bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute anterior compartment syndrome associated with psychogenic polydipsia
Authors: Maiocchi Licia , Bernardi Elsa 
Published: March 2012

Objective: The aim of this paper is to describe the association of psychogenic polydipsia with anterior compartment syndrome. Method: Case report. Results: A 31-year-old man with glucose-6-phosphate-dehydrogenase (G6PD) deficiency had a history of paranoid schizophrenia from age 16 complicated by the use of drugs. Four years after the initial diagnosis of schizophrenia, he developed psychogenic polydipsia. This was complicated by episodic severe acute hyponatraemia with seizures and, on one occasion, by generalized rhabdomyolysis. One episode of severe acute hyponatraemia with delirium led to anterior compartment syndrome in both legs. Delayed diagnosis and treatment led to extensive myonecrosis and permanent bilateral foot drop. For 6 years his polydipsia remained partially controlled in a locked psychiatric ward with limited leave, until his sudden death related to severe water intoxication. Conclusions: Anterior compartment syndrome is a rare event associated with psychogenic polydipsia. Psychiatrists, physicians and surgeons should be aware of the seriousness of anterior compartment syndrome and its potential to increase morbidity in patients with psychogenic polydipsia.
Prediction of antibody persistency from antibody titres to natalizumab
Authors: Jensen Poul Erik H , Koch-Henriksen Nils , Sellebjerg Finn , Sørensen Per S 
Published: March 2012

Background:In a subgroup of patients with multiple sclerosis natalizumab therapy causes generation of anti-natalizumab antibodies that may be transient or persistent. It is recommended to discontinue natalizumab therapy in persistently antibody-positive patients. Objective:To use titres of anti-natalizumab antibodies to predict persistency of antibodies. Patients and methods:In 525 consecutive natalizumab treated patients tested for anti-natalizumab antibodies 43 (8.2%) were antibody-positive. Thirty of the antibody-positive patients, who were tested both at three and at six months after treatment start, had antibody titres in blood measured using an extended ELISA method. Results:Samples from persistently positive patients ( N=18) had higher titre values than samples from transiently positive patients ( N=12). A cut-off value for high titre values was generated, above which patients may discontinue natalizumab therapy after three months. The method had a sensitivity of 0.83, a specificity of 1.00 and a diagnostic accuracy of 0.90. Conclusion:An extended ELISA method for measuring anti-natalizumab antibody titres in multiple sclerosis patients on natalizumab therapy may be used for evaluation of antibody persistence. A test at three months may identify patients with high titres, who should discontinue natalizumab therapy, and patients with transient low-titre antibodies, who may continue natalizumab therapy despite development of antibodies.
Exhaust gas recirculation stratification to control diesel homogeneous charge compression ignition combustion
Authors: André Mathieu , Walter Bruno , Bruneaux Gilles , Foucher Fabrice , Mounaïm–Rousselle Christine 
Published: March 2012

A single-cylinder diesel engine was used to investigate the potential of exhaust gas recirculation dilution stratification as a control technique for homogeneous charge compression ignition combustion with early direct injections. Experimental studies on both all-metal and optically accessible engines were performed to understand the processes involved when exhaust gas recirculation is introduced separately in the intake ports. Laser-induced fluorescence diagnostics were carried out in the optical engine in order to provide fuel and exhaust gas recirculation distributions. The results indicate that depending on the intake configuration, the exhaust gas recirculation stratification can be maintained until late timings corresponding to the combustion event, leading to decreased maxima of heat-release rates, as well as decreased combustion noise levels. This result suggests that exhaust gas recirculation stratification may be used as a control parameter for combustion speed and therefore may contribute to the extension of the homogeneous charge compression ignition operating range. However, although exhaust gas recirculation stratification appears to be an interesting new control technique for homogeneous charge compression ignition combustion, its effect on the combustion was shown to be very sensitive to parameters such as the intake system configuration or the exhaust gas recirculation composition, showing that industrial use of this control technique requires further understanding of the physical phenomena involved.
Arm exercise training in chronic obstructive pulmonary disease
Authors: McKeough Zoe J , Bye Peter TP , Alison Jennifer A 
Published: March 2012

The aim of this study was to compare the effects of arm endurance training, arm strength training, a combination of arm endurance and strength training, and no arm training on endurance arm exercise capacity. A randomised controlled trial was undertaken with chronic obstructive pulmonary disease subjects randomised into one of four groups to complete 8 weeks of training: (a) arm endurance training (endurance group) consisting of supported and unsupported arm exercises, (b) arm strength training (strength group) using weight machines, (c) a combination of arm endurance and arm strength training (combined group), or (d) no arm training (control group). The primary outcome measurement was endurance arm exercise capacity measured by an endurance arm crank test. Secondary outcomes included functional arm exercise capacity measured by the incremental unsupported arm exercise test and health-related quality of life. A total of 52 subjects were recruited and 38 (73%) completed the study. When comparing the arm endurance group to the control group, there was a significant increase in endurance time of 6 min (95% CI 2–10, p < 0.01) following the interventions. When comparing the combined group to each of the control, endurance and strength groups, there was a significantly greater reduction in dyspnoea and rate of perceived exertion at the end of the functional arm exercise test for the combined group following the interventions. The mode of training to be favoured to increase endurance arm exercise capacity is arm endurance training. However, combined arm endurance and strength training may also be very useful to reduce the symptoms during everyday arm tasks.
Autophagy is required for CSF-1–induced macrophagic differentiation and acquisition of phagocytic functions
Authors: Jacquel Arnaud , Obba Sandrine , Boyer Laurent , Dufies Maeva , Robert Guillaume , Gounon Pierre , Lemichez Emmanuel , Luciano Frederic , Solary Eric , Auberger Patrick 
Published: March 2012

Abstract
Autophagy is the process by which superfluous or damaged macromolecules or organelles are degraded by the lysosome. Pharmacologic and genetic evidence indicates that autophagy plays pleiotropic functions in cellular homeostasis, development, survival, and differentiation. The differentiation of human blood monocytes into macrophages is a caspase-dependent process when triggered ex vivo by colony stimulating factor-1. We show here, using pharmacologic inhibitors, siRNA approaches, and Atg7−/− mice, that autophagy initiated by ULK1 is required for proper colony stimulating factor-1–driven differentiation of human and murine monocytes. We also unravel a role for autophagy in macrophage acquisition of phagocytic functions. Collectively, these findings highlight an unexpected and essential role of autophagy during monocyte differentiation and acquisition of macrophage functions.
Primates and mouse NumtS in the UCSC Genome Browser
Authors: Calabrese Francesco Maria , Simone Domenico , Attimonelli Marcella 
Published: March 2012

Abstract

Background
NumtS (N uclear M iT ochondrial S equences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.

Results
The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.

Conclusions
Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.
Intuitive representation of surface properties of biomolecules using BioBlender
Authors: Andrei Raluca Mihaela , Callieri Marco , Zini Maria Francesca , Loni Tiziana , Maraziti Giuseppe , Pan Mike Chen , Zoppè Monica 
Published: March 2012

Abstract

Background
In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties.

Methods
Recent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work.
On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features.
Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface.

Results
A new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein.

Conclusions
Our system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
Authors: Bramucci Emanuele , Paiardini Alessandro , Bossa Francesco , Pascarella Stefano 
Published: March 2012

Abstract

Background
In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users.

Results
A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLAST, ClustalW, MUSCLE, CEalign and MODELLER) has been developed, to show how the integration of the individual steps required for homology modeling and sequence/structure analysis within the PyMOL framework can hugely simplify these tasks. Sequence similarity searches, multiple sequence and structural alignments generation and editing, and even the possibility to merge sequence and structure alignments have been implemented in PyMod, with the aim of creating a simple, yet powerful tool for sequence and structure analysis and building of homology models.

Conclusions
PyMod represents a new tool for the analysis and the manipulation of protein sequences and structures. The ease of use, integration with many sequence retrieving and alignment tools and PyMOL, one of the most used molecular visualization system, are the key features of this tool.
Source code, installation instructions, video tutorials and a user's guide are freely available at the URL http://schubert.bio.uniroma1.it/pymod/index.html
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments
Authors: Consiglio Arianna , Carella Massimo , De Caro Giorgio , Delle Foglie Gianfranco , Giovannelli Candida , Grillo Giorgio , Ianigro Massimo , Licciulli Flavio , Palumbo Orazio , Piepoli Ada , Ranieri Elena , Liuni Sabino 
Published: March 2012

Abstract

Background
It is known from recent studies that more than 90% of human multi-exon genes are subject to Alternative Splicing (AS), a key molecular mechanism in which multiple transcripts may be generated from a single gene. It is widely recognized that a breakdown in AS mechanisms plays an important role in cellular differentiation and pathologies. Polymerase Chain Reactions, microarrays and sequencing technologies have been applied to the study of transcript diversity arising from alternative expression. Last generation Affymetrix GeneChip Human Exon 1.0 ST Arrays offer a more detailed view of the gene expression profile providing information on the AS patterns. The exon array technology, with more than five million data points, can detect approximately one million exons, and it allows performing analyses at both gene and exon level. In this paper we describe BEAT, an integrated user-friendly bioinformatics framework to store, analyze and visualize exon arrays datasets. It combines a data warehouse approach with some rigorous statistical methods for assessing the AS of genes involved in diseases. Meta statistics are proposed as a novel approach to explore the analysis results. BEAT is available at http://beat.ba.itb.cnr.it.

Results
BEAT is a web tool which allows uploading and analyzing exon array datasets using standard statistical methods and an easy-to-use graphical web front-end. BEAT has been tested on a dataset with 173 samples and tuned using new datasets of exon array experiments from 28 colorectal cancer and 26 renal cell cancer samples produced at the Medical Genetics Unit of IRCCS Casa Sollievo della Sofferenza.
To highlight all possible AS events, alternative names, accession Ids, Gene Ontology terms and biochemical pathways annotations are integrated with exon and gene level expression plots. The user can customize the results choosing custom thresholds for the statistical parameters and exploiting the available clinical data of the samples for a multivariate AS analysis.

Conclusions
Despite exon array chips being widely used for transcriptomics studies, there is a lack of analysis tools offering advanced statistical features and requiring no programming knowledge. BEAT provides a user-friendly platform for a comprehensive study of AS events in human diseases, displaying the analysis results with easily interpretable and interactive tables and graphics.
Improving biomarker list stability by integration of biological knowledge in the learning process
Authors: Sanavia Tiziana , Aiolli Fabio , Da San Martino Giovanni , Bisognin Andrea , Di Camillo Barbara 
Published: March 2012

Abstract

Background
The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for biomarker discovery using microarray data often provide results with limited overlap. It has been suggested that one reason for these inconsistencies may be that in complex diseases, such as cancer, multiple genes belonging to one or more physiological pathways are associated with the outcomes. Thus, a possible approach to improve list stability is to integrate biological information from genomic databases in the learning process; however, a comprehensive assessment based on different types of biological information is still lacking in the literature. In this work we have compared the effect of using different biological information in the learning process like functional annotations, protein-protein interactions and expression correlation among genes.

Results
Biological knowledge has been codified by means of gene similarity matrices and expression data linearly transformed in such a way that the more similar two features are, the more closely they are mapped. Two semantic similarity matrices, based on Biological Process and Molecular Function Gene Ontology annotation, and geodesic distance applied on protein-protein interaction networks, are the best performers in improving list stability maintaining almost equal prediction accuracy.

Conclusions
The performed analysis supports the idea that when some features are strongly correlated to each other, for example because are close in the protein-protein interaction network, then they might have similar importance and are equally relevant for the task at hand. Obtained results can be a starting point for additional experiments on combining similarity matrices in order to obtain even more stable lists of biomarkers. The implementation of the classification algorithm is available at the link: http://www.math.unipd.it/~dasan/biomarkers.html.
RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts
Authors: Driver Ashley M , Peñagaricano Francisco , Huang Wen , Ahmad Khawaja R , Hackbart Katie S , Wiltbank Milo C , Khatib Hasan 
Published: March 2012

AbstractBackgroundA valuable tool for both research and industry, in vitro fertilization (IVF) has applications range from gamete selection and preservation of traits to cloning. Although IVF has achieved worldwide use, with approximately 339,685 bovine embryos transferred in 2010 alone, there are still continuing difficulties with efficiency. It is rare to have more than 40% of fertilized in vitro cattle oocytes reach blastocyst stage by day 8 of culture, and pregnancy rates are reported as less than 45% for in vitro produced embryos. To investigate potential influences in-vitro fertilization (IVF) has on embryonic development, this study compares in vivo- and in vitro-derived bovine blastocysts at a similar stage and quality grade (expanded, excellent quality) to determine the degree of transcriptomic variation beyond morphology using RNA-Seq.ResultsA total of 26,906,451 and 38,184,547 fragments were sequenced for in vitro and in vivo embryo pools, respectively. We detected expression for a total of 17,634 genes, with 793 genes showing differential expression between the two embryo populations with false discovery rate (FDR) < 0.05. There were also 395 novel transcribed units found, of which 45 were differentially expressed (FDR < 0.05). In addition, 4,800 genes showed evidence of alternative splicing, with 873 genes displaying differential alternative splicing between the two pools (FDR < 0.05). Using GO enrichment analysis, multiple biological pathways were found to be significantly enriched for differentially expressed genes (FDR < 0.01), including cholesterol and sterol synthesis, system development, and cell differentiation.ConclusionsThus, our results support that IVF may influence at the transcriptomic level and that morphology is limited in full characterization of bovine preimplantation embryos.
Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation
Authors: Hara Kahori , Fujii Tsuguru , Suzuki Yutaka , Sugano Sumio , Shimada Toru , Katsuma Susumu , Kawaoka Shinpei 
Published: March 2012

Abstract

Background
In the silkworm, Bombyx mori, femaleness is strongly controlled by the female-specific W chromosome. Originally, it was presumed that the W chromosome encodes female-determining gene(s), accordingly called Fem. However, to date, neither Fem nor any protein-coding gene has been identified from the W chromosome. Instead, the W chromosome is occupied with numerous transposon-related sequences. Interestingly, the silkworm W chromosome is a source of female-enriched PIWI-interacting RNAs (piRNAs). piRNAs are small RNAs of 23-30 nucleotides in length, which are required for controlling transposon activity in animal gonads. A recent study has identified a novel mutant silkworm line called KG, whose mutation in the W chromosome causes severe female masculinization. However, the molecular nature of KG line has not been well characterized yet.

Results
Here we molecularly characterize the KG line. Genomic PCR analyses using currently available W chromosome-specific PCR markers indicated that no large deletion existed in the KG W chromosome. Genetic analyses demonstrated that sib-crosses within the KG line suppressed masculinization. Masculinization reactivated when crossing KG females with wild type males. Importantly, the KG ovaries exhibited a significantly abnormal transcriptome. First, the KG ovaries misexpressed testis-specific genes. Second, a set of female-enriched piRNAs was downregulated in the KG ovaries. Third, several transposons were overexpressed in the KG ovaries.

Conclusions
Collectively, the mutation in the KG W chromosome causes broadly altered expression of testis-specific genes, piRNAs, and transposons. To our knowledge, this is the first study that describes a W chromosome mutant with such an intriguing phenotype.