bluuebunny/crossref_metadata_2025_split huggingface dataset:
PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data
Authors: Frankhouser David E. , Murphy Mark , Blachly James S. , Park Jincheol , Zoller Mike W. , Ganbat Javkhlan-Ochir , Curfman John , Byrd John C. , Lin Shili , Marcucci Guido , Yan Pearlly , Bundschuh Ralf 
Published: September 2014

AbstractMotivation : DNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques.Results : Here we present a computational method that computes nucleotide-resolution methylation values from capture-based data by incorporating fragment length profiles into a model of methylation analysis. We demonstrate that it compares favorably with nucleotide-resolution bisulfite sequencing and has better predictive power with respect to a reference than window-based methods, often used for enrichment data. The described method was used to produce the methylation data used in tandem with gene expression to produce a novel and clinically significant gene signature in acute myeloid leukemia. In addition, we introduce a complementary statistical method that uses this nucleotide-resolution methylation data for detection of differentially methylated features.Availability : Software in the form of Python and R scripts is available at http://bioserv.mps.ohio-state.edu/ premer and is free for non-commercial use.Contact : pearlly.yan@osumc.edu ; bundschuh@mps.ohio-state.eduSupplementary information: Supplementary data are available at Bioinformatics online.
VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering
Authors: Verbist Bie M.P. , Thys Kim , Reumers Joke , Wetzels Yves , Van der Borght Koen , Talloen Willem , Aerssens Jeroen , Clement Lieven , Thas Olivier 
Published: September 2014

Abstract
Motivation : In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations.
Results : A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%.
Availability : The VirVarSeq is available, together with a user’s guide and test data, at sourceforge: http://sourceforge.net/projects/virtools/?source=directory
Contact : bie.verbist@ugent.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Trans-dimensional finite-fault inversion
Authors: Dettmer Jan , Benavente Roberto , Cummins Phil R. , Sambridge Malcolm 
Published: September 2014

AbstractThis paper develops a probabilistic Bayesian approach to the problem of inferring the spatiotemporal evolution of earthquake rupture on a fault surface from seismic data with rigorous uncertainty estimation. To date, uncertainties of rupture parameters are poorly understood, and the effect of choices such as fault discretization on uncertainties has not been studied. We show that model choice is fundamentally linked to uncertainty estimation and can have profound effects on results. The approach developed here is based on a trans-dimensional self-parametrization of the fault, avoids regularization constraints and provides rigorous uncertainty estimation that accounts for model-selection ambiguity associated with the fault discretization. In particular, the fault is parametrized using self-adapting irregular grids which intrinsically match the local resolving power of the data and provide parsimonious solutions requiring few parameters to capture complex rupture characteristics. Rupture causality is ensured by parametrizing rupture-onset time by a rupture-velocity field and obtaining first rupture times from the eikonal equation. The Bayesian sampling of the parameter space is implemented on a computer cluster with a highly efficient parallel tempering algorithm.The inversion is applied to simulated and observed W-phase waveforms from the 2010 Maule (Chile) earthquake. Simulation results show that our approach avoids both over- and underparametrization to ensure unbiased inversion results with uncertainty estimates that are consistent with data information. The simulation results also show the ability of W-phase data to resolve the spatial variability of slip magnitude and rake angles. In addition, sensitivity to spatially dependent rupture velocities exists for kinematic slip models.Application to the observed data indicates that residual errors are highly correlated and likely dominated by theory error, necessitating the iterative estimation of a non-stationary data covariance matrix. The moment magnitude for the Maule earthquake is estimated to be ∼8.9, with slip concentrated in two zones updip of and north and south of the hypocentre, respectively. While this aspect of the slip distribution is similar to previous studies, we show that the slip maximum in the southern zone is poorly resolved compared to the northern zone. Both slip maxima are higher than reported in previous studies, which we speculate may be due to the lack of bias caused by the regularization used in other studies.
Transformation of vanadinite [Pb5(VO4)3Cl] by fungi
Authors: Ceci Andrea , Rhee Young Joon , Kierans Martin , Hillier Stephen , Pendlowski Helen , Gray Nia , Persiani Anna Maria , Gadd Geoffrey Michael 
Published: September 2014

SummarySaprotrophic fungi were investigated for their bioweathering effects on the vanadium‐ and lead‐containing insoluble apatite group mineral, vanadinite [Pb5(VO4)3Cl]. Despite the insolubility of vanadinite, fungi exerted both biochemical and biophysical effects on the mineral including etching, penetration and formation of new biominerals. Lead oxalate was precipitated by Aspergillus niger during bioleaching of natural and synthetic vanadinite. Some calcium oxalate monohydrate (whewellite) was formed with natural vanadinite because of the presence of associated ankerite [Ca(Fe2+,Mg)(CO3)2]. Aspergillus niger also precipitated lead oxalate during growth in the presence of lead carbonate, vanadium(V) oxide and ammonium metavanadate, while abiotic tests confirmed the efficacy of oxalic acid in solubilizing vanadinite and precipitating lead as oxalate. Geochemical modelling confirmed the complexity of vanadium speciation, and the significant effect of oxalate. Oxalate–vanadium complexes markedly reduced the vanadinite stability field, with cationic lead(II) and lead oxalate also occurring. In all treatments and geochemical simulations, no other lead vanadate, or vanadium minerals were detected. This research highlights the importance of oxalate in vanadinite bioweathering and suggests a general fungal transformation of lead‐containing apatite group minerals (e.g. vanadinite, pyromorphite, mimetite) by this mechanism. The findings are also relevant to remedial treatments for lead/vanadium contamination, and novel approaches for vanadium recovery.
Plant methyl salicylate induces defense responses in the rhizobacterium Bacillus subtilis
Authors: Kobayashi Kazuo 
Published: September 2014

SummaryBacillus subtilis is a rhizobacterium that promotes plant growth and health. Cultivation of B. subtilis with an uprooted weed on solid medium produced pleat‐like architectures on colonies near the plant. To test whether plants emit signals that affect B. subtilis colony morphology, we examined the effect of plant‐related compounds on colony morphology. Bacillus subtilis formed mucoid colonies specifically in response to methyl salicylate, which is a plant‐defense signal released in response to pathogen infection. Methyl salicylate induced mucoid colony formation by stimulating poly‐γ‐glutamic acid biosynthesis, which formed enclosing capsules that protected the cells from exposure to antimicrobial compounds. Poly‐γ‐glutamic acid synthesis depended on the DegS‐DegU two‐component regulatory system, which activated DegSU‐dependent gene transcription in response to methyl salicylate. Bacillus subtilis did not induce plant methyl salicylate production, indicating that the most probable source of methyl salicylate in the rhizosphere is pathogen‐infected plants. Methyl salicylate induced B. subtilis biosynthesis of the antibiotics bacilysin and fengycin, the latter of which exhibited inhibitory activity against the plant pathogenic fungus Fusarium oxysporum. We propose that B. subtilis may sense plants under pathogen attack via methyl salicylate, and express defense responses that protect both B. subtilis and host plants in the rhizosphere.
The Impact of Ozone Treatment on Changes in Biologically Active Substances of Cardamom Seeds
Authors: Joanna Brodowska Agnieszka , Śmigielski Krzysztof , Nowak Agnieszka , Brodowska Katarzyna , Catthoor Rik , Czyżowska Agata 
Published: September 2014

AbstractThe overall objective of this study was to develop a decontamination method against microorganisms in cardamom (Elettaria cardamomum (L.) Maton) seeds using ozone as a decontaminating agent. Ozone treatment was conducted 3 times, at 24‐h intervals, and the parameters of the process were determined assuring the least possible losses of biologically active substances (essential oils and polyphenols): ozone concentration 160 to 165.0 g/m3; flow rate 0.1 L/min; pressure 0.5 atm; time 30 min. After each step of decontamination, the microbiological profile of the cardamom seeds was studied, and the contaminating microflora was identified. Next to the microbiological profile, the total polyphenol content (TPC), composition of essential oils, free radical‐scavenging capacity, total antioxidant capacity, ferric‐reducing antioxidant power (FRAP), and LC–MS polyphenol analysis were determined. This study shows that extract from cardamom seeds after ozone treatment is characterized by a better radical scavenging activity (IC50 = 24.18 ± 0.04 mg/mL) than the control sample (IC50 = 31.94 ± 0.05 mg/mL). The extract from cardamom seeds after ozone treatment showed an improved FRAP activity as well (613.64 ± 49.79 mmol TE/g compared to 480.29 ± 30.91 mmol TE/g of control sample). The TPC and the total antioxidant capacity were negatively affected, respectively, 41.2% and 16.2%, compared to the control sample.
Neostigmine vs. sugammadex: observational cohort study comparing the quality of recovery using the Postoperative Quality Recovery Scale
Authors: AMORIM P. , LAGARTO F. , GOMES B. , ESTEVES S. , BISMARCK J. , RODRIGUES N. , NOGUEIRA M. 
Published: September 2014

BackgroundQuality of postoperative recovery is an important outcome after surgery. An observational cohort study was designed to assess the quality of postoperative recovery using the Portuguese version of the Postoperative Quality Recovery Scale (PQRS) in patients treated with neostigmine vs. sugammadex as neuromuscular blocking reversal agents.MethodsA convenience sample of 101 adult patients undergoing elective surgery with general anaesthesia and treated with neostigmine (n = 48) or sugammadex (n = 53) as neuromuscular blocking reversal agents was included. Patients were evaluated using the Portuguese PQRS version at baseline and postoperatively at 15 (T15) and 40 (T40) min and also at days 1 and 3. Recovery was defined as return to baseline values (or better) at each time points.ResultsThe PQRS overall recovery rates were similar in both groups, but recoveries in the nociceptive (96.2% vs. 81.3%, P = 0.02) and physiological (96.2% vs. 70.2%, P = 0.001) domains at T40 were higher in the sugammadex group than in the neostigmine group. Also, there was a trend that patients treated with sugammadex reported significantly better global perspective on the impact of surgery on working capacity and daily activities, as well as higher satisfaction with anaesthetic care.ConclusionsThis pilot study suggests that sugammadex may improve physiological and nociceptive postoperative recovery as well as patient satisfaction with anaesthetic care. Although we lack an explanation for a possible favourable impact of sugammadex on quality of recovery, our results may provide sufficient preliminary data to justify a randomised trial to explore this possibility.
Gastric adenocarcinoma in a diamond python (Morelia spilota spilota)
Authors: Baron HR , Allavena R , Melville LM , Doneley RJT 
Published: September 2014

Case reportA 5‐year‐old captive male diamond python (Morelia spilota spilota) was presented with a 1‐month history of regurgitation and anorexia and discrete coelomic distention. Physical examination revealed a firm, immobile mass at approximately two‐thirds of the snout–vent length from the front of the head. Ultrasound‐guided fine needle aspirate biopsy of the mass in the region of the stomach showed necrosis with bacterial infiltration and possibly neoplastic changes. A gastroscopy was conducted, but showed grossly normal gastric mucosa, confirmed by biopsy. On exploratory coeliotomy, it was confirmed the mass involved most of the stomach wall and occluded the gastric lumen. The mass was completely excised and based on histopathology, a diagnosis of gastric adenocarcinoma was made. The snake was found dead 12 h postoperatively, but no specific cause of death was found on postmortem examination.ConclusionMost cases of adenocarcinoma in snakes go undiagnosed. This case report illustrates that the architecture of gastric masses may lead to false‐negative gastric biopsy results in snakes with neoplasia.
Friendlessness and theory of mind: A prospective longitudinal study
Authors: Fink Elian , Begeer Sander , Peterson Candida C. , Slaughter Virginia , de Rosnay Marc 
Published: September 2014

Chronic friendlessness in childhood predicts adverse mental health outcomes throughout life, yet its earliest roots are poorly understood. In theory, developing a theory of mind (ToM) should help children gain mutual friends and one preschool study (Peterson & Siegal, 2002. Br J Dev Psychol, 20, 205) suggested a cross‐sectional connection. We therefore used a 2‐year prospective longitudinal design to explore ToM as a predictor of mutual friendship in 114 children from age 5 to 7 years after controlling potential confounds including language ability and group popularity. Confirming friendship's distinctiveness from group sociometric status, numerous group‐rejected children (53%) had a mutual friend whereas 23% of those highest in group status did not. Five‐year‐olds with a mutual friend significantly outperformed their friendless peers on a comprehensive ToM battery (basic and advanced false belief). Longitudinally, chronically friendless 7‐year‐olds (no friends at either testing time) stood out for their exceptionally poor Time 1 ToM understanding even after controlling for group popularity, age, and language skill. Extending previous evidence of ToM's predictive links with later social and cognitive outcomes, these results for mutual friendship suggest possible interventions to help reduce the lifelong mental health costs of chronic friendlessness.
Whose picture is this? Children's memory for item and source information
Authors: Chalmers Kerry A. 
Published: September 2014

Children aged 3½ to 6½ years viewed pictures of common objects presented either once or three times on one of two consecutive days. A different hand puppet was used to present the pictures on each day, providing both perceptual and temporal cues to source. At test, old (studied) and new (non‐studied) pictures were presented for item recognition and source identification. Results showed that both item and source accuracy were higher for older (M = 5; 9 years) than younger children (M = 4; 6 years). Significant interactions between Age and Day of study were found for both item and source accuracy. For younger children, accuracy was higher for pictures studied on Day 1 than Day 2 (significant for source identification but not item recognition), whereas older children showed the opposite pattern: Higher accuracy for Day 2 than Day 1 (significant for item recognition but not source identification). Results are interpreted with respect to proactive interference and response bias. The utility of signal detection theory measures in determining the basis of age differences in performance of source identification is discussed.
The Differential Profiling of Ubiquitin‐Proteasome and Autophagy Systems in Different Tissues before the Onset of Huntington's Disease Models
Authors: Her Lu‐Shiun , Lin Jian‐Yu , Fu Mu‐Hui , Chang Yu‐Fan , Li Chia‐Ling , Tang Ting‐Yu , Jhang Yu‐Ling , Chang Chih‐Yi , Shih Meng‐Chi , Cheng Pei‐Hsun , Yang Shang‐Hsun 
Published: September 2014

AbstractHuntington's disease (HD) is a genetic and neurodegenerative disease, leading to motor and cognitive dysfunction in HD patients. At cellular level, this disease is caused by the accumulation of mutant huntingtin (HTT) in different cells, and finally results in the dysfunction of different cells. To clean these mutant proteins, ubiquitin‐proteasome system (UPS) and autophagy system are two critical pathways in the brain; however, little is known in other peripheral tissues. As mutant HTT affects different tissues progressively and might influence the UPS and autophagy pathways at early stages, we attempted to examine two clearance systems in HD models before the onset. Here, in vitro results showed that the accumulation of UPS signals with time was observed obviously in neuroblastoma and kidney cells, not in other cells. In HD transgenic mice, we observed the impairment of UPS, but not autophagy, over time in the cortex and striatum. In heart and muscle tissues, disturbance of autophagy was observed, whereas dysfunction of UPS was displayed in liver and lung. These results suggest that two protein clearance pathways are disturbed differentially in different tissues before the onset of HD, and enhancement of protein clearance at early stages might provide a potential stratagem to alleviate the progression of HD.
Long‐term survival and conditional survival of cancer patients in Japan using population‐based cancer registry data
Authors: Ito Yuri , Miyashiro Isao , Ito Hidemi , Hosono Satoyo , Chihara Dai , Nakata‐Yamada Kayo , Nakayama Masashi , Matsuzaka Masashi , Hattori Masakazu , Sugiyama Hiromi , Oze Isao , Tanaka Rina , Nomura Etsuko , Nishino Yoshikazu , Matsuda Tomohiro , Ioka Akiko , Tsukuma Hideaki , Nakayama Tomio ,   the J‐CANSIS Research Group
Published: September 2014

Although we usually report 5‐year cancer survival using population‐based cancer registry data, nowadays many cancer patients survive longer and need to be followed‐up for more than 5 years. Long‐term cancer survival figures are scarce in Japan. Here we report 10‐year cancer survival and conditional survival using an established statistical approach. We received data on 1 387 489 cancer cases from six prefectural population‐based cancer registries in Japan, diagnosed between 1993 and 2009 and followed‐up for at least 5 years. We estimated the 10‐year relative survival of patients who were followed‐up between 2002 and 2006 using period analysis. Using this 10‐year survival, we also calculated the conditional 5‐year survival for cancer survivors who lived for some years after diagnosis. We reported 10‐year survival and conditional survival of 23 types of cancer for 15–99‐year‐old patients and four types of cancer for children (0–14 years old) and adolescent and young adults (15–29 years old) patients by sex. Variation in 10‐year cancer survival by site was wide, from 5% for pancreatic cancer to 95% for female thyroid cancer. Approximately 70–80% of children and adolescent and young adult cancer patients survived for more than 10 years. Conditional 5‐year survival for most cancer sites increased according to years, whereas those for liver cancer and multiple myeloma did not increase. We reported 10‐year cancer survival and conditional survival using population‐based cancer registries in Japan. It is important for patients and clinicians to report these relevant figures using population‐based data.
Clinical and Radiographic Comparison between Platform‐Shifted and Nonplatform‐Shifted Implant: A One‐Year Prospective Study
Authors: Glibert Maarten , Vervaeke Stijn , De Bruyn Hugo , Östman Pär‐Olov 
Published: September 2014

AbstractBackgroundDevelopments in implant hardware and biologic understanding improved treatment predictability in terms of implant survival. Current research focuses on accelerated loading protocols and crestal bone preservation.PurposeThis prospective, monocenter study analyzed the clinical and radiographic outcome of a novel parallel‐walled implant, with and without platform shift.Materials and MethodsForty‐eight consecutively treated patients (30 women, 18 men) with crowns/bridges supported by 115 implants were included. Eighty‐three percent of implants were nonocclusal, immediately loaded, and 17% were subjected to one‐stage surgery and delayed loading after 10 weeks; 39.1% were of diameter 5.0 mm, enabling platform shifting with a 4.0 mm‐wide prosthetic component; 60.9% were of diameter 4.0 mm with a 4.0 mm component. Radiographic crestal bone levels were assessed at baseline and 1 year. A multivariate statistical analysis was performed to determine factors affecting crestal bone loss after 1 year.ResultsAll implants survived and mean marginal bone loss was 0.73 mm (SD: 0.13; range: −0.60 to 5.0 mm). There was a statistically significant difference between platform‐shifted (0.63 mm; SD: 0.18) and nonplatform‐shifted (1.02 mm; SD: 0.14) implants. Implants in abundant bone volume lost significant less crestal bone (0.45 mm; SD: 0.14) compared with implants in small volume (1.20 mm; SD: 0.21). Implant diameter, loading time, anatomical position, smoking, and bone quality did not affect crestal bone loss.ConclusionAfter 1 year of loading, both implant‐prosthetic features yield a high survival and limited crestal bone loss. Crestal bone loss is minimized using platform‐shifted implants placed in sufficiently voluminous bone. To limit the crestal bone loss, an adopted implant diameter with platform shifting should be considered.