bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlates of non-random patterns of capsule switching in pneumococcus
Authors: Joshi Shreyas S. , Al-Mamun M. A. , Weinberger Daniel M. 
Published: October 2019

ABSTRACTBackgroundPneumococcus is a diverse pathogen, with >90 serotypes, each of which has a distinct polysaccharide capsule. Pneumococci can switch capsules, evading vaccine pressure. Certain serotype pairs are more likely to switch, but the drivers of these patterns are not well understood.MethodsWe used the PubMLST and Global Pneumococcal Sequencing (GPS) databases to quantify the number of genetic lineages on which different serotype pairs co-occur. We also quantified the genetic diversity of each serotype. Regression models evaluated the relationship between shared polysaccharide structural components and the frequency of serotype switching and diversity.ResultsA number of serotype pairs co-occurred on the same genetic lineage more commonly than expected. Co-occurrence of between-serogroup pairs was more common when both serotypes had glucose as a component of the capsule (and, potentially, glucuronic acid). Diversity also varied markedly by serotype and was lower for serotypes with glucuronic acid in the capsule and higher for those with galactose in the capsule.ConclusionsCertain pairs of serotypes are more likely to occur on the same genetic background, and these patterns were correlated with shared polysaccharide components. This might indicate adaptation of strains to produce capsules with particular characteristics.
Protein Phosphatase 1 activity controls a balance between collective and single cell modes of migration
Authors: Chen Yujun , Kotian Nirupama , Aranjuez George , Chen Lin , Messer C. Luke , Burtscher Ashley , Sawant Ketki , Ramel Damien , Wang Xiaobo , McDonald Jocelyn A. 
Published: October 2019

AbstractCollective cell migration is central to many developmental and pathological processes. However, the mechanisms that keep cell collectives together and coordinate movement of multiple cells are poorly understood. Using theDrosophilaborder cell migration model, we find that Protein phosphatase 1 (Pp1) activity controls collective cell cohesion and migration. Inhibition of Pp1 causes border cells to round up, dissociate, and move as single cells with altered motility. We present evidence that Pp1 promotes proper levels of cadherin-catenin complex proteins at cell-cell junctions within the cluster to keep border cells together. Pp1 further restricts actomyosin contractility to the cluster periphery rather than at internal cell-cell contacts. We show that the myosin phosphatase Pp1 complex, which inhibits non-muscle myosin-II (Myo-II) activity, coordinates border cell shape and cluster cohesion. Given the high conservation of Pp1 complexes, this study identifies Pp1 as a major regulator of collective versus single cell migration.
Integrating multiple dimensions of biodiversity to inform global parrot conservation
Authors: Burgio Kevin R. , Davis Katie E. , Dreiss Lindsay M. , Cisneros Laura M. , Klingbeil Brian T. , Presley Steven J. , Willig Michael R. 
Published: October 2019

ABSTRACTBecause biodiversity is increasingly threatened by habitat destruction and climate change, conservation agencies face challenges associated with an uncertain future. In addition to changes associated with climate and land use, parrots are threatened by hunting and capture for the pet trade, making them the most at-risk order of birds in the world. Parrots provide key ecosystem services, but remain understudied compared to other major bird orders despite their high extinction risk and ecological importance. Species richness is often used to identify high priority areas for conserving biodiversity. By definition, richness considers all species to be equally different. However, ongoing research emphasizes the importance of incorporating ecological functions (functional diversity) or evolutionary relationships (phylogenetic diversity) to more fully understand patterns of biodiversity, suggesting that using functional and phylogenetic information could improve conservation strategies. These distinctions among dimensions of biodiversity are important, because (1) areas of high species richness do not always represent areas of high functional or phylogenetic diversity, and (2) functional or phylogenetic diversity may better predict ecosystem function and evolutionary potential, which are essential for effective long-term conservation policy and management.Our objective was to create a framework for identifying areas of high species richness, functional diversity, and phylogenetic diversity within the global distribution of parrots We combined species richness, functional diversity, and phylogenetic diversity into an Integrated Biodiversity Index (IBI) to identify global biodiversity hotspots for parrots. We found important spatial mismatches among dimensions, which demonstrate that species richness is not always an effective proxy for other dimensions of parrot biodiversity. The IBI is an integrative and flexible index that can incorporate multiple dimensions of biodiversity, resulting in an intuitive and more direct way of assessing comprehensive goals in conservation planning (i.e., healthy ecosystem functioning and climate change resilience).
Ectopic HOTTIP Expression Induces Non-canonical Transactivation Pathways to Promote Growth and Invasiveness in Pancreatic Ductal Adenocarcinoma
Authors: Wong Chi Hin , Li Chi Han , He Qifang , Lam Chan Stephen , Tong Joanna Hung-Man , To Ka-Fai , Chen Yangchao 
Published: October 2019

AbstractLncRNA HOTTIP (HOXA transcript at the distal tip) is upregulated in pancreatic ductal adenocarcinoma (PDAC). However, oncogenic pathway mediated by HOTTIP is not fully understood. We identified canonical HOTTIP-HOXA13 targets: CYP26B1, CLIC5, CHI3L1 and UCP2 which were responsible for cell growth and cell invasion. Importantly, genome-wide analysis revealed that 38% of the genes regulated by HOTTIP contained H3K4me3 and HOTTIP enrichment at their promoters, without HOXA13 binding. HOTTIP complexed with WDR5-MLL1 totrans-activate oncogenic proteins CYB5R2, SULT1A1, KIF26A, SLC1A4 and TSC22D1 through directly triggering H3K4me3 at their promoters. The WDR5, MLL1 and H3K4me3 levels at their promoters and their expression levels were sensitive to HOTTIP overexpression and knockdown. These suggested the importance of non-canonicaltrans-acting HOTTIP-WDR5-MLL1 pathway in HOTTIP-regulatory mechanism by promoting the expression of oncogenic proteins. Furthermore, we dissected the mechanism by which HOTTIP was regulated by miR-497 in PDAC. Analysis of PDAC human tissues also revealed that HOTTIP was negatively correlated with miR-497 level. Our findings demonstrated that HOTTIP, upregulated in PDAC due to the loss of inhibitory miR-497, promoted PDAC progression through canonical HOTTIP-HOXA13 axis and a novel non-canonicaltrans-acting HOTTIP-WDR5-MLL1-H3K4me3 pathway.
The abstract space and the alienation of political public space in the Middle East
Authors: Zamani Farzad , Mehan Asma 
Published: October 2019

Purpose
The purpose of this paper is to explain how abstract space of the State – universally and specifically within the context of Middle Eastern cities – aims to homogenise the city and eliminate any anomaly that threatens its power structure.

Design/methodology/approach
Through a historical and discourse analysis of these policies and processes in the two case studies, this paper presents a contextualised reading of Lefebvre’s concept of abstract space and process of abstraction in relation to the alienation of political public spaces.

Findings
The paper proposes that regardless of these homogenising strategies being applied universally, they fail to respond to contextual particularities and therefore they – in a contradictory manner – may themselves produce a space of resistance and difference.

Originality/value
This paper focusses on Iran, the case of Tehran and Turkey, the case of Taksim Square and Gezi Park in Istanbul. Recent policies and strategies have been proposed and implemented to reduce, alienate and possibly neutralise the impacts of urban and political protests in these cities and socio-political contexts.
Food traceability technologies and foodborne outbreak occurrences
Authors: Magalhães Ana Elisa Vianna , Rossi Arthur Henrique Gomes , Zattar Izabel Cristina , Marques Marcos Augusto Mendes , Seleme Robson 
Published: October 2019

Purpose
The purpose of this paper is to identify the relationship between the frequency of publication on food supply chain (FSC) traceability and the occurrence of foodborne diseases outbreaks.

Design/methodology/approach
A systematic review of the literature was carried out to locate the main articles published in the literature, followed by a content analysis in order to list the main food traceability technologies and their evolutions. Finally, a Spearman’s ρ correlation analysis between the frequency of publications on FSC traceability and the annual occurrence of foodborne outbreaks in the five largest food exporting countries in the world was performed.

Findings
In these analyses, the tools of radiofrequency, deoxyribonucleic acid, wireless sensor network, hazard analysis and critical control points and Internet of Things are the most researched technologies, and they are relevant in the evolution of traceability in the FSC. With correlation coefficients above 0.700 at 0.01 significance levels, this evolution of food traceability technologies has been one of the factors reducing the number of food outbreaks in the USA and Germany, countries with greater development of the health system and food control.

Originality/value
This paper provides an evaluation of the food traceability technologies and the effects of their evolutions in the occurrence of food outbreaks. This may help in the proposal of public policies related to food and outbreak control.
Processed food choice based on the theory of planned behavior in the context of nutritional warning labels
Authors: Aliaga-Ortega Luis , Adasme-Berríos Cristian , Méndez Caren , Soto Carolina , Schnettler Berta 
Published: October 2019

Purpose
The purpose of this paper is to analyze the effect of nutritional warning (NW) labels on the behavior of consumers of processed foods, considering demographic and psychological factors associated with the theory of planned behavior (TPB).

Design/methodology/approach
The study had a descriptive and cross-sectional design. A survey was applied to 200 household food decision makers from central Chile. This questionnaire was developed based on the planned behavior theory that evaluates the psychological constructs of human behavior: Attitude (ATT), Subjective Norms (SN), Perceived Behavioral Control (PBC) and Purchase Intention (PI) toward processed foods with NW. Sociodemographic variables were also included. The data were analyzed by using a multinomial logit (MNL) model, where three types of categories are established depending on the choice made by the consumer. Thus, the dependent variable responds to the effect of the following probabilities: Eliminate from Consumption, Do Not Eliminate from Consumption and Do Not Know whether or not to eliminate from consumption when selecting a food processed with NW.

Findings
The results show that the implementation of NW has significant effects on the choice of processed foods purchases made by Chilean consumers. Consumers with negative ATT and PBC in the presence of NW on processed foods eliminated this type of food from their consumption. On the other hand, those who did not eliminate processed foods with NW from their consumption made that choice because they had a positive PBC. In addition, consumers who were unsure about eliminating or consuming processed foods with NW also had a positive PBC. In addition, SN and sociodemographic variables did not affect consumer choice.

Practical implications
The results of this study are crucial in informing public policy strategies seeking to alert consumers about the content of processed foods, thus raising awareness for decision making in order to reduce noncommunicable diseases associated with poor eating habits.

Originality/value
The study provides evidence on the effect of NWs for processed foods on consumer decisions based on the TPB.
Numerical simulation of the area shrinkage mass for the waist of elastic pantyhose by using FEM
Authors: Dan Rui , Shi Zhen 
Published: October 2019

Purpose
The area shrinkage of the body under pressure is very important to evaluate the comfort of pressure sense, and it is an important index that appraises compression garment. The purpose of this paper is to obtain the area shrinkage mass of the waist cross section by using the finite-element method (FEM), and the waist of women’s pantyhose could be designed with a different degree of elasticity during the course of design based on clothing pressure comfort.

Design/methodology/approach
This study aimed at the problems existing in the wearing of women’s elastic pantyhose, took the waist of pantyhose as the research object, and the contact between human body and pantyhose as elastic contact. The finite-element model of the waist cross section and elastic pantyhose fabric was acquired through CT scan and Mimics software. After simulating on the corresponding displacement distribution of the waist of sample elastic pantyhose during the process of dressing by using ANSYS, the authors divided the waist cross section into 24 equal regions according to angle (every 15 degrees as a region), and then the area shrinkage mass of each region was obtained by area calculation formula. According to the tendency of area shrinkage distribution, the waist of women’s elastic pantyhose could be designed for different regions of tension considering the pressure comfort, so as to guarantee that the wearing comfort can be maintained on the premise of ensuring the functionality of the elastic pantyhose.

Findings
In this paper, the authors obtained the area shrinkage mass of elastic pantyhose at waist cross section, and this area shrinkage distribution could be used as an objective evaluation index for pressure comfort. All these solutions are of great significance to the optimization design of pantyhose and can provide theoretical basis for the structural improvement of functional pantyhose and the prediction of clothing pressure.

Originality/value
This paper simulated the area shrinkage mass for the waist of elastic pantyhose by using FEM, and the waist of women’s elastic pantyhose could be designed for different regions of tension considering the pressure comfort according to the area shrinkage distribution tendency, so as to guarantee the wearing comfort during the wearing process.
Intergenerational exchange and the possibilities of role substitution for older people
Authors: Macfarlane Joanna , Stephens Christine , Taylor Joanne 
Published: October 2019

PurposeRole loss or substitution are common experiences of older adults, and a role typically held by older people – great grandparent or grandparent – is now under threat. Set within the context of a retirement village where an Intergenerational Programme (IGP) was taking place, the purpose of this paper is to understand older people’s perspectives on preschool-aged children, and the roles they adopt with them.Design/methodology/approachThe authors conducted semi-structured interviews and analysed the data using narrative analysis (n=19).FindingsFour narratives were identified, revealing that older adults adopt the roles of teacher and compromiser when interacting with children, believe they are “plugging a gap” in society through their involvement with younger generations and are reminded of life when with them.Research limitations/implicationsThe study does not feature the voice of younger children within intergenerational contact; information which would have provided a different perspective on the roles identified.Social implicationsThe bulk of global IGP practice is targeted at bringing together older and younger people who are not as young as preschool age, but this may be an opportunity missed. Retirement village operators may also want to consider intergenerational activity with preschool-aged children as a way for them to provide opportunities for role substitution within this environment.Originality/valueThe findings identify a positive perception older people have about young children in today’s society, expanding on very limited literature. How older adults perceive their role with young children is also identified within this research, highlighting how interacting with non-related preschoolers can provide some older people with a substitute role in later years.
Priority effects will impede range shifts of temperate tree species into the boreal forest
Authors: Solarik Kevin A. , Cazelles Kevin , Messier Christian , Bergeron Yves , Gravel Dominique 
Published: October 2019

Abstract

Temperate tree species are expected to expand their distribution into the boreal forest in response to climate change. However, it is becoming increasingly clear that many species will experience significant setbacks in capacity to migrate due to a series of unfavourable conditions impacting their recruitment success, and thus their ability to colonize new locations.

We quantify the relative influence of a series of factors important for tree seedling recruitment at range margins: propagule dispersal, substrate favourability and the influence of the local hetero‐specific species canopy composition. We hypothesized that boreal trees are responsible for priority effects that influence the establishment of temperate tree species seedlings. To do so, we analysed two recruitment stages (first‐year seedlings and older seedlings) for seven tree species: Abies balsamea (ABBA), Acer rubrum (ACRU), Acer saccharum (ACSA), Betula papyrifera (BEPA), Betula alleghaniensis (BEAL), Populus tremuloides (POTR) and Fagus grandifolia (FAGR) commonly found within the temperate‐boreal ecotone forests of northeastern North America.

Overall, we found that boreal canopy trees influence the distribution of substrates, more specifically the occurrence of needle cover and decayed wood in recruitment plots. Interestingly, decayed wood was a poor substrate in almost all cases. This association between canopy and substrate led to highly unfavourable substrates that affected the seedling densities of all temperate tree species. In addition, we found that seedling dispersion was highly localized, where the mean dispersal distance of all trees occurred in close proximity of parent trees.

Synthesis. Unfavourable substrates and limited mean dispersal distance of trees due to resident boreal trees generate (strong) priority effects within the temperate‐boreal ecotone. Together, these conditions promise to cause significant lags in temperate tree species migration into the boreal forest in the future.
Symbiotic interactions above treeline of long‐lived pines: Mycorrhizal advantage of limber pine (Pinus flexilis) over Great Basin bristlecone pine (Pinus longaeva) at the seedling stage
Authors: Shemesh Hagai , Boaz Briana E. , Millar Constance I. , Bruns Thomas D. 
Published: October 2019

Abstract

In response to contemporary changes in climate, many tree species are shifting upslope to find favorable habitat. In the case of obligate ectomycorrhizal species, seedling growth above upper treeline depends on fungal spore availability. In the mountain ranges of the Great Basin, a recent shift in tree species stratification has been recorded, with limber pine (LP, Pinus flexilis) leapfrogging above the ancient bristlecone pine (BCP, Pinus longaeva) forest and establishing above current treeline.

We compared the ability of LP and BCP to interact with soil spore banks collected at different microhabitats (next to dead trees, young live trees or in a treeless control) above current treeline in the White Mountains of California.

We found an ectomycorrhizal fungal spore bank community composed of 15 species that was dominated by an undescribed and a hitherto unsequenced species of Geopora and Rhizopogon, respectively. This represents a much richer community than was found previously in this system. While both LP and BCP were able to establish ectomycorrhiza, LP was twice as likely to do so, and when comparing only seedlings that were colonized, its root system was colonized to a three‐fold greater extent. BCP seedlings grown on soils collected under young live trees were much more likely to be colonized compared to soils from the other two microhabitats.

Synthesis. These differences in ectomycorrhizal receptivity might help to explain why LP is currently establishing at higher rates above the BCP treeline. Furthermore, it is possible that LP saplings above treeline can provide ectomycorrhizal facilitation for BCP seedlings, enabling the subsequent shift of BCP above treeline.
A crosstalk between c‐di‐GMP and cAMP in regulating transcription of GcsA, a diguanylate cyclase involved in swimming motility in Pseudomonas putida
Authors: Xiao Yujie , Liu Huizhong , He Meina , Nie Liang , Nie Hailing , Chen Wenli , Huang Qiaoyun 
Published: October 2019

SummaryThe ubiquitous bacterial second messenger c‐di‐GMP is synthesized by diguanylate cyclase (DGC) and degraded by phosphodiesterase (PDE). Pseudomonas putida has dozens of DGC/PDE‐encoding genes in its genome, but the phenotypical–genotypical correlation and transcriptional regulation of these genes are largely unknown. Herein, we characterize function and transcriptional regulation of a P. putida c‐di‐GMP‐metabolizing enzyme, GcsA. GcsA consists of two per‐ARNT‐sim (PAS) domains, followed by a canonical conserved central sequence pattern (GGDEF) domain and a truncated EAL domain. In vitro analysis confirmed the DGC activity of GcsA. The phenotypic observation revealed that GcsA inhibited swimming motility in an FlgZ‐dependent manner. In terms of transcriptional regulation, gcsA was found to be cooperatively regulated by c‐di‐GMP and cAMP via their effectors, FleQ and Crp respectively. The transcription of gcsA was promoted by c‐di‐GMP and inhibited by cAMP. In vitro binding analysis revealed that FleQ indirectly regulated the transcription of gcsA, while Crp directly regulated the transcription of gcsA by binding to its promoter. Besides, an inverse relationship between the cellular c‐di‐GMP and cAMP levels in P. putida was confirmed. These findings provide basic knowledge regarding the function and transcriptional regulation of GcsA and demonstrate a crosstalk between c‐di‐GMP and cAMP in the regulation of the expression of GcsA in P. putida.