bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Trust of the Muslim Nurse
Authors: Hansbrough Wendy B. , Kray Gina , Katib Faten
Published: July 2018

OBJECTIVE

This quantitative study examined patients’ trust of a nurse who represents the Muslim faith by wearing the hijab.

BACKGROUND

Presumptions about nurse trustworthiness based on religious affiliation may impede the effectiveness of the nurse-patient relationship and diminish the ability of nursing care to promote patient’s feelings of well-being.

METHODS

Hospitalized participants were randomly given a picture of a nurse either wearing the hijab or not. They completed a survey to measure their level of trust considering the nurse in the picture.

RESULTS

No difference was found in trust of the nurse between groups or in trust analyzed for between-group characteristics. In the hijab picture group, the older the patient, the lower the trust of the nurse.

CONCLUSIONS

The results may reflect the general trust of nurses as an ethical and honest professional group. A high level of general trust may transcend stereotypes toward a Muslim nurse.
Integrating global patterns and drivers of tree diversity across a continuum of spatial grains
Authors: Keil Petr , Chase Jonathan M.
Published: July 2018

What drives biodiversity and where are the most biodiverse places on Earth? The answer critically depends on spatial scale (grain), and is obscured by lack of data and mismatches in their grain. We resolve this with cross-scale models integrating global data on tree species richness (S) from 1338 local forest surveys and 287 regional checklists, enabling estimation of drivers and patterns of biodiversity at any desired grain. We uncover grain-dependent effects of both environment and biogeographic regions on S, with a positive regional effect of Southeast Asia at coarse grain that disappears at fine grains. We show that, globally, biodiversity cannot be attributed to purely environmental or regional drivers, since regions are environmentally distinct. Finally, we predict global maps of biodiversity at two grains, identifying areas of exceptional species turnover in China, East Africa, and North America. Our cross-scale approach unifies disparate results from previous studies regarding environmental versus biogeographic predictors of biodiversity, and enables efficient integration of heterogeneous data.
Reversible solidification of fission yeast cytoplasm after prolonged nutrient starvation
Authors: Heimlicher Maria B. , Bächler Mirjam , Ibeneche-Nnewihe Chieze , Florin Ernst-Ludwig , Hoenger Andreas , Brunner Damian
Published: July 2018

Cells depend on a highly ordered organization of their content and they must develop strategies to maintain the anisotropic distribution of organelles during periods of nutrient shortage. One of these strategies, observed in bacteria and in yeast cells with acutely interrupted energy production, is to solidify the cytoplasm. Here, we describe a different type of cytoplasm solidification that occurs in fission yeast cells having slowly run out of nutrients after multiple days of culturing. It provides the most profound reversible cytoplasmic solidification of yeast cells described to date. Our data suggest the involvement of a matrix with a certain mesh size that immobilizes cellular components in a size-dependent manner. We provide experimental evidence that cells need time, intrinsic nutrients and intrinsic energy sources to enter this state in the absence of external sources. Such cytoplasmic solidification may provide a robust means to protect cellular architecture in dormant cells.
SOD1 activity thresholds and TOR signalling modulate VAP(P58S) aggregation via ROS-induced proteasomal degradation in a Drosophila model of Amyotrophic Lateral Sclerosis
Authors: Chaplot Kriti , Pimpale Lokesh , Ramalingam Balaji , Deivasigamani Senthilkumar , Kamat Siddhesh S. , Ratnaparkhi Girish S.
Published: July 2018

Familial Amyotrophic Lateral Sclerosis (F-ALS) is an incurable, late onset motor neuron disease, linked strongly to various causative genetic loci. ALS8 codes for a missense mutation, P56S, in VAMP-associated Protein B (VAPB) that causes the protein to misfold and form cellular aggregates. Uncovering genes and mechanisms that affect aggregation dynamics would greatly help increase our understanding of the disease and lead to potential therapeutics.

Here, we develop a quantitative high-throughput, Drosophila S2R+ cell-based kinetic assay coupled with fluorescent microscopy to score for genes involved in the modulation of aggregates of fly ortholog, VAP(P58S), tagged with GFP. As proof of principle, we conducted a targeted RNAi screen against 900 genes, consisting of VAP genetic interactors, other ALS loci, as also genes involved in proteostasis. The screen identified 150 hits that modify aggregation, including the ALS loci SOD1, TDP43 and also genes belonging to the TOR pathway.

To validate these modifiers, we developed a system to measure the extent of VAP(P58S) aggregation in the Drosophila third instar larval brain using the UAS-GAL4 system, followed by quantitative imaging of cellular inclusions. We find that reduction of SOD1 activity or decreased TOR signalling reduces aggregation. Interestingly, we find that increase in cellular reactive oxygen species (ROS) levels, assessed by measuring oxidation of cellular lipids and proteins, in response to SOD1 knockdown or by inhibition of TOR signalling appears to be the trigger for clearing of aggregates. The mechanism of aggregate clearance is, primarily, the proteasomal machinery, and not autophagy. Increase in VAP, but not VAP(P58S) levels, appears to elevate ROS, which may in turn regulate VAP transcription in a feedback loop.

We have thus uncovered an interesting interplay between SOD1, ROS and TOR signalling that regulates the dynamics of VAP aggregation. Mechanistic processes underlying such cellular regulatory networks will lead us to a better understanding of initiation and progression of ALS.
Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism
Authors: Kuntner Matjaž , Hamilton Chris A. , Ren-Chung Cheng , Gregorič Matjaž , Lupše Nik , Lokovšek Tjaša , Lemmon Emily Moriarty , Lemmon Alan R. , Agnarsson Ingi , Coddington Jonathan A. , Bond Jason E.
Published: July 2018

Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope’s Rule (phyletic size increase), Rensch’s Rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length ≥ 2) is the norm. Nephilid genera construct webs of exaggerated proportions which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 Anchored Hybrid Enrichment (AHE) markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch’s Rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope’s Rule. Allometric analyses reject the converse, Rensch’s Rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve towards an optimum size (3.2–4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, diagnosability, and arachnological community practice. We resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous Geratonephila Poinar & Buckley 2012, Herennia Thorell 1877, Indoetra Kuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, and Trichonephila Dahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically-ancient phenotype (over 100 ma), as is eSSD, though their magnitudes vary by lineage and, to some extent, biogeographically.
CorShrink: Empirical Bayes shrinkage estimation of correlations, with applications
Authors: Dey Kushal K. , Stephens Matthew
Published: July 2018

Estimation of correlation matrices and correlations among variables is a ubiquitous problem in statistics. In many cases – especially when the number of observations is small relative to the number of variables – some kind of shrinkage or regularization is necessary to improve estimation accuracy. Here, we propose an Empirical Bayes shrinkage approach, CorShrink, which adaptively learns how much to shrink correlations by combining information across all pairs of variables. One key feature of CorShrink, which distinguishes it from most existing methods, is its flexibility in dealing with missing data. Indeed, CorShrink explicitly accounts for varying amounts of missingness among pairs of variables. Numerical studies suggest CorShrink is competitive with other popular correlation shrinkage methods, even when there is no missing data. We illustrate CorShrink on gene expression data from GTEx project, which suffers from extensive missing observations, and where existing methods struggle. We also illustrate its flexibility by applying it to estimate cosine similarities between word vectors from word2vec models, thereby generating more accurate word similarity rankings.
Varicose veins of lower extremities: insights from the first large-scale genetic study
Authors: Shadrina Alexandra S. , Sharapov Sodbo Z. , Shashkova Tatiana I. , Tsepilov Yakov A.
Published: July 2018

Varicose veins of lower extremities (VVs) are a common multifactorial vascular disease. Genetic factors underlying VVs development remain largely unknown. Here we report the first large-scale study of VVs performed on a freely available genetic data of 408,455 European-ancestry individuals. We identified 7 reliably associated loci that explain 10% of the SNP-based heritability, and prioritized the most likely causal genesCASZ1, PPP3R1, EBF1, STIM2, andHFE. Genetic correlation analysis confirmed known epidemiological associations and found genetic overlap with various traits including fluid intelligence score, educational attainment, smoking, and pain. Finally, we observed causal effects of height, weight, both fat and fat-free mass, and plasma levels of MICB and CD209 proteins.
Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite
Authors: Bruning John M. , Wang Yan , Oltrabella Francesca , Tian Boxue , Kholodar Svetlana A. , Liu Harrison , Bhattacharya Paulomi , Guo Su , Holton James M. , Fletterick Robert J. , Jacobson Matthew P. , England Pamela M.
Published: July 2018

Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinson’s disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and x-ray crystallography we show that DHI binds to the ligand binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinson’s disease.
Epi-fluorescence Microscopy of Single Molecule DNA Denaturation in situ
Authors: Sharma Pulkit
Published: July 2018

DNA can be denatured by two main methods which are: a) denaturation in solution (invitro) and b) denaturation on a slide surface (in-situ). Additionally, DNA can also be denatured in gels with urea. The method to be used depends on various factors such as the application, the source of the DNA, the length, and the techniques available to confirm the extent of denaturation. Verification of the extent of denaturation is important because of the following factors: 1) increases the chances of hybridization (especially for short probes), 2) prevents the loss of expensive probes (if the target site is not denatured then, the probes will not hybridize and will only cause a high a background), 3) a higher degree of denaturation allows for more probes to be used and therefore, more information can be derived after hybridization, and 4) essential to maximize due to extremely short probe length. It is important to ensure that DNA morphology is preserved after denaturation in order for the probes to hybridise and also for ensuring proper statistical analysis for high throughput applications. In this work, various experimental conditions for in situ denaturation of single molecule DNA is presented.

Significance Statement

The significance of this work is that it emphasizes on the importance of denaturation of target genomic DNA in DNA fibre FISH (fluorescence in situ hybridisation) experiments. If the quality of the target DNA is poor after denaturation or the target DNA is not properly denatured, then it will be very difficult or impossible to hybridize the probe DNA during FISH experiments. This will affect the final results for DNA FISH. Additionally, it is the first time that single DNA combed molecules have been shown to be denatured in situ. Most of the past work has been on gels only. Thus the work is both unique and significant.
Inducing controlled cell cycle arrest and re-entry during asexual proliferation ofPlasmodium falciparummalaria parasites
Authors: van Biljon Riëtte , Niemand Jandeli , Wyk Roelof van , Clark Katherine , Verlinden Bianca , Abrie Clarissa , Grüning Hilde von , Smidt Werner , Smit Annél , Reader Janette , Painter Heather , Llinás Manuel , Doerig Christian , Birkholtz Lyn-Marié
Published: July 2018

The life cycle of the malaria parasitePlasmodium falciparumis tightly regulated, oscillating between stages of intense proliferation and quiescence. Cyclic 48-hour asexual replication ofPlasmodiumis markedly different from cell division in higher eukaryotes, and mechanistically poorly understood. Here, we report tight synchronisation of malaria parasites during the early phases of the cell cycle by exposure to DL-α-difluoromethylornithine (DFMO), which results in the depletion of polyamines. This induces an inescapable cell cycle arrest in G1(~15 hours post-invasion) by blocking G1/S transition. Cell cycle-arrested parasites enter a quiescent G0-like state but, upon addition of exogenous polyamines, re-initiate their cell cycle in a coordinated fashion. This ability to halt malaria parasites at a specific point in their cell cycle, and to subsequently trigger re-entry into the cell cycle, provides a valuable framework to investigate cell cycle regulation in these parasites. We therefore used gene expression analyses to show that re-entry into the cell cycle involves expression of Ca2+-sensitive (cdpk4andpk2)and mitotic kinases (nimaandark2),with deregulation of the pre-replicative complex associated with expression ofpk2. Changes in gene expression could be driven through transcription factors MYB1 and two ApiAP2 family members. This new approach to parasite synchronisation therefore expands our currently limited toolkit to investigate cell cycle regulation in malaria parasites.
Comprehensive analysis of immune evasion in breast cancer by single-cell RNA-seq
Authors: Yin Jianhua , Li Zhisheng , Yan Chen , Fang Enhao , Wang Ting , Zhou Hanlin , Luo Weiwei , Zhou Qing , Zhang Jingyu , Hu Jintao , Jin Haoxuan , Wang Lei , Zhao Xing , Li Jiguang , Qi Xiaojuan , Zhou Wenbin , Huang Chen , He Chenyang , Yang Huanming , Kristiansen Karsten , Hou Yong , Zhu Shida , Zhou Dongxian , Wang Ling , Dean Michael , Wu Kui , Hu Hong , Li Guibo
Published: July 2018

The tumor microenvironment is composed of numerous cell types, including tumor, immune and stromal cells. Cancer cells interact with the tumor microenvironment to suppress anticancer immunity. In this study, we molecularly dissected the tumor microenvironment of breast cancer by single-cell RNA-seq. We profiled the breast cancer tumor microenvironment by analyzing the single-cell transcriptomes of 52,163 cells from the tumor tissues of 15 breast cancer patients. The tumor cells and immune cells from individual patients were analyzed simultaneously at the single-cell level. This study explores the diversity of the cell types in the tumor microenvironment and provides information on the mechanisms of escape from clearance by immune cells in breast cancer.

One Sentence Summary

Landscape of tumor cells and immune cells in breast cancer by single cell RNA-seq
Asymmetric perirenal brown adipose dormancy in adult humans is defined by local sympathetic activity
Authors: Jespersen Naja Z. , Feizi Amir , Andersen Eline S. , Heywood Sarah , Hattel Helle B. , Daugaard Søren , Bagi Per , Feldt-Rasmussen Bo , Schultz Heidi S. , Hansen Ninna S. , Krogh-Madsen Rikke , Pedersen Bente K. , Petrovic Natasa , Nielsen Søren , Scheele Camilla
Published: July 2018

We here detect dormant brown adipose tissue (BAT) in adult humans, occurring in most of the perirenal fat depot and characterized by a unilocular morphology. This phenotype was contrasted by multilocular BAT accumulating near the adrenal gland. Transcriptomic analysis revealed a gene expression profile of unilocular BAT that was approaching, yet was still distinct from, the expression profile of subcutaneous white adipose tissue (WAT). Candidate gene signatures were recapitulated in a murine model of unilocular brown fat induced by thermoneutrality and high fat diet. We identified SPARC as a candidate adipokine representing a dormant BAT state in the absence of sympathetic activation and CLSTN3 as a novel marker for multilocular BAT. Brown fat precursor cells were present in the entire perirenal fat depot, regardless of state. When differentiated in vitro, these cells responded to acute norepinephrine stimulation by increasing UCP1 gene expression and uncoupled respiration, confirming a BAT phenotype. We thus propose a mechanism for the reduction of functionally competent BAT in adult humans and we provide a solid data set for future research on factors that can reactivate dormant BAT as a potential strategy for combatting obesity and metabolic disease.
Recurrent pregnancy loss is associated with a pro-senescent decidual response during the peri-implantation window
Authors: Lucas Emma S , Vrljicak Pavle , Muter Joanne , Diniz-da-Costa Maria M , Brighton Paul J , Kong Chow-Seng , Lipecki Julia , Fishwick Katherine , Odendaal Joshua , Ewington Lauren J. , Quenby Siobhan , Ott Sascha , Brosens Jan J
Published: July 2018

Breakdown of the feto-maternal interface in early pregnancy causes miscarriage. The cycling endometrium becomes poised to transition to a pregnant state during the midluteal implantation window, coinciding with differentiation of stromal cells into decidual cells (DC) and emergence of senescent decidual cells (snDC). Emerging evidence suggests that DC engage uterine natural killer cells to eliminate their senescent counterparts, thus enabling formation of a robust decidual matrix in pregnancy. To examine if failure to constrain snDC during the peri-implantation window increases the risk of miscarriage, we reconstructed the decidual pathway at single-cell levelin vitroand demonstrated that, without immune surveillance, secondary senescence rapidly transforms DC into progesterone-resistant cells that abundantly express extracellular matrix remodelling factors. Additional single-cell analysis of midluteal endometrium identifiedDIO2andSCARA5as marker genes of a diverging decidual responsein vivo. Finally, we report a conspicuous link between a pro-senescent decidual response in luteal phase endometrium and recurrent pregnancy loss, suggesting that pre-pregnancy screening and intervention may reduce the burden of miscarriage.
Underlying mechanisms and ecological consequences of variation in exploratory behavior of the Argentine ant,Linepithema humile
Authors: Page Hannah , Sweeney Andrew , Pilko Anna , Pinter-Wollman Noa
Published: July 2018

Uncovering how and why animals explore their environment is fundamental for understanding population dynamics, the spread of invasive species, species interactions etc. In social animals, individuals within a group can vary in their exploratory behavior and the behavioral composition of the group can determine its collective success. Workers of the invasive Argentine ant (Linepithema humile)exhibit individual variation in exploratory behavior, which affects the colony’s collective nest selection behavior. Here we examine the mechanisms underlying this behavioral variation in exploratory behavior and determine its implications for the ecology of this species. We first establish that individual variation in exploratory behavior is repeatable and consistent across situations. We then show a relationship between exploratory behavior and the expression of genes that have been previously linked with other behaviors in social insects. Specifically, we find a negative relationship between exploratory behavior and the expression of the FOR gene. Finally, we determine how colonies allocate exploratory individuals in natural conditions. We find that ants from inside the nest are the least exploratory individuals, while workers on newly formed foraging trails are the most exploratory individuals. Furthermore, workers in the spring, when new resources emerge, are more exploratory than workers in the winter, potentially allowing the colony to find and exploit new resources. These findings reveal the importance of individual variation in behavior for the ecology of social animals and provide mechanistic and functional explanations for how such behavioral variation can emerge.
Complement C3-targeted gene therapy restricts onset and progression of neurodegeneration in chronic mouse glaucoma
Authors: Bosco Alejandra , Anderson Sarah R , Breen Kevin T , Romero Cesar O , Steele Michael R , Chiodo Vince A , Boye Sanford L , Hauswirth William W , Tomlinson Stephen , Vetter Monica L
Published: July 2018

Dysregulation of the complement system is implicated in neurodegeneration, including human and animal glaucoma. Optic nerve and retinal damage in glaucoma is preceded by local complement upregulation and activation, but whether targeting this early innate immune response could have therapeutic benefit remains undefined. Because complement signals through three pathways that intersect at complement C3 activation, here we targeted this step to restore complement balance in the glaucomatous retina, and to determine its contribution to degeneration onset and/or progression. To achieve this, we combined adeno-associated viral retinal gene therapy with the targeted C3 inhibitor CR2-Crry. We show that intravitreal injection of AAV2.CR2-Crry produced sustained Crry overexpression in the retina, and reduced deposition of the activation product complement C3d on retinal ganglion cells and the inner retina of DBA/2J mice. This resulted in neuroprotection of retinal ganglion cell axons and somata despite continued intraocular pressure elevation, suggesting a direct restriction of neurodegeneration onset and progression, and significant delay to terminal disease stages. Our study uncovers a damaging effect of complement C3 or downstream complement activation in glaucoma and establishes AAV2.CR2-Crry as a viable therapeutic strategy to target pathogenic C3-mediated complement activation in the glaucomatous retina.
Individual variations of the human corticospinal tract and its hand-related motor fibers using diffusion MRI tractography
Authors: Dalamagkas Kyriakos , Tsintou Magdalini , Rathi Yogesh , O'Donnell Lauren J , Pasternak Ofer , Gong Xue , Zhu Anne , Savadjiev Peter , Papadimitriou George M , Kubicki Marek , Yeterian Edward H , Makris Nikos
Published: July 2018

The corticospinal tract (CST) is one of the most well-studied tracts in human neuroanatomy. Its clinical significance can be demonstrated in many notable traumatic conditions and diseases such as stroke, spinal cord injury (SCI) or amyotrophic lateral sclerosis (ALS). With the advent of diffusion MRI and tractography the computational representation of the human CST in a 3D model became available. However, the representation of the entire CST and, specifically, the hand motor area has remained elusive. In this paper we proposed a novel method, using manually-drawn ROIs based on robustly identifiable neuroanatomic structures to delineate the entire CST and isolate its hand motor representation as well as to estimate their variability and generate a database of their volume, length and biophysical parameters. Using 37 healthy human subjects we performed a qualitative and quantitative analysis of the CST and the hand-related motor fiber tracts (HMFTs). Finally, we have created variability heatmaps from 37 subjects for both the aforementioned tracts, which could be utilized as reference for clinicians to explore neuropathology in both trauma and disease states.
PPARγ is a nexus controlling alternative activation of macrophages via glutamine metabolism
Authors: Nelson Victoria L. , Nguyen Hoang C.B. , Garcìa-Cañaveras Juan C. , Briggs Erika R. , Ho Wesley Y. , DiSpirito Joanna R. , Marinis Jill M. , Hill David A. , Lazar Mitchell A.
Published: July 2018

The nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) is known to regulate lipid metabolism in many tissues, including macrophages. Here we report that peritoneal macrophage respiration is enhanced by rosiglitazone, an activating PPARγ ligand, in a PPARγ-dependent manner. Moreover, PPARγ is required for macrophage respiration even in the absence of exogenous ligand. Unexpectedly, the absence of PPARγ dramatically affects the oxidation of glutamine. Both glutamine and PPARγ have been implicated in alternative activation (AA) of macrophages, and PPARγ was required for interleukin 4 (IL4)-dependent gene expression and stimulation of macrophage respiration. Indeed, unstimulated macrophages lacking PPARγ contained elevated levels of the inflammation-associated metabolite itaconate and express a proinflammatory transcriptome that, remarkably, phenocopied that of macrophages depleted of glutamine. Thus, PPARγ functions as a checkpoint, guarding against inflammation, and is permissive for AA by facilitating glutamine metabolism. However, PPARγ expression is itself markedly increased by IL4. This suggests that PPARγ functions at the center of a feed-forward loop that is central to AA of macrophages.
Variant antigen repertoires inTrypanosoma congolensepopulations and experimental infections can be profiled from deep sequence data using universal protein motifs
Authors: Silva Pereira Sara , Casas-Sánchez Aitor , Haines Lee R. , Ogugo Moses , Absolomon Kihara , Sanders Mandy , Kemp Steve , Acosta-Serrano Álvaro , Noyes Harry , Berriman Matthew , Jackson Andrew P.
Published: July 2018

African trypanosomes are vector-borne hemoparasites of humans and animals. In the mammal, parasites evade the immune response through antigenic variation. Periodic switching of the variant surface glycoprotein (VSG) coat covering their cell surface allows sequential expansion of serologically distinct parasite clones. Trypanosome genomes contain many hundreds ofVSGgenes, subject to rapid changes in nucleotide sequence, copy number, and chromosomal position. Thus, analyzing, or even quantifying, VSG diversity over space and time presents an enormous challenge to conventional techniques. Indeed, previous population genomic studies have overlooked this vital aspect of pathogen biology for lack of analytical tools. Here we present a method for analyzing population-scale VSG diversity inTrypanosoma congolensefrom deep sequencing data. Previously, we suggested thatT. congolenseVSGs segregate into defined “phylotypes” that do not recombine. In our data set comprising 41T. congolensegenome sequences from across Africa, these phylotypes are universal and exhaustive. Screening sequence contigs with diagnostic protein motifs accurately quantifies relative phylotype frequencies, providing a metric of VSG diversity, called the “variant antigen profile.” We applied our metric to VSG expression in the tsetse fly, showing that certain, rare VSG phylotypes may be preferentially expressed in infective, metacyclic-stage parasites. Hence, variant antigen profiling accurately and rapidly determines theT. congolense VSGgene and transcript repertoire from sequence data, without need for manual curation or highly contiguous sequences. It offers a tractable approach to measuring VSG diversity across strains and during infections, which is imperative to understanding the host–parasite interaction at population and individual scales.
OChemDb: the free online Open Chemistry Database portal for searching and analysing crystal structure information
Authors: Altomare Angela , Corriero Nicola , Cuocci Corrado , Falcicchio Aurelia , Moliterni Anna , Rizzi Rosanna
Published: July 2018

The Open Chemistry Database (OChemDb) is a new free online portal which uses an appropriately designed database of already solved crystal structures. It makes freely available computational and graphical tools for searching and analysing crystal-chemical information of organic, metal–organic and inorganic structures, and providing statistics on desired bond distances, bond angles, torsion angles and space groups. Atom types have been classified by an identifier code containing information about the chemical topology and local environment. The crystallographic data used by OChemDb are acquired from the CIFs contained in the free small-molecule Crystallography Open Database (COD). OChemDb offers easy-to-use and intuitive options for searching. It is updated by following the continuous growth of information stored in the COD. It can be of great utility for structural chemistry, in particular in the process of determination of a new crystal structure, and for any discipline involving crystalline structure knowledge. The use of OChemDb requires only a web browser and an internet connection. Every device (mobile or desktop) and every operating system is able to use OChemDb by accessing its web page. Examples of application of OChemDb are reported.
Single crystals of the filled Ti2N-type η-phase Ti3Zn3O
x
(x = 1.07 and 1.23) prepared using a Bi flux
Authors: Yamane Hisanori , Hiraka Keita
Published: July 2018

Single crystals of the filled Ti2Ni-type Ti3Zn3O
x
η-phase (cubic, space group Fd\overline{3}m) having {111} facets were obtained by heating Ti, Zn and ZnO with a Bi flux. The lattice parameter of a single crystal prepared at 800°C was 11.4990 (2) Å, which is close to that of Ti3Zn3O∼0.5 (a = 11.502 Å), as reported by Rogl & Nowotny [Monatsh. Chem. (1977), 108, 1167–1180]. The occupancies of the O1 (16c) and O2 (8a) sites were 1 and 0.071 (12), respectively, and the composition of the crystal was determined to be Ti3Zn3O1.04. A single crystal from the sample prepared at 650°C had the same structure type, with a lattice parameter of 11.5286 (2) Å. However, O atoms were situated at a new 32e site in addition to the original 16c and 8a sites, and the Zn-atom positions were split in accordance with the new O-atom site. The chemical formula Ti3Zn3O1.27 determined by X-ray diffraction occupancy refinement agreed with the chemical composition obtained for the cross section of the single crystal determined with an electron probe microanalyzer.
Crystal structure of a dinuclear ruthenium(II) complex with a bent CO2
2− bridge
Authors: Takase Tsugiko , Abe Ryosuke , Oyama Dai
Published: July 2018

The molecular and crystal structures of a CO2
2−-bridged dinuclear ruthenium complex is reported, namely, μ-carbonito-κ2
C:O-bis[bis(2,2′-bipyridine-κ2
N,N′)carbonylruthenium(II)] bis(hexafluoridophosphate)–acetonitrile–diethyl ether (1/1/0.5), [Ru2(CO)2(C10H8N2)4(μ:κ
2-C:O-CO2)](PF6)2·CH3CN·0.5C4H10O. The complex cation in the title compound consists of two {Ru(CO)(bpy)2}2+ units (bpy = 2,2′-bipyridine) singly bridged by a μ:κ2-C:O carbonite anion, resulting in an unsymmetrical dinuclear structure. Some of the interatomic C...O distances involving the carbonyl ligands are shorter than the sum of the van der Waals radii. There are intramolecular C—H...O and aromatic π–π contacts in the cationic complex. In the crystal, the cations are linked by pairs of C—H...F hydrogen bonds in addition to weak C—H...F interactions between the solvent molecules and PF6
− counter-anions. The equatorial F atoms of one of the PF6
− anions are disordered over two sets of sites with an occupancy ratio of 0.908 (7):0.092 (7) while the central O atom of the diethyl ether solvent molecule is disordered over an inversion centre.
Towards Industry 4.0
Authors: Ardito Lorenzo , Petruzzelli Antonio Messeni , Panniello Umberto , Garavelli Achille Claudio
Published: July 2018

Purpose

The purpose of this paper is to present a comprehensive picture of the innovative efforts undertaken over time to develop the digital technologies for managing the interface between supply chain management and marketing processes and the role they play in sustaining supply chain management-marketing (SCM-M) integration from an information processing point of view.

Design/methodology/approach

Patent analysis and actual examples are used to carry out this study. In detail, first, the authors identify the subset of enabling technologies pertaining to the fourth industrial revolution (Industry 4.0) that can be considered the most relevant for effective SCM-M integration (i.e. Industrial Internet of Things, Cloud computing, Big Data analytics and customer profiling, Cyber security). Second, the authors carry out a patent analysis aimed at providing a comprehensive overview of the patenting activity trends characterizing the set of digital technologies under investigation, hence highlighting their innovation dynamics and applications.

Findings

This research provides insightful information about which digital technologies may enable the SCM-M integration. Specifically, the authors highlight the role those solutions play in terms of information acquisition, storage and elaboration for SCM-M integration by relying on illustrative actual examples. Moreover, the authors present the organisations more involved in the development of digital technologies for SCM-M integration over time and offer an examination of their technological impact in terms of influence on subsequent technological developments.

Originality/value

So far, much has been said about why marketing and supply chain management functions should be integrated. However, a clear picture of the digital technologies that might be adopted to achieve this objective has yet to be revealed. Thus, the paper contributes to the literature on SCM-M integration and Industry 4.0 by highlighting the enabling technologies for the Industry 4.0 that may particularly serve for managing the SCM-M interface from an information processing perspective.
Managing the exploration-exploitation paradox in healthcare
Authors: Gastaldi Luca , Appio Francesco Paolo , Corso Mariano , Pistorio Andrea
Published: July 2018

Purpose

The purpose of this paper is to understand how digital technologies can help healthcare organisations and improve the exploration-exploitation paradox over time. The authors explore inputs, processes and outcomes of implementing digital transformation programs and advance four testable propositions.

Design/methodology/approach

The authors conducted multiple case studies with embedded units of analysis: digital transformation processes; hospitals; and regional healthcare systems. Primary sources come from 107 semi-structured interviews with key informants within 14 Italian hospitals between 2009 through 2011.

Findings

Three complementary paths emerge as fundamental to balance exploratory and exploitatory efforts in healthcare: assets digitalisation within hospitals; digitally based process integration; and disruptive decision-making through analytics. Intra- and inter-path characteristics are discussed to show how digital transformation can both move hospital within the exploration-exploitation space.

Research limitations/implications

By its very nature, this study is exploratory. Notwithstanding the number of cases and interviews, its generalisability is limited.

Practical implications

Digital transformation programs are fundamental to resolve the tensions raised by the exploration-exploitation paradox. Their implementation leads to better performance (cost reductions, quality improvements). A framework is provided for practitioners to make better decisions.

Originality/value

This study sheds new light on how digital technologies are actually adopted and adapted in healthcare contexts. It does it by entailing a longitudinal perspective.
Do labour unions mitigate labour conflicts in China’s manufacturing firms?
Authors: Fan Hanbing , Dong Yiming , Hu Dezhuang , Luo Lianfa
Published: July 2018

Purpose

This paper aims to examine whether labour unions influence labour conflicts and this mechanism is different in China compared with other countries.

Design/methodology/approach

This paper uses the data from the China Employer–Employee Survey that interviewed 1,208 firms and 10,087 workers in 2016 as the measurement of variables, and it uses Logit regression model to do the empirical research.

Findings

Unions cannot significantly influence labour conflicts. More active unions and unions whose leaders are appointed by the firms’ management are associated with a higher incidence of labour conflicts.

Originality/value

This paper finds a new mechanism that explains the relationship between unions and labour conflicts. The existing literature states that unions may increase labour conflicts via “monopoly power” and may also mitigate labour conflicts via “voice mechanisms”. This paper’s findings show that the positive correlation between unions and labour conflicts may be explained by the lack of “voice mechanism” rather than “monopoly power”. The findings imply that labour unions should represent the interest of workers to mitigate the increasing labour conflicts.
Hidden potentials in open-loop supply chains for remanufacturing
Authors: Kalverkamp Matthias
Published: July 2018

Purpose

The circular economy grows in popularity in sustainability-oriented environments. Remanufacturing contributes to circularity though it faces challenges regarding reverse supply chains (SCs). Literature focusses on closed-loop supply chains (CLSCs) for reverse flows of products. However, alternative SCs and different market actors provide used components (cores) for remanufacturing through “open-loops”. The purpose of this paper is to investigate the influence of independent actors on core supply and how especially middlemen implement supplier relationship management to address supply shortages in automotive remanufacturing.

Design/methodology/approach

The study follows a qualitative research approach to compare remanufacturing SCs in Europe and North America. The analysis aims to identify managerial leverage to reduce supply shortages.

Findings

Reduction of information asymmetries and transaction costs is crucial for “open-loop supply chains” to compete with more integrated CLSCs. The study identifies an e-procurement solution that addresses these issues and helps to increase the supply through “open-loops”. Furthermore, regulation may hinder or facilitate supply.

Research limitations/implications

It needs to be further investigated to what extent e-procurement and supplier relationship management can reduce shortages. Middlemen who can collaborate with the research would provide further research opportunities.

Practical implications

If supplier relationship management adapts to the requirements of remanufacturing, it can increase the supply potential through “open-loop” SCs. The e-procurement solution could serve SCs beyond automotive remanufacturing. Policy makers need to revise legislation hindering these SCs.

Originality/value

The study provides novel findings regarding independent actors, their supplier relationship management and their potential to reduce shortages in independent SCs for remanufacturing.
Identification of the similarities and differences of logistics controller, manager and specialist
Authors: Dobroszek Justyna , Mourao Paulo , Grzesiak Lena
Published: July 2018

Purpose

The purpose of this paper is to demonstrate the similarities and differences of occupational identity among logistics managers, controllers and specialists.

Design/methodology/approach

After a thorough review of the literature, the authors opted for desk research and content analysis of job advertisements for these three occupations as the major research method, focusing on a sample of 60 Polish and German advertisements.

Findings

The analysis of these data confirmed that the three occupations have their own identity (although there is a certain closeness between controllers and managers), but, from a holistic perspective of logistics management considering current trends in logistics, these three occupations should be integrated as a whole.

Originality/value

This has been the first paper comparing ads focused on logistics professionals in two relevant European economies in terms of logistics development: Poland and Germany.
High commitment human resource practices and employee behavior: a multi-level analysis
Authors: Nam Jungmin , Lee Hwansoo
Published: July 2018

Purpose

The purpose of this paper is to examine the relationship between high commitment human resource practices (HCHRPs), conceptualized at the workplace level and employees’ attitudes, including affective commitment (AC) and turnover intention (TI). The study also tests the moderating role of cooperative labor–management relations (CLMR) between HCHRPs and organizational trust (OT).

Design/methodology/approach

Based on social exchange theory and trust commitment theory, the authors build a research model that explains employee behavior and empirically prove the model by using samples of 407 employees from South Korea. This study uses hierarchical linear regression and cross-level hypotheses based on hierarchical linear modeling.

Findings

The results demonstrate the positive impact of HCHRPs on an AC and TI, through OT. However, no moderating effect of CLMR between human resource management (HRM) practices and OT is observed.

Originality/value

Few theory-based studies test the direct linkage between HRM practices and outcomes. This study is designed with a multi-level research method to provide a conceptually comprehensive and deeper understanding of how HRM practices work in an organization by testing the relationship between organizational practices and employees’ outcomes.
From outsider to insider: how creative professional service firms internationalise
Authors: McQuillan Deirdre , Scott Pamela Sharkey , Mangematin Vincent
Published: July 2018

Purpose

The management of reputation and status is central to creative professional service firms (CPSFs) rendering the internationalisation process a particular challenge. The authors build on arguments that internationalisation requires moving from outsidership to insidership within client networks and focus on how CPSFs build signals about quality to start this process. The paper aims to discuss these issues.

Design/methodology/approach

The exploration draws from the international business, professional services and organisational status bodies of literature. A multiple case study design was developed comprising ten Irish architecture firms. In-depth semi-structured interviews were conducted.

Findings

The findings clarify how relationships start in the internationalisation process through signal building about quality. This allows CPSFs to join client networks moving from outsidership to insidership. The findings systemise three different approaches for CPSFs: from outsidership to insidership within a local market network, within a global industry network and within a global project network.

Research limitations/implications

Research within other sectoral and geographical contexts could support transferability of the findings.

Practical implications

The study has implications for international business strategies as it identifies multiple paths to relevant network insidership and the tactical responses managers can use to achieve this.

Originality/value

The authors believe that incorporating signal-building mechanisms into the internationalisation process is a novel approach to theorizing about how CPSFs move from outsidership to insidership. The authors offer important theoretical insights into the international business, professional service firm and organisational status literatures. CPSF business leaders should benefit as it helps them to focus on a portfolio of signal-building approaches that can start the internationalisation process.
Gamification in aquarium context
Authors: Tan Wee Kheng
Published: July 2018

Purpose

The purpose of this paper is to consider issues related to gamification through the non-game aquarium context and explore how the intention of aquarium visitors to play a game that imparts knowledge about marine animals and promotes the conservation of these animals is influenced by visitors’ attitudes toward marine animals, motivations to visit the aquarium and perceptions of the game’s benefits.

Design/methodology/approach

This study surveyed individuals who have visited Taiwan’s National Museum of Marine Biology and Aquarium at least once in the past three years and who use smartphones. They were shown a description of a hypothetical game scenario that they were asked to imagine to be available while at the aquarium. The partial least squares method was used to analyze the data from 225 returns.

Findings

The study shows that gamification can satisfy a visitor’s desire to learn and enjoy the aquarium simultaneously. Gamification is limited by the visit motivation and the attitudes toward marine animals that visitors bring with them. The usefulness of gamification is limited when visitors desire relaxation during the visit.

Originality/value

This study considers the application of gamification in the context of aquariums and the tourism field and the non-technology-related antecedents to the use of gamification. Gamification is not silver bullet for every situation, and a good understanding of potential users is important for its success and targeting of players. The importance of intrinsic benefits over extrinsic benefits is confirmed. Thus, this study addresses several gaps in the gamification literature.