bluuebunny/crossref_metadata_2025 huggingface dataset:
MinION barcodes: biodiversity discovery and identification by everyone, for everyone
Authors: Srivathsan Amrita , Lee Leshon , Katoh Kazutaka , Hartop Emily , Kutty Sujatha Narayanan , Wong Johnathan , Yeo Darren , Meier Rudolf
Published: March 2021

Background

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via “innovation through subtraction” and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to <10 cents, and allows fast turnaround from specimen to sequence by using the portable, real-time sequencer MinION.

Results

We describe cost-effective and rapid procedures for barcoding individual specimens with MinION sequencing. We illustrate how tagged amplicons can be obtained and sequenced with the portable, real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells (“R10.3”) which suggest that each run can generate barcodes for >10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (>99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018.

Conclusions

We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle (“Flongle”) while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
Establishing farm dust as a useful viral metagenomic surveillance matrix
Authors: Kwok Kirsty T. T. , de Rooij Myrna M. T. , Messink Aniek B. , Wouters Inge M. , Smit Lidwien A. M. , Cotten Matthew , Heederik Dick J.J. , Koopmans Marion P. G. , Phan My V. T.
Published: March 2021

Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data,ParvoviridaeandPicornaviridaewere the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from thePicornaviridae. Sequences from theCaliciviridaeandAstroviridaefamiles were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
A Focused Small-Molecule Screen Identifies PHA-680626 as an Amphosteric Inhibitor Disrupting the Interaction between Aurora-A and N-Myc
Authors: Souvalidou Fani , Boi Dalila , Montanari Roberta , Polverino Federica , Marini Grazia , Capelli Davide , Pochetti Giorgio , Contestabile Roberto , Trisciuoglio Daniela , Tramonti Angela , Carpinelli Patrizia , Ascanelli Camilla , Lindon Catherine , De Leo Alessandro , Di Santo Roberto , Costi Roberta , Guarguaglini Giulia , Paiardini Alessandro
Published: March 2021

Neuroblastoma is a severe childhood disease, accounting for ~10% of all infant cancers. The amplification of the MYCN gene, coding for the N-Myc transcriptional factor, is an essential marker correlated with tumor progression and poor prognosis. In neuroblastoma cells, the mitotic kinase Aurora-A (AURKA), also frequently overexpressed in cancer, prevents N-Myc degradation, by directly binding to a highly conserved N-Myc region, i.e. Myc Box I. As a result, elevated levels of N-Myc, which are required for the growth of MYCN amplified cells, are observed. During the last years, it has been demonstrated that the ATP competitive inhibitors of AURKA CD532, MLN8054 and Alisertib also cause essential conformational changes in the structure of the activation loop of the kinase that prevent N-Myc binding, thus impairing the formation of the AURKA/N-Myc complex. In this study, starting from a screening of crystal structures of AURKA in complex with known inhibitors, we identified additional compounds affecting the conformation of the kinase activation loop. We assessed the ability of such compounds to disrupt the interaction between AURKA and N-Mycin vitro, using Surface Plasmon Resonance competition assays, and in tumor cell lines overexpressing MYCN, by performing Proximity Ligation Assays. Finally, their effects on N-Myc cellular levels and cell viability were investigated. Our results, identifying PHA-680626 as an amphosteric inhibitor bothin vitroand MYCN overexpressing cell lines, expand the repertoire of known conformational disrupting inhibitors of the AURKA/N-Myc complex, and confirm that altering the conformation of the activation loop of AURKA with a small molecule is an effective strategy to destabilize the AURKA/N-Myc interaction in neuroblastoma cancer cells.
PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools
Authors: Pockrandt Christopher , Steinegger Martin , Salzberg Steven L.
Published: March 2021

PhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments. It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF/GTF files using precomputed tracks or computes and scores multiple sequence alignments on the fly with MMseqs2.

Availability

PhyloCSF++ is released under the AGPLv3 license. Binaries and source code are available athttps://github.com/cpockrandt/PhyloCSFpp. The software can be installed through bioconda. A variety of tracks can be accessed throughftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/.

Contact

pockrandt@jhu.edu,martin.steinegger@snu.ac.kr
Tight junction ZO proteins maintain tissue fluidity, ensuring efficient collective cell migration
Authors: Skamrahl Mark , Pang Hongtao , Ferle Maximilian , Gottwald Jannis , Rübeling Angela , Maraspini Riccardo , Honigmann Alf , Oswald Tabea A. , Janshoff Andreas
Published: March 2021

Tight junctions are essential components of epithelial tissues connecting neighboring cells to provide protective barriers. Albeit their general function to seal compartments is well understood, their role in collective cell migration is largely unexplored. Here, the importance of the tight junction proteins ZO1 and ZO2 for epithelial migration is investigated employing video microscopy in conjunction with velocimetry, segmentation, cell tracking, and atomic force microscopy/spectroscopy. The results indicate that ZO proteins are necessary for fast and coherent migration. In particular, ZO1 and 2 loss (dKD) induces actomyosin remodeling away from the central cortex towards the periphery of individual cells, resulting in altered viscoelastic properties. A tug-of-war emerges between two subpopulations of cells with distinct morphological and mechanical properties: 1) smaller and highly contractile cells with an outward-bulged apical membrane, and 2) larger, flattened cells, which, due to tensile stress, display a higher proliferation rate. In response, the cell density increases, leading to crowding-induced jamming and more small cells over time. Co-cultures comprising wildtype and dKD cells display phase separation based on differences in contractility rather than differential adhesion. This study shows that ZO proteins are necessary for efficient collective cell migration by maintaining tissue fluidity and controlling proliferation.
Lamb1a regulates atrial growth by limiting excessive, contractility-dependent second heart field addition during zebrafish heart development
Authors: Derrick Christopher J. , Pollitt Eric J. G. , Uruchurtu Ashley Sanchez Sevilla , Hussein Farah , Noёl Emily S.
Published: March 2021

During early vertebrate heart development, the heart transitions from a linear tube to a complex asymmetric structure. This process includes looping of the tube and ballooning of the emerging cardiac chambers, which occur simultaneously with growth of the heart. A key driver of cardiac growth is deployment of cells from the Second Heart Field (SHF) into both poles of the heart, with cardiac morphogenesis and growth intimately linked in heart development. Laminin is a core component of extracellular matrix (ECM) basement membranes, and although mutations in specific laminin subunits are linked with a variety of cardiac abnormalities, including congenital heart disease and dilated cardiomyopathy, no role for laminin has been identified in early vertebrate heart morphogenesis. We identified dynamic, tissue-specific expression of laminin subunit genes in the developing zebrafish heart, supporting a role for laminins in heart morphogenesis.lamb1amutants exhibit cardiomegaly from 2dpf onwards, with subsequent progressive defects in cardiac morphogenesis characterised by a failure of the chambers to compact around the developing atrioventricular canal. We show that loss oflamb1aresults in excess addition of SHF cells to the atrium, revealing that Lamb1a functions to limit heart size during cardiac development by restricting SHF addition to the venous pole.lamb1amutants exhibit hallmarks of altered haemodynamics, and specifically blocking cardiac contractility inlamb1amutants rescues heart size and atrial SHF addition. Furthermore, we identify that FGF and RA signalling, two conserved pathways promoting SHF addition, are regulated by heart contractility and are dysregulated inlamb1amutants, suggesting that laminin mediates interactions between SHF deployment, heart biomechanics, and biochemical signalling during heart development. Together, this describes the first requirement for laminins in early vertebrate heart morphogenesis, reinforcing the importance of specialised ECM composition in cardiac development.
Shank3 influences mammalian sleep development
Authors: Medina Elizabeth , Schoch Hannah , Wintler Taylor , Ford Kaitlyn , Singletary Kristan G. , Peixoto Lucia
Published: March 2021

Sleep problems are prevalent in Autism Spectrum Disorder (ASD), can be observed before diagnosis, and are associated with increased restricted and repetitive behaviors. Therefore, sleep abnormalities may be a core feature of the disorder, but the developmental trajectory remains unknown. Animal models provide a unique opportunity to understand sleep ontogenesis in ASD. Previously we showed that adult mice with a truncation in the high-confidence ASD geneShank3(Shank3ΔC) recapitulate the clinical sleep phenotype. In this study we used longitudinal electro-encephalographic (EEG) recordings to define, for the first time, changes in sleep from weaning to young adulthood in an ASD mouse model. We show that Shank3ΔCmice sleep less overall throughout their lifespan, have increased rapid eye movement (REM) sleep early in life despite significantly reduced non-rapid eye movement (NREM) sleep, and have abnormal responses to increased sleep pressure that emerge during a specific developmental period. We demonstrate that the ability to fall asleep quickly in response to sleep loss develops normally between 24 and 30 days in mice. However, mutants are unable to reduce sleep latency after periods of prolonged waking and maintain the same response to sleep loss regardless of age. This phenomenon seems independent of homeostatic NREM sleep slow-wave dynamics. Overall, our study recapitulates both preclinical models and clinical studies showing that reduced sleep is consistently associated with ASD and suggests that problems falling asleep may reflect abnormal development of sleep and arousal mechanisms.

SIGNIFICANCE STATEMENT

In this first longitudinal sleep study in an Autism mouse model, we demonstrate that sleeping less seems a core feature of the disorder while problems falling asleep emerge during development.
A photoswitchable helical peptide with light-controllable interface / transmembrane topology in lipidic membranes
Authors: Gutiérrez-Salazar Mónica , Santamaría-Aranda Eduardo , Schaar Louise , Salgado Jesús , Sampedro Diego , Lorenz-Fonfria Victor A.
Published: March 2021

According to the three-step model, the spontaneous insertion and folding of helical transmembrane (TM) polypeptides into lipid bilayers is driven by three sequential equilibria: solution-to-membrane interface (MI) partition, unstructured-to-helical folding, and MI-to-TM helix insertion. However, understanding these three steps with molecular detail has been challenged by the lack of suitable experimental approaches to rapidly and reversibly perturb membrane-bound hydrophobic polypeptides out of equilibrium. Here, we report on a 24-residues-long hydrophobic α-helical polypeptide, covalently coupled to an azobenzene photoswitch (KCALP-azo), which displays a light-controllable TM/MI equilibrium in hydrated lipid bilayers. FTIR spectroscopy shows that dark-adapted KCALP-azo (transazobenzene) folds as a TM α-helix, with its central TM region displaying an average tilt of 36 ± 4° with the membrane normal (TM topology). Aftertrans-to-cisphotoisomerization of the azobenzene moiety with UV light (reversed with blue light), spectral changes by FTIR spectroscopy indicate that the helical structure of KCALP-azo is maintained but the peptide experiences a more polar environment. Interestingly, pH changes induced similar spectral alterations in the helical peptide LAH4, with a well-characterized pH-dependent TM/MI equilibrium. Polarized experiments confirmed that the membrane topology of KCALP-azo is altered by light, with its helix tilt changing reversibly from 32 ± 5° (TM topology, blue light) to 79 ± 8° (MI topology, UV light). Further analysis indicates that, while thetransisomer of KCALP-azo is ~100% TM, thecisisomer exists in a ~90% TM and ~10% MI mixture. Strategies to further increase the perturbation of the TM/MI equilibrium with the light are briefly discussed.
Differential expression of H2A isoforms contribute to tissue and lineage specificity with HIST2H2AC as a potential cancer biomarker
Authors: Girish Shah Sanket , Rashid Mudasir , Natu Abhiram , Gupta Sanjay
Published: March 2021

Recent advancements in the field of histone biology imply non-redundancy in the function of histone H2A isoforms; however, the expression of H2A isoforms in various normal tissue types, the correlation among organs and tumor/tumor type-specific expression remain poorly investigated. The profiling of sixteen H2A isoforms in eleven different normal human tissue types strongly suggests their tissue-specific or predominant expression. Further, clustering analysis shows a lineage-specific correlation of H2A isoforms. In continuation, the expression analysis in twelve human tumor types shows overexpression of HIST2H2AC. Moreover, overexpression was observed exclusively in tumor samples but not with fetal samples; highlighting the cancer-specific association of HIST2H2AC. Further,in silicoanalysis of TCGA pan-cancer data also showed tumor-specific over-expression of the HIST2H2AC isoform. Our findings provide insights into tissue-type-specificity of histone H2A isoforms expression patterns and advance our understanding of their importance in lineage specification and cancer.
Neural Basis of the Delayed Gratification
Authors: Gao Zilong , Wang Hanqing , Lu Chen , Froudist-Walsh Sean , Chen Ming , Wang Xiao-jing , Hu Ji , Sun Wenzhi
Published: March 2021

Balancing instant gratification versus delayed, but better gratification is important for optimizing survival and reproductive success. Although psychologists and neuroscientists have long attempted to study delayed gratification through human psychological and brain activity monitoring, and animal research, little is known about its neural basis. We successfully trained mice to perform a waiting-and-water-reward delayed gratification task and used these animals in physiological recording and optical manipulation of neuronal activity during the task to explore its neural basis. Our results showed that the activity of DA neurons in ventral tegmental area (VTA) increases steadily during the waiting period. Optical activation vs. silencing of these neurons, respectively, extends or reduces the duration of waiting. To interpret this data, we developed a reinforcement learning (RL) model that reproduces our experimental observations. In this model, steady increases in DAergic activity signal the value of waiting and support the hypothesis that delayed gratification involves real-time deliberation.

TEASER

Sustained ramping dopaminergic activation helps individuals to resist impulsivity and wait for laerger but later return.
Post-transcriptional regulation of glutamate metabolism ofPichia pastorisand development of a glutamate-inducible yeast expression system
Authors: Dey Trishna , Rangarajan Pundi N
Published: March 2021

Pichia pastorisharbours a unique glutamate utilization pathway in which glutamate dehydrogenase 2 (GDH2), aspartate aminotransferase 2 (AAT2) and phosphoenolpyruvate carboxykinase (PEPCK) catalyze the conversion of glutamate to α-ketoglutarate, oxaloacetate, and phosphoenolpyruvate respectively in the cytosol. GDH2 and PEPCK are glutamate-inducible enzymes and their synthesis is regulated post-transcriptionally by Rtg1p, a cytosolic basic helix-loop-helix protein via Rtg1p response elements located downstream of TATA box ofGDH2andPEPCKpromoters. Glutamate-inducible synthesis of PEPCK is abrogated inΔgdh2andΔaat2. α-ketoglutarate induces PEPCK synthesis inΔgdh2but notΔaat2. We propose that oxaloacetate derived from glutamate is the inducer of PEPCK synthesis. Enzymes of glutamate utilization pathway are synthesized during carbon starvation and they enableP. pastoristo overcome nutritional stress. Finally, green fluorescent protein can be synthesized efficiently fromGDH2andPEPCKpromoters using food-grade monosodium glutamate as inducer indicating that the post-transcriptional regulatory circuit described here can be exploited for the development of glutamate-inducibleP. pastorisexpression system.
Excitatory postsynaptic calcium transients at Aplysia sensory-motor neuron synapses allow for quantal examination of synaptic strength over multiple days in culture
Authors: Dunn Tyler W , Sossin Wayne S
Published: March 2021

The ability to monitor changes in strength at individual synaptic contacts is required to test the hypothesis that specialized synapses maintain changes in synaptic strength that underlie memory. Measuring excitatory post-synaptic calcium transients through calcium permeable AMPA receptors is one way to monitor synaptic strength at individual synaptic contacts. Using a membrane targeted genetic calcium sensor, we demonstrate that one can measure synaptic events at individual synaptic contacts in Aplysia sensory-motor neuron synapses. These results show that synaptic strength is not evenly distributed between all contacts in these cultures, but dominated by multiquantal sites of synaptic contact. The probability, quantal size and quantal content can be measured over days at individual synaptic contacts using this technique. Surprisingly, most synaptic contacts were not found opposite presynaptic varicosities, but instead at areas of pre- and post-synaptic contact with no visible thickening of membranes. This technique shows promise in being able to address whether specialized synapses maintain synaptic strength underlying memory.
Data-Driven Network Models for Genetic Circuits From Time-Series Data with Incomplete Measurements
Authors: Yeung Enoch , Kim Jongmin , Yuan Ye , Gonçalves Jorge , Murray Richard M.
Published: March 2021

Synthetic gene networks are frequently conceptualized and visualized as static graphs. This view of biological programming stands in stark contrast to the transient nature of biomolecular interaction, which is frequently enacted by labile molecules that are often unmeasured. Thus, the network topology and dynamics of synthetic gene networks can be difficult to verifyin vivoorin vitro, due to the presence of unmeasured biological states. Here we introduce the dynamical structure function as a new mesoscopic, data-driven class of models to describe gene networks with incomplete measurements. We introduce a network reconstruction algorithm and a code base for reconstructing the dynamical structure function from data, to enable discovery and visualization of graphical relationships in a genetic circuit diagram astime-dependent functionsrather than static, unknown weights. We prove a theorem, showing that dynamical structure functions can provide a data-driven estimate of the size of crosstalk fluctuations from an idealized model. We illustrate this idea with numerical examples. Finally, we show how data-driven estimation of dynamical structure functions can explain failure modes in two experimentally implemented genetic circuits, a historical genetic circuit and a newE. colibased transcriptional event detector.
Assessing the effectiveness of oxathiapiprolin towardsPhytophthora agathidicida, the causal agent of kauri dieback disease
Authors: Lacey Randy F. , Fairhurst Michael J. , Daley Kaitlyn J. , Ngata-Aerengamate Te Amohaere , Patterson Haileigh R. , Patrick Wayne M. , Gerth Monica L.
Published: March 2021

Phytophthoraspecies cause disease and devastation of plants in ecological and horticultural settings worldwide. A recently identified species,P. agathidicida, infects and ultimately kills the treasured kauri trees that are endemic to New Zealand. Currently there are few options for controlling or treatingP. agathidicida. In this study, we sought to assess the toxicity of the oomycide oxathiapiprolin against several lifecycle stages of two geographically distinctP. agathidicidaisolates. Half maximal effective concentration (EC50) values were determined to be approximately 0.1 ng/ml for inhibiting mycelial growth, indicating thatP. agathidicidamycelia are more sensitive to oxathiapiprolin than those from most otherPhytophthoraspecies that have been studied. Oxathiapiprolin was also highly effective at inhibiting the germination of zoospores (EC50= 2-9 ng/ml for the two isolates) and oospores (complete inhibition at 100 ng/ml). In addition, oxathiapiprolin delayed the onset of detached kauri leaf infection in a dose-dependent manner. Collectively, the results presented here highlight the significant potential of oxathiapiprolin as a tool to aid in the control of kauri dieback disease.
Droplet-based single cell RNA sequencing of bacteria identifies known and previously unseen cellular states
Authors: McNulty Ryan , Sritharan Duluxan , Liu Shichen , Hormoz Sahand , Rosenthal Adam Z.
Published: March 2021

Clonal bacterial populations rely on transcriptional variation to differentiate into specialized cell states that increase the community’s fitness. Such heterogeneous gene expression is implicated in many fundamental microbial processes including sporulation, cell communication, detoxification, substrate utilization, competence, biofilm formation, motility, pathogenicity, and antibiotic resistance1. To identify these specialized cell states and determine the processes by which they develop, we need to study isogenic bacterial populations at the single cell level2,3. Here, we develop a method that uses DNA probes and leverages an existing commercial microfluidic platform (10X Chromium) to conduct bacterial single cell RNA sequencing. We sequenced the transcriptome of over 15,000 individual bacterial cells, detecting on average 365 transcripts mapping to 265 genes per cell inB. subtilisand 329 transcripts mapping to 149 genes per cell inE. coli. Our findings correctly identify known cell states and uncover previously unreported cell states. Interestingly, we find that some metabolic pathways segregate into distinct subpopulations across different bacteria and growth conditions, suggesting that some cellular processes may be more prone to differentiation than others. Our high throughput, highly resolved single cell transcriptomic platform can be broadly used for understanding heterogeneity in microbial populations.
CD36 family members are TCR-independent ligands for CD1 antigen-presenting molecules
Authors: Gherardin Nicholas A. , Redmond Samuel J. , McWilliam Hamish E.G. , Almeida Catarina F. , Gourley Katherine H.A. , Seneviratna Rebecca , Li Shihan , De Rose Robert , Nguyen-Robertson Catriona V. , Su Shian , Ritchie Matthew E. , Villadangos Jose A. , Moody D. Branch , Pellicci Daniel G. , Uldrich Adam P. , Godfrey Dale I.
Published: March 2021

CD1c presents lipid-based antigens to CD1c-restricted T cells which are thought to be a major component of the human T cell pool. The study of CD1c-restricted T cells, however, is hampered by the presence of an abundantly expressed CD1c-binding partner on blood cells distinct to the T cell receptor (TCR), confounding analysis of TCR-mediated CD1c tetramer staining. Here, we identify the CD36 family (CD36, CD36-L1 and CD36-L2) as novel ligands for CD1c, CD1b and CD1d proteins, and show that CD36 is the receptor responsible for non-TCR-mediated CD1c tetramer staining of blood cells. Moreover, CD36-blockade enables tetramer-based identification of CD1c-restricted T cells and clarifies identification of CD1b- and CD1d-restricted T cells. We use this technique to characterise CD1c-restricted T cells ex vivo and show diverse phenotypic features, TCR repertoire and antigen-specific subsets. Accordingly, this work will enable further studies into the biology of CD1 and human CD1-restricted T cells.

One Sentence Summary

CD1 molecules bind CD36 family members and blockade of this interaction facilitates the study of CD1-restricted T cells.
Additive and synergistic effects of arbuscular mycorrhizal fungi, insect pollination and nutrient availability in a perennial fruit crop
Authors: Chen Ke , Kleijn David , Scheper Jeroen , Fijen Thijs P.M.
Published: March 2021

Managing ecosystem services may reduce the dependence of modern agriculture on external inputs and increase the sustainability of agricultural production. Insect pollinators and arbuscular mycorrhizal fungi (AMF) provide vital ecosystem services for crop production, but it has not been tested whether their effects on crop yield interact and how their effects are influenced by nutrient availability. Here we use potted raspberry (Rubus idaeusL.) plants in a full-factorial randomized block design to assess the interacting effects of insect pollination, AMF inoculation and four levels of fertilizer application. AMF inoculation increased the per-plant flower number by 33% and fruit number by 35%, independently from insect pollination and fertilizer application. Single berry weight furthermore increased more strongly with fertilizer application rates in AMF inoculated plants than in non-inoculated plants. As a consequence, AMF inoculation boosted raspberry yield by 43% compared to non-inoculated plants. AMF inoculation increased pollinator visitation rate under intermediate fertilizer levels, suggesting additional indirect effects of AMF on yield. Fruit yield of pollinated plants increased more strongly with fertilizer application rate than the yield of plants from which pollinators had been excluded. At maximum nutrient availability, the combined benefits of both ecosystem services resulted in a 135% higher yield than that of fertilizer-only treatments. Our results suggest that benefits of ecosystem services on yield can be additive or synergistic to the effects of conventional management practices. Intensive, high-input farming systems that do not consider the potential adverse effects of management on ecosystem service providing species may risk becoming limited by delivery of ecosystem services. Pro-actively managing ecosystem services, on the other hand, has the potential to increase crop yield at the same level of external inputs.
DFT and Raman study of all-transastaxanthin optical isomers
Authors: Yao Guohua , Guo Shuju , Yu Wenjie , Muhammad Muhammad , Liu Jianguo , Huang Qing
Published: March 2021

Astaxanthin (AST) is a xanthophyll carotenoid widely distributed in aquatic animals, which has many physiological functions such as antioxidant, anti-inflammatory, anti-hypertensive and anti-diabetic activities. Astaxanthin has three optical isomers, including a pair of enantiomers (3S,3 ‘Sand 3R,3 ‘R) and a meso form (3R,3 ‘S). Different optical isomers have differences in a variety of physiological functions. Traditionally, High Performance Liquid Chromatography (HPLC) can be used to distinguish these isomers. In this work, it’s found that Raman spectroscopy can be employed to distinguish the three optical isomers. Because the intensities of two Raman bands at 1190 cm-1and 1215 cm-1of three isomers are different. DFT calculations are performed and used to analyze the spectral differences. The calculation results show that the structures of these chiral isomers are not strictly mirror-symmetrical to each other, which leads to the difference in their Raman spectra.

Highlights

Raman spectroscopy can be utilized to distinguish three optical isomers of all-transastaxanthin.

The DFT-calculated spectrum is used to explain why the Raman bands of optical isomers at 1190 and 1215 cm-1are different.

The structural parameters of the three optical isomers have been identified.
DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
Authors: Giacopelli Brian , Wang Min , Cleary Ada , Wu Yue-Zhong , Schultz Anna Reister , Schmutz Maximilian , Blachly James S. , Eisfeld Ann-Kathrin , Mundy-Bosse Bethany , Vosberg Sebastian , Greif Philipp A. , Claus Rainer , Bullinger Lars , Garzon Ramiro , Coombes Kevin R. , Bloomfield Clara D. , Druker Brian J. , Tyner Jeffrey W. , Byrd John C. , Oakes Christopher C.
Published: March 2021

Acute myeloid leukemia (AML) is a molecularly complex disease characterized by heterogeneous tumor genetic profiles and involving numerous pathogenic mechanisms and pathways. Integration of molecular data types across multiple patient cohorts may advance current genetic approaches for improved subclassification and understanding of the biology of the disease. Here, we analyzed genome-wide DNA methylation in 649 AML patients using Illumina arrays and identified a configuration of 13 subtypes (termed “epitypes”) using unbiased clustering. Integration of genetic data revealed that most epitypes were associated with a certain recurrent mutation (or combination) in a majority of patients, yet other epitypes were largely independent. Epitypes showed developmental blockage at discrete stages of myeloid differentiation, revealing epitypes that retain arrested hematopoietic stem-cell-like phenotypes. Detailed analyses of DNA methylation patterns identified unique patterns of aberrant hyper- and hypomethylation among epitypes, with variable involvement of transcription factors influencing promoter, enhancer, and repressed regions. Patients in epitypes with stem-cell-like methylation features showed inferior overall survival along with up-regulated stem cell gene expression signatures. We further identified a DNA methylation signature involving STAT motifs associated with FLT3-ITD mutations. Finally, DNA methylation signatures were stable at relapse for the large majority of patients, and rare epitype switching accompanied loss of the dominant epitype mutations and reversion to stem-cell-like methylation patterns. These results show that DNA methylation-based classification integrates important molecular features of AML to reveal the diverse pathogenic and biological aspects of the disease.
Industry 4.0 technologies as enablers of lean and agile supply chain strategies: an exploratory investigation
Authors: Raji Ibrahim Oluwole , Shevtshenko Eduard , Rossi Tommaso , Strozzi Fernanda
Published: March 2021

Purpose

Lean and agile are essential supply chain management (SCM) strategies that enhance companies' performance. Previous studies have reported the capabilities of different SCM strategies to enhance performance; however, the emergence of Industry 4.0 technologies has bred focus on the possibility of attaining more levels of operational performance. Despite being demonstrated helpful at enabling supply chain (SC) strategies, the literature linking Industry 4.0 with SCM strategies is still in its infancy. Thus, this work investigates the degree to which “Industry 4.0 technologies” enable the implementation of lean and agile practices and subsequently assesses the potential performance implications of integrating Industry 4.0 technologies with the SC operations.

Design/methodology/approach

The work employs an exploratory case study approach using empirical data from selected organisations drawn from an Estonian manufacturing cluster and digital solution providing companies. The data collected via interviews were used to assign numerical scores and subsequently aggregated across the five cases for the research variables of interest. The work is crowned with a model grounded on the cross-case analysis to depict which technologies impact each of the lean and agile practices.

Findings

The analysis enabled comprehension of the potential impact and level of importance of the main Industry 4.0 technologies on lean and agile practices and ultimately the potential implication on performance. The findings revealed that the technologies have a high impact on the practices. Although the impacts are of varying degrees, the analysis provides means to identify the technologies with the most significant impact on lean and agile SCM and the sets of practices with the greatest likelihood of being enabled by various digital technologies.

Practical implications

The work presents various lean and agile practices that practitioners can deploy to operations, alongside the technologies that could support the implementation of the practices towards achieving the various performance measures. Also, it provides some guides for the digital solution providing companies towards understanding the SCM practices that can be improved upon by various digital technologies. This enables them to have more saleable proposals for intending companies who might be sceptical about transiting into the digital operation phase.

Originality/value

This is the first attempt to empirically address the connection between Industry 4.0 technologies and the integrated lean and agile strategies despite literature backing of the complementary nature of the two SCM strategies.
Quality objectives in management systems – their attributes, establishment and motivational function
Authors: Bugdol Marek , Jedynak Piotr
Published: March 2021

Purpose

The aim of this paper is to show the ways of setting quality objectives, their attributes and the conditions under which they can perform a motivational function.

Design/methodology/approach

Collecting relevant data, the authors used the results of previous research and theoretical assumptions concerning quality objectives. Subsequently, they carried out a survey and exemplification research based on participatory observations, document content analysis and interviews.

Findings

Goals are set mainly by top management, but the communication process itself is insufficient; the needs of system users are not taken into account. In the opinion of the employees, quality objectives are measurable and objective, although not very ambitious. For quality objectives to fulfil a motivational function, they should be objective and measurable. Also, the allocation of tasks among employees needs to be fair. Furthermore, quality objectives have to play a greater role in remuneration systems.

Originality/value

This paper is one of the first publications on the role and function of quality objectives. Its advantage is that it defines the conditions under which such objectives can have a motivational effect and encourage employees to pursue the improvement of their products and services.
Collaborative consumption sport hosting: value and consumption constraints
Authors: Goldman Michael , Brown Brandon , Schwarz Eric C.
Published: March 2021

Purpose

The purpose of this paper is to find evidence of the benefits and constraints of collaborative consumption experiences by investigating the perceptions of hosts and visitors that attended professional regular season basketball and baseball games in the USA.

Design/methodology/approach

Data were collected through four focus groups with 37 total participants and were analyzed through qualitative content analysis.

Findings

The results show that participants in a collaborative consumption experience perceive four types of value: social interaction and belonging, new fandom, travel bucket list experiences and local and sport knowledge. In addition, the results provide evidence of five consumption constraints related to collaborative consumption: expenses, average experiences, seat location, interpersonal disconnects and personal risk.

Research limitations/implications

The selection of only two sites for the study limited the data triangulation that was possible. This study should be replicated across a wider range of teams and countries to confirm the main findings of the study.

Practical implications

Practitioners can use this initial study to better understand the benefits hosts and visitors perceive in the experience, and therefore the kind of experience design that would encourage increased purchases and loyalty.

Originality/value

This paper provides qualitative insights into the benefits and detriments of a collaborative consumption sport experience, based on participants' involvement in an innovative peer-to-peer platform.
An execution environment as a service for adaptive long-running workflows
Authors: Souza-Júnior Milton Secundino de , Rosa Nelson Souto , Lins Fernando Antônio Aires
Published: March 2021

Purpose

This paper aims to present Long4Cloud (long-running workflows execution environment for cloud), a distributed and adaptive LRW execution environment delivered “as a service” solution.

Design/methodology/approach

LRWs last for hours, days or even months and their duration open the possibility of changes in business rules, service interruptions or even alterations of formal regulations of the business before the workflow completion. These events can lead to problems such as loss of intermediary results or exhaustion of computational resources used to manage the workflow execution. Existing solutions face those problems by merely allowing the replacement (at runtime) of services associated with activities of the LRW.

Findings

LONG4Cloud extends the previous works in two main aspects, namely, the inclusion of dynamic reconfiguration capabilities and the adoption of an “as a service” delivery mode. The reconfiguration mechanism uses quiescence principles, data and state management and provides multiple adaptive strategies. Long4Cloud also adopts a scenario-based analysis to decide the adaptation to be performed. Events such as changes in business rules or service failures trigger reconfigurations supported by the environment. These features have been put together in a solution delivered “as a service” that takes advantage of cloud elasticity and allows to better allocate cloud resources to fit into the demands of LRWs.

Originality/value

The original contribution of Long4Cloud is to incorporate adaptive capabilities into the LRW execution environment as an effective way to handle the specificities of this kind of workflow. Experiments using current data of a Brazilian health insurance company were carried out to evaluate Long4Cloud and show performance gains in the execution of LRWs submitted to the proposed environment.
Is it your personality, your boundary leadership or both? An integrative approach for the improvement of school management team effectiveness
Authors: Benoliel Pascale
Published: March 2021

Purpose

Reorganizing schools and managing through teams is seen as a way to achieve school goals, especially in educational contexts that are highly focused on measurable student achievements. This shift to shared leadership requires principals to play a key role in promoting school management team (SMT) outcomes. Accordingly, this study aims to investigate how principals' personality traits and behavior complement each other and combine in an integrative model of SMT effectiveness. Specifically, the research aims to examine the mediating role of principals' internal and external boundary activities between principals' traits from the Big Five typology, namely, extraversion, conscientiousness, agreeableness, openness to experience and neuroticism and SMT effectiveness.

Design/methodology/approach

Data were collected from two sources to minimize problems associated with same-source bias. In total, 92 SMTs and their principals from 92 public schools in Israel participated in the study. Overall, 295 SMT members and 92 principals were included in the sample. Data were aggregated at the school level of analysis. The theoretical model was tested with structural equation modeling. The bootstrapping procedure, to ascertain the presence of indirect effects, was employed.

Findings

The findings of structural equation modeling indicated that principal external activities partially mediated the relationship of conscientiousness and extraversion to SMT effectiveness, providing support for an integrated trait–behavioral model of leadership for SMT effectiveness.

Originality/value

As schools involve increasingly interconnected professional networks based on relationships, acknowledging that SMT effectiveness may be influenced by principals' personality traits that translate into leadership behavior may clarify the implications of principals' traits for educational teams. Importantly, the proposed integrative model points to possible mechanisms linking principal traits, behaviors and effectiveness by positioning principals' boundary activities as one possible mechanism through which principal traits facilitate SMT effectiveness. The findings can help deepen our understanding of which kinds of principals engage in boundary activities, contributing to the discussion of what factors influence principals' practices with implications for school managers' selection practices.
Prevalence and correlates of contraceptive use among vocational schools adolescents in Northern Thailand
Authors: Yau Shamsudeen , Adamu Yau , Wongsawat Pramote , Songthap Archin
Published: March 2021

Purpose

This study aimed to determine the prevalence of and factors associated with contraceptive use among school-going adolescents.

Design/methodology/approach

A cross-sectional study was conducted among vocational school students in Phitsanulok, Northern Thailand. The study employed a multistage random sampling technique to select 391 students from three schools that were purposively selected.

Findings

The prevalence of contraceptive use during the most recent sexual intercourse was 75.8%. The condom was the most commonly used contraceptive method, followed by emergency pills and the rhythm/calendar method. Being male, in the second academic year, sexual communication with parents, sex with a casual partner or sex worker and contraceptive use at sexual initiation were significant risk factors for contraceptive use (p < 0.05). The preventive factors were subdistrict municipality area residency, extended family, medium or high income and partners who drank (p < 0.05).

Originality/value

The authors found a high prevalence of contraceptive use among school-going adolescents. Maintaining and improving this trend would require a concerted effort from all stakeholders to promote early sexuality communication and ensure access and use of contraceptive services.
Events management as a community of practice
Authors: Brown Tim , Stokes Peter
Published: March 2021

Purpose

This paper examines events management as a Community of Practice (CoP) and to demonstrate that knowledge management and practice within events operate as a CoP. The paper adds to the events management literature which is currently superficial in considering events conceptually as a CoP.

Design/methodology/approach

An interpretive and inductive approach was adopted for the research which incorporated quantitative and qualitative methods undertaken in a United Kingdom setting. Twenty-five in-depth semi-structured interviews with event professionals were conducted and this was complemented by a survey of 215 event professionals.

Findings

The findings demonstrate that within the evolving events industry, as well as reflected in aspects of the academic literature, events can be depicted as a “domain” which connects event professionals to a “community”. The themes emerging revealed that there are modes of working, shared values and practices, a shared identity and a desire to work as a wider collective in order to maintain and enhance knowledge and practice, which are in keeping with a CoP framework.

Research limitations/implications

This study provides new insight on an under-researched area concerning knowledge and practice development within events management.

Originality/value

This is a novel study that considers how the emergent field of events management should be considered as a CoP. It addresses a gap in the literature pertaining to knowledge and practice creation within events management from a CoP perspective.
The Hole in the Centre: A Comment on Lowe and Pemberton, The Official History of the British Civil Service, Volume II: 1982–1997
Authors: Rutter Jill
Published: March 2021

This article looks at Prime Ministers’ attempts to reform their operation in Number Ten and their relationship with the Cabinet Office in response to frustrations they encounter trying to drive their policy agenda from the centre. Prime Ministers have developed new institutions to bolster their meagre resources in Number Ten. There is particular focus on the experience of John Major in trying to push his Citizen's Charter. It notes how resistant departments were to many of the changes. Finally the article discusses recent changes in Boris Johnson's Number Ten that marked the brief tenure of Dominic Cummings and his clear centralising mission.