bluuebunny/crossref_metadata_2025_split huggingface dataset:
The gputools package enables GPU computing in R
Authors: Buckner Joshua , Wilson Justin , Seligman Mark , Athey Brian , Watson Stanley , Meng Fan 
Published: October 2009

Abstract
Motivation: By default, the R statistical environment does not make use of parallelism. Researchers may resort to expensive solutions such as cluster hardware for large analysis tasks. Graphics processing units (GPUs) provide an inexpensive and computationally powerful alternative. Using R and the CUDA toolkit from Nvidia, we have implemented several functions commonly used in microarray gene expression analysis for GPU-equipped computers.
Results: R users can take advantage of the better performance provided by an Nvidia GPU.
Availability: The package is available from CRAN, the R project's repository of packages, at http://cran.r-project.org/web/packages/gputools More information about our gputools R package is available at http://brainarray.mbni.med.umich.edu/brainarray/Rgpgpu
Contact: bucknerj@umich.edu
An assessment of the validity of SOFA score based triage in H1N1 critically ill patients during an influenza pandemic
Authors: Khan Z. , Hulme J. , Sherwood N. 
Published: October 2009

SummarySequential Organ Failure Assessment (SOFA) score based triage of influenza A H1N1 critically ill patients has been proposed for surge capacity management as a guide for clinical decision making. We conducted a retrospective records review and SOFA scoring of critically ill patients with influenza A H1N1 in a mixed medical‐surgical intensive care unit in an urban hospital. Eight critically ill patients with influenza A H1N1 were admitted to the intensive care unit. Their mean (range) age was 39 (26–52) years with a length of stay of 11 (3–17) days. All patients met SOFA score based triage admission criteria with a modal SOFA score of five. Five patients required invasive ventilation for a mean (range) of 5 (4–11) days. Five patients would have been considered for withdrawal of treatment using SOFA scoring guidelines at 48 h. All patients survived. We conclude that SOFA score based triage could lead to withdrawal of life support in critically ill patients who could survive with an acceptably low length of stay in the intensive care unit.
Risk of pulmonary aspiration with laryngeal mask airway and tracheal tube: analysis on 65 712 procedures with positive pressure ventilation
Authors: Bernardini A. , Natalini G. 
Published: October 2009

SummaryWe compared the risk of pulmonary aspiration in patients whose lungs were mechanically ventilated through a laryngeal mask airway (35 630 procedures) or tracheal tube (30 082 procedures). Three cases of pulmonary aspiration occurred with the laryngeal mask airway and seven with the tracheal tube. There were no deaths related to pulmonary aspiration. The incidence and outcome of pulmonary aspiration detected in this study were similar to those previously reported. The adjusted odds ratio (OR) for pulmonary aspiration with the laryngeal mask airway was 1.06 (95% CI 0.20–5.62). Unplanned surgery (OR 30.5, 95% CI 8.6–108.9) and male sex (OR 8.6, 95% CI 1.1–68) were associated with an increased risk of aspiration and age < 14 years with a reduced risk (OR 0.21, 95% CI 0.07–0.64). There were contraindications and exclusions to the use of the laryngeal mask airway but in this selected population the use of an laryngeal mask airway was not associated with an increased risk of pulmonary aspiration compared with a tracheal tube.
Ontogeny of haematopoiesis: recent advances and open questions
Authors: Ottersbach Katrin , Smith Aileen , Wood Andrew , Göttgens Berthold 
Published: October 2009

SummaryUnravelling the embryonic origins of the haematopoietic system has been the subject of sustained research for more than a century. Nevertheless, many important questions are still either unanswered or remain a matter of intense debate. Recent progress in mouse and embryonic stem cell model systems as well as imaging and post‐genomic technologies has provided new insights into many of these open questions. Here we place into context recent reports on the anatomical site of blood stem cell emergence and, using red blood cells as an example, illustrate how the development of stem cells and the other blood lineages is both temporally and spatially decoupled. In addition, we outline how embryonic stem cell assays are increasingly used as a powerful surrogate for studying lineage relationships and developmental potential of early embryonic blood progenitors. Finally, we review how recent progress in the reconstruction of transcriptional regulatory networks is beginning to define the connectivity between key regulators that control early blood development. In light of these rapid recent advances, research into the embryonic origins of the haematopoietic system should remain one of the most vibrant disciplines within the wider field of haematology for the foreseeable future.
Do antineutrophil cytoplasmic antibodies (ANCA) play a key role in neutrophilic dermatoses? A case of propylthiouracil-induced neutrophilic dermatosis with positive perinuclear ANCA
Authors: Darné S. , Natarajan S. , Blasdale C. 
Published: October 2009

Summary
We report a case of neutrophilic dermatosis caused by propylthiouracil (PTU), with positive perinuclear antineutrophil cytoplasmic antibodies (p-ANCA). PTU is well known to cause vasculitis associated with positive ANCA titres, and this typically occurs late in the treatment (after months to years). PTU rarely causes neutrophilic dermatoses (three case reports). In the three cases described, ANCA was positive at the outset. Our patient’s initial ANCA testing was negative and her positive p-ANCA evolved. This may be because PTU binds to myeloperoxidase (MPO) inside neutrophils, altering its configuration and thus causing antibody formation to this abnormal MPO–PTU configuration, which would not be detected by standard laboratory techniques. ANCA has been implicated in spreading neutrophil activation and thus its pathogenic effect and clinical significance may extend beyond the realm of vasculitis alone.
Generalized eruptive lentiginosis induced by chemotherapy
Authors: De D. , Dogra S. , Kanwar A. J. , Saikia U. N. 
Published: October 2009

Summary
Lentigines are characterized by brown macules developing due to increased proliferation of melanocytes in the dermoepidermal junction. Many drugs, including immunosuppressants and immunomodulators, have been shown to cause generalized lentiginosis. We describe a case of lentiginosis induced by cancer chemotherapy, an extremely rare occurrence.
Combined effects of ocean acidification and solar UV radiation on photosynthesis, growth, pigmentation and calcification of the coralline alga Corallina sessilis (Rhodophyta)
Authors: GAO KUNSHAN , ZHENG YANGQIAO 
Published: October 2009

AbstractPrevious studies have shown that increasing atmospheric CO2 concentrations affect calcification in some planktonic and macroalgal calcifiers due to the changed carbonate chemistry of seawater. However, little is known regarding how calcifying algae respond to solar UV radiation (UVR, UVA+UVB, 280–400 nm). UVR may act synergistically, antagonistically or independently with ocean acidification (high CO2/low pH of seawater) to affect their calcification processes. We cultured the articulated coralline alga Corallina sessilis Yendo at 380 ppmv (low) and 1000 ppmv (high) CO2 levels while exposing the alga to solar radiation treatments with or without UVR. The presence of UVR inhibited the growth, photosynthetic O2 evolution and calcification rates by13%, 6% and 3% in the low and by 47%, 20% and 8% in the high CO2 concentrations, respectively, reflecting a synergistic effect of CO2 enrichment with UVR. UVR induced significant decline of pH in the CO2‐enriched cultures. The contents of key photosynthetic pigments, chlorophyll a and phycobiliproteins decreased, while UV‐absorptivity increased under the high pCO2/low pH condition. Nevertheless, UV‐induced inhibition of photosynthesis increased when the ratio of particulate inorganic carbon/particulate organic carbon decreased under the influence of CO2‐acidified seawater, suggesting that the calcified layer played a UV‐protective role. Both UVA and UVB negatively impacted photosynthesis and calcification, but the inhibition caused by UVB was about 2.5–2.6 times that caused by UVA. The results imply that coralline algae suffer from more damage caused by UVB as they calcify less and less with progressing ocean acidification.
Role of the aquatic pathway in the carbon and greenhouse gas budgets of a peatland catchment
Authors: DINSMORE KERRY J. , BILLETT MICHAEL F. , SKIBA UTE M. , REES ROBERT M. , DREWER JULIA , HELFTER CAROLE 
Published: October 2009

AbstractPeatland streams have repeatedly been shown to be highly supersaturated in both CO2 and CH4 with respect to the atmosphere, and in combination with dissolved (DOC) and particulate organic carbon (POC) represent a potentially important pathway for catchment greenhouse gas (GHG) and carbon (C) losses. The aim of this study was to create a complete C and GHG (CO2, CH4, N2O) budget for Auchencorth Moss, an ombrotrophic peatland in southern Scotland, by combining flux tower, static chamber and aquatic flux measurements from 2 consecutive years. The sink/source strength of the catchment in terms of both C and GHGs was compared to assess the relative importance of the aquatic pathway. During the study period (2007–2008) the catchment functioned as a net sink for GHGs (352 g CO2‐Eq m−2 yr−1) and C (69.5 g C m−2 yr−1). The greatest flux in both the GHG and C budget was net ecosystem exchange (NEE). Terrestrial emissions of CH4 and N2O combined returned only 4% of CO2 equivalents captured by NEE to the atmosphere, whereas evasion of GHGs from the stream surface returned 12%. DOC represented a loss of 24% of NEE C uptake, which if processed and evaded downstream, outside of the catchment, may lead to a significant underestimation of the actual catchment‐derived GHG losses. The budgets clearly show the importance of aquatic fluxes at Auchencorth Moss and highlight the need to consider both the C and GHG budgets simultaneously.
BmHrp28 is a RNA‐binding protein that binds to the female‐specific exon 4 of Bombyx mori dsx pre‐mRNA
Authors: Wang Z. , Zhao M. , Li D. , Zha X. , Xia Q. , Xiang Z. , He N. 
Published: October 2009

AbstractThe Bombyx mori sex determination gene Bmdsx is alternatively spliced in the male and female to produce the male‐ and female‐specific proteins. In an effort to better understand the mechanism of the alternative splicing regulation of Bmdsx, we conducted a gel‐shift assay followed by LC‐MS/MS analysis to identify the putative proteins bound to the cis‐element CE1+6 in the exon 4 of Bmdsx. A protein named as BmHrp28 which is homologous to the Drosophila Hrp48, a member of the hnRNPA/B family, was identified and expressed in Escherichia coli for testing RNA‐protein binding in vitro. All of the results showed that BmHrp28 specifically bound to the CE1+6 RNA probe. BmHrp28 has two RNA recognition motifs at the N‐terminal and a glycine‐rich motif at the C‐terminal. It might be one of the factors involved in the male‐specific splicing of Bmdsx.
Eight years of entomological surveillance in Italy show no evidence ofCulicoides imicolageographical range expansion
Authors: Conte A. , Gilbert M. , Goffredo M. 
Published: October 2009

Summary1.Assessing changes in species range is based on identifying new occurrences in areas where absence has been inferred due to lack of previous records. This technique depends on creating a consistent observational dataset, based on comparable detection methods.2.In Mediterranean countries, the midgeCulicoides imicolais the principal vector of bluetongue virus (BTV) that causes an infectious disease of domestic and wild ruminants. Over the last 10 years, BTV has invaded Mediterranean countries (1998) and much of Northern Europe (2006); this unprecedented spread is reported to be a possible consequence of climate change. In southern Europe, based on recent observations found in northern latitudes, BTV spread has been attributed in part to changes inC. imicoladistribution. However, current sampling ofCulicoidesspp. is far more intensive and targeted than that undertaken before the first BTV epidemics; this obviously results in new information from areas in which collections would have had little chance of positive identification in the past.3.Since 2001, a national surveillance programme based on permanent traps was established in Italy to followC. imicolapopulation dynamics in space and time. Based on data from 2000 to 2001 cross‐sectional studies, Italy was divided into three zones (I: endemicity; II: transition; III: absence) in which longitudinal data onC. imicolapresence and abundance were analysed as a function of time between 2002 and 2007 through linear and quantile regressions.4.The results from the surveillance programme demonstrate no detectable range expansion of theC. imicolapopulation in Italy between 2002 and 2007.5.Synthesis and applications. This study provides strong evidence that there has been no measurable range expansion between 2002 and 2007 in a species previously described as moving northwards as a result of climate change. For any reliable conclusions to be drawn on the range distribution ofC. imicolaor other similar vector species in Southern Europe,theCulicoidessurveillance system across all European countries should be designed to provide comparable data based on a constant detection probability over time.
Role of genetic testing in arrhythmogenic right ventricular cardiomyopathy/dysplasia
Authors: Barahona‐Dussault C , Benito B , Campuzano O , Iglesias A , Leung TL , Robb L , Talajic M , Brugada R 
Published: October 2009

Barahona‐Dussault C, Benito B, Campuzano O, Iglesias A, Leung TL, Robb L, Talajic M, Brugada R. Role of genetic testing in arrhythmogenic right ventricular cardiomyopathy/dysplasia.In a cohort of patients with confirmed or suspected arrhythmogenic right ventricular cardiomyopathy/dysplasia (ARVC/D), genetic testing is useful in confirming the diagnosis, particularly in individuals who do not completely fulfil Task Force criteria for the disease, thereby also enabling the adoption of preventive measures in family members. Due to the high percentage of novel mutations that are expected to be identified in ARVC/D, the use of genetic screening technology based on the identification of known mutations seems to have very restricted value. Our results support that the presence of certain genetic variations could play a role in the final phenotype of patients with ARVC/D, where single and compound mutation carriers would have more symptomatic forms of the disease and the polymorphism P366L could be associated to a more benign phenotype.
Multiple spinal ganglioneuromas in a patient harboring a pathogenic NF1 mutation
Authors: Bacci C , Sestini R , Ammannati F , Bianchini E , Palladino T , Carella M , Melchionda S , Zelante L , Papi L 
Published: October 2009

Bacci C, Sestini R, Ammannati F, Bianchini E, Palladino T, Carella M, Melchionda S, Zelante L, Papi L. Multiple spinal ganglioneuromas in a patient harboring a pathogenic NF1 mutation.Ganglioneuroma is a rare benign tumor originating from autonomic ganglia and is considered the benign counterpart of neuroblastoma. Ganglioneuromas may be present as an isolated finding and, rarely, in association with neurofibromatosis type 1 (NF1). However, ganglioneuromas of the cervical spine with intradural extension and multiple locations are extremely rare. We describe a 32‐year‐old woman with multiple ganglioneuromas of the cervical, dorsal and lumbar spine associated with a few café‐au‐lait spots and subcutaneous nodules. The patient lacked other NF1 stigmata, such as freckling, Lisch nodules and cutaneous neurofibromas. Although our patient did not fulfill the NF1 diagnostic criteria, molecular diagnosis revealed a pathogenic mutation in the NF1 gene. Approximately 30 patients affected by NF1 and ganglioneuromas have been reported: in all these individuals, NF1 diagnosis was made according to the clinical diagnostic criteria and no patients have molecular diagnosis. Therefore, this is the first case with multiple spinal ganglioneuromas associated with a pathogenic NF1 mutation.
Functional and anatomic assessments for transobturator vaginal tape inside‐out operation for urodynamic stress incontinence
Authors: Huang Wen‐Chu , Su Tsung‐Hsien , Lin Tzu‐Yin , Hsieh Ching‐Hung , Chen Shwu‐Shiuang , Lee Mei‐Yu 
Published: October 2009

AbstractAim:  The aim of the present study was to assess by urodynamic study and chain urethrocystography the functional and anatomic changes before and after transobturator vaginal tape inside‐out (TVT‐O) operation.Methods:  From January 2005 to February 2006, 35 women were enrolled who had urodynamic stress incontinence, with or without intrinsic sphincter deficiency, and had undergone TVT‐O with regular follow‐up. Investigations, including pelvic examination, pad test, urodynamic study, chain urethrocystography and questionnaire with short forms of Urogenital Distress Inventory and Incontinence Impact Questionnaire, were performed pre‐ and postoperatively.Results:  The mean follow‐up period was 12.8 months. The subjective and objective cure rates were 80 and 71.4%, respectively. The maximal urethral pressure was significantly decreased (from 67.0 to 58.9 cmH2O) after surgery and bladder neck mobility was reduced. Quality of life assessment revealed significant improvement after TVT‐O.Conclusion:  TVT‐O is an effective operation for female urodynamic stress incontinence. Improved postoperative bladder neck mobility showed anatomic correction, indicating a hammock effect. The decreased maximal urethral pressure may reflect neurogenic damage during surgery; thus, minimal dissection and avoidance of unnecessary dissection to prevent periurethral damage are advised.
Primary chemotherapy patterns for ovarian cancer treatment in Japan
Authors: Shirai Takako , Imanaka Yuichi , Sekimoto Miho , Ishizaki Tatsuro ,   QIP Ovarian Cancer Expert Group
Published: October 2009

AbstractAims:  Evidence‐based clinical practices can improve patient outcomes, especially in the area of chemotherapy. In Japan, it is not known how well physicians adhere to evidence‐based chemotherapy guidelines. This study aimed to assess physician compliance with national guidelines for ovarian cancer primary chemotherapy in Japan.Methods:  Using an administrative database, we analyzed 209 cases of surgical laparotomy without neoadjuvant chemotherapy as the primary intervention for adnexal cancer. Cases were identified across seven teaching hospitals between 2003 and 2006.Results:  Of the 136 patients receiving inpatient chemotherapy, 101 cases (74%) were treated with platinum–taxane therapy. In five hospitals, platinum–taxane therapy was used in more than 75% of patients, compared to 56% and 32% in the other two hospitals, respectively. The proportion of patients receiving paclitaxel and carboplatin concomitant therapy (TC therapy) was 67%, although significant variation was noted between hospitals (range 32% to 94%, P < 0.001). Of the 91 patients receiving TC therapy, 59 (65%) were given full‐dose monthly regimens, while 32 cases (35%) were treated with divided doses weekly. Weekly TC therapy was more frequently provided in hospitals with a low volume of patients receiving TC therapy. Patients under the age of 65 receiving inpatient chemotherapy were more likely to receive full‐dose regimens than patients 65 or older (68% vs 43%, P = 0.005). Publication of national treatment guidelines did not appear to substantially impact chemotherapy practice patterns.Conclusions:  Adherence to standardized chemotherapy was comparable to rates in European countries, although rates among hospitals differed significantly. Elderly patients were more likely to receive divided‐dose regimens.
Transvaginal cystocele correction: Midterm results with a transobturator tension‐free technique using a combined bovine pericardium/polypropylene mesh
Authors: Araco Francesco , Gravante Gianpiero , Overton John , Araco Placido , Dati Stefano 
Published: October 2009

AbstractAims:  To describe the benefits and complications of a combined bovine/pericardium polypropylene mesh for severe vaginal wall prolapse at midterm follow up.Methods:  Retrospective analysis of patients with stages 3 and 4 pelvic prolapse undergoing cystocele repair using the combined mesh.Results:  Between June 2004 and April 2006 36 patients were treated. The median follow up was 35 months. Two patients experienced de novo urgency (5.6%). Resolution of prolapse was achieved in 91.7% of patients. Ten percent of those with urinary incontinence continued to suffer from incontinence after surgery. There was a significant improvement in the quality of life in cases with associated urinary incontinence, and in the sexual lives and constipation of all patients. Two cases of vaginal perforation (5.6%) and three cases of vaginal erosion (8.3%) were described.Conclusions:  The use of a composite bovine pericardium/polypropylene mesh for cystocele correction is feasible and safe, yielding good results at midterm follow up.
Free peritoneal cyst with histologic properties of amniotic epithelium observed in a woman pregnant with twins
Authors: Horikoshi Tsuguhiro , Kikuchi Akihiko , Ono Kyoko , Kita Mariko , Takagi Kimiyo , Ogiso Yoshifumi 
Published: October 2009

AbstractWe report an interesting case of a free peritoneal cyst in a woman pregnant with twins. As far as we know, a cyst with histologic properties similar to the metaplastic stratified squamous epithelium of the amnion has not been reported. A 20‐year‐old Japanese woman pregnant with twins underwent cesarean section at 29 weeks of gestation. A simple serous cyst 5 cm in diameter was found at excavatio vesicouterina. The cyst was not attached to the surrounding organs, and was located independent of any other tissues in the patient's abdominal cavity. Histologic examination revealed that the cyst wall was composed of three major layers (epithelium, mesenchyme and mesothelium) with no vessels. Immunohistochemical staining with human chorionic gonadotropin (HCG), cytokeratins, vimentin, placental alkaline phosphatase (PAP) and cluster of differentiation (CD) 31, showed that the cyst wall had characteristic features of the amniotic membrane. Alleles of the patient's husband were not identified when the cyst was genotyped. Some of the patient's loci were deleted and others showed a structurally heterogeneous pattern. These findings suggest that the cyst was derived not from the ovum parthenogenesis, but from the patient's somatic cells and could have been incubated by ascites.