bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of an image guided intensity‐modulated protocol for post‐prostatectomy radiotherapy: Planning data and acute toxicity outcomes
Authors: Chua Benjamin , Min Myo , Wood Maree , Edwards Sarah , Hoffmann Matthew , Greenham Stuart , Kovendy Andrew , McKay Michael J. , Shakespeare Thomas P. 
Published: February 2013

AbstractIntroductionThere is substantial interest in implementation of image‐guided intensity‐modulated radiotherapy (IG‐IMRT) in the post‐prostatectomy setting. We describe our implementation of IG‐IMRT, and examine how often published organ‐at‐risk (OAR) constraints were met. Furthermore, we evaluate the incidence of acute genitourinary and gastrointestinal toxicities when patients were treated according to our protocol.MethodsPatients were eligible if they received post‐prostatectomy radiotherapy (PPRT). Planning data were collected prospectively, and toxicity assessments were collected before, during and after treatment.ResultsSeventy‐five eligible patients received either 64 Gy (19%) or 66 Gy (81%) in a single phase to the prostate bed. Suggested rectal dose‐constraints of V40Gy < 60% and V60Gy < 40% were met in 64 (85%) and 75 (100%) patients, respectively. IMRT‐specific rectal dose‐constraints of V40Gy < 35% and V65Gy < 17% were achieved in 5 (7%) and 57 (76%) of patients. Bladder dose‐constraint (V50Gy < 50%) was met in 58 (77%) patients. Two patients (3%) experienced new grade 3 genitourinary toxicity and one patient (1%) experienced new grade 3 gastroinestinal toxicity. All grade 3 toxicities had improved by 3‐month review. Overall deterioration in urinary and gastrointestinal symptoms occurred in 33 (44%) and 35 (47%) of patients respectively.ConclusionsWe report on our implementation of PPRT which takes into account nationally adopted guidelines, with a margin reduction supported by use of daily image guidance. Non‐IMRT OAR constraints were met in most cases. IMRT‐specific constraints were less often achieved despite margin reductions, suggesting the need for review of guidelines. Severe toxicity was rare, and most patients did not experience deterioration in urinary or bowel function attributable to radiotherapy.
Identification of Culex complex species using SNP markers based on high‐resolution melting analysis
Authors: Kang David , Sim Cheolho 
Published: February 2013

AbstractMosquitoes belonging to the Culex pipiens complex are primary vectors for diseases such as West Nile encephalitis, Eastern equine encephalitis, many arboviruses, as well as lymphatic filariases. Despite sharing physiological characteristics, each mosquito species within the Culex complex has unique behavioural and reproductive traits that necessitate a proper method of identification. Unfortunately, morphometric methods of distinguishing members of this complex have failed to yield consistent results, giving rise to the need for molecular methods of identification. In this study, we propose a novel identification method using high‐resolution melting (HRM) analysis by examining single‐nucleotide polymorphisms in the acetylcholinesterase‐2 (ace‐2) locus. Our method provides a high confidence for species determination among the three Culex complex mosquitoes.
Transformer‐4 version 2.0.1, a free multi‐platform software to quickly reformat genotype matrices of any marker type, and archive them in the Demiurge information system
Authors: Caujapé‐Castells Juli , Sabbagh Izzat , Castellano José J. , Ramos Rafael , Henríquez Víctor , Quintana Francisco M. , Medina Dailos A. , Toledo Javier , Ramírez Fernando , Rodríguez Juan F. 
Published: February 2013

AbstractTransformer‐4 version 2.0.1 (T4) is a multi‐platform freeware programmed in java that can transform a genotype matrix in Excel or XML format into the input formats of one or several of the most commonly used population genetic software, for any possible combination of the populations that the matrix contains. T4 also allows the users to (i) draw allozyme gel interpretations for any number of diploid individuals, and then generate a genotype matrix ready to be used by T4; and (ii) produce basic reports about the data in the matrices. Furthermore, T4 is the only way to optionally submit ‘genetic diversity digests’ for publication in the Demiurge online information system (http://www.demiurge-project.org). Each such digest undergoes peer‐review, and it consists of a geo‐referenced data matrix in the tfm4 format plus any ancillary document or hyperlink that the digest authors see fit to include. The complementarity between T4 and Demiurge facilitates a free, safe, permanent, and standardized data archival and analysis system for researchers, and may also be a convenient resource for scientific journals, public administrations, or higher educators. T4 and its converters are freely available (at, respectively, http://www.demiurge-project.org/download_t4 and http://www.demiurge-project.org/converterstore) upon registration in the Demiurge information system (http://demiurge-project.org/register). Users have to click on the link provided on an account validation email, and accept Demiurge's terms of use (see http://www.demiurge-project.org/termsofuse). A thorough user's guide is available within T4. A 3‐min promotional video about T4 and Demiurge can be seen at http://vimeo.com/29828406.
A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages
Authors: Pérez‐Porro A. R. , Navarro‐Gómez D. , Uriz M. J. , Giribet G. 
Published: February 2013

AbstractSponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost‐effective manner. Here we present the first NGS (next‐generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non‐reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage‐based assemblies. In that multi‐stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA‐seq for improving knowledge on functional processes along the sponge life cycle.
Genetic dissection of a motility‐associated c‐di‐GMP signalling protein of Pseudomonas putida
Authors: Österberg Sofia , Åberg Anna , Herrera Seitz M Karina , Wolf‐Watz Magnus , Shingler Victoria 
Published: February 2013

SummaryLack of the Pseudomonas putida PP2258 protein or its overexpression results in defective motility on solid media. The PP2258 protein is tripartite, possessing a PAS domain linked to two domains associated with turnover of c‐di‐GMP – a cyclic nucleotide that controls the switch between motile and sessile lifestyles. The second messenger c‐di‐GMP is produced by diguanylate cyclases and degraded by phosphodiesterases containing GGDEF and EAL or HD‐GYP domains respectively. It is common for enzymes involved in c‐di‐GMP signalling to contain two domains with potentially opposing c‐di‐GMP turnover activities; however, usually one is degenerate and has been adopted to serve regulatory functions. Only a few proteins have previously been found to have dual enzymatic activities – being capable of both synthesizing and hydrolysing c‐di‐GMP. Here, using truncated and mutant derivatives of PP2258, we show that despite a lack of complete consensus in either the GGDEF or EAL motifs, the two c‐di‐GMP turnover domains can function independently of each other, and that the diguanylate cyclase activity is regulated by an inhibitory I‐site within its GGDEF domain. Thus, motility‐associated PP2258 can be added to the short list of bifunctional c‐di‐GMP signalling proteins.
Comparison of periodontal open flap debridement versus closed debridement with Er,Cr:YSGG laser
Authors: Gupta M , Lamba AK , Verma M , Faraz F , Tandon S , Chawla K , Koli DK 
Published: February 2013

AbstractBackgroundTraditional periodontal open flap debridement (OFD) results in reduced pocket depth (PD), clinical attachment loss (CAL), gingival recession (GR) and postoperative pain and discomfort. The quest to overcome these shortcomings has led to research into Er,Cr:YSGG laser assisted pocket therapy (ELAPT). This study was designed to compare the clinical outcomes of ELAPT versus OFD.MethodsFifteen patients with a PD of ≥5 mm and ≤8 mm at two sites were selected. Test sites (Group 1) were treated by ELAPT and the control (Group 2) by OFD. Clinical parameters were recorded at baseline, 3 and 6 months and included Plaque Index (PI), Gingival Index (GI), modified Sulcular Bleeding Index (mSBI), PD, CAL and GR.ResultsBoth treatments produced a reduction in PI, GI, mSBI and PD, an increase in GR, and a gain in CAL at 3 and 6 months. The mean gain of CAL in Group 1 at 3 and 6 months (1.60 ± 0.78 and 1.80 ± 0.63) was similar (p > 0.05) to the value of Group 2 (1.93 ± 0.88 and 2.00 ± 0.54). GR increased significantly (p < 0.05) only in Group 2 at 3 and 6 months (1.80 ± 0.56 and 1.87 ± 0.64) compared to Group 1 (0.50 ± 0.68 and 0.60 ± 0.74).ConclusionsELAPT compared with OFD results in similar CAL gains with less GR and significant reductions in PD, GI and mSBI, and may be considered as an alternative to surgical therapy.
Weak Firms Follow Strong Firms in Hot IPO Markets
Authors: Chang Kiyoung , Kim Yong‐Cheol , Shim Hyeongsop 
Published: February 2013

AbstractWe investigate whether initial public offerings (IPO) occurring during hot markets are fundamentally different from those occurring during cold markets. Firms that go public during hot markets show lower survival probability, shorter survival duration, and worse long‐run performance. When hot markets are separated into two periods, we find early issuers during hot markets (pioneers) have better investment opportunities than late issuers during the same hot markets (followers). Furthermore, pioneers show higher survival probability, longer survival duration, and better long‐run performance than followers. Our evidence shows that the inferior quality of followers is a major contributor to the difference between hot and cold IPO markets.
Credit Rating Changes and Earnings Management
Authors: Kim Young S. , Kim Yura , Song Kyojik “Roy” 
Published: February 2013

AbstractWe examine whether firm managers engage in income‐increasing accruals manipulation or real activities earnings management to affect the future rating changes when firm managers have private information about the upcoming credit rating change. Using the large sample of United States data over the period 1990–2011, we find that firms with upcoming credit rating changes are likely to engage in real activities earnings management, whereas they tend to decrease discretionary accruals before credit rating changes. We also find a positive relationship between real activities management (RM) and credit rating upgrades, but no relation between RM and downgrades. The findings suggest that the firm's management tries to influence the upcoming changes of credit ratings by actively engaging in real activities earnings management rather than accruals‐based earnings management.
Immunogenicity and Contraceptive Efficacy of Escherichia coli‐Expressed Recombinant Porcine Zona Pellucida Proteins
Authors: Gupta Neha , Chakrabarti Kausiki , Prakash Krishna , Wadhwa Neerja , Gupta Tripti , Gupta Satish K. 
Published: February 2013

ProblemTo overcome availability of the purified native zona pellucida (ZP) glycoproteins for immunocontraception, porcine ZP3, and ZP4 were expressed in E. coli.Method of studyPurified recombinant proteins were characterized by SDS‐PAGE and Western blot, and immunogenicity and contraceptive efficacy determined in FvB/J female mice.ResultsPurified ZP3, ZP3 with promiscuous T‐cell epitope of tetanus toxoid, ZP4 and ZP4 incorporating promiscuous T‐cell epitope of bovine RNase revealed ~44‐, ~49‐, ~53‐, and ~55‐kDa bands by SDS‐PAGE and Western blot, respectively. Immunization of female mice with recombinant proteins elicited high antibody titers as well as T‐cell responses. Immune sera recognized mouse oocyte ZP and also inhibited in vitro fertilization. Immunized mice showed significant decrease in fertility. Recombinant proteins were able to recall memory antibody response in female mice primed with porcine native ZP.ConclusionAvailability of recombinant porcine proteins will be useful in the development of contraceptive vaccine.
Molecular characteristics of horse phospholipase C zeta (PLCζ)
Authors: Sato Kana , Wakai Takuya , Seita Yasunari , Takizawa Akiko , Fissore Rafael A. , Ito Junya , Kashiwazaki Naomi 
Published: February 2013

AbstractA sperm‐specific phospholipase C (PLC), PLCzeta (PLCζ), is thought to underlie the initiation of calcium ([Ca2+]i) oscillations that induce egg activation in mammals. In large domestic species, only bovine, porcine and recently equine PLCζ have been cloned, and the physiological functions of these molecules have not been fully characterized. Here, we evaluated the physiological functions of equine PLCζ (ePLCζ) in mouse oocytes. ePLCζ was cloned from testis using RT‐PCR. The expression of ePLCζ messenger RNA was confirmed in testis but not in other tissues. Microinjection of ePLCζ complementary RNA (cRNA) into mouse oocytes induced long‐lasting [Ca2+]i oscillations, and most of the injected oocytes formed pronuclei (PN). The injection of cRNAs encoding horse, mouse, human and cow PLCζ into mouse oocytes showed that ePLCζ had the highest [Ca2+]i oscillation‐inducing activity among the species tested. Mutation of D202R, which renders the protein inactive, abrogated the activity of ePLCζ. The nuclear translocation ability of ePLCζ was defective when expressed in mouse oocytes. Taken together, our findings show for the first time that ePLCζ has highest activity of the mammalian species studied to date. Our findings will be useful for the improvement of reproductive technologies in the horse.
Exploring the role and influence of expectations in achieving VLE benefit success
Authors: Jackson Stephen , Fearon Colm 
Published: February 2013

AbstractThe aim of this paper is to investigate the role and influence of expectations management in realising benefit success when adopting a virtual learning environment (VLE). Based on a discussion of findings from a further and higher education college in the UK, a conceptual expectations management model is developed that explores the factors influencing the formulation and realisation of expected benefits from a case study of VLE adoption over time (2003–2012). The importance of avoiding unrealistic expectations as well as proactive user involvement, change control, training and clearly defined pedagogical reasons for introducing a VLE are discussed. Finally, a number of key learning points, which managers and practitioners should address when adopting VLEs, are also considered, along with suggestions for future research.
Surgical correction of vesico‐ureteric reflux for recurrent febrile urinary tract infections after kidney transplantation
Authors: Dinckan Ayhan , Aliosmanoglu Ibrahim , Kocak Huseyin , Gunseren Filiz , Mesci Ayhan , Ertug Zeki , Yucel Selcuk , Suleymanlar Gultekin , Gurkan Alihan 
Published: February 2013

Objective
To evaluate the outcome of anti‐reflux revision surgery in patients diagnosed with at least a grade 3 reflux at voiding cysto‐urethrography in patients with recurrent urinary tract infection (UTI) after renal transplantation.
Patients and Methods
We identified 60 patients with a diagnosis of recurrent febrile UTI and post‐transplantation vesico‐ureteric reflux (VUR) who underwent open surgical correction of reflux.
Patient characteristics, including the aetiology of end‐stage renal disease, age, time to VUR correction, type of VUR correction, serum creatinine levels, and number of UTIs before and after correction were documented.
Results
The median (range) age of the patients was 31.5 (9–65) years. A total of 30 patients underwent uretero‐ureterostomy or pyelo‐ureterostomy and 30 underwent extravesical or intravesical ureteric reimplantation.
The median (range) creatinine levels before and after correction were 1.5 (0.8–4.5) mg/dL and 1.3 (0.7–4.5) mg/dL (P < 0.05), respectively.
The median (range) number of UTI episodes reported before the correction surgery was 4 (3–12), whereas number of UTI episodes after the surgery was 1 (0–12), the difference being significant (P < 0.05).
Conclusions
Open surgical correction of post‐transplant VUR is an effective and safe method of decreasing UTI episodes and stopping reflux.
Surgical correction of reflux may prolong the life of the renal graft.
Dysembryoplastic Neuroepithelial Tumors Share with Pleomorphic Xanthoastrocytomas and Gangliogliomas BRAFV600E Mutation and Expression
Authors: Chappé Céline , Padovani Laetitia , Scavarda Didier , Forest Fabien , Nanni‐Metellus Isabelle , Loundou Anderson , Mercurio Sandy , Fina Frédéric , Lena Gabriel , Colin Carole , Figarella‐Branger Dominique 
Published: February 2013

AbstractPediatric cortical glioneuronal benign tumors mainly include gangliogliomas (GG) [differential diagnoses pilocytic astrocytomas (PA) and pleomorphic xanthoastrocytomas (PXA)] and dysembryoplastic neuroepithelial tumor (DNT). DNT include the specific form and the controversial non‐specific form that lack the specific glioneuronal element. Our aims were to search for BRAFV600E mutation and CD34 expression in DNT, PXA, GG and PA to correlate BRAFV600E mutation with BRAFV600E expression and to evaluate their diagnostic and prognostic values. Ninety‐six children were included. BRAFV600E mutation was studied by sequencing and immunohistochemistry; CD34 expression was analyzed by immunohistochemistry. BRAFV600E mutation was detected in PXA (60%), GG (38.7%), DNT (30%, including 3/11 specific and 3/9 non‐specific forms) and PA (12.5%). BRAFV600E expression was recorded in PXA (60%), GG (45.2%) and DNT (30%). CD34 expression was recorded in PXA (60%), GG (58.1%), DNT (25%) and PA (12.5%). Neither CD34 expression nor BRAFV600E status was predictive of prognosis, except for PA tumors where CD34 expression was associated with a shorter overall survival. In conclusion, DNT shared with PXA and GG, BRAFV600E mutation and/or CD34 expression, which represent molecular markers for these tumors, and we recommend searching for CD34 expression and BRAFV600E mutation in all DNT, especially the non‐specific forms.
Osteonecrosis of the Jaw after Implant Surgery in Patients Treated with Bisphosphonates – A Presentation of Six Consecutive Cases
Authors: Tam Yvonne , Kar Kian , Nowzari Hessam , Cha Hyun‐Suk , Ahn Kang‐Min 
Published: February 2013

AbstractBackgroundOsteonecrosis of the jaws in patients treated with bisphosphonates is mostly associated with intravenous bisphosphonates while the incidence associated with oral bisphosphonates is not significant.PurposeThe purpose of this paper is to describe a series of cases of jaw osteonecrosis that may be associated with dental implant placement in patients who had taken nitrogen containing bisphosphonates via oral and/or intravenous route.PatientsSix female patients were treated for osteonecrosis of the jaw after implant placement. An average age was 71.8 ± 6.5 years old and they had a history of bisphosphonate use. Two patients suffered from cancer and the other patients had osteoporosis. Two osteoporosis patients had taken only oral bisphosphonate and the other patients received intravenous bisphosphonates.ResultsResection of necrotized bone, implant removal, and primary closure were performed in five patients and four patients showed uneventful healing. One patient presented recurrence at the maxilla and underwent further extraction and resection. One patient presented with an exposure of the bone after implant placement was treated with an advanced flap closure, and the implants were preserved.ConclusionUnusual jaw necrosis after dental implant surgery might be related with oral and/or intravenous bisphosphonates. Wide resection of necrotic bone, collagen graft, and primary closure are key factors for successful healing.
Clinical, microbiological, and salivary biomarker profiles of dental implant patients with type 2 diabetes
Authors: Tatarakis Nikolaos , Kinney Janet S. , Inglehart Marita , Braun Thomas M. , Shelburne Charles , Lang Niklaus P. , Giannobile William V. , Oh Tae‐Ju 
Published: February 2013

AbstractObjectiveRegulators of peri‐implant bone loss in patients with diabetes appear to involve multiple risk factors that have not been clearly elucidated. This study was conducted to explore putative local etiologic factors on implant bone loss in relation to type 2 diabetes mellitus, including clinical, microbial, salivary biomarker, and psychosocial factors.Materials and methodsThirty‐two subjects (divided into type 2 diabetes mellitus and non‐diabetic controls), having at least one functional implant and six teeth, were enrolled in a 1‐year longitudinal investigation. Analyses of clinical measurements and standardized intra‐oral radiographs, saliva and serum biomarkers (via protein arrays for 20 selected markers), and plaque biofilm (via qPCR for eight periodontal pathogens) were performed at baseline and 1 year. In addition, the subjects were asked to respond to questionnaires to assess behavioral and psychosocial variables.ResultsThere was a significant increase from baseline to 1 year in the probing depth of implants in the diabetes group (1.95 mm to 2.35 mm, P = 0.015). The average radiographic bone loss during the study period marginally increased at dental implants compared to natural teeth over the study period (0.08 mm vs. 0.05 mm; P = 0.043). The control group harbored higher levels of Treponema denticola at their teeth at baseline (P = 0.046), and the levels of the pathogen increased significantly over time around the implants of the same group (P = 0.003). Salivary osteoprotegerin (OPG) levels were higher in the diabetes group than the control group at baseline only; in addition, the salivary levels of IL‐4, IL‐10, and OPG associated with host defense were significantly reduced in the diabetes group (P = 0.010, P = 0.019, and P = 0.024), while controls showed an increase in the salivary OPG levels (P = 0.005). For psychosocial factors, there were not many significant changes over the observation period, except for some findings related to coping behaviors at baseline.ConclusionsThe study suggests that the clinical, microbiological, salivary biomarker, and psychosocial profiles of dental implant patients with type 2 diabetes who are under good metabolic control and regular maintenance care are very similar to those of non‐diabetic individuals. Future studies are warranted to validate the findings in longer‐term and larger clinical trials (ClinicalTrials.gov # NCT00933491).