bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predators attacking virtual prey reveal the costs and benefits of leadership
Authors: Ioannou Christos C. , Rocque Florence , Herbert-Read James E. , Duffield Callum , Firth Josh A. 
Published: April 2019

Significance
Across a wide range of animals, it is assumed that leading from the front of a group exposes individuals to greater predation risk, generating a cost that explains variation between individuals in their tendencies to lead and follow. Remarkably, there is scant empirical evidence to support this, and there are no experimental tests. By presenting real predators with a simulation of collective behavior, we were able to exclude any correlation between social behavior and other traits that could confound effects on predation risk. We show that virtual prey leading others were preferentially attacked, but leaders were still safer than solitary prey. Leaders benefit from being followed, and they should act to maintain group cohesion and avoid splitting from their followers.
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays
Authors: Reith Frank , Verboom William , Pate John , Chittleborough David 
Published: April 2019

AbstractBackground and AimsPrevious studies have described the laying down of specific B horizons in south-western Australian ecosystems. This paper presents biomolecular, morphological and physicochemical analyses elucidating the roles of specific woody plant taxa and rhizosphere bacteria in producing these phenomena.MethodsClayey deposits within lateral root systems of eucalypts and appropriate background soil samples were collected aseptically at multiple locations on sand dunes flanking Lake Chillinup. Bacterial communities were profiled using tagged next-generation sequencing (Miseq) of the 16S rRNA gene and assigned to operational taxonomic units. Sedimentation, selective dissolution and X-ray diffraction analyses quantitatively identified clay mineral components. Comparisons were made of pedological features between the above eucalypt systems, giant podzols under proteaceous woodland on sand dunes at the study site of Jandakot and apparently similar systems observed elsewhere in the world.Key ResultsBacterial communities in clay pods are highly diverse, resolving into 569 operational taxonomic units dominated by Actinobacteria at 38.0–87.4 % of the total reads. Multivariate statistical analyses of community fingerprints demonstrated substrate specificity. Differently coloured pods on the same host taxon carry distinctive microfloras correlated to diversities and abundances of Actinobacteria, Acidobacteria, Firmicutes and Proteobacteria. A number of these microbes are known to form biominerals, such as phyllosilicates, carbonates and Fe-oxides. A biogenic origin is suggested for the dominant identified mineral precipitates, namely illite and kaolinite. Comparisons of morphogenetic features of B horizons under eucalypts, tree banksias and other vegetation types show remarkably similar developmental trajectories involving pods of precipitation surrounding specialized fine rootlets and their orderly growth to form a continuous B horizon.ConclusionsThe paper strongly supports the hypothesis that B-horizon development is mediated by highly sophisticated interactions of host plant and rhizosphere organisms in which woody plant taxa govern overall morphogenesis and supply of mineral elements for precipitation, while rhizosphere microorganisms execute biomineralization processes.
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA
Authors: Gong Sha , Zhang Chengxin , Zhang Yang 
Published: April 2019

Abstract

Motivation
Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search.

Results
We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments.

Availability and implementation
https://zhanglab.ccmb.med.umich.edu/RNA-align/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda)
Authors: Kerkhove Thomas R H , Boyen Jens , De Backer Annelies , Mol Jan H , Volckaert Filip A M , Leliaert Frederik , De Troch Marleen 
Published: April 2019

AbstractThe recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.
Healing through Connection: An Aboriginal Community Designed, Developed and Delivered Cultural Healing Program for Aboriginal Survivors of Institutional Child Sexual Abuse
Authors: Black Carlina , Frederico Margarita , Bamblett Muriel 
Published: April 2019

AbstractThe wrongs experienced by Aboriginal people have caused life-long and intergenerational impacts that demand culturally grounded healing approaches, yet this is not experienced by Aboriginal people in mainstream services. This article details a culturally informed approach by sharing the findings of a Cultural Healing Program (CHP) designed, developed and delivered by an Aboriginal Community Controlled Organisation. The program was for Aboriginal survivors of institutional child sexual abuse who had also experienced cultural abuse having been forcibly removed from their families as children and in the process disconnected from their communities, culture and land. This study of the development, implementation and evaluation of the CHP included a review of literature, interviews with survivors and facilitators, pre- and post-participant surveys, facilitator journals, participant–observer reflections and short films exploring impacts. The study drew upon the experiences of the survivors and facilitators to identify outcomes of the program. Connection with culture and the collective approach were key to healing for all survivors. The paper identifies key learnings that can inform social work practice and discusses implications regarding program design and implementation.
Public Health Importance of Invasive Methicillin-sensitive Staphylococcus aureus Infections: Surveillance in 8 US Counties, 2016
Authors: Jackson Kelly A , Gokhale Runa H , Nadle Joelle , Ray Susan M , Dumyati Ghinwa , Schaffner William , Ham David C , Magill Shelley S , Lynfield Ruth , See Isaac 
Published: April 2019

Abstract

Background
Public health and infection control prevention and surveillance efforts in the United States have primarily focused on methicillin-resistant Staphylococcus aureus (MRSA). We describe the public health importance of methicillin-susceptible S. aureus (MSSA) in selected communities.

Methods
We analyzed Emerging Infections Program surveillance data for invasive S. aureus (SA) infections (isolated from a normally sterile body site) in 8 counties in 5 states during 2016. Cases were considered healthcare-associated if culture was obtained &gt;3 days after hospital admission; if associated with dialysis, hospitalization, surgery, or long-term care facility (LTCF) residence within 1 year prior; or if a central venous catheter was present ≤2 days prior. Incidence per 100 000 census population was calculated, and a multivariate logistic regression model with random intercepts was used to compare MSSA risk factors with those of MRSA.

Results
Invasive MSSA incidence (31.3/100 000) was 1.8 times higher than MRSA (17.5/100 000). Persons with MSSA were more likely than those with MRSA to have no underlying medical conditions (adjusted odds ratio [aOR], 2.06; 95% confidence interval [CI], 1.26–3.39) and less likely to have prior hospitalization (aOR, 0.70; 95% CI, 0.60–0.82) or LTCF residence (aOR, 0.37; 95% CI, 0.29–0.47). MSSA accounted for 59.7% of healthcare-associated cases and 60.1% of deaths.

Conclusions
Although MRSA tended to be more closely associated with healthcare exposures, invasive MSSA is a substantial public health problem in the areas studied. Public health and infection control prevention efforts should consider MSSA prevention in addition to MRSA.
Clinical practice and implementation of guidelines for the prevention, diagnosis and management of cardiac implantable electronic device infections: results of a worldwide survey under the auspices of the European Heart Rhythm Association
Authors: Traykov Vassil , Bongiorni Maria Grazia , Boriani Giuseppe , Burri Haran , Costa Roberto , Dagres Nikolaos , Deharo Jean-Claude , Epstein Laurence M , Erba Paola Anna , Snygg-Martin Ulrika , Nielsen Jens Cosedis , Poole Jeanne E , Saghy Laszlo , Starck Christoph , Strathmore Neil , Blomström-Lundqvist Carina 
Published: April 2019

Abstract

Aims
Cardiac implantable electronic device (CIED) infection rates are increasing. Worldwide compliance and disparities to published guidelines for the prevention, diagnosis and management of these conditions are not well elucidated. The purpose of this survey, therefore, was to clarify these issues through an inquiry to arrhythmia-related associations and societies worldwide.

Methods and results
A questionnaire comprising 15 questions related to CIED infections was distributed among members of seven arrhythmia societies worldwide. A total of 234 centres in 62 countries reported implantation rates of which 159 (68.0%) performed more than 200 device implantations per year and 14 (6.0%) performed fewer than 50 implantations per year. The reported rates of CIED infections for 2017 were ≤2% in 78.7% of the centres, while the infection rates exceeded 5% in 7.8% of the centres. Preventive measures for CIED infection differed from published recommendations and varied among different regions mainly in terms of pocket irrigation and administering post-operative antimicrobial therapy the use of which was reported by 39.9% and 44% of the respondents, respectively. Antibacterial envelopes were used by 37.7% of the respondents in selected circumstances. In terms of pocket infection management, 62% of the respondents applied complete system removal as an initial step. Diagnostic pocket needle aspiration and pocket surgical debridement were reported by 15.8% and 11.8% of centres, respectively.

Conclusion
Clinical practices for prevention and management of CIED do not fully comply with current recommendations and demonstrate considerable regional disparities. Further education and programmes for improved implementation of guidelines are mandatory.
Characterizing the first wave of fish and invertebrate colonization on a new offshore petroleum platform
Authors: Todd Victoria L G , Williamson Laura D , Cox Sophie E , Todd Ian B , Macreadie Peter I 
Published: April 2019

Abstract
Offshore Oil & Gas (O&G) infrastructure creates artificial reef complexes that support marine communities in oceans. No studies have characterized the first wave of colonization, which can reveal information about habitat attraction and ecological connectivity. Here we used opportunistically-collected industrial Remotely Operated Vehicles (ROVs) to investigate fish and invertebrate colonization on a new North Sea O&G platform and trenching of an associated pipeline. We observed rapid colonization of fish communities, with increases in species richness (S), abundance (N), and diversity (H′) over the first four days (the entire study period). By contrast, there was minimal change in motile invertebrate communities over the survey period. After trenching, invertebrate S, N and H′ decreased significantly, whilst fish S, N and H′ increased. This study is the first to report on the pioneer wave of fish and invertebrate colonization on O&G infrastructure, thereby providing rare insight into formation of new reef communities in the sea. These short and opportunistic data are valuable in terms of showing what can be discovered from analysis of ‘pre-installation’ ROV footage of O&G structures, of which there are terabytes of data held by O&G companies waiting to be analyzed by environmental scientists.
The variable effectiveness of hedging strategies
Authors: Ciorciari John D 
Published: April 2019

AbstractGovernments often adopt hedging strategies to mitigate risks they face in international affairs. They hedge in the conventional, financial sense of the term by seeking to offset risks in global markets. They also adopt strategies to hedge against international security hazards by preserving strategic ambiguity, forging limited security alignments, and cultivating modest self-protection in case potential threats materialize. Both types of hedging typically are seen as prudent behavior. However, hedging strategies sometimes fail. Risks can be difficult to calculate, and the measures needed to hedge against them can be costly. Hedging international security risks can be particularly challenging, as governments sometimes lack access to adequate protective options at any price. This article illustrates the argument with two contrasting cases: relatively successful Southeast Asian hedging against the risk of financial calamity after the 1997 crisis and less effective efforts by some of the same states to hedge against the security risk of Chinese encroachment in the South China Sea.
Four versus six weeks of antibiotic therapy for osteoarticular infections after implant removal: a randomized trial
Authors: Benkabouche Mohamed , Racloz Guillaume , Spechbach Hervé , Lipsky Benjamin A , Gaspoz Jean-Michel , Uçkay Ilker 
Published: April 2019

AbstractBackgroundThe optimal duration of antibiotic therapy for treating orthopaedic implant infections after surgical drainage and complete implant removal is unknown.MethodsThis was a single-centre, unblinded, prospective trial randomizing (1:1) eligible patients to either 4 or 6 weeks of systemic, pathogen-targeted antibiotic therapy. Clinical trial registration number: ClinicalTrials.gov (NCT0362209).ResultsWe analysed 123 eligible patients (62 in the 4 week antibiotic arm and 61 in the 6 week arm) in the ITT analysis. The patients’ median age was 64 years, 75 (61%) were men and 38 (31%) were immunocompromised. The most common types of infection treated included: two-stage exchange procedure for prosthetic joint infection (n = 38); orthopaedic plate infection (44) and infected nail implants (11). The median duration of post-explant intravenous antibiotic therapy was 4 days. Overall, 120 episodes (98%) were cured microbiologically and 116 (94%) clinically after a median follow-up period of 2.2 years. During follow-up, four patients had a clinical recurrence with a pathogen other than the initial causative agent. We noted recurrence of clinical infection in four patients in the 4 week arm and three patients in the 6 week arm (4/62 versus 3/61; χ2 test; P = 0.74); in all cases, this occurred at around 2 months following the end of antibiotic treatment.ConclusionsWe found no statistically significant difference in the rates of clinical or microbiological remission between patients randomized to only 4 compared with 6 weeks of systemic antibiotic therapy after removal of an infected osteoarticular implant.
Deontic modals and hyperintensionality
Authors: Faroldi Federico L G 
Published: April 2019

Abstract
In this paper I argue that deontic modals are hyperintensional, i.e. logically equivalent contents cannot be substituted in their scope. I give two arguments, one deductive and the other abductive. First, I show that the contrary thesis (that deontic modals are not hyperintensional) leads to falsity; second, I argue that a hyperintensional theory of deontic modals fares better than its rivals in terms of elegance, theoretical simplicity and explanatory power (e.g. Ross’s paradox, the Gentle Murderer, The Good Samaritan, Free Choice Permission and the Miners’ Paradox disappear). I then propose a philosophical analysis of this thesis and outline some consequences. In Section 1 I introduce and define deontic modality and hyperintensionality. In Section 2 I give a reductio for the hyperintensionality of deontic modals. If the argument is sound, a useful corollary is that deontic modals are also non-intensional, and therefore possible-world semantics accounts are illfitted for them. I then show how the main result can be strengthened or weakened by varying the definition of logical validity. In Section 3 I give an abductive argument for the hyperintensionality of deontic modals, arguing that with a single move we are able to solve many paradoxes and puzzles traditionally troubling deontic logic. I present a version of a hyperintensional deontic logic in an appendix, which I prove is sound and complete with respect to a version of truthmaker semantics.
Proof theory for quantified monotone modal logics
Authors: Negri Sara , Orlandelli Eugenio 
Published: April 2019

Abstract
This paper provides a proof-theoretic study of quantified non-normal modal logics (NNML). It introduces labelled sequent calculi based on neighbourhood semantics for the first-order extension, with both varying and constant domains, of monotone NNML, and studies the role of the Barcan formulas in these calculi. It will be shown that the calculi introduced have good structural properties: invertibility of the rules, height-preserving admissibility of weakening and contraction and syntactic cut elimination. It will also be shown that each of the calculi introduced is sound and complete with respect to the appropriate class of neighbourhood frames. In particular, the completeness proof constructs a formal derivation for derivable sequents and a countermodel for non-derivable ones, and gives a semantic proof of the admissibility of cut.
Dose–volume parameters and local tumor control in cervical cancer treated with central-shielding external-beam radiotherapy and CT-based image-guided brachytherapy
Authors: Okazaki Shohei , Murata Kazutoshi , Noda Shin-ei , Kumazaki Yu , Hirai Ryuta , Igari Mitsunobu , Abe Takanori , Komatsu Shuichiro , Nakano Takashi , Kato Shingo 
Published: April 2019

AbstractDefinitive radiotherapy for cervical cancer consists of external-beam radiotherapy (EBRT) and brachytherapy. In EBRT, a central shield (CS) reduces the dose to the rectum and bladder. The combination of whole-pelvic (WP)- and CS-EBRT and brachytherapy is the standard radiotherapy protocol in Japan. Despite clinical studies, including multi-institutional clinical trials, showing that the Japanese treatment protocol yields favorable treatment outcomes with low rates of late radiation toxicities, dose–volume parameters for the Japanese treatment protocol remain to be established. We conducted a retrospective dose–volume analysis of 103 patients with uterine cervical cancer treated with the Japanese protocol using computed tomography–based adaptive brachytherapy. The 2-year overall survival and 2-year local control rates according to FIGO stage were 100% and 100% for Stage I, 92% and 94% for Stage II, and 85% and 87% for Stage III–IV, respectively. Late adverse effects in the rectum and bladder were acceptable. Receiver operating characteristic analysis discriminated recurrence within the high-risk clinical target volume (HR-CTV) (n = 5) from no local recurrence (n = 96), with the optimal response obtained at a dose of 36.0 GyEQD2 for HR-CTV D90 and 28.0 GyEQD2 for HR-CTV D98. These values were used as cut-offs in Fisher exact tests to show that high HR-CTV D90 and HR-CTV D98 doses for brachytherapy sessions were significantly associated with tumor control within the HR-CTV. These data suggest a contribution of brachytherapy to local tumor control in WP- and CS-EBRT and brachytherapy combination treatment, warranting validation in multi-institutional prospective studies.
Towards a Refugee Livelihoods Approach: Findings from Cameroon, Jordan, Malaysia and Turkey
Authors: Wake Caitlin , Barbelet Veronique 
Published: April 2019

Abstract
This note from the field explores the purpose, process and value of using a sustainable-livelihoods framework and operational map to study refugee livelihoods. The current absence of a livelihoods framework specifically tailored to refugees has created a gap not only in research, but in policy development and application. This article reflects on the utility of this methodology to generate insight into the lives of refugees in four diverse contexts: Central African Republic (CAR) refugees in Cameroon; Rohingya refugees in Kuala Lumpur, Malaysia; Syrian refugees in Zarqa, Jordan; and Syrian refugees in Istanbul, Turkey. The framework was helpful in that it enabled us to explore how refugees perceive their context, risks and possibilities as well their objectives, actions and strategies. As per Levine’s methodology, starting with refugees and their perceptions unlocked a new way of looking at the environment within which refugees try to sustain themselves and a deeper understanding of how refugees’ perceptions dictate their livelihood goals, strategies and actions. This article extends analysis to consider the broader policy implications that this specific methodological approach supports.
The Wandering Palestinian as Reflected in the Novel Imra’at Al-Risāla by The Palestinian Writer Rajā’ Bakriyya
Authors: Gottesfeld Dorit 
Published: April 2019

Abstract
The article examines the writing of Rajā’ Bakriyya, who is considered a prominent new generation Palestinian woman writer in Israel, focusing on her latest novel, Imra’at al-risāla (The Letter Woman, 2007). It points to the way Bakriyya feminizes the novel from every possible aspect, even the national-political dimension which is integrated into the novel, creating a narrative which is truly her own. The article focuses on the integration of the national-political reality into the text, especially the female protagonist’s journey of wandering between homeland and exile, which is presented as a metaphor for the wandering Palestinian. Bakriyya articulates this journey in a unique way, as a journey between the beloved and a lover. Leaving the homeland is described as leaving the beloved while returning to the homeland is described as a returning to the eternal beloved one. The uniqueness of the novel lies in the innovative and unconventional way in which it describes this journey.