bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prokaryotic taxonomy in the sequencing era – the polyphasic approach revisited
Authors: Kämpfer Peter , Glaeser Stefanie P. 
Published: October 2011

SummaryThe ultimate goal of taxonomy is to establish a system that mirrors the ‘order in nature’. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as ‘backbone of prokaryote taxonomy’ at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far behind their accumulation. Genes and genomes do not function on its own and can only display their potential within the cell as the basic unit of evolution (and hence taxonomy). It is the phenotype and the natural selection that ‘drive’ evolution in a given environment. In this context, the ‘polyphasic taxonomic approach’ should be revisited again, taking into account the novel insights into genomes and other ‘omic’ sciences in a more strict and detailed context with the phenotype. This approach allows a more holistic view and provides a sound basis for describing the diversity of prokaryotes and has the potential to become the foundation of a more stable, in‐depth taxonomy of the prokaryotes.
Metagenomic analysis of DNA viruses in a wastewater treatment plant in tropical climate
Authors: Tamaki Hideyuki , Zhang Rui , Angly Florent E. , Nakamura Shota , Hong Pei‐Ying , Yasunaga Teruo , Kamagata Yoichi , Liu Wen‐Tso 
Published: October 2011

SummaryViruses have been detected in the different stages of wastewater treatment plants (WWTPs) at concentrations of 108–1010 ml−1 of virus‐like particles (VLPs), 10–1000 times higher than in natural aquatic environments, suggesting that WWTPs can be considered as an important reservoir and source of viruses. This study revealed novel diversity and function with the DNA viral communities in the influent, activated sludge, anaerobic digester, and effluent of a domestic WWTP using metagenomics. WWTP was a very specific environment, with less than 5% of the > 936 000 metagenomic sequences obtained (∼70–119 Mbp per sample) similar to sequences present in other environmental viromes. Many viruses found in the WWTP were novel, resulting in only < 5–20% of the reads being phylogenetically or functionally assigned. DNA metabolism was observed as the most abundant function with DNA methylase detected at levels 4.2‐fold higher than other published viromes, while carbohydrate and amino acids metabolisms were 3.7‐ and 4.2‐fold less abundant respectively. These specific aspects of the WWTP community functions are likely due to high biomass concentration, turnover rate and microbial activity in WWTPs, and likely include mechanisms that help viruses increase their infectivity. Among ∼500 genotypes estimated in individual WWTP viromes, > 82% were shared. These data suggested that VLPs of most viral types could be present between 1 and 30 days in the process before they were discharged. Viruses in WWTP and the discharged ones can have potential impacts on the functioning of the wastewater treatment system and on the dynamics of microbial community in the surrounding aquatic environments respectively.
The morphology of the pecten oculi in the common buzzard (Buteo buteo)
Authors: Gültiken Murat E. , Yıldız Dinçer , Onuk Burcu , Karayiğit Mehmet Ö. 
Published: October 2011

AbstractObjective  The pecten oculi are an intraocular, vascular, and pigmented structure peculiar to the avian eye. In this study, we investigated the pecten oculi of the common buzzard (Buteo buteo) using stereomicroscopy and light and scanning electron microscopy (SEM).Procedures  Twenty eyes from 10 adult buzzards were studied. Specimens from each buzzard were preserved in 10% buffered formalin and observed stereomicroscopically before being embedded in paraffin, sectioned, and stained with three stains: Mallory’s triple staining technique as modified by Crossman, Hematoxylin‐Eosin (HE), and Safranin O, and for examination by light microscopy. Specimens from two buzzards were also prepared for SEM.Results  Stereomicroscopy and SEM examination showed the pecten oculi in the common buzzard to be pleated—consisting of 17–18 100 μm thick folds. These folds are connected to one another by bands of connective tissue extending vertically between the plications. Blood vessels, approximately 30–40 μm in diameter, were seen on the surface of the each fold. These vessels arise from the base of pecten, becoming thinner toward the apical end of the structure. A network of capillary vessels at the base of the plicated structure resembles contour lines. At high amplification, melanin granule accumulations were observed around the vascular structures of the plica on SEM images. Light microscopy supported the SEM observations.Conclusions  These findings reveal that the pecten oculi in the common buzzard are plicated and are remarkably similar to that of the other diurnal raptors.
Canine neurogenic Keratoconjunctivitis sicca: 11 cases (2006–2010)
Authors: Matheis Franziska L. , Walser‐Reinhardt Ladina , Spiess Bernhard M. 
Published: October 2011

AbstractObjective To describe the clinical data of dogs with neurogenic Keratoconjunctivitis sicca (KCS) and an ipsilateral dry nose without other neurologic deficits.Procedure The retrospective case study included 11 dogs diagnosed with neurogenic KCS and an ipsilateral dry nose between 2006 and 2010. Medical records were reviewed for breed, age, sex, history, suspected cause of neurogenic KCS, clinical signs, and treatment modalities. Follow‐up information was obtained by re‐examination of patients or completion of a telephone survey with the referring veterinarian or the owners.Results Mean age of the dogs was 6.6 ± 4.5 years. Neurogenic KCS was diagnosed in three females, five spayed females, one male, and two castrated males representing 10 different breeds. Ophthalmic signs of KCS (mean Schirmer tear test [STT] value of 1.9 ± 2.9 mm/min) combined with an ipsilateral dry nose were diagnosed in seven left and four right eyes. The suspected cause of neurogenic KCS was idiopathic in nine and trauma in two cases. Systemic therapy consisted of oral pilocarpine 1–2% eye drops combined with case‐specific topical treatment with cyclosporine 0.2% and tear substitutes. Duration of systemic treatment with pilocarpine until healing was 125 days (range 84–204, median 98 days) for five dogs. One dog was lost to follow‐up, and the remaining five dogs are still under systemic treatment with pilocarpine.Conclusions Neurogenic KCS with an ipsilateral dry nose seems to be a predominantly idiopathic disease of middle‐aged female dogs without breed predisposition, which may be self‐limiting in some cases.
The sternum V glands in Lepidoptera
Authors: Djernæs Marie 
Published: October 2011

Djernæs, M. 2011. The sternum V glands in Lepidoptera. —Acta Zoologica (Stockholm) 00: 1–16.AbstractI investigated representatives for all lepidopteran families known to possess the sternum V glands (Micropterigidae, Agathiphagidae, Heterobathmiidae, Erio‐craniidae and Lophocoronidae) as well as representatives for the two families (Neopseustidae and Nepticulidae) known to posses fenestrae on sternum IV, structures associated with the sternum V glands in Eriocraniidae. I found significant variation in the gland structure. The gland opening is associated with a variety of cuticular modifications, several of which provide enlarged evaporative surfaces for enhanced dispersal of gland products. The gland reservoir was surrounded by musculature in all families except Agathiphagidae and Nepticulidae, providing means of rapid expulsion of gland products. The fenestra in female Eriocraniidae, Neopseustidae and Nepticulidae are perforated. Furthermore, the fenestra in female Neopseustidae and Nepticulidae are associated with what appears to be functional sternum V glands consisting of a reservoir and secretory tissue albeit without a gland duct. I discuss the evolutionary history and functional considerations of the sternum V gland in Lepidoptera.
Lumbar glands in the frog genera Pleurodema and Somuncuria (Anura: Leiuperidae): histological and histochemical perspectives
Authors: Ferraro Daiana P. , Topa Pascual E. , Hermida Gladys N. 
Published: October 2011

Ferraro, D.P., Topa, P.E. and Hermida, G.N. 2011. Lumbar glands in the frog genera Pleurodema and Somuncuria (Anura: Leiuperidae): histological and histochemical perspectives. —Acta Zoologica (Stockholm) 00: 1–14.AbstractThe skin in the lumbar region of nine species of Pleurodema and in the monotypic genus Somuncuria (Anura: Leiuperidae) bears macroglands [lumbar gland (LG)]. Lumbar glands of Pleurodema bibroni, P. borellii, P. brachyops, P. bufoninum, P. cinereum, P. cordobae, P. kriegi, and P. thaul, as well as Somuncuria somuncurensis, were examined using histological and histochemical methods. The epidermis and the dermis of LGs are described. Also, skin of LGs presents characteristic features as the interruption of the Eberth–Katschenko layer and the presence of a differentiated type of gland only observed in macrogland and not previously described for Pleurodema or Somuncuria; this is termed lumbar serous gland. These glands are filled with a granular product, which occasionally is immersed in a matrix. Differences in the secretory products of mucous and serous glands are described, as well as inter‐ and intraspecific variability of gland structure. The mode of toxin expulsion from macroglands and the homology between lumbar and inguinal glands among anuran families are discussed.
Infection after transrectal ultrasonography‐guided prostate biopsy: increased relative risks after recent international travel or antibiotic use
Authors: Patel Uday , Dasgupta Prokar , Amoroso Peter , Challacombe Ben , Pilcher James , Kirby Roger 
Published: October 2011

Study Type – Prognosis (case series)Level of Evidence 4What's known on the subject? and What does the study add?Septicaemia is the most frequent cause of hospitalization after transtrectal prostate biopsy; fatalities have been reported and the incidence is on the rise. This study shows that men with a history of recent international travel or antibiotic use have up to four times increased risk of septicaemia and hospitalization. When they do occur, infections are usually due to multi‐resistant E coli and additional care, e.g. delay before biopsy, different antibiotic prophylaxis or transperineal biopsy, should be considered in these cases.OBJECTIVE
To study the infection rate after prostate biopsy in those who have travelled overseas or used antibiotics in the 4 weeks before biopsy.
PATIENTS AND METHODS
A total of 316 men with a mean (range) age of 61 (45–85) years were studied. All had undergone transrectal ultrasonography (TRUS)‐guided prostate biopsy after standard antibiotic prophylaxis.
Before their biopsy the patients were risk stratified and a history of recent international travel or antibiotic use was recorded.
Those who suffered sufficiently severe infection/sepsis so as to require hospitalization were identified at the end of the study period.
The characteristics of these patients and the types of infections were explored and the relative risk (RR) of infection after recent travel or antibiotic use was calculated.
RESULTS
Of the 316 men, 16 were hospitalized with infection.
The group with (n= 16) and without (n= 300) infection were equivalent in age, prostate‐specific antigen level, disease status and number of biopsy cores taken.
Either recent travel or antibiotic use were independent risk factors for infection [travel: 8/16 vs 76/300; P= 0.04; RR 2.7 and antibiotic use: 4/16 vs 20/300; P= 0.025; RR 4]. There was no significant pattern in the countries visited or the type of antibiotic used.
Culture results were positive in 10/16 men, and all cultures grew multiresistant Escherichia coli. The strains were uniformly resistant to ciprofloxacin and amoxycillin, and variably resistant to gentamicin and co‐amoxiclav, but nearly all were sensitive to meropenem.
All patients made a full recovery after antibiotic and supportive treatment.
CONCLUSIONS
Either recent international travel or antibiotic use are independent risk factors for severe infection after TRUS‐guided prostate biopsy.
When infection does occur it should be treated aggressively as the causative agent is usually a multiresistant E. coli.
The renin‐angiotensin system: a link between obesity, inflammation and insulin resistance
Authors: Kalupahana N. S. , Moustaid‐Moussa N. 
Published: October 2011

SummaryThe renin‐angiotensin system (RAS) is classically known for its role in regulation of blood pressure, fluid and electrolyte balance. Recently, several local RASs in organs such as brain, heart, pancreas and adipose tissue have also been identified. Evidence from clinical trials suggests that in addition to anti‐hypertensive effects, pharmacological inhibition of RAS also provides protection against the development of type‐2 diabetes. Moreover, animal models with targeted inactivation of RAS genes exhibit improved insulin sensitivity and are protected from high‐fat diet‐induced obesity and insulin resistance. Because there is evidence for RAS overactivation in obesity, it is possible that RAS is a link between obesity and insulin resistance. This review summarizes the evidence and mechanistic insights on the associations between RAS, obesity and insulin resistance, with special emphasis on the role of adipose tissue RAS in the pathogenesis of metabolic derangements in obesity.
Secular trends in the prevalence of general and abdominal obesity among Chinese adults, 1993–2009
Authors: Xi B. , Liang Y. , He T. , Reilly K. H. , Hu Y. , Wang Q. , Yan Y. , Mi J. 
Published: October 2011

SummaryThe objective of this study is to examine the trends in body mass index (BMI), waist circumference (WC) and prevalence of overweight (BMI 25–27.49 kg m−2), general obesity (BMI ≥ 27.5 kg m−2) and abdominal obesity (WC ≥ 90 cm for men and ≥80 cm for women) among Chinese adults from 1993 to 2009. Data were obtained from the China Health and Nutrition Survey, which was conducted from 1993 to 2009 and included a total of 52,621 Chinese adults. During the period of 1993–2009, mean BMI values increased by 1.6 kg m−2 among men and 0.8 kg m−2 among women; mean WC values increased by 7.0 cm among men and 4.7 cm among women. The prevalence of overweight increased from 8.0 to 17.1% among men (P < 0.001) and from 10.7 to 14.4% among women (P < 0.001); the prevalence of general obesity increased from 2.9 to 11.4% among men (P < 0.001) and from 5.0 to 10.1% among women (P < 0.001); the prevalence of abdominal obesity increased from 8.5 to 27.8% among men (P < 0.001) and from 27.8 to 45.9% among women (P < 0.001). Similar significant trends were observed in nearly all age groups and regions for both men and women. The prevalence of overweight, general obesity and abdominal obesity among Chinese adults has increased greatly during the past 17 years.
Estimating Progression-Free Survival in Paediatric Brain Tumour Patients When Some Progression Statuses are Unknown
Authors: Yuan Ying , Thall Peter F. , Wolff Johannes E. 
Published: October 2011

SummaryIn oncology, progression-free survival time, which is defined as the minimum of the times to disease progression or death, often is used to characterize treatment and covariate effects. We are motivated by the desire to estimate the progression time distribution on the basis of data from 780 paediatric patients with choroid plexus tumours, which are a rare brain cancer where disease progression always precedes death. In retrospective data on 674 patients, the times to death or censoring were recorded but progression times were missing. In a prospective study of 106 patients, both times were recorded but there were only 20 non-censored progression times and 10 non-censored survival times. Consequently, estimating the progression time distribution is complicated by the problems that, for most of the patients, either the survival time is known but the progression time is not known, or the survival time is right censored and it is not known whether the patient's disease progressed before censoring. For data with these missingness structures, we formulate a family of Bayesian parametric likelihoods and present methods for estimating the progression time distribution. The underlying idea is that estimating the association between the time to progression and subsequent survival time from patients having complete data provides a basis for utilizing covariates and partial event time data of other patients to infer their missing progression times. We illustrate the methodology by analysing the brain tumour data, and we also present a simulation study.
BayesianL-Optimal Exact Design of Experiments for Biological Kinetic Models
Authors: Gilmour Steven G. , Trinca Luzia A. 
Published: October 2011

SummaryData from experiments in steady state enzyme kinetic studies and radioligand binding assays are usually analysed by fitting non-linear models developed from biochemical theory. Designing experiments for fitting non-linear models is complicated by the fact that the variances of parameter estimates depend on the unknown values of these parameters and Bayesian optimal exact design for non-linear least squares analysis is often recommended. It has been difficult to implement Bayesian L-optimal exact design, but we show how it can be done by using a computer algebra package to invert the information matrix, sampling from the prior distribution to evaluate the optimality criterion for candidate designs and implementing an exchange algorithm to search for candidate designs. These methods are applied to finding optimal designs for the motivating applications in biological kinetics, in the context of which some practical problems are discussed. A sensitivity study shows that the use of a prior distribution can be essential, as is careful specification of that prior.
Conventional brain MRI in neuromyelitis optica
Authors: Cabrera‐Gomez J. A. , Kister I. 
Published: October 2011

Background and purpose:  Numerous case series have demonstrated that lesions on brain MRI are common in neuromyelitis optica (NMO), but there has not been an attempt to survey and synthesize the literature on neuro‐radiology of brain findings in NMO.Objectives:  To review the studies on conventional brain MRI in NMO and to propose to incorporate characteristic brain MRI lesions into the diagnostic criteria of NMO.Methods:  We searched for articles with descriptions of brain MRI findings in NMO in EBSCO, EMBASE, PubMed/Medline, Science Citation Index, and SCOPUS.Results:  Brain abnormalities are seen in majority of NMO patients as disease duration increases. A minority of NMO patients meet Barkhof criteria for space dissemination in multiple sclerosis (MS), and these criteria should not be used to exclude NMO diagnosis. Distinctive brain lesions of NMO are cataloged and described.Conclusions:  Brain lesions in NMO are a consistent feature of the disease. International consensus MRI criteria are needed for NMO analogous to the existing criteria for MS.
Are there ethnic differences in impulsive/compulsive behaviors in Parkinson’s disease?
Authors: Chiang H.‐L. , Huang Y.‐S. , Chen S.‐T. , Wu Y.‐R. 
Published: October 2011

Background and purpose: Recent studies have suggested increased prevalence of impulsive/compulsive behaviors (ICB) in patients with Parkinson’s disease (PD) as compared to general population in different ethnic groups. The spectrum of these behaviors includes dopamine dysregulation syndrome (DDS), punding, pathological gambling (PG), hypersexuality (HS), binge eating (BE), and compulsive shopping (CS).Methods: Two hundred and seventy‐eight consecutive patients with idiopathic PD regularly followed‐up at an outpatient clinic were interviewed and screened for the ICB between September 2008 and December 2008 using designated diagnostic criteria. All patients who screened positive for ICB or obsessive‐compulsive disorder (OCD) were further confirmed by an experienced psychiatrist.Results: Of all the studied patients, 15 patients confirmed to have ICB (lifetime prevalence: 5.60%), 3 (1.12%) were diagnosed to have DDS, 1 (0.37%) punding, 4 (1.49%) PG, 8 (2.99%) HS, 1 (0.37%) BE, 0 (0%) CS. OCD was found in one patient (0.37%).Conclusions: The prevalence of ICB is lower in Taiwan as compared with the Caucasians, with similar risk factors. The possible reasons include differences in ethnicity, environmental, cultural, and social factors as well as the dosage and selection of dopaminergic medications.
Characterization of the Asian myopathy patients with VCP mutations
Authors: Shi Z. , Hayashi Y. K. , Mitsuhashi S. , Goto K. , Kaneda D. , Choi Y.‐C. , Toyoda C. , Hieda S. , Kamiyama T. , Sato H. , Wada M. , Noguchi S. , Nonaka I. , Nishino I. 
Published: October 2011

Background and purpose:  Mutations in the valosin‐containing protein (VCP) gene are known to cause inclusion body myopathy with Paget’s disease of bone and frontotemporal dementia (IBMPFD) and familial amyotrophic lateral sclerosis (ALS). Despite an increasing number of clinical reports, only one Asian family with IBMPFD has been described.Methods:  To characterize patients with VCP mutations, we screened a total of 152 unrelated Asian families who were suspected to have rimmed vacuolar myopathy.Results:  We identified VCP mutations in seven patients from six unrelated Asian families. Five different missense mutations were found, including a novel p.Ala439Pro substitution. All patients had adult‐onset progressive muscle wasting with variable involvement of axial, proximal, and distal muscles. Two of seven patients were suggested to have mild brain involvement including cerebellar ataxia, and only one showed radiological findings indicating a change in bone. Findings from skeletal muscle indicated mixed neurogenic and myogenic changes, fibers with rimmed vacuoles, and the presence of cytoplasmic and nuclear inclusions. These inclusions were immunopositive for VCP, ubiquitin, transactivation response DNA‐binding protein 43, and also histone deacetylase 6 (HDAC6), of which function is regulated by VCP. Evidence of early nuclear and mitochondrial damage was also characteristic.Conclusions:  Valosin‐containing protein mutations are not rare in Asian patients, and gene analysis should be considered for patients with adult‐onset rimmed vacuolar myopathy with neurogenic changes. A wide variety of central and peripheral nervous system symptoms coupled with rare bone abnormalities may complicate diagnosis.