bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating biogeographical patterns using point‐based cartograms
Authors: Keddy Alexander , Beiko Robert G. 
Published: December 2017

AbstractAimVisualization is an important tool in the investigation of phylogenetic distributions of species. Several tools have been developed that allow a researcher to overlay species distributions and phylogenetic trees on a map. However, when samples span a large range but also have high density in some regions, it can be difficult to appreciate both the global and the local context of biodiversity in a single view.InnovationWe have developed an algorithm for cartogram construction that extends the Gastner–Newman approach to point‐based rather than region‐based data. Cartogram construction is controlled by parameters that impact the magnitude and extent of the distortion. We also introduce the geographically coupled phylogenetic distance (GCPD), a quantitative measure that combines phylogenetic diversity with geographical distance, as a criterion for distorting a map.Main conclusionsWe used our cartogram approach to develop enhanced geographical visualizations of datasets, including an outbreak of Vibrio cholerae in Haiti and the distribution of the salamander Aneides lugubris in California, U.S.A. In both examples, our cartogram approach allowed the concurrent visualization of local distributional patterns while preserving the broader context of the survey. Our implementation in the GenGIS software package allows joint visualization of cartogram, phylogenetic and other types of data.
Are the radiations of temperate lineages in tropical alpine ecosystems pre‐adapted?
Authors: Nürk Nicolai M. , Michling Florian , Linder H. Peter 
Published: December 2017

AbstractAimTropical mountains around the world harbour an extraordinarily rich pool of plant species and are hotspots of biodiversity. Climatically, they can be zoned into montane climates at mid‐altitudes and tropical alpine climates above the tree line. Around half of the tropical alpine species belong to plant lineages with a temperate ancestry, although these regions are often geographically distant. We test the hypothesis that these temperate lineages are pre‐adapted to the tropical alpine climate.LocationNew World, with a focus on tropical alpine Andes.Time periodMiocene to present.Major taxa studiedFlowering plants.MethodsWe build multidimensional environmental models representing the full space of New World climates. We quantify the environmental similarity between the tropical alpine ecosystem and those of potential source areas, while correcting for regional differences by kernel density smoothers. Based on spatial observations of the genus Hypericum (St John's Wort), we quantify niche overlap and test for niche conservatism following intercontinental dispersal using density‐weighted nonparametric tests. A dated species tree, biogeographical estimation, multi‐optima Ornstein–Uhlenbeck models and model selection approaches are used to test for niche shifts during establishment in the tropical alpine Andes.ResultsThe tropical alpine ecosystem is isolated by its climate from adjacent regions and is climatically similar to temperate lowland biomes of both hemispheres. Niche conservatism is evident in the study group, except in the tropical alpine lineage that is characterized by niche expansion and shifts in temperature optima.Main conclusionsOur results reject the pre‐adaptation hypothesis and instead suggest pronounced niche evolution during colonization of tropical alpine ecosystems. Establishment involved substantial niche shifts, mainly in temperature‐related variables, and resulted in a tremendous proliferation of species in the newly invaded tropical alpine ecosystem.
Identifying perception behaviours in people with profound intellectual and multiple disabilities
Authors: Roemer Miriam , Verheul Ellen , Velthausz Frank 
Published: December 2017

BackgroundTo support people with profound intellectual and multiple disabilities (PIMD), it is essential to understand how they experience their environment. Insight into perception behaviour may provide an entry point for improved understanding.Materials and MethodsA random sample of a 30‐min video registration of five participants with PIMD was used to code behaviours per second based on an ethogram containing 157 different perception behaviours in nine categories.ResultsEighty‐nine different perception behaviours were observed, of which movements with eyes, head and arms were most common. The senses used most were seeing, hearing and touching. Finally, the function of five perception patterns was established in relation to their function:awareness, focusing attention and tension regulation.ConclusionsClose observation using an observation ethogram provides insight into how people with PIMD perceive their environment.
Shift in the subgingival microbiome following scaling and root planing in generalized aggressive periodontitis
Authors: Liu Guojing , Luan Qingxian , Chen Feng , Chen Zhibin , Zhang Qian , Yu Xiaoqian 
Published: December 2017

AbstractAimTo investigate the shift in the subgingival microbiota under scaling and root planing (SRP) in patients with generalized aggressive periodontitis (GAgP).Materials and MethodsAfter undergoing supragingival scaling, 12 individuals with GAgP were enrolled in this longitudinal study. Full‐mouth SRP was accomplished in 3 weeks and re‐evaluated 6 weeks later. Pooled subgingival samples (posterior‐mesial, posterior‐buccal, anterior‐mesial, and anterior‐buccal) were obtained from each patient before SRP (pre‐treatment group) and at the time of re‐evaluation (post‐treatment group). 16S rRNA PCR products were generated and sequenced after DNA isolation.ResultsUnder SRP, the diversity of the subgingival community was consistent, whereas genus‐level biomarkers transformed from Porphyromonas, Treponema, and Fretibacterium to Actinomyces, Streptococcus, and Haemophilus. In a network analysis, pathogen‐related and non‐pathogen‐related components were identified in both the pre‐ and post‐treatment groups; the pathogen component was dramatically augmented, while the non‐pathogen component shrank after treatment. Hubs were also distributed in both components pre‐treatment and were confined to the pathogen component post‐treatment.ConclusionsScaling and root planing decreased periodontal pathogens in the subgingival microbiota of patients with GAgP. However, the shift in the microbiota composition was characterized by the expansion of pathogen‐related components and the contraction of non‐pathogen‐related components 6 weeks after SRP. Clinicaltrials.gov #NCT03090282.
Software and package applicating for network meta‐analysis: A usage‐based comparative study
Authors: Xu Chang , Niu Yuming , Wu Junyi , Gu Huiyun , Zhang Chao 
Published: December 2017

AbstractObjectiveTo compare and analyze the characteristics and functions of software applications for network meta‐analysis (NMA).MethodsPubMed, EMbase, The Cochrane Library, the official websites of Bayesian inference Using Gibbs Sampling (BUGS), Stata and R, and Google were searched to collect the software and packages for performing NMA; software and packages published up to March 2016 were included. After collecting the software, packages, and their user guides, we used the software and packages to calculate a typical example. All characteristics, functions, and computed results were compared and analyzed.ResultsTen types of software were included, including programming and non‐programming software. They were developed mainly based on Bayesian or frequentist theory. Most types of software have the characteristics of easy operation, easy mastery, exact calculation, or excellent graphing. However, there was no single software that performed accurate calculations with superior graphing; this could only be achieved through the combination of two or more types of software.ConclusionThis study suggests that the user should choose the appropriate software according to personal programming basis, operational habits, and financial ability. Then, the choice of the combination of BUGS and R (or Stata) software to perform the NMA is considered.
Skin colour assessment of replanted fingers in digital images and its reliability for the incorporation of images in nursing progress notes
Authors: Terashima Taiko , Yoshimura Sadako 
Published: December 2017

Aims and objectivesTo determine whether nurses can accurately assess the skin colour of replanted fingers displayed as digital images on a computer screen.BackgroundColour measurement and clinical diagnostic methods for medical digital images have been studied, but reproducing skin colour on a computer screen remains difficult.DesignThe inter‐rater reliability of skin colour assessment scores was evaluated. In May 2014, 21 nurses who worked on a trauma ward in Japan participated in testing.MethodsSix digital images with different skin colours were used. Colours were scored from both digital images and direct patient's observation. The score from a digital image was defined as the test score, and its difference from the direct assessment score as the difference score. Intraclass correlation coefficients were calculated. Nurses’ opinions were classified and summarised.ResultsThe intraclass correlation coefficients for the test scores were fair. Although the intraclass correlation coefficients for the difference scores were poor, they improved to good when three images that might have contributed to poor reliability were excluded. Most nurses stated that it is difficult to assess skin colour in digital images; they did not think it could be a substitute for direct visual assessment. However, most nurses were in favour of including images in nursing progress notes.DiscussionAlthough the inter‐rater reliability was fairly high, the reliability of colour reproduction in digital images as indicated by the difference scores was poor. Nevertheless, nurses expect the incorporation of digital images in nursing progress notes to be useful. This gap between the reliability of digital colour reproduction and nurses’ expectations towards it must be addressed.ConclusionsHigh inter‐rater reliability for digital images in nursing progress notes was not observed. Assessments of future improvements in colour reproduction technologies are required.Relevance to clinical practiceFurther digitisation and visualisation of nursing records might pose challenges.
Changes in the dysphagia and nutritional status of patients with brain injury
Authors: Kim Hyeyeoung , Suh Yeonok 
Published: December 2017

Aims and objectivesTo evaluate the degree of improvement in the dysphagia and nutritional status of patients with brain injuries after removal of the nasogastric tube.BackgroundThe nurse should assess patients’ dysphagia, after removal of the nasogastric tube, and immediately reflect the changes in patient care. Accordingly, the critical roles of nurses in caring for patients with dysphagia involve providing appropriate nutritional therapy as well as preventing aspiration pneumonia and nutritional imbalance. Assessment of the patient's dysphagia on a regular basis and analysis of nutritional status according to the degree of dysphagia are necessary to determine the appropriate timing for providing nursing interventions and to develop protocols for the provision of a therapeutic diet.DesignProspective observational study.MethodsThis study was conducted on 56 patients with dysphagia after a brain injury. Data were collected using the Gugging Swallowing Screen (GUSS) test and Swallowing Symptom Questionnaire (SSQ). Descriptive statistics, chi‐square tests, t tests, and MANOVA were analysed using SPSS 22.0.ResultsPatient's dysphagia was observed over the course of 2 weeks. After 14 days, the severity of dysphagia decreased from 91.1%–35.7%, while the number of participants with normal swallowing increased from 1.8%–58.9%. Dysphagia in patients with brain injury improved gradually over time. A significant difference was observed in the serum albumin level of patients with dysphagia (F = 9.51, p = .003, Wilk's λ = .034).ConclusionsMost of the patients with brain injury developed moderate dysphagia immediately after removal of the nasogastric tube. However, after 14 days had elapsed, the percentage of patients recovering from dysphagia increased to 58.9%. Proper dietary patterns were not adequately provided depending on the degree of patient's dysphagia after removal of the nasogastric tube. Assessing the degree of dysphagia using the GUSS test and providing appropriate diet prevent malnutrition in patients with dysphagia.Relevance to clinical practiceThis study was conducted in patients who developed complications of dysphagia after a brain injury. Using the Gugging Swallowing Screen (GUSS) test, the changes in the degree of dysphagia were repeatedly measured at different times: 4, 7 and 14 days after the removal of the nasogastric tube. Provision of appropriate diet and changes in the nutritional status were analysed to determine the proper timing for nursing intervention in patients with dysphagia. The data obtained from this study could serve as a basis for developing diet provision protocols for patients with dysphagia.
Living with relapsed myeloma: Symptoms and self‐care strategies
Authors: Cormican Orlaith , Dowling Maura 
Published: December 2017

Aims and ObjectivesTo explore which symptoms relapsed myeloma patients experience and what self‐care strategies are used.MethodsThis was a qualitative study utilising focus group interviews (n = 4) with relapsed myeloma patients (n = 15) and carers (n = 9). The focus groups were analysed and guided by thematic analysis.ResultsThree major themes with subthemes were identified following analysis of the interview data: “difficult symptoms; “self‐care” and “feeling vulnerable.” These findings indicate the challenges relapsed myeloma patients experience with ongoing symptoms and highlight the importance of continuity of care.ConclusionsSymptom management for myeloma patients remains complex due to the array of treatments given. These patients require holistic care and thorough regular assessments to help them cope with the adverse effects on their physical and psychological health. For patients with a long‐term diagnosis of myeloma, self‐management workshops and regular education sessions may be of benefit.Relevance to clinical practiceThis study highlights the key role of healthcare professionals in going beyond assessment of symptoms to offering advice and support to assist relapsed myeloma patients in managing their symptoms.
Experiences of Chinese immigrant women following “Zuo Yue Zi” in British Columbia
Authors: Chang Sylvia Hsi‐Ching , Hall Wendy A , Campbell Suzanne , Lee Lily 
Published: December 2017

Aims and objectivesTo describe Chinese women's experiences with “zuo yue zi” in British Columbia, Canada.BackgroundWomen born in China and Taiwan are increasingly immigrating to westernised countries. Many women choose to follow traditional Chinese postpartum practices, also called “zuo yue zi.” Few studies have examined women's use of traditional practices in western countries.DesignThe study used a qualitative descriptive design.MethodsWe recruited 13 mothers who were: aged 19 or older, immigrants from mainland China, Hong Kong or Taiwan in the last 5 years, and caring for infants born in the previous 6 weeks. Semistructured interviews were conducted in Mandarin, translated into English, transcribed and analysed using inductive content analysis.ResultsThe core theme was Chinese women's novel encounters with “zuo yue zi.” The women's expectations of “zuo yue zi” were acquired through birth experiences or interactions with family and friends. The participants struggled with implementing traditional practices because social support and formal institutional structures were lacking. They modified their expectations about “zuo yue zi.” Factors affecting their practices were catalysts and deterrents. Catalysts included help from Chinese family members, friends and informed healthcare providers. Deterrents included unregulated paid helpers, uninformed care providers, financial constraints and structural limitations in their new environments.ConclusionsChinese immigrant women struggled to modify and implement traditional practices in their adopted country when they encountered financial constraints, unregulated paid helpers and varying support from health care providers.Relevance to clinical practiceSome postpartum women following “zuo yue zi” believed that the practice would prevent chronic illness and strengthen their intrafamily relationships. Immigrant mothers require nursing support to follow traditional postpartum practices. Nurses can advocate on patients’ behalf to increase care providers’ knowledge about “zuo yue zi” and public awareness for necessary regulated institutional structures.
A Single Mechanosensitive Channel Protects Francisella tularensis subsp. holarctica from Hypoosmotic Shock and Promotes Survival in the Aquatic Environment
Authors: Williamson David R. , Dewan Kalyan K. , Patel Tanmay , Wastella Catherine M. , Ning Gang , Kirimanjeswara Girish S. 
Published: December 2017

ABSTRACT

Francisella tularensis
subsp.
holarctica
is found in North America and much of Europe and causes the disease tularemia in humans and animals. An aquatic cycle has been described for this subspecies, which has caused waterborne outbreaks of tularemia in at least 10 countries. In this study, we sought to identify the mechanosensitive channel(s) required for the bacterium to survive the transition from mammalian hosts to freshwater, which is likely essential for the transmission of the bacterium between susceptible hosts. A single 165-amino-acid MscS-type mechanosensitive channel (
Ft
MscS) was found to protect
F. tularensis
subsp.
holarctica
from hypoosmotic shock, despite lacking much of the cytoplasmic vestibule domain found in well-characterized MscS proteins from other organisms. The deletion of this channel did not affect virulence within the mammalian host; however,
Ft
MscS was required to survive the transition from the host niche to freshwater. The deletion of
Ft
MscS did not alter the sensitivity of
F. tularensis
subsp.
holarctica
to detergents, H
2
O
2
, or antibiotics, suggesting that the role of
Ft
MscS is specific to protection from hypoosmotic shock. The deletion of
Ft
MscS also led to a reduced average cell size without altering gross cell morphology. The mechanosensitive channel identified and characterized in this study likely contributes to the transmission of tularemia between hosts by allowing the bacterium to survive the transition from mammalian hosts to freshwater.

IMPORTANCE
The contamination of freshwater by
Francisella tularensis
subsp.
holarctica
has resulted in a number of outbreaks of tularemia. Invariably, the contamination originates from the carcasses or excreta of infected animals and thus involves an abrupt osmotic downshock as the bacteria enter freshwater. How
F. tularensis
survives this drastic change in osmolarity has not been clear, but here we report that a single mechanosensitive channel protects the bacterium from osmotic downshock. This channel is functional despite lacking much of the cytoplasmic vestibule domain that is present in better-studied organisms such as
Escherichia coli
; this report builds on previous studies that have suggested that parts of this domain are dispensable for downshock protection. These findings extend our understanding of the aquatic cycle and ecological persistence of
F. tularensis
, with further implications for mechanosensitive channel biology.
Covalent Structure and Bioactivity of the Type AII Lantibiotic Salivaricin A2
Authors: Geng Mengxin , Austin Frank , Shin Ronald , Smith Leif 
Published: December 2017

ABSTRACT

Lantibiotics are a class of lanthionine-containing, ribosomally synthesized, and posttranslationally modified peptides (RiPPs) produced by Gram-positive bacteria. Salivaricin A2 belongs to the type AII lantibiotics, which are generally considered to kill Gram-positive bacteria by binding to the cell wall precursor lipid II via a conserved ring A structure. Salivaricin A2 was first reported to be isolated from a probiotic strain,
Streptococcus salivarius
K12, but the structural and bioactivity characterizations of the antibiotic have remained limited. In this study, salivaricin A2 was purified and its covalent structure was characterized. N-terminal analogues of salivaricin A2 were generated to study the importance for bioactivity of the length and charge of the N-terminal amino acids. Analogue salivaricin A2(3-22) has no antibacterial activity and does not have an antagonistic effect on the native compound. The truncated analogue also lost its ability to bind to lipid II in a thin-layer chromatography (TLC) assay, suggesting that the N-terminal amino acids are important for binding to lipid II. The creation of N-terminal analogues of salivaricin A2 promoted a better understanding of the bioactivity of this antibiotic and further elucidated the structural importance of the N-terminal leader peptide. The antibacterial activity of salivaricin A2 is due not only to the presence of the positively charged N-terminal amino acid residues, but to the length of the N-terminal linear peptide.

IMPORTANCE
The amino acid composition of the N-terminal linear peptide of salivaricin A2 is crucial for function. Our study shows that the length of the amino acid residues in the linear peptide is crucial for salivaricin A2 antimicrobial activity. Very few type AII lantibiotic covalent structures have been confirmed. The characterization of the covalent structure of salivaricin A2 provides additional support for the predicted lanthionine and methyl-lanthionine ring formations present in this structural class of lantibiotics. Removal of the N-terminal Lys1 and Arg2 residues from the peptide causes a dramatic shift in the chemical shift values of amino acid residues 7 through 9, suggesting that the N-terminal amino acids contribute to a distinct structural conformer for the linear peptide region. The demonstration that the bioactivity could be partially restored with the substitution of N-terminal alanine residues supports further studies aimed at determining whether new analogues of salivaricin A2 for novel applications can be synthesized.