bluuebunny/crossref_metadata_2025_split huggingface dataset:
Striatal mitochondria in subjects with chronic undifferentiated vs. chronic paranoid schizophrenia
Authors: Somerville Shahza M. , Conley Robert R. , Roberts Rosalinda C. 
Published: September 2011

AbstractSchizophrenia (SZ) is a heterogeneous disease with a spectrum of symptoms, risk factors, and etiology. Abnormalities in mitochondria, the energy‐producing organelles of the cell, have been observed in mixed cohorts of subjects with SZ. The purpose of the present study was to determine if striatal mitochondria were differentially affected in two different DSM‐IV subgroups of SZ. Postmortem striatal tissue was examined from normal controls (NC), chronic paranoid SZs (SZP), and chronic undifferentiated SZs (SZU). Tissue was processed for calbindin immunohistochemistry to identify striosomal compartments, prepared for electron microscopy and analyzed using stereological methods. In both caudate and putamen, the density of mitochondria in the neuropil was decreased in SZP compared to both NCs and SZU. In the putamen, both the SZP and the SZU subgroups had fewer mitochondria per synapse than did NCs. When examining patch matrix compartments, striatal compartments associated with different circuitry and function, only the matrix exhibited changes. In the caudate matrix, the SZP subgroup had fewer mitochondria in the neuropil than did the SZU and NCs. In the putamen matrix, the SZP had fewer mitochondria in the neuropil as compared to NCs, but not the SZU. The numbers of mitochondria per synapse in both the SZP and the SZU groups were similar to each other and fewer than that of NCs. A decrease in mitochondrial density in the neuropil distinguishes the SZP from the SZU subgroup, which could be associated with the symptoms of paranoia and/or could represent a protective mechanism against some of the symptoms that are less pronounced in this subtype than in the SZU subgroup such as cognitive and emotional deficits. Synapse, 2012. © 2011 Wiley Periodicals, Inc.
Atmospheric stability and turbulence fluxes at Horns Rev—an intercomparison of sonic, bulk and WRF model data
Authors: Peña Alfredo , Hahmann Andrea N. 
Published: September 2011

ABSTRACTDirect estimations of turbulent fluxes and atmospheric stability were performed from a sonic anemometer at 50 m height on a meteorological mast at the Horns Rev wind farm in the North Sea. The stability and flux estimations from the sonic measurements are compared with bulk results from a cup anemometer at 15 m height and potential temperature differences between the water and the air above. Surface flux estimations from the advanced weather research and forecast (WRF) model are also validated against the sonic and bulk data. The correlation between the sonic and bulk estimates of friction velocity is high and the highest among all velocity comparisons. From the sonic–bulk–WRF inter‐comparison, it is found that the atmospheric stability measures at the sonic height tend to be closer to the neutral value than the WRF and bulk estimates, which are performed within an air layer closer to the surface, not only from a systematic bulk and WRF under‐prediction of the friction velocity when compared with the sonic value but also because of the lower magnitude of the sonic heat flux compared with that from the WRF simulations. Although they are not measured but parameterized or estimated, the bulk–WRF comparisons of friction velocity and 10 m wind speed show good agreement. It is also shown that on a long‐term basis, the WRF and bulk estimates of stability are nearly equal and that a correction towards a slightly stable atmospheric condition has to be applied to the long‐term wind profile at Horns Rev and at other locations over the North Sea, the correction being larger for points close to the coast. Copyright © 2011 John Wiley & Sons, Ltd.
Effect of Alcohol in Starch‐Thickened Fillings on the Storage Stability of Dark Chocolate Pralines
Authors: Böhme Birgit , Kretzschmar Rene , Schneider Yvonne , Fiala Petra , Rohm Harald 
Published: September 2011

AbstractCommercial praline shells made from dark chocolate were filled with a mixture of invert sugar syrup, wine distillate and sucrose, which was adjusted to a viscosity of approximately 4 Pa·s by addition of pregelatinized starch. The pralines which also contained malt extract were subjected to storage at 20 and 24 °C. The liquefaction rate induced by enzymes of the malt extract depended on ethanol (0–15% w/w) and moisture content (approximately 30%) of the filling, and on storage temperature. The decay of apparent viscosity immediately after adding malt extract was delayed when ethanol was present in the filling, implying that viscosity stability after mixing and during subsequent processing is improved. Softening of the praline shells and fat bloom formation also depended on the ethanol concentration of the filling. A cross‐comparison with praline shells which were filled with pure invert sugar syrup implies that the enzymes of the malt extract do not exhibit a negative influence on praline shell firmness. Electron micrographs give evidence that ethanol in contact with chocolate causes structural damage which results in a partial solubilization of praline shells.
MONTH OF BIRTH, SOCIOECONOMIC BACKGROUND AND HEIGHT IN RURAL CHINESE MEN
Authors: ZHANG WEIGUO 
Published: September 2011

SummaryThis study examines the effects of birth month and socioeconomic factors on height in rural Chinese men. The analysis of sample data of 833 adult men, 18–52 years of age, collected from 600 families in rural Hebei in 2005, shows that adult men born in winter months (November to January) are, on average, 1.04 cm shorter (p<0.01) than those born during the rest of the year. In addition to the conventional OLS regression models, the household fixed and random effects models also indicate that the month-of-birth effect exists when socioeconomic variables are controlled for. The birth-month effect on height is, however, smaller than effects of socioeconomic variables, including the household registration status, household economy and father's class status.
The efficacy of novel arylimidamides against Trypanosoma cruzi in vitro
Authors: DA SILVA CRISTIANE FRANÇA , DALIRY ANISSA , DA SILVA PATRÍCIA BERNARDINO , AKAY SENOL , BANERJEE MOLOY , FARAHAT ABDELBASSET A. , FISHER MARY K. , HU LAIXING , KUMAR ARVIND , LIU ZONGYING , STEPHENS CHAD E. , BOYKIN DAVID W. , CORREIA SOEIRO MARIA DE NAZARÉ 
Published: September 2011

SUMMARYThe present study aimed to determine the in vitro biological efficacy and selectivity of 7 novel AIAs upon bloodstream trypomastigotes and intracellular amastigotes of Trypanosoma cruzi. The biological activity of these aromatic compounds was assayed for 48 and 24 h against intracellular parasites and bloodstream forms of T. cruzi (Y strain), respectively. Additional assays were also performed to determine their potential use in blood banks by treating the bloodstream parasites with the compounds diluted in mouse blood for 24 h at 4°C. Toxicity against mammalian cells was evaluated using primary cultures of cardiac cells incubated for 24 and 48 h with the AIAs and then cellular death rates were determined by MTT colorimetric assays. Our data demonstrated the outstanding trypanocidal effect of AIAs against T. cruzi, especially DB1853, DB1862, DB1867 and DB1868, giving IC50 values ranging between 16 and 70 nanomolar against both parasite forms. All AIAs presented superior efficacy to benznidazole and some, such as DB1868, also demonstrated promising activity as a candidate agent for blood prophylaxis. The excellent anti-trypanosomal efficacy of these novel AIAs against T. cruzi stimulates further in vivo studies and justifies the screening of new analogues with the goal of establishing a useful alternative therapy for Chagas disease.
The Hybrid II assay: a sensitive and specific real-time hybridization assay for the diagnosis ofTheileria parvainfection in Cape buffalo (Syncerus caffer) and cattle
Authors: PIENAAR RONEL , POTGIETER FRED T. , LATIF ABDALLA A. , THEKISOE ORIEL M. M. , MANS BEN J. 
Published: September 2011

SUMMARYCorridor disease is an acute, fatal disease of cattle caused by buffalo-adaptedTheileria parva. This is a nationally controlled disease in South Africa and strict control measures apply for the movement of buffalo, which includes mandatory testing for the presence ofT. parvaand other controlled diseases. Accurate diagnosis of theT. parvacarrier state in buffalo using the official real-time hybridization PCR assay (Sibekoet al.2008), has been shown to be affected by concurrent infection withT.sp. (buffalo)-like parasites. We describe the Hybrid II assay, a real-time hybridization PCR method, which compares well with the official hybridization assay in terms of specificity and sensitivity. It is, however, not influenced by mixed infections ofT.sp. (buffalo)-like parasites and is as such a significant improvement on the current hybridization assay.
Toxoplasma gondii: the changing paradigm of congenital toxoplasmosis
Authors: LINDSAY D. S. , DUBEY J. P. 
Published: September 2011

SUMMARYResearchers have learned much concerning the population biology ofToxoplasma gondiiover the past 2 decades. It is now apparent that many atypical genotypes exist besides the typical 3 genotypes (type I, type II and type III) first described from samples from Europe and the United States. These genotypes can differ in pathogenicity and transmissibility from the typical genotypes that have been used in the majority of scientific research over the past 70 years. These differences impact much of what we used to believe as facts about congenital toxoplasmosis (CT) and will be important in developing new recommendations for prevention of CT and the monitoring of women at risk for developing CT. The present review highlights new information onT. gondiigenotypes and how this information will change the way we convey information about CT to pregnant women, physicians and students.
Involvement of sulfated glycosaminoglycans on the development and attachment of Trypanosoma cruzi to the luminal midgut surface in the vector, Rhodnius prolixus
Authors: GONZALEZ MARCELO S. , SILVA LUIZ-CLAUDIO F. , ALBUQUERQUE-CUNHA J. M. , NOGUEIRA NADIR F. S. , MATTOS DÉBORA P. , CASTRO DANIELE P. , AZAMBUJA PATRICIA , GARCIA ELOI S. 
Published: September 2011

SUMMARYIn the present study, we investigated the involvement of sulfated glycosaminoglycans in both the in vivo development and adhesion of T. cruzi epimastigotes to the luminal surface of the digestive tract of the insect vector, Rhodnius prolixus. Pre-incubation of T. cruzi, Dm 28c epimastigotes with heparin, chondroitin 4-sulfate, chondroitin 6-sulfate or protamine chloridrate inhibited in vitro attachment of parasites to the insect midgut. Enzymatic removal of heparan sulfate moieties by heparinase I or of chondroitin sulfate moieties by chondroitinase AC from the insect posterior midgut abolished epimastigote attachment in vitro. These treatments also reduced the labelling of anionic sites exposed at the luminal surface of the perimicrovillar membranes in the triatomine midgut epithelial cells. Inclusion of chondroitin 4-sulfate or chondroitin 6-sulfate and to a lesser extent, heparin, in the T. cruzi-infected bloodmeal inhibited the establishment of parasites in R. prolixus. These observations indicate that sulfated glycosaminoglycans are one of the determinants for both adhesion of the T. cruzi epimastigotes to the posterior midgut epithelial cells of the triatomine and the parasite infection in the insect vector, R. prolixus.
FLASH: fast length adjustment of short reads to improve genome assemblies
Authors: Magoč Tanja , Salzberg Steven L. 
Published: September 2011

Abstract
Motivation: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome.
Results: We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads &gt;99% of the time on simulated reads with an error rate of &lt;1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
Availability and Implementation: The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash.
Contact: t.magoc@gmail.com
survcomp: an R/Bioconductor package for performance assessment and comparison of survival models
Authors: Schröder Markus S. , Culhane Aedín C. , Quackenbush John , Haibe-Kains Benjamin 
Published: September 2011

Abstract
Summary: The survcomp package provides functions to assess and statistically compare the performance of survival/risk prediction models. It implements state-of-the-art statistics to (i) measure the performance of risk prediction models; (ii) combine these statistical estimates from multiple datasets using a meta-analytical framework; and (iii) statistically compare the performance of competitive models.
Availability: The R/Bioconductor package survcomp is provided open source under the Artistic-2.0 License with a user manual containing installation, operating instructions and use case scenarios on real datasets. survcomp requires R version 2.13.0 or higher. http://bioconductor.org/packages/release/bioc/html/survcomp.html
Contact: bhaibeka@jimmy.harvard.edu; mschroed@jimmy.harvard.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Protein–protein binding affinity prediction on a diverse set of structures
Authors: Moal Iain H. , Agius Rudi , Bates Paul A. 
Published: September 2011

AbstractMotivation: Accurate binding free energy functions for protein–protein interactions are imperative for a wide range of purposes. Their construction is predicated upon ascertaining the factors that influence binding and their relative importance. A recent benchmark of binding affinities has allowed, for the first time, the evaluation and construction of binding free energy models using a diverse set of complexes, and a systematic assessment of our ability to model the energetics of conformational changes.Results: We construct a large set of molecular descriptors using commonly available tools, introducing the use of energetic factors associated with conformational changes and disorder to order transitions, as well as features calculated on structural ensembles. The descriptors are used to train and test a binding free energy model using a consensus of four machine learning algorithms, whose performance constitutes a significant improvement over the other state of the art empirical free energy functions tested. The internal workings of the learners show how the descriptors are used, illuminating the determinants of protein–protein binding.Availability: The molecular descriptor set and descriptor values for all complexes are available in the Supplementary Material. A web server for the learners and coordinates for the bound and unbound structures can be accessed from the website: http://bmm.cancerresearchuk.org/~AffinityContact: paul.bates@cancer.org.ukSupplementary Information: Supplementary data are available at Bioinformatics online.
First Report of Squash Mosaic Virus in Ornamental Pumpkin in the Czech Republic
Authors: Svoboda J. , Leisova-Svobodova L. 
Published: September 2011

In August 2010, yellow mosaic and leaf deformation were observed on leaves of field planted ornamental pumpkin (Cucurbita pepo L. convar. microcarpina Grebenščikov) plants near Tasovice Village in the Znojmo District of the Czech Republic. These symptoms were typical of a virus infection. Nine leaf samples were collected and examined for the presence of commonly occurring cucurbit viruses by double-antibody sandwich (DAS)-ELISA. Eight samples were infected with Zucchini yellow mosaic virus (ZYMV), seven with Watermelon mosaic virus-2 (WMV-2), five with Cucumber mosaic virus (CMV), and two with Squash mosaic virus (SqMV). Some aphid species were observed on inspected plants but we did not carried out a search for vectors. SqMV isolates, Tas-1 and Tas-5, were also infected with ZYMV and WMV-2. SqMV was separated from the other viruses by mechanical inoculation onto the resistant plant species Cucumis sativus L. ‘Taichung Mou Gua-1’, which is resistant to ZYMV and WMV-2 (3). The virus was transmitted back to C. pepo plants, and DAS-ELISA used for testing for multiple viruses proved the presence of SqMV alone. A C. pepo leaf sample was examined by electron microscopy to validate the presence of the virus. Isometric particles of approximately 30 nm in diameter, corresponding in size and shape to the described particles of SqMV (2), were observed. The presence of SqMV was verified by reverse transcription (RT)-PCR using specific primers designed on the sequence for coat proteins of SqMV found in NCBI and EMBL databases (SqMV-F: TGTGTACAAGATTGGTGGAGATGC; SqMV-R: AGGCTTCTAAAGCGAACTGGG). The obtained amplicons of approximately 1,900 bp were sequenced (GenBank Accession No. JF922966), and by using nucleotide blast analysis (4), identified as a part of RNA-2 genome. Blast analysis showed that the Czech SqMV isolates, Tas-1 and Tas-5, were identical and similar to published SqMV sequences from the United States, Japan, and China. The highest similarity was found between the Czech isolates and one isolate from the United States (Accession No. M96148; E = 0, nucleotide sequence identity = 90%) and one from China (Accession No. AF059533; E = 0, nucleotide sequence identity = 90%). To our knowledge, this is the first report of a natural occurrence of SqMV in the Czech Republic. SqMV can be transmitted via infected seeds by as much as 35% (1); therefore, protection against epidemics should be based on clean seed programs. References: (1) M. Alvarez et al. Phytopathology 68:257, 1978. (2) H. M. Mazzone et al. Biochim. Biophys. Acta 55:164, 1962. (3) T. Wai et al. J. Hered. 88:454, 1997. (4) Z. Zhang et al. J. Comput. Biol. 7:203, 2000.
Paediatric B‐cell precursor acute lymphoblastic leukaemia with t(1;19)(q23;p13): clinical and cytogenetic characteristics of 47 cases from the Nordic countries treated according to NOPHO protocols
Authors: Andersen Mette K. , Autio Kirsi , Barbany Gisela , Borgström Georg , Cavelier Lucia , Golovleva Irina , Heim Sverre , Heinonen Kristina , Hovland Randi , Johannsson Johann H. , Johansson Bertil , Kjeldsen Eigil , Nordgren Ann , Palmqvist Lars , Forestier Erik 
Published: September 2011

SummaryThe translocation t(1;19)(q23;p13)/der(19)t(1;19) is a risk stratifying aberration in childhood B‐cell precursor acute lymphoblastic leukaemia (BCP ALL) in the Nordic countries. We have identified 47 children/adolescents with t(1;19)/der(19)t(1;19)‐positive BCP ALL treated on two successive Nordic Society of Paediatric Haematology and Oncology (NOPHO) protocols between 1992 and 2007 and have reviewed the clinical and cytogenetic characteristics of these cases, comprising 1·8% of all cases. The translocation was balanced in 15 cases (32%) and unbalanced in 29 cases (62%). The most common additional chromosome abnormalities were del(9p), i(9q), del(6q), and del(13q). The median age was 7 years, the median white blood cell (WBC) count was 16 × 109/l, and the female/male ratio was 1·2. The predicted event‐free survival (EFS) at 5 and 10 years was 0·79, whereas the predicted overall survival (OS) at 5 and 10 years was 0·85 and 0·82, respectively. Nine patients had a bone marrow relapse after a median of 23 months; no patient had a central nervous system relapse. Additional cytogenetic abnormalities, age, gender, WBC count or whether the t(1;19) was balanced or unbalanced did not influence EFS or OS. Compared to cases with t(12,21) and high hyperdiploidy, EFS was similar, but overall survival was worse in patients with t(1;19)/der(19)t(1;19) (P = 0·004).
KRN5500, a spicamycin derivative, exerts anti‐myeloma effects through impairing both myeloma cells and osteoclasts
Authors: Miki Hirokazu , Ozaki Shuji , Nakamura Shingen , Oda Asuka , Amou Hiroe , Ikegame Akishige , Watanabe Keiichiro , Hiasa Masahiro , Cui Qu , Harada Takeshi , Fujii Shiro , Nakano Ayako , Kagawa Kumiko , Takeuchi Kyoko , Yata Ken‐ichiro , Sakai Akira , Abe Masahiro , Matsumoto Toshio 
Published: September 2011

SummaryThe spicamycin analogue KRN5500 alters glycoprotein processing and induces damage in the endoplasmic reticulum (ER)‐Golgi apparatus in cancer cells. In the present study, we explored the cytotoxic effects of KRN5500 on multiple myeloma (MM) cells and the bone marrow microenvironment with special reference to ER stress. Cell proliferation assay showed that KRN5500 induced G1 arrest and apoptosis in MM cells in a time‐ and dose‐dependent manner. KRN5500 enhanced ER stress independently of caspase activation in MM cells. This cell death was observed even in the presence of bone marrow stroma cells or osteoclasts. Notably, KRN5500 induced cell death also in osteoclasts. In vivo effects of KRN5500 were evaluated using two xenograft models established in severe combined immunodeficient (SCID) mice by either subcutaneous injection of RPMI 8226 cells or intra‐bone injection of INA‐6 cells to subcutaneously implanted rabbit bones (SCID‐rab model). KRN5500 significantly inhibited tumour growth in both animal models, and decreased the number of osteoclasts, which resulted in prevention of bone destruction in the SCID‐rab model. These results suggest that KRN5500 exerts anti‐MM effects through impairing both MM cells and osteoclasts. Therefore, this unique mechanism of KRN5500 might be a useful therapeutic option in patients with MM.
Fibroproliferative activity in patients with immune thrombocytopenia (ITP) treated with thrombopoietic agents
Authors: Ghanima Waleed , Junker Peter , Hasselbalch Hans Carl , Boiocchi Leonardo , Geyer Julia T. , Feng Xingmin , Gudbrandsdottir Sif , Orazi Attilio , Bussel James B. 
Published: September 2011

SummaryThis study assessed the grade of bone marrow (BM) fibrosis and its association with a seromarker for collagen‐III formation and fibrosis‐related cytokines in 25 immune thrombocytopenia (ITP) patients treated with thrombopoietin receptor agonists (Tpo‐RA) who had at least one BM biopsy. Assessment of 8 pre‐ and on‐treatment BM biopsies revealed statistically significant increases in reticulin. Reticulin in biopsies performed after a median of 1·4 years of treatment was graded: MF‐0 in 3 (12%), MF‐1 in 19 (76%), MF‐2 in 2 (8%) and MF‐3 in 1 (4%). No cytogenetic or flow‐cytometric abnormalities were detected. Median pretreatment Procollagen III N‐propeptide (PIIINP) (6·6 μg/l) was significantly higher than on‐treatment levels (5·6 μg/l); both were higher than controls (3·4 μg/l; P < 0·001). PIIINP was negatively correlated with treatment duration (r = −0·49) suggesting a decelerated reticulin production over time. There was a trend towards an association between grade of reticulin and PIIINP. Transforming growth factor (GF)‐beta and basic‐Fibroblast GF were not different between patients and controls but Hepatocyte GF (HGF), an anti‐fibrotic cytokine, was significantly elevated in patients. In conclusion, low‐grade BM reticulin fibrosis is seen in most ITP patients on Tpo‐RA. The novel findings of decreasing PIIINP and elevated HGF need further investigation to explore their significance in BM fibrogenesis.