bluuebunny/crossref_metadata_2025 huggingface dataset:
Rh‐based Biphasic Isomerization of Carbon–Carbon Double Bonds in Natural Oils
Authors: Quirino Rafael L. , Larock Richard C.
Published: December 2011

The biphasic conjugation of soybean and other natural oils, as well as the isomerization of various alkenes, was examined using a rhodium catalyst. A maximum yield, of conjugated soybean oil, of 96% was obtained when the reaction was run at 80 °C under argon with ethanol as the polar solvent, using triphenylphosphine monosulfonate sodium salt (tppms) as the ligand, and the surfactant sodium dodecyl sulfate (SDS). The optimized conditions were tested with other substrates, and the products were analyzed by 1H NMR, GC/MS, and ICP‐MS.
Selecting Products Safely
Authors: Stanton Carina
Published: December 2011

With a focus on multiple stakeholders working together, AORN's “Recommended practices for product selection in perioperative practice settings” provides a source of information to help facilities choose safe and efficient perioperative products, including medical devices and other products used in the perioperative settings.
The association between Internet addiction and psychiatric disorder: A review of the literature
Authors: Ko C.-H. , Yen J.-Y. , Yen C.-F. , Chen C.-S. , Chen C.-C.
Published: December 2011

Internet addiction is a newly emergent disorder. It has been found to be associated with a variety of psychiatric disorders. Information about such coexisting psychiatric disorders is essential to understand the mechanism of Internet addiction. In this review, we have recruited articles mentioning coexisting psychiatric disorders of Internet addiction from the PubMed database as at November 3, 2009. We describe the updated results for such disorders of Internet addiction, which include substance use disorder, attention-deficit hyperactivity disorder, depression, hostility, and social anxiety disorder. We also provide discussion for possible mechanisms accounting for the coexistence of psychiatric disorders and Internet addiction. The review might suggest that combined psychiatric disorders mentioned above should be evaluated and treated to prevent their deteriorating effect on the prognosis of Internet addiction. On the other hand, Internet addiction should be paid more attention to when treating people with these coexisting psychiatric disorders of Internet addiction. Additionally, we also suggest future necessary research directions that could provide further important information for the understanding of this issue.
Variation in the BDNF Val66Met polymorphism and response to cognitive-behavior therapy in obsessive-compulsive disorder
Authors: Fullana M.A. , Alonso P. , Gratacòs M. , Jaurrieta N. , Jiménez-Murcia S. , Segalàs C. , Real E. , Estivill X. , Menchón J.M.
Published: December 2011

Background

Recent research suggests that the brain-derived neurotrophic factor (BDNF) may play a role in extinction learning. The goal of this study was to test whether variation in the BDNF Val66Met polymorphism is related to treatment response to exposure-based cognitive-behavior therapy (CBT), a form of extinction learning, in obsessive-compulsive disorder (OCD).

Methods

One hundred and six OCD patients from a specialized clinic, who underwent a standardized CBT treatment after partial or non-response to a 12-week pharmacological trial, were genotyped for the BDNF Val66Met and the relationship between genotype and treatment response was analyzed.

Results

Among 98 CBT completers, 36% of those carrying the BDNF Met allele were rated as CBT responders compared to 60% of nonMet allele carriers (P = 0.027). When analyzing the different obsessive-compulsive symptom dimensions, in patients with contamination/cleaning symptoms, the Met allele was associated with a significantly worse CBT response (P<0.0001) and a lower obsessions severity decrease from pre- to posttreatment (P = 0.046).

Conclusion

Genetic variation in BDNF may be associated with treatment response in exposure-based CBT in OCD, especially in those patients exhibiting contamination/cleaning symptoms.
In patients with schizophrenia, symptoms improvement can be uncorrelated with quality of life improvement
Authors: Wilson-d’Almeida K. , Karrow A. , Bralet M.-C. , Bazin N. , Hardy-Baylé M.-C. , Falissard B.
Published: December 2011

Objectives

Quality of life has been found to be associated with symptoms in patients with schizophrenia. Nevertheless, the mechanism that underlies this association is still unclear. The objective of this paper is to prospectively evaluate the quality of life of patients with schizophrenia in relation to the concurrent evolution of their symptoms, their expectations and their perceived position in life.

Methods

Participants included 306 outpatients with schizophrenia who were interviewed at baseline, 6 and 12 months, about their quality of life (Outcome revealed by Preference in Schizophrenia, OPS) and symptoms (Positive and Negative Syndrome Scale, PANSS).

Results

Quality of life relative to subject expectations remained stable over time. A decrease in symptoms was correlated to an increase in both expectations and perceived position in life but did not correlate to quality of life.

Conclusion

The level of expectations seems to play a major role in the subjective assessment of quality of life in patients with schizophrenia. Symptom improvement is not necessarily associated with quality of life improvement relative to subject expectations. Caregivers should be aware of this result so as to deal with possible disappointments in patients receiving a new efficient treatment.
Characteristics Associated With Use of Homeopathic Drugs for Psychiatric Symptoms in the General Population
Authors: Grolleau A. , Bégaud B. , Verdoux H.
Published: December 2011

Objective

To explore which patient characteristics are associated in naturalistic conditions with the lifetime use of homeopathic treatment for psychiatric symptoms.

Method

Lifetime use of psychotropic treatment was explored in a sample of 36,785 persons, participating in the Mental Health Survey in the General Population. Characteristics associated with use of homeopathic treatments, associated or not with conventional psychotropic drugs, were explored using multivariate analyses.

Results

Use of homeopathic treatment for psychiatric symptoms was reported by 1.3% of persons. Younger age, female gender and high educational level were associated with use of homeopathy. Half of homeopathy users presented at least one Mini International Neuropsychiatric Interview (MINI) diagnosis, most frequently anxiety disorders. Their diagnostic profile was similar to that of persons reporting use of anxiolytics or hypnotics. Compared to persons with no lifetime use of psychotropic drugs, persons using homeopathy were more likely to present with a diagnosis of mood disorder or anxiety disorder. Compared to those using conventional psychotropic drugs, they presented less frequently with psychiatric disorders, with the exception of anxiety disorders.

Conclusion

Homeopathic treatment for psychiatric symptoms appears to be used mainly to reduce anxiety symptoms in the general population.
Mutational analysis of Sep‐tRNA:Cys‐tRNA synthase reveals critical residues for tRNA‐dependent cysteine formation
Authors: Helgadóttir Sunna , Sinapah Sylvie , Söll Dieter , Ling Jiqiang
Published: December 2011

In methanogenic archaea, Sep‐tRNA:Cys‐tRNA synthase (SepCysS) converts Sep‐tRNACys to Cys‐tRNACys. The mechanism of tRNA‐dependent cysteine formation remains unclear due to the lack of functional studies. In this work, we mutated 19 conserved residues in Methanocaldococcus jannaschii SepCysS, and employed an in vivo system to determine the activity of the resulting variants. Our results show that three active‐site cysteines (Cys39, Cys42 and Cys247) are essential for SepCysS activity. In addition, combined with structural modeling, our mutational and functional analyses also reveal multiple residues that are important for the binding of PLP, Sep and tRNA. Our work thus represents the first systematic functional analysis of conserved residues in archaeal SepCysSs, providing insights into the catalytic and substrate binding mechanisms of this poorly characterized enzyme.
The yeast metacaspase is implicated in oxidative stress response in frataxin‐deficient cells
Authors: Lefevre Sophie , Sliwa Dominika , Auchère Françoise , Brossas Caroline , Ruckenstuhl Christoph , Boggetto Nicole , Lesuisse Emmanuel , Madeo Frank , Camadro Jean-Michel , Santos Renata
Published: December 2011

Friedreich ataxia is the most common recessive neurodegenerative disease and is caused by reduced expression of mitochondrial frataxin. Frataxin depletion causes impairment in iron–sulfur cluster and heme biosynthesis, disruption of iron homeostasis and hypersensitivity to oxidants. Currently no pharmacological treatment blocks disease progression, although antioxidant therapies proved to benefit patients. We show that sensitivity of yeast frataxin‐deficient cells to hydrogen peroxide is partially mediated by the metacaspase. Metacaspase deletion in frataxin‐deficient cells results in recovery of antioxidant capacity and heme synthesis. In addition, our results suggest that metacaspase is associated with mitochondrial respiration, intracellular redox control and genomic stability.
Balanced autosomal translocation and double Robertsonian translocation in cases of primary amenorrhea in an Indian population
Authors: Kopakka Neeraja , Dalvi Rupa , Shetty Dhanlaxmi L. , Das Bibhu R. , Mandava Swarna
Published: December 2011

Objective

To assess the frequency of balanced autosomal translocations in patients with primary amenorrhea in an Indian population.

Methods

Cytogenetic analysis was carried out among women referred from all parts of India for primary amenorrhea between 2002 and 2010. Clinical history and laboratory findings were taken into consideration to determine the diagnosis. G‐banding with trypsin–Giemsa was performed to detect chromosome abnormalities.

Results

There were 15 balanced autosomal translocations in 1100 patients. Two novel translocations were identified: 1 with mosaic pattern of X chromosome monosomy and male karyotype, together with balanced autosomal translocation of chromosomes 11 and 20 in both cell lines; and 1 with double Robertsonian translocation of chromosomes 14 and 21.

Conclusion

Autosomal genes have a crucial role in reproductive development. More candidate genes need to be recognized for appropriate genetic counseling and clinical management.
Imperatives of the science of operations and supply‐chain management
Authors: Singhal Kalyan , Singhal Jaya
Published: December 2011

Although knowledge in operations and supply‐chain management (O&SCM) has advanced substantially during the last six decades, our community has not fully utilized the potential for radical innovations. We identify two sets of opportunities for pursuing radical innovations. First, there is an opportunity to pursue all phases of science, including exploratory and qualitative research, developing theories, causation and internal validity, and testing models and theories for external validity (the ability to generalize knowledge to other situations). This would broaden the domain covered by each research effort, minimize the bias resulting from the choice of research paradigm and research domain, to enhance external validity, and to minimize the gap between our research efforts and the real world our community seeks to reshape. Second, there is an opportunity to pursue multiple perspectives because a scientific conclusion valid for a narrow domain may prove to be partially true or even false if one obtains multiple perspectives. Multiple perspectives can be obtained by investigating different parts of the system, by employing different methods of analysis, by using different sources of data, or by using different subsets of the same data. Developing scientific knowledge requires pursuit of all phases of science and of multiple perspectives. In a separate paper, we propose and analyze ways to accomplish it.
Environmental changes in southeastern Amazonia during the last 25,000 yr revealed from a paleoecological record
Authors: Hermanowski Barbara , da Costa Marcondes Lima , Behling Hermann
Published: December 2011

New pollen, micro-charcoal, sediment and mineral analyses of a radiocarbon-dated sediment core from the Serra Sul dos Carajás (southeast Amazonia) indicate changes between drier and wetter climatic conditions during the past 25,000 yr, reflected by fire events, expansion of savanna vegetation and no-analog Amazonian forest communities. A cool and dry last glacial maximum (LGM) and late glacial were followed by a wet phase in the early Holocene lasting for ca. 1200 yr, when tropical forest occurred under stable humid conditions. Subsequently, an increasingly warm, seasonal climate established. The onset of seasonality falls within the early Holocene warm period, with possibly longer dry seasons from 10,200 to 3400 cal yr BP, and an explicitly drier phase from 9000 to 3700 cal yr BP. Modern conditions with shorter dry seasons became established after 3400 cal yr BP. Taken together with paleoenvironmental evidence from elsewhere in the Amazon Basin, the observed changes in late Pleistocene and Holocene vegetation in the Serra Sul dos Carajás likely reflect large-scale shifts in precipitation patterns driven by the latitudinal displacement of the Inter-Tropical Convergence Zone and changes in sea-surface temperatures in the tropical Atlantic.
Predicting Fear of Flying and Positive Emotions Towards Air Travel
Authors: Martinussen Monica , Gundersen Elisabeth , Pedersen Reidar
Published: December 2011

The purpose of this study was to assess both fear of flying and positive emotions regarding air travel. A sample of 270 participants recruited at the local airport and from a university campus completed a questionnaire measuring fear of flying (Flight Anxiety Situations Questionnaire) as well as positive emotions toward flying. Hierarchical regression analyses were used to examine a model for predicting both fear of flying and positive emotions regarding air travel. Fear of flying was predicted by sex, recent flying experience, and stress/worry regarding check-in and security checks. Positive emotions were unrelated to demographic variables and flying experience, but were predicted by satisfaction with check-in and security checks.
Helicopter Accidents at Night
Authors: de Voogt Alex
Published: December 2011

Night conditions constrain the operations of a helicopter. Helicopter crews that fly at night have limited landing possibilities in times of emergency and suffer from limited visual cues during operations. This study compares the underlying causes and factors that differentiate daytime and nighttime helicopter accidents. From the US National Transportation and Safety Board (NTSB) online database, 4,755 helicopter accidents were selected for which the characteristics of day and night flights were compared. The number of fatal accidents occurring at night was significantly higher than during the daytime (χ2 = 95.04, df = 1, p < .001). Helicopter accidents that occur at night also show significantly fewer engine failures and autorotations but significantly more weather-related causes. The relative absence of engine failures at night is partly explained by the absence of specific helicopter operations. The combination of night flights and adverse weather conditions is shown to be particularly fatal in accidents. It is concluded that pilots require more conservative planning particularly in the vicinity of adverse weather systems.
Diagnostic Accuracy of CEUS in the Differential Diagnosis of Small (≤ 20 mm) and Subcentimetric (≤ 10 mm) Focal Liver Lesions in Comparison with Histology
Authors: Strobel D. , Bernatik T. , Blank W. , Schuler A. , Greis C. , Dietrich C. , Seitz K.
Published: December 2011

Hintergrund: Evaluierung der diagnostischen Treffsicherheit der Kontrastmittelsonografie in der Differenzialdiagnose kleiner Leberläsionen.

Material und Methoden: 1349 Patienten mit im B-Bild und Power Doppler unklarem Lebertumor wurden prospektiv mittels KM-Sono multizentrisch mit standardisiertem Protokoll (mechanischer Index < 0,4, Phase/Puls-Inversion-Technik, Sonovue-Bolus-Injektion) untersucht. Die Differenzialdiagnose im KM-Sono basierte auf tumortypischen Vaskularisationsmustern in der arteriellen, portalvenösen Phase und Spätphase (EFSUMB-Leitlinie). 335 Patienten mit fokalen Leberläsionen (FLLs) ≤ 20 mm wurden analysiert. Die Tumorklassifizierung nach KM-Sono wurde mit der Histologie (73,2 %) oder in einigen Fällen mit CT und/oder MRT verglichen.

Ergebnisse: Eine definitive Tumordiagnose war in 329 FLLs möglich. Die Enddiagnose der ≤ 20 mm FLLs mit histologischer Sicherung (n = 241) beinhaltete 87 benigne und 154 maligne Tumore. Die diagnostische Treffsicherheit des KM-Sono bei ≤ 20 mm histologisch gesicherten FLLs war 83,8 %. Die KM-Sono identifizierte 144 /154 maligne FLLs (Sensitivität 93,5 %) und 58 /87 benigne FLLs (Spezifität 66,7 %). 24 /241 FLLs blieben nach der KM-Sono unklar (9,9 %). Die KM-Sono klassifizierte 15 /241 FLLs (6,2 %) falsch (12 benigne und 3 maligne FLLs). Die positive Voraussagekraft der KM-Sono bei malignen FLLs war 92,3 %, die negative Voraussagekraft 95,1 %. Von 241 histologisch gesicherten FLLs waren 62 FLLs ≤ 10 mm (diagnostische Treffsicherheit KM-Sono 80,6 %) und 179 FLLs > 10 mm ≤ 20 mm (diagnostische Treffsicherheit KM-Sono 80,6 %).

Schlussfolgerung: Die KM-Sonografie hat eine hohe diagnostische Treffsicherheit in der Differenzierung kleiner und kleinster (≤ 1 cm) FLL im klinischen Alltag.
Punched Nerve Syndrome: Ultrasonographic Appearance of Functional Vascular Nerve Impairment
Authors: Loizides A. , Peer S. , Plaikner M. , Djurdjevic T. , Gruber H.
Published: December 2011

Purpose: The mechanical impact of a neighboring vessel on a “punched” nerve segment is thought to be one possible cause of compression neuropathy but has not been proven definitively. We report on 9 subjects with unclear clinical mononeuropathies in whom we could clearly define peripheral nerve impairment by such vessels on real-time high-resolution ultrasound (HRUS).

Materials and Methods: Nine subjects with unclear mononeuropathy based on clinical neurological examination were referred to our department for HRUS assessment. The shape, inner and outer echotexture, size and diameter, and overall integrity of these nerves were assessed including an exact analysis of the surrounding soft tissues to search for potentially extraneural pathology. This included duplex imaging to identify even tiny atypical vascular structures.

Results: In all patients duplex HRUS showed the pulsatile and “punching” character of the relevant vessels and the direct mechanical impact of these vessel. The involved nerve segments appeared enlarged with a hypoechoic change of echotexture including at least partial masking of their inner fascicular texture.

Conclusion: Although rare, a “punching” vessel can be the cause of a compression neuropathy. Therefore, duplex HRUS must be included in every HRUS examination of patients with otherwise unclear mononeuropathy.
Frequency of Tumor Entities among Liver Tumors of Unclear Etiology Initially Detected by Sonography in the Noncirrhotic or Cirrhotic Livers of 1349 Patients
Authors: Seitz K. , Greis C. , Schuler A. , Bernatik T. , Blank W. , Dietrich C. , Strobel D.
Published: December 2011

Ziel: Untersuchung der Häufigkeit von verschiedenen soliden fokalen Leberläsionen (SFLL) in nicht zirrhotischen und zirrhotischen Lebern unter besonderer Berücksichtigung der Häufigkeit der Metastasierung in Zirrhoselebern.

Material und Methoden: Das Patientenkollektiv der DEGUM-Multicenterstudie (n = 1349) wurde reevaluiert und in ein Subkollektiv A ohne (n = 1067) und B mit Zirrhose (n = 282) unterteilt. Die verschiedenen Tumorentitäten waren zu 74,6 % histologisch gesichert (n = 1006). 

Ergebnisse: Im Subkollektiv A fanden sich 385 Fälle mit Metastasen (36,4 %) und 65 mit HCC (6,1 %), demgegenüber waren an benignen Läsionen Hämangiome mit 237 Fällen (22,4 %) und FNH mit 170 Fällen (16,1 %) am häufigsten. Im Subkollektiv B fanden sich 216 Fälle von HCC (76,6 %) und 12 Metastasen (4,3 %), sowie 42 benigne Läsionen (14,9 %). CCC waren im Subkollektiv A (3,3 %) und im Subkollektiv B (2,5 %) selten. Eine Tumoranamnese erhöht die Wahrscheinlichkeit für eine maligne SFLL im Subkollektiv A 1,8-fach, nicht jedoch im Subkollektiv B.

Schlussfolgerung: Die Häufigkeit der verschieden Tumorentitäten unterscheidet sich bei Patienten mit und ohne Zirrhose grundlegend. In nicht zirrhotischen Lebern sind maligne und benigne SFLL etwa gleich häufig. Im Vordergrund stehen Metastasen, Hämangiome und FNH, CCC sind selten. Eine Tumorvorgeschichte erhöht die Wahrscheinlichkeit auf eine maligne SFLL. Bei Zirrhose dominieren HCC, HCC sind 18-mal häufiger als Metastasen. Benigne SFLL und CCC sind selten
Intravenous Application of Second-Generation Ultrasound Contrast Agents in Children: A Review of the Literature
Authors: Piskunowicz M. , Kosiak W. , Batko T.
Published: December 2011

CEUS examinations using second-generation ultrasound contrast agents (UCA) are conducted in children, despite not being registered for individuals less than 18 years of age. We searched the Medline® database through Pubmed® and Scopus database, in order to find articles in which UCA were administered intravenously in patients under the age of 18. We analyzed in detail 9 papers (7 case reports, 2 original research studies), describing the examinations with intravenous administration of the UCA in children, and 23 original papers, in which the study group included at least one individual under the age of 18. Neither of the analyzed studies included any reports of adverse effects after UCA administration.
Incidentally Detected Splenic Lesions in Ultrasound: Does Contrast-Enhanced Ultrasonography Improve the Differentiation of Benign Hemangioma/Hamartoma from Malignant Lesions?
Authors: Stang A. , Keles H. , Hentschke S. , von Seydewitz C.-U. , Dahlke J. , Habermann C. , Wessling J.
Published: December 2011

Ziel: Ziele dieser Arbeit waren die Identifikation und die Validierung von unterschiedlichen tumorspezifischen Kontrastmittelmustern für die Differenzialdiagnose zwischen benignen vaskulären Neoplasien (Typ Hämangiom/Hamartom) und malignen Milzherden in der Kontrastmittelsonografie (CEUS).

Material und Methoden: 136 Milzläsionen (58 benigne vaskuläre Neoplasien, 78 maligne Läsionen) wurden jeweils in der B-Bild-Sonografie (US) und nachfolgend in der Kontrastmittelsonografie nach Sulfur-Hexafluoride-Injektion untersucht und dokumentiert. Zwei On-site-Reader analysierten das Kontrastmittelverhalten der Milzläsionen während der arteriellen und parenchymalen Phase. Mittels univariater und multivariater Analyse wurden tumorspezifische Kontrastmittelmuster, die signifikant mit einer der beiden Tumordiagnosen korreliert waren, identifiziert. Zwei geblindete Off-site-Reader benutzten diese tumorspezifischen Kontrastmittelmuster als Diagnosekriterien und stellten unabhängig voneinander anhand der Befunde der B-Bild-Sonografie und der Kontrastmittelsonografie eine Diagnose der Milzherde. Die diagnostische Treffsicherheit und Confidence (Az-Werte) sowie die Übereinstimmung der Off-site-Reader (қ-Werte) wurden kalkuliert. Referenzstandards waren Histopathologie oder CT und/oder MRI mit klinischem Verlauf.

Ergebnisse: In der multivariate Analyse waren arterielles Hyper- oder Isoenhancement unabhängige Prediktoren für eine benigne vaskuläre Neoplasie (Odds Ratio, 3,558; p < 0,0017). In der Subgruppe der iso- oder hypoechogenen Läsionen war arterielles Hyperenhancement praktisch beweisend für eine benigne vaskuläre Neoplasie (Odds Ratio, 21,333; p < 0,001). In der geblindeten Situation verbesserte sich die diagnostische Treffsicherheit und Confidence (Az-Werte) für beide Off-site Reader signifikant von 63,2 % und 70,6 % (0,785 und 0,818) in der B-Bild-Sonografie auf 87,5 % und 88,2 % (0,915 und 0,908) in der Kontrastmittelsonografie (p < 0,001). Die Interreaderübereinstimmung verbesserte sich ebenfalls (қ = 0,52 für B-Bild-Sonografie vs. қ = 0,88 nach Kontrastmittelsonografie).

Schlussfolgerung: Die Kontrastmittelsonografie verbessert die Differenzialdiagnose zwischen benigen vaskulären Neoplasien und malignen Tumoren in der Milz und scheint besonders hilfreich bei unklaren, zufällig im Ultraschall entdeckten hypoechogenen Milzherden.
Actin disassembly clock determines shape and speed of lamellipodial fragments
Authors: Ofer Noa , Mogilner Alexander , Keren Kinneret
Published: December 2011

A central challenge in motility research is to quantitatively understand how numerous molecular building blocks self-organize to achieve coherent shape and movement on cellular scales. A classic example of such self-organization is lamellipodial motility in which forward translocation is driven by a treadmilling actin network. Actin polymerization has been shown to be mechanically restrained by membrane tension in the lamellipodium. However, it remains unclear how membrane tension is determined, what is responsible for retraction and shaping of the rear boundary, and overall how actin-driven protrusion at the front is coordinated with retraction at the rear. To answer these questions, we utilize lamellipodial fragments from fish epithelial keratocytes which lack a cell body but retain the ability to crawl. The absence of the voluminous cell body in fragments simplifies the relation between lamellipodial geometry and cytoskeletal dynamics. We find that shape and speed are highly correlated over time within individual fragments, whereby faster crawling is accompanied by larger front-to-rear lamellipodial length. Furthermore, we find that the actin network density decays exponentially from front-to-rear indicating a constant net disassembly rate. These findings lead us to a simple hypothesis of a disassembly clock mechanism in which rear position is determined by where the actin network has disassembled enough for membrane tension to crush it and haul it forward. This model allows us to directly relate membrane tension with actin assembly and disassembly dynamics and elucidate the role of the cell membrane as a global mechanical regulator which coordinates protrusion and retraction.
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data
Authors: Fuchsberger Christian , Taliun Daniel , Pramstaller Peter P. , Pattaro Cristian
Published: December 2011

Summary: The GWAtoolbox is an R package that standardizes and accelerates the handling of data from genome-wide association studies (GWAS), particularly in the context of large-scale GWAS meta-analyses. A key feature of GWAtoolbox is its ability to perform quality control (QC) of any number of files in a matter of minutes. The implemented workflow has been structured to check three particular data quality aspects: (i) data formatting, (ii) quality of the GWAS results and (iii) data consistency across studies. Output consists of an extensive list of quality statistics and plots which allow inspection of individual files and between-study comparison to identify systematic bias.

Availability:  http://www.eurac.edu/GWAtoolbox

Contact:  cfuchsb@umich.edu; daniel.taliun@eurac.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids
Authors: Gonçalves-Almeida V. M. , Pires D. E. V. , de Melo-Minardi R. C. , da Silveira C. H. , Meira W. , Santoro M. M.
Published: December 2011

Motivation: Protein–protein interfaces contain important information about molecular recognition. The discovery of conserved patterns is essential for understanding how substrates and inhibitors are bound and for predicting molecular binding. When an inhibitor binds to different enzymes (e.g. dissimilar sequences, structures or mechanisms what we call cross-inhibition), identification of invariants is a difficult task for which traditional methods may fail.

Results: To clarify how cross-inhibition happens, we model the problem, propose and evaluate a methodology called HydroPaCe to detect conserved patterns. Interfaces are modeled as graphs of atomic apolar interactions and hydrophobic patches are computed and summarized by centroids (HP-centroids), and their conservation is detected. Despite sequence and structure dissimilarity, our method achieves an appropriate level of abstraction to obtain invariant properties in cross-inhibition. We show examples in which HP-centroids successfully predicted enzymes that could be inhibited by the studied inhibitors according to BRENDA database.

Availability:  www.dcc.ufmg.br/~raquelcm/hydropace

Contact:  valdetemg@ufmg.br; raquelcm@dcc.ufmg.br; santoro@icb.ufmg.br

Supplementary information:  Supplementary data are available at Bioinformatics online.
SitePainter: a tool for exploring biogeographical patterns
Authors: Gonzalez Antonio , Stombaugh Jesse , Lauber Christian L. , Fierer Noah , Knight Rob
Published: December 2011

As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies.

Availability:  https://sourceforge.net/projects/sitepainter

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  antoniog@colorado.edu, Rob.Knight@colorado.edu
Detection of microRNAs in color space
Authors: Marco Antonio , Griffiths-Jones Sam
Published: December 2011

Motivation: Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs.

Results: Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3′ end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs.

Availability and implementation: A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/

Contact: antonio.marco@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures
Authors: Muth Thilo , García-Martín Juan A. , Rausell Antonio , Juan David , Valencia Alfonso , Pazos Florencio
Published: December 2011

Summary: We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces.

Availability and implementation:  JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.

Contact:  pazos@cnb.csic.es
Reclassification of

Bacillus beijingensis

Qiu et al. 2009 and

Bacillus ginsengi

Qiu et al. 2009 as Bhargavaea beijingensis comb. nov. and Bhargavaea ginsengi comb. nov. and emended description of the genus

Bhargavaea
Authors: Verma Pankaj , Pandey Prashant Kumar , Gupta Arvind Kumar , Seong Chi Nam , Park Seong Chan , Choe Han Na , Baik Keun Sik , Patole Milind Shivaji , Shouche Yogesh Shreepad
Published: December 2011

We have carried out a polyphasic taxonomic characterization of

Bacillus beijingensis

DSM 19037T and

Bacillus ginsengi

DSM 19038T, which are closely related phylogenetically to

Bhargavaea cecembensis

LMG 24411T. All three strains are Gram-stain-positive, non-motile, moderately halotolerant and non-spore-forming. 16S rRNA gene sequence analyses showed that the strains constituted a coherent cluster, with sequence similarities between 99.7 and 98.7 %. The percentage similarity on the basis of amino acid sequences deduced from partial gyrB gene nucleotide sequences of these three type strains was 96.1–92.7 %. Phylogenetic trees based on the 16S rRNA gene and GyrB amino acid sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a deeply rooted cluster separated from the clades represented by the genera

Bacillus

,

Planococcus

,

Planomicrobium

,

Sporosarcina

,

Lysinibacillus

,

Viridibacillus

,

Kurthia

and

Geobacillus

, supporting their placement in the genus

Bhargavaea

. All three type strains have menaquinone MK-8 as the major respiratory quinone and showed similar fatty acid profiles. The main polar lipids present in the three type strains were diphosphatidylglycerol and phosphatidylglycerol, and the three strains showed peptidoglycan type A4α with l-lysine as the diagnostic diamino acid. The DNA G+C contents of

Bacillus beijingensis

DSM 19037T,

Bacillus ginsengi

DSM 19038T and

Bhargavaea cecembensis

LMG 24411T were 53.1, 50.2 and 53.7 mol%, respectively. The level of DNA–DNA hybridization among the three strains was 57–39 %, indicating that they are members of different species of the genus

Bhargavaea

. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data, we have emended the description of the genus

Bhargavaea

and propose the reclassification of

Bacillus beijingensis

and

Bacillus ginsengi

to the genus

Bhargavaea

, as Bhargavaea beijingensis comb. nov. (type strain ge10T  = DSM 19037T  = CGMCC 1.6762T) and Bhargavaea ginsengi comb. nov. (type strain ge14T  = DSM 19038T  = CGMCC 1.6763T).
Multilocus sequence analysis of

Bosea

species and description of Bosea lupini sp. nov., Bosea lathyri sp. nov. and Bosea robiniae sp. nov., isolated from legumes
Authors: De Meyer Sofie E. , Willems Anne
Published: December 2011

Gram-negative, rod-shaped bacteria were isolated from root nodules of Lupinus polyphyllus, Lathyrus latifolius and Robinia pseudoacacia. Based on the 16S rRNA gene phylogeny, they were closely related to

Bosea

species (100–97 % similarity), belonging to the class

Alphaproteobacteria

, family

Bradyrhizobiaceae

. The closest relatives of LMG 26383T, LMG 26379T and LMG 26381T were respectively the type strains of

Bosea thiooxidans

(99.6 %),

B. eneae

(98.3 %) and

B. minatitlanensis

(99.0 %). Chemotaxonomic data, including major fatty acid profiles, supported the assignment of our strains to the genus

Bosea

. Analysis of the concatenated sequences of five housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) and the results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from each other and from the five

Bosea

species with validly published names. No nodA or nodC genes could be amplified, while nifH PCR gave non-specific products. On the basis of genotypic and phenotypic data, three novel species, Bosea lupini sp. nov. (type strain LMG 26383T  = CCUG 61248T  = R-45681T), Bosea lathyri sp. nov. (type strain LMG 26379T  = CCUG 61247T  = R-46060T) and Bosea robiniae sp. nov. (type strain LMG 26381T  = CCUG 61249T  = R-46070T), are proposed.
Aquamicrobium ahrensii sp. nov. and Aquamicrobium segne sp. nov., isolated from experimental biofilters
Authors: Lipski André , Kämpfer Peter
Published: December 2011

Two groups of Gram-negative, aerobic bacterial strains previously isolated from experimental biofilters were investigated to determine their taxonomic position. Based on their 16S rRNA gene sequences, these isolates formed two distinct groups within the genus

Aquamicrobium

. The gene sequence similarities of the new isolates to the type strains of

Aquamicrobium

species were below 98.3 %. The presence of ubiquinone-10, C18 : 1
cis 11 as the predominant fatty acid and a polar lipid pattern with phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and phosphatidylethanolamine was in accordance with the characteristics of this genus. The results of DNA–DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from all recognized species of the genus

Aquamicrobium

. Therefore, the isolates were assigned to two novel species of this genus for which the names Aquamicrobium ahrensii sp. nov. (type strain 905/1T = DSM 19730T = CCUG 55251T) and Aquamicrobium segne sp. nov. (type strain 1006/1T = DSM 19714T = CCUG 55250T) are proposed. An emended description of the genus Aquamicrobium is also presented.
The Limbic System Conception and Its Historical Evolution
Authors: Roxo Marcelo R. , Franceschini Paulo R. , Zubaran Carlos , Kleber Fabrício D. , Sander Josemir W.
Published: December 2011

Throughout the centuries, scientific observers have endeavoured to extend their knowledge of the interrelationships between the brain and its regulatory control of human emotions and behaviour. Since the time of physicians such as Aristotle and Galen and the more recent observations of clinicians and neuropathologists such as Broca, Papez, and McLean, the field of affective neuroscience has matured to become the province of neuroscientists, neuropsychologists, neurologists, and psychiatrists. It is accepted that the prefrontal cortex, amygdala, anterior cingulate cortex, hippocampus, and insula participate in the majority of emotional processes. New imaging technologies and molecular biology discoveries are expanding further the frontiers of knowledge in this arena. The advancements of knowledge on the interplay between the human brain and emotions came about as the legacy of the pioneers mentioned in this field. The aim of this paper is to describe the historical evolution of the scientific understanding of interconnections between the human brain, behaviour, and emotions.
Cell Intrinsic Roles of Apoptosis-Associated Speck-Like Protein in Regulating Innate and Adaptive Immune Responses
Authors: Hassan Hoda , Amer Amal O.
Published: December 2011

The role of apoptosis-associated speck-Like protein (ASC) in the assembly of the inflammasome complex within macrophages has been elucidated in several studies. In this particular role, ASC functions as an adaptor protein by linking nod-like receptors (NLRs) and procaspase-1, thereby leading to the activation of caspase-1 to cleave inflammatory cytokines IL-1βand IL-18 and inducing pyroptosis. It has been noted that ASC maintains inflammasome-independent roles, including but not limited to controlling the expression of Dock2 and mitogen-activated protein kinases (MAPK/ERK2) and regulating the NF-κB pathway. This paper will emphasize the major roles of ASC during pathogen infection, the mechanisms by which it mediates inflammation, and discuss its more recently discovered functions.
A CCCH-Type Zinc Finger Nucleic Acid-Binding Protein Quantitatively Confers Resistance against Rice Bacterial Blight Disease
Authors: Deng Hanqing , 卿 邓汉 , Liu Hongbo , 波 刘红 , Li Xianghua , 花 李香 , Xiao Jinghua , 华 肖景 , Wang Shiping , 平 王石
Published: December 2011

Bacterial blight is a devastating disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv oryzae (Xoo). Zinc finger proteins harboring the motif with three conserved cysteine residues and one histidine residue (CCCH) belong to a large family. Although at least 67 CCCH-type zinc finger protein genes have been identified in the rice genome, their functions are poorly understood. Here, we report that one of the rice CCCH-type zinc finger proteins, C3H12, containing five typical CX8-CX5-CX3-H zinc finger motifs, is involved in the rice-Xoo interaction. Activation of C3H12 partially enhanced resistance to Xoo, accompanied by the accumulation of jasmonic acid (JA) and induced expression of JA signaling genes in rice. In contrast, knockout or suppression of C3H12 resulted in partially increased susceptibility to Xoo, accompanied by decreased levels of JA and expression of JA signaling genes in rice. C3H12 colocalized with a minor disease resistance quantitative trait locus to Xoo, and the enhanced resistance of randomly chosen plants in the quantitative trait locus mapping population correlated with an increased expression level of C3H12. The C3H12 protein localized in the nucleus and possessed nucleic acid-binding activity in vitro. These results suggest that C3H12, as a nucleic acid-binding protein, positively and quantitatively regulates rice resistance to Xoo and that its function is likely associated with the JA-dependent pathway.
The RPT2 Subunit of the 26S Proteasome Directs Complex Assembly, Histone Dynamics, and Gametophyte and Sporophyte Development inArabidopsis
Authors: Lee Kwang-Hee , Minami Atsushi , Marshall Richard S. , Book Adam J. , Farmer Lisa M. , Walker Joseph M. , Vierstra Richard D.
Published: December 2011

The regulatory particle (RP) of the 26S proteasome contains a heterohexameric ring of AAA-ATPases (RPT1-6) that unfolds and inserts substrates into the core protease (CP) for degradation. Through genetic analysis of the Arabidopsis thaliana gene pair encoding RPT2, we show that this subunit plays a critical role in 26S proteasome assembly, histone dynamics, and plant development. rpt2a rpt2b double null mutants are blocked in both male and female gamete transmission, demonstrating that the subunit is essential. Whereas rpt2b mutants are phenotypically normal, rpt2a mutants display a range of defects, including impaired leaf, root, trichome, and pollen development, delayed flowering, stem fasciation, hypersensitivity to mitomycin C and amino acid analogs, hyposensitivity to the proteasome inhibitor MG132, and decreased 26S complex stability. The rpt2a phenotype can be rescued by both RPT2a and RPT2b, indicative of functional redundancy, but not by RPT2a mutants altered in ATP binding/hydrolysis or missing the C-terminal hydrophobic sequence that docks the RPT ring onto the CP. Many rpt2a phenotypes are shared with mutants lacking the chromatin assembly factor complex CAF1. Like caf1 mutants, plants missing RPT2a or reduced in other RP subunits contain less histones, thus implicating RPT2 specifically, and the 26S proteasome generally, in plant nucleosome assembly.
Possible Host Adaptation as an Evolution Factor of Cowpea aphid‐borne mosaic virus Deduced by Coat Protein Gene Analysis
Authors: Nicolini Cícero , Rabelo Filho Francisco A. C. , Resende Renato O. , Andrade Genira. P. , Kitajima Elliot W. , Pio‐Ribeiro Gilvan , Nagata Tatsuya
Published: December 2011

Cowpea aphid‐borne mosaic virus (CABMV) causes major diseases in cowpea and passion flower plants in Brazil and also in other countries. CABMV has also been isolated from leguminous species including, Cassia hoffmannseggii, Canavalia rosea, Crotalaria juncea and Arachis hypogaea in Brazil. The virus seems to be adapted to two distinct families, the Passifloraceae and Fabaceae. Aiming to identify CABMV and elucidate a possible host adaptation of this virus species, isolates from cowpea, passion flower and C. hoffmannseggii collected in the states of Pernambuco and Rio Grande do Norte were analysed by sequencing the complete coat protein genes. A phylogenetic tree was constructed based on the obtained sequences and those available in public databases. Major Brazilian isolates from passion flower, independently of the geographical distances among them, were grouped in three different clusters. The possible host adaptation was also observed in fabaceous‐infecting CABMV Brazilian isolates. These host adaptations possibly occurred independently within Brazil, so all these clusters belong to a bigger Brazilian cluster. Nevertheless, African passion flower or cowpea‐infecting isolates formed totally different clusters. These results showed that host adaptation could be one factor for CABMV evolution, although geographical isolation is a stronger factor.
Evaluation of Hydrangea macrophylla for Resistance to Leaf‐Spot Diseases
Authors: Mmbaga Margaret T. , Kim Mee‐Sook , Mackasmiel Lucas , Li Yonghao
Published: December 2011

Garden hydrangea (Hydrangea macrophylla) is a popular ornamental plant that can be devastated by leaf‐spot diseases. Information is needed to determine susceptibility of commercial cultivars to leaf‐spot diseases. To address this need, 88 cultivars of H. macrophylla were evaluated for their resistance to leaf‐spot diseases in full‐shade (2007–2008), full‐sun (2007–2008) and partial‐shade (2009–2010) environments in McMinnville, TN, USA. Ten cultivars [‘Ami Pasquier’, ‘Ayesha’, ‘Blue Bird’, ‘Forever Pink’, ‘Fuji Waterfall’ (‘Fujinotaki’), ‘Miyama‐yae‐Murasaki’, ‘Seafoam’, ‘Taube’, ‘Tricolor’ and ‘Veitchii’] were rated resistant (R) or moderately resistant to leaf spot under each of the three environments. In 2007–2008, approximately 51% of the cultivars were rated R in full shade, but only 5% were R in full sun. In 2009–2010, only 1% of the cultivars were rated R in partial shade. Although environmental parameters including temperature and rainfall influence disease severity and host reaction, a shaded environment was least favourable for leaf‐spot disease development, which demonstrates that establishing hydrangea in shaded environment can be an effective tool along with cultivar selection for managing leaf‐spot diseases on hydrangea. Six pathogens, Corynespora cassiicola, Cercospora spp., Myrothecium roridum, Glomerella cingulata (Anamorph: Colletotrichum gloeosporioides), Phoma exigua and Botrytis cinerea, were associated with leaf‐spot diseases of garden hydrangea. Of the leaf‐spot pathogens, C. cassiicola was most frequently isolated (55% of all isolates), followed by Cercospora spp. (20%) and other pathogens (25%). Because symptoms attributed to each leaf‐spot pathogen were similar, cultivars were selected for resistance to multiple leaf‐spot pathogens.