bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing Motional Correlations in Molecular Dynamics using Geometric Deformations
Authors: Fioravante M. , Shook A. , Thorpe I. , Rheingans P. 
Published: July 2013

AbstractIn 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

AbstractParticle 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

AbstractAs 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

AbstractJulia 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

AbstractAimConfocal 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.MethodA 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.ResultsIn 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).ConclusionCLE, 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.
Common Counsel, Common Policy: Healthcare, Missions and the Rise of the ‘Voluntary Sector’ in Colonial Tanzania
Authors: Jennings Michael 
Published: July 2013

ABSTRACTAnalysis 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

AbstractObjectivesThe 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.MethodsPremolars 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.ConclusionsThe 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

AbstractBeta 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

SummaryReasons for performing studySepsis 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.ObjectivesTo identify temporal trends in prevalence of bacteria isolated from foals with sepsis between 1979 and 2010.Study designRetrospective review of medical records.MethodsAll 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.ResultsThe 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.ConclusionsWhereasGram‐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

Summary

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

AbstractObjectivesTo 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.DesignDiscrete choice experiment administered within a face‐to‐face interview.SettingAn intermediate care service in a large city within the United Kingdom.ParticipantsThe 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.InterventionsNot applicable.Main Outcome MeasureThe degree of preference, measured using single utility score, for individual service characteristics presented within a series of potential care packages.ResultsLocation 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.ConclusionsPatients 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

AimTo investigate the value of α‐methylacyl‐CoA racemase (AMACR) immunohistochemistry for predicting neoplastic progression in Barrett's oesophagus (BO).Methods and resultsWe 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%).ConclusionsStrong 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.
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

AbstractIn 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.
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 ObjectivePeriodontal 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 MethodsCD44 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.ResultsPDL 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).ConclusionsThe 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.