarm's behavior within the search space. In principle, our method can be used for any optimization algorithm where a swarm of individuals searches within a discrete search space. Our approach is verified with a case study for the PSO algorithm HelixPSO that predicts the secondary structure of RNA molecules.
Augmenting Visualization with Natural Language Translation of Interaction: A Usability Study
Authors: Nafari M. , Weaver C.
Published: July 2013

As visualization tools get more complicated, users often find it increasingly difficult to learn interaction sequences, recall past queries, and interpret visual states. We examine a query‐to‐question (Q2Q) supporting system that takes advantage of natural language generation (NLG) techniques to automatically translate and display query interactions as natural language questions. We focus on a symmetric pattern of multiple coordinated views, cross‐filtered views, that involves only nominal/categorical data. We describe a study of the effects of pairing a visualization with a Q2Q interface on several aspects of usability. Q2Q produces considerable improvements in learnability, efficiency, and memorability of visualization in terms of speed and the length of interaction sequences that users follow, along with a modest decrease in error ratio. From a visual language perspective, we analyze how Q2Q speeds up users’ comprehension of interaction, particularly when a visualization representation has deficiencies in illustrating hidden items or relationships.
Visual Explanation of the Complexity in Julia Sets
Authors: Schrijvers Okke , van Wijk Jarke J.
Published: July 2013

Julia sets based on quadratic polynomials have a very simple definition, yet a highly intricate shape. Our contribution is to provide a visual explanation for this complexity. To this end we show the construction of Julia sets as a dynamic process, in contrast to showing just a static image of the set itself. Our method is based on the Inverse Iteration Method (IIM). We start with a disk, which is successively distorted. The crucial step is to show an animation of the effect of taking a root of a subset of the complex plane. We present four different approaches for this, using a Riemann surface, a corkscrew, a fan, and disks as metaphors. We packaged our results in an interactive tool with a simple interface, such that everybody can view and inspect these for different Julia sets. The results are useful for teaching complex analysis, promoting mathematics, entertainment, and, above all, as a visual explanation for the complexity of Julia sets.
Meta‐analysis of confocal laser endomicroscopy for the detection of colorectal neoplasia
Authors: Dong Y.‐Y. , Li Y.‐Q. , Yu Y.‐B. , Liu J. , Li M. , Luan X.‐R.
Published: July 2013

Aim

Confocal laser endomicroscopy (CLE) is a recently developed technique used to image colorectal neoplasia. Trials have shown varied results when it is compared with conventional colonoscopy. A meta‐analysis was performed to determine the diagnostic accuracy of CLE in the detection of colorectal neoplasia.

Method

A search was performed for studies assessing the accuracy of CLE in colorectal neoplasia. Studies comparing CLE diagnostic accuracy with conventional endoscopy in the detection of colorectal neoplasia were included. Exclusion criteria included case reports or case series, reviews, duplicate reports or insufficient data in the paper. Seventy‐eight titles came up in the initial search and six studies were selected. These were subjected to a meta‐analysis. In all, 284 patients with 1030 lesions were included. Each patient underwent conventional colonoscopy and CLE. Per‐lesion sensitivity and specificity with 95% CI were calculated.

Results

In the individual studies, the sensitivity ranged from 33.3% to 100% and specificity from 71.6% to 99.4%. The weighted and total pooled result (random effects model) for sensitivity was 81% (95% CI 77–85) and for specificity was 88% (95% CI 85–90). The area under the weighted symmetric summary receiver operating curve was 0.9186. In the endoscope‐based CLE subgroup, the sensitivity was 82% (95% CI 69–91) and specificity was 94% (95% CI 91–96). In the probe‐based CLE subgroup, the sensitivity was 81% (95% CI 76–85) and the specificity was 75% (95% CI 69–81).

Conclusion

CLE, using either the endoscope‐based CLE or probe‐based CLE technique, has high sensitivity and specificity. It could therefore be considered as an alternative endoscopic method to distinguish neoplastic from non‐neoplastic lesions.
FOR BETTER OR FOR WORSE, BUT HOW ABOUT A RECESSION?
Authors: ARKES JEREMY , SHEN YU‐CHU
Published: July 2013

In light of the current economic crisis, we estimate hazard models of divorce to determine how state and national unemployment rates affect the likelihood of a divorce or separation. With data in the United States over the 1978–2008 period from the 1979 NLSY, we find some evidence indicating that a higher unemployment rate increases the risk of a marriage ending for couples in years 6–10 of marriage (suggesting counter‐cyclical divorce/separation probabilities) but has no significant effect for couples in years 1–5 of marriage and those married longer than 10 years. The estimates are generally stronger in magnitude when using national instead of state unemployment rates and when considering just divorces rather than the first observed divorce or separation. (JELJ12)
Common Counsel, Common Policy: Healthcare, Missions and the Rise of the ‘Voluntary Sector’ in Colonial Tanzania
Authors: Jennings Michael
Published: July 2013

Analysis of the voluntary sector in sub‐Saharan Africa has tended to focus on the role of the NGO, and the types of relationships this institution establishes and maintains with donors, national governments and the communities with which they work. The voluntary sector in Africa is therefore usually defined through, and often treated as synonymous with, the institution of the NGO. As a result, the boundaries of understandings of the ‘third sector’ space occupied by the vast number of NGOs — its origins, the nature of the relationship of voluntary sector actors to the state, the types of organizations that characterize the sector — have tended to reflect a narrow concern with the NGO type and its experiences. This article suggests that this view is too narrow in its gaze. The voluntary sector was not a creation of a post‐colonial (and especially post‐1970s) development crisis. It emerged from an evolving relationship between colonial‐era non‐state (voluntary) actors and governments determined to demonstrate that they were meeting their commitments to the welfare of Africans under their charge. Missions and mission welfare services, expanding across much of rural sub‐Saharan Africa by the beginnings of the twentieth century, and increasingly coordinated from the late 1920s and early 1930s, created the foundations for the emergence of sub‐Saharan Africa's formal voluntary sector as it exists today. This matters for more than just historical accuracy. To understand the constraints, challenges and opportunities faced by NGOs, we need to move beyond a narrow focus on the institution of the NGO itself, and look in addition to the environment in which it operates: its history, its evolution and the shifts that created those conditions.
Metal tooth‐like surgical templates for tooth autotransplantation in adolescents
Authors: Ashkenazi Malka , Levin Liran
Published: July 2013

Objectives

The aim of this study was to suggest a way to fabricate surgical templates to assist the surgeon in preparing the recipient socket when performing premolar autotransplantation.

Methods

Premolars used previously for extractions of periodontal ligament (PDL) fibroblasts were used in this study as archetype of models for tooth transplantation. Eighty‐four mandibular and maxillary first and second extracted premolars were reviewed. All teeth were extracted for orthodontic reasons. From these teeth, eight teeth were selected to serve as archetype of models in which all the other teeth were at equal size or smaller in maximum 2 mm in M‐D or B‐L dimension. These teeth were sent to dental technician to perform identical archetype stainless steel templates. During autotransplantation immediately following donor tooth extraction, the appropriate template is chosen out of the toothlike stainless steel surgical templates and the donor tooth is then immediately replaced in its socket. This enables the surgeon to prepare the recipient site without manipulating the donor tooth and thus preventing damage to the PDL cells of the donor tooth. Only after the recipient site had been prepared to the appropriate size and shape according to the template, the donor tooth is removed from its socket, immediately placed at the recipient site and splinted as recommended.

Conclusions

The advantage of the presented metal tooth‐like surgical templates described in this study is that a set of stents has been produced by replicating different common shape adolescent premolars that reflect the biological variation in size and shape of these teeth.
Beta diversity as the variance of community data: dissimilarity coefficients and partitioning
Authors: Legendre Pierre , De Cáceres Miquel
Published: July 2013

Beta diversity can be measured in different ways. Among these, the total variance of the community data table Y can be used as an estimate of beta diversity. We show how the total variance of Y can be calculated either directly or through a dissimilarity matrix obtained using any dissimilarity index deemed appropriate for pairwise comparisons of community composition data. We addressed the question of which index to use by coding 16 indices using 14 properties that are necessary for beta assessment, comparability among data sets, sampling issues and ordination. Our comparison analysis classified the coefficients under study into five types, three of which are appropriate for beta diversity assessment. Our approach links the concept of beta diversity with the analysis of community data by commonly used methods like ordination and anova. Total beta can be partitioned into Species Contributions (SCBD: degree of variation of individual species across the study area) and Local Contributions (LCBD: comparative indicators of the ecological uniqueness of the sites) to Beta Diversity. Moreover, total beta can be broken up into within‐ and among‐group components by manova, into orthogonal axes by ordination, into spatial scales by eigenfunction analysis or among explanatory data sets by variation partitioning.
Temporal trends in prevalence of bacteria isolated from foals with sepsis: 1979–2010
Authors: Theelen M. J. P. , Wilson W. D. , Edman J. M. , Magdesian K. G. , Kass P. H.
Published: July 2013

Reasons for performing study

Sepsis is an important cause of death in foals. Knowledge of which pathogens are likely to be involved is important for selection of antimicrobial drugs for initial treatment.

Objectives

To identify temporal trends in prevalence of bacteria isolated from foals with sepsis between 1979 and 2010.

Study design

Retrospective review of medical records.

Methods

All foals ≤30 days of age presented to theVeterinaryMedicalTeachingHospital (VMTH)at the University of California,Davis between 1979 and 2010, with a diagnosis of sepsis confirmed by culture of bacteria from blood or internal organs (antemortemor at necropsy), were included in the study. Conventional microbiological methods were used to identify isolated organisms. TheCochran–Armitage trend test was used for statistical analysis.

Results

The percentage ofGram‐positive isolates increased significantly over the years. The percentageEnterobacteriacea,andKlebsiellaspp. in particular,decreased over time.Enterococcusspp. isolates were cultured more often in recent years.

Conclusions

WhereasGram‐negative bacteria, particularlyEnterobacteriaceae, remain the most common isolates from neonatal foals with sepsis, the prevalence ofGram‐positive bacteria is increasing. This trend underlines the importance of including antimicrobial drugs active against bothGram‐positive andGram‐negative bacteria in treatment protocols while awaiting the results of bacteriological culture and susceptibility tests. The increased prevalence ofEnterococcusspp. is of concern because antimicrobial susceptibility patterns for enterococci are unpredictable and enterococci can also act as donors of antimicrobial resistance genes to other bacteria.
Patterns of density dependence in growth, reproduction and survival in the invasive freshwater snail Pomacea canaliculata in Japanese rice fields
Authors: Yoshida Kazuhiro , Hoshikawa Kazuo , Wada Takashi , Yusa Yoichi
Published: July 2013

Patterns of density dependence in growth, reproduction and survival are important for predicting the population dynamics of a species. The patterns may change with environmental factors, such as the harshness of winter, but very little is known about such patterns and their mechanisms in unmanipulated natural populations of invasive animal species.

We studied the extent of density dependence in the growth, reproduction and survival of an invasive freshwater snail, Pomacea canaliculata, in rice fields in Nara (cold district) and Kumamoto (warm district), Japan, over 2‐ and 1‐year periods, respectively.

In both areas, growth was negatively density dependent within the same generation, and the density of snails in the parental generation negatively affected the growth of offspring. The number of eggs per unit area was independent of adult density, suggesting eggs per adult female were few at high densities. Survival over the cold winter of 2005–2006 was independent of density in Nara. However, survival over the warm winter of 2006–2007 in both Nara and Kumamoto was negatively density dependent.

Irrespective of the various negative density‐dependent patterns, population density tended to show positive correlations with the density of the previous generation. This appears to reflect the substantial capacity of this snail to resist extremely low densities due to the various negative density‐dependent patterns rather than indicating susceptibility to extinction at low densities.
Assessing patient preferences for the delivery of different community‐based models of care using a discrete choice experiment
Authors: Dixon Simon , Nancarrow Susan A. , Enderby Pamela M. , Moran Anna M. , Parker Stuart G.
Published: July 2013

Objectives

To assess patient preferences for different models of care defined by location of care, frequency of care and principal carer within community‐based health‐care services for older people.

Design

Discrete choice experiment administered within a face‐to‐face interview.

Setting

An intermediate care service in a large city within the United Kingdom.

Participants

The projected sample size was calculated to be 200; however, 77 patients were recruited to the study. The subjects had recently been discharged from hospital and were living at home and were receiving short‐term care by a publicly funded intermediate care service.

Interventions

Not applicable.

Main Outcome Measure

The degree of preference, measured using single utility score, for individual service characteristics presented within a series of potential care packages.

Results

Location of care was the dominant service characteristics with care at home being the strongly stated preference when compared with outpatient care (0.003), hospital care (<0.001) and nursing home care (<0.001) relative to home care, although this was less pronounced among less sick patients. Additionally, the respondents indicated a dislike for very frequent care contacts. No particular type of professional carer background was universally preferred but, unsurprisingly, there was evidence that sick patients showed a preference for nurse‐led care.

Conclusions

Patients have clear preferences for the location for their care and were able to state preferences between different care packages when their ideal service was not available. Service providers can use this information to assess which models of care are most preferred within resource constraints.
Value of α‐methylacyl‐CoA racemase immunochemistry for predicting neoplastic progression in Barrett's oesophagus
Authors: Kastelein Florine , Biermann Katharina , Steyerberg Ewout W , Verheij Joanne , Kalisvaart Marit , Looijenga Leendert H J , Stoop Hans A , Walter Laurens , Kuipers Ernst J , Spaander Manon C W , Bruno Marco J ,   ProBar study group
Published: July 2013

Aim

To investigate the value of α‐methylacyl‐CoA racemase (AMACR) immunohistochemistry for predicting neoplastic progression in Barrett's oesophagus (BO).

Methods and results

We conducted a case–control study within a prospective cohort of 720 BO patients. Patients who developed high‐grade dysplasia or oesophageal adenocarcinoma were classified as cases, and patients without neoplastic progression as controls. AMACR expression was determined by immunohistochemistry in 12 127 biopsies from 635 patients, and was scored independently by two expert pathologists. Relative risks adjusted for age, gender, BO length and oesophagitis (RRa) were calculated in log‐linear models. During a median follow‐up of 6.6 years, 49 patients (8%) developed high‐grade dysplasia or oesophageal adenocarcinoma. Although mild AMACR expression was associated with a trend towards an increased risk of neoplastic progression (RRa 1.6, 95% CI 0.9–3.1), the risk was especially elevated with strong AMACR expression (RRa 4.8, 95% CI 1.9–12.6). The positive predictive value of strong AMACR expression was slightly higher than that of low‐grade dysplasia (22% versus 15%); the negative predictive value was slightly lower (91% versus 93%).

Conclusions

Strong AMACR expression is associated with an increased risk of neoplastic progression in BO. However, AMACR expression appears to be a less powerful predictor for neoplastic progression than low‐grade dysplasia.
Malignant Hemangioendothelioma of the Skin
Authors: HORI YOSHIAKI
Published: July 2013

Three cases of malignant hemangioendotheliomas in elderly individuals are recounted. All of them died shortly after onset of the malignancies in spite of radical surgery in one; radical surgery, chemotherapy, and radiotherapy in another; and chemotherapy and radiotherapy in the third. Findings from studies of specimens of the malignancies by conventional microscopy, histochemistry, and electron microscopy are described.
Surgical Management of Congenital Giant Hairy Pigmented Nevi
Authors: PITANGUY IVO
Published: July 2013

The author describes his experience with surgical ablation of truly giant hairy pigmented nevi in 26 cases, three in detail of which two were on the face and one on the back. In a comprehensive table, salient clinical, histopathologic, and surgical data on the 26 cases are given.
A New Dermatome for Surgical Treatment of Rhinophyma
Authors: STREMPEL HARTMUT
Published: July 2013

A new instrument is suggested for surgical treatment of rhinophyma. It is an electrically driven dermatome that has been used beneficially in surgery on the palate. Its use offers several advantages over other instruments and methods currently used for the management of rhinophyma. It avoids the danger of shaving too deeply because the depth of each sweep is both predictable and constant. The size of the blade allows fine sculpturing even in narrow spaces.
Soft‐Tissue Resection for Ingrowing Toenails
Authors: MURRAY WILLIAM R. , ROBB JAMES E.
Published: July 2013

Soft‐tissue resection was carried out on 25 toes of 20 patients who had suffered recurrence of ingrowing toenails following avulsion of their afflicted nails. A cure rate of 60% was achieved. The virtue of the procedure is discussed.
Learning loops – interactions between guided reflection and experience‐based learning in a serious game activity
Authors: Cowley B. , Heikura T. , Ravaja N.
Published: July 2013

In a study on experience‐based learning in serious games, 45 players were tested for topic comprehension by a questionnaire administered before and after playing the single‐player serious game Peacemaker (Impact Games 2007). Players were divided into two activity conditions: 20 played a 1‐h game with a 3‐min half‐time break to complete an affect self‐report form while 25 also participated in a 20‐min reflective group discussion during their half‐time break. During the discussion, they were asked by an experimenter to reflect on a set of topics related to the game. We present the analysis of the questionnaires, which illustrates that contrary to our expectations the reflection period had a negative effect on the learning of the players as judged by their performance on closed‐form questions at levels 1–5 (out of 6) on the Bloom taxonomy of learning outcomes. The questionnaire also included a few open questions which gave the players a possibility to display deep (level 6) learning. The players did not differ significantly between conditions regarding the questions measuring deep learning.
The relationship between emergence from spawning gravel and growth in farmed rainbow trout Oncorhynchus mykiss
Authors: Andersson M. Å. , Laursen D. C. , Silva P. I. M. , Höglund E.
Published: July 2013

The relationship between the timing of emergence from spawning gravel and growth after emergence was investigated in farmed Oncorhynchus mykiss. A relationship between the time of emergence and growth became evident after 6 months of rearing, where individuals with an intermediate emergence time had grown larger compared with early and late emerging individuals.
Comparative life histories of fishes in the genus Phallichthys (Pisces: Poeciliidae)
Authors: Regus J. U. , Johnson J. B. , Webb S. A. , Reznick D. N.
Published: July 2013

This study presents a description of the life histories of all four species of the genus Phallichthys, found primarily in the Atlantic slope of Central America (ranging from northern Panama to Mexico), based on a combination of data collected from preserved and living specimens. All species produced a single litter of offspring before developing another brood (i.e. no superfoetation). In the laboratory, the mean time interval between successive litters ranged from 24 to 48 days, further suggesting that they lack superfoetation. Embryos lose from 15 to 65% of their dry mass during development, meaning all or the large majority of resources required for development are provided prior to fertilization (lecithotrophy). All mature male size distributions were platykurtotic and appeared either bimodal or multimodal. Multimodal and skewed size distributions have been associated with genetic polymorphisms for size at maturity in other species of Poeciliidae. As the sister clade to Phallichthys includes genera in which all species have superfoetation (Neoheterandria and Poeciliopsis), these results suggest that their common ancestor with Phallichthys also had superfoetation and that the trait has been lost.
Reproductive biology of female bigeye tunaThunnus obesusin the western Pacific Ocean
Authors: Sun C. L. , Yeh S. Z. , Chang Y. J. , Chang H. Y. , Chu S. L.
Published: July 2013

The reproductive biology of female bigeye tunaThunnus obesuswas assessed by examining 888 fish (ranging from 84·9 to 174·4 cm fork length,LF) caught by Taiwanese offshore longliners in the western Pacific Ocean from November 1997 to November 1998 and November to December 1999 and 258 gonad samples from these fish. The overall sex ratio of the catch during the sampling differed significantly from 0·5, but males were predominant in sizes >140 cmLF. Reproductive activity (assessed by histology), a gonado‐somatic index, and the size‐frequency distributions of whole oocytes indicated that spawning occurred throughout the year and the major spawning season appeared to be from February to September. The estimated sizes at 50% maturity (LF50) of females was 102·85 cm (95%c.i.: 90·79–110·21 cm) and the smallest mature female was 99·7 cmLF. They are multiple spawners and oocytes develop asynchronously. The proportion of mature (0·63) and reproductively active (0·70) females with ovaries containing postovulatory follicles indicated that they spawn almost daily. Batch fecundity for 15 females with the most advanced oocytes (>730 µm) ranged from 0·84 to 8·56 million eggs (mean ± s.d. = 3·06 ± 2·09). The relationships between batch fecundity (FB, in millions of eggs) andLF(cm) and round mass (MR, kg) were(r2 = 0·84) and(r2 = 0·80), respectively. The parameters estimated in this study are key information for stock assessments ofT. obesusin the western Pacific Ocean and will contribute to the conservation and sustainable yield of this species.
Eruptive and functional changes in periodontal ligament fibroblast orientation in CD44 wild‐type vs. knockout mice
Authors: Popowics T. , Boyd T. , Hinderberger H.
Published: July 2013

Background and Objective

Periodontal ligament (PDL) fibroblasts establish principal fibers of the ligament during tooth eruption, and maintain these fibers during occlusion. PDL development and occlusal adaptation includes changes in the orientation of PDL fibroblasts; however, the mechanism for these changes in orientation is unclear. The objective of this study was to compare PDL fibroblast orientation in different stages corresponding with first molar eruption and occlusion in CD44 wild‐type (WT) and knockout (KO) mice.

Material and Methods

CD44 WT and KO mice were raised to six postnatal stages corresponding with first molar (M1) eruption (postnatal day 8, 11, 14 and 18) and occlusion (postnatal day 26 and 41). Coronal sections of the first mandibular molar (M1) were prepared and the orientation of fibroblasts in the cervical root region was measured. Angle measurements were compared across developmental stages and between strains using Watson–Williams F‐test (oriana software) and ANCOVA.

Results

PDL fibroblast orientation increased significantly in CD44 WT (9–87°) and KO mice (14–93°; p ≤ 0.05) between intraosseous eruption (day 11), mucosal penetration (day 14) and preocclusal eruption (day 18); however, the PDL fibroblast orientation did not change significantly with the onset of occlusion (day 26) or continued function (day 41). Within each strain, the variance in fibroblast orientation during preocclusal eruption (day 18) was significantly higher than the variance of all other time points (p < 0.0005). CD44 WT and KO mice showed a similar pattern of PDL development and eruption with a significant difference in CD44 WT vs. KO fibroblast orientations only during early function (day 26, 92° vs 116°; p = 0.05).

Conclusions

The development of PDL fibroblast orientation is highly similar between CD44 WT and KO mice. Between early (day 11) and late (day 18) eruptive stages PDL fibroblast orientation increases, corresponding with the upward movement of M1. The PDL fibroblast orientation established in preocclusal eruption (day 18) is maintained during early (day 26) and late (day 41) stages of occlusal function, suggesting that PDL cells adapt to mechanical loads in the oral cavity before M1 occlusion.