bluuebunny/crossref_metadata_2025 huggingface dataset:
Playing by Ear
Authors: Woody Robert H.
Published: December 2012

Many people divide musicians into two types: those who can read music and those who play by ear. Formal music education tends to place great emphasis on producing musically literate performers but devotes much less attention to teaching students to make music without notation. Some would suggest that playing by ear is a specialized skill that is useful only to jazz and popular musicians. There are, however, many reasons to reconsider this position. Around the world, aural transmission of music and ear-based performance are the norm. Music pedagogues have described ear playing as a necessary developmental precursor to becoming a truly fluent music reader. Research supports the idea that playing by ear is a foundational skill that contributes to other aspects of musicianship, including improvising, sight-reading, and performing from memory. Ear playing has even been shown to be a contributor to skilled performance of rehearsed music, the traditional mainstay of school music. Ear-driven activities can involve student musicians in composing and arranging, musical collaboration with peers, and lifelong individual artistic expression.
Reframing Student Practice to Facilitate Lifelong, Joyful Musicianship
Authors: Smeltz Hannah
Published: December 2012

Teaching students to practice independently is an important part of a music teacher’s work. Yet, many common techniques used to teach and enforce student practicing, such as practice charts and performance tests, can backfire, causing students to practice inefficiently or lose their love of music. In search of a method of teaching practicing that promotes enduring, joyful musicianship, I surveyed eighty-nine adult musicians about their practice habits and attitudes. This survey data, along with a review of current research about music learning and motivation, became the basis of a strategic approach to teaching practicing. I taught this approach to my middle school band students and evaluated its success through parent surveys, student interviews, and analysis of videotaped practice sessions. Findings indicate that it is possible to increase the effectiveness of students’ practicing without decreasing their joy. This article details this research and provides a model for reframing practicing as a personally satisfying and healthful lifetime endeavor.
From “Five Angry Women” to “Kick-ass Community”: Gentrification and Environmental Activism in Brooklyn and Beyond
Authors: Hamilton Trina , Curran Winifred
Published: December 2012

In this article, a new conceptual framework is advocated to evaluate the range of environmental activism in already-gentrifying neighbourhoods and to recognise the agency and resilience of long-term residents. The category of gentrifier-enhanced environmental activism is meant to account for attempts to forge coalitions (however uneasy they may turn out to be) between long-term residents and gentrifiers. This includes attempts by long-term residents to mitigate environmental gentrification by ‘schooling’ gentrifiers in communities’ longstanding concerns and needs, framing these concerns as a common cause rather than allowing for the takeover of local environmental politics often associated with environmental gentrification. The example is used of the fight to clean up Newtown Creek in Greenpoint, Brooklyn, as a case study in how environmental veterans made strategic alliances with gentrifiers who brought new resources to the area in order to achieve political pressure for change and to promote more just sustainabilities.
Age of onset, length of residence, language aptitude, and ultimate L2 attainment in three linguistic domains
Authors: Granena Gisela , Long Michael H
Published: December 2012

A study was conducted to identify the scope and timing of maturational constraints in three linguistic domains within the same individuals, as well as the potential mediating roles of amount of second language (L2) exposure and language aptitude at different ages in different domains. Participants were 65 Chinese learners of Spanish and 12 native speaker controls. Results for three learner groups defined by age of onset (AO) – 3–6, 7–15, and 16–29 years – confirmed previous findings of windows of opportunity closing first for L2 phonology, then for lexis and collocation and, finally, in the mid-teens, for morphosyntax. All three age functions exhibited the discontinuities in the rate of decline with increasing AO associated with sensitive periods. Significant correlations were found between language aptitude, measured using the LLAMA test (Meara, 2005), and pronunciation scores, and between language aptitude and lexis and collocation scores, in the AO 16–29 group.
Biomechanical Analysis of a Double-Loaded Glenoid Anchor Configuration
Authors: Kamath Ganesh V. , Hoover Stephen , Creighton R. Alexander , Weinhold Paul , Barrow Aaron , Spang Jeffrey T.
Published: December 2012

Background:

Bankart repair with multiple anchor holes concentrated in the anterior-inferior glenoid may contribute to glenoid weakening and potentially may induce glenoid failure.

Purpose:

To compare the biomechanical strength of a Bankart repair construct that used 3 single-loaded suture anchors versus a repair construct that used 2 double-loaded suture anchors.

Study Design:

Comparative laboratory study.

Methods:

A standard Bankart lesion was created in 18 human cadaveric shoulders (9 matched pairs). Within each matched pair, 1 repair construct used 3 single-loaded anchors, whereas the other used 2 double-loaded suture anchors. Measured outcomes (load, stiffness, and energy absorbed) were recorded at failure and at 2 mm of labral displacement. Constructs were loaded to failure with a materials testing device that had differential variable reluctance transducers for displacement measurements.

Results:

The double-loaded anchor construct had a significantly higher ultimate tensile load (944 ± 231 vs 784 ± 287 N; P = .03). For the other measures (load at 2 mm of displacement, energy absorbed at failure and at 2 mm of displacement and stiffness), there were no significant differences between tested constructs.

Conclusion:

A Bankart repair construct that used 2 double-loaded anchors was either superior to or equal to a repair construct that used 3 single-loaded anchors in all measured outcomes.

Clinical Relevance:

Using 2 double-loaded suture anchors for a Bankart repair may limit anchor holes in the glenoid and reduce the risk of postsurgical glenoid fracture while providing a stable repair construct.
Attachment, Activity Limitation, and Health Symptoms in Later Life
Authors: Consedine Nathan S. , Fiori Katherine L. , Tuck Natalie L. , Merz Eva-Maria
Published: December 2012

Objectives: Patterns of attachment—normative styles of relating to significant others—impact relationships across adulthood. Preliminary studies link attachment with health outcomes but have yet to examine older adults or functional impairment, and the mechanisms behind this relationship remain unclear. This report investigated how attachment predicted symptoms and functional impairment and tested the mediating roles of positive affect (PA) and negative affect (NA). Methods: 1,118 older adults completed measures of attachment, health symptoms, and functional impairment, together with confounds including age, sex, and income. Results: As expected, security and fearful avoidance predicted greater symptomology, but only fearful avoidance predicted greater functional impairment. Negative affect partially mediated links between attachment and outcomes, but only for fearful avoidance. Discussion: Understanding links between attachment, symptom reports, and functional impairment will facilitate better understanding of positive aging versus premature decline, help identify at risk individuals, and guide interventions to assist optimal functioning in later life.
Mainstreaming climate change adaptation in Indian cities
Authors: Sharma Divya , Tomar Sanjay
Published: December 2012

If climate change is perceived as a global threat, this can mean that too little attention is paid to the ways in which it affects local populations and settlements. This also means too little attention to the importance of locally driven adaptation, both to reduce risks and to be better prepared to cope with consequences. This paper reviews the many initiatives underway in India that respond to climate change, and discusses what else is needed to mainstream effective adaptation, as well as identifying what currently constrains this. It also discusses how adaptation has to be mainstreamed within urban development and urban governance. Most municipal authorities in India are already grappling with large deficits in infrastructure and services and do not see climate change adaptation as a priority or as their responsibility. However, their attention may be engaged if they can see the co-benefits between adaptation and measures to address development and environmental health concerns.
The challenges of local environmental problems facing the urban poor in Chittagong, Bangladesh: a scale-sensitive analysis
Authors: Maksudur Rahman M. , Haughton Graham , Jonas Andrew E G
Published: December 2012

This paper explores local environmental problems at both the household and neighbourhood levels in Chittagong, based on a broad spectrum household survey. The survey shows that households in poor areas are very exposed to localized environmental problems and thus necessarily develop a wide range of coping strategies around the living space. Yet poorer households are less likely to express their concerns about neighbourhood environmental issues, despite experiencing many problems at this level. This paper investigates the interface between household and neighbourhood environmental problems.
Recent developments in plans for Dharavi and for the airport slums in Mumbai
Authors: Arputham Jockin , Patel Sheela
Published: December 2012

This is the fourth in a series of papers chronicling the negotiations over plans to redevelop Dharavi, Mumbai’s vast informal settlement. It also describes current plans to redevelop land beside Mumbai’s international airport, where more than 85,000 households live on a 110-hectare (275 acres) site. In both these settlements, each with populations equivalent to a sizeable city, the government plans appear to be driven more by an intent to support commercial developments than to address the needs of their residents.
Vulnerability of poor urban coastal communities to flooding in Lagos, Nigeria
Authors: Adelekan Ibidun O
Published: December 2012

This paper considers the risks from and vulnerabilities to flooding in four urban poor communities close to the coast in Lagos, Nigeria. Drawing on interviews with inhabitants and key informants and also on group discussions, it documents the scale and frequency of flooding in these settlements and the impacts, as well as the individual, household and community responses. It also considers the factors that have contributed to increasing flood risks in Lagos, including the uncontrolled expansion of the built-up area, the lack of infrastructure and the failure not only to expand stormwater drainage but also to maintain existing drainage systems. The paper also considers changes in the frequency and intensity of rainstorms on Lagos Island between 1971 and 2005, which suggest that on average these have become less frequent but more intense.
Impact of Community Policing on Public Satisfaction and Perception of Police
Authors: Kumar T. K. Vinod
Published: December 2012

Community policing has over the last four decades developed into a widely accepted method for police to engage the public. It is now being used extensively in diverse countries. The Janamaitri community policing program in Kerala state in India is one initiative that is being implemented in a programmatic manner. This article examines the components of the Janamaitri program, and whether it had any impact on public satisfaction with police services and perception of police in community. The study is conducted through an initial overview of the program, followed by a survey of people in the area. It illuminates the immediate impact of the program on different aspects of police–public relations such as greater accessibility, better behavior of police, greater sense of security among the populace, and better perception of police. It also demonstrates how these different factors are interrelated. The study demonstrates the importance of community policing, especially in developing societies, as a way forward for better police service delivery and reforms.
Rooting Out Waste, Fraud, and Abuse
Authors: Parker David C. W. , Dull Matthew
Published: December 2012

Scholars have long bemoaned congressional disinterest in oversight. We explain varied congressional attention to oversight by advancing the contingent oversight theory. We show how the structure of congressional committees, partisan majorities, and theories of delegation together explain when, why, and for how long Congress investigated executive branch malfeasance between 1947 and 2004. Divided government, partisan committees, and committees characterized by broad statutory discretion generate more investigations, whereas distributive committees and unified government dampen Congress’ investigatory vigor. The conduct of oversight depends on more than a desire to produce good government or the incentive structures faced by individual members of Congress.
Childhood ADHD Symptoms Are Associated With Lifetime and Current Illicit Substance-Use Disorders and In-Site Health Risk Behaviors in a Representative Sample of Latino Prison Inmates
Authors: González Rafael A. , Vélez-Pastrana María C. , Ruiz Varcárcel José J. , Levin Frances R. , Albizu-García Carmen E.
Published: December 2012

Objective: This study aimed to explore retrospective childhood ADHD symptomatology, psychiatric comorbidity, rates of substance-use disorders (SUD), as well as their association with high-risk health behaviors in prison and adverse health outcomes. Method: A randomly selected representative sample of inmates in the Puerto Rico correctional system ( N = 1,179) was assessed with the Spanish-language Wender Utah Rating Scale (WURS); the Composite International Diagnostic Interview (CIDI) modules for lifetime/current major depression disorder (MDD), generalized anxiety disorder (GAD), and SUD; the Davidson Trauma Scale (DTS; posttraumatic stress disorder [PTSD]); and self-reports of in-site high-risk behaviors. Results: Wald χ2 tests revealed significant associations of ADHD with MDD and PTSD, as well as increased risk for overdosing and intravenous drug use in prison. A logistic regression model adjusted for mood and anxiety comorbidity predicted lifetime SUD diagnosis (odds ratio = 2.38; 95% confidence interval = [1.15, 4.94]). Conclusion: Our results provide further evidence on the association of drug dependence and ADHD symptoms, and their overrepresentation among prison inmates.
Understanding of emotions based on counterfactual reasoning in children with autism spectrum disorders
Authors: Begeer Sander , De Rosnay Marc , Lunenburg Patty , Stegge Hedy , Terwogt Mark Meerum
Published: December 2012

The understanding of emotions based on counterfactual reasoning was studied in children with high-functioning autism spectrum disorders ( n = 71) and in typically developing children ( n = 71), aged 6–12 years. Children were presented with eight stories about two protagonists who experienced the same positive or negative outcome, either due to their own action or by default. Relative to the comparison group, children with high-functioning autism spectrum disorder were poor at explaining emotions based on downward counterfactual reasoning (i.e. contentment and relief). There were no group differences in upward counterfactual reasoning (i.e. disappointment and regret). In the comparison group, second-order false-belief reasoning was related to children’s understanding of second-order counterfactual emotions (i.e. regret and relief), while children in the high-functioning autism spectrum disorder group relied more on their general intellectual skills. Results are discussed in terms of the different functions of counterfactual reasoning about emotion and the cognitive style of children with high-functioning autism spectrum disorder.
Healing Diabetic Foot Ulcers Step by Step
Authors: Jiang Yufeng , Xu Zhangrong , Fu Xiaobing
Published: December 2012

Diabetic foot is a leading cause of admission, amputation, and mortality in diabetic patients. A multidisciplinary team approach is highly recommended for the management of patients with foot problems. To heal diabetic foot ulcers, all methods have to be conducted step by step under an efficient program, and all specialists should be well organized also, which was confirmed by the 2 cases described in this article.
Justice and Legitimacy: Rawls, Schmitt and the Normativity of Law
Authors: Olney Charles
Published: December 2012

This article argues that the later work of John Rawls offers the best hope for establishing a justifiable and sustainable concept of liberalism. The context for this concern is the work of Carl Schmitt, whose attack on liberal legal practices exposes a deep weakness in most liberal approaches to the concept of law. The divide between positivism and normative legal approaches (expressed in the debates among H.L.A. Hart, Ronald Dworkin, and Hans Kelsen) seems to wither in the face of Schmittian critique, leaving only a depoliticized husk of legal practice. Rawls offers a different approach, a justificatory regime capable of engaging the problem of the sovereign exception while preserving the force of liberal normativity.
Berlusconi on Berlusconi? An analysis of digital terrestrial television coverage on commercial broadcast news in Italy
Authors: Padovani Cinzia
Published: December 2012

This article examines how Italian commercial broadcast news on Mediaset’s three terrestrial channels has covered the transition to digital terrestrial television. Mediaset is the largest commercial broadcaster in the country and is owned by former prime minister Silvio Berlusconi. By drawing on critical discourse analysis of broadcast news, it is argued that linguistic elements such as pronouns, choice of words, and metaphors, together with tendentious editing and framing of interviews, were part of a strategy of positive representation of the broadcaster’s interests in the transition and negative representation of media policies opposing such interests. In particular, the analysis brings to the surface the ideological usage of interviews. Interviews in this case did not function as an act of control over the powerful, but as a way to illuminate the broadcaster’s strategic interests while obfuscating the reasons behind attempts to regulate the transition to digital television and open the market to competition. The data attest that the way in which news programs covered the digital transition exposes the connections between media content, media ownership, and governmental institutions. Indeed, all three news programs, TG5, TG4, and Studio Aperto, despite their different target audience and the reputation of one of them (TG5) as the most objective and authoritative newscast on Italian commercial television, echoed each other in unified support of the sort of interests and media legislation that best fitted the corporation, especially at times when those interests were threatened. The corpus consists of 13 newscasts grouped in two clusters aired in 2006 and 2009. The main participants in the story were Mediaset’s president, often interviewed as the ‘expert’ on the TV industry, the communications minister for the center-left Prodi government (in the 2006 cluster), and the communications undersecretary for the center-right Berlusconi government (in the 2009 cluster). Citizens and consumer groups were never given the opportunity to voice their positions or be an active part of the narration.
NLRX1 does not inhibit MAVS-dependent antiviral signalling
Authors: Soares Fraser , Tattoli Ivan , Wortzman Michael E , Arnoult Damien , Philpott Dana J , Girardin Stephen E
Published: December 2012

NLRX1 is a member of the Nod-like receptor family of intracellular sensors of microbial- and danger-associated molecular patterns. NLRX1 has a N-terminal mitochondrial addressing sequence that localizes the protein to the mitochondrial matrix. Recently, conflicting reports have been presented with regard to the putative implication of NLRX1 as a negative regulator of MAVS-dependent cytosolic antiviral responses. Here, we generated a new NLRX1 knockout mouse strain and observed that bone marrow-derived macrophages and murine embryonic fibroblasts from NLRX1-deficient mice displayed normal antiviral and inflammatory responses following Sendai virus infection. Importantly, wild type and NLRX1-deficient mice exhibited unaltered antiviral and inflammatory gene expression following intranasal challenge with influenza A virus or i.p. injection of Poly (I:C). Together, our results demonstrate that NLRX1 does not participate in the negative regulation of MAVS-dependent antiviral responses.
In vivo generation of transplantable human hematopoietic cells from induced pluripotent stem cells
Authors: Amabile Giovanni , Welner Robert S. , Nombela-Arrieta Cesar , D'Alise Anna Morena , Di Ruscio Annalisa , Ebralidze Alexander K. , Kraytsberg Yevgenya , Ye Min , Kocher Olivier , Neuberg Donna S. , Khrapko Konstantin , Silberstein Leslie E. , Tenen Daniel G.
Published: December 2012

Key Points

Human hematopoietic cells develop within human iPSC-derived teratomas in immunodeficient mice. Co-transplantation of OP9 stromal cells along with human iPSCs increases hematopoietic specification within teratomas.
Some higher order Hardy inequalities
Authors: Kufner Alois , Kuliev Komil , Persson Lars-Erik
Published: December 2012

We investigate the k-th order Hardy inequality (1.1) for functions satisfying rather general boundary conditions (1.2), show which of these conditions are admissible and derive sufficient, and necessary and sufficient, conditions (for 0 < q < ∞, p > 1) on u, v for (1.1) to hold.
Comparative evaluation of set-level techniques in predictive classification of gene expression samples
Authors: Holec Matěj , Kléma Jiří , Železný Filip , Tolar Jakub
Published: December 2012

Background

Analysis of gene expression data in terms of a priori-defined gene sets has recently received significant attention as this approach typically yields more compact and interpretable results than those produced by traditional methods that rely on individual genes. The set-level strategy can also be adopted with similar benefits in predictive classification tasks accomplished with machine learning algorithms. Initial studies into the predictive performance of set-level classifiers have yielded rather controversial results. The goal of this study is to provide a more conclusive evaluation by testing various components of the set-level framework within a large collection of machine learning experiments.

Results

Genuine curated gene sets constitute better features for classification than sets assembled without biological relevance. For identifying the best gene sets for classification, the Global test outperforms the gene-set methods GSEA and SAM-GS as well as two generic feature selection methods. To aggregate expressions of genes into a feature value, the singular value decomposition (SVD) method as well as the SetSig technique improve on simple arithmetic averaging. Set-level classifiers learned with 10 features constituted by the Global test slightly outperform baseline gene-level classifiers learned with all original data features although they are slightly less accurate than gene-level classifiers learned with a prior feature-selection step.

Conclusion

Set-level classifiers do not boost predictive accuracy, however, they do achieve competitive accuracy if learned with the right combination of ingredients.

Availability

Open-source, publicly available software was used for classifier learning and testing. The gene expression datasets and the gene set database used are also publicly available. The full tabulation of experimental results is available at http://ida.felk.cvut.cz/CESLT.
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
Authors: Riehle Kevin , Coarfa Cristian , Jackson Andrew , Ma Jun , Tandon Arpit , Paithankar Sameer , Raghuraman Sriram , Mistretta Toni-Ann , Saulnier Delphine , Raza Sabeen , Diaz Maria Alejandra , Shulman Robert , Aagaard Kjersti , Versalovic James , Milosavljevic Aleksandar
Published: December 2012

Background

Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings.

Methods

To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis. The Toolset drives hypothesis generation by providing a wide range of analyses including alpha diversity and beta diversity, phylogenetic profiling, supervised machine learning, and feature selection.

Results

We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from the irritable bowel syndrome.

Conclusions

By lowering the barrier to performing a comprehensive set of microbiome analyses, the Toolset empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.
A cross-validation scheme for machine learning algorithms in shotgun proteomics
Authors: Granholm Viktor , Noble William Stafford , Käll Lukas
Published: December 2012

Peptides are routinely identified from mass spectrometry-based proteomics experiments by matching observed spectra to peptides derived from protein databases. The error rates of these identifications can be estimated by target-decoy analysis, which involves matching spectra to shuffled or reversed peptides. Besides estimating error rates, decoy searches can be used by semi-supervised machine learning algorithms to increase the number of confidently identified peptides. As for all machine learning algorithms, however, the results must be validated to avoid issues such as overfitting or biased learning, which would produce unreliable peptide identifications. Here, we discuss how the target-decoy method is employed in machine learning for shotgun proteomics, focusing on how the results can be validated by cross-validation, a frequently used validation scheme in machine learning. We also use simulated data to demonstrate the proposed cross-validation scheme's ability to detect overfitting.
An amputation resets positional information to a proximal identity in the regenerating zebrafish caudal fin
Authors: Azevedo Ana Sofia , Sousa Sara , Jacinto António , Saúde Leonor
Published: December 2012

Background

Zebrafish has emerged as a powerful model organism to study the process of regeneration. This teleost fish has the ability to regenerate various tissues and organs like the heart, spinal cord, retina and fins. In this study, we took advantage of the existence of an excellent morphological reference in the zebrafish caudal fin, the bony ray bifurcations, as a model to study positional information upon amputation. We investigated the existence of positional information for bifurcation formation by performing repeated amputations at different proximal-distal places along the fin.

Results

We show that, while amputations performed at a long distance from the bifurcation do not change its final proximal-distal position in the regenerated fin, consecutive amputations done at 1 segment proximal to the bifurcation (near the bifurcation) induce a positional reset and progressively shift its position distally. Furthermore, we investigated the potential role of Shh and Fgf signalling pathways in the determination of the bifurcation position and observed that they do not seem to be involved in this process.

Conclusions

Our results reveal that, an amputation near the bifurcation inhibits the formation of the regenerated bifurcation in the pre-amputation position, inducing a distalization of this structure. This shows that the positional memory for bony ray bifurcations depends on the proximal-distal level of the amputation.
Transcriptome profiling of the demosponge Amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions
Authors: Conaco Cecilia , Neveu Pierre , Zhou Hongjun , Arcila Mary Luz , Degnan Sandie M , Degnan Bernard M , Kosik Kenneth S
Published: December 2012

Background

The biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the Porifera (sponges), which are the earliest branching metazoans. The demosponge, Amphimedon queenslandica, undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. While the genome of A. queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unclear how this is drawn upon to coordinate changing morphological features and ecological demands throughout the sponge life cycle.

Results

To identify genome-wide events that accompany the pelagobenthic transition in A. queenslandica, we compared global gene expression profiles at four key developmental stages by sequencing the poly(A) transcriptome using SOLiD technology. Large-scale changes in transcription were observed as sponge larvae settled on the benthos and began metamorphosis. Although previous systematics suggest that the only clear homology between Porifera and other animals is in the embryonic and larval stages, we observed extensive use of genes involved in metazoan-associated cellular processes throughout the sponge life cycle. Sponge-specific transcripts are not over-represented in the morphologically distinct adult; rather, many genes that encode typical metazoan features, such as cell adhesion and immunity, are upregulated. Our analysis further revealed gene families with candidate roles in competence, settlement, and metamorphosis in the sponge, including transcription factors, G-protein coupled receptors and other signaling molecules.

Conclusions

This first genome-wide study of the developmental transcriptome in an early branching metazoan highlights major transcriptional events that accompany the pelagobenthic transition and point to a network of regulatory mechanisms that coordinate changes in morphology with shifting environmental demands. Metazoan developmental and structural gene orthologs are well-integrated into the expression profiles at every stage of sponge development, including the adult. The utilization of genes involved in metazoan-associated processes throughout sponge development emphasizes the potential of the genome of the last common ancestor of animals to generate phenotypic complexity.
Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya
Authors: Aryal Rishi , Yang Xiaozeng , Yu Qingyi , Sunkar Ramanjulu , Li Lei , Ming Ray
Published: December 2012

Background

The small RNAs (sRNA) are a regulatory class of RNA mainly represented by the 21 and 24-nucleotide size classes. The cellular sRNAs are processed by RNase III family enzyme dicer (Dicer like in plant) from a self-complementary hairpin loop or other type of RNA duplexes. The papaya genome has been sequenced, but its microRNAs and other regulatory RNAs are yet to be analyzed.

Results

We analyzed the genomic features of the papaya sRNA population from three sRNA deep sequencing libraries made from leaves, flowers, and leaves infected with Papaya Ringspot Virus (PRSV). We also used the deep sequencing data to annotate the micro RNA (miRNA) in papaya. We identified 60 miRNAs, 24 of which were conserved in other species, and 36 of which were novel miRNAs specific to papaya. In contrast to the Chargaff’s purine-pyrimidine equilibrium, cellular sRNA was significantly biased towards a purine rich population. Of the two purine bases, higher frequency of adenine was present in 23nt or longer sRNAs, while 22nt or shorter sRNAs were over represented by guanine bases. However, this bias was not observed in the annotated miRNAs in plants. The 21nt species were expressed from fewer loci but expressed at higher levels relative to the 24nt species. The highly expressed 21nt species were clustered in a few isolated locations of the genome. The PRSV infected leaves showed higher accumulation of 21 and 22nt sRNA compared to uninfected leaves. We observed higher accumulation of miRNA* of seven annotated miRNAs in virus-infected tissue, indicating the potential function of miRNA* under stressed conditions.

Conclusions

We have identified 60 miRNAs in papaya. Our study revealed the asymmetric purine-pyrimidine distribution in cellular sRNA population. The 21nt species of sRNAs have higher expression levels than 24nt sRNA. The miRNA* of some miRNAs shows higher accumulation in PRSV infected tissues, suggesting that these strands are not totally functionally redundant. The findings open a new avenue for further investigation of the sRNA silencing pathway in plants.
Multi-objective dynamic population shuffled frog-leaping biclustering of microarray data
Authors: Liu Junwan , Li Zhoujun , Hu Xiaohua , Chen Yiming , Liu Feifei
Published: December 2012

Background

Multi-objective optimization (MOO) involves optimization problems with multiple objectives. Generally, theose objectives is used to estimate very different aspects of the solutions, and these aspects are often in conflict with each other. MOO first gets a Pareto set, and then looks for both commonality and systematic variations across the set. For the large-scale data sets, heuristic search algorithms such as EA combined with MOO techniques are ideal. Newly DNA microarray technology may study the transcriptional response of a complete genome to different experimental conditions and yield a lot of large-scale datasets. Biclustering technique can simultaneously cluster rows and columns of a dataset, and hlep to extract more accurate information from those datasets. Biclustering need optimize several conflicting objectives, and can be solved with MOO methods. As a heuristics-based optimization approach, the particle swarm optimization (PSO) simulate the movements of a bird flock finding food. The shuffled frog-leaping algorithm (SFL) is a population-based cooperative search metaphor combining the benefits of the local search of PSO and the global shuffled of information of the complex evolution technique. SFL is used to solve the optimization problems of the large-scale datasets.

Results

This paper integrates dynamic population strategy and shuffled frog-leaping algorithm into biclustering of microarray data, and proposes a novel multi-objective dynamic population shuffled frog-leaping biclustering (MODPSFLB) algorithm to mine maximum bicluesters from microarray data. Experimental results show that the proposed MODPSFLB algorithm can effectively find significant biological structures in terms of related biological processes, components and molecular functions.

Conclusions

The proposed MODPSFLB algorithm has good diversity and fast convergence of Pareto solutions and will become a powerful systematic functional analysis in genome research.
Identification and recombinant expression of anandamide hydrolyzing enzyme from Dictyostelium discoideum
Authors: Neelamegan Dhamodharan , Schoenhofen Ian C , Richards James C , Cox Andrew D
Published: December 2012

Background

Anandamide (Arachidonoyl ethanolamide) is a potent bioactive lipid studied extensively in humans, which regulates several neurobehavioral processes including pain, feeding and memory. Bioactivity is terminated when hydrolyzed into free arachidonic acid and ethanolamine by the enzyme fatty acid amide hydrolase (FAAH). In this study we report the identification of a FAAH homolog from Dictyostelium discoideum and its function to hydrolyze anandamide.

Results

A putative FAAH DNA sequence coding for a conserved amidase signature motif was identified in the Dictyostelium genome database and the corresponding cDNA was isolated and expressed as an epitope tagged fusion protein in either E.coli or Dictyostelium. Wild type Dictyostelium cells express FAAH throughout their development life cycle and the protein was found to be predominantly membrane associated. Production of recombinant HIS tagged FAAH protein was not supported in E.coli host, but homologous Dictyostelium host was able to produce the same successfully. Recombinant FAAH protein isolated from Dictyostelium was shown to hydrolyze anandamide and related synthetic fatty acid amide substrates.

Conclusions

This study describes the first identification and characterisation of an anandamide hydrolyzing enzyme from Dictyostelium discoideum, suggesting the potential of Dictyostelium as a simple eukaryotic model system for studying mechanisms of action of any FAAH inhibitors as drug targets.
Percutaneous ultrasonographically guided liver punctures: an analysis of 1961 patients over a period of ten years
Authors: Mueller Michael , Kratzer Wolfgang , Oeztuerk Suemeyra , Wilhelm Manfred , Mason Richard Andrew , Mao Ren , Haenle Mark Martin
Published: December 2012

Background

Ultrasonographically guided punctures of the liver represent a decisive tool in the diagnosis of many diseases of the liver. Objective of the study was to determine the extent to which the complication rate for ultrasonographically guided punctures of the liver is affected by less comprehensively studied risk factors.

Methods

A total of 2,229 liver biopsies were performed in 1,961 patients (55.5% males; 44.5% females). We recorded actual complications and assessed the following risk factors: needle gauge, puncture technique, examiner experience, coagulation status, puncture target (focal lesion versus parenchyma), lesion size, patient sex and age.

Results

he rate of complications stood at 1.2% (n = 27), of which 0.5% (n = 12) were major and 0.7% (n = 15) minor complications. A significant increase in complications involving bleeding was observed with larger-gauge needles compared with smaller-gauge needles and for cutting biopsy punctures compared with aspiration biopsies (Menghini technique). In the bivariate analysis complications were 2.7 times more frequent in procedures performed by experienced examiners compared with those with comparatively less experience. Lower values for Quick’s test and higher partial thromboplastin times were associated with a higher rate of bleeding. Neither the puncture target, lesion size or patient sex exerted any measurable influence on the puncture risk. Advanced patient age was associated with a higher rate of complications involving bleeding.

Conclusions

Our study helps to establish the importance of potential and less comprehensively studied risk factors and may contribute to further reduction in complications rates in routine clinical practice.
LINE-1 methylation shows little intra-patient heterogeneity in primary and synchronous metastatic colorectal cancer
Authors: Matsunoki Aika , Kawakami Kazuyuki , Kotake Masanori , Kaneko Mami , Kitamura Hirotaka , Ooi Akishi , Watanabe Go , Minamoto Toshinari
Published: December 2012

Background

Long interspersed nucleotide element 1 (LINE-1) hypomethylation is suggested to play a role in the progression of colorectal cancer (CRC). To assess intra-patient heterogeneity of LINE-1 methylation in CRC and to understand its biological relevance in invasion and metastasis, we evaluated the LINE-1 methylation at multiple tumor sites. In addition, the influence of stromal cell content on the measurement of LINE-1 methylation in tumor tissue was analyzed.

Methods

Formalin-fixed paraffin-embedded primary tumor tissue was obtained from 48 CRC patients. Matched adjacent normal colon tissue, lymph node metastases and distant metastases were obtained from 12, 18 and 7 of these patients, respectively. Three different areas were microdissected from each primary tumor and included the tumor center and invasive front. Normal mucosal and stromal cells were also microdissected for comparison with the tumor cells. The microdissected samples were compared in LINE-1 methylation level measured by multicolor MethyLight assay. The assay results were also compared between microdissected and macrodissected tissue samples.

Results

LINE-1 methylation within primary tumors showed no significant intra-tumoral heterogeneity, with the tumor center and invasive front showing identical methylation levels. Moreover, no difference in LINE-1 methylation was observed between the primary tumor and lymph node and distant metastases from the same patient. Tumor cells showed significantly less LINE-1 methylation compared to adjacent stromal and normal mucosal epithelial cells. Consequently, LINE-1 methylation was significantly lower in microdissected samples compared to macrodissected samples. A trend for less LINE-1 methylation was also observed in more advanced stages of CRC.

Conclusions

LINE-1 methylation shows little intra-patient tumor heterogeneity, indicating the suitability of its use for molecular diagnosis in CRC. The methylation is relatively stable during CRC progression, leading us to propose a new concept for the association between LINE-1 methylation and disease stage.
Orbital glomus tumor in an Asian patient
Authors: Chang Minwook , Lee Youngseok , Baek Sehyun , Lee Tae Soo
Published: December 2012

Background

This report describes a recurrent orbital glomus tumor in an Asian patient.

Case presentation

A healthy 50-year-old Korean man had progressive right exophthalmos and a soft mass on his right lower lid for 6 months. We evaluated the mass using CT and MRI, and performed excisional biopsy and pathologic examination. Pathologically, the mass was a glomus tumor. Although proptosis of the right eye decreased, one month after surgery it increased to almost the same level as before surgery.

Conclusions

This is the first report of an Asian patient with an orbital glomus tumor that demonstrated rapid re-growth after incision without pain or visual problems.
Elevated serum levels of Chromogranin A in hepatocellular carcinoma
Authors: Biondi Antonio , Malaguarnera Giulia , Vacante Marco , Berretta Massimiliano , D’Agata Velia , Malaguarnera Michele , Basile Francesco , Drago Filippo , Bertino Gaetano
Published: December 2012

Background

During the past three decades, the incidence of hepatocellular carcinoma in the United States has tripled. The neuroendocrine character has been observed in some tumor cells within some hepatocellular carcinoma nodules and elevated serum chromogranin A also been reported in patients with hepatocellular carcinoma. The aim of this work was to investigate the role of serum concentration of chromogranin A in patients with hepatocellular carcinoma at different stages.

Methods

The study population consisted of 96 patients (63 males and 33 females age range 52-84) at their first hospital admission for hepatocellular carcinoma. The control group consisted of 35 volunteers (20 males and 15 females age range 50-80). The hepatocellular carcinoma patients were stratified according the Barcelona-Clinic Liver Cancer classification. Venous blood samples were collected before treatment from each patients before surgery, centrifuged to obtain serum samples and stored at -80° C until assayed.

Results

The chromogranin A serum levels were elevated (> 100 ng/ml) in 72/96 patients with hepatocellular carcinoma. The serum levels of chromogranin A were significantly correlated (p<0.05) with alpha-fetoprotein. In comparison with controls, the hepatocellular carcinoma patients showed a significant increase (p<0.001) vs controls. The chromogranin A levels in the Barcelona staging of hepatocellular carcinoma was higher in stage D compared to stage C (p<0.01), to stage B (p<0.001), and to stage A (p<0.001).

Conclusions

Molecular markers, such as chromogranin A, could be very useful tools for hepatocellular carcinoma diagnosis. However the molecular classification should be incorporated into a staging scheme, which effectively separated patients into groups with homogeneous prognosis and response to treatment, and thus serves to aid in the selection of appropriate therapy.
Single cell oil of oleaginous fungi from the tropical mangrove wetlands as a potential feedstock for biodiesel
Authors: Khot Mahesh , Kamat Srijay , Zinjarde Smita , Pant Aditi , Chopade Balu , RaviKumar Ameeta
Published: December 2012

Background

Single cell oils (SCOs) accumulated by oleaginous fungi have emerged as a potential alternative feedstock for biodiesel production. Though fungi from mangrove ecosystem have been reported for production of several lignocellulolytic enzymes, they remain unexplored for their SCO producing ability. Thus, these oleaginous fungi from the mangrove ecosystem could be suitable candidates for production of SCOs from lignocellulosic biomass. The accumulation of lipids being species specific, strain selection is critical and therefore, it is of importance to evaluate the fungal diversity of mangrove wetlands. The whole cells of these fungi were investigated with respect to oleaginicity, cell mass, lipid content, fatty acid methyl ester profiles and physicochemical properties of transesterified SCOs in order to explore their potential for biodiesel production.

Results

In the present study, 14 yeasts and filamentous fungi were isolated from the detritus based mangrove wetlands along the Indian west coast. Nile red staining revealed that lipid bodies were present in 5 of the 14 fungal isolates. Lipid extraction showed that these fungi were able to accumulate > 20% (w/w) of their dry cell mass (4.14 - 6.44 g L-1) as lipids with neutral lipid as the major fraction. The profile of transesterified SCOs revealed a high content of saturated and monounsaturated fatty acids i.e., palmitic (C16:0), stearic (C18:0) and oleic (C18:1) acids similar to conventional vegetable oils used for biodiesel production. The experimentally determined and predicted biodiesel properties for 3 fungal isolates correlated well with the specified standards. Isolate IBB M1, with the highest SCO yield and containing high amounts of saturated and monounsaturated fatty acid was identified as Aspergillus terreus using morphotaxonomic study and 18 S rRNA gene sequencing. Batch flask cultures with varying initial glucose concentration revealed that maximal cell biomass and lipid content were obtained at 30gL-1. The strain was able to utilize cheap renewable substrates viz., sugarcane bagasse, grape stalk, groundnut shells and cheese whey for SCO production.

Conclusion

Our study suggests that SCOs of oleaginous fungi from the mangrove wetlands of the Indian west coast could be used as a potential feedstock for biodiesel production with Aspergillus terreus IBB M1 as a promising candidate.