bluuebunny/crossref_metadata_2025_split huggingface dataset:
A literature review exploring the efficacy of case formulations in clinical practice. What are the themes and pertinent issues?
Authors: Aston Robert 
Published: April 2009

AbstractThere is a paucity of research exploring the validity, reliability and impact on clinical outcome of Cognitive Behavioural Psychotherapy (CBP) case formulations. This review considers a variety of literature that relates to formulations and their use, it also draws on other types of psychotherapy where there appears to be a more established and robust research base. The literature review explores the research that has taken place within CBP and considers the themes that emerge from this research. Several themes were identified and these relate to decision-making and experience, specific guidelines to aid quality of formulations and a significant lack of understanding of clients' views on the formulation process and its outcome. It is unclear whether formulations do influence the successfulness of therapy. Recommendations are made as to what further research is needed and the form this should take.
Collusion in clinical supervision: literature review and case study in self-reflection
Authors: Milne Derek L. , Leck Caroline , Choudhri Nasim Z. 
Published: April 2009

AbstractInterpersonal dynamics are a recurring impediment to effective clinical supervision and can lead to phenomena like collusion between the supervisor and supervisee. Collusion involves both supervisor and supervisee engaging in safety behaviours that serve to conveniently avoid and escape from difficult topics and challenging methods. Whilst minimizing the short-term threat to supervisor and supervisee, collusion will tend to undermine the effectiveness of supervision and limit significantly its long-term value to patients. In order to consider how best to address collusion, we review the cognitive-behavioural therapy (CBT) and related literature on collusion, focusing on how it has been formulated and managed. We then provide a case study featuring a supervisor who was colluding with the supervisee's avoidance behaviours (i.e. filling supervision sessions with superficial reflections on his casework) by not challenging these reflections or moving to another learning mode (e.g. experimenting). We develop a CBT formulation of this pattern of supervision as part of the self-reflection process, led by a consultant. Self-reflection appeared to be a useful tool for improving the supervisor's understanding of this dysfunctional process, and strengthened the supervisor's confidence in utilizing relevant skills in the future.
When is enough enough? Structuring the organization of treatment to maximize patient choice and control
Authors: Carey Timothy A. , Spratt Margaret B. 
Published: April 2009

AbstractThe psychological treatment offered to clients is important. However, an equally important consideration may be the way the treatment is delivered. Reducing waiting lists and improving access to services are priorities for many health services. So is increasing patient control over their own health-care outcomes. While waiting times and access to services have typically been addressed by increasing the numbers of clinicians available, our work suggests that a strategy of providing patients with the ability to determine the frequency and duration of their treatment may be an option that is simpler, more effective, and financially more attractive. After describing policy and ethical guidelines as well as empirical and theoretical information, we provide data from our work in one GP practice about the improvements in waiting times and access to services that occurred when we adopted an approach that allowed patients rather than clinicians to decide how the organization of treatment would occur. There seem to be many benefits to this approach; however, it may also raise dilemmas for clinicians when patients' preferences differ from their own. Ultimately, these conundrums can only be reconciled by the individual clinicians based on their attitudes to mental health problems and service provision.
Curating Genetic Association Literature for Common Diseases
Authors: Silver Elana , Halperin Eran , Kober Kord , Padhukasahasram Badri , Patil Nila , Sommargren Michelle , Stephan Dietrich , Thomas Daryl , Trumbower Heather , Cargill Michele 
Published: April 2009

AbstractPapers describing genetic associations with common diseases are currently being published at a rapid rate. These new papers add to an already large body of literature which includes candidate gene studies, genome wide association studies, review papers, and meta-analyses. Related papers describe the basic epidemiology of these common diseases, as well as interactions between genes and environment, other genes, and drugs (pharmacogenomics), all of which may affect disease predisposition and management. As the field of personalized genomics continues to grow and mature, this body of literature is being synthesized in various ways. One aspect of utmost importance is to track gene-disease associations over time to see if they are replicated in different populations by different authors. This has historically^1^ been a limitation of genetic association studies and if not addressed, can be a major barrier to the adoption of personalized genomics. Another key need is to systematically collect data on the magnitude of the gene-disease effect (typically an odds ratio), variant identifier, allele frequency, risk and non-risk alleles, and other key information from the papers. This is often made more complicated the way that the data is presented by authors (in particular, it is often difficult to tell which is the risk allele), as well as by DNA strand issues. We have built a literature curation database that addresses these two key needs, using Ruby on Rails with MySQL. Lack of consistent standards for the reporting of gene-disease associations, either by journal editors or other consortia or agencies, make automated computer curation infeasible at this time. Thus, Navigenics does all curation manually, employing a team of epidemiologists and human geneticists. To minimize human error, we have incorporated quality control measures, including two independent literature reviews, into the data collection system. Methods for the collection, interpretation, storage, and retrieval of genetic association data from large numbers of papers will be discussed.
Genome Network Project: An Integrated Genomic Platform
Authors: Clemente Jose , Nakagawa So , Ikeo Kazuho , Gojobori Takashi 
Published: April 2009

AbstractWith the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on transcriptional control and transcription-factor related protein-protein interactions (PPI). This data has been collected and organized into the Genome Network Platform ("http://genomenetwork.nig.ac.jp/":http://genomenetwork.nig.ac.jp/) at the National Institute of Genetics. Expression data was obtained through CAGE (Cap Analysis Gene Expression), qRT-PCR, tiling array, microarray and short RNA analysis, while PPI information was gathered through yeast two hybrid (Y2H), mammalian two hybrid (M2H) and in vitro virus (IVV) methods. The Genome Network Platform Viewer provides an integrated user interface to the complete database, including services of gene search, whole genome browsing, PPI network viewer, and expression profile analysis. Our platform represents an extremely useful resource for researchers in the field of genomics, and provides access to high quality data through the combination of intuitive browsing and visualization capabilities.
HGNC: The Why and How of Standardised Gene Nomenclature
Authors: Seal Ruth , Gordon Susan , Lush Michael , Wright Mathew , Bruford Elspeth 
Published: April 2009

AbstractThe HUGO Gene Nomenclature Committee (HGNC) aims to approve a unique gene symbol and gene name for every human gene. Standardisation of gene symbols is necessary to allow researchers and curators to refer to the same gene without ambiguity. Consistent use of gene symbols in publications and across different websites makes it easy for researchers to find all relevant information for a particular gene and facilitates data mining and retrieval. For each gene that we name we curate relevant information including symbol aliases, chromosomal location, locus type, sequence accessions and links to relevant databases. Therefore, our website is a central resource for human genetics. We endeavour to approve gene symbols that are acceptable to researchers to encourage widespread use of our symbols. In order to achieve this, we contact researchers that work on particular genes for advice before approving symbols and allow researchers to submit gene symbols to us directly for our consideration. We attend conferences to discuss difficult nomenclature matters and to gain community agreement. We interact with annotators of genes and proteins to provide symbols and names that accurately reflect the nature of each gene and its products. We also work with the gene nomenclature committees for other organisms, and aim to approve equivalent gene symbols for orthologous genes in human and other vertebrate species, especially mouse and rat. We will demonstrate the steps that are required to name a gene, and will show how and where the nomenclature of a particular gene is used. We will also explain the nature of our collaborations with particular journals and other databases in striving to achieve the use of a common gene nomenclature by all.
Bringing Text Miners and Biologists Closer Together
Authors: Lourenço Anália , Carneiro Sónia , Carreira Rafael , Rocha Miguel , Rocha Isabel , Ferreira Eugénio 
Published: April 2009

AbstractThe boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap between text miners and biologists. Beyond the development of enhanced entity recognisers and the construction of relationship extraction systems, now, more than ever, it is the time for applying available tools to real-world scenarios. Moreover, it is crucial to develop end-user tools that can assist biologists in their research activities. Such tools should be able to emulate biologist conventional curation, recurring to the same knowledge bases and making the same assumptions that biologists usually do, whereas delivering automated capabilities. The search and selection of PubMed articles, the construction of dictionaries from the contents of available Molecular Biology repositories, the implementation of description environments for rule specification, the implementation of dictionary- and rule-based entity recognisers, the development of flexible and extensible relationship extraction systems and the development of easy-to-use manual curation environments are of foremost importance.Our software, named @Note, aims to be a framework and a workbench for BioTM, i.e., it has been conceived for delivering end-user applications, whereas enabling collaboration with other BioTM groups. As a framework, it provides a reusable design for BioTM software systems and a set of pre-assembled software building blocks that programmers can use, extend and customise for their specific needs. As a workbench, it helps developing BioTM applications by integrating Natural Language Processing and Data Mining tools and supporting major Information Retrieval and Information Extraction processes. Moreover, it encompasses a flexible and extensible manual curation environment that enables the interaction with biologists, correcting former annotations and enhancing dictionary contents. We successfully applied @Note in the study of the stringent response on Escherichia coli, an important subject within the analysis of stress responses in bacteria. This joint effort allowed biologists to contribute to the enhancement of our manual curation environment and to identify new functionalities for the existing plug-ins and the specification of new plug-ins.
Challenges in Whole-Genome Annotation of Pyrosequenced Fungal Genomes
Authors: Kuo Alan , Grigoriev Igor 
Published: April 2009

AbstractPyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454 sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~10k genes. ~12% of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~9% rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also, >90% of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. We conclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.
UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web
Authors: Redaschi Nicole , Consortium UniProt 
Published: April 2009

AbstractThe UniProt knowledgebase (UniProtKB) is a comprehensive repository of protein sequence and annotation data. We collect information from the scientific literature and other databases and provide links to over one hundred biological resources. Such links between different databases are an important basis for data integration, but the lack of a common standard to represent and link information makes data integration an expensive business. At UniProt we have started to tackle this problem by using the Resource Description Framework ("http://www.w3.org/RDF/":http://www.w3.org/RDF/) to represent our data. RDF is a core technology for the World Wide Web Consortium's Semantic Web activities ("http://www.w3.org/2001/sw/":http://www.w3.org/2001/sw/) and is therefore well suited to work in a distributed and decentralized environment. The RDF data model represents arbitrary information as a set of simple statements of the form subject-predicate-object. To enable the linking of data on the Web, RDF requires that each resource must have a (globally) unique identifier. These identifiers allow everybody to make statements about a given resource and, together with the simple structure of the RDF data model, make it easy to combine the statements made by different people (or databases) to allow queries across different datasets. RDF is thus an industry standard that can make a major contribution to solve two important problems of bioinformatics: distributed annotation and data integration.
Growth of 𝐿^{𝑝} Lebesgue constants for convex polyhedra and other regions
Authors: Ash J. , De Carli Laura 
Published: April 2009

For any convex polyhedron

W
W

in

R

m

\mathbb {R}^{m}

,

p
∈

(
1
,
∞
)

p\in \left (1,\infty \right )

, and

N
≥
1

N\geq 1

, there are constants

γ

1

(
W
,
p
,
m
)

\gamma _{1}\left (W,p,m\right )

and

γ

2

(
W
,
p
,
m
)

\gamma _{2}\left (W,p,m\right )

such that
\[

γ

1

N

m

(
p
−
1
)

≤

∫

T

m

|

∑

k
∈
N
W

e

(
k
⋅
x
)

|

p

d
x
≤

γ

2

N

m

(
p
−
1
)

.

\gamma _{1}N^{m\left (p-1\right ) }\leq \int _{\mathbb {T}^{m}}\left \vert \sum _{k\in NW}e\left (k\cdot x\right ) \right \vert ^{p}dx\leq \gamma _{2}N^{m\left (p-1\right )}.

\]
Similar results hold for more general regions. These results are various special cases of the inequalities
\[

γ

1

N

m

(
p
−
1
)

≤

∫

T

m

|

∑

k
∈
N
B

e

(
k
⋅
x
)

|

p

d
x
≤

γ

2

ϕ

(
N
)

,

\gamma _{1}N^{m\left (p-1\right ) }\leq \int _{\mathbb {T}^{m}}\left \vert \sum _{k\in NB}e\left (k\cdot x\right ) \right \vert ^{p}dx\leq \gamma _{2} \phi \left (N\right ),

\]
where

ϕ

(
N
)

=

N

p

(
m
−
1
)

/

2

\phi \left (N\right )=N^{p\left (m-1\right ) /2}

when

p
∈

(
1
,

2
m

m
+
1

)

p\in \left ( 1,\frac {2m}{m+1}\right )

,

ϕ

(
N
)

=

N

p

(
m
−
1
)

/

2

log

\phi \left (N\right )=N^{p\left (m-1\right ) /2}\log

N
N

when

p
=

2
m

m
+
1

p=\frac {2m}{m+1}

, and

ϕ

(
N
)

=

N

m

(
p
−
1
)

\phi \left (N\right )=N^{m\left ( p-1\right ) }

when

p
>

2
m

m
+
1

p>\frac {2m}{m+1}

, where

B
B

is a bounded subset of

R

m

\mathbb {R}^{m}

with non-empty interior.
Igusa-type functions associated to finite formed spaces and their functional equations
Authors: Klopsch Benjamin , Voll Christopher 
Published: April 2009

We study symmetries enjoyed by the polynomials enumerating non-degenerate flags in finite vector spaces, equipped with a non-degenerate alternating bilinear, Hermitian or quadratic form. To this end we introduce Igusa-type rational functions encoding these polynomials and prove that they satisfy certain functional equations.

Some of our results are achieved by expressing the polynomials in question in terms of what we call parabolic length functions on Coxeter groups of type

A
A

. While our treatment of the orthogonal case exploits combinatorial properties of integer compositions and their refinements, we formulate a precise conjecture how in this situation, too, the polynomials may be described in terms of parabolic length functions.
Flow invariance for nonlinear partial differential delay equations
Authors: Ruess Wolfgang 
Published: April 2009

Several fundamental results on existence, flow-invariance, regularity, and linearized stability of solutions to the nonlinear partial differential delay equationu˙(t)+Bu(t)∋F(ut),t≥0,u0=φ,\dot {u}(t) + Bu(t) \ni F(u_t), t\geq 0, u_0 = \varphi ,withB⊂X×XB\subset X\times Xω−\omega -accretive, are developed for a general Banach spaceX.X.In contrast to existing results, with the history-responseFFglobally defined and, at least, Lipschitz on bounded sets, the results are tailored for situations withFFdefined on (possibly) thin subsets of the initial-history spaceEEonly, and are applied to place several classes of population models in their naturalL1−L^1-setting. The main result solves the open problem of a subtangential condition for flow-invariance of solutions in the fully nonlinear case, paralleling those known for the cases of (a) no delay, (b) ordinary delay equations withB≡0,B\equiv 0,and (c) the semilinear case.
VARNA: Interactive drawing and editing of the RNA secondary structure
Authors: Darty Kévin , Denise Alain , Ponty Yann 
Published: April 2009

Abstract
Description: VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
Features: VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.
Availability: VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr
Contact: ponty@lri.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Long‐term prognosis of medically treated patients with functional mitral regurgitation and left ventricular dysfunction
Authors: Agricola Eustachio , Ielasi Alfonso , Oppizzi Michele , Faggiano Pompilio , Ferri Luca , Calabrese Alice , Vizzardi Enrico , Alfieri Ottavio , Margonato Alberto 
Published: April 2009

AimsTo assess long‐term prognosis in patients with functional mitral regurgitation (FMR) and left ventricular (LV) dysfunction, receiving current standard pharmacological therapy.Methods and resultsWe prospectively enrolled 404 consecutive patients (mean age 70.2 ± 10 years) with ischaemic (76.5%) and non‐ischaemic (23.5%) LV dysfunction (ejection fraction 34.4 ± 10.8%) and at least mild MR. Results are reported at 4 years' follow‐up. Survival free of all‐cause mortality was 53% and cardiac death was 74%. Survival free of all‐cause mortality was 50% (95% CI 35–72) for patients with moderate MR, 49% (95% CI 27–65) for severe MR, and 64% (95% CI 47–78) for mild MR (P = 0.03). Survival free of cardiac death was 57% (95% CI 38–74) for patients with moderate MR, 55% (95% CI 30–77) for severe MR, and 94% (95% CI 59–98) for mild MR (P = 0.003). Moderate‐to‐severe MR [relative risk (RR) 2.7, 95% CI 1.2–6.1, P = 0.003] was an independent predictor of cardiac death but not of all‐cause mortality. Survival free of heart failure (HF) was 32%. Survival free of HF was 20% (95% CI 17–35) for patients with moderate MR, 18% (95% CI 15–32) for severe MR, and 62% (95% CI 45–72) for mild MR (P = 0.0001). Moderate‐to‐severe MR (RR 3.2, 95% CI 1.9–5.2, P = 0.0001) was an independent predictor of HF.ConclusionThe mortality and morbidity of patients with LV dysfunction and FMR remain high despite current standard pharmacological therapy. Moderate‐to‐severe MR is an independent predictor of cardiac death and HF.
Study of the immunological profile towards Mycobacterium bovis antigens in naturally infected cattle
Authors: Blanco Federico C. , Schierloh Pablo , Bianco María Verónica , Caimi Karina , Meikle Virginia , Alito Alicia E. , Cataldi Angel A. , Sasiain María del Carmen , Bigi Fabiana 
Published: April 2009

ABSTRACTA number of studies have determined the contribution of Th1 and Th2 responses to the protective immunity and pathology of Mycobacterium bovis infection. However, much of that information is derived from experimentally infecting cattle with M. bovis and few data from naturally infected animals are available. The aim of this study was to characterize the immunological profile towards M. bovis antigens of naturally infected cattle by measurement of cytokine mRNA expression in PBMC, and to determine which lymphocyte subsets are involved in recall responses of PBMC from M. bovis infected cattle to M. bovis antigens. Consistent with data from cattle experimentally infected with M. bovis, naturally infected animals were found to display a Th1 cytokine profile in response to M. bovis PPDB stimulation. Production of IFN‐γ mRNA by PBMC after PPDB stimulation statistically distinguishes between infected and healthy herds, suggesting that this molecule is usable as an M. bovis‐infection marker. As happens in experimentally infected cows, CD4, CD8 and γδTCR cells from a herd naturally infected with M. bovis are the predominant T cell subsets expanded in response to PPDB.