bluuebunny/crossref_metadata_2025 huggingface dataset:
A fuzzy-registration approach to track cell divisions in time-lapse fluorescence microscopy
Authors: Amarteifio Saoirse , Fallesen Todd , Pruessner Gunnar , Sena Giovanni
Published: September 2018

Background

Particle-tracking in 3D is an indispensable computational tool to extract critical information on dynamical processes from raw time-lapse imaging. This is particularly true with in vivo time-lapse fluorescence imaging in cell and developmental biology, where complex dynamics are observed at high temporal resolution. Common tracking algorithms used with time-lapse data in fluorescence microscopy typically assume a continuous signal where background, recognisable keypoints and independently moving objects of interest are permanently visible. Under these conditions, simple registration and identity management algorithms can track the objects of interest over time. In contrast, here we consider the case of transient signals and objects whose movements are constrained within a tissue, where standard algorithms fail to provide robust tracking.

Results

To optimize 3D tracking in these conditions, we propose the merging of registration and tracking tasks into a fuzzy registration algorithm to solve the identity management problem. We describe the design and application of such an algorithm, illustrated in the domain of plant biology, and make it available as an open-source software implementation. The algorithm is tested on mitotic events in 4D data-sets obtained with light-sheet fluorescence microscopy on growing Arabidopsis thaliana roots expressing CYCB::GFP. We validate the method by comparing the algorithm performance against both surrogate data and manual tracking.

Conclusion

This method fills a gap in existing tracking techniques, following mitotic events in challenging data-sets using transient fluorescent markers in unregistered images.
Initial Sequencing and Characterization of Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Reveals Abnormally High Levels of Potentially Starch Metabolizing Bacteria in the General Population
Authors: Batool Maria , Ali Syed Baqir , Jaan Ali , Khalid Kehkishan , Ali Syeda Aba , Kamal Kainat , Raja Afraz Ahmed , Gul Farzana , Pedroso Inti , Apte Zachary , Nasir Arshan
Published: September 2018

We describe the characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults representing seven major geographies and six ethnicities in the country. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m2, and were early-career students or professionals belonging to 25 major cities of the country. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. Using the crude measure of percentage overlap or similarity between the gut microbiota profile of Pakistani and uBiome dataset as proxy for health, our sequencing indicated that the Pakistani gut microbiota was moderately healthy relative to the uBiome dataset and Pakistani women appeared healthier relative to men. The Pakistani gut microbiome seemed susceptible to obesity and weight gain, levels of probiotics was very high likely due to the popularity of milk-based and fermented foods in the Pakistani diet, and bacteria that metabolize starch and carbohydrates (typically seen in the gut microbiota of honey bee) were abnormally enriched in the gut of Pakistani men. Our investigations reveal serious issues with the dietary habits and lifestyle of Pakistani individuals of consuming food enriched in high carbohydrates and fats, overcooked in oil and spices, following a sedentary lifestyle, little or no daily intake of fresh fruits, over-consumption of antibiotics from a very early age, and health and hygiene standards that do not meet international standards. Our sequencing is the first step towards generating a country-wide understanding of the impact of the local diet and lifestyle on Pakistani gut microbiota and can help understand its overall association with health and wellness.
Surface sediment samples from early age of seafloor exploration can provide a late 19th century baseline of the marine environment
Authors: Rillo Marina C. , Kucera Michal , Ezard Thomas H. G. , Giles Miller C.
Published: September 2018

Ocean-floor sediment samples collected up to 150 years ago represent an important historical archive to benchmark global changes in the seafloor environment, such as species’ range shifts and invasions and pollution trends. Such benchmarking requires that the historical sediment samples represent the state of the environment at or shortly before the time of collection. However, early oceanographic expeditions sampled the ocean floor using devices like the sounding tube or a dredge, which potentially disturb the sediment surface and recover a mix of Holocene (surface) and deeper, Pleistocene sediments. Here we use climate-sensitive microfossils as a fast biometric method to assess if historical seafloor samples contain a mixture of modern and glacial sediments. Our assessment is based on comparing the composition of planktonic foraminifera (PF) assemblages in historical samples with Holocene and Last Glacial Maximum (LGM) global reference datasets. We show that eight out of the nine historical samples contain PF assemblages more similar to the Holocene than to the LGM PF assemblages, but the comparisons are only significant when there is a high local species’ temporal turnover (from the LGM to the Holocene). When analysing temporal turnover globally, we show that upwelling and temperate regions had greatest species turnover, which are areas where our methodology would be most diagnostic. Our results suggest that sediment samples from historical collections can provide a baseline of the state of marine ecosystems in the late 19th century, and thus be used to assess ocean global change trends.
Genetic hubs: a phylogeographer’s widget for pinpointing of ancestral populations
Authors: Ondřej Mikula
Published: September 2018

Statistical phylogeography benefits from the development of increasingly realistic models of spatially structured genetic variation. Their fitting, however, is computationally demanding and requires population and/or genomic sampling that is not available for many species of interest. ‘Genetic hubs’ is a method that can be used for exploratory analyses of various kinds of genetic data, including those as typical in mitochondrial phylogeography, i.e. many small samples of single locus genotypes scattered throughout the species distributional range. ‘Genetic hubs’ allows to quantify and visualize gradients of genetic variation with the aim to pinpoint possible origin of expansion. It estimates local genetic variability as an accessibility of all genetic variation from the site in question and it allows to take dissimilarity of genotypes into account. The method represents fast and versatile tool that can be used whenever history of range expansion is assumed to shape the observed distribution of genetic variation and it is useful especially for preliminary analyses whose purpose is to provide sound basis for formulation of testable hypotheses and design of follow-up studies.
WFD ecological status indicator shows poor correlation with flow parameters in a large Alpine catchment
Authors: Larsen Stefano , Bruno Maria Cristina , Zolezzi Guido
Published: September 2018

Since the implementation of the Water Framework Directive, the ecological status of European running waters has been evaluated using a set of harmonised ecological indicators that should guide conservation and restoration actions. Among these, the restoration of the natural flow regime (ecological flows) is considered indispensable for the achievement of the good ecological status, and yet the sensitivity of the current biological indicators to hydrologic parameters remains understudied. The Italian Star_ICMi well represents other similar WFD indicators; it is a macroinvertebrate-based multimetric index officially adopted to assess the ecological status of running waters at the national level. Recent legislation has also included the Star_ICMi as one of the indicators used to assess and prescribe ecological flows in river reaches regulated by water abstraction. However, the relationship between river hydrology and the Star_ICMi index is so far virtually unknown. Using data from the Trentino - Alto Adige Alpine region, we first assessed the relationship between the Star_ICMi and synthetic descriptors of the physico-chemical (LIMeco) and morphological (MQI) status of respectively 280 and 184 river reaches. Then, we examined the relation between the Star_ICMi and a set of ecologically-relevant hydrologic parameters derived from discharge time-series measured at 21 hydrometric stations, representing both natural and regulated river reaches. Although the Star_ICMi showed significant and linear relationships with the physico-chemical character and, slightly, with the morphological quality of the reaches, its response to flow parameters appeared weak or non-existent when examined with linear models. Mixed quantile regressions allowed the identification of flow parameters that represented limiting factors for macroinvertebrate communities and the associated Star_ICMi scores. In particular, the index showed ‘negative floors’ where lower values were observed in reaches with large temporal variation in flow magnitude as well as frequent low and high flow events. The modelled quantiles also tracked the transition of the index from acceptable to unacceptable conditions.

The results suggest that while the central tendency of the Star_ICMi index is not strongly influenced by river flow character, some key flow parameters represent limiting factors that allow the index to reach its lowest values, eventually ‘pushing’ the site towards unacceptable ecological conditions. The identification of limiting flow parameters can aid the setting of hydrologic thresholds over which ecological impairment is likely to occur. Overall, however, results imply caution is needed in using biological indicator like the Star_ICMi for the quantitative assessment and design of ecological flows.
Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques
Authors: Reed Eric , Moses Elizabeth , Xiao Xiaohui , Liu Gang , Campbell Joshua , Perdomo Catalina , Monti Stefano
Published: September 2018

The need to reduce per sample cost of RNA-seq profiling for scalable data generation has led to the emergence of highly multiplexed RNA-seq. These technologies utilize barcoding of cDNA sequences in order to combine samples into single sequencing lane to be separated during data processing. In this study, we report the performance of one such technique denoted as sparse full length sequencing (SFL), a ribosomal RNA depletion-based RNA sequencing approach that allows for the simultaneous sequencing of 96 samples and higher. We offer comparisons to well established single-sample techniques, including: full coverage Poly-A capture RNA-seq and microarray, as well as another low-cost highly multiplexed technique known as 3’ digital gene expression (3’DGE). Data was generated for a set of exposure experiments on immortalized human lung epithelial (AALE) cells in a two-by-two study design, in which samples received both genetic and chemical perturbations of known oncogenes/tumor suppressors and lung carcinogens. SFL demonstrated improved performance over 3’DGE in terms of coverage, power to detect differential gene expression, and biological recapitulation of patterns of differential gene expression from in vivo lung cancer mutation signatures.
Cutting tree branches to pick OTUs: a novel method of provisional species delimitation
Authors: Ondřej Mikula
Published: September 2018

Delimitation of species is crucial in all studies of biodiversity, its geographic patterns and evolutionary dynamics as well as in the corresponding conservation applications. In practice, operational taxonomic units (OTUs) are often used as provisional surrogates of the species, whose evidence-based and robust delimitation requires too extensive data and complex analyses. The novel method for this provisional species delimitation is suggested, which uses any phylogenetic tree with meaningful branch lengths as an input and delimits OTUs on it by identification of branches whose removal significantly changes structure of the tree. Such branches are considered to reflect interspecific differentiation that is assumed generally more erratic than intraspecific branching. It is called branch-cutting method as it evaluates structural importance of the branch by its cutting (shrinking to zero length) and inspecting impact of this operation on the average pairwise distances between tree tips. Tree tips can be also constrained to be either conspecific or heterospecific which allows the method to achieve more robust and informed delimitations and to focus on particular phylogenetic scale. Usefulness of the method is demonstrated on four empirical examples and comparison with similar methods is performed.
MMseqs2 desktop and local web server app for fast, interactive sequence searches
Authors: Mirdita Milot , Steinegger Martin , Söding Johannes
Published: September 2018

The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.

Availability and implementation

The app is easy to install for non-experts. Source code, prebuilt desktop app packages for Windows, macOS and Linux, Docker images for the web server application, and a demo web server are available at https://search.mmseqs.com.

Contact

martin.steinegger@mpibpc.mpg.de or soeding@mpibpc.mpg.de
Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases
Authors: Shalaeva Daria N. , Cherepanov Dmitry A. , Galperin Michael Y. , Mulkidjanian Armen Y.
Published: September 2018

The activity of cellular nucleoside triphosphatases (NTPases) must be tightly controlled to prevent spontaneous ATP hydrolysis leading to cell death. While most P-loop NTPases require activation by arginine or lysine fingers, some of the apparently ancestral ones are, instead, activated by potassium ions, but not by sodium ions. We combined comparative structure analysis of P-loop NTPases of various classes with molecular dynamics (MD) simulations of Mg-ATP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures, the conserved P-loop motif keeps the triphosphate chains of enzyme-bound NTPs in an extended, catalytically prone conformation, similar to that attained by ATP in water in the presence of potassium or ammonium ions bound between alpha- and gamma-phosphate groups. The smaller sodium ions could not reach both alpha- and gamma-phosphates of a protein-bound extended phosphate chain and therefore are unable to activate most potassium-dependent P-loop NTPases.
Cryo-EM structures reveal bilayer remodeling during Ca2+ activation of a TMEM16 scramblase
Authors: Falzone Maria E. , Rheinberger Jan , Lee Byoung-Cheol , Peyear Thasin , Sasset Linda , Raczkowski Ashleigh , Eng Edward , Lorenzo Annarita Di , Andersen Olaf S. , Nimigean Crina M. , Accardi Alessio
Published: September 2018

The lipid distribution of plasma membranes of eukaryotic cells is asymmetric and phospholipid scramblases disrupt this asymmetry by mediating the rapid nonselective transport of lipids down their concentration gradients. As a result, phosphatidylserine is exposed to the outer leaflet of membrane, an important step in extracellular signaling networks controlling processes such as apoptosis, blood coagulation, membrane fusion and repair. Several members of the TMEM16 family have been identified as Ca2+-activated scramblases but the mechanisms underlying their Ca2+-dependent gating and their effects on the surrounding lipid bilayer remain poorly understood. Here we describe three high-resolution cryo-electron microscopy structures of a fungal scramblase from Aspergillus fumigatus, afTMEM16, reconstituted in lipid nanodiscs, revealing large Ca2+-dependent conformational changes of the protein as well as significant, function dependent membrane reorganization.
Functional retinal imaging using adaptive optics swept-source OCT at 1.6MHz
Authors: Azimipour Mehdi , Migacz Justin V. , Zawadzki Robert J. , Werner John S. , Jonnal Ravi S.
Published: September 2018

Objective optical assessment of photoreceptor function may permit earlier diagnosis of retinal disease than current methods such as perimetry, electrophysiology, and clinical imaging. In this work, we describe an adaptive optics (AO) optical coherence tomography (OCT) system designed to measure functional responses of single cones to visible stimuli. The OCT subsystem consisted of a raster-scanning Fourier-domain mode-locked laser that acquires A-scans at 1.64MHz with a center wavelength of 1063nm, and an AO subsystem providing diffraction-limited imaging. Analysis of serial volumetric images revealed phase changes of cone photoreceptors consistent with outer segment elongation and proportional to stimulus intensity, as well as other morphological changes in the outer segment and retinal pigment epithelium.
Bidirectional Control of Coronary Vascular Resistance by Eicosanoids via a Novel GPCR
Authors: Alkayed Nabil J. , Cao Zhiping , Qian Zu Yuan , Nagarajan Shanthi , Liu Xuehong , Nelson Jonathan , Xie Fuchun , Li Bingbing , Fan Wei , Liu Lijuan , Grafe Marjorie R. , Xiao Xiangshu , Barnes Anthony P. , Kaul Sanjiv
Published: September 2018

Arachidonic acid metabolites epoxyeicosatrienoates (EETs) and hydroxyeicosatetraenoates (HETEs) are important regulators of myocardial blood flow and coronary vascular resistance (CVR), but their mechanisms of action are not fully understood. We identified G protein-coupled receptor 39 (GPR39)as a microvascular smooth muscle cell (mVSMC) receptor antagonistically regulated by two endogenous eicosanoids: 15-HETE, which stimulates GPR39 to increase mVSMC intracellular calcium and augment microvascular CVR, and 14,15-EET, which inhibits these actions. Furthermore, zinc ion acts as an allosteric modulator of GPR39 to potentiate the efficacy of the two ligands. Our findings will have a major impact on understanding the roles of eicosanoids in cardiovascular physiology and disease, and provide an opportunity for the development of novel GPR39-targeting therapies for cardiovascular disease.

One Sentence Summary

GPR39 is a microvascular smooth muscle cell receptor regulated by two vasoactive eicosanoids with opposing actions.
Genomic sequence capture of haemosporidian parasites: Methods and prospects for enhanced study of host-parasite evolution
Authors: Barrow Lisa N. , Allen Julie M. , Huang Xi , Bensch Staffan , Witt Christopher C.
Published: September 2018

Avian malaria and related haemosporidians (Plasmodium, [Para]Haemoproteus, and Leucocytoozoon) represent an exciting multi-host, multi-parasite system in ecology and evolution. Global research in this field accelerated after 1) the publication in 2000 of PCR protocols to sequence a haemosporidian mitochondrial (mtDNA) barcode, and 2) the development in 2009 of an open-access database to document the geographic and host ranges of parasite mtDNA haplotypes. Isolating haemosporidian nuclear DNA from bird hosts, however, has been technically challenging, slowing the transition to genomic-scale sequencing techniques. We extend a recently-developed sequence capture method to obtain hundreds of haemosporidian nuclear loci from wild bird samples, which typically have low levels of infection, or parasitemia. We tested 51 infected birds from Peru and New Mexico and evaluated locus recovery in light of variation in parasitemia, divergence from reference sequences, and pooling strategies. Our method was successful for samples with parasitemia as low as ∼0.03% (3 of 10,000 blood cells infected) and mtDNA divergence as high as 15.9% (one Leucocytozoon sample), and using the most cost-effective pooling strategy tested. Phylogenetic relationships estimated with >300 nuclear loci were well resolved, providing substantial improvement over the mtDNA barcode. We provide protocols for sample preparation and sequence capture including custom probe kit sequences, and describe our bioinformatics pipeline using aTRAM 2.0, PHYLUCE, and custom Perl and Python scripts. This approach can be applied to the tens of thousands of avian samples that have already been screened for haemosporidians, and greatly improve our understanding of parasite speciation, biogeography, and evolutionary dynamics.
The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks
Authors: Tarasov Sergei
Published: September 2018

What constitutes a morphological character versus character state has been long discussed in the systematics literature but the consensus on this issue is still missing. Different methods of classifying organismal features into characters and character states can dramatically affect the results of phylogenetic analyses. Here, I show that the modular structure of the gene regulatory network (GRN) underlying trait development, and the hierarchical nature of GRN evolution, essentially remove the distinction between morphological character and character state, thus endowing the character and character state with an invariant property with respect to each other. This property allows representing the states of one character as several individual characters and vice versa. In practice, this means that a phenotype can be encoded using a set of characters or just one complex character with numerous states. The representation of a phenotype using one complex character requires a selection of an appropriate penalty for the state transitions.
Different capsid-binding patterns of the β-herpesvirus-specific tegument protein pp150 (pM32/pUL32) in murine and human cytomegaloviruses
Authors: Liu Wei , Dai Xinghong , Jih Jonathan , Chan Karen , Trang Phong , Yu Xuekui , Balogun Rilwan , Mei Ye , Liu Fenyong , Zhou Z. Hong
Published: September 2018

The phosphoprotein pp150 is a structurally, immunogenically, and regulatorily important capsid-associated tegument protein abundant in β-herpesviruses including cytomegaloviruses (CMV), but absent in α-herpesviruses and Γ-herpesviruses. In human CMV (HCMV), bridging across each triplex and three adjacent major capsid proteins (MCPs) is a group of three pp150 subunits in a “△”-shapedfortifyingconfiguration, 320 of which encase and stabilize the genome-containing capsid. Because murine CMV (MCMV) has been used as a model for HCMV pathogenesis and therapeutic studies, one might expect that pp150 and the capsid in MCMV and HCMV have similar structures. Here, by cryoEM and sub-particle reconstructions, we have obtained structures of MCMV capsid and pp150 at near atomic resolutions and built their atomic models. Surprisingly, the capsid-binding patterns of pp150 differ between HCMV and MCMV despite their highly similar capsid structures. In MCMV, pp150 is absent on triplex Tc and exists as a “Λ”-shaped dimer on other triplexes, leading to only 260 groups of two pp150 subunits per capsid in contrast to 320 groups of three pp150 subunits encasing each HCMV capsid. Many more amino acids contribute to pp150-pp150 interactions in MCMV than in HCMV, making MCMV pp150 dimer inflexible thus incompatible to instigate triplex Tc-binding as observed in HCMV. While pp150 is essential in HCMV, pp150-deleted MCMV mutants remained viable though with attenuated infectivity and exhibiting defects in retaining viral genome. These results support targeting capsid proteins, but invalidate targeting pp150, when using MCMV as a model for HCMV pathogenesis and therapeutic studies.

Importance

CMV infection is a leading viral cause of congenital birth defects and often responsible for life-threating complications in immunocompromised individuals like AIDS and post-organ transplantation patients. Absence of effective vaccines and potent drugs against CMV infections has motivated animal-based studies, mostly based on the mouse model with MCMV, both for understanding pathogenesis of CMV infections and for developing therapeutic strategies. Here, we present the first atomic structures of MCMV and show that the organization patterns of capsid-associated tegument protein pp150 between human and mouse CMV are different despite their highly similar capsid structures. Our functional studies demonstrate that deleting pp150 does not eliminate MCMV infection in contrast to pp150’s essential role in HCMV infections. These results thus establish the validity to target capsid proteins, but raise concerns to target pp150, when using MCMV as HCMV model for pathogenesis and therapeutic studies.
Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants
Authors: de la Torre Vanesa S. Garcia , Majorel-Loulergue Clarisse , Gonzalez Dubiel A. , Soubigou-Taconnat Ludivine , Rigaill Guillem J. , Pillon Yohan , Barreau Louise , Thomine Sé;bastien , Fogliani Bruno , Burtet-Sarramegna Valérie , Merlot Sylvain
Published: September 2018

The Anthropocene epoch is associated with the spreading of metals in the environment increasing oxidative and genotoxic stress on living organisms1,2. Once regarded as a curiosity, plants hyperaccumulating metals are now envisioned as an opportunity to remediate metal contaminated soils. About 500 plant species adapted to metalliferous soils acquired the capacity to hyperaccumulate (>0.1% of dry weight) nickel in their shoot3. The phylogenetic distribution of these hyperaccumulators in 50 families suggest that this complex trait evolved multiple times independently from basic mechanisms involved in metal homeostasis. However, the exact nature of these mechanisms and whether they are shared between various lineages is not known. Here, using cross-species transcriptomic analyses in different plant families, we have identified convergent functions that may represent major nodes in the evolution of nickel hyperaccumulation. In particular, our data point out that constitutive high expression of IREG/Ferroportin transporters recurrently emerged as a mechanism involved in nickel hyperaccumulation.
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Authors: Dyrdak Robert , Mastafa Monika , Hodcroft Emma B. , Neher Richard A. , Albert Jan
Published: September 2018

Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. To investigate diversity, spread, and evolution of EV-D68 we performed near full-length deep sequencing in 54 samples obtained in Sweden during the 2014 and 2016 outbreaks. In most samples, intrapatient variability was low and dominated by rare synonymous variants, but three patients showed evidence of dual infections with distinct EV-D68 variants from the same subclade. Interpatient evolution showed a very strong temporal signal, with an evolutionary rate of 0.0039 ± 0.0001 substitutions per site and year. Phylogenetic trees reconstructed from the sequences suggest that EV-D68 was introduced into Stockholm several times during the 2016 outbreak. Putative neutralization targets in the BC and DE loops of the VP1 protein were slightly more diverse within-host and tended to undergo more frequent substitution than other genomic regions. However, evolution in these loops did not appear to have been driven the emergence of the 2016 B3-subclade directly from the 2014 B1-subclade. Instead, the most recent ancestor of both clades was dated to 2009. The study provides a comprehensive description of the intra- and interpatient evolution of EV-D68, including the first report of intrapatient diversity and dual infections. The new data along with publicly available EV-D68 sequences are included in an interactive phylodynamic analysis on nextstrain.org/enterovirus/d68 to facilitate timely EV-D68 tracking in the future.
Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines
Authors: Esteban Oscar , Blair Ross W , Nielson Dylan M , Varada Jan C , Marrett Sean , Thomas Adam G , Poldrack Russell A , Gorgolewski Krzysztof J
Published: September 2018

The neuroimaging community is steering towards increasingly large sample sizes, which are highly heterogeneous because they can only be acquired by multi-site consortia. The visual assessment of every imaging scan is a necessary quality control step, yet arduous and time-consuming. A sizeable body of evidence shows that images of low quality are a source of variability that may be comparable to the effect size under study. We present the MRIQC Web-API, an open crowdsourced database that collects image quality metrics extracted from MR images and corresponding manual assessments by experts. The database is rapidly growing, and currently contains over 100,000 records of image quality metrics of functional and anatomical MRIs of the human brain, and over 200 expert ratings. The resource is designed for researchers to share image quality metrics and annotations that can readily be reused in training human experts and machine learning algorithms. The ultimate goal of the database is to allow the development of fully automated quality control tools that outperform expert ratings in identifying subpar images.
The extracellular gate shapes the energy profile of an ABC exporter
Authors: Hutter Cedric A.J. , Timachi M. Hadi , Hürlimann Lea M. , Zimmermann Iwan , Egloff Pascal , Göddeke Hendrik , Kucher Svetlana , Štefanic Saša , Karttunen Mikko , Schäfer Lars V. , Bordignon Enrica , Seeger Markus A.
Published: September 2018

ABC exporters harness the energy of ATP to pump substrates across membranes. Extracellular gate opening and closure are key steps of the transport cycle, but the underlying mechanism is poorly understood. Here, we generated a synthetic single domain antibody (sybody) that recognizes the heterodimeric ABC exporter TM287/288 exclusively in the presence of ATP, which was essential to solve a 3.2 Å crystal structure of the outward-facing transporter. The sybody binds to an extracellular wing and strongly inhibits ATPase activity by shifting the transporter’s conformational equilibrium towards the outward-facing state, as shown by double electron-electron resonance (DEER). Mutations that facilitate extracellular gate opening resulted in a comparable equilibrium shift and strongly reduced ATPase activity and drug transport. Using the sybody as conformational probe, we demonstrate that efficient extracellular gate closure is required to dissociate the NBD dimer after ATP hydrolysis to reset the transporter back to its inward-facing state.
Emergence of collective oscillations in adaptive cells
Authors: Wang Shou-Wen , Tang Lei-Han
Published: September 2018

Collective oscillations of cells in a population appear under diverse biological contexts. Here, we establish a set of common principles by categorising the response of individual cells against a time-varying signal. A positive intracellular signal relay of sufficient gain from participating cells is required to sustain the oscillations, together with phase matching. The two conditions yield quantitative predictions for the onset cell density and frequency in terms of measured single-cell and signal response functions. Through mathematical constructions, we show that cells that adapt to a constant stimulus fulfil the phase requirement by developing a leading phase in an active frequency window that enables cell-to-signal energy flow. Analysis of dynamical quorum sensing in several cellular systems with increasing biological complexity reaffirms the pivotal role of adaptation in powering oscillations in an otherwise dissipative cell-to-cell communication channel. The physical conditions identified also apply to synthetic oscillatory systems.
Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes
Authors: Prabh Neel , Roeseler Waltraud , Witte Hanh , Eberhardt Gabi , Sommer Ralf J. , Rödelsperger Christian
Published: September 2018

The widespread identification of genes without detectable homology in related taxa is a hallmark of genome sequencing projects in animals, together with the abundance of gene duplications. Such genes have been called novel, young, taxon-restricted, or orphans, but little is known about the mechanisms accounting for their origin, age, and mode of evolution. Phylogenomic studies relying on deep and systematic taxon sampling and using the comparative method can provide insight into the evolutionary dynamics acting on novel genes. We used a phylogenomic approach for the nematode model organism Pristionchus pacificus and sequenced six additional Pristionchus and two outgroup species. This resulted in 10 genomes with a ladder-like phylogeny, sequenced in one laboratory using the same platform and analyzed by the same bioinformatic procedures. Our analysis revealed that 68%–81% of genes are assignable to orthologous gene families, the majority of which defined nine age classes with presence/absence patterns that can be explained by single evolutionary events. Contrasting different age classes, we find that older age classes are concentrated at chromosome centers, whereas novel gene families preferentially arise at the periphery, are weakly expressed, evolve rapidly, and have a high propensity of being lost. Over time, they increase in expression and become more constrained. Thus, the detailed phylogenetic resolution allowed a comprehensive characterization of the evolutionary dynamics of Pristionchus genomes indicating that distribution of age classes and their associated differences shape chromosomal divergence. This study establishes the Pristionchus system for future research on the mechanisms that drive the formation of novel genes.
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome
Authors: Goltsman Daniela S. Aliaga , Sun Christine L. , Proctor Diana M. , DiGiulio Daniel B. , Robaczewska Anna , Thomas Brian C. , Shaw Gary M. , Stevenson David K. , Holmes Susan P. , Banfield Jillian F. , Relman David A.
Published: September 2018

Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.
Crystal structure of Arabidopsis thaliana peroxiredoxin A C119S mutant
Authors: Yang Ye , Cai Wenguang , Wang Junchao , Pan Weimin , Liu Lin , Wang Mingzhu , Zhang Min
Published: September 2018

Peroxiredoxins (Prxs), a large family of antioxidant enzymes, are abundant in all living organisms. Peroxiredoxin A (PrxA) from Arabidopsis thaliana belongs to the typical 2-Cys Prx family and is localized in the chloroplast. This article reports the crystal structure of a PrxA C119S mutant refined to 2.6 Å resolution. The protein exists as a decamer both in the crystal structure and in solution. The structure is in the reduced state suitable for the approach of peroxide, though conformational changes are needed for the resolving process.
Fuzzy model predictive control for 2-DOF robotic arms
Authors: Yang Weilin , Zhang Wentao , Xu Dezhi , Yan Wenxu
Published: September 2018

Purpose

Robotic arm control is challenging due to the intrinsic nonlinearity. Proportional-integral-derivative (PID) controllers prevail in many robotic arm applications. However, it is usually nontrivial to tune the parameters in a PID controller. This paper aims to propose a model-based control strategy of robotic arms.

Design/methodology/approach

A Takagi–Sugeno (T-S) fuzzy model, which is capable of approximating nonlinear systems, is used to describe the dynamics of a robotic arm. Model predictive control (MPC) based on the T-S fuzzy model is considered, which optimizes system performance with respect to a user-defined cost function.

Findings

The control gains are optimized online according to the real-time system state. Furthermore, the proposed method takes into account the input constraints. Simulations demonstrate the effectiveness of the fuzzy MPC approach. It is shown that asymptotic stability is achieved for the closed-loop control system.

Originality/value

The T-S fuzzy model is discussed in the modeling of robotic arm dynamics. Fuzzy MPC is used for robotic arm control, which can optimize the transient performance with respect to a user-defined criteria.
A study on the factors to measure employer brand: the case of undergraduate senior students
Authors: Lee Chi-Cheng , Kao Rui-Hsin , Lin Chia-Jung
Published: September 2018

Purpose

This paper aims to develop the structure of employer brand and discuss whether employees and employers have the same view on the elements of employer brand.

Design/methodology/approach

The employer brand of Taiwan, which includes 5 facets and 20 eight terms, was obtained. Management, welfare, interest and environment are the common facets of employer brand in China and Western countries. In addition, family and atmosphere is an important factor that merges both Western and Eastern job applicants. Its contents emphasize family life, which is only found in applicants from Taiwan and China.

Findings

The results showed that enterprises utilize functional factors in order to connect emotions closely and satisfy psychological sustenance, which have true attraction to young Taiwanese applicants and the current workforce of employees.

Originality/value

In general, after 20 years of establishment and empirical research, the achievements are rich and many practical opinions are provided. However, most of the existing literatures come from the researches of Western scholars, and they may be affected by the Western social value. This study has explored the Oriental and Western literatures. In the study field of Taiwan, it is found that employer brand will definitely show different style features due to the cultural difference. Therefore, when an enterprise applies the relevant connotation of the employer brand, it is necessary considering the cultural difference. This shows the importance of cross-cultural study of employer brand recently. At the same time, this also highlights the contribution of this study on theory and practice.
Fatigue life prediction of cord–rubber composite structures based on progressive damage analysis
Authors: Jha Niraj Kumar , Nackenhorst Udo
Published: September 2018

Purpose

The purpose of this paper is to develop a progressive damage framework to predict the fatigue life of cord-reinforced rubber composite under cyclic loadings. Special attention has been paid to failure mechanisms, like cord–rubber interfacial debonding, and rubber matrix damage.

Design/methodology/approach

The constitutive modeling is based on the continuum damage mechanics (CDMs) and the thermodynamics of irreversible process. The damage in rubber is described by an istropic law, whereas elasto-plastic continuum model has been proposed for cord–rubber interphase layer. The numerical framework is implemented into commercial finite element code Abaqus/Standard via user subroutine (UMAT).

Findings

One of the most important findings obtained from reviewing various techniques is that meso-level fatigue damage modeling based on developed framework can simulate competitive damage scenarios, e.g. debonding, delamination or matrix failure.

Originality/value

A systematic framework for predicting failure in cord-reinforced rubber composite is formulated within the context of CDMs that can also be applied for industrial components, such as tires and airsprings.
New Wella Salon: a journey towards popularizing the services (B)
Authors: Sattar Muhammad Muzamil , Pathan Nabeel Nisar , Raza Ali
Published: September 2018

Subject area

Entrepreneurship, Entrepreneurial Marketing and Services Marketing.

Study level/applicability

The New Wella Salon case (B) is suitable for teaching at MBA level and last-year students of undergraduate-level courses in services marketing and entrepreneurship.

Case overview

This case discusses the challenges faced by a young entrepreneur Mr Meer, who has successfully brought a new trend in the salon industry of Sukkur City. The new trend focuses on trendier and sophisticated services keeping in mind the changing mindset of consumer and services provided by leading salons of Pakistan. Though, the new salon has proved to be a great success. But recent developments have badly shaken the well-established brand. The most challenging issue was the loss of customers to competition, showing a negative sign for the future of this leading brand of local salon industry. He was confused and upset about the future of the leading salon brand of the local industry. He knew that he has to make some strategic decisions to secure his career and family business but appeared to be confused about how to operationalize these. He soon realized that word-of-mouth publicity and running a Facebook page would not be enough to promote his business effectively; so, he has to explore some new ways to promote his unique and nascent service other than advertising. But what should those be? To capture the growing demand of trendy services and scattered populations as a result of growing competition from similar salons, Meer has chalked down two different options: open another salon at a promising avenue and/or offer more services.

Expected learning outcomes

To identify and differentiate between traits of an entrepreneur and traditional businessman. To discuss how services companies can create and sustain competitive advantage. To understand the various strategic aspects of the small businesses that lever their decision-making. To work out strategic choices available to a new entrepreneurial firm, evaluate the alternatives and devise strategies for successful expansion of the business. To assess the usefulness of traditional and non-traditional marketing channels for promoting a small business.

Supplementary materials

Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 8: Marketing.
An efficient numerical method to solve the Falkner-Skan problem over an isothermal moving wedge
Authors: Delkhosh Mehdi , Parand Kourosh , Ganji D.D.
Published: September 2018

Purpose

This paper aims to solve the Falkner–Skan problem over an isothermal moving wedge using the combination of the quasilinearization method and the fractional order of rational Chebyshev function (FRC) collocation method on a semi-infinite domain.

Design/methodology/approach

The quasilinearization method converts the equation into a sequence of linear equations, and then by using the FRC collocation method, these linear equations are solved. The governing nonlinear partial differential equations are reduced to the nonlinear ordinary differential equation by similarity transformations.

Findings

The entropy generation and the effects of the various parameters of the problem are investigated, and various graphs for them are plotted.

Originality/value

Very good approximation solutions to the system of equations in the problem are obtained, and the convergence of numerical results is shown by using plots and tables.
Perceived price and service quality as mediators between price fairness and perceived value in business banking relationships
Authors: Zietsman Mariëtte Louise , Mostert Pierre , Svensson Göran
Published: September 2018

Purpose

The purpose of this paper is to test perceived price and service quality as mediators between price fairness and perceived value in service encounters between micro-enterprises and their banks.

Design/methodology/approach

The study is based on a self-administered and internet-based questionnaire conducted in the banking industry. The sample consists of 381 micro-enterprises in South Africa that employ one or two staff members.

Findings

The findings of this paper provide evidence for both theory and practice that perceived price and service quality influence the relationship between business banking customers’ perception of price fairness and the value of the service offered.

Research limitations/implications

The measurement and structural properties reported are satisfactory. This paper confirms the hypothesized relationships in the tested research model, and rejects a tested rival model. Limitations are reported, and suggestions for further research are provided.

Practical implications

This paper offers banking executives guidance in managing the pricing structure of their services, and highlights the value of offering greater transparency with regards to service charges and interest rates.

Originality/value

This paper contributes to insights into the mediating effects of perceived price and service quality between price fairness and perceived value in business relationships between micro-enterprises and their banks.
Value co-creation through digital service capabilities: the role of human factors
Authors: Saunila Minna , Ukko Juhani , Rantala Tero
Published: September 2018

Purpose

The purpose of this paper is to explore the different human factor characteristics that are emphasized when co-creating value through digital service capabilities.

Design/methodology/approach

Empirical data are gathered from two small companies that deliver digital services and products in business-to-business markets.

Findings

The study highlights the role and importance of human factors as reflected in employees’ customer orientation while delivering digital service capabilities. The role of human factors also changes during the digital service production process.

Originality/value

Developing digital service capability is positively associated with value co-creation, but it requires new skills: firms need to evaluate their mechanisms for supporting continuous learning about the properties of digital technologies. To the authors’ knowledge, this is the first study to focus on the role of human factors in in developing digital service capabilities.