183 research outputs found

    Data production models for the CDF experiment

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    The data production for the CDF experiment is conducted on a large Linux PC farm designed to meet the needs of data collection at a maximum rate of 40 MByte/sec. We present two data production models that exploits advances in computing and communication technology. The first production farm is a centralized system that has achieved a stable data processing rate of approximately 2 TByte per day. The recently upgraded farm is migrated to the SAM (Sequential Access to data via Metadata) data handling system. The software and hardware of the CDF production farms has been successful in providing large computing and data throughput capacity to the experiment.Comment: 8 pages, 9 figures; presented at HPC Asia2005, Beijing, China, Nov 30 - Dec 3, 200

    Zootechnical and genetic aspects of a Prolific Merino Program

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    In a Prolific Merino nucleus herd of 200 ewes the ovulation rate (OR) test results obtained in 169 animals between 1988 and 1993 were compared with those of 113 ewes from the same herd in 1996. Whereas earlier the ratio of individuals showing an OR ≥ 4 was only 32%, that of the group checked in 1996 was 59%. This increase could be attributed to 40 ewes, both of whose parents had proven to be homozygous carriers of the prolific gene. To develop the Prolific Merino breed, 21 Booroola Merino rams were imported from New Zealand, and mostly their frozen semen was used. Of these rams, one was not a prolific gene carrier, 8 were homozygous carriers, 10 were heterozygous carriers and two had not been identified yet. Of the 36 home-bred rams, 9 proved to be homozygous by parents, 11 heterozygous, 8 homozygous, one proved to be a non-carrier, and 7 rams and their frozen semen were to be progeny tested. Six thousand doses of frozen semen from a total of 33 animals (16 imported rams and their 17 home-bred offspring) are stored in plastic straws. Sixty-three % of this is semen reserve from rams of the FecBFecBgenotype, belonging to 10 ram lines. The remaining 37% is gene reserve intended for creating homozygous ram lines. Only one ram (no. 3244) was bought for the nucleus herd, the other ram lines were introduced into the herd by assortative mating, using intrauterine insemination. The average conception rate found after 472 intrauterine inseminations was 53% with large (occasionally 10-100%) individual ram differences

    Data processing model for the CDF experiment

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    The data processing model for the CDF experiment is described. Data processing reconstructs events from parallel data streams taken with different combinations of physics event triggers and further splits the events into datasets of specialized physics datasets. The design of the processing control system faces strict requirements on bookkeeping records, which trace the status of data files and event contents during processing and storage. The computing architecture was updated to meet the mass data flow of the Run II data collection, recently upgraded to a maximum rate of 40 MByte/sec. The data processing facility consists of a large cluster of Linux computers with data movement managed by the CDF data handling system to a multi-petaByte Enstore tape library. The latest processing cycle has achieved a stable speed of 35 MByte/sec (3 TByte/day). It can be readily scaled by increasing CPU and data-handling capacity as required.Comment: 12 pages, 10 figures, submitted to IEEE-TN

    Характеристика корів симентальської породи за господарськи корисними ознаками в умовах Львівщини

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    There are indicators data of body weight, body parts measurements, reproductive ability, milk production, morphological and functional properties of udder, the duration of use and economic reasons of disposal of Simmental cows in terms of Lviv oblast. It was established that the experimental cows by live weight during their growth in all ages have been prevailing minimum requirements of breed standard. They are marked by peculiar to combined breed type of body structure with well–defined not only milk but also meat forms, they had strong skeleton and were quite tall (withers height – 131.1 cm). However, the width of the breast in most cows, that is not enough for combined breed (on an average 41.4 cm). Simmentals age at the moment of the 1st insemination was 19.7, while during the 1st calving – 29.0 months, the duration of the service–period, depending on lactation, was within 96.8 – 112.0, of inter–calving period – within 381.6 – 396.9 day. They were characterized by an average fertility and high adaptablity. Simmentals milk yield, depending on lactation, was 3026,4–3810,2 kg, fat content in milk – 3.76 – 3.81% and quantity of milk fat 113.6 – 145.0 kg. Cows after the 4th calving had the highest milk productivity. During the all studied lactations cows milk yield and quantity of milk fat predominated breed standard. They had a well developed udder. 68.2% cows after the first calving had cupped udder, 25.9% – wash–tub and 6.9% – round udder. Their intensity of milk yield was 1.53 kg/min. Simmental cows duration of economic use in the conditions of Lviv oblast was 1.904.1 day or 5.3 lactations, lifetime yield – 18011, lifetime quantity of milk fat – 688 kg. Most reasons for dropped out of the herd was dysfunction of reproduction (35.7%) and low productivity (21.3%).Наведено дані щодо показників живої маси, промірів статей тіла, відтворювальної здатності, молочної продуктивності, морфо–функціональних властивостей вимені, тривалості господарського використання та причин вибуття корів симентальської породи в умовах Львівщини. Встановлено, що піддослідні корови за живою масою у період їх вирощування у всі вікові періоди переважали мінімальні вимоги стандарту породи. Вони відзначалися характерним для комбінованих порід типом будови тіла з добре вираженими не лише молочними, але й м'ясними формами, мали міцний кістяк і були досить високими (висота в холці – 131,1 см). Проте, ширина грудей у більшості особин, як для тварин комбінованого напряму продуктивності, є дещо недостатньою (в середньому 41,4 см). Вік сименталів при І осіменінні становив 19,7, а при І отеленні –29,0 місяців, тривалість сервіс–періоду, залежно від лактації, знаходилася в межах 96,8 – 112,0, міжотельного періоду – в межах 381,6 – 396,9 дня. Вони характеризувалися середньою плодючістю та високою адаптаційною здатністю. Надій корів симентальської породи, залежно від лактації, становив 3026,4 – 3810,2 кг, вміст жиру в молоці – 3,76 – 3,81% та кількість молочного жиру 113,6 – 145,0 кг. Найвищі показники молочної продуктивності спостерігалися у тварин з четвертим отеленням. За всі досліджувані лактації піддослідні корови переважали за надоєм та кількістю молочного жиру стандарт породи. У них була добре розвинута молочна залоза. 68,2 % первісток мали чашоподібну форму вимені, 25,9% – ванноподібну і 6,9% – округлу. Інтенсивність молоковіддачі у них становила 1,53 кг/хв. У корів симентальської породи в умовах Львівщини тривалість господарського використання складала 1904,1 дня або 5,3 лактацій, довічний надій – 18011, довічна кількість молочного жиру – 688 кг. Найбільше тварин вибувало зі стада через порушення функції відтворення (35,7%) та низьку продуктивність (21,3%)

    An Evaluation of Putative Sympatric Speciation within Limnanthes (Limnanthaceae)

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    Limnanthes floccosa ssp. floccosa and L. floccosa ssp. grandiflora are two of five subspecies within Limnanthes floccosa endemic to vernal pools in southern Oregon and northern California. Three seasons of monitoring natural populations have quantified that L. floccosa ssp. grandiflora is always found growing sympatrically with L. floccosa ssp. floccosa and that their flowering times overlap considerably. Despite their subspecific rank within the same species crossing experiments have confirmed that their F1 hybrids are sterile. An analysis of twelve microsatellite markers, with unique alleles in each taxon, also shows exceedingly low levels of gene flow between populations of the two subspecies. Due to the lack of previous phylogenetic resolution among L. floccosa subspecies, we used Illumina next generation sequencing to identify single nucleotide polymorphisms from genomic DNA libraries of L. floccosa ssp. floccosa and L. floccosa ssp. grandiflora. These data were used to identify single nucleotide polymorphisms in the chloroplast, mitochondrial, and nuclear genomes. From these variable loci, a total of 2772 bp was obtained using Sanger sequencing of ten individuals representing all subspecies of L. floccosa and an outgroup. The resulting phylogenetic reconstruction was fully resolved. Our results indicate that although L. floccosa ssp. floccosa and L. floccosa ssp. grandiflora are closely related, they are not sister taxa and therefore likely did not diverge as a result of a sympatric speciation event

    Effect of axillary brachial plexus blockade on baroreflex-induced skin vasomotor responses: Assessing the effectiveness of sympathetic blockade

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    Background: The combination of laser Doppler flowmetry and non-invasive blood pressure monitoring allows the continuous observation of cutaneous vascular resistance (CVR). Continuous recording of unmodulated skin blood flow (SBF) is very sensitive to artefacts, rendering the method unreliable. In contrast, intermittent short lasting challenges of the CVR by cardiovascular autonomic reflexes may provide information about the responsiveness of the sympathetic nervous system in the skin. Methods: Eleven patients with below-wrist hand surgery (six males and five females; aged 35.2 ± 7.1 years) performed Valsalva maneuver following axillary blockade. Skin blood flow was continuously monitored on the forearm of the side axillary blockade, as well as on the contra-lateral forearm, which was used as the control. The responses were expressed as changes compared with the baseline level derived from a resting period of 30s. The maxima

    Genotyping of black grouse MHC class II B using reference Strand-Mediated Conformational Analysis (RSCA)

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    <p>Abstract</p> <p>Background</p> <p>The Major Histocompatibility Complex (MHC) is a cluster of genes involved in the vertebrate immune system and includes loci with an extraordinary number of alleles. Due to the complex evolution of MHC genes, alleles from different loci within the same MHC class can be very similar and therefore difficult to assign to separate loci. Consequently, single locus amplification of MHC genes is hard to carry out in species with recently duplicated genes in the same MHC class, and multiple MHC loci have to be genotyped simultaneously. Since amplified alleles have the same length, accurate genotyping is difficult. Reference Strand-Mediated Conformational Analysis (RSCA), which is increasingly used in studies of natural populations with multiple MHC genes, is a genotyping method capable to provide high resolution and accuracy in such cases.</p> <p>Findings</p> <p>We adapted the RSCA method to genotype multiple MHC class II B (BLB) genes in black grouse (<it>Tetrao tetrix</it>), a non-model galliform bird species, using a 96-Capillary Array Electrophoresis, the MegaBACE™ 1000 DNA Analysing System (GE Healthcare). In this study we used fluorescently labelled reference strands from both black grouse and hazel grouse and observed good agreement between RSCA and cloning/sequencing since 71 alleles were observed by cloning/sequencing and 76 alleles by RSCA among the 24 individuals included in the comparison. At the individual level however, there was a trend towards more alleles scored with RSCA (1-6 per individual) than cloning/sequencing (1-4 per individual). In 63% of the pair-wise comparison, the identical allele was scored in RSCA as in cloning/sequencing. Nine out of 24 individuals had the same number of alleles in RSCA as in cloning/sequencing. Our RSCA protocol allows a faster RSCA genotyping than presented in many other RSCA studies.</p> <p>Conclusions</p> <p>In this study, we have developed the RSCA typing method further to work on a 96-Capillary Array Electrophoresis (MegaBACE™ 1000). Our RSCA protocol can be applied to fast and reliable screening of MHC class II B diversity of black grouse populations. This will facilitate future large-scale population studies of black grouse and other galliformes species with multiple inseparable MHC loci.</p

    Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England

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    BACKGROUND: Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform infection control. Here, we describe a protracted hospital outbreak of multidrug-resistant A. baumannii, in which whole-genome sequencing (WGS) was used to obtain a high-resolution view of the relationships between isolates. METHODS: To delineate and investigate the outbreak, we attempted to genome-sequence 114 isolates that had been assigned to the A. baumannii complex by the Vitek2 system and obtained informative draft genome sequences from 102 of them. Genomes were mapped against an outbreak reference sequence to identify single nucleotide variants (SNVs). RESULTS: We found that the pulsotype 27 outbreak strain was distinct from all other genome-sequenced strains. Seventy-four isolates from 49 patients could be assigned to the pulsotype 27 outbreak on the basis of genomic similarity, while WGS allowed 18 isolates to be ruled out of the outbreak. Among the pulsotype 27 outbreak isolates, we identified 31 SNVs and seven major genotypic clusters. In two patients, we documented within-host diversity, including mixtures of unrelated strains and within-strain clouds of SNV diversity. By combining WGS and epidemiological data, we reconstructed potential transmission events that linked all but 10 of the patients and confirmed links between clinical and environmental isolates. Identification of a contaminated bed and a burns theatre as sources of transmission led to enhanced environmental decontamination procedures. CONCLUSIONS: WGS is now poised to make an impact on hospital infection prevention and control, delivering cost-effective identification of routes of infection within a clinically relevant timeframe and allowing infection control teams to track, and even prevent, the spread of drug-resistant hospital pathogens
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