bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
Authors: Wu Jiansheng , Liu Hongde , Duan Xueye , Ding Yan , Wu Hongtao , Bai Yunfei , Sun Xiao 
Published: November 2008

Abstract
Motivation: In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical–chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class.
Results: The results show that the RF model achieves 91.41% overall accuracy with Matthew's correlation coefficient of 0.70 and an area under the receiver operating characteristic curve (AUC) of 0.913. To our knowledge, the RF method using the hybrid feature is currently the computationally optimal approach for predicting DNA-binding sites in proteins from amino acid sequences without using three-dimensional (3D) structural information. We have demonstrated that the prediction results are useful for understanding protein–DNA interactions.
Availability: DBindR web server implementation is freely available at http://www.cbi.seu.edu.cn/DBindR/DBindR.htm.
Contact: xsun@seu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays
Authors: Davis Oliver S. P. , Plomin Robert , Schalkwyk Leonard C. 
Published: November 2008

Abstract
Summary: Large-scale genome-wide association (GWA) studies using thousands of high-density SNP microarrays are becoming an essential tool in the search for loci related to heritable variation in many phenotypes. However, the cost of GWA remains beyond the reach of many researchers. Fortunately, the majority of statistical power can still be obtained by estimating allele frequencies from DNA pools, reducing the cost to that of tens, rather than thousands of arrays. We present a set of software tools for processing SNPMaP (SNP microarrays and pooling) data from CEL files to Relative Allele Scores in the rich R statistical computing environment.
Availability: The SNPMaP package is available from http://cran.r-project.org/ under the GNU General Public License version 3 or later.
Contact: snpmap@iop.kcl.ac.uk
Supplementary information: Additional resources and test datasets are available at http://sgdp.iop.kcl.ac.uk/snpmap/
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
Authors: Brouwer Rutger W. W. , van Hijum Sacha A. F. T. , Kuipers Oscar P. 
Published: November 2008

Abstract
Summary: We have developed MINOMICS, a tool that allows facile and in-depth visualization of prokaryotic transcriptomic and proteomic data in conjunction with genomics data. MINOMICS generates interactive linear genome maps in which multiple experimental datasets are displayed together with operon, regulatory motif, transcriptional promoter and transcriptional terminator information.
Availability: MINOMICS is freely accessible at http://www.minomics.nl
Contact: sacha.vanhijum@nizo.nl; o.p.kuipers@rug.nl
Supplementary information: http://bioinformatics.biol.rug.nl/supplementary/minomics/
Stability of Vitamin E in Wheat Flour and Whole Wheat Flour During Storage
Authors: Nielsen Merete M⊘ller , Hansen Åse 
Published: November 2008

ABSTRACTThe stability of vitamin E during 297 days of storage of wheat flour and whole wheat flour ground on a stone mill or a roller mill, respectively, were studied. One day after milling, the total content of vitamin E, expressed in vitamin E equivalents (α‐TE), was 18.7 α‐TE and 10.8 α‐TE for stone‐milled and roller‐milled wheat flour, respectively. The difference in total vitamin E content was primarily due to the absence of the germ and bran fractions in the roller‐milled flour. The total loss of vitamin E during storage was 24% for stone‐milled wheat flour but 50% for roller‐milled wheat flour. These results indicate that vitamin E, which is present in high amounts in wheat germ, functions as an antioxidant in the stone‐milled wheat flour. Hexanal formation showed that lipid oxidation in roller‐milled flour occurred just after milling, whereas the formation of hexanal in the germ fraction displayed a lack period of 22 days, confirming that vitamin E functions as an effective antioxidant in the wheat germ. Results showed no significant difference in total loss of vitamin E for stone‐milled and roller‐milled whole wheat flour. Total loss after 297 days of storage for both milling methods was ≈32%.
Effects of Selected Barley Cultivars and Their Pearling Fractions on Inhibition of Human LDL Oxidation In Vitro Using a Modified Conjugated Dienes Method
Authors: Abdel‐Aal E.‐S. M. , Gamel T. H. 
Published: November 2008

ABSTRACTOxidation of LDL cholesterol is an important factor in the development of atherosclerosis and heart disease. In this study, selected Canadian and Egyptian barley cultivars and their pearling fractions were evaluated for antioxidant capacity to inhibit human LDL oxidation in vitro. Measurement of conjugated dienes (CD) at 234 nm was optimized to determine the degree of LDL oxidation. Dilution of oxidized LDL with iso‐propanol gave a distinct diene conjugation peak. Significant differences in total phenols content (TPC) were found between the cultivars tested, with the hulless barley having greater TPC and inhibition capacity compared with hulled barleys. The outer layers fraction contained the highest TPC, lowest CD formation, and longest lag time, whereas the inner, or endosperm fraction, had the lowest inhibition effects. The middle pearling and hull fractions possessed intermediate inhibition effects. The inhibitory effect of barley extracts was dependent on phenols concentration following a linear or quadratic pattern. The results suggest that barley whole meals, outer layers, middle pearling, or hull fraction would be a potential LDL antioxidant.
Rheological Properties of Wheat Flour Dough and Their Relationship with Bread Volume. II. Dynamic Oscillation Measurements
Authors: Van Bockstaele Filip , De Leyn Ingrid , Eeckhout Mia , Dewettinck Koen 
Published: November 2008

ABSTRACTThe rheological properties of 17 pure European wheat cultivars were analyzed and evaluated in relation to the bread volume. Rheological testing included two empirical rheological methods, farinograph and alveograph, in addition to more fundamental rheological methods, specifically the creep‐recovery and dynamic oscillation measurements. The four rheological methods revealed large differences in dough rheological properties among the 17 wheat cultivars. Phase angle δ and the moduli were strongly correlated. The dynamic oscillation parameters also correlated significantly with protein content, Zeleny sedimentation value, damaged starch content, and farinograph water absorption. A nonlinear relationship (power) between the maximum creep or recovery strain and the dynamic moduli was found for both shear stresses (100 and 250 Pa). Phase angle δ showed a positive relationship with the maximum creep or recovery strain. The dynamic oscillation parameters could be related to the bread volume. Phase angle δ could explain ≈70% of the variance in bread volume among the wheat cultivars. The dynamic moduli showed an inverse relationship with the bread volume. A nonlinear relationship with the bread volume could be established for G′ (r2 = 0.75), G″ (r2 = 0.72), and |G*| (r2 = 0.74).
Outbreak of Bacterial Blossom Blight Caused by Pseudomonas viridiflava on Actinidia chinensis Kiwifruit Plants in Italy
Authors: Balestra G. M. , Mazzaglia A. , Rossetti A. 
Published: November 2008

During the springs from 2006 to 2008, a new disease was observed on 4- to 5-year-old Actinidia chinensis (cv. Jin Tao) trees in different commercial kiwifruit-production areas in northern Italy (Lombardy). Initially, disease occurrence was sporadic but later became widespread. Symptoms on flowers appeared as a dark brown rot of anthers, filaments, sepals, and whole buds. Blossoms abscised prematurely from buds. Symptoms appeared as confluent brown spots often present on rolled margins. Bacteria were isolated from symptomatic tissue on nutrient agar medium supplemented with 5% sucrose. The isolated bacteria were aerobic; produced a diffusible fluorescent pigment on King's B medium; levan, oxidase, and arginine dihydrydrolase negative, and catalase positive; rotted potato tuber tissue; caused a hypersensitive response on tobacco; and failed to reduce nitrate or utilize sucrose and were ice nuclease-positive at –5°C, suggesting the organism was P. viridiflava (1,3). Inoculation of 2-year-old A. chinensis cv. Jin Tao plants were carried out in the greenhouse under controlled environmental conditions (15 to 27°C, night/day; relative humidity up to 70%) by spraying five plants in bloom with a suspension (1 × 108 CFU/ml) of isolated bacteria with a hand-held sprayer that produced large spray droplets. Symptoms, similar to those in nature, were observed on flowers and buds 3 to 5 days after inoculation and on leaves after 7 to 10 days. Using the same tests described above with the original strains, the strains that were isolated from symptomatic tissue were identified as Pseudomonas viridiflava. Seven bacterial strains (PV508–PV1108) were identified by sequencing 1,481 bp of their 16S rDNA region (2) and using BlastN (4) for the most similar sequences in the INSD (GenBank, EMBL, and DDBJ). Our sequences shared 99.53% (1,474 of 1,481 bp) to 99.9% (1480 of 1,481 bp) identity with the analogous sequences of P. viridiflava available in the database. To our knowledge, this is the first report of an outbreak of blossom blight caused by P. viridiflava on A. chinensis cv. Jin Tao kiwifruit plants in Italy. Previously, it was reported on A. deliciosa cv. Hayward (3). Because of the risk of bacterial contamination among the different cultivars of kiwifruit, further investigation and development of control measures are in progress. References: (1) R. A. Lelliott and D. E. Stead. Methods for the Diagnosis of Bacterial Diseases of Plants. Blackwell Scientific, Oxford, UK, 1987. (2) E. R. B. Moore et al. Syst. Appl. Microbiol. 19:478, 1996. (3) L. Varvaro et al. Inf. Fitopatol. 6:49, 1990. (4) Z. Zhang et al. J. Comput. Biol. 7(1-2):203, 2000.
First Report of Tomato chlorosis virus Infecting Tomato Crops in Brazil
Authors: Barbosa J. C. , Teixeira A. P. M. , Moreira A. G. , Camargo L. E. A. , Filho A. Bergamin , Kitajima E. W. , Rezende J. A. M. 
Published: November 2008

During 2006 and 2007 in the region of Sumaré, state of São Paulo, Brazil, surveys were done on tomato (Solanum lycopersicum L.) virus diseases in three open field-grown crops. The data revealed low incidence (0.25 to 3.42%) of randomly distributed plants exhibiting interveinal chlorosis and some necrosis on the basal leaves. Symptoms were only observed on old fruit-bearing plants. Preliminary analysis of thin sections of symptomatic leaves from one plant by transmission electron microscopy revealed the presence of aggregates of thin, flexible, and elongated particles in some phloem vessels, suggesting infection with a member of the genus Crinivirus, family Closteroviridae. Total RNA was extracted separately from leaves of 10 symptomatic plants and used for one-step reverse transcription (RT)-PCR using the HS-11/HS-12 primer pair, which amplifies a fragment of 587 bp from the highly conserved region of the heat shock protein (HSP-70) homolog gene reported for Tomato infectious chlorosis virus (TICV) and Tomato chlorosis virus (ToCV) (1). The RT-PCR product was subsequently tested by nested-PCR for single detection of TICV and ToCV using primer pairs TIC-3/TIC-4 and ToC-5/ToC-6, respectively (1). Only one fragment of approximately 463 bp was amplified from 7 of the 10 plants with the primer pair specific for ToCV. No amplification was obtained with the primers specific for TICV. Two amplicons of 463 bp were purified and directly sequenced in both directions. Sequence comparisons of the 463-bp consensus sequence (GenBank Accession No. EU868927) revealed 99% identity with the reported sequence of ToCV from the United States (GenBank Accession No. AY903448) (3). Virus-free adults of Bemisia tabaci biotype B confined on symptomatic tomato leaves for a 24-h acquisition access period were able to transmit the virus to healthy tomato plants, which reproduced the original symptoms on the bottom leaves 65 days after inoculation under greenhouse conditions. Infection from transmission was confirmed by RT-PCR using the HS-11/HS-12 primer pair. In addition to B. tabaci biotype B, the greenhouse whitefly, Trialeurodes vaporariorum, has also been reported as a vector of ToCV, although it is less efficient than the B. tabaci biotype B in transmission of this virus (4). T. vaporariorum, which was previously considered limited to greenhouses, was recently reported in tomato and green bean (Phaseolus vulgaris L.) crops under field conditions in São Paulo State (2). Therefore, it might also contribute to the spread of ToCV in tomato crops in São Paulo. To our knowledge, this is the first report of ToCV in Brazil and South America. References: (1) C. I. Dovas et al. Plant Dis.86:1345, 2002. (2) A. L. Lourenção et al. Neotrop. Entomol. 37:89, 2008. (3) W. M. Wintermantel et al. Arch. Virol. 15:2287, 2005. (4) W. M. Wintermantel and G. C. Wisler. Plant Dis. 90:814, 2006.
Blufensin1Negatively Impacts Basal Defense in Response to Barley Powdery Mildew
Authors: Meng Yan , Moscou Matthew J. , Wise Roger P. 
Published: November 2008

AbstractPlants have evolved complex regulatory mechanisms to control the defense response against microbial attack. Both temporal and spatial gene expression are tightly regulated in response to pathogen ingress, modulating both positive and negative control of defense. BLUFENSIN1 (BLN1), a small peptide belonging to a novel family of proteins in barley (Hordeum vulgare), is highly induced by attack from the obligate biotrophic fungus Blumeria graminis f. sp. hordei (Bgh), casual agent of powdery mildew disease. Computational interrogation of the Bln1 gene family determined that members reside solely in the BEP clade of the Poaceae family, specifically, barley, rice (Oryza sativa), and wheat (Triticum aestivum). Barley stripe mosaic virus-induced gene silencing of Bln1 enhanced plant resistance in compatible interactions, regardless of the presence or absence of functional Mla coiled-coil, nucleotide-binding site, Leu-rich repeat alleles, indicating that BLN1 can function in an R-gene-independent manner. Likewise, transient overexpression of Bln1 significantly increased accessibility toward virulent Bgh. Moreover, silencing in plants harboring the Mlo susceptibility factor decreased accessibility to Bgh, suggesting that BLN1 functions in parallel with or upstream of MLO to modulate penetration resistance. Collectively, these data suggest that the grass-specific Bln1 negatively impacts basal defense against Bgh.
Incidence of bleeding lesions within reach of conventional upper and lower endoscopes in patients undergoing double‐balloon enteroscopy for obscure gastrointestinal bleeding
Authors: FRY L. C. , BELLUTTI M. , NEUMANN H. , MALFERTHEINER P. , MÖNKEMÜLLER K. 
Published: November 2008

SummaryBackground  Double‐balloon enteroscopy (DBE) is a useful method for evaluation of obscure gastrointestinal bleeding (OGIB).Aim To determine the incidence of lesions within reach of conventional upper and lower endoscopes as the cause of OGIB in patients referred for DBE.Methods All patients undergoing DBE for OGIB during a 3.5‐year period at a university hospital were studied. OGIB was defined according to American Gastroenterological Association (AGA) guidelines.Results One hundred and forty‐three DBEs were performed in 107 patients for obscure overt (n = 85) and obscure occult (n = 22) GIB. Lesions outside the SB as possible sources of GIB were found in 51 patients (47.6%) and a definite source of bleeding outside the small bowel (SB) was detected in 26 patients (24.3%). Lesions considered to explain a definite source of GIB were: gastric ulcer (n = 3), duodenal ulcer (n = 3), Cameron’s lesions (n = 2), gastric antral vascular ectasias (n = 4), radiation proctitis (n = 1), radiation ileitis (n = 2), duodenal angiodysplasias (n = 1), haemorrhoids with stigmata of recent bleed (n = 1), colon angiodysplasias (n = 3), colon diverticulosis (n = 3), colonic Crohn’s disease (n = 1), anastomotic ulcers (n = 1).Conclusions The frequency of non‐SB lesions definitely explaining the source of GIB in patients referred for DBE was 24.3%. Therefore, repeat esophago‐gastroduodenoscopy (EGD) and ileocolonoscopy should be taken into consideration before DBE.
Investigating the selectivity of weed harrowing with new methods
Authors: RASMUSSEN J , BIBBY B M , SCHOU A P 
Published: November 2008

SummaryIn six field experiments on post‐emergence weed harrowing in spring barley, the effects of row spacing, timing, direction and orientation on crop/weed selectivity were investigated. The efficacies of increasing intensities of harrowing generated either by increasing number of passes or increasing driving speed were also tested. Selectivity was defined as the relationship between crop burial in soil immediately after treatment and weed control. To estimate crop burial, digital image analysis was used in order to make objective estimations. The study showed that narrow row spacing decreased selectivity in a late crop growth stage, whereas row spacing in the range 5.3–24 cm had no effects at an early growth stage. Harrowing across rows decreased selectivity in one out of two experiments. Whether repeated passes with the harrow were carried out in the same orientation along the rows or in alternative orientations forth and back was unimportant. There were indications that a high harrowing intensity produced by a single pass at high speed gave a lower selectivity than a similar intensity produced by several passes at a low speed. Impacts on selectivity, however, were small and only significant at high degrees of weed control. Timing had no significant impact on selectivity.
Assessment of Sperm DNA Fragmentation in Stallion (Equus caballus) and Donkey (Equus asinus) Using the Sperm Chromatin Dispersion Test
Authors: Cortés‐Gutiérrez EI , Crespo F , Serres‐Dalmau C , Gutiérrez de las Rozas AL , Dávila‐Rodríguez MI , López‐Fernández C , Gósalvez J 
Published: November 2008

ContentsSperm DNA fragmentation (sDF) is an important parameter to assessing sperm quality. Information about sperm quality is not available for donkeys, especially in some breeds at risk of extinction. The objectives of this research were to test the four commercial variants of sperm chromatin dispersion test (SCD; sperm Halomax test), originally developed to assess sDF in boars, bulls, rams and stallions, in order to scrutinize their applicability in the study of sDF in a donkey breed at risk of extinction (Zamorano‐Leonesa), for which there is no specific test available to analyze sperm at present. Only the SCD test, originally developed for stallions, produced stable and consistent results, and was deemed suitable to assess DNA fragmentation in sperm samples from donkeys. Image analysis was used to compare differences between the SCD methodology applied to stallion and donkey semen samples processed under the same experimental conditions. The extent of SCD in the SCD test was approximately 20% lower in donkey sperm than in stallion sperm. Yet, the ratio of chromatin sperm dispersion achieved in fragmented and unfragmented nuclei did not differ significantly between species. These data suggest that a similar protein depletion treatment can cause differences in protein removal in equivalent cells from different species and that sperm chromatin may be organized differently in stallions and donkeys.
Ultrasonographic and Endocrine Evaluation of Three Regimes for Oestrus and Ovulation Synchronization for Sheep in the Subtropics
Authors: Ali A , Hayder M , Saifelnaser EOH 
Published: November 2008

ContentsThis study aimed to evaluate three regimes for oestrus and ovulation synchronization in Farafra ewes in the subtropics. During autumn, 43 ewes were assigned to (i) controlled internal drug releasing (CIDR)‐eCG group, treated with CIDR for 12 days and eCG at insert withdrawal, n = 13; (ii) PGF2α‐PGF2α group, treated with two PGF2α injections at 11 days interval, n = 14; and (iii) GnRH‐PGF2α‐GnRH group, treated with GnRH, followed 5 days later with PGF2α and 24 h later with a second GnRH, n = 16. Oestrus‐mating detection was carried out at 4 h intervals starting on day 0 [the day of CIDR withdrawal (CIDR‐eCG group), the day of second PGF2α treatment (PGF2α‐PGF2α group) and the day of PGF2α treatment (GnRH‐PGF2α‐GnRH group)]. Ovarian dynamics was monitored by ultrasound every 12 h beginning on day 0 and continued for 4 days. Blood samples were obtained daily for progesterone (P4) and oestradiol 17β (E2) estimation starting on day 0 and continued for 4 days. The obtained results showed that, oestrus expression, ovulation and conception were greater (p < 0.05) in CIDR‐eCG and PGF2α‐PGF2α groups than in GnRH‐PGF2α‐GnRH group. All ewes of PGF2α‐PGF2α group presented, on day of second PGF2α injection with mature CL (P4 > 2.0 ng/ml), compared to 42.9% in GnRH‐PGF2α‐GnRH group (p = 0.01). The peak of oestrus occurred 32–52, 48–60 and 28–96 h after the end of treatment in CIDR‐eCG, PGF2α‐PGF2α and GnRH‐PGF2α‐GnRH groups, respectively. Ovulation started 48 h after treatment in all groups and extended for 24, 36 and 48 h for CIDR‐eCG, PGF2α‐PGF2α and GnRH‐PGF2α‐GnRH groups, respectively. Results demonstrated that oestrus and ovulation synchronization could be efficiently achieved in Farafra ewes using either CIDR‐eCG or PGF2α‐PGF2α regimes; however, the GnRH‐PGF2α‐GnRH treatment induced a more spread oestrus and ovulation that may make the protocol inadequate for timed artificial insemination.