bluuebunny/crossref_metadata_2025 huggingface dataset:
Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest
Authors: Marx Hannah E. , Jorgensen Stacy A. , Wisely Eldridge , Li Zheng , Dlugosch Katrina M. , Barker Michael S.
Published: April 2020

Premise of the study:Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes.

Methods:We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content.

Results:We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated genes between diploid and polyploid transcriptomes.

Discussion:Our resource provides new RNA-seq datasets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers clear opportunities for large scale studies at the intersection of ecology and genomics.
Impact of glycan positioning on HIV-1 Env glycan shield density, function, and antibody recognition
Authors: Wei Qing , Hargett Audra A. , Knoppova Barbora , Duverger Alexandra , Rawi Reda , Shen Chen-Hsiang , Farney S. Katie , Hall Stacy , Brown Rhubell , Keele Brandon F. , Heath Sonya L. , Saag Michael S. , Kutsch Olaf , Chuang Gwo-Yu , Kwong Peter D. , Moldoveanu Zina , Raska Milan , Renfrow Matthew B. , Novak Jan
Published: April 2020

N-glycans, which represent >50% mass of the HIV-1 envelope (Env) trimer, play important roles for virus-cell entry and immune evasion. How each glycan unit interacts to shape the Env protein-sugar complex and affects Env function is not well understood. Here, high-resolution glycomics analysis of two Env variants from the same donor, with differing functional characteristics and N-glycosylation-site composition, revealed that changes to key N-glycosylation-site not only affected the Env structure at distant locations, but also had a ripple effect on Env-wide glycan processing, virus infectivity, and antibody recognition and virus neutralization. Specifically, the N262 glycan, although not located in the CD4-binding site, controlled Env binding to the CD4 receptor, affected the recognition of Env by several glycan-dependent broadly neutralizing antibodies, and altered heterogeneity of glycosylation at several sites, with N156, N160, and N448 displaying limited glycan processing. Molecular dynamic simulations visualized how specific oligosaccharide positions can move to compensate for loss of a glycan. This study demonstrates how changes in individual glycan units can alter molecular dynamics and processing of the Env-glycan shield and, consequently, Env function.
On the Relation of Gene Essentiality to Intron Structure: A Computational and Deep Learning Approach
Authors: Schonfeld Ethan , Vendrow Edward , Vendrow Joshua , Schonfeld Elan
Published: April 2020

Identification and study of human-essential genes has become of practical importance with the realization that disruption or loss of nearby essential genes can introduce latent-vulnerabilities to cancer cells. Essential genes have been studied by copy-number-variants and deletion events, which are associated with introns. The premise of our work is that introns of essential genes have characteristic properties that are distinct from the introns of nonessential genes. We provide support for the existence of characteristic properties by training a deep learning model on introns of essential and nonessential genes and demonstrated that introns alone can be used to classify essential and nonessential genes with high accuracy (AUC of 0.846). We further demonstrated that the accuracy of the same deep-learning model limited to first introns will perform at an increased level, thereby demonstrating the critical importance of introns and particularly first introns in gene essentiality. Using a computational approach, we identified several novel properties of introns of essential genes, finding that their structure protects against deletion and intron-loss events, and that these traits are especially centered on the first intron. We showed that GC density is increased in the first introns of essential genes, allowing for increased enhancer activity, protection against deletions, and improved splice-site recognition. Furthermore, we found that first introns of essential genes are of remarkably smaller size than their nonessential counterparts, and to protect against common 3’ end deletion events, essential genes carry an increased number of (smaller) introns. To demonstrate the importance of the seven features we identified, we trained a feature–based model using only information from these features and achieved high accuracy (AUC of 0.787).
Granadaene Photobleaching Reduces the Virulence and Increases Antimicrobial Susceptibility ofStreptococcus agalactiae
Authors: Jusuf Sebastian , Dong Pu-Ting , Hui Jie , Ulloa Erlinda R. , Liu George Y. , Cheng Ji-Xin
Published: April 2020

Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is increasingly recognized as a major cause of soft tissue and invasive diseases in the elderly and diabetic populations. Antibiotics like penicillin are used with great frequency to treat these infections, although antimicrobial resistance is increasing among GBS strains and underlines a need for alternative methods not reliant on traditional antibiotics. GBS hemolysin/cytolysin and granadaene pigment are two major linked virulence factors that contribute to GBS pathogenicity. Here we show that photobleaching of the antioxidant granadaene renders the pathogen more susceptible to killing by mouse macrophages and to hydrogen peroxide killing. Photo-treatment also leads to loss of activity of the linked hemolysin/cytolysin although photobleaching disproportionally affected the activity of the two factors. Treatment with light also affected GBS membrane permeability and contribute to increased susceptibility to the cell membrane active antibiotic daptomycin and to penicillin. Overall our study demonstrates a dual effect of photobleaching on the virulence and antimicrobial susceptibility of GBS and suggests a novel approach for the treatment of GBS infection. Our findings further provide new insight on the relationship between GBS hemolysin and the granadaene pigment.

Importance

For elderly individuals or those with chronic underlying conditions (such as diabetes), skin infections caused byStreptococcus agalactiaerepresent a significant risk for the development of invasive disease.S. agalactiaestrains are becoming increasingly resistant to antibiotics. By utilizing blue light to neutralize the granadaene pigment present inS. agalactiae, this paper presents a non-invasive and non-antibiotic reliant process capable of reducing GBS virulence while increasing the antimicrobial susceptibility of the bacterium. The differential effect of blue light on the linked GBS hemolysin/cytolysin and granadene pigment further provides new insight on the relationship between the two virulence factors. Overall photo-treatment represents a novel strategy for the treatment ofS. agalactiaeinfections.
Genetic program activity delineates risk, relapse, and therapy responsiveness in Multiple Myeloma
Authors: Wall Matthew A. , Turkarslan Serdar , Wu Wei-Ju , Danziger Samuel A. , Reiss David J. , Mason Mike J. , Dervan Andrew P. , Trotter Matthew W.B. , Bassett Douglas , Hershberg Robert M. , de Lomana Adrián López García , Ratushny Alexander V. , Baliga Nitin S.
Published: April 2020

Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to their previous therapies. Although many therapies exist with diverse mechanisms of action, it is not yet clear how the differences in MM biology across patients impacts the likelihood of success for existing therapies and those in the pipeline. Therefore, we not only need the ability to predict which patients are at high risk for disease progression, but also a means to understand the mechanisms underlying their risk. We hypothesized that knowledge of the biological networks that give rise to MM, specifically the transcriptional regulatory network (TRN) and the mechanisms by which mutations impact gene regulation, would enable improved predictions of disease progression and actionable insights for treatment. Here we present a method to infer TRNs from multi-omics data and apply it to the generation of a MM TRN that links chromosomal abnormalities and somatic mutations to downstream effects on gene expression via perturbation of transcriptional regulators. We find that 141 genetic programs underlie the disease and that the activity profile of these programs fall into one of 25 distinct transcriptional states. These transcriptional signatures prove to be more predictive of outcomes than do mutations and reveal plausible mechanisms for relapse, including the establishment of an immuno-suppressive microenvironment. Moreover, we observe subtype-specific vulnerabilities to interventions with existing drugs and motivate the development of new targeted therapies that appear especially promising for relapsed refractory MM.
Two-Step Bacterial Artificial Chromosome (BAC) Engineering: Preparation of Shuttle Vector DNA
Authors: Heintz Nathaniel , Gong Shiaoching
Published: April 2020

In two-step bacterial artificial chromosome (BAC) engineering, a single plasmid is introduced into the BAC-carrying cell lines. The shuttle vector pLD53.SCAB (or pLD53.SCAEB) carries the recA gene and the R6Kγ origin, which requires the π protein to replicate. PIR2 cells, expressing π, are typically used for the amplification of the vector and maintain about 15 copies/cell of the donor vector, which is relatively stable in this host.
Structural characterization of human O-phosphoethanolamine phospho-lyase
Authors: Vettraino Chiara , Peracchi Alessio , Donini Stefano , Parisini Emilio
Published: April 2020

Human O-phosphoethanolamine phospho-lyase (hEtnppl; EC 4.2.3.2) is a pyridoxal 5′-phosphate-dependent enzyme that catalyzes the degradation of O-phosphoethanolamine (PEA) into acetaldehyde, phosphate and ammonia. Physiologically, the enzyme is involved in phospholipid metabolism, as PEA is the precursor of phosphatidylethanolamine in the CDP-ethanolamine (Kennedy) pathway. Here, the crystal structure of hEtnppl in complex with pyridoxamine 5′-phosphate was determined at 2.05 Å resolution by molecular replacement using the structure of A1RDF1 from Arthrobacter aurescens TC1 (PDB entry 5g4i) as the search model. Structural analysis reveals that the two proteins share the same general fold and a similar arrangement of active-site residues. These results provide novel and useful information for the complete characterization of the human enzyme.
Mechanism and quantitative evaluation model of slip-induced loosening for bolted joints
Authors: Sun Qingchao , Lin Qingyuan , Yang Bin , Zhang Xianlian , Wang Lintao
Published: April 2020

Purpose

Bolted joints are the most common type of mechanical connections, and improving the anti-loosening performance of bolts for the reliable performance of mechanical and building structures is highly significant.

Design/methodology/approach

Because of the lack of sufficient theoretical basis for the evaluation and design of anti-loosening bolts, a quantitative evaluation model exhibiting the following two evaluation criteria for anti-loosening bolts is introduced: bolt rotation angular acceleration criterion and critical transverse load criterion. Based on the relationship among bolt tension, transverse load and bolt rotation angular acceleration, a critical transverse load calculation model is put forward, and the mechanism by which the critical transverse load increases with the increase of bolt tension is revealed.

Findings

Based on the above model, a new type of anti-loosening bolt is designed, which generates additional bolt tension when the transverse load increases, and then improves the critical transverse load of the bolt. The effectiveness of the new type of anti-loosening bolt is verified by theoretical calculations and experiments.

Originality/value

The proposed model and method set a preliminary theoretical foundation for the evaluation of bolt anti-loosening performance and the design of a new anti-loosening bolt.
Unfurling the cultural value of street art experiences
Authors: Green Amelia , Gray Steffen
Published: April 2020

Purpose

The purpose of this paper is to begin unfurling the cultural value of street art experiences by opening up an audience-centred research stream sensitive to the nuances of this art form.

Design/methodology/approach

The paper develops a two-part model through which to investigate how everyday citizens experience street art. The methodology involves a purposeful literature review, and direct assessment of how the nuances of street art could pertain to audience experiences.

Findings

The first part of the model conceptualises the characteristics that distinguish contemporary street art from other art forms. To help further guide future research, the second part distinguishes six layers that frame street art audience experiences: (1) “the art”, (2) artist's intentions for the art, (3) the street artist, (4) experiential context, (5) social contexts and (6) audience interpretive lenses.

Research limitations/implications

The investigative model provides a constructive stimulus for substantive empirical inquiries into the dynamics, complexities and implications of everyday street art experiences.

Practical implications

The research stream developed could inform appropriate approaches to facilitating street art, and collaboration amongst street artists, facilitators, municipal representatives and policymakers.

Originality/value

The paper helps to open up an audience-centred approach to street art that intersects with recent developments in arts experience, cultural value and arts marketing.
Towards a spectacularly dynamic and pluralist “normal science”: pragmatism, communication, IMP and BtoB marketing research
Authors: Lowe Sid , Rod Michel , Hwang Ki-Soon
Published: April 2020

Purpose

The purpose of this paper is to promote the use of pragmatism within industrial marketing and purchasing (IMP), business-to-business (B2B)/network research with its enhanced emphasis on developing adaptable, workable solutions to practical problems. The usability of findings and the study produced means that implications and impact become a natural part of the research process rather than an afterthought concluding a research project. Although the reader might feel that the approach oscillates between viewing pragmatism in its everyday sense (through the use of terminology such as “a pragmatic approach […].,” the intent is to elevate the discussion to one where pragmatism is viewed as a guiding philosophy.

Design/methodology/approach

It blends literature review and conceptual contemplation and challenges convention by “reading against the grain” (Brown and Wijland, 2018).

Findings

The authors do this to challenge convention and advocate for pluralism and diversity, theoretical evolution based on empirical evidence and increased sensitivity to the critical role of discourse, semiotics and abduction as a catalyst between theory, method and empirical activities. This conceptual blending portrays “activities” and beliefs as mutually constituted through the symbolic mediation of rhetoric and discourse.

Research limitations/implications

Existing elements of American pragmatism and discourse are identified as already a tacit constituent of the IMP oeuvre. Combining these approaches more explicitly is advocated as a suitable basis for a potential future “IMP 3” research agenda with significant potentials afforded to IMP and B2B marketing research.

Originality/value

This paper contributes to the development and dissemination of alternative and critical perspectives in marketing theory. The implication is that activities must usually be justified by actors within communication as believable and this process always involves mixtures of rational and non-rational appeals. Existing elements of American pragmatism and discourse are identified as already a tacit constituent of the IMP oeuvre. Combining these approaches more explicitly is advocated as a suitable basis for a potential future “IMP 3” research agenda with significant potentials afforded to IMP and B2B marketing research.
FDI and tourism futures: a dynamic investigation for a panel of small island economies
Authors: Fauzel Sheereen
Published: April 2020

Purpose

Based on a panel vector error correction model (PVECM), this study aims to investigate the impact of foreign direct investment (FDI) on tourism development in a selected group of 17 small island economies during 1995-2018. In the long run, a positive and direct relationship was found between foreign investment and tourists’ arrival. Moreover, economic performance and tourists’ income were also found to be key determinants of tourism development. It is further observed that there is bidirectional causality between the two variables. Hence, one can argue that FDI is a key element for tourism development. So, if the countries can attract more FDI and grow economically, these elements will contribute positively to the sector in the future.

Design/methodology/approach

This work uses rigorous dynamic time series analysis, namely, a dynamic PVECM, which takes into account dynamism and endogeneity issues in tourism modelling. Furthermore, the PVECM is also appropriately suited for integrating short- and long-run analysis.

Findings

The results confirm that FDI has been an important ingredient in the tourism development of the island economies in the long run. Interestingly, a bidirectional causality between FDI and tourism development is validated. Moreover, growth will as well be important. So, if the country can attract more FDI and grow economically, these elements will attract the tourists of the future.

Originality/value

Relatively few studies have rigorously studied the relationships between FDI and tourism development, particularly with respect to developing countries and small island states which rely heavily on tourism as well as FDI. As such existing research has neglected dynamic and reverse causality analysis in their respective FDI-tourism modelling. This study thus attempts to address the above and supplement the literature by investigating the direct and indirect relationship between FDI and tourism development for the case of small island economies over the period 1995-2018. Moreover, the implication of foreign capital inflows on tourism futures will as well be developed.
Fabrication and characterization of mixed thin-/thick-film thermoelectric microgenerator based on constantan/chromium and silver arms
Authors: Gierczak Mirosław Gracjan , Prociów Eugeniusz , Dziedzic Andrzej
Published: April 2020

Purpose

This paper aims to focus on the fabrication and characterization of mixed thin-/thick-film thermoelectric microgenerators, based on magnetron sputtered constantan (copper–nickel alloy) and screen-printed silver. To improve the adhesion of the constantan layer to the applied substrates, the additional chromium sublayer was used. The aim of the study was to investigate the influence of chromium sublayer on the electrical and thermoelectric properties of such hybrid microgenerators.

Design/methodology/approach

Fabrication of such structures consisted of several steps – magnetron sputtering of the chromium and then constantan layer, exposing the first arms of thermocouples, applying the second arms by screen-printing technology and firing the prepared structures in a belt furnace. The structures were made both on Al2O3 (alumina) and low temperature co-fired ceramics (LTCC) substrates.

Findings

To the best of the authors’ knowledge, for the first time, laser ablation process was applied to fabricate the first arms of thermocouples from a layer of constantan only or constantan with a chromium sublayer. Geometric measurements have shown that the mapping of mask pattern by laser ablation technique is very accurate.

Originality/value

The determined Seebeck coefficient of the realized structures was about 40.4 µV/K. After firing the exemplary structures at 850°C peak temperature, Seebeck coefficient is increased to an average value of 51 µV/K.
Magnesium sulphate for fetal neuroprotection at imminent risk for preterm delivery: a systematic review with meta‐analysis and trial sequential analysis
Authors: Wolf HT , Huusom LD , Henriksen TB , Hegaard HK , Brok J , Pinborg A
Published: April 2020

Background

Ordinary meta‐analyses indicate that magnesium sulphate (MgSO4) treatment in women at imminent risk for preterm delivery decreases the offspring's risk of cerebral palsy (CP). However, repetitive testing of cumulative data calls for statistical caution, e.g. by trial sequential analysis (TSA), for which there are previously insufficient samples to draw a firm conclusion. Recently, a randomised controlled trial (RCT) provided additional data that potentially increased the sample size such that a new TSA might detect a statistically significant effect.

Objectives

To assess the possible fetal neuroprotective effect of MgSO4for women at imminent risk for preterm delivery in an updated systematic review with meta‐analysis and TSA.

Search strategy

We searched MEDLINE, Embase, Cochrane andClinicalTrials.govon 8 October 2019. The search strategy clustered terms describing the MgSO4intervention and preterm delivery.

Selection criteria

RCTs.

Data collection and analysis

Two reviewers extracted the data. Summary relative risks (RRs) and 95% confidence intervals (CIs) were calculated using fixed‐effects models. A TSA was applied to the primary outcome, CP. The quality of the evidence was assessed using GRADE. The protocol was registered in PROSPERO (registration: CRD42019151441).

Main results

We identified six eligible trials (5917 women). MgSO4intervention in women at imminent risk for preterm birth decreased the offspring's CP risk (meta‐analysis RR 0.68, 95% CI 0.54–0.85; TSA RR 0.69, 95% CI 0.48–0.97).

Conclusions

This systematic review with meta‐analysis and TSA shows conclusively that MgSO4, when given to women at imminent risk for preterm delivery, decreases the offspring's CP risk.

Tweetable abstract

Antenatal magnesium sulphate decreases the risk of cerebral palsy in children born preterm.
Phylogenetic and sequence analyses of insect transferrins suggest that only transferrin 1 has a role in iron homeostasis
Authors: Najera Diana G. , Dittmer Neal T. , Weber Jacob J. , Kanost Michael R. , Gorman Maureen J.
Published: April 2020

Iron is essential to life, but surprisingly little is known about how iron is managed in nonvertebrate animals. In mammals, the well‐characterized transferrins bind iron and are involved in iron transport or immunity, whereas other members of the transferrin family do not have a role in iron homeostasis. In insects, the functions of transferrins are still poorly understood. The goals of this project were to identify the transferrin genes in a diverse set of insect species, resolve the evolutionary relationships among these genes, and predict which of the transferrins are likely to have a role in iron homeostasis. Our phylogenetic analysis of transferrins from 16 orders of insects and two orders of noninsect hexapods demonstrated that there are four orthologous groups of insect transferrins. Our analysis suggests that transferrin 2 arose prior to the origin of insects, and transferrins 1, 3, and 4 arose early in insect evolution. Primary sequence analysis of each of the insect transferrins was used to predict signal peptides, carboxyl‐terminal transmembrane regions, GPI‐anchors, and iron binding. Based on this analysis, we suggest that transferrins 2, 3, and 4 are unlikely to play a major role in iron homeostasis. In contrast, the transferrin 1 orthologs are predicted to be secreted, soluble, iron‐binding proteins. We conclude that transferrin 1 orthologs are the most likely to play an important role in iron homeostasis. Interestingly, it appears that the louse, aphid, and thrips lineages have lost the transferrin 1 gene and, thus, have evolved to manage iron without transferrins.
Synthesis of triethylene tetramine–modified water‐insoluble corn flour caged in magnetic chitosan resin and its adsorption application for removal of patulin from apple juice
Authors: Guo Caixia , Han Li , Guo Meng , Li Meiping , Yu Ligang , Yang Yukun
Published: April 2020

In this study, triethylene tetramine–modified water‐insoluble corn flour caged in magnetic chitosan resin (TETA‐WICF/MCR) was firstly prepared, which indicates novel aspects for immobilization and chemically modification of mycotoxin adsorbents. The TETA‐WICF/MCR was characterized using zoom stereo microscope, scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, X‐ray diffractometer (XRD), and magnetic separation performance analysis. Experimental results confirmed successful layer by layer modification of chitosan, biosorbent water‐insoluble corn flour (WICF), TETA onto the surface of magnetic beads. The mean diameter of the TETA‐WICF/MCR was 2.63 mm with good magnetic‐responsive ability. Subsequently, the adsorption performance of the TETA‐WICF/MCR obtained toward patulin was assessed in batch adsorption system and the results demonstrated that the adsorption process was strongly depended on adsorbent dosage, contact time, temperature, and initial patulin concentration. The results of SEM images and FTIR analysis showed obvious changes in the porous structure of TETA‐WICF/MCR after adsorbing patulin, and ‐NH2 and ‐OH groups were predominantly involved in the adsorption of patulin. Furthermore, the adsorption kinetics followed the mechanism of pseudo‐second‐order model, and equilibrium data were well fitted in the Freundlich isotherm model. It was also found that the TETA‐WICF/MCR had good reusability without any adverse changes in apple juice.

Practical Application

Patulin is a regulated toxin biosynthesized by certain fungi that contaminate agricultural commodities, such as fruits, juices, and other beverages. Several approaches have been studied to reduce patulin levels in apple juice and other aqueous systems. There is need for more low‐cost and eco‐friendly adsorbent capable of detoxifying patulin contaminated. In this sense, triethylene tetramine–modified water‐insoluble corn flour caged in magnetic chitosan resin (TETA‐WICF/MCR) was first prepared and exhibits easy solid–liquid separation and high adsorption capacity for removing patulin from contaminated apple juice.
The association between arterial pulse waveform analysis device and in‐hospital mortality in high‐risk non‐cardiac surgeries
Authors: Takeda Chikashi , Takeuchi Masato , Mizota Toshiyuki , Yonekura Hiroshi , Nahara Isao , Joo Woo J. , Dong Li , Kawasaki Yohei , Kawakami Koji
Published: April 2020

Background

Perioperative goal‐directed fluid therapy is used for haemodynamic optimization in high‐risk surgeries. Cardiac output monitoring can be performed by a specialized pressure transducer for arterial pulse waveform analysis (S‐APWA). No study has assessed whether real‐world use of S‐APWA is associated with post‐operative outcomes; therefore, using a Japanese administrative claims database, we retrospectively investigated whether S‐APWA use is associated with in‐hospital mortality among patients undergoing high‐risk surgery under general anaesthesia.

Methods

Adult patients who underwent high‐risk surgery under general anaesthesia and arterial catheterization between 2014 and 2016 were divided into S‐APWA and conventional arterial pressure transducer groups, then compared regarding baseline factors and outcomes. Logistic regression analysis was performed to compare in‐hospital mortality. Subgroup analyses evaluated S‐APWA efficacy and outcomes based on the type of surgery and patients’ comorbidity.

Results

S‐APWA was used in 6859 of 23 655 (29.0%) patients; the crude in‐hospital mortality rate was 3.5%. Adjusted analysis showed no significant association between S‐APWA use and in‐hospital mortality rate (adjusted odds ratio [aOR] = 0.91; 95% confidence interval [CI]: 0.76‐1.07; P = .25). S‐APWA use was associated with significantly lower in‐hospital mortality in patients undergoing vascular surgery (aOR = 0.67; 95% CI: 0.49‐0.94), and significantly higher in‐hospital mortality in patients undergoing lower limb amputation (aOR = 2.63; 95% CI: 1.32‐5.22). S‐APWA use and in‐hospital mortality were not significantly associated with other subgroups.

Conclusion

S‐APWA use was not associated with in‐hospital mortality in the entire study population. However, S‐APWA was associated with decreased in‐hospital mortality among vascular surgery and increased in‐hospital mortality among lower limb amputation.
Distribution and abundance of large herbivores in a northern Australian tropical savanna: A multi‐scale approach
Authors: Reid Angela M. , Murphy Brett P. , Vigilante Tom ,   Wunambal Gaambera Aboriginal Corporation, Bowman David M. J. S.
Published: April 2020

Australian mammals have exhibited exceptionally high rates of decline since European settlement 230 years ago with much focus on small mammals in northern tropical savannas. In these systems, little scientific attention has been given to the suite of grazing macropods, family Macropodidae, (common wallaroo (Osphranter robustus), antilopine wallaroo (O. antilopinus) and agile wallaby (Notamacropus agilis)). These species may be impacted by feral herbivores and contemporary fire regimes, two threats linked to small mammal declines. A multi‐scale approach using aerial surveys, road surveys and camera trapping was utilised to determine the effects of feral cattle and fire on the distribution and abundance of large macropods in the North Kimberley bioregion. Feral cattle density and biomass exceeded that of macropods regardless of survey technique. Density estimates for cattle were up to 125 times higher (0.3–10.0 km−2) than estimates for macropods (0.08–0.49 km−2). Cattle biomass, based on the aerial survey estimates (corrected for perception bias), were 15 and 95 times higher than macropods for infertile (279 vs. 19 kg km−2) and fertile savannas (518 vs. 5 kg km−2), respectively. Proximity to the nearest pastoral station was a significant predictor of the aerial sightings of feral cattle (P ≤ 0.05). Abundance and foraging activity of cattle were positively associated (P ≤ 0.05) with recently burnt areas. In contrast, camera trapping showed agile wallaby and wallaroo occurrence and foraging were associated with longer unburnt areas (P ≤ 0.05). Agile wallaby and wallaroo were negatively associated with cattle (P ≤ 0.05) and showed substantial diurnal and seasonal separation consistent with an antagonistic interspecific interaction. Results also suggest that the agile wallaby is the primary prey of the dingo, not wallaroo. Collectively, this study suggests that recent landscape changes such as altered fire regimes and introduced herbivores have negatively impacted large grazing macropod species.
Structural and ultrastructural characteristics of the tongue of the Collared Peccary (Pecari tajacu, Linnaeus, 1758)
Authors: Barbosa Gabriela Klein , dos Santos Jacob Carolina , Pimentel Neto Jurandyr , de Oliveira Moacir Franco , Rici Rose Eli Grassi , Watanabe Ii‐Sei , Ciena Adriano Polican
Published: April 2020

The tongue is an important organ in species due to its feeding functions, and its structure is influenced by the habitat and diet. The Collared Peccary (Pecari tajacu, Linnaeus, 1758) is a terrestrial mammal that is distributed on the American continents and has an omnivorous diet. This study aimed to describe the morphological characteristics of the tongue, lingual papillae and the connective tissue cores (CTCs) of the Collared Peccary. Eight tongues were collected from the Wild Animals Multiplication Center. The samples (n = 6) were processed for three‐dimensional analysis of their dorsal epithelium, and their CTCs by scanning electron microscopy and the other samples (n = 2) were used to observe ultrastructural characteristics by transmission electron microscopy. Filiform papillae were observed in the lingual apex and body with their conical CTC demonstrating ripples in their extent. Two types of fungiform papillae were observed, the first in the apex and body with a dome‐shaped CTC and the second forming a dorsolateral line with a radial pattern CTC. The vallate papillae were bilateral in the caudal region with the CTCs, characterised by numerous projections, and foliate papilla were not observed. We found a new type of papilla anteriorly to the vallate papilla with an irregular groove and a CTC formed by triangular‐shaped projections with a duct opening at the top. We concluded that the lingual papillae of the Collared Peccary resemble those papillae of other mammals, however, were revealed another form of their CTCs and a new lingual papillae morphological description.
Distribution of dendritic cells in the septate uterus: An immunological perspective
Authors: Negishi Yasuyuki , Kato Masahiko , Ono Shuichi , Kuwabara Yoshimitsu , Morita Rimpei , Takahashi Hidemi , Takeshita Toshiyuki
Published: April 2020

Problem

Septate uterus is associated with spontaneous abortion. Surgical intervention of the uterine septa (US) is frequently performed following spontaneous abortion; however, immunological mechanisms for spontaneous abortion in patients with septate uterus remain completely unknown.

Method of study

A total of 12 women with septate uterus who underwent hysteroscopic metroplasty and 10 women with uterine leiomyoma who underwent total hysterectomy were enrolled as the experimental and control groups, respectively. Immune cells, dendritic cells (DCs), macrophages, T cells, natural killer cells, invariant natural killer cells, and chemokine receptors in US and uterine myometrium tissue (UMT) were analyzed using flow cytometry and immunohistochemical staining. Additionally, the chemokine production of macrophage inflammatory protein 1 alpha (MIP‐1α), regulated upon activation normal T‐cell express sequence (RANTES), and macrophage inflammatory protein 3 beta (MIP‐3β) from the viable cells obtained from the US and UMT samples was evaluated in an ex vivo study.

Results

The percentage of CD141+ DCs in US was significantly lower than that in UMT. Both US and UMT showed CCR1 and CCR5 expression on CD141+ DCs; however, the production of chemokines, MIP‐1α, RANTES, and MIP‐3β was abundant in UMT‐obtained viable cells.

Conclusion

The accumulation of CD141+ DCs was lower in US than that in UMT. This phenomenon may be caused by low chemokine productions in US. Our findings support the benefit of surgical intervention for septate uterus—that is, the elimination of inappropriate implantation sites.
Tofacitinib for ulcerative colitis: results of the prospective Dutch Initiative on Crohn and Colitis (ICC) registry
Authors: Biemans Vince B. C. , Sleutjes Jasmijn A. M. , de Vries Annemarie C. , Bodelier Alexander G. L. , Dijkstra Gerard , Oldenburg Bas , Löwenberg Mark , van Bodegraven Adriaan A. , van der Meulen‐de Jong Andrea E. , de Boer Nanne K. H. , Srivastava Nidhi , West Rachel L. , Römkens Tessa E. H. , Horjus Talabur Horje Carmen S. , Jansen Jeroen M. , van der Woude C. Janneke , Hoekstra Jildou , Weersma Rinse K. , van Schaik Fiona D. M. , Hoentjen Frank , Pierik Marieke J. ,   the Dutch Initiative on Crohn and Colitis (ICC)
Published: April 2020

Background

Tofacitinib is a Janus kinase inhibitor approved for the treatment of ulcerative colitis (UC).

Aim

To evaluate effectiveness, safety and use of tofacitinib in daily practice.

Methods

UC patients initiating tofacitinib were prospectively enrolled in 15 hospitals in the Netherlands. Corticosteroid‐free clinical remission (short clinical colitis activity index [SCCAI] ≤2), biochemical remission (faecal calprotectin level ≤250 µg/g), combined corticosteroid‐free clinical and biochemical remission, predictors of remission, safety outcomes, treatment dose and effect on lipids were determined at weeks 12 and 24. Endoscopic outcomes were evaluated in centres with routine endoscopic evaluation.

Results

In total, 123 UC patients (95% anti‐TNF, 62% vedolizumab and 3% ustekinumab experienced) were followed for a median duration of 24 weeks (interquartile range 12‐26). The proportion of patients in corticosteroid‐free clinical, biochemical, and combined corticosteroid‐free clinical and biochemical remission rate at week 24 was 29% (n: 22/77), 25% (n: 14/57), and 19% (n: 11/57) respectively. Endoscopic remission (Mayo = 0) was achieved in 21% of patients at week 12 (n: 7/33). Prior vedolizumab exposure was associated with reduced clinical remission (odds ratio 0.33, 95% confidence interval [CI] 0.11‐0.94). At week 24, 33% (n: 14/42) of patients still on tofacitinib treatment used 10 mg twice daily. In total, 33 tofacitinib‐related adverse events (89 per 100 patient years) occurred, 7 (6% of total cohort) resulted in discontinuation. Cholesterol, HDL and LDL levels increased during induction treatment by 18% (95% CI 9‐26), 18% (95% CI 8‐28) and 21% (95% CI 14‐39) respectively.

Conclusion

Tofacitinib is an effective treatment for UC after anti‐TNF and vedolizumab failure. However, a relatively high rate of adverse events was observed resulting in discontinuation in 6% of patients.
Some days are more satisfying than others: A daily‐diary study on optimism, pessimism, coping, and academic satisfaction
Authors: Boileau Laurence , Gaudreau Patrick , Gareau Alexandre , Chamandy Melodie
Published: April 2020

Background

Feelings of satisfaction fluctuate across time and situations, and focusing on within‐person experiences opens up the door to a better understanding of the daily lives of university students.

Aims

Our overarching goal was to situate academic satisfaction not only as a relatively enduring characteristic but also as a transient state that fluctuates across days in the lives of student. In the present study, we explored how optimism and pessimism related to inter‐individual differences in academic satisfaction. We also investigated the association between coping and academic satisfaction at both the between‐ and within‐person levels.

Sample

A sample of 235 undergraduate students (Mage = 19.14) participated in this study.

Method

Students completed baseline measures of optimism and pessimism. They were then asked to complete daily‐diary measures of academic coping strategies and academic satisfaction during six consecutive days.

Results

At the between‐person level, results from multilevel mediation analyses demonstrated that optimism was associated with greater academic satisfaction and that task‐oriented coping was a significant mediator of this association. At the within‐person level, our analyses revealed that the daily satisfaction of students varies according to the coping strategies used on those specific days. Almost half of the variance in academic satisfaction can be attributable to daily fluctuations.

Conclusions

This source of within‐person variance is non‐negligible and supports the need to also conceive academic satisfaction as a question of when. These findings illustrate the importance of considering the role of personality and daily coping to better conceptualize and understand academic satisfaction of university students.
Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere
Authors: Sutherland Ben J. G. , Rycroft Claire , Ferchaud Anne‐Laure , Saunders Rob , Li Li , Liu Sheng , Chan Amy M. , Otto Sarah P. , Suttle Curtis A. , Miller Kristina M.
Published: April 2020

Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self‐sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery‐farmed) or naturalized/wild oysters to move onto a farm (naturalized‐farmed). It is therefore important to understand genetic variation among populations and farm types. Here, we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double‐digest RAD‐sequencing in 182 naturalized, 112 hatchery‐farmed, and 72 naturalized‐farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean FST = 0.0019) and low differentiation between countries in the Japan–Canada–France historical translocation lineage (France–Canada FST = 0.0024; Japan–Canada FST = 0.0060). Chinese populations were more differentiated (China–Japan FST = 0.0241). Hatchery‐propagated populations had higher interindividual relatedness suggesting family structure. Within‐population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were lower in one farm population. Moving oysters from nature onto farms did not result in strong within‐generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting nonlocal origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery‐farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.
Geomorphological features drive spatiotemporal dynamics of young‐of‐the‐year brown trout populations in a large New Zealand river catchment
Authors: Mikheev Pavel B. , Jarvis Matt G. , Matthaei Christoph D. , Ingram Travis , Nikiforov Andrey I. , Closs Gerard P.
Published: April 2020

Determining the factors driving population dynamics of stream salmonids across broad landscapes is important for understanding stream ecosystem functioning and for the management and conservation of the populations of such fish. A few studies have described the determinants of the early life history of salmonids across catchments, but none of them have examined how this spatial variation develops temporally.

We hypothesised that: (1) spatiotemporal dynamics of young‐of‐the‐year (YoY) trout populations vary within the catchment, with loss rates (emigration plus mortality) being higher in lower elevation, downstream reaches than in higher elevation, upstream ones; and (2) loss rate would be density dependent, leading to reduced intra‐ and inter‐cohort competition and supporting establishment of resident populations.

We tested the first hypothesis by examining relationships between geomorphic characteristics of spawning streams and temporal dynamics of YoY brown trout density, loss rate and biological traits through an austral summer across the catchment of New Zealand's fourth‐longest river, the Taieri River. To test the second hypothesis, we examined whether initial YoY density in spring and other biotic determinants affected loss rate and cohort structure dynamics, resulting in density‐dependent self‐thinning of YoY fish to avoid resource limitation.

Spring YoY density and subsequent loss rate was higher in low elevation sites, corresponding to stream accessibility to migratory spawners. These significant correlations of YoY density and related biotic variables with elevation disappeared later in the season, indicating that regardless of their origin, brown trout YoY tend to form stream resident populations with multicohort structure and densities low enough to limit intraspecific competition.

Our findings provide evidence that geomorphological features of the landscape affect temporal dynamics of YoY trout populations driven by density‐dependent self‐regulatory mechanisms that can control the abundance of growing fish.
Climate and local environment structure asynchrony and the stability of primary production in grasslands
Authors: Gilbert Benjamin , MacDougall Andrew S. , Kadoya Taku , Akasaka Munemitsu , Bennett Joseph R. , Lind Eric M. , Flores‐Moreno Habacuc , Firn Jennifer , Hautier Yann , Borer Elizabeth T. , Seabloom Eric W. , Adler Peter B. , Cleland Elsa E. , Grace James B. , Harpole William Stanley , Esch Ellen H. , Moore Joslin L. , Knops Johannes , McCulley Rebecca , Mortensen Brent , Bakker Jonathan , Fay Philip A.
Published: April 2020

Aim

Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when a decrease in performance by some species is offset by an increase in performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species that reduce buffering. Local conditions, such as soil nutrients, can also alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling experiment.

Location

Grasslands in North America, Europe and Australia.

Time period

Annual surveys over 5 year intervals occurring between 2007 and 2014.

Major taxa studied

Herbaceous plants.

Methods

We sampled annually the per species cover and aboveground community biomass [net primary productivity (NPP)], plus soil chemical properties, in 29 grasslands. We tested how soil conditions, combined with variability in precipitation and temperature, affect species richness, asynchrony and temporal stability of primary productivity. We used bivariate relationships and structural equation modelling to examine proximate and ultimate relationships.

Results

Climate variability strongly predicted asynchrony, whereas NPP stability was more related to soil conditions. Species richness was structured by both climate variability and soils and, in turn, increased asynchrony. Variability in temperature and precipitation caused a unimodal asynchrony response, with asynchrony being lowest at low and high climate variability. Climate impacted stability indirectly, through its effect on asynchrony, with stability increasing at higher asynchrony owing to lower inter‐annual variability in NPP. Soil conditions had no detectable effect on asynchrony but increased stability by increasing the mean NPP, especially when soil organic matter was high.

Main conclusions

We found globally consistent evidence that climate modulates species asynchrony but that the direct effect on stability is low relative to local soil conditions. Nonetheless, our observed unimodal responses to variability in temperature and precipitation suggest asynchrony thresholds, beyond which there are detectable destabilizing impacts of climate on primary productivity.