bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimally invasive surgery of neuroblastic tumors in children: Indications depend on anatomical location and image‐defined risk factors
Authors: Irtan Sabine , Brisse Hervé J. , Minard‐Colin Véronique , Schleiermacher Gudrun , Canale Sandra , Sarnacki Sabine 
Published: October 2014

BackgroundMinimally invasive surgery (MIS) is still not a well‐accepted surgical approach to remove neuroblastic tumors. We aimed to assess the indications and limits of MIS in this childhood tumor according to tumor location and image‐defined risk factors (IDRFs).ProcedureBetween 2006 and 2012, 39 patients underwent MIS for neuroblastic tumors, using thoracoscopic (n = 20), retroperitoneoscopic (n = 1) or laparoscopic approaches (n = 18). The tumor locations were paravertebral (n = 18; thoracic n = 15, lumbar n = 3), perivascular (n = 5; abdominal n = 2; thoracic n = 3), adrenal (n = 13), pleural (n = 2) and pelvic (n = 1). Two patients were treated for relapses. According to the INRG staging system, IDRFs were absent in 20 patients and present in 19 patients. Ten patients received chemotherapy preoperatively. Mean largest diameter was 35 mm for thoracic tumors (range: 7–85 mm) and 34 mm for abdominal tumors (range: 10–75 mm). Mean follow‐up was 25 months (range: 5–116 months).ResultsResection was macroscopically incomplete (R2) for six thoracic tumors and one adrenal tumor. Conversion was necessary for three thoracic L2 tumors. Postoperative complications consisted of chylothorax in three patients with L2 paravertebral thoracic tumors, Horner's syndrome in a patient with a cervicothoracic tumor, and renal atrophy in a patient with a L2 abdominal tumor. No perioperative or postoperative complications occurred in patients with adrenal and abdominal paravertebral tumors. The overall survival rate was 98%.ConclusionIn carefully selected cases, MIS permits safe and efficient resection of neuroblastic tumors in children. Open surgical approach should be considered if organ or vascular control or quality of resection is jeopardized. Pediatr Blood Cancer 2015;62:257–261. © 2014 Wiley Periodicals, Inc.
Vehicle refuelling, use of domestic wood heaters and the risk of childhood brain tumours: Results from an Australian case–control study
Authors: Greenop Kathryn R. , Hinwood Andrea L. , Fritschi Lin , Scott Rodney J. , Attia John , Ashton Lesley J. , Heath John A. , Armstrong Bruce K. , Milne Elizabeth 
Published: October 2014

BackgroundThe aetiology of childhood brain tumours (CBT) is largely unknown. Damage to germ cells after parental exposure to airborne carcinogens, such as volatile organic compounds and polycyclic aromatic hydrocarbons is one plausible pathway. This analysis aimed to investigate whether parental refuelling of vehicles or the use of domestic wood heaters in key time periods relating to the child's birth was associated with an increased risk of CBT.ProcedureCases <15 years of age were recruited through 10 paediatric oncology centres around Australia; controls were recruited through nationwide random‐digit dialling, frequency matched to cases on age, sex and State of residence. Exposure to refuelling and wood heaters was ascertained through questionnaires from both parents. Odds ratios (ORs) and confidence intervals (CIs) were estimated using unconditional logistic regression, adjusting for relevant covariates.ResultsData were available for 306 case and 950 control families. Paternal refuelling ≥4 times/month was associated with an increased risk of CBT (OR 1.59, 95% CI: 1.11, 2.29), and a dose‐dependent trend was observed (P = 0.004). No association was seen for maternal refuelling. Use of closed, but not open, wood heaters before (OR 1.51, 95% CI: 1.05, 2.15) and after (OR 1.44, 95% CI: 1.03, 2.01) the child's birth was associated with increased risk of CBT, but dose‐response relationships were weak or absent.ConclusionsPaternal refuelling of vehicles ≥4 times/month and the use of closed wood heaters before the child's birth may increase the risk of CBT. Replication in larger studies is needed. Pediatr Blood Cancer 2015;62:229–234. © 2014 Wiley Periodicals, Inc.
Brooding rumination as a mediator in the relation between early maladaptive schemas and symptoms of depression and social anxiety in adolescents
Authors: Orue Izaskun , Calvete Esther , Padilla Patricia 
Published: October 2014

ABSTRACTTheory states that different cognitive constructs can be included in an integrated sequential model. This 3‐wave longitudinal study assessed whether schema domains predict brooding rumination and brooding in turn predict depression and social anxiety symptoms among adolescents. A total of 1170 adolescents (Mage = 13.44 years old, SDage = 1.30) completed measures of schema domains, brooding rumination, depression and social anxiety symptoms at baseline, 6‐ and 12‐month follow‐up (T1, T2, T3, respectively). Results revealed that the Disconnection and Rejection schema domain at T1 predicted prospective depression symptoms at T3 directly but not through brooding rumination. However, this schema domain did not predict social anxiety symptoms. The Other‐Directedness schema domain at T1 predicted social anxiety symptoms at T3 both directly and through brooding at T2. Furthermore, this schema domain also predicted depression symptoms at T3 through brooding at T2. Identifying specific schema domains and the mechanisms through which these domains predict psychological symptoms has implications for interventions with adolescents.
Neonatal intrahippocampal HIV‐1 protein Tat1–86 injection: neurobehavioral alterations in the absence of increased inflammatory cytokine activation
Authors: Moran Landhing M. , Fitting Sylvia , Booze Rosemarie M. , Webb Katy M. , Mactutus Charles F. 
Published: October 2014

AbstractPediatric AIDS caused by human immunodeficiency virus type 1 (HIV‐1) remains one of the leading worldwide causes of childhood morbidity and mortality. HIV‐1 proteins, such as Tat and gp120, are believed to play a crucial role in the neurotoxicity of pediatric HIV‐1 infection. Detrimental effects on development, behavior, and neuroanatomy follow neonatal exposure to the HIV‐1 viral toxins Tat1–72 and gp120. The present study investigated the neurobehavioral effects induced by the HIV‐1 neurotoxic protein Tat1–86, which encodes the first and second exons of the Tat protein. In addition, the potential effects of HIV‐1 toxic proteins Tat1–86 and gp120 on inflammatory pathways were examined in neonatal brains. Vehicle, 25 μg Tat1–86 or 100 ng gp120 was injected into the hippocampus of male Sprague–Dawley pups on postnatal day 1 (PD1). Tat1–86 induced developmental neurotoxic effects, as witnessed by delays in eye opening, delays in early reflex development and alterations in prepulse inhibition (PPI) and between‐session habituation of locomotor activity. Overall, the neurotoxic profile of Tat1–86 appeared more profound in the developing nervous system in vivo relative to that seen with the first exon encoded Tat1–72 (Fitting et al., 2008b), as noted on measures of eye opening, righting reflex, and PPI. Neither the direct PD1 CNS injection of the viral HIV‐1 protein variant Tat1–86, nor the HIV‐1 envelope protein gp120, at doses sufficient to induce neurotoxicity, necessarily induced significant expression of the inflammatory cytokine IL‐1β or inflammatory factors NF‐κβ and I‐κβ. The findings agree well with clinical observations that indicate delays in developmental milestones of pediatric HIV‐1 patients, and suggest that activation of inflammatory pathways is not an obligatory response to viral protein‐induced neurotoxicity that is detectable with behavioral assessments. Moreover, the amino acids encoded by the second tat exon may have unique actions on the developing hippocampus.
Using the plurality of codon positions to identify deleterious variants in human exomes
Authors: Subramanian Sankar 
Published: October 2014

Abstract
Motivation: A codon position could perform different or multiple roles in alternative transcripts of a gene. For instance, a non-synonymous position in one transcript could be a synonymous site in another. Alternatively, a position could remain as non-synonymous in multiple transcripts. Here we examined the impact of codon position plurality on the frequency of deleterious single-nucleotide variations (SNVs) using data from 6500 human exomes.
Results: Our results showed that the proportion of deleterious SNVs was more than 2-fold higher in positions that remain non-synonymous in multiple transcripts compared with that observed in positions that are non-synonymous in one or some transcript(s) and synonymous or intronic in other(s). Furthermore, we observed a positive relationship between the fraction of deleterious non-synonymous SNVs and the number of proteins (alternative splice variants) affected. These results demonstrate that the plurality of codon positions is an important attribute, which could be useful in identifying mutations associated with diseases.
Contact: s.subramanian@griffith.edu.au
Supplementary Information: Supplementary data are available at Bioinformatics online
An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs
Authors: Luijk René , Goeman Jelle J. , Slagboom Eline P. , Heijmans Bastiaan T. , van Zwet Erik W. 
Published: October 2014

AbstractIntroduction : An increasing number of studies investigates the influence of local genetic variation on DNA methylation levels, so-called in cis methylation quantitative trait loci (meQTLs). A common multiple testing approach in genome-wide cis meQTL studies limits the false discovery rate (FDR) among all CpG–SNP pairs to 0.05 and reports on CpGs from the significant CpG–SNP pairs. However, a statistical test for each CpG is not performed, potentially increasing the proportion of CpGs falsely reported on. Here, we presented an alternative approach that properly control for multiple testing at the CpG level.Results : We performed cis meQTL mapping for varying window sizes using publicly available single-nucleotide polymorphism (SNP) and 450 kb data, extracting the CpGs from the significant CpG–SNP pairs ( FDR&lt;0.05 ). Using a new bait-and-switch simulation approach, we show that up to 50% of the CpGs found in the simulated data may be false-positive results. We present an alternative two-step multiple testing approach using the Simes and Benjamini–Hochberg procedures that does control the FDR among the CpGs, as confirmed by the bait-and-switch simulation. This approach indicates the use of window sizes in cis meQTL mapping studies that are significantly smaller than commonly adopted.Discussion : Our approach to cis meQTL mapping properly controls the FDR at the CpG level, is computationally fast and can also be applied to cis eQTL studies.Availability and implementation : An examplary R script for performing the Simes procedure is available as supplementary material.Contact : e.w.van_zwet@lumc.nl or b.t.heijmans@lumc.nlSupplementary information : Supplementary data are available at Bioinformatics online.
SIST: stress-induced structural transitions in superhelical DNA
Authors: Zhabinskaya Dina , Madden Sally , Benham Craig J. 
Published: October 2014

Abstract
Summary : Supercoiling imposes stress on a DNA molecule that can drive susceptible sequences into alternative non-B form structures. This phenomenon occurs frequently in vivo and has been implicated in biological processes, such as replication, transcription, recombination and translocation. SIST is a software package that analyzes sequence-dependent structural transitions in kilobase length superhelical DNA molecules. The numerical algorithms in SIST are based on a statistical mechanical model that calculates the equilibrium probability of transition for each base pair in the domain. They are extensions of the original stress-induced duplex destabilization (SIDD) method, which analyzes stress-driven DNA strand separation. SIST also includes algorithms to analyze B-Z transitions and cruciform extrusion. The SIST pipeline has an option to use the DZCB trans algorithm, which analyzes the competition among these three transitions within a superhelical domain.
Availability and implementation : The package and additional documentation are freely available at https://bitbucket.org/benhamlab/sist_codes .
Contact : dzhabinskaya@ucdavis.edu
Evaluation of Commercial Kits for Dual Extraction of DNA and RNA from Human Body Fluids,,
Authors: Schweighardt Andrew J. , Tate Courtney M. , Scott Kristina A. , Harper Kathryn A. , Robertson James M. 
Published: October 2014

AbstractSTR typing of DNA evidence can identify the donor with a high power of discrimination but cannot identify the tissue origin of a body‐fluid stain. Using RNA to attribute a crime scene stain to a particular tissue may aid in reconstruction efforts. With blood from 10 donors, four DNA and RNA coextraction kits were evaluated by measuring yields and STR and mRNA profiles. T tests indicated some significant differences in kit performance. The Zymo Research ZR‐Duet™ kit performed best based on average DNA (41.4 ng) and mRNA (4.07 ng) yields and was the only kit to provide complete DNA/RNA profiles for all samples. The consistency of this kit was challenged by data from additional blood and saliva donors. Further testing is advised before a superior kit is unequivocally chosen. Stand‐alone DNA or RNA purification generally offers higher yield, but coextraction may still allow successful STR profiling and tissue source identification.
Columnar‐Thin‐Film‐Assisted Visualization of Depleted Sebaceous Fingermarks on Nonporous Metals and Hard Plastics
Authors: Williams Stephanie F. , Pulsifer Drew P. , Lakhtakia Akhlesh , Shaler Robert C. 
Published: October 2014

AbstractA fingermark on a nonporous substrate can be developed by depositing a columnar thin film (CTF) on it, but the CTF technique's sensitivity for low‐quality fingermarks is unknown. The optimized CTF and traditional development of several depletion series of sebaceous‐loaded fingermarks were compared using a split‐print methodology as well as subjective and objective grading schemes, in a limited laboratory trial. CTF development was superior to development with selected traditional techniques on brass, anodized aluminum, black acrylonitrile butadiene styrene (ABS), and white nylon. On white ABS and black nylon, the CTF technique performed poorly but still as well as the best‐performing traditional development technique. The CTF technique was more sensitive on brass and anodized aluminum than, and as sensitive on the four hard plastics and stainless steel as, the best‐performing traditional technique. Thus, the CTF technique is useful to develop friction‐ridge detail from limited fingermark residue on some smooth substrates.
Learning the “Craft” of Auditing: A Dynamic View of Auditors' On‐the‐Job Learning
Authors: Westermann Kimberly D. , Bedard Jean C. , Earley Christine E. 
Published: October 2014

AbstractWe investigate how auditors learn the technical aspects of their professional role while performing client engagements, and how that learning process has been shaped by changes in societal, economic, and regulatory forces. Prior studies explicitly recognize that auditors need social skills and demeanor consistent with professional norms as well as requisite knowledge, but those studies generally focus on the processes through which new auditors are molded toward consistency with social norms. In contrast, we focus on forces affecting the transfer of technical knowledge from supervisor (guide) to subordinate (learner) in the everyday work setting. Our evidence derives from semi‐structured interviews with 30 relatively new and more experienced audit partners at one Big 4 firm, thus spanning multiple “generations” of experience. Results confirm that auditors primarily acquire technical knowledge on the job, through the interactions among individual engagement team members. However, partners express concern about changes in the practice environment that may limit effectiveness of on‐the‐job learning, including characteristics of personnel, the approach to formal training at induction, supervisors' reluctance to provide candid feedback, regulatory and economic pressures, and the increased distraction, and reduced interpersonal contact associated with the use of information technology. At the end of the day, our findings raise implications for practice regarding the difficulty of developing effective learning conditions for auditors in the face of these challenges.
Subgingival bacterial recolonization after scaling and root planing in smokers with chronic periodontitis
Authors: Feres M , Bernal MAC , Matarazzo F , Faveri M , Duarte PM , Figueiredo LC 
Published: October 2014

AbstractBackgroundThe aim of this study was to compare subgingival bacterial recolonization patterns after scaling and root planing in current smokers and non‐smokers.Methods15 smokers and 15 non‐smokers with chronic periodontitis received scaling and root planing in six visits lasting one hour each, over a period of 21 days. Clinical monitoring was performed at baseline and 180 days, and microbiological monitoring was performed at baseline, immediately after scaling and root planing (Day 0) and at 42, 63 and 180 days post‐therapy. Subgingival plaque samples were analysed by checkerboard DNA–DNA hybridization.ResultsAn improvement in clinical condition was observed for smokers and non‐smokers; however, non‐smokers showed a greater reduction in mean clinical attachment level in intermediate sites in comparison with smokers (p < 0.05). At Day 0, there was a significant reduction in the mean counts of the three pathogens from the red complex, Eubacterium nodatum and Parvimonas micra only in non‐smokers (p < 0.05). There was a significant increase in the proportion of host‐compatible species in non‐smokers and smokers from baseline to 180 days post‐therapy (p < 0.05). However, a significant decrease in the pathogenic species was observed only in non‐smokers.ConclusionsSmokers were more susceptible to the re‐establishment of a pathogenic subgingival biofilm than non‐smokers.
Inhibition of transforming growth factor beta/SMAD signal by MiR‐155 is involved in arsenic trioxide‐induced anti‐angiogenesis in prostate cancer
Authors: Ji Hui , Li Yuan , Jiang Fei , Wang Xingxing , Zhang Jianping , Shen Jian , Yang Xiaojun 
Published: October 2014

Prostate cancer is the most common cause of cancer‐related deaths in men. Current practices for treatment of prostate cancer are less than satisfactory because of metastasis and recurrence, which are primarily attributed to angiogenesis. Hence, anti‐angiogenesis treatment is becoming a promising new approach for prostate cancer therapy. In addition to treating acute promyelocytic leukemia, arsenic trioxide (As2O3) suppresses other solid tumors, including prostate cancer. However, the effects of As2O3 on angiogenesis in prostate cancer cells, and the underlying molecular mechanisms remain unclear. In the present study, As2O3 attenuated angiogenic ability through microRNA‐155 (miR‐155)‐mediated inhibition of transforming growth factor beta (TGF‐β)/SMAD signal pathway in human prostate cancer PC‐3 and LNCaP cells in vitro and in vivo. Briefly, As2O3 inhibited the activations/expressions of both TGFβ‐induced and endogenous SMAD2/3. Furthermore, As2O3 improved the expression of miR‐155 via DNA‐demethylation. MiR‐155, which targeted the SMAD2‐3′UTR, decreased the expression and function of SMAD2. Knockdown of miR‐155 abolished the As2O3‐induced inhibitions of the TGF‐β/SMAD2 signaling, the vascular endothelial growth factor secretion and angiogenesis. Through understanding a novel mechanism whereby As2O3 inhibits angiogenic potential of prostate cancer cells, our study would help in the development of As2O3 as a potential chemopreventive agent when used alone or in combination with other current anticancer drugs.
Use of a modified Delphi approach to develop research priorities for the Association of Coloproctology of Great Britain and Ireland
Authors: Tiernan J. , Cook A. , Geh I. , George B. , Magill L. , Northover J. , Verjee A. , Wheeler J. , Fearnhead N. 
Published: October 2014

AbstractAimThe modified Delphi approach is an established method for reaching a consensus opinion among a group of experts in a particular field. We have used this technique to survey the entire membership of the Association of Coloproctology of Great Britain and Ireland (ACPGBI) to reach a consensus on prioritizing clinical research questions in colorectal disease.MethodThree rounds of surveys were conducted using a web‐based tool. In the first, the ACPGBI membership was invited to submit research questions. In Rounds 2 and 3 they were asked to score questions on priority. A steering group analysed the results of each round to identify those questions ranked as being of highest priority.ResultsFive hundred and two questions were submitted in Round 1. Following two rounds of voting and analysis, a list of 25 priority questions was produced, including 15 cancer‐related and 10 noncancer‐related questions.ConclusionIt is anticipated that these results will: (i) set the research agenda over the next few years for the study of colorectal disease in the United Kingdom, (ii) promote development and (iii) define funding of new research and prioritize areas of unmet clinical need where the potential clinical impact is greatest.
Gracilis muscle interposition for rectovaginal and anovaginal fistula repair: a systematic literature review
Authors: Hotouras A. , Ribas Y. , Zakeri S. , Murphy J. , Bhan C. , Chan C. L. 
Published: October 2014

AbstractBackgroundRepair of rectovaginal fistula (RVF) is associated with high recurrence. For this reason gracilis muscle interposition is increasingly being used.AimTo evaluate the efficacy of this procedure for RVF repair.Method/Search strategyA search of PubMed and Medline databases was performed in November 2013 using the text terms and MESH headings ‘rectovaginal fistula/fistulation’, and ‘gracilis muscle’, spanning 1980–2013. The search strategy was restricted to articles written in English with available abstracts. Sample size, aetiology of RVF, previous repair attempts, follow‐up period, healing rates and complications were recorded and analysed.ResultsSeventeen studies involving 106 patients were analysed. The cause of RVF included inflammatory bowel disease (n = 37 [34.9%]: Crohn's disease [34], ulcerative colitis [3]), pelvic surgery (37 [34.9%]), obstetric injury (9 [8.5%]), malignancy (7 [6.6%]), trauma (5 [4.7%]), miscellaneous (idiopathic, endometriosis, radiation: 11 [10.4%]). Patients had undergone a median number of two previous unsuccessful repairs. At a median follow‐up of 21 months, healing had occurred in 33–100% (median 100%) with the largest studies reporting rates between 60% and 90%. Thirteen studies did not report any complications, with the remainder reporting only minor morbidity.ConclusionGracilis interposition appears to have a reasonable success rate for RVF repair with acceptable morbidity. It may be considered as one of the first‐line treatment options for recurrent RVF.