bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection limits of quantitative and digital PCR assays and their influence in presence–absence surveys of environmental DNA
Authors: Hunter Margaret E. , Dorazio Robert M. , Butterfield John S. S. , Meigs‐Friend Gaia , Nico Leo G. , Ferrante Jason A. 
Published: October 2016

AbstractA set of universal guidelines is needed to determine the limit of detection (LOD) in PCR‐based analyses of low‐concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species’ presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp (Ctenopharyngodon idella) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty—indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis and forensic and clinical diagnostics.
The titles of Petra in the sixth century: the evidence from the Petra papyri
Authors: Al‐Nasarat Mohammed I. , Twissi Sa'ad A. 
Published: October 2016

Since their discovery in 1993, the Petra papyri have drawn the attention of both historians and archaeologists because of the amount of information they contain. The content of the papyri essentially deals with the property inheritance and transaction of a certain Theodoros son of Obodianos and his family in Petra and its vicinity, in the period between AD 537 and 593. The present paper focuses on the titles of Petra mentioned in these papyri and on their importance for the understanding of Petra in the Roman and Byzantine periods. Petra's full titles are: ‘Imperial Colony Antoniana, Distinguished, Holy (?), Mother of the Colonies, Hadriana Petra, and Metropolis of [the Province] Tertia Palaestina Salutaris’. The main components of these titles are attested elsewhere, but they appear in their entirety in the Petra papyri for the first time.The various titles of Petra as they appear in the papyri concerned clearly indicate that Petra continued to style itself as an important place in the Byzantine Empire. The picture that emerges from Petra's titles and other evidence from the papyri is that, in the sixth century Petra was still a place inhabited by relatively wealthy people, which had a major role in the economy of the Byzantine Empire.
Transoral robotic surgery: implementation as a tool in head and neck surgery – a single‐centre Australian experience
Authors: Hirshoren Nir , Ruskin Olivia , Fua Tsien , Kleid Stephen , Magarey Matthew , Dixon Benjamin 
Published: October 2016

BackgroundTransoral robotic surgery (TORS) is now a well‐validated technique for resection of head and neck cancers. Benefits include reduced patient morbidity, swallowing preservation and rationalization of adjuvant therapies.MethodsThis was a single‐centre, retrospective review of 35 patients who underwent TORS of oro‐, retro‐ and parapharyngeal tumours between March 2014 and August 2015. Outcome measures included resection margins, swallowing function and impact on post‐operative radiotherapy.ResultsMedian age was 63.7 years and the number of male patients was 22 (62.9%). Tongue base was the most common site (51.4%), followed by tonsil (25.7%). Nine patients (25.7%) had previous radiotherapy. A total of 24 patients had squamous cell carcinoma and the clear margin rate for primary TORS was 93.3%. Median hospital stay was 5.5 days, longer for previously irradiated patients (9 days). Median nasogastric tube dependence was 3.5 days. Four patients (11.4%) received a gastrostomy and two patients remained dependent on the tube at the time of last review. There were two major complications (5.7%): bleeding requiring return to theatre (1) and pulmonary embolism (1). Post‐operative radiotherapy was either avoided or reduced in 22 patients (81.5%).Conclusion
TORS is a safe and effective tool, providing surgical access to oropharyngeal and other difficult to access areas. Patient selection and a multidisciplinary approach are essential to ensure adequate margins can be achieved and therefore to reduce adjuvant therapies.
Micrometastasis in colorectal cancer: does it affect staging?
Authors: Mohajeri Gholamreza , Hejab Kavak , Sheikhbahaei Saba , Mohajeri Mohammadreza , Niknam Negar , Mohammadi Alireza 
Published: October 2016

BackgroundMicrometastasis (MM) in colorectal cancer (CRC) is not considered in tumour‐node‐metastasis (TNM) staging currently and also the prognostic significance of these occult tumoural cells is not proven yet. This study was designed to find whether MM to bone marrow (BM) and/or liver cause upstaging of the tumour according to conventional staging system and if it may alter the survival rate.MethodsThirty‐eight CRC patients who were candidates of surgical procedure were enrolled in our cross‐sectional study. Liver and BM biopsy were obtained during the surgery to be looked for tissue‐specific marker of CRC, CK20. CK20 expression in BM and liver was assessed by the two methods of reverse transcriptase polymerase chain reaction and immunohistochemistry.ResultsAmong the 38 submitted patients, a total number of 14 MM, including 10 BM (23%) and seven hepatic (18%) were detected. There was no significant difference in clinicopathological aspects including size, location, stage, grade, local invasion to vessels and neurons, TNM staging and relapse rate of tumour among patients with/without disseminated tumoural cells. The result did not demonstrate a survival difference between patients receiving neoadjuvant chemotherapy compared to other patients.ConclusionOur study did not confirm that the presence of MM influences TNM staging and overall survival of the patients. Additional clinical investigations with longer follow‐up period and larger number of cases are required to decide on administration of neoadjuvant therapy in CRC patients.
Misplaced Paternalism and other Mistakes in the Debate over Kidney Sales
Authors: Semrau Luke 
Published: October 2016

AbstractErik Malmqvist defends the prohibition on kidney sales as a justifiable measure to protect individuals from harms they have not autonomously chosen. This appeal to ‘group soft paternalism’ requires that three conditions be met. It must be shown that some vendors will be harmed, that some will be subject to undue pressure to vend, and that we cannot feasibly distinguish between the autonomous and the non‐autonomous. I argue that Malmqvist fails to demonstrate that any of these conditions are likely to obtain. His argument involves two common errors. First, he, like many, proceeds on a mistaken understanding of how to assess harm. What matters is not the balance of costs and benefits of vending, but a comparison of potential vendors’ welfare across two possible courses of action. Second, Malmqvist's concerns about third‐party pressure are predicated on an empirically unrealistic understanding of the operation of a regulated market. A widely underappreciated fact is that kidney sales will be relatively rare, and most who try to vend will be unable to. Because pressure on another to vend will not result in the desired outcome, few will exert it.
Assisted Suicide in Switzerland: Clarifying Liberties and Claims
Authors: Hurst Samia A. , Mauron Alex 
Published: October 2016

AbstractAssisting suicide is legal in Switzerland if it is offered without selfish motive to a person with decision‐making capacity. Although the ‘Swiss model’ for suicide assistance has been extensively described in the literature, the formally and informally protected liberties and claims of assistors and recipients of suicide assistance in Switzerland are incompletely captured in the literature. In this article, we describe the package of rights involved in the ‘Swiss model’ using the framework of Hohfeldian rights as modified by Wenar. After outlining this framework, we dissect the rights involved in suicide assistance in Switzerland, and compare it with the situation in England and Germany. Based on this approach, we conclude that in Switzerland, claim rights exist for those requesting suicide assistance, and for those who are considering providing such assistance, even though no entitlements exist toward suicide assistance. We then describe the implementation of the ‘Swiss model’ and difficulties arising within it. Clarifying these issues is important to understand the Swiss situation, to evaluate what features of it may or may not be worth correcting or emulating, and to understand how it can impact requests for suicide assistance in other countries due to ‘suicide tourism’. It is also important to understand exactly what sets Switzerland apart from other countries with different legislations regarding suicide assistance.
Survival differences between patients with Hodgkin lymphoma treated inside and outside clinical trials. A study based on the EORTC‐Netherlands Cancer Registry linked data with 20 years of follow‐up
Authors: Liu Lifang , Giusti Francesco , Schaapveld Michael , Aleman Berthe , Lugtenburg Pieternella , Meijnders Paul , Hutchings Martin , Lemmens Valery , Bogaerts Jan , Visser Otto 
Published: October 2016

SummaryThe survival of patients diagnosed with Hodgkin lymphoma (HL) has improved from 70% to 90% in clinical trials. However, population‐based data has shown lower survival. In this study, clinical trial data were linked with cancer registry to identify trial and non‐trial participants and differences in overall survival and associated factors were assessed. In 1986–2004, 27% of HL patients aged 15–70 years participated in clinical trials. Compared to non‐trial participants, trial participants were younger (median age, 31 vs. 34 years), had staging registered more accurately and had an 8% higher 20‐year survival rate (73% vs. 65%). After adjusting for baseline differences, no differences in survival (hazard ratio = 0·96, 95% confidence interval 0·82–1·12), or in subgroup analysis according to stage, remained. Over time, increased administration of chemotherapy in combination with radiotherapy, together with the decreased use of radiotherapy alone was observed among the trial population. This trend was later followed in non‐trial participants, coinciding with a similar ‘take‐up’ in survival. The observed superior survival among patients with HL treated in clinical trials can be largely explained by the differences in baseline characteristics, particularly younger age. High trial participation rate and centralized expertise facilitates the implementation of trial findings to real‐world practice.
Whole body magnetic resonance imaging in newly diagnosed multiple myeloma: early changes in lesional signal fat fraction predict disease response
Authors: Latifoltojar Arash , Hall‐Craggs Margaret , Rabin Neil , Popat Rakesh , Bainbridge Alan , Dikaios Nikolaos , Sokolska Magdalena , Rismani Ali , D'Sa Shirley , Punwani Shonit , Yong Kwee 
Published: October 2016

SummaryCross‐sectional imaging techniques are being increasingly used for disease evaluation in patients with multiple myeloma. Whole body magnetic resonance imaging (WB‐MRI) scanning is superior to plain radiography in baseline assessment of patients but changes following treatment have not been systematically explored. We carried out paired WB‐MRI scans in 21 newly diagnosed patients prior to, and 8‐weeks after, starting chemotherapy, and analysed stringently selected focal lesions (FLs) for parametric changes. A total of 323 FLs were evaluated, median 20 per patient. At 8 weeks, there was a reduction in estimated tumour volume (eTV), and an increase in signal fat fraction (sFF) and apparent diffusion coefficient (ADC) in the group as a whole (P < 0·001). Patients who achieved complete/very good partial response (CR/VGPR) to induction had a significantly greater increase in sFF compared to those achieving ≤ partial response (PR; P = 0·001). When analysed on a per‐patient basis, all patients achieving CR/VGPR had a significant sFF increase in their FL's, in contrast to patients achieving ≤PR. sFF changes in patients reaching maximal response within 100 days (fast responders) were greater compared to slow responders (P = 0·001). Receiver Operator Characteristic analysis indicated that sFF changes at 8 weeks were the best biomarker (area under the Curve 0·95) for an inferior response (≤PR). We conclude that early lesional sFF changes may provide important information on depth of response, and are worthy of further prospective study.
Strategies for reducing the treatment‐related physical burden of childhood acute myeloid leukaemia – a review
Authors: Hasle Henrik , Kaspers Gertjan J. L. 
Published: October 2016

SummaryOver the last four decades the survival of paediatric patients with acute myeloid leukaemia has gradually increased to 70% in high‐income countries. The therapy is very intensive and associated with many acute and long‐term side effects. The early death rate has been reduced to 1–4%. The acute toxicity is a limiting factor for improving survival in low‐income countries. Transplant is associated with more endocrinological late effects while cardiotoxicity is more common after relapse. Reducing the physical costs of therapy without jeopardizing survival may be accomplished by optimal supportive care, less cardiotoxic anthracyclines, less consolidation courses and strict indications for stem cell transplantation. Analysing scenarios with different frequency of transplantation in first complete remission show similar overall survival rates, indicating that almost all patients can be spared the procedure in first remission. Reducing relapse risk is an effective way of reducing toxicity and more targeted therapy and improved risk group stratifications are needed.
Improving participation outcomes and interventions in neurodisability: co‐designing future research
Authors: McAnuff J. , Brooks R. , Duff C. , Quinn M. , Marshall J. , Kolehmainen N. 
Published: October 2016

SummaryThere is an urgent, agreed need to improve participation outcomes and interventions for children and young people with neurodisability. We worked together with service users and providers to design research into participation outcomes and interventions in neurodisability. We built on existing evidence about participation outcomes and interventions and the WHO International Classification of Functioning, Disability and Health. We: (1) specified seven participation outcome categories for measurement; (2) prioritized these for improvement: self‐care, friends and social, and physical activity ranked the highest; (3) identified 11 potential intervention categories for targeting the top priority, self‐care, through eight hypothesized change mechanisms and agreed for the interventions to be delivered as a ‘Menu of Interventions’ for personalized self‐care support; and (4) designed a before‐and‐after mixed methods feasibility study to evaluate the Menu with children and young people (0–12 years) and their parents and therapists.
Implant survival following sinus membrane elevation without grafting and immediate implant installation with a one‐stage technique: an up‐to‐40‐month evaluation
Authors: Stefanski Sebastian , Svensson Börje , Thor Andreas 
Published: October 2016

AbstractPurposeVarious augmentation procedures involving the maxillary sinus, using bone substitutes or bone, have been used to enhance bone support for dental implants. The aim of this study was to retrospectively evaluate the status of implants in patients who had undergone a maxillary sinus lift and immediate implant placement without the addition of graft material.Materials and MethodsNineteen patients who had required bone augmentation of their maxillary sinus floor were evaluated in this study. After a bone window in the lateral wall of the sinus has been prepared and the Schneiderian membrane had been carefully elevated, dental implants were inserted in the residual bone, creating a membrane elevation. Resorbable collagenous membrane was used to seal the lateral access window of the maxillary sinus after implant placement. Clinical and radiological follow‐up was carried out up to 40 months after implant installation.ResultsA total of 28 implants in lengths of 10 and 12 mm were placed in a one‐stage healing protocol, with an average residual bone height of 5.25 mm (SD = 1.48). All implants remained stable, with a survival rate of 100%. An increase in mean bone height of 4.75 mm (SD = 1.13) was gained. The marginal bone levels relative to the coronal aspect of the implant shoulder exhibited a mean change of 1.01 mm (SD = 0.49) from the baseline. Of the 19 patients, none showed a plaque index or gingival index greater than 2, and 14 patients showed no presence of plaque.ConclusionThe findings of the study regarding the immediate placement of implants without the use of bone grafts or other bone substitute materials demonstrate a successful approach for new bone formation around implants in the posterior part of the maxilla, when the preoperative height of the subantral bone is moderate and enough to achieve primary stability.
A roadmap for knowledge exchange and mobilization research in conservation and natural resource management
Authors: Nguyen Vivian M. , Young Nathan , Cooke Steven J. 
Published: October 2016

AbstractScholars across all disciplines have long been interested in how knowledge moves within and beyond their community of peers. Rapid environmental changes and calls for sustainable management practices mean the best knowledge possible is needed to inform decisions, policies, and practices to protect biodiversity and sustainably manage vulnerable natural resources. Although the conservation literature on knowledge exchange (KE) and knowledge mobilization (KM) has grown in recent years, much of it is based on context‐specific case studies. This presents a challenge for learning cumulative lessons from KE and KM research and thus effectively using knowledge in conservation and natural resources management. Although continued research on the gap between knowledge and action is valuable, overarching conceptual frameworks are now needed to enable summaries and comparisons across diverse KE‐KM research. We propose a knowledge‐action framework that provides a conceptual roadmap for future research and practice in KE/KM with the aim of synthesizing lessons learned from contextual case studies and guiding the development and testing of hypotheses in this domain. Our knowledge‐action framework has 3 elements that occur at multiple levels and scales: knowledge production (e.g., academia and government), knowledge mediation (e.g., knowledge networks, actors, relational dimension, and contextual dimension), and knowledge‐based action (e.g., instrumental, symbolic, and conceptual). The framework integrates concepts from the sociology of science in particular, and serves as a guide to further comprehensive understanding of knowledge exchange and mobilization in conservation and sustainable natural resource management.
Fractions We Cannot Ignore: The Nonsymbolic Ratio Congruity Effect
Authors: Matthews Percival G. , Lewis Mark R. 
Published: October 2016

AbstractAlthough many researchers theorize that primitive numerosity processing abilities may lay the foundation for whole number concepts, other classes of numbers, like fractions, are sometimes assumed to be inaccessible to primitive architectures. This research presents evidence that the automatic processing of nonsymbolic magnitudes affects processing of symbolic fractions. Participants completed modified Stroop tasks in which they selected the larger of two symbolic fractions while the ratios of the fonts in which the fractions were printed and the overall sizes of the compared fractions were manipulated as irrelevant dimensions. Participants were slower and less accurate when nonsymbolic dimensions of printed fractions were incongruent with the symbolic comparison decision. Results indicated a robust basic sensitivity to nonsymbolic ratios that exceeds prior conceptions about the accessibility of fraction values. Results also indicated a congruity effect for overall fraction size, contrary to findings of prior research. These findings have implications for extending theory about the nature of human number sense and mathematical cognition more generally.
Do Bilinguals Automatically Activate Their Native Language When They Are Not Using It?
Authors: Costa Albert , Pannunzi Mario , Deco Gustavo , Pickering Martin J. 
Published: October 2016

AbstractMost models of lexical access assume that bilingual speakers activate their two languages even when they are in a context in which only one language is used. A critical piece of evidence used to support this notion is the observation that a given word automatically activates its translation equivalent in the other language. Here, we argue that these findings are compatible with a different account, in which bilinguals “carry over” the structure of their native language to the non‐native language during learning, and where there is no activation of translation equivalents. To demonstrate this, we describe a model in which language learning involves mapping native language phonological relationships to the non‐native language, and we show how it can explain the results attributed to automatic activation of translation equivalents.
Prioritization of Marine Turtle Management Projects: A Protocol that Accounts for Threats to Different Life History Stages
Authors: Klein Carissa J. , Beher Jutta , Chaloupka Milani , Hamann Mark , Limpus Colin , Possingham Hugh P. 
Published: October 2016

AbstractProject prioritization protocols are an important tool for allocating conservation resources efficiently, and have been applied to a range of species and ecosystems. Current approaches are inadequate when applied to species with distinct threats impacting different and/or multiple life history stages, such as sea turtles. We develop a model that integrates the benefit of any management project on a population by way of its expected population growth rate, including projects targeting different and/or multiple life history stages. To illustrate its utility, we prioritize projects for investment relevant to Australia's eastern population of Flatback turtle (Natator depressus). We rely upon expert‐elicitation to estimate individual benefit parameters, feasibility, and cost, and calculate the cost‐effectiveness of each project. The most cost‐effective project was not the most feasible, cheapest, or most beneficial. Our approach will help managers make efficient decisions that account for the full range of threats operating on a population.