bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic flux analysis using 13C peptide label measurements
Authors: Mandy Dominic E. , Goldford Joshua E. , Yang Hong , Allen Doug K. , Libourel Igor G.L. 
Published: November 2013

Summary13C metabolic flux analysis (MFA) has become the experimental method of choice to investigate the cellular metabolism of microbes, cell cultures and plant seeds. Conventional steady‐state MFA utilizes isotopic labeling measurements of amino acids obtained from protein hydrolysates. To retain spatial information in conventional steady‐state MFA, tissues or subcellular fractions must be dissected or biochemically purified. In contrast, peptides retain their identity in complex protein extracts, and may therefore be associated with a specific time of expression, tissue type and subcellular compartment. To enable ‘single‐sample’ spatially and temporally resolved steady‐state flux analysis, we investigated the suitability of peptide mass distributions (PMDs) as an alternative to amino acid label measurements. PMDs are the discrete convolution of the mass distributions of the constituent amino acids of a peptide. We investigated the requirements for the unique deconvolution of PMDs into amino acid mass distributions (AAMDs), the influence of peptide sequence length on parameter sensitivity, and how AAMD and flux estimates that are determined through deconvolution compare to estimates from a conventional GC–MS measurement‐based approach. Deconvolution of PMDs of the storage protein β–conglycinin of soybean (Glycine max) resulted in good AAMD and flux estimates if fluxes were directly fitted to PMDs. Unconstrained deconvolution resulted in inferior AAMD and flux estimates. PMD measurements do not include amino acid backbone fragments, which increase the information content in GC–MS‐derived analyses. Nonetheless, the resulting flux maps were of comparable quality due to the precision of Orbitrap quantification and the larger number of peptide measurements.
Spatial Epidemiology ofEscherichia coliO157:H7 in Dairy Cattle in Relation to Night Roosts OfSturnus vulgaris(European Starling) inOhio,USA(2007–2009)
Authors: Swirski A. L. , Pearl D. L. , Williams M. L. , Homan H. J. , Linz G. M. , Cernicchiaro N. , LeJeune J. T. 
Published: November 2013

SummaryThe goal of our study was to use spatial scan statics to determine whether the night roosts ofEuropean starlings (Sturnus vulgaris) act as point sources for the dissemination ofEscherichia coliO157:H7 among dairy farms. From 2007 to 2009, we collected bovine faecal samples (n = 9000) and starling gastrointestinal contents (n = 430) from 150 dairy farms in northeasternOhio,USA. Isolates ofE. coliO157:H7 recovered from these samples were subtyped using multilocus variable‐number tandem repeat analysis (MLVA). GeneratedMLVAtypes were used to construct a dendrogram based on a categorical multistate coefficient and unweighted pair‐group method with arithmetic mean (UPGMA). Using a focused spatial scan statistic, we identified statistically significant spatial clusters among dairy farms surrounding starling night roosts, with an increased prevalence ofE. coliO157:H7‐positive bovine faecal pats, increased diversity of distinguishableMLVAtypes and a greater number of isolates withMLVAtypes from bovine‐starling clades versus bovine‐only clades. Thus, our findings are compatible with the hypothesis that starlings have a role in the dissemination ofE. coliO157:H7 among dairy farms, and further research into starling management is warranted.
The MARVEL Domain Protein Nce102 Regulates Actin Organization and Invasive Growth of Candida albicans
Authors: Douglas Lois M. , Wang Hong X. , Konopka James B. 
Published: November 2013

ABSTRACT

Invasive growth of the fungal pathogen
Candida albicans
into tissues promotes disseminated infections in humans. The plasma membrane is essential for pathogenesis because this important barrier mediates morphogenesis and invasive growth, as well as secretion of virulence factors, cell wall synthesis, nutrient import, and other processes. Previous studies showed that the Sur7 tetraspan protein that localizes to MCC (membrane compartment occupied by Can1)/eisosome subdomains of the plasma membrane regulates a broad range of key functions, including cell wall synthesis, morphogenesis, and resistance to copper. Therefore, a distinct tetraspan protein found in MCC/eisosomes, Nce102, was investigated. Nce102 belongs to the MARVEL domain protein family, which is implicated in regulating membrane structure and function. Deletion of
NCE102
did not cause the broad defects seen in
sur7Δ
cells. Instead, the
nce102Δ
mutant displayed a unique phenotype in that it was defective in forming hyphae and invading low concentrations of agar but could invade well in higher agar concentrations. This phenotype was likely due to a defect in actin organization that was observed by phalloidin staining. In support of this, the invasive growth defect of a
bni1Δ
mutant that mislocalizes actin due to lack of the Bni1 formin was also reversed at high agar concentrations. This suggests that a denser matrix provides a signal that compensates for the actin defects. The
nce102Δ
mutant displayed decreased virulence and formed abnormal hyphae in mice. These studies identify novel ways that Nce102 and the physical environment surrounding
C. albicans
regulate morphogenesis and pathogenesis.

IMPORTANCE
The plasma membrane promotes virulence of the human fungal pathogen
Candida albicans
by acting as a protective barrier around the cell and mediating dynamic activities, such as morphogenesis, cell wall synthesis, secretion of virulence factors, and nutrient uptake. To better understand how the plasma membrane contributes to virulence, we analyzed a set of eight genes encoding MARVEL family proteins that are predicted to function in membrane organization. Interestingly, deletion of one gene,
NCE102
, caused a strong defect in formation of invasive hyphal growth
in vitro
and decreased virulence in mice. The
nce102Δ
mutant cells showed defects in actin organization that underlie the morphogenesis defect, since mutation of a known regulator of actin organization caused a similar defect. These studies identify a novel way in which the plasma membrane regulates the actin cytoskeleton and contributes to pathogenesis.
Injuries in elite and recreational snowboarders
Authors: Wijdicks Coen A , Rosenbach Brandon S , Flanagan Troy R , Bower Gillian E , Newman Kelly E , Clanton Thomas O , Engebretsen Lars , LaPrade Robert F , Hackett Tom R 
Published: November 2013

BackgroundThe relatively young sport of snowboarding exhibits high injury rates. The current efforts to characterise the injury pattern of snowboarders focus largely on the general snowboard population and upper extremity injuries, the most common injury site in snowboarders as a whole.MethodsIn an effort to describe the current published information available on snowboarding injuries in the elite-level population, a literature search was performed and the articles related to snowboarding injuries were analysed. Additionally, the literature pertaining to biomechanical analyses of injury and injury prevention was included.ResultsStudies rarely stratify the snowboarders by skill level, a classification which has a profound effect on the riding activities of snowboarders and the resultant injury patterns. Elite-level snowboarders are often injured when performing difficult manoeuvres at high velocities and with amplified levels of force to the lower limbs. Consequently, elite-level snowboarders suffer from injuries that are of higher severity and have decidedly greater lower extremity injury rates. Conversely, injuries to the upper extremities are decreased in the elite snowboarders. Furthermore, little has been published regarding the biomechanical analyses and injury prevention for the protection of the lower extremities in snowboarding.ConclusionsSnowboarding continues to evolve as a sport. This includes a steady progression in the degree of difficulty of the manoeuvres conducted by athletes and an increase in the number of snowboarders attempting such manoeuvres. The injury patterns across the skill levels are markedly different, and it is imperative that the research directed towards understanding the disparate lower extremity injury pattern of elite-level snowboarders is increased.
The impact of neurological disorders on the risk for falls in the community dwelling elderly: a case-controlled study
Authors: Homann Barbara , Plaschg Annemarie , Grundner Marion , Haubenhofer Alice , Griedl Theresa , Ivanic Gerd , Hofer Edith , Fazekas Franz , Homann Carl Nikolaus 
Published: November 2013

ObjectivesOwing to a lack of data, our aim was to evaluate and compare the impact of various common neurological diseases on the risk for falls in independent community dwelling senior citizens.DesignProspective case-controlled study.SettingGeneral hospital.ParticipantsOf 298 consecutive patients and 214 controls enrolled, 228 patients (aged 74.5±7.8; 61% women) and 193 controls (aged 71.4±6.8; 63% women) were included. The exclusion criteria were as follows: for patients, severe disability, disabling general condition or severe cognitive impairment; for controls, any history of neurological disorders or disabling medical conditions; and for both, age below 60 years. A matching process led to 171 age-matched and gender-matched pairs of neurological patients and healthy controls.Main outcome measuresA 1-year incidence of falls based on patients' 12-month recall; motor and non-motor function tests to detect additional risk factors.Results46% of patients and 16% of controls fell at least once a year. Patients with stroke (89%), Parkinson’s disease (77%), dementia (60%) or epilepsy (57%) had a particularly high proportion of fallers, but even subgroups of patients with the least fall-associated neurological diseases like tinnitus (30%) and headache (28%) had a higher proportion of fallers than the control group. Neuropathies, peripheral nerve lesions and Parkinson's disease were predisposing to recurrent falls. A higher number of neurological comorbidities (p<0.001), lower Barthel Index values (p<0.001), lower Activities-Specific Balance Confidence scores (p<0.001) and higher Center of Epidemiological Studies Depression scores (p<0.001) as well as higher age (p<0.001) and female gender (p=0.003) proved to further increase the risk of falls.ConclusionsMedical practitioners, allied health professionals and carers should be aware that all elderly neurological patients seen in outpatient settings are potentially at high risk for falls; they should query them routinely about previous falls and fall risks and advise them on preventive strategies.
The cost-effectiveness of a structured education pulmonary rehabilitation programme for chronic obstructive pulmonary disease in primary care: the PRINCE cluster randomised trial
Authors: Gillespie Paddy , O'Shea Eamon , Casey Dympna , Murphy Kathy , Devane Declan , Cooney Adeline , Mee Lorraine , Kirwan Collette , McCarthy Bernard , Newell John ,   for the PRINCE study team
Published: November 2013

ObjectiveTo assess the cost-effectiveness of a structured education pulmonary rehabilitation programme (SEPRP) for chronic obstructive pulmonary disease (COPD) relative to usual practice in primary care. The programme consisted of group-based sessions delivered jointly by practice nurses and physiotherapists over 8 weeks.DesignCost-effectiveness and cost-utility analysis alongside a cluster randomised controlled trial.Setting32 general practices in Ireland.Participants350 adults with COPD, 69% of whom were moderately affected.InterventionsIntervention arm (n=178) received a 2 h group-based SEPRP session per week over 8 weeks delivered jointly by a practice nurse and physiotherapist at the practice surgery or nearby venue. The control arm (n=172) received the usual practice in primary care.Main outcome measuresIncremental costs, Chronic Respiratory Questionnaire (CRQ) scores, quality-adjusted life years (QALYs) gained estimated using the generic EQ5D instrument, and expected cost-effectiveness at 22 weeks trial follow-up.ResultsThe intervention was associated with an increase of €944 (95% CIs 489 to 1400) in mean healthcare cost and €261 (95% CIs 226 to 296) in mean patient cost. The intervention was associated with a mean improvement of 1.11 (95% CIs 0.35 to 1.87) in CRQ Total score and 0.002 (95% CIs −0.006 to 0.011) in QALYs gained. These translated into incremental cost-effectiveness ratios of €850 per unit increase in CRQ Total score and €472 000 per additional QALY gained. The probability of the intervention being cost-effective at respective threshold values of €5000, €15 000, €25 000, €35 000 and €45 000 was 0.980, 0.992, 0.994, 0.994 and 0.994 in the CRQ Total score analysis compared to 0.000, 0.001, 0.001, 0.003 and 0.007 in the QALYs gained analysis.ConclusionsWhile analysis suggests that SEPRP was cost-effective if society is willing to pay at least €850 per one-point increase in disease-specific CRQ, no evidence exists when effectiveness was measured in QALYS gained.Trial RegistrationCurrent Controlled TrialsISRCTN52 403 063.
The CopenHeartSF trial—comprehensive sexual rehabilitation programme for male patients with implantable cardioverter defibrillator or ischaemic heart disease and impaired sexual function: protocol of a randomised clinical trial
Authors: Johansen Pernille Palm , Zwisler Ann-Dorthe , Hastrup-Svendsen Jesper , Frederiksen Marianne , Lindschou Jane , Winkel Per , Gluud Christian , Giraldi Annamaria , Steinke Elaine , Jaarsma Tiny , Berg Selina Kikkenborg 
Published: November 2013

IntroductionSexuality is an important part of people’s physical and mental health. Patients with heart disease often suffer from sexual dysfunction. Sexual dysfunction has a negative impact on quality of life and well-being in persons with heart disease, and sexual dysfunction is associated with anxiety and depression. Treatment and care possibilities seem to be lacking. Studies indicate that non-pharmacological interventions such as exercise training and psychoeducation possess the potential of reducing sexual dysfunction in patients with heart disease. The CopenHeartSF trial will investigate the effect of a comprehensive sexual rehabilitation programme versus usual care.Methods and analysisCopenHeartSF is an investigator-initiated randomised clinical superiority trial with blinded outcome assessment, with 1:1 central randomisation to sexual rehabilitation plus usual care versus usual care alone. Based on sample size calculations, 154 male patients with impaired sexual function due to implantable cardioverter defibrillator or ischaemic heart disease will be included from two university hospitals in Denmark. All patients receive usual care and patients allocated to the experimental intervention group follow a 12-week sexual rehabilitation programme consisting of an individualised exercise programme and psychoeducative consultation with a specially trained nurse. The primary outcome is sexual function measured by the International Index of Erectile Function. The secondary outcome measure is psychosocial adjustment to illness by the Psychosocial Adjustment to Illness Scale, sexual domain. A number of explorative analyses will also be conducted.Ethics and disseminationCopenHeartSF is approved by the regional ethics committee (no H-4-2012-168) and the Danish Data Protection Agency (no 2007-58-0015) and is performed in accordance with good clinical practice and the Declaration of Helsinki in its latest form.RegistrationClinicaltrials.gov identifier:NCT01796353.
Chapter 10 Biogeography of Ordovician linguliform and craniiform brachiopods
Authors: Popov Leonid E. , Holmer Lars E. , Bassett Michael G. , Pour Mansoureh Ghobadi , Percival Ian G. 
Published: November 2013

Abstract
The biogeographical patterns shown by Ordovician linguliform and craniiform brachiopods are greatly influenced by their dominance in low-diversity associations in marginal environments. This is particularly evident in the Early Ordovician, when linguliform-dominated dysaerobic assemblages are widely distributed along the deep shelves of Gondwana, the Kazakhstanian terranes and in Baltica. By the Darriwilian, micromorphic linguliforms are characteristic components of the pantropical climatic-controlled faunas of Laurentia, Cuyania and Kazakhstanian terranes, which – in spite of separation by extensive oceans – retain a distinct similarity. Analysis of craniiform biogeographical distribution is impeded significantly by the poor state of craniide taxonomy and lack of reliable data from most regions. However, in general their biogeographical dispersion is similar to other groups of the Palaeozoic Evolutionary Fauna. Unlike the linguliforms, which are important members of the Cambrian Evolutionary Fauna, there is no convincing Cambrian craniiform record; they may have evolved and dispersed from Gondwana and associated microcontinents and island arcs. The earliest well-established record is from the late Tremadocian of temperate to high-latitude peri-Gondwana. During most of the Ordovician, they have a peri-Iapetus distribution. They are very rare or absent in tropical Gondwana, South China and Kazakhstanian terranes and are not yet documented from Siberia. The trimerellides probably evolved in tropical peri-Gondwanan island arc settings. Their dispersion and major features of biogeography mirror those of atrypides.
Chapter 12 A review of the Early Palaeozoic biogeography of bryozoans
Authors: Buttler Caroline J. , Jackson Patrick N. Wyse , Ernst Andrej , Mckinney Frank K. 
Published: November 2013

Abstract
The palaeogeographical distributions of Early Palaeozoic bryozoan faunas are reviewed. Previous studies are examined and new databases have been assembled of the stratigraphical and geographical distribution of Ordovician and Silurian taxa. Analysis was carried out using cluster analysis based on Jaccard’s coefficient and paired group method, as well as principal coordinate analysis based on Jaccard’s coefficient, to examine the relationships between different localities. Bryozoan faunas increased in diversity throughout the Ordovician peaking with 133 genera during the Katian. In the earliest Ordovician provincialism is difficult to determine, but by the Darriwilian five distinct provinces developed, decreasing to four in the Sandbian. There was a decrease in provinciality throughout the Katian as faunas became less endemic, caused by the reduction of geographical barriers. Following the extinction of many genera at the end of the Ordovician, early Silurian faunas contain remnant taxa. Subsequently fenestrates began to dominate faunas. During the Llandovery bryozoans began to show distinct provincialism, but this declined during the Wenlock, only to re-emerge during the Ludlow. Late Silurian (Pridoli) faunas are sparse but nevertheless show possible division into two provinces.
Chapter 14 Palaeobiogeography of Ordovician echinoderms
Authors: Lefebvre Bertrand , Sumrall Colin D. , Shroat-Lewis Rene A. , Reich Mike , Webster Gary D. , Hunter Aaron W. , Nardin Elise , Rozhnov Sergei V. , Guensburg Thomas E. , Touzeau Alexandra , Noailles Fleur , Sprinkle James 
Published: November 2013

Abstract
The palaeobiogeographical distribution of the six major clades of Ordovician echinoderms (asterozoans, blastozoans, crinoids, echinozoans, edrioasteroids and stylophorans) is analysed based on a comprehensive and up-to-date database compiling 3701 occurrences (1938 species recorded from 331 localities) of both complete specimens and isolated ossicles. Although historically biased towards a limited number of regions (Europe, North America, Russia), the resulting dataset makes it possible to identify six main palaeobiogeographical provinces for Ordovician echinoderms: Laurentia, Baltica, West Gondwana, East Gondwana, Avalonia and Siberia. At a global scale, the high endemicity of echinoderms during the Early to Middle Ordovician coincides with the time of maximum dispersal of continental masses. Late Ordovician faunas tend to become more cosmopolitan, possibly as a consequence of changing palaeogeography and/or relatively higher sea-levels in the Sandbian–Katian interval. Regional biodiversity patterns of Ordovician echinoderms confirm that their major diversification during the Ordovician is not a single, universal evolutionary event, but rather results from the complex addition of contrasted local evolutionary trends.
Chapter 15 Biogeography of Ordovician and Silurian gastropods, monoplacophorans and mimospirids
Authors: Ebbestad Jan Ove R. , Frýda Jiří , Wagner Peter J. , Horný Radvan J. , Isakar Mare , Stewart Sarah , Percival Ian G. , Bertero Verònica , Rohr David M. , Peel John S. , Blodgett Robert B. , Högström Anette E. S. 
Published: November 2013

Abstract
The biogeographical distribution of Ordovician and Silurian gastropods, monoplacophorans and mimospirids has been analysed on a generic level. The dataset contains 334 genera and 2769 species, yielding 1231 records of genera with 2274 occurrences worldwide. There is a bias towards eastern Laurentia, Baltica and Perunica records. Some 53.1% of the records are Ordovician. The study demonstrates that these molluscs are well suited to being used to improve understanding of Ordovician and Silurian biogeographical provinciality. Specific points are that: a Lower Ordovician assemblage is evident in Laurentia; the fauna of the Argentinean Precordillera is Laurentian until the Darriwilian, when taxa are shared with North China; Late Silurian gastropods from the Alexander terrane (SE Alaska) are unknown in Laurentia, but support a rift origin of this terrane from NE Siberia; Perunica, Ibero-Armorica and Morocco cluster together throughout the Ordovician but Perunica and Morocco are closer; Darriwilian–Sandbian deep-water Bohemian taxa occur in Baltica; a Laurentian–Baltica proximity is unsupported until the Silurian; Siberia clusters with North China and eastern Laurentia during the Tremadocian–Darriwilian; during the Gorstian–Pridoli Siberia clusters with the Farewell and Alexander terranes; North China may have been close to Laurentia and the Argentinean margin of Gondwana; and the affinity of Tarim taxa is problematic.
Chapter 17 Biogeographical distribution patterns in Early Palaeozoic Rostroconchia (Mollusca)
Authors: Amler Michael R. W. , Rogalla Nicole S. 
Published: November 2013

Abstract

The geographical distribution of rostroconch taxa of the orders Ribeirioida and Conocardiida, mostly across the equatorial continents and oceans, is compiled for six presumed diversity acmes in the early Early Ordovician (
c.
485 Ma), the late Early–early Middle Ordovician (
c.
475 Ma), the Late Ordovician (
c.
455 Ma), the Early Silurian (
c.
435 Ma), the late Early–early Late Silurian (
c.
425 Ma) and the early Early Devonian (
c.
415 Ma), based on our present, uneven knowledge. Rostroconchs show distribution patterns which enable a provisional separation of biogeographical provinces at least from the Silurian onward, comparable with Late Palaeozoic rostroconch distributional patterns. The distributions of tabulate corals, trilobites and bivalves appear roughly comparable, but not the nektic and planktic groups. A restriction to low latitudes (‘tropical’ realms) is clear for members of
Ribeiria
and
Eopteria
in the Early Ordovician, similar to proven patterns for hippocardiid rostroconchs from the Late Silurian onward until the Middle Permian. Preliminary rostroconch provinces or subprovinces, respectively, are currently discernable in the Silurian and Devonian for northwestern Laurentia, south-central Laurentia/Baltica and the north-central margin of Gondwana (i.e. Perunica, Bohemia). Rostroconch distributional data for SE Asia, China, Kazakhstan, Siberia and Australia are sparse and require further studies.