bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed Composition Analyses of Diverse Oat Genotype Kernels Grown in Different Environments in North Dakota
Authors: Doehlert Douglas C. , Simsek Senay , Thavarajah Dil , Thavarajah Pushparajah , Ohm Jae‐Bom 
Published: July 2013

ABSTRACTNutritional composition of oat kernels from 18 genotypes grown in six environments in North Dakota, U.S.A., was analyzed by chemical means. Of the macronutrients, mean starch concentration was 56.5%, protein was 18.1%, oil was 7.9%, neutral detergent fiber (insoluble fiber) was 6.0%, β‐glucan (soluble fiber) was 5.2%, ash was 1.9%, and soluble carbohydrate was 0.6%. These add up to 96.2%, which appears to account for most of the mass of the oat kernel. Protein amino acid analysis indicated 4.5% lysine and 1.8% methionine. Free amino acid analysis indicated 1,129 μg of asparagine per gram of flour. The 18:1 and 18:2 fatty acids were the most abundant in oat lipids. Mean micronutrient concentrations in oat kernels included potassium (3,419 ppm), magnesium (1,416 ppm), calcium (441 ppm), iron (52 ppm), zinc (26 ppm), and selenium (0.38 ppm). Analysis of variance indicated significant genotypic and environmental variation, as well as significant genotype × environmental interaction for most of the nutritional components. In general, protein was higher in drier, hotter environments, whereas oil, β‐glucan, and starch were higher in wetter, cooler environments. The results provide a unique database of a collection of compositional components for specific oat genotypes in diverse environments.
First Molecular Detection of Ramularia Leaf Spot (Ramularia collo-cygni) in Seeds and Leaves of Barley in Argentina
Authors: Havis N. D. , Gorniak K. , Carmona M. A. , Formento A. N. , Luque A. G. , Scandiani M. M. 
Published: July 2013

The fungus Ramularia collo-cygni B. Sutton & J. M. Waller (Rcc) was identified as the causal agent of this emerging disease on barley (Hordeum vulgare L.) based on symptoms and signs on leaves and attributes of the fungus. The common name given to the disease was “necrotic sprinkling.” This disease was found for the first time on barley in fields of Buenos Aires Province, Argentina, in 2001, with severities ranging from 60 to 100% (2). During the spring of 2012, the disease spread throughout most barley growing areas of the Pampean region, affecting almost all varieties of barley in the Buenos Aires, Entre Ríos, and Santa Fe provinces. The disease showed typical symptoms of small, brown spots on leaves, sheaths, and awns, and caused rapid loss of green leaf area and significant economic damage. The diagnosis of this disease is difficult by conventional techniques and has caused some confusion. In order to obtain appropriate information about the incidence of this pathogen in the most important barley growing region of Argentina, as well as to confirm its presence on seed, 39 seed samples containing 200 seeds each and eight leaf samples were analyzed using a real-time PCR diagnostic test (4). Thirty-five of the 37 seed samples had Rcc DNA levels above the minimum detection level (0.13 pg DNA). Ramularia has been described as a seedborne fungus previously (1) and seed infection could hasten the spread of the fungus to new geographically distinct areas. Moreover, leaf samples were microscopically assessed for conidophore presence and then ground for DNA extraction. Rcc DNA was detected by PCR in all eight leaf samples. To our knowledge, this is the first report about molecular detection of R. collo-cygni in barley seed of harvested samples from Argentina. Seeds infected/infested may also lead to new strains of the fungus arriving in barley fields and provide a source of inoculum for future epidemics (3). References: (1) N. D. Havis et al. FEMS Microbiol. Lett. 256:217, 2006. (2) M. Khier et al. Salpicado necrótico, nueva enfermedad de la cebada en Argentina causada por Ramularia collo-cygni. Page 47 in: Resúmenes XI Jornadas Fitosanitarias Argentinas, 26–29 June 2002, Río Cuarto, Córdoba, 2002. (3) P. Matusinsky et al. J. Plant Pathol. 3:679, 2011. (4) J. M. G. Taylor et al. Lett. Appl. Microbiol. 50:493, 2010.
Lactobacillus rhamnosus GG on Rotavirus‐Induced Injury of Ileal Epithelium in Gnotobiotic Pigs
Authors: Liu Fangning , Li Guohua , Wen Ke , Wu Shaoping , Zhang Yongguo , Bui Tammy , Yang Xingdong , Kocher Jacob , Sun Jun , Jortner Bernard , Yuan Lijuan 
Published: July 2013

ABSTRACTObjective:The aim of this study was to study the effect of continued Lactobacillus rhamnosus GG strain (LGG) feeding on rotavirus gastroenteritis in the gnotobiotic (Gn) pig model of virulent human rotavirus (HRV) infection.Methods:Gn pigs were assigned to treatment groups: mock control, LGG only, HRV only, or LGG plus HRV. Nine days before HRV inoculation (3 days of age), pigs were fed LGG with a daily dose increase of 10‐fold from 103 to 1012 colony‐forming units (CFU). The 1012 CFU/dose of LGG feeding continued until post‐HRV inoculation day (PID) 6. Clinical sign (diarrhea), rotavirus fecal shedding, histopathology of the ileum, adherent junction and tight junction protein expression in the ileal epithelial cells, mucin production in the large and small intestinal contents, and serum cytokine responses from PID 2 to 6 were examined and compared among the treatment groups.Results:Clinically, the percentage of pigs developing diarrhea, the mean duration of diarrhea, and the mean cumulative fecal scores were lower in the LGG fed pigs compared to the nonfed pigs after HRV inoculation. LGG partially protected ileal epithelium against HRV‐induced compensatory increases of the adherent junction protein α‐catenin and β‐catenin, tight junction protein occludin, claudin‐3 and claudin‐4, and leak protein claudin‐2. LGG promoted mucin production because the mucin levels in the large intestinal contents of the LGG+HRV pigs were significantly higher than the HRV‐only pigs on PID 2. Additionally, LGG maintained the anti‐inflammatory cytokine transforming growth factor‐β level in serum after HRV infection.Conclusions:LGG is moderately effective for ameliorating rotavirus diarrhea by partially preventing injuries to the epithelium.
Case of chromoblastomycosis with pulmonary involvement
Authors: Camara‐Lemarroy Carlos R. , Soto‐Garcia Anally J. , Preciado‐Yepez Cesar I. , Moreno‐Hoyos Francisco , Hernandez‐Rodriguez Pedro A. , Galarza‐Delgado Dionicio A. 
Published: July 2013

AbstractChromoblastomycosis is a slowly growing chronic cutaneous mycosis associated with a variety of cutaneous lesions. Extra‐dermal involvement is rare. A 58‐year‐old man was admitted to the hospital with nausea, vomiting, weakness and a history of weight loss. On inspection, he had a large verrucous mass in the sacral region, and two large subcutaneous nodules in the anterior thoracic wall. He claimed the lesions were several years old. Biopsy and histological studies were positive for chromoblastomycosis. Routine chest radiography showed hilar enlargement, and a chest computed tomography was ordered. Pulmonary nodules were evident, and endoscopically acquired samples were also positive for chromoblastomycosis. Extra‐dermal and systemic involvement in chromoblastomycosis is exceedingly rare and often associated with immunosuppression. There is only one other case of pulmonary chromoblastomycosis reported in the published work.
Density‐dependent life history and the dynamics of small populations
Authors: Mugabo Marianne , Perret Samuel , Legendre Stéphane , Le Galliard Jean‐François 
Published: July 2013

Summary

Small population dynamics depend importantly on the strength and shape of density dependence. Unfortunately, the lack of reliable life‐history data often prevents to make accurate demographic predictions for populations regulated by density dependence.

We created a gradient from low to high densities in small experimental populations of common lizards (Zootoca vivipara) and investigated the shape and strength of the density dependence of life‐history traits during a yearly cycle. We then analysed stochastic population dynamics using one‐sex and two‐sex age‐structured matrix models.

Body growth and reproductive performances decreased with density, yearling and adult survival and body size at birth were density‐independent, and juvenile survival increased with density. The density dependence of reproduction was partly explained by positive effects of body size on age at first reproduction and clutch size.

Parturition date decreased with density in sparse populations and then increased, providing one of the first empirical evidence of a component Allee effect in the phenology of reproduction.

Population growth rate (λ) was most affected by variations in juvenile and yearling survival. However, density at equilibrium was most affected by juvenile access to reproduction and yearling clutch size.

Stochastic simulations revealed that negative density dependence buffers the effects of initial density on extinction probability, has positive effects on the persistence of sparse populations and interacts with sex ratio fluctuations to shape extinction dynamics.

This study demonstrates that negative density dependence modifies the dynamics of small populations and should be investigated together with Allee effects to predict extinction risks.
Paralogous metabolism: S‐alkyl‐cysteine degradation in Bacillus subtilis
Authors: Chan Che‐Man , Danchin Antoine , Marlière Philippe , Sekowska Agnieszka 
Published: July 2013

SummaryMetabolism is prone to produce analogs of essential building blocks in the cell (here named paralogous metabolism). The variants result from lack of absolute accuracy in enzyme‐templated reactions as well as from molecular aging. If variants were left to accumulate, the earth would be covered by chemical waste. The way bacteria cope with this situation is essentially unexplored. To gain a comprehensive understanding of Bacillus subtilis sulphur paralogous metabolism, we used expression profiling with DNA arrays to investigate the changes in gene expression in the presence of S‐methyl‐cysteine (SMeC) and its close analog, methionine, as sole sulphur source. Altogether, more than 200 genes whose relative strength of induction was significantly different depending on the sulphur source used were identified. This allowed us to pinpoint operon ytmItcyJKLMNytmO_ytnIJ_rbfK_ytnLM as controlling the pathway cycling SMeC directly to cysteine, without requiring sulphur oxygenation. Combining genetic and physiological experiments, we deciphered the corresponding pathway that begins with protection of the metabolite by acetylation. Oxygenation of the methyl group then follows, and after deprotection (deacetylation), N‐formyl cysteine is produced. This molecule is deformylated by the second deformylase present in B. subtilis DefB, yielding cysteine. This pathway appears to be present in plant‐associated microbes.
American crows as carriers of vancomycin‐resistant enterococci with vanA gene
Authors: Oravcova Veronika , Zurek Ludek , Townsend Andrea , Clark Anne B. , Ellis Julie C. , Cizek Alois , Literak Ivan 
Published: July 2013

SummaryWe studied the vanA‐carrying vancomycin‐resistant enterococci (VRE) isolated from American crows in the United States during the winter 2011/2012. Faecal samples from crows were cultured selectively for VRE and characterized. Pulsed‐field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to examine epidemiological relationships of vanA‐containing VRE. Isolates were tested in vitro for their ability to horizontally transfer the vancomycin resistance trait. VRE with the vanA gene were found in 15 (2.5%) of 590 crows samples, from which we obtained 22 different isolates. Enterococcal species were Enterococcus faecium (14) and E. faecalis (8). One, two and 19 isolates originated from Kansas, New York State and Massachusetts, respectively. Based on MLST analysis, E. faecium isolates were grouped as ST18 (6 isolates), ST555 (2), and novel types ST749 (1), ST750 (3), ST751 (1), ST752 (1). Enterococcus faecalis isolates belonged to ST6 (1), ST16 (3) and ST179 (4). All isolates were able to transfer the vancomycin resistance trait via filter mating with very high transfer range. Clinically important enterococci with the vanA gene occur in faeces of wild American crows throughout the United States. These migrating birds may contribute to the dissemination of VRE in environment over large distances. [Correction added after first online publication on 06 August 2013: The number of E. faecium ST752 isolate is now amended to ‘1’, consistent with that shown in the ‘Results’ section and Figure 2.]
Revealing underlying vulnerable emotion in couple therapy: impact on session and final outcome
Authors: McKinnon Jacqueline M. , Greenberg Leslie S. 
Published: July 2013

This study examined how the revealing of underlying vulnerable emotion relates to session and final outcome in the context of emotion‐focused therapy for couples. Segments of videotaped therapy sessions were rated on a measure of underlying vulnerable emotional expression for twenty‐five couples. Results indicated that partners rated sessions in which underlying vulnerable emotion was expressed significantly more positively than control sessions on a measure of session outcome. Moreover, from pre to post, couples who were found to have expressed underlying vulnerable emotion at least once improved significantly more on a measure of trust, and marginally significantly more on a measure of unfinished business, than couples who were not found to have expressed underlying vulnerable emotion. Recommendations for treatment are provided in light of the findings.Practitioner points
It is recommended that couple therapists help partners to access and express underlying vulnerable emotion, because this appears to be associated with better session and final outcomes.
When an underlying vulnerable emotion begins to emerge, it is recommended that the therapist maintain the focus on this emotion and help to facilitate its full expression.
Using the Bayesian Improved Surname Geocoding Method (BISG) to Create a Working Classification of Race and Ethnicity in a Diverse Managed Care Population: A Validation Study
Authors: Adjaye‐Gbewonyo Dzifa , Bednarczyk Robert A. , Davis Robert L. , Omer Saad B. 
Published: July 2013

ObjectiveTo validate classification of race/ethnicity based on the Bayesian Improved Surname Geocoding method (BISG) and assess variations in validity by gender and age.Data Sources/Study SettingSecondary data on members of Kaiser Permanente Georgia, an integrated managed care organization, through 2010.Study DesignFor 191,494 members with self‐reported race/ethnicity, probabilities for belonging to each of six race/ethnicity categories predicted from the BISG algorithm were used to assign individuals to a race/ethnicity category over a range of cutoffs greater than a probability of 0.50. Overall as well as gender‐ and age‐stratified sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. Receiver operating characteristic (ROC) curves were generated and used to identify optimal cutoffs for race/ethnicity assignment.Principal FindingsThe overall cutoffs for assignment that optimized sensitivity and specificity ranged from 0.50 to 0.57 for the four main racial/ethnic categories (White, Black, Asian/Pacific Islander, Hispanic). Corresponding sensitivity, specificity, PPV, and NPV ranged from 64.4 to 81.4 percent, 80.8 to 99.7 percent, 75.0 to 91.6 percent, and 79.4 to 98.0 percent, respectively. Accuracy of assignment was better among males and individuals of 65 years or older.ConclusionsBISG may be useful for classifying race/ethnicity of health plan members when needed for health care studies.
HIV Testing in the Nation's Opioid Treatment Programs, 2005–2011: The Role of State Regulations
Authors: D'Aunno Thomas , Pollack Harold A. , Jiang Lan , Metsch Lisa R. , Friedmann Peter D. 
Published: July 2013

ObjectiveTo identify the extent to which clients in a national sample of opioid treatment programs (OTPs) received HIV testing in 2005 and 2011; to examine relationships between state laws for informed consent and pretest counseling and rates of HIV testing among OTP clients.Data SourceData were collected from a nationally representative sample of OTPs in 2005 (n = 171) and 2011 (n = 200).Study DesignRandom‐effects logit and interval regression analyses were used to examine changes in HIV testing rates and the relationship of state laws to HIV testing among OTPs.Data CollectionData on OTP provision of HIV testing were collected in phone surveys from OTP managers; data also were collected on state laws for HIV testing.Principal FindingsThe percentage of OTPs offering HIV testing decreased significantly from 93 percent in 2005 to 64 percent in 2011. Similarly, the percentage of clients tested decreased from an average of 41 percent in 2005 to 17 percent in 2011. OTPs located in states whose laws do not require pretest counseling and that use opt‐out consent were more likely to provide HIV testing and to test higher percentages of clients.ConclusionsThe results show the need to increase HIV testing among OTP clients; the results also underscore the beneficial possibilities of dropping pretest counseling as a requirement for HIV testing and of using the opt‐out approach to informed consent for testing.
Report ofAkabosia matsudoensis Kinoshita (Collembola;Paronellidae) fromKorea, with notes on theKorean aquatic springtail fauna
Authors: Kang Sangkyu , Park Kyung‐Hwa 
Published: July 2013

AbstractA hygrophilous collembolan species,Akabosia matsudoensisis redescribed and illustrated with a list and key to other aquatic fauna belonging toEntomobryoidea fromKorea. Specimens inhabiting the damp area near a creek were collected with hand net and aspirator. This species is characterized by the absence of scale, having 2 + 2 macrosetae on the vertex of the head, 2 feathered prelabial setae, dens crenulated and the base of mucro with bladder like appendage. GenusAkabosiareported only one species,A. matsudoensis, that was originally recorded inJapan;Korea is the second recorded country and it is the onlyParonellidae fromKorea.
Microbial production and chemical transformation of poly‐γ‐glutamate
Authors: Ashiuchi Makoto 
Published: July 2013

SummaryPoly‐γ‐glutamate (PGA), a novel polyamide material with industrial applications, possesses a nylon‐like backbone, is structurally similar to polyacrylic acid, is biodegradable and is safe for human consumption. PGA is frequently found in the mucilage of natto, a Japanese traditional fermented food. To date, three different types of PGA, namely a homo polymer of d‐glutamate (D‐PGA), a homo polymer of l‐glutamate (L‐PGA), and a random copolymer consisting of d‐ and l‐glutamate (DL‐PGA), are known. This review will detail the occurrence and physiology of PGA. The proposed reaction mechanism of PGA synthesis including its localization and the structure of the involved enzyme, PGA synthetase, are described. The occurrence of multiple carboxyl residues in PGA likely plays a role in its relative unsuitability for the development of bio‐nylon plastics and thus, establishment of an efficient PGA‐reforming strategy is of great importance. Aside from the potential applications of PGA proposed to date, a new technique for chemical transformation of PGA is also discussed. Finally, some techniques for PGA and its derivatives in advanced material technology are presented.
Magnetic resonance imaging appearances in primary and secondary angiosarcoma of the breast
Authors: O'Neill Ailbhe C , D'Arcy Clare , McDermott Enda , O'Doherty Ann , Quinn Cecily , McNally Sorcha 
Published: July 2013

SummaryAngiosarcomas are malignant tumours of endovascular origin. They are rare tumours accounting for 0.04–1% of all breast malignancies. Two different forms are described: primary, occurring in young women, and secondary angiosarcoma, which occurs in older women with a history of breast‐conserving surgery and radiation therapy. Imaging findings on mammography and ultrasound are non‐specific, but magnetic resonance imaging with dynamic contrast enhancement is more informative. We present two cases – one of primary and one of secondary angiosarcoma – and review the imaging findings.
Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome
Authors: Bourgeois Yann X. C. , Lhuillier Emeline , Cézard Timothée , Bertrand Joris A. M. , Delahaie Boris , Cornuault Josselin , Duval Thomas , Bouchez Olivier , Milá Borja , Thébaud Christophe 
Published: July 2013

AbstractHere, we present an adaptation of restriction‐site‐associated DNA sequencing (RAD‐seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white‐eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least 386 000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80 000 SNPs that could be mapped unambiguously and are evenly distributed across the genome. Thus, our approach provides a good illustration of the high potential of paired‐end RAD sequencing of pooled DNA samples combined with comparative assembly to the zebra finch genome to build large contigs and characterize vast numbers of informative SNPs in nonmodel passerine bird species in a very efficient and cost‐effective way.
Minor impact of ocean acidification to the composition of the active microbial community in an Arctic sediment
Authors: Tait Karen , Laverock Bonnie , Shaw Jennifer , Somerfield Paul J. , Widdicombe Steve 
Published: July 2013

SummaryEffects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO2 concentrations [380 (present day), 540, 750, 1120 and 3000 μatm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO2 treatments. Only when the highest and lowest pCO2 treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO2 concentration, indicating that these groups may be able to take advantage of changing pH or pCO2 conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore‐water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO2 on sediment physicochemical parameters, biogeochemistry and microbial community dynamics.