bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scaffolding pre-assembled contigs using SSPACE
Authors: Boetzer Marten , Henkel Christiaan V. , Jansen Hans J. , Butler Derek , Pirovano Walter 
Published: December 2010

Abstract
Summary: De novo assembly tools play a main role in reconstructing genomes from next-generation sequencing (NGS) data and usually yield a number of contigs. Using paired-read sequencing data it is possible to assess the order, distance and orientation of contigs and combine them into so-called scaffolds. Although the latter process is a crucial step in finishing genomes, scaffolding algorithms are often built-in functions in de novo assembly tools and cannot be independently controlled. We here present a new tool, called SSPACE, which is a stand-alone scaffolder of pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. SSPACE shows promising results on both prokaryote and eukaryote genomic testsets where the amount of initial contigs was reduced by at least 75%.
Availability: www.baseclear.com/bioinformatics-tools/.
Contact: walter.pirovano@baseclear.com
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of a Group 16SrII Phytoplasma Associated with Witches'-Broom of Eggplant in Oman
Authors: Al-Subhi A. M. , Al-Saady N. A. , Khan A. J. , Deadman M. L. 
Published: December 2010

Eggplant (Solanum melongena L.) belongs to the family Solanaceae and is an important vegetable cash crop grown in most parts of Oman. In February 2010, plants showing phyllody symptoms and proliferation of shoots resembling those caused by phytoplasma infection were observed at Khasab, 500 km north of Muscat. Total genomic DNA was extracted from healthy and two symptomatic plants with a modified (CTAB) buffer method (2) and analyzed by direct and nested PCR with universal phytoplasma 16S rDNA primers P1/P7 and R16F2n/ R16R2, respectively. PCR amplifications from all infected plants yielded an expected product of 1.8 kb with P1/P7 primers and a 1.2-kb fragment with nested PCR, while no products were evident with DNA from healthy plants. Restriction fragment length polymorphism (RFLP) profiles of the 1.2-kb nested PCR products of two eggplant phyllody phytoplasma and five phytoplasma control strains belonging to different groups used as positive control were generated with the restriction endonucleases RsaI, AluI, Tru9I, T-HB8I, and HpaII. The eggplant phytoplasma DNA yielded patterns similar to alfalfa witches'-broom phytoplasma (GenBank Accession No. AF438413) belonging to subgroup 16SrII-D, which has been recorded in Oman (1). The DNA sequence of the 1.8-kb direct PCR product was deposited in GenBank (Accession No. HQ423156). Sequence homology results using BLAST revealed that the eggplant phyllody phytoplasma shared >99% sequence identity with Scaevola witches'-broom phytoplasma (Accession No. AB257291.1), eggplant phyllody phytoplasma (Accession No. FN257482.1), and alfalfa witches'-broom phytoplasma (Accession No. AY169323). The RFLP and BLAST results of 16S rRNA gene sequences confirm that eggplant phyllody phytoplasma is similar to the alfalfa phytoplasma belonging to subgroup 16SrII-D. To our knowledge, this is the first report of a phytoplasma of the 16SrII-D group causing witches'-broom disease on eggplant in Oman. References: (1) A. J. Khan et al. Phytopathology 92:1038, 2002. (2) M. A. Saghai-Maroof et al. Proc. Natl. Acad. Sci. USA, 81:8014, 1984.
Cost‐effectiveness of plant and animal biodiversity indicators in tropical forest and agroforest habitats
Authors: Kessler Michael , Abrahamczyk Stefan , Bos Merijn , Buchori Damayanti , Putra Dadang Dwi , Robbert Gradstein S. , Höhn Patrick , Kluge Jürgen , Orend Friederike , Pitopang Ramadhaniel , Saleh Shahabuddin , Schulze Christian H. , Sporn Simone G. , Steffan‐Dewenter Ingolf , Tjitrosoedirdjo Sri S. , Tscharntke Teja 
Published: December 2010

Summary 1. Biodiversity data are needed for conservation and management of tropical habitats, but the high diversity of these ecosystems makes comprehensive surveys prohibitively expensive and indicator taxa reflecting the biodiversity patterns of other taxa are frequently used. Few studies have produced the necessary comprehensive data sets to assess the quality of the indicator groups, however, and only one previous study has considered the monetary costs involved in sampling them. 2. We surveyed four plant groups (herbs, liverworts, trees, lianas) and eight animal groups (ants, canopy and dung beetles, birds, butterflies, bees, wasps and the parasitoids of the latter two) in 15 plots of 50 × 50 m2 each, representing undisturbed rainforest and two types of cacao agroforest in Sulawesi, Indonesia. We calculated three biodiversity measures (α and β diversity; percentage of species indicative of habitat conditions), built simple and multiple regression models among species groups (single groups, combinations of 2–11 groups, averaged relative diversity of all 12 groups), and related these to three measures of survey cost (absolute costs and two approaches correcting for different sampling intensities). 3. Determination coefficients (R2 values) of diversity patterns between single study groups were generally low (<0·25), while the consideration of several study groups increased R2 values to up to 0·8 for combinations of four groups, and to almost 1·0 for combinations of 11 groups. Survey costs varied 10‐fold between study groups, but their cost‐effectiveness (indicator potential versus monetary cost) varied strongly depending on the biodiversity aspect taken into account (α or β diversity, single or multiple groups, etc.). 4. Synthesis and applications. We found that increasing the number of taxa resulted in best overall biodiversity indication. We thus propose that the most cost‐efficient approach to general tropical biodiversity inventories is to increase taxonomic coverage by selecting taxa with the lowest survey costs.
Chromosomal instability in enterohaemorrhagic Escherichia coli O157:H7: impact on adherence, tellurite resistance and colony phenotype
Authors: Bielaszewska Martina , Middendorf Barbara , Tarr Phillip I. , Zhang Wenlan , Prager Rita , Aldick Thomas , Dobrindt Ulrich , Karch Helge , Mellmann Alexander 
Published: December 2010

SummaryTellurite (Tel) resistant enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is a global pathogen. In strain EDL933 Tel resistance (TelR) is encoded by duplicate ter cluster in O islands (OI) 43 and 48, which also harbour iha, encoding the adhesin and siderophore receptor Iha. We identified five EHEC O157:H7 strains that differentiate into large (L) colonies and small (S) colonies with high and low Tel minimal inhibitory concentrations (MICs) respectively. S colonies (Tel‐MICs ≤ 4 µg ml−1) sustained large internal deletions within the TelR OIs via homologous recombination between IS elements and lost ter and iha. Moreover, complete excision of the islands occurred by site‐specific recombination between flanking direct repeats. Complete excision of OI 43 and OI 48 occurred in 1.81 × 10−3 and 1.97 × 10−4 cells in culture, respectively; internal deletion of OI 48 was more frequent (9.7 × 10−1 cells). Under iron limitation that promotes iha transcription, iha‐negative derivatives adhered less well to human intestinal epithelial cells and grew slower than did their iha‐positive counterparts. Experiments utilizing iha deletion and complementation mutants identified Iha as the major factor responsible for these phenotypic differences. Spontaneous deletions affecting TelR OIs contribute to EHEC O157 genome plasticity and might impair virulence and/or fitness.
Tandem use of selenocysteine: adaptation of a selenoprotein glutaredoxin for reduction of selenoprotein methionine sulfoxide reductase
Authors: Kim Moon‐Jung , Lee Byung Cheon , Jeong Jaeho , Lee Kong‐Joo , Hwang Kwang Yeon , Gladyshev Vadim N. , Kim Hwa‐Young 
Published: December 2010

SummarySeveral engineered selenocysteine (Sec)‐containing glutaredoxins (Grxs) and their enzymatic properties have been reported, but natural selenoprotein Grxs have not been previously characterized. We expressed a bacterial selenoprotein Grx from Clostridium sp. (also known as Alkaliphilus oremlandii) OhILAs in Escherichia coli and characterized this selenoenzyme and its natural Cys homologues in Clostridium and E. coli. The selenoprotein Grx had a 200‐fold higher activity than its Sec‐to‐Cys mutant form, suggesting that Sec is essential for catalysis by this thiol‐disulfide oxidoreductase. Kinetic analysis also showed that the selenoprotein Grx had a 10‐fold lower Km than Cys homologues. Interestingly, this selenoenzyme efficiently reduced a Clostridium selenoprotein methionine sulfoxide reductase A (MsrA), suggesting that it is the natural reductant for the protein that is not reducible by thioredoxin, a common reductant for Cys‐containing MsrAs. We also found that the selenoprotein Grx could not efficiently reduce a Cys version of Clostridium MsrA, whereas natural Clostridium and E. coli Cys‐containing Grxs, which efficiently reduce Cys‐containing MsrAs, poorly acted on the selenoprotein MsrA. This specificity for MsrA reduction could explain why Sec is utilized in Clostridium Grx and more generally provides a novel example of the use of Sec in biological systems.
Posterior reversible encephalopathy syndrome after liver transplantation in children: A rare complication related to calcineurin inhibitor effects
Authors: Santos Maria M. , Tannuri Ana Cristina A. , Gibelli Nelson E. , Ayoub Ali A. , Maksoud‐Filho João G. , Andrade Wagner C. , Velhote Manoel C. P. , Silva Marcos M. , Pinho Maria L. , Miyatani Helena T. , Susuki Liza , Tannuri Uenis 
Published: December 2010

Santos MM, Tannuri ACA, Gibelli NE, Ayoub AA, Maksoud‐Filho JG, Andrade WC, Velhote MCP, Silva MM, Pinho ML, Miyatani HT, Suzuki L, Tannuri U. Posterior reversible encephalopathy syndrome after liver transplantation in children: A rare complication related to calcineurin inhibitor effects. Pediatr Transplantation 2011: 15:157–160. © 2010 John Wiley & Sons A/S.Abstract:  PRES is a neuroclinical and radiological syndrome that results from treatment with calcineurin inhibitor immunosuppressives. Severe hypertension is commonly present, but some patients may be normotensive. We report herein two children who received liver transplants, as treatment for biliary atresia in the first case and for Alagille’s syndrome in the second one. In the early postoperative, both patients presented hypertension and seizures. In both cases, the image findings suggested the diagnosis of PRES. The CT scan showed alterations in the posterior area of the brain, and brain MRI demonstrated parietal and occipital areas of high signal intensity. Both children were treated by switching the immunosuppressive regimen and controlling arterial blood pressure. They displayed full recuperation without any neurologic sequelae. Probably, the pathophysiology of PRES results from sparse sympathetic innervation of the vertebrobasilar circulation, which is responsible for supplying blood to the posterior areas of the brain. In conclusion, all liver‐transplanted children who present with neurological symptoms PRES should be considered in the differential diagnosis, although this is a rare complication. As treatment, we recommend rigorous control of arterial blood pressure and switching the immunosuppressive regimen.
Minimizing steroid use in pediatric kidney recipients
Authors: Grenda Ryszard 
Published: December 2010

Grenda R. Minimizing steroid use in pediatric kidney recipients. Pediatr Transplantation 2011: 15:32–36. © 2010 John Wiley & Sons A/S.Abstract:  Outcomes of pediatric kidney transplantation have improved significantly over the years, such that the majority of graft recipients survive to become adolescents and adults. In this article, the findings of some of the important trials that shaped the current therapeutic landscape of immunosuppression will be reviewed. As an evolving landscape, novel strategies are continuously being sought to address the significant challenges in pediatric transplantation. Among these challenges is the development of immunosuppressive strategies that not only minimize the risk of allograft rejection but also allow normal growth and developmental patterns in children. To that end, the growing clinical evidence that indicates that the use of steroid‐sparing regimens is effective will be reviewed. Finally, a brief description of the TWIST study will be provided. This large‐scale comparative study has been designed specifically to assess the effect of early steroid withdrawal on growth in pediatric renal transplant recipients. An overview of the preliminary analysis of the eagerly anticipated results of this landmark trial will also be provided.
Blood conservation and pain control in scoliosis corrective surgery: an online survey of UK practice
Authors: Bird Scott , McGill Neil 
Published: December 2010

SummaryBackground:  Discussion at local meetings led to the realization of the diversity in anaesthetic practice for pediatric and adolescent scoliosis surgery. This diversity was assessed using an online survey, the aim being to provoke discussion and highlight areas of future research.Methods:  Of the 24 centers practicing pediatric and adolescent scoliosis surgery, 21 completed questionnaires, a response rate of 88%.Results:  Blood conservation; the area of greatest clinical variability was seen in dosing regimes for Tranexamic acid. Thromboprophylaxis; both mechanical and pharmacological regimes showed wide range in both application and timing. Pain control; eight different types of postoperative pain relief were utilized across the centres, some in isolation but many in combination.Conclusions:  The results from our survey show wide variation nationally and hopefully will provoke discussion and ultimately national multi‐centred research to define best practice.
Fractal geometry of angular momentum evolution in near-Keplerian systems
Authors: Gürkan M. Atakan 
Published: December 2010

Abstract
In this Letter, we propose a method to study the nature of resonant relaxation in near-Keplerian systems. Our technique is based on measuring the fractal dimension of the angular momentum trails and we use it to analyse the outcome of N-body simulations. With our method, we can reliably determine the time-scale for resonant relaxation, as well as the rate of change of angular momentum in this regime. We find that growth of angular momentum is more rapid than random walk, but slower than linear growth. We also determine the presence of long-term correlations arising from the bounds on angular momentum growth. We develop a toy model that reproduces all essential properties of angular momentum evolution.
MEASUREMENTS OF NORMAL AND COLLATERAL CORONARY BLOOD FLOW BY CLOSE‐ARTERIAL AND INTRAMYOCARDIAL INJECTION OF KRYPTON85 AND XENON133
Authors: LINDER ERLAND 
Published: December 2010

ABSTRACTA recent method for measuring collateral blood flow in the myocardium of dogs was based on an analysis of the composite clearance of Krypton85 administered close‐arterially (Johansson, Linder and Seeman 1964, 1966). This method has been critically analysed and various sources of possible errors in the estimations are discussed.Comparisons between paired measurements by this technique and results obtained by recordings of the wash‐out rate of intramuscularly injected Xenon133 depots, in the well‐perfused and ischemic myocardial areas respectively, strongly suggest that the method is fairly accurate and reliable, despite the fact that it has obvious theoretical limitations.The results also reveal that the collateral flow to the ischemic area is not entirely uniform. Within a narrow border zone there is a steep reduction of blood flow, with a more gradual diminution towards central parts of the ischemic zone. This regional heterogeneity in collateral flow could not for several reasons, be analysed in exact detail from the composite curve alone, but was revealed by recordings of clearance of strictly localized, intramuscular tracer injections.Peak flow during reactive hyperemia could also be fairly satisfactorily measured, provided certain precautions were taken. The results suggest that it is, in addition, possible to make a fair estimation of the mass of the ischemic tissue from the composite curve.The method may prove to be useful in experimental studies designed to investigate different means for improving collateral blood supply to an ischemic myocardial area.
Unusual clinical presentations of new‐onset herpetic eye disease after ocular surgery
Authors: Jhanji Vishal , Ferdinands Mervyn , Sheorey Harsha , Sharma Namrata , Jardine Darren , Vajpayee Rasik B. 
Published: December 2010

AbstractPurpose:  To report five cases of new‐onset herpetic eye disease with unusual presentation after ocular surgery.Methods:  Herpetic eye disease was suspected in five cases, three after cataract surgery and two after lamellar corneal transplantation surgery. Of these, four cases presented within 2–6 weeks of surgery. The clinical presentation was in the form of an epithelial defect, suspected epithelial down growth, graft oedema with unexplained anterior chamber inflammation and graft–host interface infection. A swab for viral detection with real‐time polymerase chain reaction was performed in all the described cases.Results:  Herpes simplex disease was detected in all cases. All cases responded to the antiherpetic medications.Conclusions:  Our study shows that new‐onset herpetic eye disease may occur after cataract surgery and lamellar corneal transplantation, and a high index of suspicion may be necessary for the diagnosis in such cases.
The chromium isotopic composition of Almahata Sitta
Authors: QIN Liping , RUMBLE Douglas , ALEXANDER Conel M. O’D. , CARLSON Richard W. , JENNISKENS Peter , SHADDAD Muawia H. 
Published: December 2010

Abstract– Nine ureilitic fragments of the anomalous polymict ureilite Almahata Sitta have been analyzed for their Cr isotopic compositions. All the samples, including both nonmagnetic and magnetic portions, show essentially the same ε54Cr deficit (−0.77 ± 0.10), relative to the terrestrial Cr standard. This contrasts with the variable positive 54Cr anomalies observed for carbonaceous chondrites, but agrees with the values measured for eucrites, diogenites, and mesosiderites (Trinquier et al. 2007). This implies that, contrary to previous suggestions based on O isotopes, ureilites were not derived from any known carbonaceous chondrite parent body. Instead, the Almahata Sitta parent body may have accreted in a nebular region/environment similar to that of the howardite, eucrite, and diogenite (HED) parent body. In addition, the lack of variation in ε54Cr combined with variable O isotopic compositions in the meteorite fragments suggests that whatever process(es) caused the O isotopic heterogeneity of the solar system was probably not responsible for heterogeneity in ε54Cr. The samples show resolvable variations in ε53Cr (0.15–0.41) that are correlated with Mn/Cr ratios, suggesting that live 53Mn was present at the time of formation of Almahata Sitta. The isochron yields an initial 53Mn/55Mn value of 3.1 (±1.1) × 10−6, corresponding to an age of 4563.6 ± (2.2) Ma when related to U‐Pb and Mn‐Cr data for the D’Orbigny angrite. This age is consistent with the Mn‐Cr and Al‐Mg ages of two other polymict ureilites (Goodrich et al. 2010). Magmatic activity on the ureilites’ parent body seems to have postdated the formation of refractory inclusions by approximately 4–5 Ma.
Inhomogeneity of asteroid 2008 TC3 (Almahata Sitta meteorites) revealed through magnetic susceptibility measurements
Authors: KOHOUT Tomáš , JENNISKENS Peter , SHADDAD Muawia H. , HALODA Jakub 
Published: December 2010

Abstract– Magnetic susceptibility measurements were performed on freshly fallen Almahata Sitta meteorites. Most recovered samples are polymict ureilites. Those found in the first 4 months since impact, before the meteorites were exposed to rain, have a magnetic susceptibility in the narrow range of 4.92 ± 0.08 log 10−9 Am2 kg−1 close to the range of other ureilite falls 4.95 ± 0.14 log 10−9 Am2 kg−1 reported by Rochette et al. (2009). The Almahata Sitta samples collected 1 yr after the fall have similar values (4.90 ± 0.06 log 10−9 Am2 kg−1), revealing that the effect of 1 yr of terrestrial weathering was not severe. However, our reported values are higher than derived from polymict (brecciated) ureilites 4.38 ± 0.47 log 10−9 Am2 kg−1 (Rochette et al. 2009) containing both falls and finds, confirming that these are significantly weathered. Additionally, other fresh‐looking meteorites of nonureilitic compositions were collected in the Almahata Sitta strewn field. Magnetic susceptibility measurements proved to be a convenient nondestructive method for identifying nonureilitic meteorites among those collected in the Almahata Sitta strewn field, even among fully crusted. Three such meteorites, no. 16, 25, and 41, were analyzed and their composition determined as EH6, H5, and EL6, respectively (Zolensky et al. 2010). A high scatter of magnetic susceptibility values among small (<5 g) samples revealed high inhomogeneity within the 2008 TC3 material at scales below 1–2 cm.
In Vitro
Activity and Single-Step Mutational Analysis of Rifamycin SV Tested against Enteropathogens Associated with Traveler's Diarrhea and
Clostridium difficile
Authors: Farrell David J. , Putnam Shannon D. , Biedenbach Douglas J. , Moro Luigi , Bozzella Roberta , Celasco Giuseppe , Jones Ronald N. 
Published: December 2010

ABSTRACT

Rifamycin SV is a broad-spectrum, poorly absorbed antimicrobial agent that, when coupled with MMX technology, is being targeted for the oral treatment of traveler's diarrhea (TD) and
Clostridium difficile
-associated disease (CDAD). Rifamycin SV was tested for activity against 911 TD-associated enteropathogens and 30
C. difficile
isolates collected from several global surveillance studies. Rifamycin SV demonstrated similar antimicrobial activity levels against the
Enterobacteriaceae
, with MIC
50
values ranging from 32 to 128 μg/ml for all but one strain (an enterotoxigenic
Escherichia coli
at >512 μg/ml). For non-
Enterobacteriaceae
strains, MIC
50
values ranged from 2 to 8 μg/ml, with the exception of
Campylobacter
spp., for which all strains had MIC values of >512 μg/ml. Rifamycin SV also demonstrated excellent activity (MIC
50
of ≤0.03 μg/ml) against most
C. difficile
strains (including one hypervirulent NAP1 strain), and this activity was even superior to the potency observed for vancomycin, metronidazole, and rifaximin. In mutational passaging studies, rifamycin SV induced stable resistance and showed a mutation frequency in
E. coli
similar to that of rifampin. This study presents the potency of rifamycin SV for enteropathogens commonly recovered from patients with TD and CDAD. Additional
in vitro
and
in vivo
studies appear necessary to determine the utility of rifamycin SV as an oral agent for the prevention and treatment of TD and CDAD.
Interspecies Dissemination of the
bla
Gene Encoding PER-1 Extended-Spectrum β-Lactamase
Authors: Bae Il Kwon , Jang Sook Jin , Kim Juwon , Jeong Seok Hoon , Cho Byungkyu , Lee Kyungwon 
Published: December 2010

ABSTRACT

PER-1 extended-spectrum β-lactamase-producing Gram-negative bacilli are resistant to oxyimino-cephalosporins. However, the
bla
PER-1
gene has never been reported in
Klebsiella pneumoniae
. Here, we studied interspecies dissemination of the
bla
PER-1
gene by horizontal transfer of Tn
1213
among
Acinetobacter baumannii
,
Pseudomonas aeruginosa
, and
K. pneumoniae.
In a
K. pneumoniae
clinical isolate, the
bla
PER-1
gene was located on a 150-kbp incompatibility group A/C plasmid.