bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional study of the ABC transporter-encoding genes in response to fungicide treatment and during plant infection in the phytopathogenic fungusBotrytis cinerea
Authors: Loisel Elise , Goncalves Isabelle R. , Poussereau Nathalie , Grosjean-Cournoyer Marie-Claire , Villalba François , Bruel Christophe 
Published: December 2016

AbstractThe grey mould fungusBotrytis cinereacauses worldwide losses of commercially important fruits, vegetables and ornamentals. Various fungicides, with different modes of action, are effective against this pathogen, but isolates with multiple fungicide-resistance phenotypes (Multi Drug Resistance, MDR) have been observed with increasing frequency. In fungi, ATP binding cassette (ABC) transporters participate in drug efflux and we report here on the parallel transcriptional study of the predicted ABC transporter-encoding genes inB. cinerea.During plant infection, transcription of all of these genes was activated and over-expression was observed for a few of these genes if the plants were treated with a fungicide prior to infection. In the absence of plant, most of the genes were transcriptionally activated in response to two different fungicides. Both common and specific transcriptional signatures were observed.
A Unique Ribosome Signature Reveals Bacterial Translation Initiation Sites
Authors: Giess Adam , Ndah Elvis , Jonckheere Veronique , Van Damme Petra , Valen Eivind 
Published: December 2016

ABSTRACTWhile methods for annotation of genes are increasingly reliable the exact identification of the translation initiation site remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Using these unique signatures we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic samples, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and elongations of annotated coding sequences. These re-annotations are supported by the presence of Shine-Dalgarno sequences, structural and sequence based features and N-terminal peptides. Finally, our model identifies 61 novel genes previously undiscovered in the genome.
The Liquid Structure of Elastin
Authors: Rauscher Sarah , Pomès Régis 
Published: December 2016

ABSTRACTThe protein elastin imparts extensibility, elastic recoil, and resilience to tissues including arterial walls, skin, lung alveoli, and the uterus. Elastin and elastin-like peptides are intrinsically disordered hydrophobic proteins that undergo liquid-liquid phase separation upon self-assembly. Despite extensive study for over eighty years, the structure of elastin remains controversial. We use molecular dynamics simulations on a massive scale to elucidate the structural ensemble of aggregated elastin-like peptides. Consistent with the entropic nature of elastic recoil, the aggregated state is stabilized both by the hydrophobic effect and by conformational entropy. The polypeptide backbone forms transient, sparse hydrogen-bonded turns and remains significantly hydrated even as self-assembly triples the extent of nonpolar side-chain contacts. The assembly approaches a maximally-disordered, melt-like state, which may be called the liquid state of proteins. These findings resolve long-standing controversies regarding elastin structure and function and afford insight of broad relevance to the phase separation of disordered proteins.
Behavioural, modeling, and electrophysiological evidence for domain-generality in human metacognition
Authors: Faivre Nathan , Filevich Elisa , Solovey Guillermo , Kühn Simone , Blanke Olaf 
Published: December 2016

AbstractMetacognition, or the capacity to introspect on one’s own mental states, has been mostly characterized through confidence reports in visual tasks. A pressing question is to what extent the results from visual studies generalize to other domains. Answering this question allows determining whether metacognition operates through shared, domain-general mechanisms, or through idiosyncratic, domain-specific mechanisms. Here, we report three new lines of evidence for decisional and post-decisional mechanisms arguing for the domain-generality of metacognition. First, metacognitive efficiency correlated between auditory, tactile, visual, and audiovisual tasks. Second, confidence in an audiovisual task was best modeled using supramodal formats based on integrated representations of auditory and visual signals. Third, confidence in correct responses involved similar electrophysiological markers for visual and audiovisual tasks that are associated with motor preparation preceding the perceptual judgment. We conclude that the domain-generality of metacognition relies on supramodal confidence estimates and decisional signals that are shared across sensory modalities.
Noninvasive Prenatal Screening at Low Fetal Fraction: Comparing Whole-Genome Sequencing and Single-Nucleotide Polymorphism Methods
Authors: Artieri Carlo G. , Haverty Carrie , Evans Eric A. , Goldberg James D. , Haque Imran S. , Yaron Yuval , Muzzey Dale 
Published: December 2016

AbstractObjectivePerformance of noninvasive prenatal screening (NIPS) methodologies when applied to low fetal fraction samples is not well established. The single-nucleotide polymorphism (SNP) method fails samples below a predetermined fetal fraction threshold, whereas some laboratories employing the whole-genome sequencing (WGS) method report aneuploidy calls for all samples. Here, the performance of the two methods was compared to determine which approach actually detects more fetal aneuploidies.MethodsComputational models were parameterized with up-to-date published data and used to compare the performance of the two methods at calling common fetal trisomies (T21, T18, T13) at low fetal fractions. Furthermore, clinical experience data were reviewed to determine aneuploidy detection rates based on compliance with recent invasive screening recommendations.ResultsThe SNP method’s performance is dependent on the origin of the trisomy, and is lowest for the most common trisomies (maternal M1 nondisjunction). Consequently, the SNP method cannot maintain acceptable performance at fetal fractions below ~3%. In contrast, the WGS method maintains high specificity independent of fetal fraction and has >80% sensitivity for trisomies in low fetal fraction samples.ConclusionThe WGS method will detect more aneuploidies below the fetal fraction threshold at which many labs issue a no-call result, avoiding unnecessary invasive procedures.
Doubling: there’s no escape from terror/doubling: there’s an escape from commodification …?
Authors: Letiche Hugo 
Published: December 2016

Purpose
Commodification doubles self and work, life and object, uniqueness and standardization and art and management. For the artist, the unicity, beauty, inspiration and creativity of art is doubled in the sale, marketing, display, distribution and mass production of “art works”. Making art is intimate, personal and individual; selling art requires public display, pleasing the all important customer(s) and dealing with many sorts of in-betweens. What commodification is on the artist/art work level is doubling on the I/me, self/persona, private/public and in-group/out-group level. This paper aims to examine the commodification and doubling in the case of the Gee’s Bend quilt makers. The quilts foreshadowed the modernist aesthetic and are of the highest aesthetic quality. But, they were made in a traditional rural society by very poor, uneducated black women. The quilts were not made to be sold but were dedicated to familial remembrance and to immediate aesthetic pleasure. But now that they are on display: is escape from commodification possible?

Design/methodology/approach
Reprint for special issue.

Findings
Doubling, in the original article below, was tendentious but artistically and politically to be overcome; doubling currently seems much more ominous, omnipresent and out of control. Signifyin(g) has become bomb throwing. Present day doubling apparently produces terror and not just commodification.

Originality/value
Invited for publication.
What Types of Policy Uncertainties Matter for Business?
Authors: Morikawa Masayuki 
Published: December 2016

AbstractThis paper reports data from the author's original survey of Japanese companies concerning the distributions on subjective uncertainties over economic policies and their effects on business operations. Companies perceive uncertainty over the future course of certain economic policies, such as the social security system and international trade policy. Policy uncertainty regarding the tax system, trade policy and environmental policy can have substantial effects on managerial decisions, especially on equipment investment and overseas activities. According to the companies’ subjective probability distributions on their sales outlook, manufacturers face greater uncertainty than non‐manufacturing companies do. Uncertainty over economic policies substantially reduces the expected sales growth rate.
Nonperforming Loans and Purchase of Loans by Public Asset Management Companies in Malaysia and Thailand
Authors: Inoguchi Masahiro 
Published: December 2016

AbstractThis paper explores the factors which eliminated the nonperforming loan (NPL) problem in Malaysia and Thailand following the 1997 Asian financial crisis. The number of NPL, which expanded in the aftermath of the crisis, has since declined in most South‐East Asian countries. Although previous studies have explored the causes of the increase in NPL numbers, few have analysed the factors that contributed to the reduction in their number in Asia. In Malaysia and Thailand, authorities put in place several measures to manage NPL. As a vehicle to acquire NPL from banks, Malaysia established the Pengurusan Danaharta Nasional Berhad (Danaharta) in 1998, while Thailand established the Thai Asset Management Corporation (TAMC) in 2001. We analyse whether the characteristic features of banks, improvements in macroeconomic conditions, and facilities for purchasing loans caused a reduction in the number of NPL in Malaysia and Thailand. The results suggest that selling loans to a public asset management company was effective in reducing the number of NPL in Thailand. While macroeconomic conditions influenced the decline in NPL ratios in Thailand, in Malaysia, well performing commercial banks and large commercial and investment banks generally had smaller NPL ratios throughout and following the crisis.
Impact of an education session on clinical handover between medical shifts in an emergency department: A pilot study
Authors: Blyth Caroline , Bost Nerolie , Shiels Sue 
Published: December 2016

AbstractObjectiveTo evaluate the impact of a medical education session on the implementation of a new change of shift medical clinical handover format in an urban hospital ED.MethodsThis pilot study used a pre‐ and post‐intervention design. The intervention consisted of a 1 h education session to teach a new handover format, SBARM (Situation, Background, Assessment, Recommendation, Medication). Data were collected through observations of doctors performing clinical handover and individual interviews with participants.ResultsThe educational intervention led to an increased focus on checking medication charts, but had minimal effect on changing other aspects of clinical handover at doctors’ change of shift times. Perceived increased time spent on handover using the new system was seen as a major barrier to the implementation of SBARM. The addition of ‘M’ to ‘SBAR’ heightened awareness of checking medication and fluid charts.ConclusionTime pressures need to be taken into consideration when introducing changes to current processes. Also, it is recommended that, in addition to ongoing education, senior clinicians are engaged during the planning and execution stages of changes to practice.
Serial changes of computed tomographic peritoneogram in patients with symptomatic ultrafiltration failure complicating continuous ambulatory peritoneal dialysis
Authors: Cheung Michelle , Chu Ferdinand SK , Kwan Lorraine PY 
Published: December 2016

AbstractIntroductionIt is well‐known that continuous ambulatory peritoneal dialysis (CAPD) is associated with complications. And some of these complications are well‐demonstrated as abnormalities on computed tomographic peritoneogram (CTP). The objective of our study is to document the serial changes of these complications.MethodsWe retrospectively reviewed 125 patients treated with CAPD for end staged renal failure (ESRF) who had CTP conducted in our hospital between December 2006 and August 2015. A total of 164 (n = 164) CTPs were performed. Patients with only one CTP performed were excluded from our study. A retrospective review of 68 serial CTPs studies on 28 patients during the 9‐year period was undertaken. We looked into the serial changes on CTP.ResultsAmong the 28 patients who had serial imaging, 46.43% of patients were found to have retroperitoneal leakage; 92.31% of them showed resolution in subsequent serial CTP. 21.43% of patients had anterior abdominal wall leakage; none of them resolved in subsequent CTP. 14.29% of patients were found to have inguinal hernias; 75% of them showed interval progression in subsequent serial CTPs.ConclusionRetroperitoneal leakage is a common complication in patients on CAPD and tends to resolve whereas other complications including anterior abdominal wall leakage and hernias are unlikely to resolve and may progress further.
Cardiac risk index as a simple geometric indicator to select patients for the heart‐sparing radiotherapy of left‐sided breast cancer
Authors: Sung KiHoon , Choi Young Eun , Lee Kyu Chan 
Published: December 2016

AbstractIntroductionThis is a dosimetric study to identify a simple geometric indicator to discriminate patients who meet the selection criterion for heart‐sparing radiotherapy (RT). The authors proposed a cardiac risk index (CRI), directly measurable from the CT images at the time of scanning.MethodsTreatment plans were regenerated using the CT data of 312 consecutive patients with left‐sided breast cancer. Dosimetric analysis was performed to estimate the risk of cardiac mortality using cardiac dosimetric parameters, such as the relative heart volumes receiving ≥25 Gy (heart V25). For each CT data set, in‐field heart depth (HD) and in‐field heart width (HW) were measured to generate the geometric parameters, including maximum HW (HWmax) and maximum HD (HDmax). Seven geometric parameters were evaluated as candidates for CRI. Receiver operating characteristic (ROC) curve analyses were used to examine the overall discriminatory power of the geometric parameters to select high‐risk patients (heart V25 ≥ 10%).ResultsSeventy‐one high‐risk (22.8%) and 241 low‐risk patients (77.2%) were identified by dosimetric analysis. The geometric and dosimetric parameters were significantly higher in the high‐risk group. Heart V25 showed the strong positive correlations with all geometric parameters examined (r > 0.8, p < 0.001). The product of HDmax and HWmax (CRI) revealed the largest area under the curve (AUC) value (0.969) and maintained 100% sensitivity and 88% specificity at the optimal cut‐off value of 14.58 cm2.ConclusionsCardiac risk index proposed as a simple geometric indicator to select high‐risk patients provides useful guidance for clinicians considering optimal implementation of heart‐sparing RT.
Exercise therapy in oncology rehabilitation in Australia: A mixed‐methods study
Authors: Dennett Amy M , Peiris Casey L , Shields Nora , Morgan Delwyn , Taylor Nicholas F 
Published: December 2016

AbstractAimOncology rehabilitation improves outcomes for cancer survivors but little is known about program availability in Australia. The aims of this study were: to describe oncology rehabilitation programs in Australia: determine whether the exercise component of programs is consistent with guidelines: and to explore barriers and facilitators to program implementation.MethodsA sequential, explanatory mixed‐methods study was completed in two phases: (1) a survey of Australian oncology rehabilitation programs; and (2) purposively sampled follow‐up semistructured interviews with senior clinicians working in oncology rehabilitation who were involved with exercise prescription.ResultsHospitals and/or cancer centers from 42 public hospital health networks (representing 163 hospitals) and 39 private hospitals were contacted to identify 31 oncology rehabilitation programs. All 31 surveys were returned (100% response rate). Programs were typically multidisciplinary, ran twice weekly, provided education and exercise and included self‐management strategies. Exercise prescription and progression was patient centered and included a combination of resistance and aerobic training supplemented by balance, pelvic floor, and core stability exercises. Challenges to implementation included a lack of awareness of programs in the community and organizational barriers such as funding. Strong links with oncologists facilitated program referrals.ConclusionDespite evidence to support oncology rehabilitation, there are few programs in Australia and there are challenges that limit it becoming part of standard practice. Programs that exist are multidisciplinary with a focus on exercise with the majority of programs following a cardiac rehabilitation model of care.
Afatinib successfully treated leptomeningeal metastasis during erlotinib treatment in a patient with EGFR‐mutant (Exon18:G719S) lung adenocarcinoma as a second‐line chemotherapy
Authors: Tamiya Motohiro , Shiroyama Takayuki , Nishihara Takashi , Nishida Takuji , Hayama Manabu , Tanaka Ayako , Morishita Naoko , Suzuki Hidekazu , Okamoto Norio , Hirashima Tomonori 
Published: December 2016

AbstractExon18 mutations are detected in 3.6% of epidermal growth factor receptor mutations. Exon 18 mutations as driver mutations have higher sensitivities in vitro to second‐generation (G)‐tyrosine kinase inhibitors (TKIs) than to first G‐ and third G‐TKIs at clinically relevant doses. In clinical trial, first G‐TKIs have moderate but insufficient efficacy, and afatinib was more active in uncommon epidermal growth factor receptor mutations. Here, we present a case of a woman who was initially prescribed erlotinib for lung adenocarcinoma with an exon18 mutation. She developed a leptomeningeal metastasis during treatment and was switched to afatinib. Subsequently, her symptoms improved and she is currently treated with maintenance afatinib therapy. This report suggests improved efficacy of afatinib compared to erlotinib for refractory leptomeningeal metastasis in exon18 mutation.
The architecture of submarine monogenetic volcanoes – insights from 3D seismic data
Authors: Reynolds Peter , Schofield Nick , Brown Richard J. , Holford Simon Paul 
Published: December 2016

AbstractMany prospective sedimentary basins contain a variety of extrusive volcanic products that are ultimately sourced from volcanoes. However, seismic reflection‐based studies of magmatic rift basins have tended to focus on the underlying magma plumbing system, meaning that the seismic characteristics of volcanoes are not well understood. Additionally, volcanoes have similar morphologies to hydrothermal vents, which are also linked to underlying magmatic intrusions. In this study, we use high resolution 3D seismic and well data from the Bass Basin, offshore southern Australia, to document 34 cone‐ and crater‐type vents of Miocene age. The vents overlie magmatic intrusions and have seismic properties indicative of a volcanic origin: their moderate–high amplitude upper reflections and zones of “wash‐out” and velocity pull‐up beneath. The internal reflections of the vents are similar to those found in lava deltas, suggesting they are composed of volcaniclastic material. This interpretation is corroborated by data from exploration wells which penetrated the flanks of several vents. We infer that the vents we describe are composed of hyaloclastite and pyroclasts produced during submarine volcanic eruptions. The morphology of the vents is typical of monogenetic volcanoes, consistent with the onshore record of volcanism on the southern Australian margin. Based on temporal, spatial and volumetric relationships, we propose that submarine volcanoes can evolve from maars to tuff cones as a result of varying magma‐water interaction efficiency. The morphologies of the volcanoes and their links to the underlying feeder systems are superficially similar to hydrothermal vents. This highlights the need for careful seismic interpretation and characterization of vent structures linked to magmatic intrusions within sedimentary basins.
General health influences episodes of xerostomia: a prospective population‐based study
Authors: da Silva Luciana , Kupek Emil , Peres Karen G. 
Published: December 2016

AbstractObjectivesThe aim of this study was to investigate the associated factors of changes in symptoms of xerostomia (SOX) in adults aged 20–59.MethodsA prospective population‐based study was conducted in 2009 (n = 1720) and 2012 (n = 1222) in the urban area of Florianópolis, SC, Brazil. Information on SOX was collected in both years together with age, family income, years of schooling, smoking habit, alcohol consumption, changes in the body mass index (BMI; kg/m²), medicine use, self‐reported diagnosis of chronic diseases, change in hypertension status and in the use and need for dentures, and number of remaining teeth. Associated factors with changes in SOX were investigated using multinomial logistic regression, considering those who had never reported this symptom as the reference.ResultsPrevalence of regular SOX was equal to 3.8% (95% CI: 2.9–5.1) and irregular (one period only) equal to 12.2% (95% CI: 10.2–14.5). Age, smoking habit, medicine use, self‐reported diagnosis of depression, and weight gain increased the probability of regular SOX, whereas highest schooling level was associated with lower probability of this symptom.ConclusionsGeneral and psychosocial health influenced the number of episodes of xerostomia symptoms, calling for multidisciplinary actions to prevent common risk behaviors for oral and general diseases.