bluuebunny/crossref_metadata_2025_split huggingface dataset:
A resource for the in silico identification of fungal polyketide synthases from predicted fungal proteomes
Authors: DELGADO JAVIER A. , AL‐AZZAM OMAR , DENTON ANNE M. , MARKELL SAMUEL G. , GOSWAMI RUBELLA S. 
Published: November 2011

SUMMARYThe goal of this study was to develop a tool specifically designed to identify iterative polyketide synthases (iPKSs) from predicted fungal proteomes. A fungi‐based PKS prediction model, specifically for fungal iPKSs, was developed using profile hidden Markov models (pHMMs) based on two essential iPKS domains, the β‐ketoacyl synthase (KS) domain and acyltransferase (AT) domain, derived from fungal iPKSs. This fungi‐based PKS prediction model was initially tested on the well‐annotated proteome of Fusarium graminearum, identifying 15 iPKSs that matched previous predictions and gene disruption studies. These fungi‐based pHMMs were subsequently applied to the predicted fungal proteomes of Alternaria brassicicola, Fusarium oxysporum f.sp. lycopersici, Verticillium albo‐atrum and Verticillium dahliae. The iPKSs predicted were compared against those predicted by the currently available mixed‐kingdom PKS models that include both bacterial and fungal sequences. These mixed‐kingdom models have been proven previously by others to be better in predicting true iPKSs from non‐iPKSs compared with other available models (e.g. Pfam and TIGRFAM). The fungi‐based model was found to perform significantly better on fungal proteomes than the mixed‐kingdom PKS model in accuracy, sensitivity, specificity and precision. In addition, the model was capable of predicting the reducing nature of fungal iPKSs by comparison of the bit scores obtained from two separate reducing and nonreducing pHMMs for each domain, which was confirmed by phylogenetic analysis of the KS domain. Biological confirmation of the predictions was obtained by polymerase chain reaction (PCR) amplification of the KS and AT domains of predicted iPKSs from V. dahliae using domain‐specific primers and genomic DNA, followed by sequencing of the PCR products. It is expected that the fungi‐based PKS model will prove to be a useful tool for the identification and annotation of fungal PKSs from predicted proteomes.
Seasonal changes in vertical distribution patterns of cod (Gadus morhua) in the Bornholm Basin, central Baltic Sea
Authors: SCHABER MATTHIAS , HINRICHSEN HANS‐HARALD , GRÖGER JOACHIM 
Published: November 2011

AbstractHydroacoustic single fish detection and corresponding hydrographic measurements were used to study seasonal changes in vertical distribution of adult cod (Gadus morhua) in relation to ambient environmental conditions in the Bornholm Basin, central Baltic Sea. Sampling was conducted in April, June and August covering the years 2006–2009. Vertical distribution of individual fish was resolved from hydroacoustic single‐target detection in combination with a fish‐tracking algorithm and related to ambient hydrographic conditions. Based on a generalized linear effect model, both salinity and oxygen concentration were identified as key parameters affecting cod vertical distribution. Results also showed a clear seasonal effect with a more shallow distribution as the spawning season progressed and oxygen concentrations in the deep parts of the basin deteriorated. The upper limit of the distributional range was mostly constituted by the halocline and remained rather constant, whereas increasing oxygen depletion in the deep water layers lifted the lower boundary of the vertical distribution, leading to the observed upward shift in the overall distribution pattern. The results presented in this study highlight a significant shortcoming of the assessment survey design established for this species, as the observed shift in vertical distribution is not taken into account, thus introducing a potential bias into a data series used to tune the ICES standard stock assessment of this species.
Direct medical costs of care for Chinese patients with colorectal neoplasia: a health care service provider perspective
Authors: Wong Carlos K. H. , Lam Cindy L. K. , Poon Jensen T. C. , McGhee Sarah M. , Law Wai‐Lun , Kwong Dora L. W. , Tsang Janice , Chan Pierre 
Published: November 2011

AbstractObjectives  To estimate the direct medical cost of colorectal neoplasia (CRN) from newly diagnosed to the completion of the tumour‐specific treatment in the initial year of disease across stages and tumour primary sites.Methods  Only direct medical costs from the perspective of the health care service provider were incorporated in the cost analysis (in 2009 USD) using a bottom‐up approach. Tumour‐specific treatments of surgery, chemotherapy and radiotherapy data in the initial year of disease were identified from the 401 CRN adult patients by a review of their medical records. Service utilization for diagnosis, staging, pre‐operative assessment and post‐operative follow‐up consultations was estimated from the recommendations of established surveillance and clinical practice guidelines.Results  Direct medical cost for the care of a newly diagnosed CRN was ranging from $1941 for low‐risk polyp to $45 115 for stage IV colorectal cancer in the initial year of care. Costs of care showed a gradient increase from $1748 for low‐risk colonic polyps to $42 899 for stage IV colon cancer, and from $2232 for low‐risk rectal polyps to $48 453 for stage IV rectal cancers. Diagnostic/pre‐operative assessment and treatment accounted for most of total costs of colorectal polyp (58.9–76.7%) and cancer (60.8–85.2%) care.Conclusion  The results provided stage and site‐specific estimations of the direct medical costs of CRN in a Chinese population that can assist policy decision making and facilitate health care service planning and cost‐effectiveness evaluations.
Haloarchaeal myovirus φCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities
Authors: Klein R. , Rössler N. , Iro M. , Scholz H. , Witte A. 
Published: November 2011

SummaryThe φCh1 myovirus, which infects the haloalkaliphilic archaeon Natrialba magadii, contains an invertible region that comprises the convergent open reading frames (ORFs) 34 and 36, which code for the putative tail fibre proteins gp34 and gp36 respectively. The inversion leads to an exchange of the C‐termini of these proteins, thereby creating different types of tail fibres. Gene expression experiments revealed that only ORF34 is transcribed, indicating that φCh1 produces tail fibre proteins exclusively from this particular ORF. Only one of the two types of tail fibres encoded by ORF34 is able to bind to Nab. magadii in vitro. This is reflected by the observation that during the early phases of the infection cycle, the lysogenic strain L11 carries its invertible region exclusively in the orientation that produces that specific type of tail fibre. Obviously, Nab. magadii can only be infected by viruses carrying this particular type of tail fibre. By mutational analysis, the binding domain of gp34 was localized to the C‐terminal part of the protein, particularly to a galactose‐binding domain. The involvement of galactose residues in cell adhesion was supported by the observation that the addition of α‐D‐galactose to purified gp34 or whole virions prevented their attachment to Nab. magadii.
The genetic and structural basis of two distinct terminal side branch residues in stewartan and amylovoran exopolysaccharides and their potential role in host adaptation
Authors: Wang Xiaolei , Yang Fan , von Bodman Susanne B. 
Published: November 2011

SummaryStewartan and amylovoran exopolysaccharide (EPS) produced by the plant pathogenic bacteria Pantoea stewartii and Erwinia amylovora are virulence factors in the cause of Stewart's vascular wilt and fire blight. The biosynthesis of amylovoran and stewartan is encoded by a set of homologous operons that have been partially characterized, although some annotations are solely on the basis of sequence homology. The major distinguishing features of these two EPS forms are the presence of a terminal pyruvate in amylovoran and glucose in stewartan, even though the gene systems to account for both are conserved and present in each bacterium. This study explores the genetic, structural and functional differences of amylovoran and stewartan, and their potential role in host adaptation. We report that the pyruvyl transferase gene in P. stewartii is non‐functional, while the terminal glucosyl transferase is catalytically active. Conversely, in E. amylovora, the homologous glucosyl transferase activity appears to be relatively ineffective, while the pyruvyl transferase function predominates. We also show that the terminally pyruvylated versus glucosylated EPS require specific repeating unit translocases (Wzx). We discuss the evolutionary, functional and biological implications of the terminally pyruvylated and glucosylated polymers and their potential contribution to plant and insect host adaptation.
Pediatric health‐related quality of life after intestinal transplantation
Authors: Ngo K. D. , Farmer D. G. , McDiarmid S. V. , Artavia K. , Ament M. E. , Vargas J. , Busuttil R. W. , Colangelo J. , Esmailian Y. , Gordon‐Burroughs S. , Duffy J. , Venick R. S. 
Published: November 2011

Ngo KD, Farmer DG, McDiarmid SV, Artavia K, Ament ME, Vargas J, Busuttil RW, Colangelo J, Esmailian Y, Gordon‐Burroughs S, Duffy J, Venick RS. Pediatric health‐related quality of life after intestinal transplantation.  Pediatr Transplantation 2011: 15: 849–854. © 2011 John Wiley & Sons A/S.Abstract:  As outcomes after ITx improve, greater emphasis is needed on HRQOL. The primary aims of this study were to (i) assess the feasibility of measuring HRQOL in pediatric ITx recipients, (ii) measure HRQOL using validated instruments, and (iii) compare HRQOL in ITx recipients to healthy normal (NL) children. The CHQ and Pediatric Quality of Life (PedsQL4.0) instruments were administered to both patients and parents at outpatient visits. All 24 eligible patients were enrolled. The median age at study enrollment was 6.0 yr (range: 2–18 yr), and the median time from transplant to study enrollment was 2.8 yr (range: 0.5–11.8 yr). The majority of subjects were male (58%), Latino (58%), and liver‐inclusive (92%) recipients. For CHQ and PedsQL4.0, parental responses were significantly lower in multiple categories including physical health and social functioning compared to healthy norms. Patient responses were not different from NL using CHQ but using PedsQL4.0 were significantly lower in the school functioning subcategory and psychosocial health summary score. HRQOL as reported by children and families after ITx is significantly lower in multiple categories compared to NL.
Variable disease progression after successful stem cell transplantation: Prospective follow‐up investigations in eight patients with Hurler syndrome
Authors: Grigull Lorenz , Sykora Karl‐Walter , Tenger Andreas , Bertram Harald , Meyer‐Marcotty Max , Hartmann Hans , Bültmann Eva , Beilken Andreas , Zivicnjak Miroslaw , Mynarek Martin , Osthaus Alexander W. , Schilke Reinhard , Kollewe Katja , Lücke Thomas 
Published: November 2011

Grigull L, Sykora K‐W, Tenger A, Bertram H, Meyer‐Marcotty M, Hartmann H, Bültmann E, Beilken A, Zivicnjak M, Mynarek M, Osthaus AW, Schilke R, Kollewe K, Lücke T. Variable disease progression after successful stem cell transplantation: Prospective follow‐up investigations in eight patients with Hurler syndrome.  Pediatr Transplantation 2011: 15: 861–869. © 2011 John Wiley & Sons A/S.Abstract:  We report the results of a prospective, standardized follow‐up programme of eight children (median age at SCT 1.2 yr) with mucopolysaccharidosis (MPS1H, M. Hurler) transplanted using a fludarabine‐based SCT. SCT resulted in stable engraftment without transplant‐related mortality. All patients are alive, engrafted and in ambulatory care. During follow‐up (median five yr, 1.9–8 yr), six of eight showed developmental delay (two severe, two mild/no), all eight had spinal deformities and one received hip surgery for acetabular dysplasia. Hand surgery for carpal tunnel release and trigger digits was required in five of the patients. The cranio‐cervical junction was narrowed in four patients, one child having already received surgery. CC was present in all patients prior to SCT. It remained unchanged in seven and regressed in one child. Severe cardiac dysfunction was present in two of the eight children before SCT. Cardiac pump function was normal in six patients and ameliorated in two, while valve abnormalities could be detected in six patients. Currently, transplantation seems no longer the major obstacle for MPS1H patients, but the variable musculoskeletal disease progression after successful SCT remains a challenge. Patients with Hurler syndrome need specialized follow‐up care because of their manifold health problems. The standardized follow‐up presented here is a step to optimize care for MPS children and their families after SCT.
Autoimmune hemolytic anemia and idiopathic thrombocytopenic purpura in pediatric solid organ transplant recipients, report of five cases and review of the literature
Authors: Miloh Tamir , Arnon Ronen , Roman Elizabeth , Hurlet Anne , Kerkar Nanda , Wistinghausen Birte 
Published: November 2011

Miloh T, Arnon R, Roman E, Hurlet A, Kerkar N, Wistinghausen B. Autoimmune hemolytic anemia and idiopathic thrombocytopenic purpura in pediatric solid organ transplant recipients, report of five cases and review of the literature.  Pediatr Transplantation 2011: 15: 870–878. © 2011 John Wiley & Sons A/S.Abstract:  Cytopenias are common among pediatric SOT; however, autoimmune cytopenias are infrequently reported. We report five cases of autoimmune cytopenias in pediatric LT patients: two with isolated IgG‐mediated AIHA, two with ITP, and one with Evans syndrome (ITP and AIHA). All patients were maintained on tacrolimus as immunosuppression. Viral illness commonly preceded the autoimmune cytopenias. All patients responded well to medical therapy (steroids, intravenous immunoglobulin, and rituximab) and lowering tacrolimus serum level. Prognosis appears to be worse when more than one cell line (e.g., Evans syndrome) is affected, and/or there is no preceding viral illness. A critical literature review of autoimmune cytopenias in children following SOT is conducted. Autoimmune cytopenias are a rarely reported complication of pediatric SOT, but clinicians taking care of pediatric transplant recipients need to be aware of this complication.
Practitioner characteristics and the treatment of children and adolescents with attention deficit hyperactivity disorder
Authors: Mitchell Philip B , Levy Florence , Hadzi‐Pavlovic Dusan , Concannon Patrick E , Hutchins Paul , Mulcahy Desmond L , Clarke Simon D , Salmelainen Pia A , Warner Alexandra , Hughes Clifford F 
Published: November 2011

Aim:  To investigate whether recent Australian practice conforms to the draft 2009 National Health and Medical Research Council (NHMRC) guidelines on the management of attention deficit hyperactivity disorder.Methods:  Data from the 2007 Special Review on Attention Deficit Hyperactivity Disorder in Children and Adolescents in New South Wales (NSW) were examined.Results:  Two hundred seven approved stimulant prescribers in NSW responded to a detailed survey on treatment practice (including 121 paediatricians and 67 psychiatrists). Overall, the practice identified in this survey of NSW approved stimulant prescribers was consistent with that recommended in the draft NHMRC guidelines. Paediatricians were more likely to inform families of developmental therapies. Most prescribers (67%) considered stimulants to be the first line of treatment for at least half of their patients. Psychiatrists were more likely to use stimulants as first‐line treatments, while those recently qualified were less likely to prescribe. Half of the prescribers were willing to consider prescribing for children 4 years of age and younger. Paediatricians were more likely to consider prescribing to this age group, while those recently qualified were less likely. There were no significant differences in prescribing practice between child and adult psychiatrists. Most prescribers (67–97%) routinely monitored patients on stimulants for weight, height, blood pressure and academic progress. Psychiatrists were less likely to review these parameters than paediatricians, with this difference being largely due to adult psychiatrists.Conclusions:  There are significant differences in prescribing practice between paediatricians and psychiatrists. These variations may reflect differing training programs and patient populations, and merit close consideration in any review arising from the publication of the recent NHMRC guideline.
Association of adrenergic receptor gene polymorphisms with adolescent obesity in Taiwan
Authors: Chou Yi‐Chun , Tsai Chi‐Neu , Lee Yun‐Shien , Pei Jen‐Sheng 
Published: November 2011

AbstractBackground:  Polymorphisms of β2‐adrenergic receptor (ADRB2) and β3‐adrenergic receptor (ADRB3) have been reported to be associated with obesity in adults and adolescents, although study results have been controversial. The aim of the present study was to investigate the association of polymorphisms of ADRB2 (Arg16Gly, Gln27Glu) and ADRB3 (Trp64Arg) with adolescent obesity in Taiwan.Methods:  A total of 559 adolescent volunteers with equal numbers female and male were enrolled. Participants were divided into two groups: obese (body mass index [BMI]≥ 95th percentile) and normal weight (BMI 15th–85th percentile). Genomic DNA was extracted from buccal mucosa cells and genotyped in TaqMan assays. Genotype results and clinical subject characteristics were analyzed.Results:  Among the three ADRB polymorphisms, only Arg16Gly polymorphism was found to be significantly correlated with adolescent obesity, especially in girls. Girls with genotype Gly/Gly had a lower probability of obesity than those with genotypes Arg/Gly or Arg/Arg (P= 0.006; Arg/Gly: odds ratio [OR], 2.57, 95% confidence interval [95%CI]: 1.22–5.41; Arg/Arg: OR, 3.03, 95%CI: 1.50–6.12). Girls with genotype Gly/Gly had lower BMI than those with genotype Arg/Arg (P= 0.049). Obese adolescents with genotype Gly/Gly had a lower probability of hypertension than those with genotype Arg/Gly or Arg/Arg (P= 0.005).Conclusions:  Arg16Gly polymorphism of ADRB2 was significantly associated with obesity in female adolescents, and those with the Gly/Gly genotype were associated with a lower possibility of obesity and lower BMI. This polymorphism was also associated with a lower probability of hypertension in obese adolescents. The other two polymorphisms of ADRB (Gln27Glu and Trp64Arg) were not associated with adolescent obesity in Taiwan.
ENVIRONMENTAL DYNAMICS AND THE LINKS BETWEEN GROWTH, VOLATILITY AND MORTALITY
Authors: Varvarigos Dimitrios 
Published: November 2011

ABSTRACTI construct a model of a growing economy with pollution. The analysis of the model shows that the interactions between capital accumulation, endogenous lifetime and environmental quality determine both the long‐run growth rate and the pattern of convergence (i.e., monotonic or cyclical) towards the balanced growth path. I argue that such interactions can provide a possible explanatory factor behind the, empirically observed, negative correlation between growth and volatility. Furthermore, the model may capture the observed pattern whereby economic growth and mortality rates appear to be negatively related in the long run, but positively related in the short run.
Y‐chromosome O3 Haplogroup Diversity in Sino‐Tibetan Populations Reveals Two Migration Routes into the Eastern Himalayas
Authors: Kang Longli , Lu Yan , Wang Chuanchao , Hu Kang , Chen Feng , Liu Kai , Li Shilin , Jin Li , Li Hui ,   The Genographic Consortium
Published: November 2011

SummaryThe eastern Himalayas are located near the southern entrance through which early modern humans expanded into East Asia. The genetic structure in this region is therefore of great importance in the study of East Asian origins. However, few genetic studies have been performed on the Sino‐Tibetan populations (Luoba and Deng) in this region. Here, we analyzed the Y‐chromosome diversity of the two populations. The Luoba possessed haplogroups D, N, O, J, Q, and R, indicating gene flow from Tibetans, as well as the western and northern Eurasians. The Deng exhibited haplogroups O, D, N, and C, similar to most Sino‐Tibetan populations in the east. Short tandem repeat (STR) diversity within the dominant haplogroup O3 in Sino‐Tibetan populations showed that the Luoba are genetically close to Tibetans and the Deng are close to the Qiang. The Qiang had the greatest diversity of Sino‐Tibetan populations, supporting the view of this population being the oldest in the family. The lowest diversity occurred in the eastern Himalayas, suggesting that this area was an endpoint for the expansion of Sino‐Tibetan people. Thus, we have shown that populations with haplogroup O3 moved into the eastern Himalayas through at least two routes.
Niche partitioning of fish assemblages in a mountain stream with frequent natural disturbances – an examination of microhabitat in riffle areas
Authors: Lee Pey‐Yi , Suen Jian‐Ping 
Published: November 2011

Abstract – Microhabitat usage by different species of fish was studied to examine the potential for niche partitioning in riffle areas of a mountain river characterised by frequent natural disturbances. We randomly sampled 96 riffle‐area plots (mostly 1 m × 1 m) in a stream in south‐western Taiwan for fish abundance and microhabitat characteristics during the dry season from November 2008 to March 2009. Density and electivity values associated with microhabitat usage indicate the presence of niche partitioning among four major species of fish based largely on flow velocity and water depth. Hemimyzon formosanum, a herbivore, prefers higher velocity and shallower water but avoids sandy substrate. Onychostoma alticorpus, a herbivore, prefers lower velocity and deeper water. Rhinogobius nantaiensis, an omnivore, prefers higher velocity, shallower water and gravel‐sized substrate but avoids boulder substrate. Acrossocheilus paradoxus, an omnivore, prefers lower velocity and deeper water but avoids pebble‐sized substrate. The existence of differentiation of microhabitat preference and overlap of microhabitat usage suggests that interspecific competition is a factor affecting the structure of this fish assemblage, which may remain at early successional stages because of frequent disturbances in the stream. Study results also show that density and electivity detect preference differently. Density detects microhabitat preference for two herbivores while electivity detects microhabitat preference for two omnivores.