bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alzheimer's Disease Management Guideline: Update 2008
Authors: Segal‐Gidan Freddi , Cherry Debra , Jones Randi , Williams Bradley , Hewett Linda , Chodosh Joshua 
Published: May 2011

BackgroundFrequent review and update of guidelines are necessary for them to remain current and useful for clinical practices. This second revision of the postdiagnostic management of Alzheimer's disease (AD) guideline by the California Workgroup was prompted by significant advances in knowledge about appropriate care management, including pharmacologic and nonpharmacologic approaches to treatment of the disease, accompanying behavioral problems, and functional decline. The focus remains explicitly on primary care, where the majority of it occurs for those with AD and other dementias.MethodsIn all, 40 experts in dementia care were recruited from a variety of disciplines across California. Four workgroups were created that reviewed recent research findings from a total of 569 publications since 2002. The revised Guideline incorporates 305 new references, including 11 state and federal laws, in addition to 78 references from the previous version.ResultsThe Guideline is divided into four sections that address postdiagnostic management: (1) assessment, (2) treatment, (3) patient and family education and support, and (4) legal considerations associated with AD. Significant revisions and changes in each area and the underlying research to support the recommendations are presented in this article. New topics related to early stage and end‐of‐life were identified and recommendations were developed for these specific populations.ConclusionsThe Guideline recommendations provide a framework to inform and improve medical care for AD by primary health care providers.
Effects of dietary seaweed extract supplementation in sows and post-weaned pigs on performance, intestinal morphology, intestinal microflora and immune status
Authors: Leonard S. G. , Sweeney T. , Bahar B. , Lynch B. P. , O'Doherty J. V. 
Published: May 2011

The present study investigated the effects of dietary supplementation of a seaweed extract (SWE) to sows and weaned pigs on post-weaning growth performance, intestinal morphology, intestinal microflora, volatile fatty acid concentrations and immune status of pigs at days 11 and 117 post-weaning. Gestating sows (n20) were supplemented with a SWE (0v.10·0 g/d) from day 107 of gestation until weaning (day 26). At weaning, pigs (four pigs per sow) were divided into two groups based on sow diet during lactation and supplemented with a SWE (0v.2·8 g/kg diet), resulting in four treatment groups: (1) BB (basal sows–basal pigs); (2) BS (basal sows–treated pigs); (3) SB (treated sows–basal pigs); (4) SS (treated sows–treated pigs). Pigs weaned from SWE-supplemented sows had a higher average daily gain (ADG) between days 0 and 21 (P < 0·05) post-weaning compared with pigs weaned from non-SWE-supplemented sows. Pigs offered post-weaning diets (PW) containing SWE had decreased colonicEscherichia colipopulations on day 11 (P < 0·01) and decreased colonic Enterobacteriaceae numbers on day 117 (P < 0·05). Pigs offered PW containing SWE had a greater mRNA abundance ofMUC2in the colon at day 11 post-weaning (P < 0·05) compared with pigs offered unsupplemented diets. In conclusion, these results demonstrate that SWE supplementation post-weaning provides a dietary means to improve gut health and to enhance growth performance in starter pigs. Dietary SWE supplementation increased ADG during the grower–finisher (GF) phases. However, there was no growth response to SWE inclusion in GF diets when pigs were weaned from SWE-supplemented sows.
Using photovoice with older adults: some methodological strengths and issues
Authors: NOVEK SHEILA , MORRIS-OSWALD TONI , MENEC VERENA 
Published: May 2011

ABSTRACTPhotovoice is a qualitative research technique in which participants record and reflect on their community through photography. The technique is gaining popularity as a participatory research methodology. Few studies, however, have described the use of photovoice with older adults. This paper examines the application of photovoice in a qualitative, participatory research study examining age-friendly community characteristics in four communities in Manitoba, Canada. Thirty older adults were provided with cameras and took photographs to illustrate how age-friendly their communities are and participated in group discussions to identify priorities in becoming more age-friendly. The research process and results were analysed in order to assess the application of the methodology with older adults. Photovoice is an effective tool for eliciting older persons’ perceptions of their communities, giving voice to the unique concerns of older adults, and identifying strategies for change. If adapted to accommodate the needs of seniors, this methodology provides an innovative approach to community-based gerontological research. On the other hand, there are a number of challenges to be overcome if photovoice is to be a truly effective research instrument, including recruitment, photography training, retrieving consent forms, and issues of time and distance.
Global Constitutionalism and the Objective Purport of the International Legal Order
Authors: VAN MULLIGEN JOHANNES GERALD 
Published: May 2011

AbstractGlobal constitutionalists argue that the international legal order can only be meaningfully construed as having an objective, value-based purport. There is, however, something hybrid about the constitutionalist argument, as constitutionalists espouse a normative agenda whilst at the same time setting out to ground their approach in positive international law. It is contended that to avoid both this foundational problem and the charge of utopianism, and as a rejoinder to positivistic arguments for the denial of objective purport, constitutionalists are forced to reason along indirect, transcendental lines. Thus, constitutionalists are to be construed as avouching global values as necessary conditions for making sense of existing international legal practice, rather than merely invoking direct, positivistic evidence and/or mere normative arguments to ground their position. Moreover, it is submitted, first, that global constitutionalists would do better by adopting a less objectivist stance as regards global values, as on the ideal-agent theory of value. Second, it is argued that even though there might be room for so-called constitutionalist ‘mindsets’, these fall short of establishing the objective purport of the international legal order. Third, d'Aspremont's positivistic argument contra objective purport is construed as (also) an argument to the effect that the rules and architecture of the international legal order only warrant the existence of Hobbesian interests as necessary conditions for making sense of it. The constitutionalist case for objective purport, then, hinges on the issue of whether constitutionalism is necessitated by considerations as regards the intelligibility of international legal argument, by explanatory desiderata regarding trends in international law-making, and as a viable response to the problems posed by fragmentation, deformalization, and international legal scepticism.
Waiting for Godot: An Analysis of the Advisory Opinion on Kosovo
Authors: JACOBS DOV , RADI YANNICK 
Published: May 2011

AbstractThe Kosovo Advisory Opinion gave rise to responses that suggest that the Court went too far, or not far enough, depending on one's perspective. In this article, the authors argue that the Court should either have done nothing or gone all the way. By accepting an inadequately drafted question, the Court was necessarily going to give an inadequate answer. This article adopts a strict approach to the legal nature of the question and considers that the ICJ should have declined its competence, not as an exercise of its discretion, but as a preservation of its core judicial function, which does not include primarily the conduct of non-state entities. Going further, the authors suggest that the Court could have rephrased the question and sought to establish the international responsibility of the United Nations, and, ultimately, of Kosovo, which, it is argued, is in fact implicitly recognized by the Court, both politically and legally.
The Kosovo Advisory Opinion Scrutinized
Authors: VIDMAR JURE 
Published: May 2011

AbstractIn the Kosovo Advisory Opinion, the International Court of Justice took the position that Kosovo's unilateral declaration of independence did not violate any applicable rules of international law. This article does not dispute the final finding, but rather critically examines the Court's somewhat controversial reasoning and considers the added value of the opinion for the clarification of legal doctrine in relation to unilateral declarations of independence. An argument is made that the Court's interpretation of the question and the identification of the authors of the declaration had significant implications for the Court's final finding. Yet, the Court cannot be criticized for not answering the question of whether or not Kosovo is a state, whether Kosovo Albanians are beneficiaries of the right of self-determination, or even whether the ‘right to remedial secession’ is applicable. However, the Court may well have implicitly answered that recognition of Kosovo is not illegal.
Equipping Church Leaders for Mission in the Anglican Church of Kenya
Authors: Nkonge Dickson 
Published: May 2011

AbstractLeadership remains the biggest challenge facing the Church in Africa today. The Anglican Church in Kenya (ACK) was started in 1844, but was it was not until 1888 that the official training of church leaders was commenced with the opening of a Divinity School at Frere Town. Since its inception the ACK has experienced a tremendous growth in membership, growing at the rate of about 6.7 per cent per annum. In spite of this rapid growth, the ACK is in leadership crises due to lack of enough and well-equipped clergy to run it. The Anglican population of about 3,711,890 Christians is served by only about 1555 clergy, translating to clergy per Christians ratio of about 1 : 2400. This affects the Church's mission in that it is impossible for one clergy to effectively provide spiritual care to 2400 Christians. On top of this, the majority of the clergy currently serving in the ACK are not properly trained to match the rapidly changing Kenyan society. About 83 per cent of these clergy have diploma and below theological qualifications. If the ACK has to be successful in its mission in this century, it has to reconsider its training systems.
Characterizing plasma mirrors near breakdown
Authors: Geissel Matthias , Schollmeier Marius S. , Kimmel Mark W. , Rambo Patrick K. , Schwarz Jens , Atherton Briggs W. , Brambrink Erik 
Published: May 2011

Experiments dedicated to the characterization of plasma mirrors with a high energy, single shot short-pulse laser were performed at the 100 TW target area of the Z-Backlighter Facility at Sandia National Laboratories. A suite of beam diagnostics was used to characterize a high energy laser pulse with a large aperture through focus imaging setup. By varying the fluence on the plasma mirror around the plasma ignition threshold, critical performance parameters were determined and a more detailed understanding of the way in which a plasma mirror works could be deduced. It was found, that very subtle variations in the laser near field profile will have strong effects on the reflected pulse if the maximum fluence on the plasma mirror approaches the plasma ignition threshold.
Identifying splits with clear separation: a new class discovery
method for gene expression data
Authors: von Heydebreck Anja , Huber Wolfgang , Poustka Annemarie , Vingron Martin 
Published: May 2011

Abstract
We present a new class discovery method for microarray gene expression data. Based on a collection of gene expression profiles from different tissue samples, the method searches for binary class distinctions in the set of samples that show clear separation in the expression levels of specific subsets of genes. Several mutually independent class distinctions may be found, which is difficult to obtain from most commonly used clustering algorithms. Each class distinction can be biologically interpreted in terms of its supporting genes. The mathematical characterization of the favored class distinctions is based on statistical concepts. By analyzing three data sets from cancer gene expression studies, we demonstrate that our method is able to detect biologically relevant structures, for example cancer subtypes, in an unsupervised fashion.
Contact: heydebre@molgen.mpg.de
Feature selection for DNA methylation based cancer

classification
Authors: Model Fabian , Adorján Péter , Olek Alexander , Piepenbrock Christian 
Published: May 2011

Abstract
Molecular portraits, such as mRNA expression or DNA methylation patterns, have been shown to be strongly correlated with phenotypical parameters. These molecular patterns can be revealed routinely on a genomic scale. However, class prediction based on these patterns is an under-determined problem, due to the extreme high dimensionality of the data compared to the usually small number of available samples. This makes a reduction of the data dimensionality necessary. Here we demonstrate how phenotypic classes can be predicted by combining feature selection and discriminant analysis. By comparing several feature selection methods we show that the right dimension reduction strategy is of crucial importance for the classification performance. The techniques are demonstrated by methylation pattern based discrimination between acute lymphoblastic leukemia and acute myeloid leukemia.
Contact: Fabian.Model@epigenomics.com
Non-symmetric score matrices and the detection of homologous
transmembrane proteins
Authors: Müller Tobias , Rahmann Sven , Rehmsmeier Marc 
Published: May 2011

Abstract
Given a transmembrane protein, we wish to find related ones by a database search. Due to the strongly hydrophobic amino acid composition of transmembrane domains, suboptimal results are obtained when general-purpose scoring matrices such as BLOSUM are used. Recently, a transmembrane-specific score matrix called PHAT was shown to perform much better than BLOSUM. In this article, we derive a transmembrane score matrix family, called SLIM, which has several distinguishing features. In contrast to currently used matrices, SLIM is non-symmetric. The asymmetry arises because different background compositions are assumed for the transmembrane query and the unknown database sequences. We describe the mathematical model behind SLIM in detail and show that SLIM outperforms PHAT both on simulated data and in a realistic setting. Since non-symmetric score matrices are a new concept in database search methods, we discuss some important theoretical and practical issues.
Contact: muelle_t@molgen.mpg.de
Fast optimal leaf ordering for hierarchical clustering
Authors: Bar-Joseph Ziv , Gifford David K. , Jaakkola Tommi S. 
Published: May 2011

Abstract
We present the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering. Hierarchical clustering has been extensively used to analyze gene expression data, and we show how optimal leaf ordering can reveal biological structure that is not observed with an existing heuristic ordering method. For a tree with n leaves, there are 2n−1 linear orderings consistent with the structure of the tree. Our optimal leaf ordering algorithm runs in time O(n4), and we present further improvements that make the running time of our algorithm practical.
Contact: {zivbj,gifford}@mit.edu; tommi@ai.mit.edu
Improved prediction of the number of residue contacts in
proteins by recurrent neural networks
Authors: Pollastri Gianluca , Baldi Pierre , Fariselli Pietro , Casadio Rita 
Published: May 2011

Abstract
Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and/or scoring remote homology searches. Here we use an ensemble of bi-directional recurrent neural network architectures and evolutionary information to improve the state-of-the-art in contact prediction using a large corpus of curated data. The ensemble is used to discriminate between two different states of residue contacts, characterized by a contact number higher or lower than the average value of the residue distribution. The ensemble achieves performances ranging from 70.1% to 73.1% depending on the radius adopted to discriminate contacts (6Âto 12Â). These performances represent gains of 15% to 20% over the base line statistical predictors always assigning an aminoacid to the most numerous state, 3% to 7% better than any previous method. Combination of different radius predictors further improves the performance.
Server: http://promoter.ics.uci.edu/BRNN-PRED/
Contact: pfbaldi@ics.uci.edu
*To whom all correspondence should be addressed.
Rich probabilistic models for gene expression
Authors: Segal Eran , Taskar Ben , Gasch Audrey , Friedman Nir , Koller Daphne 
Published: May 2011

Abstract
Clustering is commonly used for analyzing gene expression data. Despite their successes, clustering methods suffer from a number of limitations. First, these methods reveal similarities that exist over all of the measurements, while obscuring relationships that exist over only a subset of the data. Second, clustering methods cannot readily incorporate additional types of information, such as clinical data or known attributes of genes. To circumvent these shortcomings, we propose the use of a single coherent probabilistic model, that encompasses much of the rich structure in the genomic expression data, while incorporating additional information such as experiment type, putative binding sites, or functional information. We show how this model can be learned from the data, allowing us to discover patterns in the data and dependencies between the gene expression patterns and additional attributes. The learned model reveals context-specific relationships, that exist only over a subset of the experiments in the dataset. We demonstrate the power of our approach on synthetic data and on two real-world gene expression data sets for yeast. For example, we demonstrate a novel functionality that falls naturally out of our framework: predicting the “cluster” of the array resulting from a gene mutation based only on the gene’s expression pattern in the context of other mutations.
Contact: eran@cs.stanford.edu
Separation of samples into their constituents using gene
expression data
Authors: Venet D. , Pecasse F. , Maenhaut C. , Bersini H. 
Published: May 2011

Abstract
Gene expression measurements are a powerful tool in molecular biology, but when applied to heterogeneous samples containing more than one cellular type the results are difficult to interpret. We present here a new approach to this problem allowing to deduce the gene expression profile of the various cellular types contained in a set of samples directly from the measurements taken on the whole sample.
Contact: davenet@ulb.ac.be
Separating real motifs from their artifacts
Authors: Blanchette Mathieu , Sinha Saurabh 
Published: May 2011

Abstract
The typical output of many computational methods to identify binding sites is a long list of motifs containing some real motifs (those most likely to correspond to the actual binding sites) along with a large number of random variations of these. We present a statistical method to separate real motifs from their artifacts. This produces a short list of high quality motifs that is sufficient to explain the over-representation of all motifs in the given sequences. Using synthetic data sets, we show that the output of our method is very accurate. On various sets of upstream sequences in S. cerevisiae , our program identifies several known binding sites, as well as a number of significant novel motifs.
Contact: blanchem@cs.washington.edu; saurabh@cs.washington.edu
‡The two authors contributed equally to the paper.
Probe selection algorithms with applications in the analysis of
microbial communities
Authors: Borneman James , Chrobak Marek , Della Vedova Gianluca , Figueroa Andres , Jiang Tao 
Published: May 2011

Abstract
We propose two efficient heuristics for minimizing the number of oligonucleotide probes needed for analyzing populations of ribosomal RNA gene (rDNA) clones by hybridization experiments on DNA microarrays. Such analyses have applications in the study of microbial communities. Unlike in the classical SBH (sequencing by hybridization) procedure, where multiple probes are on a DNA chip, in our applications we perform a series of experiments, each one consisting of applying a single probe to a DNA microarray containing a large sample of rDNA sequences from the studied population. The overall cost of the analysis is thus roughly proportional to the number of experiments, underscoring the need for minimizing the number of probes. Our algorithms are based on two well-known optimization techniques, i.e. simulated annealing and Lagrangian relaxation, and our preliminary tests demonstrate that both algorithms are able to find satisfactory probe sets for real rDNA data.
Contact: jiang@cs.ucr.edu
An efficient algorithm for finding short approximate non-tandem

repeats
Authors: Adebiyi Ezekiel F. , Jiang Tao , Kaufmann Michael 
Published: May 2011

Abstract
We study the problem of approximate non-tandem repeat †extraction. Given a long subject string S of length N over a finite alphabet Σ and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact repeats) required by the algorithm, and prove a sublinear bound on their expected numbers. Using this result, we present a sub-quadratic algorithm for finding all short (i.e., of length O(log N)) approximate repeats. The running time of our algorithm is O(DN3pow(ε)−1log N), where ε = D/P and pow(ε) is an increasing, concave function that is 0 when ε = 0 and about 0.9 for DNA and protein sequences.
Contact: adebiyi@informatik.uni-tuebingen.de
†Throughout the paper we only consider non-tandem repeats.
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
Authors: Friedman Carol , Kra Pauline , Yu Hong , Krauthammer Michael , Rzhetsky Andrey 
Published: May 2011

Abstract
Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.
Contact: friedman.carol@dmi.columbia.edu