bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Two Approaches to Defining Extinction Risk under the U.S. Endangered Species Act
Authors: Thompson Grant G. , Maguire Lynn A. , Regan Tracey J. 
Published: January 2018

AbstractThe predominant definition of extinction risk in conservation biology involves evaluating the cumulative distribution function (CDF) of extinction time at a particular point (the “time horizon”). Using the principles of decision theory, this article develops an alternative definition of extinction risk as the expected loss (EL) to society resulting from eventual extinction of a species. Distinct roles are identified for time preference and risk aversion. Ranges of tentative values for the parameters of the two approaches are proposed, and the performances of the two approaches are compared and contrasted for a small set of real‐world species with published extinction time distributions and a large set of hypothetical extinction time distributions. Potential issues with each approach are evaluated, and the EL approach is recommended as the better of the two. The CDF approach suffers from the fact that extinctions that occur at any time before the specified time horizon are weighted equally, while extinctions that occur beyond the specified time horizon receive no weight at all. It also suffers from the fact that the time horizon does not correspond to any natural phenomenon, and so is impossible to specify nonarbitrarily; yet the results can depend critically on the specified value. In contrast, the EL approach has the advantage of weighting extinction time continuously, with no artificial time horizon, and the parameters of the approach (the rates of time preference and risk aversion) do correspond to natural phenomena, and so can be specified nonarbitrarily.
A Systems‐Based Risk Assessment Framework for Intentional Electromagnetic Interference (IEMI) on Critical Infrastructures
Authors: Oakes Benjamin Donald , Mattsson Lars‐Göran , Näsman Per , Glazunov Andrés Alayón 
Published: January 2018

AbstractModern infrastructures are becoming increasingly dependent on electronic systems, leaving them more vulnerable to electrical surges or electromagnetic interference. Electromagnetic disturbances appear in nature, e.g., lightning and solar wind; however, they may also be generated by man‐made technology to maliciously damage or disturb electronic equipment. This article presents a systematic risk assessment framework for identifying possible, consequential, and plausible intentional electromagnetic interference (IEMI) attacks on an arbitrary distribution network infrastructure. In the absence of available data on IEMI occurrences, we find that a systems‐based risk assessment is more useful than a probabilistic approach. We therefore modify the often applied definition of risk, i.e., a set of triplets containing scenario, probability, and consequence, to a set of quadruplets: scenario, resource requirements, plausibility, and consequence. Probability is “replaced” by resource requirements and plausibility, where the former is the minimum amount and type of equipment necessary to successfully carry out an attack scenario and the latter is a subjective assessment of the extent of the existence of attackers who possess the motivation, knowledge, and resources necessary to carry out the scenario. We apply the concept of intrusion areas and classify electromagnetic source technology according to key attributes. Worst‐case scenarios are identified for different quantities of attacker resources. The most plausible and consequential of these are deemed the most important scenarios and should provide useful decision support in a countermeasures effort. Finally, an example of the proposed risk assessment framework, based on notional data, is provided on a hypothetical water distribution network.
Somatic diversification of the B cell repertoire requires two cell subsets
Authors: Cohn M. 
Published: January 2018

AbstractEvolution found itself in a Catch‐22 situation when selecting for the somatically derived paratopic repertoire of the humoral immune system. The B cell BCR repertoire can only be somatically diversified from a substrate of paratopes that is encoded in the germline. In order for the cells expressing that substrate to also be a target of germline selection, their BCRs must, independently, be of selective value by being expressed in a functionally important way in each individual. A somatically derived repertoire scrambles this substrate so that its specificities are lost, making it unselectable in the germline. Consequently, evolution faced an incompatibility. Here, we explore what it takes to resolve it.
Fixed point method and its improvement for the system of Volterra-Fredholm integral equations of the second kind
Authors: Hasan Talaat Ismahel , Salleh Shaharuddin 
Published: January 2018

In this paper, we consider the system of Volterra-Fredholm integral equations of the second kind (SVFI-2). We proposed fixed point method (FPM) to solve SVFI-2 and improved fixed point method (IFPM) for solving the problem. In addition, a few theorems and two new algorithms are introduced. They are supported by numerical examples and simulations using Matlab. The results are reasonably good when compared with the exact solutions.
Analysis of a mathematical model of the dynamics of contagious bovine pleuropneumonia
Authors: Aligaz Achamyelesh Amare , Munganga Justin Manango W. 
Published: January 2018

Contagious bovine pleuropneumonia (CBPP) is a disease of cattle and water buffalo caused by Mycoplasma mycoides subspecies mycoides (Mmm). It attacks the lungs and the membranes that line the thoracic cavity. The disease is transmitted by inhaling droplets disseminated through coughing by infected cattle. In this paper a deterministic mathematical model for the transmission of Contagious Bovine plueropnemonia is presented. The model is a five compartmental model consisting of susceptible, Exposed, Infectious, Persistently infected and Recovered compartments. We derived a formula for the basic reproduction number R0. For R0 ≤ 1, the disease free equilibrium is globally asymptotically stable, thus CBPP dies out; whereas for R0 > 1, the unique endemic equilibrium is globally asymptotically stable and hence the disease persists. Elasticity indices for R0 with respect to different parameters are calculated; indicating parameters that are important for control strategies to bring R0 below 1, the effective contact rate β has the largest elasticity index. As the disease control options are associated to these parameters, for some values of these parameters, R0 < 1, thus the disease can be controlled.
Whole-Genome Sequence of the Novel Temperate
Enterobacter
Bacteriophage Tyrion, Isolated from the Gut of the Formosan Subterranean Termite
Authors: Tikhe Chinmay Vijay , Gissendanner Chris R. , Husseneder Claudia 
Published: January 2018

ABSTRACT

We sequenced the genome of the novel
Enterobacter
bacteriophage Tyrion isolated from termite gut. The bacteriophage is temperate in nature and belongs to the
Podoviridae
family. Many predicted bacteriophage genes showed similarity to prophage regions of the genomes of
Enterobacteriaceae
bacteria. This is the second bacteriophage isolated from termite gut.
Draft Genome Sequence of the Vanadium-Leaching Bacterium
Pseudomonas chlororaphis
Strain L19
Authors: Peng Qingjing , Yi Langbo , Zhou Lulu , Peng Qingzhong 
Published: January 2018

ABSTRACT

Pseudomonas chlororaphis
strain L19, isolated from stone coal soil, has the ability to perform bioleaching to release vanadium ions from mineral ore. Here, we report the draft genome sequence and annotation of the vanadium-leaching bacterium
Pseudomonas chlororaphis
L19. These data provide information for understanding the genomic properties and mineral bioleaching mechanisms of strain L19.
Metagenomics Study of Contaminated Sediments from the Yamuna River at Kalindi Kunj, Delhi, India
Authors: Sahu Nishi , Deori Maushumi , Ghosh Ilora 
Published: January 2018

ABSTRACT
The Yamuna River is the backbone of domestic, irrigation, and industrial activities in Delhi, India, yet the complex dynamics of its microbes and their contribution to biogeochemical cycles in a polluted environment remain elusive. This is an introductory report describing the microbial community in the Yamuna River, using high-throughput metagenomics.
Draft Genome Sequence of
Marinobacter
sp. Strain ANT_B65, Isolated from Antarctic Marine Sponge
Authors: de França Paula , Camilo Esther , Fantinatti-Garboginni Fabiana 
Published: January 2018

ABSTRACT

Marinobacter
sp. strain ANT_B65 was isolated from sponge collected in King George Island, Antarctica. The draft genome of 4,173,840 bp encodes 3,743 protein-coding open reading frames. The genome will provide insights into the strain’s potential use in the production of natural products.
Complete Genome Sequence of a Lineage II Peste des Petits Ruminants Virus from Sierra Leone
Authors: Dundon William G. , Adombi Caroline M. , Kanu Saidu , Loitsch Angelika , Cattoli Giovanni , Diallo Adama 
Published: January 2018

ABSTRACT
The complete genome sequence of a peste des petits ruminants virus (PPRV) from goat samples collected in Sierra Leone in 2011 is reported here. The genome shows a higher nucleotide sequence identity (98.9%) with a lineage II PPRV from Senegal than to PPRVs from neighboring Liberia and Ivory Coast.
Acanthamoebakeratitis in 194 patients: risk factors for bad outcomes and severe inflammatory complications
Authors: Carnt Nicole , Robaei Dana , Minassian Darwin C , Dart John K G 
Published: January 2018

Background/aimsTo determine demographic and clinical features of patients withAcanthamoebakeratitis (AK) that are independent risk factors both for bad outcomes and for severe inflammatory complications (SIC).MethodsA retrospective audit of medical records of AK cases at Moorfields Eye Hospital from July 2000 to April 2012, including 12 earlier surgical cases. Cases with a bad outcome were defined as those having one or more of the following: corneal perforation, keratoplasty, other surgery (except biopsy), duration of antiamoebic therapy (AAT) ≥10.5 months (the 75th percentile of the whole cohort) and final visual acuity ≤20/80. SICs were defined as having scleritis and/or a stromal ring infiltrate. Multivariable analysis was used to identify independent risk factors for both bad outcomes and SICs.ResultsRecords of 194 eyes (194 patients) were included, having bad outcomes in 93 (48%). Bad outcomes were associated with the presence of SIC, aged >34 years, corticosteroids used before giving AAT and symptom duration >37 days before AAT. The development of SIC was independently associated with aged >34 years, corticosteroids used before giving AAT and herpes simplex virus (HSV) keratitis treatment before AAT.ConclusionsThe prompt diagnosis of AK, avoidance of a misdiagnosis of HSV keratitis and corticosteroid use before the exclusion of AK as a potential cause of keratitis are essential to the provision of a good outcome for patients and for the avoidance of SIC. Older age is an unmodifiable risk factor that may reflect differences in the immune response to AK in this patient subset.
Multicentre prospective evaluation of real-time optical diagnosis of T1 colorectal cancer in large non-pedunculated colorectal polyps using narrow band imaging (the OPTICAL study)
Authors: Backes Yara , Schwartz Matthijs P , ter Borg Frank , Wolfhagen Frank H J , Groen John N , de Vos tot Nederveen Cappel Wouter H , van Bergeijk Jeroen , Geesing Joost M J , Spanier Bernhard W M , Didden Paul , Vleggaar Frank P , Lacle Miangela M , Elias Sjoerd G , Moons Leon M G 
Published: January 2018

ObjectiveThis study evaluated the preresection accuracy of optical diagnosis of T1 colorectal cancer (CRC) in large non-pedunculated colorectal polyps (LNPCPs).DesignIn this multicentre prospective study, endoscopists predicted the histology during colonoscopy in consecutive patients with LNPCPs using a standardised procedure for optical assessment. The presence of morphological features assessed with white light, and vascular and surface pattern with narrow-band imaging (NBI) were recorded, together with the optical diagnosis, the confidence level of prediction and the recommended treatment. A risk score chart was developed and validated using a multivariable mixed effects binary logistic least absolute shrinkage and selection (LASSO) model.ResultsAmong 343 LNPCPs, 47 cancers were found (36 T1 CRCs and 11 ≥T2 CRCs), of which 11 T1 CRCs were superficial invasive T1 CRCs (23.4% of all malignant polyps). Sensitivity and specificity for optical diagnosis of T1 CRC were 78.7% (95% CI 64.3 to 89.3) and 94.2% (95% CI 90.9 to 96.6), and 63.3% (95% CI 43.9 to 80.1) and 99.0% (95% CI 97.1 to 100.0) for optical diagnosis of endoscopically unresectable lesions (ie, ≥T1 CRC with deep invasion), respectively. A LASSO-derived model using white light and NBI features discriminated T1 CRCs from non-invasive polyps with a cross-validation area under the curve (AUC) of 0.85 (95% CI 0.80 to 0.90). This model was validated in a temporal validation set of 100 LNPCPs (AUC of 0.81; 95% CI 0.66 to 0.96).ConclusionOur study provides insights in the preresection accuracy of optical diagnosis of T1 CRC. Sensitivity is still limited, so further studies will show how the risk score chart could be improved and finally used for clinical decision making with regard to the type of endoresection to be used and whether to proceed to surgery instead of endoscopy.Trial registration numberNTR5561.
AutomatedPlasmodiumdetection by the Sysmex XN hematology analyzer
Authors: Dumas Cécile , Bienvenu Anne-Lise , Girard Sandrine , Picot Stéphane , Debize Gisèle , Durand Brigitte 
Published: January 2018

BackgroundMalaria is a potentially severe disease affecting nearly 200 million people per year. Early detection of the parasite even in unsuspected patients remains the challenging aim for effective patient care. Automated complete blood counts that are usually performed for any febrile patient might represent a tool to ascertain malaria infection.AimsTo evaluate the ability of the new generation of the Sysmex hematology analyzer (XN-series) to detect malaria.MethodsWe retrospectively studied 100 blood samples performed with the recent Sysmex XN analyzer that were positive forPlasmodiumand explored its ability to detect the parasite. 100 samples from patients uninfected by malaria were used as control group.ResultsSpecific abnormalities such as additional events in the mature neutrophil/eosinophil area of the white blood cells differential (WDF) scattergram were noted for 1.1% ofPlasmodium falciparumsamples and 56.2% of otherPlasmodiumspecies samples. Mature parasite stages (schizonts or gametocytes) were observed on blood smears among those samples. WDF scattergrams were able to detect 80.0% (12/15) ofPlasmodiummature stages. Furthermore, the differential in white blood counts between WDF and white cell nucleated (WNR) channels was a predictive signal ofPlasmodiummature stages in 73.3% (11/15) of samples and may be explained by a differential destruction of particles with the analyzer reagent.ConclusionAssociated to thrombocytopaenia, a Sysmex XNPlasmodiumpattern may represent a useful warning forPlasmodiumdetection in unsuspected patients, particularly when mature parasite stages are present.
Which role does multiphoton interference play in small phase estimation in quantum Fourier transform interferometers?
Authors: Zimmermann Olaf , Tamma Vincenzo 
Published: January 2018

Recently, quantum Fourier transform interferometers have been demonstrated to allow a quantum metrological enhancement in phase sensitivity for a small number [Formula: see text] of identical input single photons [J. P. Olson, K. R. Motes, P. M. Birchall, N. M. Studer, M. LaBorde, T. Moulder, P. P. Rohde and J. P. Dowling, Phys. Rev. A 96 (2017) 013810; K. R. Motes, J. P. Olson, E. J. Rabeaux, J. P. Dowling, S. J. Olson and P. P. Rohde, Phys. Rev. Lett. 114 (2015) 170802; O. Zimmermann, Bachelor Thesis (Ulm University, 2015) arXiv: 1710.03805.]. However, multiphoton distinguishability at the detectors can play an important role from an experimental point of view [V. Tamma and S. Laibacher, Phys. Rev. Lett. 114 (2015) 243601.]. This raises a fundamental question: How is the phase sensitivity affected when the photons are completely distinguishable at the detectors and therefore do not interfere? In other words, which role does multiphoton interference play in these schemes? Here, we show that for small phase values, the phase sensitivity achievable in the proposed schemes with indistinguishable photons is enhanced only by a constant factor with respect to the case of completely distinguishable photons at the detectors. Interestingly, this enhancement arises from the interference of only a polynomial number (in [Formula: see text]) of the total [Formula: see text] multiphoton path amplitudes in the [Formula: see text]-port interferometer. These results are independent of the number [Formula: see text] of single photons and of the phase weight factors employed at each interferometer channel.
CCR5+ Myeloid-Derived Suppressor Cells Are Enriched and Activated in Melanoma Lesions
Authors: Blattner Carolin , Fleming Viktor , Weber Rebekka , Himmelhan Bianca , Altevogt Peter , Gebhardt Christoffer , Schulze Torsten J. , Razon Hila , Hawila Elias , Wildbaum Gizi , Utikal Jochen , Karin Nathan , Umansky Viktor 
Published: January 2018

Abstract
Accumulation of myeloid-derived suppressor cells (MDSC) in melanoma microenvironment is supported by chemokine receptor/chemokine signaling. Although different chemokines were suggested to be involved in this process, the role of CCR5 and its ligands is not established. Using a Ret transgenic mouse melanoma model, we found an accumulation of CCR5+ MDSCs in melanoma lesions associated with both increased concentrations of CCR5 ligands and tumor progression. Tumor-infiltrating CCR5+ MDSCs displayed higher immunosuppressive activity than their CCR5− counterparts. Upregulation of CCR5 expression on CD11b+Gr1+ myeloid cells was induced in vitro by CCR5 ligands and other inflammatory factors. In melanoma patients, CCR5+ MDSCs were enriched at the tumor site and correlated with enhanced production of CCR5 ligands. Moreover, they exhibited a stronger immunosuppressive pattern compared with CCR5− MDSCs. Blocking CCR5/CCR5 ligand interactions increased survival of tumor-bearing mice and was associated with reduced migration and immunosuppressive potential of MDSCs in tumor lesions. Our findings define a critical role for CCR5 in recruitment and activation of MDSCs, suggesting a novel strategy for melanoma treatment.
Significance: These findings validate the importance of the CCR5/CCR5 ligand axis not only for MDSC recruitment but also for further activation of their immunosuppressive functions in the tumor microenvironment, with potentially broad therapeutic implications, given existing clinically available inhibitors of this axis. Cancer Res; 78(1); 157–67. ©2017 AACR.
Translating Science into Survival: Report on the Third International Cancer Immunotherapy Conference
Authors: Diken Mustafa , Chu Karen K. , Brodsky Arthur N. 
Published: January 2018

Abstract
On September 6 to 9, 2017, in Mainz, Germany, the Third International Cancer Immunotherapy Conference was hosted jointly by the Cancer Research Institute, the Association for Cancer Immunotherapy, the European Academy of Tumor Immunology, and the American Association for Cancer Research. For the third straight year, more than 1,400 people attended the four-day event, which covered the latest advances in cancer immunology and immunotherapy. This report provides an overview of the main topics discussed. Cancer Immunol Res; 6(1); 10–13. ©2017 AACR.
Does John 8:44 Imply That the Devil Has a Father?
Authors: Llewelyn Stephen Robert , Robinson Alexandra , Wassell Blake Edward 
Published: January 2018

Abstract
John 8:44 has been a source of concern because of its ambiguity. Is it to be read “of (your) father, the devil” or “of the father of the devil”? This article contends that the former, traditional reading is not ungrammatical as suggested in the grammars and more recently by DeConick and that accordingly the verse cannot be considered pro-gnostic.
The Lord’s Prayer as Song: Performance, Gesture and Meaning
Authors: Haste Amanda J. 
Published: January 2018

The Lord’s Prayer is a central text in Christian liturgy, generally recited rather than sung, often as a communal act of worship. The text has also provided inspiration for many musical settings, a process of ‘musicking’ [musikierung] which takes the text out of its traditional worship environment. The internet – and specifically video-streaming sites such as YouTube – are now providing a medium for the dissemination of stage, screen, studio and audio performances of the Lord’s Prayer as song, and these are now reaching – and speaking to – new audiences up to eighty years after they were made; the fact that individuals continue to post video and audio content of the Lord’s Prayer as song reflects their desire to share something which has moved them, whether musically or spiritually, with a worldwide audience.In liberating the text from its liturgical context and releasing it as song into classical, jazz, rock, and pop performance arenas, many questions are raised about the transformation of textual meaning and ritual significance. The aim of this study is to examine the meaningfulness of the musico-textual setting for the receiver, firstly through the question of ownership of the text as a communal prayer, and secondly in arguing that perception and reception of the performer are contributory factors in the relative positivity or negativity of the receiver’s response. The research was carried out by examining a selection of the legion twentieth- and twenty-first-century musical settings of the Lord’s Prayer readily accessible through YouTube, using ethnographic data from on-line comments and from the author’s on-line survey of Christian worshippers to explore the issues raised by these musical settings. These include the perceived right of an individual to ‘perform’ a mutually-owned prayer; the loss of ritual functionality engendered by the ‘musicking’ of the text and its release into the popular domain; and the additional layers of meaning afforded to the text by gestures in performance, which can in turn lead to a transformation and renewal of ritual significance for the receiver. The inclusion of hyperlinks to YouTube video content throughout the article encourages the reader to engage with the performances themselves, from which it is hoped that a fruitful discussion of the issues will emerge.