bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractObjectiveTo assess the frequency of balanced autosomal translocations in patients with primary amenorrhea in an Indian population.MethodsCytogenetic 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.ResultsThere 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.ConclusionAutosomal 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

AbstractAlthough 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.
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

Zusammenfassung
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

Abstract
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

Zusammenfassung
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

AbstractCEUS 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

Zusammenfassung
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.
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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
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

AbstractBacterial 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

AbstractThe 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

AbstractCowpea 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.