bluuebunny/crossref_metadata_2025 huggingface dataset:
An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea)
Authors: Evangelista Dominic A. , Wipfler Benjamin , Béthoux Olivier , Donath Alexander , Fujita Mari , Kohli Manpreet K. , Legendre Frédéric , Liu Shanlin , Machida Ryuichiro , Misof Bernhard , Peters Ralph S. , Podsiadlowski Lars , Rust Jes , Schuette Kai , Tollenaar Ward , Ware Jessica L. , Wappler Torsten , Zhou Xin , Meusemann Karen , Simon Sabrina
Published: January 2019

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, andLamproblattabeing the closest relative to the social and wood-feedingCryptocercusand termites. Consequently, we propose new names for various clades in Blattodea:Cryptocercus+ termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.
Isoniazid resistance in Mycobacterium tuberculosis is a heterogeneous phenotype comprised of overlapping MIC distributions with different underlying resistance mechanisms
Authors: Ghodousi Arash , Tagliani Elisa , Karunaratne Eranga , Niemann Stefan , Perera Jennifer , Köser Claudio U. , Cirillo Daniela Maria
Published: January 2019

MIC testing using the BACTEC 960 MGIT system of 70 phylogenetically diverse, isoniazid-resistant clinical strains of Mycobacterium tuberculosis revealed a complex pattern of overlapping MIC distributions. Whole-genome sequencing could explain most of the level of resistance observed. The MIC distribution of strains with only inhA promoter mutations was split by the current concentration that is endorsed by the Clinical Laboratory Standards Institute to detect low-level resistance to isoniazid and is therefore likely not optimally set.
Moraxellaceae and Moraxella interact with the altered airway mycobiome in asthma
Authors: Liu Hai-yue , Li Chun-xi , Liang Zhen-yu , Zhang Shi-yu , Yang Wan-ying , Ye Yan-mei , Lin Yan-xia , Chen Rong-chang , Zhou Hong-wei , Su Jin
Published: January 2019

Airway microbial-microbial interaction plays an important role in chronic airway inflammatory diseases such as asthma. Moraxella is widely regarded as a human respiratory tract pathogen. We aimed to investigate the interactions among Moraxella, Moraxellaceae (to which Moraxella belongs) and the airway microbiome in asthma. Induced sputum samples were obtained from 116 asthma patients and 29 healthy individuals, and the bacterial/fungal communities were profiled using 16S rRNA and ITS1 DNA gene sequencing. We found that asthma patients harboured significantly greater airway bacterial and fungal α-diversity than that of healthy individuals. Moraxellaceae, Moraxella and Moraxella otu19 (bacteria), and Schizophyllaceae, Polyporaceae, Aspergillus, Schizophyllum and Candida (fungi) were increased in the airway of asthma. Moreover, Moraxellaceae, Schizophyllaceae, Polyporaceae and Candida were positively associated with airway fungal α-diversity. Correlation networks revealed Moraxellaceae and Moraxella as microbial “hubs” in asthma that had significant negative connections with multiple bacterial communities, such as Leptotrichiaceae, Lachnospiraceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotella, Veillonella, Rothia and Leptotrichia, but positive interactions with fungal communities such as Schizophyllaceae, Polyporaceae, Candida and Meyerozyma. Together, our finding revealed an altered microbiome and complex microbial-microbial interactions in the airway of asthma. Moraxellaceae and Moraxella showed significant interactions with the airway mycobiome, providing potential insights into the novel pathogenic mechanisms of asthma.

IMPORTANCE

With the advent of culture-independent techniques, growing evidence suggests that the airway microbiome is closely correlated with chronic respiratory diseases such as asthma. The complex microbial-microbial interaction exists in the airways of both healthy individuals and patients with respiratory diseases, which is of great significance for the pathogenesis and disease progression of asthma. In this study, we evaluated the airway dysbiosis in asthma patients, described the interaction between Moraxellaceae, Moraxella and airway bacterial/fungal communities, and it contributes to further understanding the pathogenic mechanisms of asthma.
Structural Insights into GluK3-kainate Receptor Desensitization and Recovery
Authors: Kumari Jyoti , Vinnakota Rajesh , Kumar Janesh
Published: January 2019

GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play key role in regulation of synaptic transmission. For better understanding of structural changes that underlie receptor recovery from desensitized state, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. We show that receptor recovery from desensitization requires major rearrangements of the ligand binding domains (LBD) while the amino terminal (ATD) and transmembrane domains remain virtually unaltered. While, the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a partially “recovered” state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using these structures as guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. Mutational analysis also identifies putative N-glycan interacting residues. These results provide a molecular framework for understanding gating properties unique to GluK3 and identify role of N-linked glycosylation in their modulation.
The transferability of lipid loci across African, Asian and European cohorts
Authors: Telkar Nikita , Reiker Theresa , Walters Robin G. , Lin Kuang , Eriksson Anders , Gurdasani Deepti , Gilly Arthur , Southam Lorraine , Tsafantakis Emmanouil , Karaleftheri Maria , Seeley Janet , Kamali Anatoli , Asiki Gershim , Millwood Iona Y. , Holmes Michael , Du Huaidong , Guo Yu ,   Understanding Society Scientific Group, Kumari Meena , Dedoussis George , Li Liming , Chen Zhengming , Sandhu Manjinder S. , Zeggini Eleftheria , Kuchenbaecker Karoline
Published: January 2019

The majority of genetic studies for cardiometabolic traits were based on samples with European ancestry. Our aim was to assess whether genetic variants associated with blood lipids, a major risk factor for CVD, are shared across different populations.

We compared genetic associations with lipids between samples from Uganda (N=6,407), China (N=21,295), Japan (N=162,255), the UK (N=9,961) and Greece (N=3,586). Using simulations, we established trans-ethnic colocalization as a method to distinguish shared from population-specific trait loci.

Genetic correlations for HDL, LDL and triglycerides between European ancestry and Asian cohorts were close to 1. A polygenic score based on established LDL-cholesterol-associated loci from European discovery samples had consistent effects on serum levels in samples from the UK, Uganda and Greek population isolates (r=0.23 to 0.28, p<1.9x10−14). Overall, ~75% of the major lipid loci from European discovery studies displayed evidence of replication at p<10−3, except triglyceride loci in the Ugandan samples of which only 10% replicated. Specific replicating loci were identified using trans-ethnic colocalization. Ten of the fourteen lipid loci that did not replicate in the Ugandan population had pleiotropic associations with BMI in European ancestry samples while none of the replicating loci did. While lipid associations were highly consistent across European and Asian populations, there was a lack of replication particularly for established triglyceride loci in the Ugandan population. These loci might affect lipids by modifying food intake or metabolism in an environment offering diets rich in certain nutrients. This suggests that gene-environment interactions could play an important role for the transferability of complex trait loci.
Cortical tethering of mitochondria by the dynein anchor Mcp5 enables uniparental mitochondrial inheritance during fission yeast meiosis
Authors: Mehta Kritika , Ananthanarayanan Vaishnavi
Published: January 2019

During sexual reproduction in eukaryotes, processes such as active degradation and dilution of paternal mitochondria ensure maternal mitochondrial inheritance. In the isogamous organism fission yeast, we employed high-resolution fluorescence microscopy to visualize mitochondrial inheritance during meiosis by differentially labeling mitochondria of the two parental cells. Remarkably, mitochondria, and thereby, mitochondrial DNA from the parental cells did not mix upon zygote formation, but remained segregated at the poles by attaching to clusters of the dynein anchor Mcp5 via its coiled-coil domain. We observed that this tethering of parental mitochondria to the poles results in uniparental inheritance of mitochondria, wherein two of the four spores formed subsequently contained mitochondria from one parent and the other spores, mitochondria from the other parent. Further, the presence of dynein on an Mcp5 cluster precluded the attachment of mitochondria to the same cluster. Taken together, we reveal a distinct mechanism that achieves uniparental inheritance by segregation of parental mitochondria.
Modular structure of human olfactory receptor codes reflects the bases of odor perception
Authors: Bak Ji Hyun , Jang Seogjoo J. , Hyeon Changbong
Published: January 2019

The circuits of olfactory signaling are reminiscent of complex computational devices. The olfactory receptor code, which represents the responses of receptors elicited by olfactory stimuli, is effectively an input code for the neural computation of odor sensing. Here, analyzing a recent dataset of the odorant-dependent responses of human olfactory receptors (ORs), we show that the space of human olfactory receptor codes is partitioned into a modular structure where groups of receptors are “labeled” for key olfactory features. Our analysis reveals a low-dimensional structure in the space of human odor perception, with the receptor groups as the bases to represent major features in the perceptual odor space. These findings provide a novel evidence that some fundamental olfactory features are already hard-coded at the level of ORs, separately from the higher-level neural circuits.
Characterisation of type 2 diabetes progression with regulatory network
Authors: Barrera Maria , Hiriart Marcia , Cocho Germinal , Villarreal Carlos
Published: January 2019

Type 2 diabetes develops due to beta cell exhaustion with accompanying decrease in insulin secretion, leading to hyperglycemia and eventual damage of nerve, kidney, and eye tissues. It is usually preceded by metabolic alterations related to insulin signaling, inflammatory pathways, or intracellular glucose processing, encompassed as metabolic syndrome. We propose a regulatory network for components of pancreatic-beta cells playing an essential role in the disease. The network interactions are expressed as continuous fuzzy logic propositions. The dynamical modeling of the network allows to portray the disease progression as a transit between steady states associated to health, metabolic syndrome, and diabetes, each state defined by specific expression patterns of the network components. Transitions between equilibrium states are due to altered expression or functional exhaustion associated to modifications of characteristic decay rates of cellular components. This approach let us identify functional modules that may eventually drive the transit from health to diabetes. The analysis reveals that underexpression of protein kinase B and X-box binding protein 1, with concomitant overexpression of lipopolysaccharides and thioredoxin interacting protein are key factors in the transition from health to disease.
14-(4-Chlorophenyl)-14H-dibenzo[a,j]xanthene
Authors: Roy Choudhury Anuradha , Paul Satya B. , Choudhury Sudip
Published: January 2019

In the title compound, C27H17ClO, the xanthene fused-ring system adopts a shallow butterfly conformation [dihedral angle between the two halves of the ring system = 22.9 (1)°. The dihedral angle between the central heteroyclic ring and the pendant chlorophenyl group is 87.60 (8)°. In the crystal, molecules are linked by weak C—H...π interactions.
The external affairs of the Hong Kong SAR: UK-Hong Kong economic relations
Authors: Summers Tim
Published: January 2019

Purpose

The purpose of this paper is to examine economic relations between Hong Kong and the UK, especially since 2012, in order to shed light on the management of Hong Kong’s external relations.

Design/methodology/approach

The context for the research is discussion of “grey areas” between Hong Kong’s external relations and foreign affairs. Research is based on textual analysis of British and some Hong Kong policy documents, government statements and media reports, as well as personal discussions with many involved in UK-Hong Kong ties.

Findings

The paper finds that the UK-Hong Kong economic relationship is managed autonomously, demonstrating Hong Kong’s external economic affairs and bilateral exchanges being practised with a high degree of autonomy. It also shows the importance that the British government attaches to its economic relationship with Hong Kong in its own right, and the likely increase in that importance as Brexit unfolds.

Originality/value

The paper engages in detailed analysis of economic relations between the UK and Hong Kong, in contrast to most post-1997 studies which have focused on Hong Kong’s ties with the USA or European Union.
The problematic chemsex journey: a resource for prevention and harm reduction
Authors: Platteau Tom , Pebody Roger , Dunbar Nia , Lebacq Tim , Collins Ben
Published: January 2019

Purpose

Chemsex is a phenomenon that has gained increasing attention in recent years. The purpose of this paper is to differentiate chemsex from other sexualized substance use, and clarify differences between recreational and problematic chemsex use. Despite plentiful publications, little has been published on underlying determinants that predispose individuals to chemsex, and their process toward problematic chemsex use.

Design/methodology/approach

During the second European Chemsex Forum, people who engage in chemsex, community organizers, researchers, clinicians, therapists, social workers and (peer) counselors discussed potential pathways to problematic chemsex. In this manuscript, we translate findings from these discussions into a framework to understand the initiation and process toward problematic chemsex.

Findings

Six stages (loneliness and emptiness, search for connection, sexual connection, chemsex connection, problematic chemsex and severe health impact) and a set of factors facilitating the transition from one stage to the next have been identified.

Originality/value

It is hoped that this “Journey towards problematic chemsex use” will stimulate reflection and debate, with the ultimate goal of improving prevention and care for people engaging in chemsex.
Obtaining laboratory accreditation – required activities
Authors: Macchi Silva Vítor Vasata , Ribeiro José Luis Duarte
Published: January 2019

Purpose

The purpose of this paper is to describe the activities needed to meet specified requirements to assist laboratory staff running tests and calibrations and to obtain ISO/IEC 17025 accreditation.

Design/methodology/approach

The relevant literature that contributes to establishing activities that help laboratory staff to obtain ISO/IEC 17025 accreditation was studied. Laboratory researchers specializing in electro-medical equipment quality control were questioned about the criteria to be observed when selecting, developing and validating analytical steps.

Findings

Results revealed the analytical method criteria to be observed, which demonstrated their essentially quantitative nature.

Originality/value

This study presents a model that improves selecting, developing and validating analytical steps and contributes to producing reliable test and calibration results. These improvements can help laboratory testing and calibration to meet clients’ needs, satisfy specified requirements and provide reliable results.
Functions of peer mentoring, satisfaction and the “real” relationship in postgraduate psychology education
Authors: Quinlan Elly , Crowe Trevor , Deane Frank P. , Whittington Meredith
Published: January 2019

Purpose

The purpose of this paper is to examine how a peer mentoring relationship may support provisional psychologists engaged in postgraduate education in Australia. The theoretical lens for this study draws from the real relationship framework and significant events literature.

Design/methodology/approach

Quantitative and qualitative data were obtained via a web survey from a sample of 23 mentors and 41 mentees. Participants had engaged in a one-year peer mentoring program on a volunteer basis. The survey contained measures of functions of mentoring, perceived genuineness and realism in the relationship, and overall satisfaction with peer mentoring. Participants also provided accounts of helpful events, hindering events and open feedback.

Findings

Perceived satisfaction was significantly correlated with greater genuineness and realism in the relationship. Satisfaction was associated with psychosocial and clinical functions of mentoring for both mentors and mentees, and career functions for mentees only. Qualitative findings indicated that the most helpful events included psychosocial support, mutual understanding and skill development. The most frequent hindering events were logistics/time, lack of structure and mentor technique/activity.

Practical implications

Peer mentors show great promise for supporting provisional psychologists. Recommendations for higher education providers include providing peer mentors with guidance regarding the importance of psychosocial support, clinical skill development and creating genuine and real relationships. Peer mentor training would also benefit from the inclusion of career development strategies and psychoeducation on transference.

Originality/value

This study is the first to apply the real relationship framework and significant events analysis to the psychology peer mentoring context.
Examining pre-post results
Authors: Waite Roberta , Mensinger Janell , Wojciechowicz Christine , Colistra Angela , Gambescia Stephen
Published: January 2019

Purpose

The purpose of this paper is to examine changes in scores from the Kouzes and Posner Student Leadership Practices Inventory of undergraduate students in the health professions who were engaged in a nine-month leadership program. The authors also assessed changes in scores on the same inventory for several observers who rated the students’ leadership competence and examined differences between the students’ self-assessment on leadership practices and those of their observers.

Design/methodology/approach

A pre-post survey design using repeated measures factorial ANOVA, Pearson correlations and paired t-tests was used to investigate the data. An α level of 0.05 was used.

Findings

Statistically significant changes were found in the pre- to post-surveys of students on three of the five subscales but only one of the five subscales for observers. Students’ and observers’ ratings were largely uncorrelated, with the exception of Encouraging the Heart ratings at post-program.

Research limitations/implications

Participants were recruited from one setting at a private university in the USA and the sample size was small. A control group was not available to offer a comparison for the outcomes of the leadership program and only quantitative data were assessed.

Originality/value

Data capturing undergraduate leadership practices on students in the health professions using a validated tool bring value to better understanding strategies that university faculty can use to improve students’ leadership skills.
Variation in plant functional traits is best explained by the species identity: Stability of trait‐based species ranking across meadow management regimes
Authors: Mudrák Ondřej , Doležal Jiří , Vítová Alena , Lepš Jan
Published: January 2019

It is commonly assumed in trait‐based studies that plant functional traits are species‐specific, being more variable among species than among different environmental conditions. If the environment affects traits, it is assumed that species react in a similar direction and conserve the functional distances. The rank of species based on the trait values is then unchanged, which justifies the use of species trait averages from database values. Such assumptions of species specificity are, however, increasingly disputed by studies showing overall high intraspecific trait variability.

To test the species specificity and ranking stability of functional traits, we sampled plant individuals of almost all species (66 in total) within each plot of a long‐term (19 years) land use management experiment, which comprised a factorial combination of fertilization, mowing and removal of the dominant species Molinia caerulea in an oligotrophic wet meadow in the Czech Republic. Plant individuals were measured for eight commonly used traits: height, leaf dry matter content (LDMC), specific leaf area (SLA), leaf δ13C content, leaf carbon content, leaf δ15N content and leaf nitrogen content. Height, LDMC and SLA were also extracted from the LEDA trait database for comparison.

Species identity consistently explained the largest portion of trait variability (40%‐68%). Land use managements had a considerably lower effect (0.4%–9% of explained trait variability for individual traits). The species trait averages computed for each land use management regime separately were mutually correlated, showing the stable trait‐based species ranking. Ranking stability of species trait averages was observed despite land use management changing absolute trait values and despite the tremendous intraspecific trait variability (causing substantial overlap of trait values for different species). For all treatments, our measured species averages for LDMC and SLA were also stably ranked with species averages from the LEDA database.

Synthesis. Our results showed that species conserve the functional distances in different environmental conditions from where they were measured. Species trait averages can describe general trends in functional composition, although averaging reduces the ecologically interesting information of the intraspecific trait variability.

A plain language summary is available for this article.
Nitrogen acquisition of Central European herbaceous plants that differ in their global naturalization success
Authors: Liu Yanjie , van Kleunen Mark
Published: January 2019

It is frequently assumed that species capable of fast nitrogen (N) acquisition under different N‐availability conditions should have a higher establishment success after their introduction into new regions. However, few experimental studies have explicitly tested this. Our multispecies experiment tested whether global naturalization success of plant species native to Central Europe is related to a high N‐acquisition ability.

We selected 41 common herbaceous species native to Germany that have all become naturalized, and thus been introduced, elsewhere. Twenty‐two of these species are widely naturalized and 19 are less widely naturalized. We grew the 41 grassland species, sampled in Germany, under low and high N‐conditions in a greenhouse experiment, and assessed their N‐acquisition abilities.

Although the widely naturalized species grew faster on average, they had a significantly lower N‐uptake rate than the less widely naturalized ones. The widely naturalized species, however, had a marginally significantly higher root‐mass fraction. Despite these differences, the total plant N‐content did on average not differ between the two groups of species. However, N‐addition tended to increase the total plant N‐content more for the widely naturalized species than for the less widely naturalized species. Nitroge addition also increased biomass production and N‐uptake rate, and decreased the root‐mass fraction of plants, but these responses did not differ between widely and less widely naturalized species.

We conclude that although fast‐growing species tend to have a higher global naturalization success than slow‐growing species, the naturalization success of plants is not necessarily related to a high N‐acquisition ability.

Aplain language summaryis available for this article.
Experimental N and P additions alter stream macroinvertebrate community composition via taxon‐level responses to shifts in detrital resource stoichiometry
Authors: Demi Lee M. , Benstead Jonathan P. , Rosemond Amy D. , Maerz John C.
Published: January 2019

Increases in nitrogen (N) and phosphorus (P) availability are changing animal communities, partly by altering stoichiometric imbalances between consumers and their food. Testing relationships between resource stoichiometry and consumer assemblage structure requires ecosystem‐level manipulations that have been lacking to date.

We analysed patterns of macroinvertebrate community composition in five detritus‐based headwater streams subject to experimental whole‐stream N and P additions that spanned a steep gradient in dissolved N:P ratio (2:1, 8:1, 16:1, 32:1, 128:1) over 2 years, following a 1‐year pre‐treatment period.

We predicted that shifts in leaf litter stoichiometry would drive overall patterns of community composition via greater responses of shredders to enrichment than other taxa, as shredders dominate primary consumer biomass and experience larger consumer–resource elemental imbalances than other functional groups in stream ecosystems. Specifically, we expected litter C:P to be a significant predictor of shredder biomass given the greater relative imbalances between shredder and litter C:P than C:N. Finally, we tested whether shredder responses to enrichment were related to other taxon‐level traits, including body size and stoichiometry, larval life span and growth rate.

Whole‐community composition shifted similarly across the five streams after enrichment, largely driven by increased shredder and predator biomass. These shifts were limited to the autumn/winter seasons and related to decreased leaf litter C:P, highlighting important links between the quality of seasonal litter subsidies and community phenology.

Among 10 taxa that drove structural shifts, two declined while other taxa from the same functional/taxonomic groups responded positively, suggesting that specific life‐history traits may determine sensitivity to enrichment.

Increases in total shredder biomass, and in biomass of several common shredders, were associated with lower litter C:P. Body C:P did not predict shredder response to enrichment. However, weak negative relationships between shredder response and body size, and larval life span, suggest that small‐bodied and short‐lived taxa may be more responsive to shifting resource stoichiometry.

Moderate anthropogenic increases in N and P availability affect resource stoichiometry and can alter animal communities, influencing additional food web and ecosystem properties. We provide support for ecological stoichiometry as a framework for predicting such outcomes based on changes in the elemental composition of resource pools.

A plain language summary is available for this article.
Association of a plant‐based dietary pattern in relation to gestational diabetes mellitus
Authors: Zamani Behzad , Milajerdi Alireza , Tehrani Hatav , Bellissimo Nick , Brett Neil R. , Azadbakht Leila
Published: January 2019

Aim

The prevalence of gestational diabetes mellitus (GDM), which has adverse effects on mothers and their offspring, is increasing worldwide. The role of a plant‐based dietary pattern as a determinant of GDM is not well understood. Therefore, we examined the association between plant‐based dietary patterns and the risk of GDM.

Methods

We enrolled 460 pregnant women in this case–control study, of them 200 were cases and 260 were controls. Dietary intake of participants was evaluated using three 24‐hour dietary records. Adherence to the plant‐based dietary patterns was scored using three indices of the overall plant‐based dietary index (PDI), healthy plant‐based diet (hPDI) and unhealthy plant‐based diet index (uPDI). The risk of GDM was compared across tertiles of PDI, hPDI and uPDI.

Results

After multivariable adjustment, we demonstrated that the high PDI score was inversely associated with risk of GDM (OR = 0.47; 95% CI: 0.28–0.78, P = 0.004), but there was no significant association between hPDI (OR = 1.03; 95% CI: 0.64–1.65, P = 0.884) or uPDI (OR = 1.65; 95% CI: 0.98–2.78, P = 0.06) and GDM risk.

Conclusions

We found that following an overall plant‐based diet was associated with lower risk of GDM. Future studies are warranted with longitudinal designs to confirm these findings.
CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases
Authors: Zizka Alexander , Silvestro Daniele , Andermann Tobias , Azevedo Josué , Duarte Ritter Camila , Edler Daniel , Farooq Harith , Herdean Andrei , Ariza María , Scharn Ruud , Svantesson Sten , Wengström Niklas , Zizka Vera , Antonelli Alexandre
Published: January 2019

Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo‐referencing or dating, can diminish their usefulness. Manual cleaning is time‐consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records.

Here, we present CoordinateCleaner, an r‐package to scan datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo‐referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio‐temporal tests for fossils.

We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic.

All cleaning functions and the biodiversity institution database are open‐source and available within the CoordinateCleaner r‐package.
Identifying Predictors of Undertriage in Injured Older Adults After Implementation of Statewide Geriatric Trauma Triage Criteria
Authors: Amoako Jeffrey , Evans Sara , Brown Nicole V. , Khaliqdina Salman , Caterino Jeffrey M.
Published: January 2019

Objectives

The objective was to identify factors associated with transport of injured older adults meeting statewide geriatric trauma triage criteria to a trauma center.

Methods

An observational retrospective cohort study using the 2009 to 2011 Ohio Trauma Registry. Subjects were adults ≥ 70 years old who met Ohio's geriatric triage criteria for trauma center transport by emergency medical services. We created multivariable logistic regression models to identify predictors of initial and ultimate (e.g., interfacility transfer) transport to a Level I or II trauma center and to a Level I, II, or III center.

Results

Of 10,411 subjects, 47% were initially and 59% were ultimately transported to a Level I or II trauma center with rates of 66 and 74%, respectively, for transport to a Level I, II, or III center. For initial transport to a Level I or II center, age 80 to 89 (odds ratio [OR] = 0.89), age ≥ 90 (OR = 0.76), and either only a Level 3 (OR = 0.3) or no trauma center (OR = 0.11) in county of residence had decreased odds of transport, while male sex (OR = 1.38), black race (OR = 2.07), Injury Severity Score (ISS) 10–15 (OR = 1.99), ISS > 15 (OR = 2.85), and Glasgow Coma Scale score < 9 (OR = 2.11) had increased odds. Results were similar for ultimate transport to a Level I or II center. Analyzing transport to a Level I, II, or III center demonstrated similar results except a Level III trauma center in county of residence was associated with increased odds (OR = 2.00 for initial and 2.21 for ultimate) of transport to a Level I, II, or III center.

Conclusions

We identified factors independently associated with failure to transport injured older adults to trauma centers in statewide data collected after adoption of geriatric triage criteria. Lack of a trauma center in the county of residence remained a factor even in analyses that included ultimate transport.
Mediterranean diet and the risk of poor semen quality: cross‐sectional analysis of men referring to an Italian Fertility Clinic
Authors: Ricci E. , Bravi F. , Noli S. , Ferrari S. , De Cosmi V. , La Vecchia I. , Cavadini M. , La Vecchia C. , Parazzini F.
Published: January 2019

Background

Several diet patterns have been suggested as involved in processes of spermatogenesis and thus in male subfertility. To study the relation between Mediterranean diet and abnormal sperm parameters in men of subfertile couples, we performed a cross‐sectional analysis of baseline data from a prospective cohort study.

Methods

Patients were enrolled in an Italian Fertility Clinic. Couples undergoing assisted reproduction techniques (ART) were interviewed to obtain information on personal and health history, lifestyle habits, and diet, on the day of oocyte retrieval. On the same day, a semen sample was also collected and analyzed to proceed with ART. Adherence to Mediterranean diet was evaluated using a Mediterranean Diet Score (MDS). Odds ratios (OR) and 95% confidence intervals (CI) were calculated for semen volume <1.5 mL, sperm concentration <15 mil/mL, and total count <39 mil.

Results

Three hundred nine men, age range 27–60, were enrolled: 19.3% had semen volume < 1.5 mL, 30.5% sperm concentration <15 mil/mL, and 32.1% total count <39 mil. MDS was low (0–3) in 86 men (27.8%), intermediate (4–5) in 131 (42.4%), and high (6–9) in 92 (29.8%). Semen volume was not associated with MDS. Compared to the highest MDS category (6–9), the ORs for low sperm concentration were 1.34 (95% CI 0.69–2.50) for MDS 4–5 and 2.42 (95% CI 1.21–4.83) for MDS 0–3, with significant trend (p = 0.011). The corresponding estimates for total count were 1.26 (95% CI 0.66–2.42) and 2.08 (95% CI 1.05–4.12), with significant trend (p = 0.034). These findings were consistent in strata of history of reproductive organ diseases.

Conclusions

Mediterranean Diet Score was positively associated with normal sperm concentration and total count, but not with semen volume.
Effects of forage source and particle size on chewing activity, ruminal pH, and saliva secretion in lactating Holstein cows
Authors: Jiang Fu‐Gui , Lin Xue‐Yan , Yan Zhen‐Gui , Hu Zhi‐Yong , Wang Yun , Wang Zhong‐Hua
Published: January 2019

The present study investigated the effects of dietary forage source (quality) and particle size on chewing activity, saliva secretion, and ruminal pH. Twelve multiparous lactating Holstein cows, four of which were ruminally cannulated, were used in a replicated 4 × 4 Latin square experimental design with a 2 × 2 factorial arrangement of treatments. Cows fed wild‐rye hay diets had longer daily eating times than cows fed oaten hay diets. Treatments had no effect on ruminating time; therefore, resting time varied inversely to eating time. Neither the rate nor the amount of saliva secretion while eating, ruminating, or resting was affected by diet, resulting in similar total daily saliva secretions across treatments (231 L/day). Total volatile fatty acids (VFAs) in the ruminal fluid from animals fed oaten hay diets were higher than those from animals fed wild‐rye hay diets; further, VFAs increased with decreasing forage particle size (FPS). Consistent with elevated VFA concentrations, reducing FPS and including oaten hay in the diet decreased mean ruminal pH and increased the daily time of ruminal pH under 5.8. Results of this study suggest that forage source and particle size affect ruminal pH might be via variations in VFA production rather than increased salivary recycling of buffering substrates.
Population pharmacokinetics of brodalumab in patients with moderate to severe plaque psoriasis
Authors: Timmermann Stine , Hall Anders
Published: January 2019

Brodalumab is a fully human monoclonal antibody targeting the IL‐17 receptor A leading to an inhibition of the biological effect of IL‐17A, IL‐17F, IL‐17A/F heterodimer, IL‐17C and IL‐17E isoforms. It has shown to be efficacious in the treatment of moderate to severe plaque psoriasis (210 mg administered subcutaneously at weeks 0, 1 and 2 followed by 210 mg every 2 weeks [Q2W+1]). A population pharmacokinetic model based on psoriasis patients only from six clinical trials was developed to describe the pharmacokinetics and identify sources of variability. In patients with psoriasis, Brodalumab exhibits non‐linear pharmacokinetics due to target‐mediated drug disposition resulting in concentration‐dependent clearance. The pharmacokinetics was best described by a two‐compartment model with linear absorption and combined linear and Michaelis‐Menten elimination. The subcutaneous bioavailability of Brodalumab was 55%, absorption rate was 0.30 day−1, and body‐weight was found to affect the volume of distribution and clearance. For a reference patient with plaque psoriasis (body‐weight of 90 kg), the estimates were 0.16 L/d for linear serum clearance, 6.1 mg/d for the maximum non‐linear clearance rate, and 4.7 and 2.4 L for central and peripheral volume of distribution, respectively. For the approved dosing regimen, time to maximum concentration was 4 days and 90% of steady‐state was achieved after 10 weeks for a reference patient. Following last dose at steady‐state, 90% of the population of reference patients will reach serum concentrations below lower limit of quantification after 45 days.
Interest Arbitration and the Narcotic Effect: Evidence from Three Decades of Collective Bargaining in Ontario
Authors: Campolieti Michele , Riddell Chris
Published: January 2019

We study whether there is increased reliance on interest arbitration, that is, a narcotic or addictive effect or, alternatively, positive state dependence, in public sector contract settlements. We use contract data from three sectors (police, firefighters and hospitals) in the Canadian province of Ontario, which covers 1981 to 2012. The length of our study period yields much longer bargaining histories than previously used, which should provide more compelling evidence on whether there is increased reliance on interest arbitration to settle bargaining impasses over time. We obtain our estimates using a dynamic probit model with random effects that models the initial conditions. Our estimates indicate — across all the sectors we consider and some robustness checks — that there is a narcotic effect in interest arbitration usage despite very different average propensities to use arbitration across sectors.
Who Will Get the Job? Hiring Practices and Inequalities in the Chilean Labour Market
Authors: Undurraga Rosario
Published: January 2019

This article explores the ways in which recruitment and hiring practices can promote and sustain social inequality in a highly neoliberal country: Chile. The article analyses six steps in the selection process. It provides evidence of discriminatory practices in the job market by analysing employers' and recruiters' practices, hiring methods, and the experiences of professionals applying for a job. The research is based on 43 interviews with managers, human resources consultants, and candidates. It uses intersectional analysis to unpack dynamics of inequality in the selection processes in Chile. The findings demonstrate high levels of explicit and severe discrimination in the labour market.
Iron accumulation in microglia triggers a cascade of events that leads to altered metabolism and compromised function in APP/PS1 mice
Authors: McIntosh Allison , Mela Virginia , Harty Conor , Minogue Aedin M. , Costello Derek A. , Kerskens Christian , Lynch Marina A.
Published: January 2019

Among the changes that typify Alzheimer’s disease (AD) are neuroinflammation and microglial activation, amyloid deposition perhaps resulting from compromised microglial function and iron accumulation. Data from Genome Wide Association Studies (GWAS) identified a number of gene variants that endow a significant risk of developing AD and several of these encode proteins expressed in microglia and proteins that are implicated in the immune response. This suggests that neuroinflammation and the accompanying microglial activation are likely to contribute to the pathogenesis of the disease. The trigger(s) leading to these changes remain to be identified. In this study, we set out to examine the link between the inflammatory, metabolic and iron‐retentive signature of microglia in vitro and in transgenic mice that overexpress the amyloid precursor protein (APP) and presenilin 1 (PS1; APP/PS1 mice), a commonly used animal model of AD. Stimulation of cultured microglia with interferon (IFN)γ and amyloid‐β (Aβ) induced an inflammatory phenotype and switched the metabolic profile and iron handling of microglia so that the cells became glycolytic and iron retentive, and the phagocytic and chemotactic function of the cells was reduced. Analysis of APP/PS1 mice by magnetic resonance imaging (MRI) revealed genotype‐related hypointense areas in the hippocampus consistent with iron deposition, and immunohistochemical analysis indicated that the iron accumulated in microglia, particularly in microglia that decorated Aβ deposits. Isolated microglia prepared from APP/PS1 mice were characterized by a switch to a glycolytic and iron‐retentive phenotype and phagocytosis of Aβ was reduced in these cells. This evidence suggests that the switch to glycolysis in microglia may kick‐start a cascade of events that ultimately leads to microglial dysfunction and Aβ accumulation.
One‐off export events
Authors: Geishecker Ingo , Schröder Philipp J. H. , S⊘rensen Allan
Published: January 2019

Isolated single‐month, one‐off export transactions (observed once in a 49‐month window) turn out to be the dominant spell length in granular firm–product–destination trade data. Moreover, on average, for an export‐active firm, such one‐off events generate a significant part of foreign sales. These patterns cannot be explained by the lumpiness of trade (e.g., seasonal shipments), nor do they sit well with available trade models. To reconcile theory with the data, we introduce passive (i.e., unsolicited buyer‐side driven) exporting in addition to proactive exporting. Our empirical investigation establishes novel stylized facts on firm and destination characteristics associated with one‐off exporting.
A total evidence analysis of the phylogeny of hatchet‐faced treefrogs (Anura: Hylidae: Sphaenorhynchus)
Authors: Araujo‐Vieira Katyuscia , Blotto Boris L. , Caramaschi Ulisses , Haddad Celio F. B. , Faivovich Julián , Grant Taran
Published: January 2019

The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships among its species, we performed a total evidence phylogenetic analysis of sequences of three mitochondrial and three nuclear genes, and 193 phenotypic characters from all species of Sphaenorhynchus. Our results support the monophyly of Sphaenorhynchus with molecular and phenotypic evidence, with S. pauloalvini as the earliest diverging taxon, followed by S. carneus, as the sister taxon of all remaining species of the genus. We recognize three species groups in Sphaenorhynchus (the S. lacteus, S. planicola and S. platycephalus groups), to facilitate its taxonomic study; only three species (S. carneus, S. pauloalvini and S. prasinus) remain unassigned to any group. Sequence data were not available for only two species (S. bromelicola and S. palustris) for which we scored phenotypic data; wildcard behaviour was detected only in S. bromelicola nested inside the S. platycephalus group. On the basis of the resulting phylogenetic hypothesis, we discuss the evolution of oviposition site and a number of phenotypic characters that could be associated with heterochronic events in the evolutionary history of this group.
Mosaic nature in the skeleton of East Asian crocodylians fills the morphological gap between “Tomistominae” and Gavialinae
Authors: Iijima Masaya , Kobayashi Yoshitsugu
Published: January 2019

Crocodylian systematics has long been confounded by conflicting hypotheses of higher level relationships—although molecular data sets strongly supported the sister‐taxon relationship ofTomistomaandGavialis, morphological data sets placedGavialisas sister to all other living taxa. One of the perceived difficulties in interpreting morphological character evolution on the molecular tree is the extensive character reversal occurring in Gavialinae, the mechanism of which has yet to be explained. Here, we provide evidence of gavialine‐specific atavistic characters from East Asian “tomistomines”Penghusuchus paniandToyotamaphimeia machikanensis. These taxa exhibit a mosaic assembly of “tomistomine” and gavialine features, which fill the gap between the two longirostrine groups. Although the parsimony analysis of morphological data (69 taxa, 254 characters) still supports the previous morphological hypothesis, the alternative tree that was forced to fit the molecular hypothesis was insignificantly (5/954 steps; 0.52%) longer than the unconstrained tree, suggesting that morphological evolution can also be interpreted on the molecular tree. Although the problem of stratigraphic gaps remains, future studies may be directed to resolving the interrelationships within Gavialoidea, a large longirostrine group of crocodylians, in the molecular tree context.