bluuebunny/crossref_metadata_2025_split huggingface dataset:
LTBI: latent tuberculosis infection or lasting immune responses toM. tuberculosis? A TBNET consensus statement
Authors: Mack U. , Migliori G. B. , Sester M. , Rieder H. L. , Ehlers S. , Goletti D. , Bossink A. , Magdorf K. , Hölscher C. , Kampmann B. , Arend S. M. , Detjen A. , Bothamley G. , Zellweger J. P. , Milburn H. , Diel R. , Ravn P. , Cobelens F. , Cardona P. J. , Kan B. , Solovic I. , Duarte R. , Cirillo D. M. ,   C. Lange for the TBNET
Published: April 2009

Tuberculosis control relies on the identification and preventive treatment of individuals who are latently infected withMycobacterium tuberculosis. However, direct identification of latent tuberculosis infection is not possible. The diagnostic tests used to identify individuals latently infected withM. tuberculosis, thein vivotuberculin skin test and theex vivointerferon-γ release assays (IGRAs), are designed to identify an adaptive immune response against, but not necessarily a latent infection with,M. tuberculosis. The proportion of individuals who truly remain infected withM. tuberculosisafter tuberculin skin test or IGRA conversion is unknown. It is also uncertain how long adaptive immune responses towards mycobacterial antigens persist in the absence of live mycobacteria. Clinical management and public healthcare policies for preventive chemotherapy against tuberculosis could be improved, if we were to gain a better understanding onM. tuberculosislatency and reactivation. This statement by the TBNET summarises knowledge and limitations of the currently available tests used in adults and children for the diagnosis of latent tuberculosis infection.In summary, the main issue regarding testing is to restrict it to those who are known to be at higher risk of developing tuberculosis and who are willing to accept preventive chemotherapy.
Efficient context-dependent model building based on clustering posterior distributions for non-coding sequences
Authors: Baele Guy , Van de Peer Yves , Vansteelandt Stijn 
Published: April 2009

Abstract

Background
Many recent studies that relax the assumption of independent evolution of sites have done so at the expense of a drastic increase in the number of substitution parameters. While additional parameters cannot be avoided to model context-dependent evolution, a large increase in model dimensionality is only justified when accompanied with careful model-building strategies that guard against overfitting. An increased dimensionality leads to increases in numerical computations of the models, increased convergence times in Bayesian Markov chain Monte Carlo algorithms and even more tedious Bayes Factor calculations.

Results
We have developed two model-search algorithms which reduce the number of Bayes Factor calculations by clustering posterior densities to decide on the equality of substitution behavior in different contexts. The selected model's fit is evaluated using a Bayes Factor, which we calculate via model-switch thermodynamic integration. To reduce computation time and to increase the precision of this integration, we propose to split the calculations over different computers and to appropriately calibrate the individual runs. Using the proposed strategies, we find, in a dataset of primate Ancestral Repeats, that careful modeling of context-dependent evolution may increase model fit considerably and that the combination of a context-dependent model with the assumption of varying rates across sites offers even larger improvements in terms of model fit. Using a smaller nuclear SSU rRNA dataset, we show that context-dependence may only become detectable upon applying model-building strategies.

Conclusion
While context-dependent evolutionary models can increase the model fit over traditional independent evolutionary models, such complex models will often contain too many parameters. Justification for the added parameters is thus required so that only those parameters that model evolutionary processes previously unaccounted for are added to the evolutionary model. To obtain an optimal balance between the number of parameters in a context-dependent model and the performance in terms of model fit, we have designed two parameter-reduction strategies and we have shown that model fit can be greatly improved by reducing the number of parameters in a context-dependent evolutionary model.
Identifying genes related to choriogenesis in insect panoistic ovaries by Suppression Subtractive Hybridization
Authors: Irles Paula , Bellés Xavier , Piulachs M Dolors 
Published: April 2009

Abstract

Background
Insect ovarioles are classified into two categories: panoistic and meroistic, the later having apparently evolved from an ancestral panoistic type. Molecular data on oogenesis is practically restricted to meroistic ovaries. If we aim at studying the evolutionary transition from panoistic to meroistic, data on panoistic ovaries should be gathered. To this end, we planned the construction of a Suppression Subtractive Hybridization (SSH) library to identify genes involved in panoistic choriogenesis, using the cockroach Blattella germanica as model.

Results
We constructed a post-vitellogenic ovary library by SSH to isolate genes involved in choriogenesis in B. germanica. The tester library was prepared with an ovary pool from 6- to 7-day-old females, whereas the driver library was prepared with an ovary pool from 3- to 4-day-old females. From the SSH library, we obtained 258 high quality sequences which clustered into 34 unique sequences grouped in 19 contigs and 15 singlets. The sequences were compared against non-redundant NCBI databases using BLAST. We found that 44% of the unique sequences had homologous sequences in known genes of other organisms, whereas 56% had no significant similarity to any of the databases entries. A Gene Ontology analysis was carried out, classifying the 34 sequences into different functional categories. Seven of these gene sequences, representative of different categories and processes, were chosen to perform expression studies during the first gonadotrophic cycle by real-time PCR. Results showed that they were mainly expressed during post-vitellogenesis, which validates the SSH technique. In two of them corresponding to novel genes, we demonstrated that they are specifically expressed in the cytoplasm of follicular cells in basal oocytes at the time of choriogenesis.

Conclusion
The SSH approach has proven to be useful in identifying ovarian genes expressed after vitellogenesis in B. germanica. For most of the genes, functions related to choriogenesis are postulated. The relatively high percentage of novel genes obtained and the practical absence of chorion genes typical of meroistic ovaries suggest that mechanisms regulating chorion formation in panoistic ovaries are significantly different from those of meroistic ones.
Evaluation of the effect of stent strut profile on shear stress distribution using statistical moments
Authors: Mejia Juan , Ruzzeh Bilal , Mongrain Rosaire , Leask Richard , Bertrand Olivier F 
Published: April 2009

Abstract

Background
In-stent restenosis rates have been closely linked to the wall shear stress distribution within a stented arterial segment, which in turn is a function of stent design. Unfortunately, evaluation of hemodynamic performance can only be evaluated with long term clinical trials. In this work we introduce a set of metrics, based on statistical moments, that can be used to evaluate the hemodynamic performance of a stent in a standardized way. They are presented in the context of a 2D flow study, which analyzes the impact of different strut profiles on the wall shear stress distribution for stented coronary arteries.

Results
It was shown that the proposed metrics have the ability to evaluate hemodynamic performance quantitatively and compare it to a common standard. In the context of the simulations presented here, they show that stent's strut profile significantly affect the shear stress distribution along the arterial wall. They also demonstrates that more streamlined profiles exhibit better hemodynamic performance than the standard square and circular profiles. The proposed metrics can be used to compare results from different research groups, and provide an improved method of quantifying hemodynamic performance in comparison to traditional techniques.

Conclusion
The strut shape found in the latest generations of stents are commonly dictated by manufacturing limitations. This research shows, however, that strut design can play a fundamental role in the improvement of the hemodynamic performance of stents. Present results show that up to 96% of the area between struts is exposed to wall shear stress levels above the critical value for the onset of restenosis when a tear-drop strut profile is used, while the analogous value for a square profile is 19.4%. The conclusions drawn from the non-dimensional metrics introduced in this work show good agreement with an ordinary analysis of the wall shear stress distribution based on the overall area exposed to critically low wall shear stress levels. The proposed metrics are able to predict, as expected, that more streamlined profiles perform better hemodynamically. These metrics integrate the entire morphology of the shear stress distribution and as a result are more robust than the traditional approach, which only compares the relative value of the local wall shear stress with a critical value of 0.5 Pa. In the future, these metrics could be employed to compare, in a standardized way, the hemodynamic performance of different stent designs.
A rapid method of fruit cell isolation for cell size and shape measurements
Authors: McAtee Peter A , Hallett Ian C , Johnston Jason W , Schaffer Robert J 
Published: April 2009

AbstractBackgroundCell size is a structural component of fleshy fruit, contributing to important traits such as fruit size and texture. There are currently a number of methods for measuring cell size; most rely either on tissue sectioning or digestion of the tissue with cell wall degrading enzymes or chemicals to release single cells. Neither of these approaches is ideal for assaying large fruit numbers as both require a considerable time to prepare the tissue, with current methods of cell wall digestions taking 24 to 48 hours. Additionally, sectioning can lead to a measurement of a plane that does not represent the widest point of the cell.ResultsTo develop a more rapid way of measuring fruit cell size we have developed a protocol that solubilises pectin in the middle lamella of the plant cell wall releasing single cells into a buffered solution. Gently boiling small fruit samples in a 0.05 M Na2CO3solution, osmotically balanced with 0.3 M mannitol, produced good cell separation with little cellular damage in less than 30 minutes. The advantage of combining a chemical treatment with boiling is that the cells are rapidly killed. This stopped cell shape changes that could potentially occur during separation. With this method both the rounded and angular cells of the apple cultivars SciRos 'Pacific Rose' and SciFresh 'Jazz'™ were observed in the separated cells. Using this technique, an in-depth analysis was performed measuring cell size from 5 different apple cultivars. Cell size was measured using the public domain ImageJ software. For each cultivar a minimum of 1000 cells were measured and it was found that each cultivar displayed a different distribution of cell size. Cell size within cultivars was similar and there was no correlation between flesh firmness and cell size. This protocol was tested on tissue from other fleshy fruit including tomato, rock melon and kiwifruit. It was found that good cell separation was achieved with flesh tissue from all these fruit types, showing a broad utility to this protocol.ConclusionWe have developed a method for isolating single cells from fleshy fruit that reduces the time needed for fruit cell separation. This method was used to demonstrate differences in cell size and shape for 5 different apple cultivars. While firmness between the different cultivars is independent of cell size, apples with more angular cells appear to be firmer.
Social influences upon injection initiation among street-involved youth in Vancouver, Canada: a qualitative study
Authors: Small Will , Fast Danya , Krusi Andrea , Wood Evan , Kerr Thomas 
Published: April 2009

AbstractBackgroundStreet-involved youth are a population at risk of adopting injection as a route of administration, and preventing the transition to injection drug use among street youth represents a public health priority. In order to inform epidemiological research and prevention efforts, we conducted a qualitative study to investigate the initiation of injection drug use among street-involved youth in Vancouver, Canada.MethodsQualitative interviews with street youth who inject drugs elicited descriptions of the adoption of injection as a route of administration. Interviewees were recruited from the At-Risk Youth Study (ARYS), a cohort of street-involved youth who use illicit drugs in Vancouver, Canada. Audio recorded interviews were transcribed verbatim and a thematic analysis was conducted.Results26 youth aged 16 to 26 participated in this study, including 12 females. Among study participants the first injection episode frequently featured another drug user who facilitated the initiation of injecting. Youth narratives indicate that the transition into injecting is influenced by social interactions with drug using peers and evolving perceptions of injecting, and rejecting identification as an injector was important among youth who did not continue to inject. It appears that social conventions discouraging initiating young drug users into injection exist among established injectors, although this ethic is often ignored.ConclusionThe importance of social relationships with other drug users within the adoption of injection drug use highlights the potential of social interventions to prevent injection initiation. Additionally, developing strategies to engage current injectors who are likely to initiate youth into injection could also benefit prevention efforts.
Further validation of the Health Scale of Traditional Chinese Medicine (HSTCM)
Authors: Wu Darong , Lai Shilong , Zhou Luojing , Guo Xinfeng , Liang Weixiong , Wen Zehuai , Ou Aihua , Zhang Guangqing , Chen Keji 
Published: April 2009

Abstract

Background
Few health measurement scales are based on Chinese medicine theory. The Health Scale of Traditional Chinese Medicine (HSTCM) was developed to fill this gap. The aim of this study is to validate the HSTCM.

Methods
A convenience sample of 630 participants was recruited in 11 settings. All participants were asked to complete the HSTCM and World Health Organization Quality of Life Measure-Abbreviated Version (WHOQOL-BREF).

Results
Properties of the HSTCM were tested. Intra-class correlation coefficient representing the inter-interviewer reliability was 0.99 (95%CI) for the overall instrument. Spearman-Brown correlation coefficient and Cronbach's coefficient alpha were 0.81 and 0.94 respectively, indicating satisfactory internal reliability and inter-interviewer reliability. Spearman's rho correlation coefficient between the HSTCM and WHOQOL-BREFF was -0.67. A receiver operating characteristic (ROC) curve analysis was performed to test the discriminate validation. Areas under the ROC curve analysis for the HSTCM and its domains ranged 0.71–0.87 and all the lower levels of 95%CI were greater than 0.50.

Conclusion
The HSTCM was validated as a generic health scale and may complement existing health measurement scales in Chinese medicine health care.
Tumour-associated tenascin-C isoforms promote breast cancer cell invasion and growth by matrix metalloproteinase-dependent and independent mechanisms
Authors: Hancox Rachael A , Allen Michael D , Holliday Deborah L , Edwards Dylan R , Pennington Caroline J , Guttery David S , Shaw Jacqueline A , Walker Rosemary A , Pringle J Howard , Jones J Louise 
Published: April 2009

Abstract
Introduction
The stromal microenvironment has a profound influence on tumour cell behaviour. In tumours, the extracellular matrix (ECM) composition differs from normal tissue and allows novel interactions to influence tumour cell function. The ECM protein tenascin-C (TNC) is frequently up-regulated in breast cancer and we have previously identified two novel isoforms – one containing exon 16 (TNC-16) and one containing exons 14 plus 16 (TNC-14/16).

Methods
The present study has analysed the functional significance of this altered TNC isoform profile in breast cancer. TNC-16 and TNC-14/16 splice variants were generated using PCR-ligation and over-expressed in breast cancer cells (MCF-7, T47D, MDA-MD-231, MDA-MB-468, GI101) and human fibroblasts. The effects of these variants on tumour cell invasion and proliferation were measured and compared with the effects of the large (TNC-L) and fully spliced small (TNC-S) isoforms.

Results
TNC-16 and TNC-14/16 significantly enhanced tumour cell proliferation (P < 0.05) and invasion, both directly (P < 0.01) and as a response to transfected fibroblast expression (P < 0.05) with this effect being dependent on tumour cell interaction with TNC, because TNC-blocking antibodies abrogated these responses. An analysis of 19 matrix metalloproteinases (MMPs) and tissue inhibitor of matrix metalloproteinases 1 to 4 (TIMP 1 to 4) revealed that TNC up-regulated expression of MMP-13 and TIMP-3 two to four fold relative to vector, and invasion was reduced in the presence of MMP inhibitor GM6001. However, this effect was not isoform-specific but was elicited equally by all TNC isoforms.

Conclusions
These results demonstrate a dual requirement for TNC and MMP in enhancing breast cancer cell invasion, and identify a significant role for the tumour-associated TNC-16 and TNC-14/16 in promoting tumour invasion, although these isoform-specific effects appear to be mediated through MMP-independent mechanisms.
Post-traumatic stress disorder and attachment: possible links with borderline personality disorder
Authors: de Zulueta Felicity 
Published: April 2009

SummaryThis article discusses the aetiology of both simple and complex post-traumatic stress disorders (PTSDs) in terms of attachment theory, and points out the similarities between the diagnosis of complex PTSD and of borderline personality disorder. Case vignettes illustrate an outline of the assessment and treatment of the psychobiological symptoms of PTSD informed by attachment research.
Minimal-medication approaches to treating schizophrenia
Authors: Calton Tim , Spandler Helen 
Published: April 2009

SummaryUK guidelines for treating people diagnosed with schizophrenia currently emphasise the primacy of antipsychotic medication, with or without psychosocially based interventions as circumstances dictate. We now see increasing calls, most notably from mental health service users, for the provision of ‘whole-person-based’, minimal-medication approaches to treating people with this diagnosis. This article is intended to locate the development of such approaches within the history of modern and pre-modern psychiatry and, in doing so, summarise the available evidence base that underpins their efficacy.
Introducing compassion-focused therapy
Authors: Gilbert Paul 
Published: April 2009

SummaryShame and self-criticism are transdiagnostic problems. People who experience them may struggle to feel relieved, reassured or safe. Research suggests that a specialised affect regulation system (or systems) underpins feelings of reassurance, safeness and well-being. It is believed to have evolved with attachment systems and, in particular, the ability to register and respond with calming and a sense of well-being to being cared for. In compassion-focused therapy it is hypothesised that this affect regulation system is poorly accessible in people with high shame and self-criticism, in whom the ‘threat’ affect regulation system dominates orientation to their inner and outer worlds. Compassion-focused therapy is an integrated and multimodal approach that draws from evolutionary, social, developmental and Buddhist psychology, and neuroscience. One of its key concerns is to use compassionate mind training to help people develop and work with experiences of inner warmth, safeness and soothing, via compassion and self-compassion.
How to make good-enough risk decisions
Authors: Carroll Andrew 
Published: April 2009

SummaryMaking decisions in the context of risk is an integral part of psychiatric work. Despite this, decision-making skills are rarely systematically taught and the processes behind decisions are rarely made explicit. This article attempts to apply contemporary evidence from cognitive and social psychology to common dilemmas faced by psychiatrists when assessing and managing risk. It argues that clinical decision-making should acknowledge both the value and limitations of intuitive approaches in dealing with complex dilemmas. After discussing the various ways in which clinical decision-making is commonly derailed, the article outlines a framework that accommodates both rational and intuitive modes of thinking, with the aim of optimising decision-making in high-risk situations.
Drug treatments for attention-deficit hyperactivity disorder in young people
Authors: Bates Gordon 
Published: April 2009

SummaryThe central role of medication in the treatment of attention-deficit hyperactivity disorder (ADHD) in children and adolescents is the focus of controversy once more. Questions about the safety and appropriateness of medication have arisen both within and without the medical community. This coincides with the disappointing results for long-term ADHD treatment, illustrated recently by the first major outcome study to be published. Clinicians have had to contend with a number of public health scares following on from the actions of drug regulatory bodies, in addition to misinformation and misunderstanding from the media. Ironically, this comes at a time when we have an ever-widening range of medications and formulations available to us, and better-quality studies to inform treatment decisions. The recently published National Institute for Health and Clinical Excellence guidelines address some of these issues and provide a welcome summary and reference point for beleaguered clinicians.
Issues concerning feedback about genetic testing and risk of depression
Authors: Wilhelm Kay , Meiser Bettina , Mitchell Philip B. , Finch Adam W. , Siegel Jennifer E. , Parker Gordon , Schofield Peter R. 
Published: April 2009

BackgroundRecent studies show that adverse life events have a significantly greater impact on depression onset for those with the s/s allele of the genotype for the 5-HT gene-linked promoter region. Research in genes related to risk of depression leads to the question of how this information is received by individuals.AimsTo investigate factors related to the response to receiving one's own serotonin transporter genotype results.MethodPredictors of the impact of receiving individual genotype data were assessed in 128 participants in a study of gene–environment interaction in depression onset.ResultsTwo-thirds decided to learn their individual genotype results (receivers) and prior to disclosure this decision was associated with a perception of greater benefit from receipt of the information (P=0.001). Receivers completing the 2-week (n=76) and 3-month follow-up (n=78) generally reported feeling pleased with the information and having had a more positive experience than distress. However, distress was related to genotype, with those with the s/s allele being most affected.ConclusionsThere was high interest in, and satisfaction with, learning about one's serotonin transporter genotype. Participants appeared to understand that the gene conferred susceptibility to depression rather than a direct causal effect.