bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating forage biomass and quality in a mixed sown pasture based on partial least squares regression with waveband selection
Authors: Kawamura Kensuke , Watanabe Nariyasu , Sakanoue Seiichi , Inoue Yoshio 
Published: August 2008

AbstractAlthough partial least squares (PLS) regression, a full‐spectrum bilinear regression method, is widely used in laboratory calibrations of pasture quality, increasing evidence indicates that PLS models include some redundant wavelengths. Consequently, more careful wavelength selection might improve their predictive accuracy, especially in field applications. We compared the predictive ability of PLS models using whole and selected wavebands from in situ canopy reflectance spectra over 400–2350 nm to predict above‐ground biomass (BM) and concentrations of crude protein (CP), acid detergent fiber (ADF) and neutral detergent fiber in herbage. Canopy reflectance measurements and plant sampling were conducted at 86 selected points in a mixed sown pasture in Hokkaido, Japan, in August 2006. Removing the minimum value of the weighted regression coefficient in the PLS model enabled stepwise waveband selection. For all pasture parameters, cross‐validated coefficients of determination () and root mean square error values, respectively, increased and decreased with removal of wavebands until the optimum number of wavebands was reached. The number of selected wavebands ranged between six (2.2% of full 277 wavebands) and 47 (17%), suggesting that over 83% wavebands were redundant or useless. Overall, higher R2 values and lower root mean squared errors of prediction were obtained using selected wavebands in the PLS model. Particularly, waveband selection greatly improved BM (R2 = 0.51–0.72) and ADF (R2 = 0.30–0.65) predictions when using the first derivative reflectance spectrum, and CP (R2 = 0.38–0.62) prediction for reflectance. These results suggest that pasture quality and BM can be predicted by in situ canopy reflectance using a PLS regression model, and that the predictive ability of the model can be improved by optimizing important wavebands.
Effects of levels of nitrogen fertilizer on oxalate and some mineral contents in napiergrass (Pennisetum purpureum Schumach)
Authors: Rahman Mohammad Mijanur , Ishii Yasuyuki , Niimi Mitsuhiro , Kawamura Osamu 
Published: August 2008

AbstractIn a number of plant species, nitrogen fertilization leads to a higher oxalate content of the plant. Various tropical grasses sometimes contain oxalate in sufficient concentrations to induce calcium deficiency in grazing animals. The present study was undertaken to investigate the effect of increasing level of N (0, 10, 30, 60 and 90 g N m−2 using urea) on oxalate and some mineral contents in napiergrass (cv. dwarf‐late). We found that the total dry matter yield increased significantly (P < 0.001) with increasing N up to 30 g N m−2 applied, but no significant difference was observed among the N levels of 30, 60 and 90 g m−2. The oxalate content was not increased with increased levels of N fertilization in all cut forages, except for insoluble oxalate content at third‐cut forage which increased significantly (P < 0.05) with increased level of N fertilizer. The content of soluble oxalate in plants was positively correlated (r2 = 0.76, P < 0.001) with potassium concentration, while the content of insoluble oxalate was positively correlated with calcium (r2 = 0.69, P < 0.001) and magnesium (r2 = 0.65, P < 0.001) concentrations. The study suggests that while applying N fertilizer as urea during cultivation of napiergrass, oxalate accumulation may not be a matter of concern.
Genetic diversity of chloroplast DNA in Zoysia and other warm‐season turfgrasses
Authors: Tsuruta Shin‐ichi , Hosaka Fumiko , Otabara Tesshu , Hashiguchi Masatsugu , Yamamoto Toshiya , Akashi Ryo 
Published: August 2008

AbstractAlthough information on chloroplast genomes has been available and used for phylogenetic analysis in some Poaceae species, they are limited in warm‐season turfgrass species including Zoysia. Twenty‐four chloroplast DNA (cpDNA) regions of Zoysia japonica cultivar Asagake were amplified using primer pairs designed from the complete chloroplast genome sequences of Oryza sativa and Zea mays. The nucleotide sequences of each fragment ranged 330–1230 bp in length, with a total of 16 780 bp. Of the 24 cpDNA regions, six amplified regions –trnK intron (matK), intergenic region of trnD‐psbM, atpA‐rps14, petE‐psaJ, atpB‐rbcL and rps3‐rps12 – were polymorphic among seven turfgrass species. The nucleotide sequences of these regions were used for the phylogenetic clustering of seven turfgrasses and two cereal crops. The phylogenetic tree showed that these nine genera segregated into three major groups corresponding to the four grass subfamilies, suggesting that the diversity of nucleotide sequences in these six cpDNA regions could be useful for assessing the phylogenetic relationships among turfgrass species. Chloroplast microsatellite markers were developed using nucleotide sequences of the amplification products with the 24 primer pairs from Z. japonica cultivar Asagake. Based on this 16 780‐bp nucleotide sequence, 21 chloroplast microsatellites were developed from 18 regions. Ten of the 21 primer pairs exhibited polymorphisms among three species of Zoysia. These informative markers should be valuable tools in the study of genetic relationships across Zoysia species.
Effects of Photodynamic Therapy Evaluated in a Novel Three‐dimensional Squamous Cell Carcinoma Organ Construct of the Skin
Authors: Obrigkeit Daniela Hoeller , Jugert Frank K. , Beermann Torsten , Baron Jens M. , Frank Jorge , Merk Hans F. , Bickers David R. , Abuzahra Faris 
Published: August 2008

AbstractSquamous cell carcinoma (SCC) of the skin is a malignant neoplasm that occurs in all ethnic groups primarily due to chronic sun exposure and constitutes a major health problem worldwide. Novel therapies for SCC are in development but as yet no in vitro models capable of screening these therapies and their mechanism of action before proceeding to clinical trials in human subjects have emerged. For this reason we have developed and characterized a novel three‐dimensional human SCC construct and validated it using photodynamic therapy (PDT), a well‐established modality for treating in situ SCCs. Histologic and immunohistochemical characterization of these SCC constructs revealed epidermal and dermal de‐differentiation, increased cell proliferation and expression of immunohistochemical markers specific for cutaneous SCC. Application of PDT to these constructs led to tumor regression with widespread apoptosis and necrosis within 5 days. This in vitro model consistently reproduces the tumor development and dynamics of growing SCCs in vivo and provides a useful approach for screening new treatment modalities for this form of cutaneous cancer.
Quantitative FRET Analysis With the E0GFP‐mCherry Fluorescent Protein Pair
Authors: Albertazzi Lorenzo , Arosio Daniele , Marchetti Laura , Ricci Fernanda , Beltram Fabio 
Published: August 2008

AbstractFluorescence resonance energy transfer (FRET) between fluorescent proteins (FPs) is a powerful tool to investigate protein–protein interaction and even protein modifications in living cells. Here, we analyze the E0GFP‐mCherry pair and show that it can yield a reproducible quantitative determination of the energy transfer efficiency both in vivo and in vitro. The photophysics of the two proteins is reported and shows good spectral overlap (Förster radius R0 = 51 Å), low crosstalk between acceptor and donor channels, and independence of the emission spectra from pH and halide ion concentration. Acceptor photobleaching (APB) and one‐ and two‐photon fluorescence lifetime imaging microscopy (FLIM) are used to quantitatively determine FRET efficiency values. A FRET standard is introduced based on a tandem construct comprising donor and acceptor together with a 20 amino acid long cleavable peptidic linker. Reference values are obtained via enzymatic cleavage of the linker and are used as benchmarks for APB and FLIM data. E0GFP‐mCherry shows ideal properties for FLIM detection of FRET and yields high accuracy both in vitro and in vivo. Furthermore, the recently introduced phasor approach to FLIM is shown to yield straightforward and accurate two‐photon FRET efficiency data even in suboptimal experimental conditions. The consistence of these results with the reference method (both in vitro and in vivo) reveals that this new pair can be used for very effective quantitative FRET imaging.
Isolation and characterization of 12 dinucleotide microsatellites in the European eel, Anguilla anguilla L., and tests of amplification in other species of eels
Authors: WIELGOSS S. , WIRTH T. , MEYER A. 
Published: August 2008

AbstractTwelve polymorphic dinucelotide microsatellites in the freshwater eel Anguilla anguilla L. were isolated and characterized. Genetic diversity was assessed in eels from Lake Constance, Germany. Allele numbers ranged from five to 26 per locus with observed heterozygosities between 0.125 and 0.875. A portion of locus AangCT77 aligns with a transcribed region of the zebrafish gene crystallin beta B2. Cross‐species amplification of most markers was possible for nine other Anguilla eel species. The newly developed primer pairs will facilitate population and conservation genetic studies in order to refine the understanding of the subtle population genetic structure typical of eels, and to identify interspecies admixture due to global trade.
Isolation and characterization of microsatellite markers for the tree‐root endophytes Phialocephala subalpina and Phialocephala fortinii s.s.
Authors: QUELOZ VALENTIN , DUÒ ANGELO , GRÜNIG CHRISTOPH R. 
Published: August 2008

AbstractSpecies of the Phialocephala fortinii s.l.–Acephala applanata complex are the dominant dark septate endophytes (DSE) in roots of species belonging to the Pinaceae. The two species Phialocephala subalpina and P. fortinii s.s. belong to the most widely distributed species within this complex. In the present study, 15 polymorphic microsatellite loci were developed for these two closely related species. Strains of a community which were analysed previously using single‐copy restriction fragment length polymorphism were screened with the new markers. Microsatellites were suitable to classify the two species and to recognize individuals within species.
Pseudoexfoliation syndrome at Jordan University Hospital
Authors: Al‐Bdour Muawyah D. , Al‐Till Maha I. , Idrees Ghaida M. , Abu Samra Khawla M. 
Published: August 2008

Abstract.Purpose:  This study aimed to estimate the prevalence of pseudoexfoliation syndrome (PXS) and analyse its association with particular ocular diseases in patients attending the Department of Ophthalmology at Jordan University Hospital.Methods:  A total of 1195 consecutive patients, aged 40–90 years, who attended the Department of Ophthalmology at Jordan University Hospital between December 2005 and March 2007 were included in the study. Each patient underwent complete ophthalmic evaluation, including: relevant history; visual acuity testing; slit‐lamp examination, applanation tonometry, gonioscopy and dilated fundus examination. Patients with typical pseudoexfoliative material on the anterior lens surface and/or the pupillary margin in either or both eyes were labelled as having PXS.Results:  Of the 1195 patients, 9.1% had pseudoexfoliation (PXF). Their mean age was 68.3 years (standard deviation [SD] 9.57). The prevalence of PXS had a tendency to increase with age but had no sex predilection. Pseudoexfoliation was bilateral in 65.7% of cases. It was significantly associated with cataract, glaucoma and phacodenesis. Of the eyes with PXF, 92.1% had cataract, 33.1% had glaucoma and 7.9% had phacodenesis.Conclusions:  Although this study was not population‐based, its findings increase our knowledge of PXS in a Middle Eastern country. Few data on PXS are available from this part of the world.
Alternatives for Youth's Advocacy Program: Reducing Minority Youth Incarceration Placements in Cleveland, Ohio
Authors: Mallett Christopher A. , Julian Linda 
Published: August 2008

ABSTRACTDetaining and incarcerating juvenile delinquents is ineffective and costly juvenile justice policy. These placements, indicative of the “tough on crime” approach, become problematic for many of these youths who do not have the advantage of legal counsel because they waive this right. In addition, a majority of these youths have a mental health or special education disability that does not get addressed in correctional facilities. Alternatives for Youth's Advocacy Program (AFY) in Cleveland, Ohio (Cuyahoga County) is addressing these issues using a holistic approach that includes the provision of civil legal representation to assist youths in accessing disability services and defense attorney support in dispositional planning to reduce juvenile offender placements. This article reports the results of an experimental design pilot study evaluation of AFY that randomly referred and evaluated 82 felony‐offending youths over 21 months. This initial review of the AFY program found it reduced detention center placement days by 47% and decreased state facility incarceration days by 74% (total cost savings $625,898). With 3,000 youths detained in the Cuyahoga County, Ohio, Detention Center and 1,800 incarcerated in Ohio state facilities annually, policy implications and recommendations are set forth.
Phylogenetic Characterization of Two Novel Commensal Bacteria Involved with Innate Immune Homeostasis inDrosophila melanogaster
Authors: Roh Seong Woon , Nam Young-Do , Chang Ho-Won , Kim Kyoung-Ho , Kim Min-Soo , Ryu Ji-Hwan , Kim Sung-Hee , Lee Won-Jae , Bae Jin-Woo 
Published: August 2008

ABSTRACTDuring a previous study on the molecular interaction between commensal bacteria and host gut immunity, two novel bacterial strains, A911Tand G707T, were isolated from the gut ofDrosophila melanogaster. In this study, these strains were characterized in a polyphasic taxonomic study using phenotypic, genetic, and chemotaxonomic analyses. We show that the strains represent novel species in the familyAcetobacteraceae. Strain G707T, a highly pathogenic organism, represents a new species in the genusGluconobacter, “Gluconobacter morbifer” sp. nov. (type strain G707 = KCTC 22116T= JCM 15512T). Strain A911T, dominantly present in the normalDrosphilagut community, represents a novel genus and species, designated “Commensalibacter intestini” gen. nov., sp. nov. (type strain A911 = KCTC 22117T= JCM 15511T).
Growth Temperature Exerts Differential Physiological and Transcriptional Responses in Laboratory and Wine Strains of
Saccharomyces cerevisiae
Authors: Pizarro Francisco J. , Jewett Michael C. , Nielsen Jens , Agosin Eduardo 
Published: August 2008

ABSTRACT

Laboratory strains of
Saccharomyces cerevisiae
have been widely used as a model for studying eukaryotic cells and mapping the molecular mechanisms of many different human diseases. Industrial wine yeasts, on the other hand, have been selected on the basis of their adaptation to stringent environmental conditions and the organoleptic properties that they confer to wine. Here, we used a two-factor design to study the responses of a standard laboratory strain, CEN.PK113-7D, and an industrial wine yeast strain, EC1118, to growth temperatures of 15°C and 30°C in nitrogen-limited, anaerobic, steady-state chemostat cultures. Physiological characterization revealed that the growth temperature strongly impacted the biomass yield of both strains. Moreover, we found that the wine yeast was better adapted to mobilizing resources for biomass production and that the laboratory yeast exhibited higher fermentation rates. To elucidate mechanistic differences controlling the growth temperature response and underlying adaptive mechanisms between the strains, DNA microarrays and targeted metabolome analysis were used. We identified 1,007 temperature-dependent genes and 473 strain-dependent genes. The transcriptional response was used to identify highly correlated gene expression subnetworks within yeast metabolism. We showed that temperature differences most strongly affect nitrogen metabolism and the heat shock response. A lack of stress response element-mediated gene induction, coupled with reduced trehalose levels, indicated that there was a decreased general stress response at 15°C compared to that at 30°C. Differential responses among strains were centered on sugar uptake, nitrogen metabolism, and expression of genes related to organoleptic properties. Our study provides global insight into how growth temperature affects differential physiological and transcriptional responses in laboratory and wine strains of
S. cerevisiae
.
Early Attachment Sites for Shiga-Toxigenic
Escherichia coli
O157:H7 in Experimentally Inoculated Weaned Calves
Authors: Dean-Nystrom Evelyn A. , Stoffregen William C. , Bosworth Brad T. , Moon Harley W. , Pohlenz Joachim F. 
Published: August 2008

ABSTRACT

Weaned 3- to 4-month-old calves were fasted for 48 h, inoculated with 10
10
CFU of Shiga toxin-positive
Escherichia coli
(STEC) O157:H7 strain 86-24 (STEC O157) or STEC O91:H21 strain B2F1 (STEC O91), Shiga toxin-negative
E. coli
O157:H7 strain 87-23 (Stx
−
O157), or a nonpathogenic control
E. coli
strain, necropsied 4 days postinoculation, and examined bacteriologically and histologically. Some calves were treated with dexamethasone (DEX) for 5 days (3 days before, on the day of, and 1 day after inoculation). STEC O157 bacteria were recovered from feces, intestines, or gall bladders of 74% (40/55) of calves 4 days after they were inoculated with STEC O157. Colon and cecum were sites from which inoculum-type bacteria were most often recovered. Histologic lesions of attaching-and-effacing (A/E) O157
+
bacteria were observed in 69% (38/55) of the STEC O157-inoculated calves. Rectum, ileocecal valve, and distal colon were sites most likely to contain A/E O157
+
bacteria. Fecal and intestinal levels of STEC O157 bacteria were significantly higher and A/E O157
+
bacteria were more common in DEX-treated calves than in nontreated calves inoculated with STEC O157. Fecal STEC O157 levels were significantly higher than Stx
−
O157, STEC O91, or control
E. coli
; only STEC O157 cells were recovered from tissues. Identifying the rectum, ileocecal valve, and distal colon as early STEC O157 colonization sites and finding that DEX treatment enhances the susceptibility of weaned calves to STEC O157 colonization will facilitate the identification and evaluation of interventions aimed at reducing STEC O157 infection in cattle.
Salmonella
and
Escherichia coli
O157:H7 Contamination on Hides and Carcasses of Cull Cattle Presented for Slaughter in the United States: an Evaluation of Prevalence and Bacterial Loads by Immunomagnetic Separation and Direct Plating Methods
Authors: Brichta-Harhay Dayna M. , Guerini Michael N. , Arthur Terrance M. , Bosilevac Joseph M. , Kalchayanand Norasak , Shackelford Steven D. , Wheeler Tommy L. , Koohmaraie Mohammad 
Published: August 2008

ABSTRACT

The hide and carcass hygiene of cull cattle at slaughter in four geographically distant regions of the United States was examined from July 2005 to April 2006 by measuring the aerobic plate counts (APC) and the prevalences and loads of
Salmonella
and
Escherichia coli
O157:H7. The geometric mean log
10
APC CFU/100 cm
2
levels on hides and preevisceration and postintervention carcasses ranged from 6.17 to 8.19, 4.24 to 6.47, and 1.46 to 1.96, respectively, and were highest in the summer (
P
< 0.0001). The average prevalences of
Salmonella
on hides and preevisceration and postintervention carcasses were 89.6% (95% confidence interval [CI], 85.1 to 94.0), 50.2% (95% CI, 40.9 to 59.5), and 0.8% (95% CI, 0.18 to 1.42), respectively. The prevalences of
E. coli
O157:H7 were 46.9% (95% CI, 37.3 to 56.6) and 16.7% (95% CI, 9.8 to 23.6) on hides and preevisceration carcasses, respectively. Examination of the concomitant incidence of
Salmonella
and
E. coli
O157:H7 showed that, on average, 33.3% (95% CI, 15.9 to 69.8) of cattle hide and 4.1% (95% CI, 0.98 to 17.3) of preevisceration carcass samples were contaminated with both pathogens. The pathogen prevalence on hides and carcasses was not significantly affected by the season; however, significant differences were observed between plants with respect to the incoming pathogen load and the ability to mitigate hide-to-carcass transfer. In spite of these differences, postintervention carcass contamination was significantly reduced (
P
< 0.001), likely as a result of the use of one or more of the processing interventions employed at each of the four processing plants examined.
Diversity and Distribution of Commensal FecalEscherichia coliBacteria in Beef Cattle Administered Selected Subtherapeutic Antimicrobials in a Feedlot Setting
Authors: Sharma Ranjana , Munns Krysty , Alexander Trevor , Entz Toby , Mirzaagha Parasto , Yanke L. Jay , Mulvey Michael , Topp Edward , McAllister Tim 
Published: August 2008

ABSTRACTEscherichia colistrains isolated from fecal samples were screened to examine changes in phenotypic and genotypic characteristics including antimicrobial susceptibility, clonal type, and carriage of resistance determinants. The goal of this 197-day study was to investigate the influence of administration of chlortetracycline alone (T) or in combination with sulfamethazine (TS) on the development of resistance, dissemination of defined strain types, and prevalence of resistance determinants in feedlot cattle. Inherent tetracycline resistance was detected in cattle with no prior antimicrobial exposure. Antimicrobial administration was not found to be essential for the maintenance of inherently ampicillin-resistant and tetracycline-resistant (Tetr)E. coliin control animals; however, higher TetrE. colishedding was observed in animals subjected to the two treatments. At day 0, high tetracycline (26.7%), lower sulfamethoxazole-tetracycline (19.2%), and several other resistances were detected, which by the finishing phase (day 197) were restricted to ampicillin-tetracycline (47.5%), tetracycline (31.7%), and ampicillin-tetracycline-sulfamethoxazole (20.8%) from both treated and untreated cattle. Among the determinants,blaTEM1,tet(A), andsul2were prevalent at days 0 and 197. Further,E. colifrom day 0 showed diverse antibiogram profiles and strain types, which by the finishing phase were limited to up to three, irrespective of the treatment. Some genetically identical strains expressed different phenotypes and harbored diverse determinants, indicating that mobile genetic elements contribute to resistance dissemination. This was supported by an increased linked inheritance of ampicillin and tetracycline resistance genes and prevalence of specific strains at day 197. Animals in the cohort shed increasingly similar genotypes by the finishing phase due to animal-to-animal strain transmission. Thus, characterizing inherent resistance and propagation of cohort-specific strains is crucial for determining antimicrobial resistance in cattle.
Isolation and Identification ofBifidobacteriaceaefrom Human Saliva
Authors: Beighton David , Gilbert Steven C. , Clark Douglas , Mantzourani Maria , al-Haboubi Mustafa , Ali Farida , Ransome Elizabeth , Hodson Nicholas , Fenlon Michael , Zoitopoulos Liana , Gallagher Jennifer 
Published: August 2008

ABSTRACTBifidobacteriaceaewere isolated from saliva and infected dentine by using a mupirocin-based selective medium. Of the saliva samples, 94% harbored bifids. The mean concentration (± the standard error) was 4.46 (±0.12) log10(CFU per ml + 1), and the predominant isolates wereBifidobacterium dentium, B. longum, Scardovia inopinata, Parascardovia denticolens, andAlloscardovia omnicolens.