bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD-HIT: accelerated for clustering the next-generation sequencing data
Authors: Fu Limin , Niu Beifang , Zhu Zhengwei , Wu Sitao , Li Weizhong 
Published: October 2012

Abstract
Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions.
Availability: http://cd-hit.org.
Contact: liwz@sdsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Gladiolus Corm Rot Caused by Fusarium proliferatum in Oman
Authors: Mahmooli I. H. Al , Balushi F. Al , Doyle O. , Sadi A. M. Al , Deadman M. L. 
Published: October 2012

Hybrid gladiolus varieties have potential as a major ornamental crop in Oman. Grown for the cut-flower industry, their production has increased significantly in recent years. In 2010, during a field trial of two hybrid varieties (Red Majesty and Mascagni) grown in sandy soil at Al Moballah, Muscat, approximately 3% of Red Majesty plants and 12% of Mascagni plants showed signs of wilting and yellowing prior to plant death. In all cases, tissue taken from 20 diseased corms yielded Fusarium-like colonies on potato dextrose agar (PDA). Colonies were light to dark purple in color with dense and abundant aerial mycelium; macroconidia were 33.8 × 4.8 μm with 3 to 5 septa per spore; microconidia were 13.5 × 4.8 μm with 0 to 1 septa per spore and were in chains (mean of 50 spores in both cases). No chlamydospores were observed. In vitro characters and spore measurements conformed to previously described features of Fusarium proliferatum (Matsushima) Nirenberg (2). Mycelial plugs (5 mm in diameter) were taken from 5-day-old cultures of F. proliferatum grown on 2.5% PDA and wrapped on the base of Gladiolus corms using Parafilm and wet cotton. The Parafilm was removed after 7 days of inoculation. The corms were kept in moistened polythene bags for and symptoms were recorded. Control corms were inoculated using PDA (1). Artificial inoculations resulted in rot symptoms on all corms within 14 days and fungal colonies identical to initial isolations were recovered from artificially infected corms. Rotting was not observed in corms inoculated using PDA alone. Identification of F. proliferatum was confirmed using sequences of the internal transcribed spacer (ITS) of the ribosomal DNA (ITS1 and ITS4 primers) and sequences of the translation elongation factor alpha (TEF-1) gene (EF-1-986 and EF-728 primers). The ITS and TEF-1 sequences were found to share 99.8% and 99.6% nucleotide similarity to previously published sequences of the ITS (HQ113948) and EF (JN092351) regions of F. proliferatum in GenBank, respectively. The ITS sequence of one isolate was assigned GenBank Accession No. JN86006. To our knowledge, this is the first report of the occurrence of F. proliferatum in Oman or in the Arabian Peninsula. References: (1) C. Linfield. Ann. Appl. Biol. 121:175, 1983. (2) P. E. Nelson et al. Fusarium Species: An Illustrated Manual for Identification. Pennsylvania State University Press, USA, 1983.
First Report of Orobanche purpurea on Achillea wilhelmsii in Iran
Authors: Yousefi A. R. , Jamshidi K. , Oveisi M. , Karimojeni H. , Pouryosef M. 
Published: October 2012

Achillea wilhelmsii C. Koch (Asteraceae) is a wild herb widely disturbed in Iran and known locally as yarrow. This plant is an important medicinal plant and it has been used for its analgesic, antiphlogistic, antispasmodic, and antibacterial effects in Iranian folk medicine. Field surveys revealed infestations of yarrow broomrape, Orobanche purpurea Jacq., on A. wilhelmsii plants in two locations in province of Zanjan (Zanjan, 36°37′19.85″ N, 48°27′16.87″ E, 1,707.4 m elevation, and Qolabar, 36°19′19.85″ N, 48°19′16.41″ E, 1,663.9 m elevation) in northwestern Iran in May 2012. The annual mean air temperature and the average maximum and minimum air temperatures were 11, 18, and 4°C, respectively. The annual mean precipitation was 298 mm. The infestation of A. wilhelmsii was confirmed by verifying the attachment of the yarrow broomrape to the A. wilhelmsii roots. Broomrape plant heights were between 24 and 37 cm. The stems were erect, unbranched, slender, and swollen near the base at contact with host, 0.5 to 10 mm diameter. The leaves were reduced to scale or bracts up to 10 to 15 mm long. The flowers were in dense terminal spikes, usually restricted to the top third or half of the shoot. There was one bract and two bracteoles surrounding each flower. The bracts measured 7 to 10 mm, had ovate lanceolates shorter than the calyces, and lanceolate bracteoles were 5 to 10 mm. The calyces were gamosepalous, entire, and whitish. Corollas were 13 to 18 mm long, and were dull bluish-purple with dark veins, suffused with whitish-yellow at the base. The upper part was slightly curved forwards. Stamens were epipetalous, inserted 4 to 7 mm above the corolla base, with filaments glabrous. The anthers were glabrous along sutures. Stigma lobes were white. Fruit was an oval capsule, 0.9 to 10 mm. Botanists at the College of Agriculture of Zanjan University confirmed the identity of O. purpurea. A. millefolium has been reported as a host plant for yarrow broomrape (1,2). However, to our knowledge, this is the first report of yarrow broomrape on A. wilhelmsii in Iran. Since production and farming of A. wilhelmsii as a medicinal plant has recently started on a commercial scale in Iran, the parasite weed could pose a serious threat to production of this plant. References: (1) B. Prajs. Biodiv. Res. Conserve. 17:33, 2010. (2) J. Rumsey and S. L. Jury. Watsonia. 18:257, 1991.
Excision of the Posterior Longitudinal Ligament During Anterior Cervical Corpectomy
Authors: Daubs Michael D. , Patel Alpesh A. , Lawrence Brandon D. , Brodke Darrel S. 
Published: October 2012

Study Design:
An in vitro biomechanical study of the cervical spine.

Objective:
To evaluate the biomechanical significance of the posterior longitudinal ligament (PLL) after anterior cervical corpectomy and reconstruction with a strut graft and anterior plate.

Summary of Background Data:
Routine excision of the PLL during anterior cervical corpectomy is controversial. Many surgeons believe that maintaining the PLL after cervical corpectomy adds stability to the reconstruction, whereas others believe it can be excised without sequelae. There are no biomechanical studies to our knowledge evaluating the biomechanical significance of excising the PLL during corpectomy and whether this affects the stability of a reconstruction consisting of a strut graft and anterior plate. The purpose of this study was to evaluate the biomechanical effects of PLL excision during a complete anterior cervical corpectomy reconstructed with a strut graft and anterior plate.

Methods:
Seven human cadaveric fresh-frozen cervical spines C2–T1 were tested for range of motion before surgery and reconstruction. A complete C6 corpectomy was performed and an interbody strut spacer with load cell was placed along with an anterior plate. Range of motion was measured with ±2.5 Nm of torque in flexion-extension, lateral bending, and axial rotation. Load-sharing data were recorded with incremental axial loads. The PLL was excised and range of motion and load-sharing testing was repeated.

Results:
There were no significant differences in range of motion or load sharing with an anterior corpectomy and reconstruction after PLL excision.

Conclusions:
Excision of the PLL during anterior cervical corpectomy reconstructed with a strut graft and anterior plate does not significantly affect the construct stability or load sharing of the graft.
Comparative analysis of PET findings and clinical outcome in patients with primary mediastinal seminoma
Authors: Koizumi Tomonobu , Katou Akane , Ikegawa Kayoko , Kosaka Mitsuru , Tateishi Kazunari , Yokoyama Toshiki , Ushiki Atsuto , Kanda Shintaro , Tsushima Kenji , Yamamoto Hiroshi , Hanaoka Masayuki , Kubo Keishi , Yoshida Kazuo , Oguchi Kazuhiko 
Published: October 2012

AbstractBackgroundPrimary mediastinal seminoma is a rare neoplasm. Cisplatin‐based chemotherapy is the standard treatment, but management of post‐chemotherapy seminoma residuals is still controversial. We encountered four cases of primary mediastinal seminoma and reviewed the clinical characteristics and outcomes, focusing on tumor size and F‐18 fluorodeoxyglucose positron emission tomography (FDG‐PET) findings after chemotherapy.MethodsA retrospective review was performed of four consecutive patients with primary mediastinal seminoma treated in our institution between 2006 and 2010. All patients were young adult males with a median age of 31.3 years (range: 20–46 years). All patients were treated with three to four cycles of a combination of cisplatin, bleomycin, and etoposide, and FDG‐PET was performed after chemotherapy.ResultsThe response to chemotherapy was good in all patients. After chemotherapy, the findings of the FDG‐PET were negative in three subjects. Two of the patients, with tumors measuring over 30 mm, underwent surgical resection for the residual mass and revealed necrotic tissues and no viable cells. A third patient remained stable without salvage surgery. The size of the residual mass in the remaining patient was less than 30 mm, but the FDP‐PET result was positive and the mass considered inoperable because of the involvement of large vessels. Subsequently, radiotherapy was added for the residual tumor, but disease progression was seen seven months after the initiation of chemotherapy.ConclusionsFDG‐PET findings after chemotherapy could be useful as a tool for the prediction of viable residual tumor in post chemotherapy residual mediastinal seminoma.
Microsatellite variation in the equine MHC
Authors: Brinkmeyer‐Langford C. L. , Cai J. J. , Gill C. A. , Skow L. C. 
Published: October 2012

SummaryGenes within the major histocompatibility complex (MHC) encode proteins involved in innate and adaptive immune responses. Genetic variation in this region can influence the immune response of an individual animal to challenges from a variety of pathogens; however, a complete documentation of genetic variation in the MHC is lacking for most domestic animals, including horses. To provide additional genetic markers for study of the horse MHC, or ELA (equine lymphocyte antigen), we identified 37 polymorphic microsatellite repeats in ELA and used these variations separately and together with published SNPs to investigate linkage disequilibrium (LD) and haplotype structure in a sample of Thoroughbred horses. ELA SNPs alone detected little LD, but microsatellites, either separately or combined with SNPs, revealed substantially more LD. A subset of markers in very high LD across the breadth of ELA may be predictive of structural polymorphisms or linked epistases that are important drivers of haplotype structure in Thoroughbreds.
The Prevalence Of Cervical Regulatory T Cells in HPV‐Related Cervical Intraepithelial Neoplasia (CIN) Correlates Inversely with Spontaneous Regression of CIN
Authors: Kojima Satoko , Kawana Kei , Tomio Kensuke , Yamashita Aki , Taguchi Ayumi , Miura Shiho , Adachi Katsuyuki , Nagamatsu Takeshi , Nagasaka Kazunori , Matsumoto Yoko , Arimoto Takahide , Oda Katsutoshi , Wada‐Hiraike Osamu , Yano Tetsu , Taketani Yuji , Fujii Tomoyuki , Schust Danny J. , Kozuma Shiro 
Published: October 2012

ProblemLocal adaptive cervical regulatory T cells (Tregs) are the most likely direct suppressors of the immune eradication of cervical intraepithelial lesion (CIN). PD‐1 expression on T cells induces Tregs. No studies have quantitatively analyzed the Tregs and PD‐1+ cells residing in CIN lesions.Method of studyCervical lymphocytes were collected using cytobrushes from CIN patients and analyzed by FACS analysis. Comparisons were made between populations of cervical Tregs and PD‐1+ CD4+ T cells in CIN regressors and non‐regressors.ResultsA median of 11% of cervical CD4+ T cells were Tregs, while a median of 30% were PD‐1+ cells. The proportions of cervical CD4+ T cells that were Tregs and/or PD‐1+ cells were significantly lower in CIN regressors when compared with non‐regressors.ConclusionsThe prevalence of cervical tolerogenic T cells correlates inversely with spontaneous regression of CIN. Cervical Tregs may play an important role in HPV‐related neoplastic immunoevasion.
Parenting and problem behaviors in children of substance abusing parents
Authors: Burlew A. Kathleen , Johnson Candace , Smith Stephanie , Sanders Alexis , Hall Ritchie , Lampkin Beatrice , Schwaderer Mary 
Published: October 2012

BackgroundThis study examined parenting practices, parental stress, and problem behaviors among urban Children of Substance Abusing Parents.MethodOne hundred and seven children completed the Child Rating Scale and the Children's Depression Inventory. Parents completed the Parenting Practices Scale‐Parent Version, Parenting Stress Index, and internalizing and externalizing scales on the Parent Observation of Classroom Adaptation.ResultsStructural Equation Modeling findings support an indirect effects pathway in which unfavorable parenting practices predict parental stress and parental stress predicts internalizing and externalizing behaviors.ConclusionThe results argue for assessing parental stress and including activities to improve the parent‐child bond in family intervention programs.
Prognostic value of tgfb1 protein in endometrioid adenocarcinoma
Authors: Soufla Giannoula , Sifakis Stavros , Porichis Filippos , Spandidos Demetrios A. 
Published: October 2012

Eur J Clin Invest 2012AbstractBackground  Angiogenesis is a prerequisite for tumour development, progression and metastasis; however, its underlying molecular mechanisms in endometrial carcinoma are poorly understood.Design  In this study, the mRNA and protein expression profiles of two key regulators of angiogenesis, vascular endothelial growth factor (VEGF) and transforming growth factor beta‐1 (TGFB1), were evaluated by real‐time PCR and western blot analysis in 23 endometrial cancer tissue‐paired specimens (malignant vs. adjacent normal tissues). We aimed to investigate whether VEGF and TGFB1 serve as markers of the malignant transformation of the endometrium and whether VEGF or TGFB1 expression can constitute a useful prognostic marker of survival in patients with endometrial carcinoma.Results  Tissue‐pair analysis revealed VEGF transcriptional up‐regulation and TGFB1 mRNA down‐regulation as the most frequent transcriptional features. VEGF and TGFB1 mRNA were positively correlated (P < 0·001). VEGF protein levels were higher in endometrioid‐type tissue pairs (P = 0·047). TGFB1 protein and mRNA levels were negatively correlated (P = 0·042). TGFB1 protein expression was related to survival only in patients with endometrioid adenocarcinoma (P = 0·045).Conclusions  Tissue‐pair mRNA and protein analysis reveals VEGF transcriptional up‐regulation and TGFB1 down‐regulation that are correlated with the malignant transformation of the endometrium, while post‐transcriptional mechanisms control VEGF and TGFB1 protein. TGFB1 protein demonstrated a prognostic value only in endometrioid adenocarcinoma.
Acinetobacter baumannii FolD ligand complexes – potent inhibitors of folate metabolism and a re‐evaluation of the structure of LY374571
Authors: Eadsforth Thomas C. , Maluf Fernando V. , Hunter William N. 
Published: October 2012

The bifunctional N5,N10‐methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram‐negative pathogen Acinetobacter baumanni and determined high‐resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed.DatabaseThe coordinates have been deposited in the Protein Data Bank under accession numbers: 4B4U, 4B4V and 4B4W.Structured digital abstract

AbFolD and AbFolD bind by x-ray crystallography (View interaction)
Individual and combined effects of fish predation and bed disturbance on stream benthic communities: a streamside channel experiment
Authors: HERRMANN PETER B. , TOWNSEND COLIN R. , MATTHAEI CHRISTOPH D. 
Published: October 2012

Summary1. The composition and spatiotemporal dynamics of biological communities are influenced by biotic processes, such as predation and competition, but also by physical disturbances, such as floods in running waters. However, the interplay of disturbance with predation is still poorly understood, especially in frequently disturbed streams. Further, different predator species can affect prey communities in different ways depending on their feeding mode and efficiency.2. We investigated the individual and combined effects of flood‐induced bed disturbance and fish predation on the benthos for 4 weeks in 18 streamside channels fed by a flood‐prone New Zealand river. Bed movements caused by floods were simulated by tumbling the substratum in half the channels. Six channels each were stocked with introduced brown trout (Salmo trutta) or native upland bully (Gobiomorphus breviceps) or had fish excluded. We studied algal biomass and both invertebrate density and daytime activity on surface stones on several dates after the disturbance, invertebrate community composition in the substrata of the entire channels on day 28 and leaf decomposition rates over the 28‐day period.3. Disturbance affected algal biomass and density, richness and activity of surface stone invertebrates, and overall density and richness of channel invertebrates. Presence or absence of fish, by contrast, did not influence overall invertebrate standing stocks when subsurface substrata were included but did affect invertebrate densities on surface stones in 45% of all analysed cases and invertebrate activity on surface stones in all cases. Leaf decomposition rates were not influenced at all by the experimental manipulations.4. Native upland bullies featured more often than exotic brown trout in causing invertebrate density changes and equally often in causing changes to grazer behaviour. Overall, our results imply that fish predation can have strong effects on the benthic invertebrate community in frequently disturbed streams, especially via behavioural changes.
Concordance between realised and fundamental niches in three IberianSigaraspecies (Hemiptera: Corixidae) along a gradient of salinity and anionic composition
Authors: CARBONELL J. A. , MILLÁN A. , VELASCO J. 
Published: October 2012

Summary1. We test the hypothesis that the physiological tolerance of corixids for saline conditions determines, at least partially, their occurrence along a salinity gradient that encompasses a variety of anionic compositions.2. Three species ofSigara,S. nigrolineata(fresh waters),S. scripta(hyposaline waters) andS. selecta(mesosaline and hypersaline waters) were selected, and it was predicted that species occurring in the most saline waters would be ion regulation specialists that are more tolerant of higher salinity, while species living in fresh or hyposaline waters would be generalist regulators in relation to different anions, and therefore less tolerant of higher salinity.3. Niche breadth was quantified using field data for both water conductivity and anionic composition (realised niche). In addition, physiological tolerance in relation to conductivity and anionic composition (fundamental niche) was estimated in laboratory tests using eggs, nymphs and adults of all species.4. Sigara nigrolineataadults showed the most limited conductivity tolerance and were generalists in relation to different anionic water compositions.Sigara scriptademonstrated tolerance of hyposaline and mesosaline waters and higher survival rates in sulphated waters.Sigara selectawas the only species occupying hypersaline waters that showed a preference for anion chloride.5. Sigara scriptawas the only species coexisting with the other two species. This can be explained by the overlap found in conductivity and anionic composition niche dimensions at the lower (S. nigrolineata) and upper (S. selecta) tolerance limits.6. Young life‐stages of the species showed similar responses but less tolerance of higher salinity than adults; this was the case for eggs ofS. nigrolineataand nymphs ofS. scriptaandS. selecta.7. Physiological limitations were not found in relation to fresh and less saline waters inS. selecta,so other factors, probably involving biotic interactions, may play an important role in this species.
Interobserver agreement among pathologists regarding core tissue specimens obtained with a new endoscopic ultrasound histology needle; a prospective multicentre study in 50 cases
Authors: Petrone Maria Chiara , Poley Jan‐Werner , Bonzini Matteo , Testoni Pier Alberto , Abdulkader Ihab , Biermann Katharina , Monges Genevieve , Rindi Guido , Doglioni Claudio , Bruno Marco J , Giovannini Marc , Iglesias‐Garcia Julio , Larghi Alberto , Arcidiacono Paolo Giorgio 
Published: October 2012

AimTo evaluate the interobserver agreement among pathologists in grading the quality of specimens obtained with a new 19‐gauge endoscopic ultrasound histology needle.Methods and resultsThis multicentre prospective study involved 50 slides prepared using material obtained with the new needle. Five experienced pathologists independently reviewed all of the samples, and made assessments of the following features: the presence of a core, the adequacy of the specimen, the interpretability of the specimen, and the possibility of performing additional analyses using the material. Interobserver agreement, determined by Fleiss' kappa statistic and 95% confidence intervals (CIs), was used as the primary outcome measure. Overall, the presence of a core was reported in 88% of cases with good agreement among the pathologists (κ = 0.61; 95% CI 0.52–0.70). The specimens were adequate in 91.2% of cases, and Fleiss' κ was 0.73 (95% CI 0.61–0.81). The interpretation of the specimens was reported to be ‘easy’ in approximately 87% of cases, with moderate agreement among the pathologists (κ = 0.44; 95% CI 0.35–0.53). The possibility of performing additional analyses from the same sample was rated as positive in approximately 91%, with good agreement (κ = 0.66; 95% CI 0.58–0.75).ConclusionsThere was excellent interobserver agreement among pathologists in the assessment of the histological material, especially with regard to sample adequacy.