bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural genomic variation leads to unexpected genetic differentiation in Lake Tanganyika’s sardines
Authors: Junker Julian , Rick Jessica A. , McIntyre Peter B. , Kimirei Ismael , Sweke Emmanuel A. , Mosille Julieth B. , Wehrli Bernhard , Dinkel Christian , Mwaiko Salome , Seehausen Ole , Wagner Catherine E.
Published: October 2019

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika’s two sardine species,Limnothrissa miodonandStolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, whereL. miodonwas introduced in 1959. Our results reveal unexpected differentiation within bothS. tanganicaeandL. miodonthat is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large segregating inversion inL. miodon. We found all inversion karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient, and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation-by-distance, even over the hundreds of kilometers covered by our sampling, but we do find shallow population structure.
A unified framework for dopamine signals across timescales
Authors: Kim HyungGoo R. , Malik Athar N. , Mikhael John G. , Bech Pol , Tsutsui-Kimura Iku , Sun Fangmiao , Zhang Yajun , Li Yulong , Watabe-Uchida Mitsuko , Gershman Samuel J. , Uchida Naoshige
Published: October 2019

Rapid phasic activity of midbrain dopamine neurons are thought to signal reward prediction errors (RPEs), resembling temporal difference errors used in machine learning. Recent studies describing slowly increasing dopamine signals have instead proposed that they represent state values and arise independently from somatic spiking activity. Here, we developed novel experimental paradigms using virtual reality that disambiguate RPEs from values. We examined the dopamine circuit activity at various stages including somatic spiking, axonal calcium signals, and striatal dopamine concentrations. Our results demonstrate that ramping dopamine signals are consistent with RPEs rather than value, and this ramping is observed at all the stages examined. We further show that ramping dopamine signals can be driven by a dynamic stimulus that indicates a gradual approach to a reward. We provide a unified computational understanding of rapid phasic and slowly ramping dopamine signals: dopamine neurons perform a derivative-like computation over values on a moment-by-moment basis.
Widespread inhibition, antagonism, and synergy in mouse olfactory sensory neurons in vivo
Authors: Inagaki Shigenori , Iwata Ryo , Iwamoto Masakazu , Imai Takeshi
Published: October 2019

Sensory information is selectively or non-selectively inhibited and enhanced in the brain, but it remains unclear whether this occurs commonly at the peripheral stage. Here, we performed two-photon calcium imaging of mouse olfactory sensory neurons (OSNs) in vivo and found that odors produce not only excitatory but also inhibitory responses at their axon terminals. The inhibitory responses remained in mutant mice, in which all possible sources of presynaptic lateral inhibition were eliminated. Direct imaging of the olfactory epithelium revealed widespread inhibitory responses at OSN somata. The inhibition was in part due to inverse agonism toward the odorant receptor. We also found that responses to odor mixtures are often suppressed or enhanced in OSNs: Antagonism was dominant at higher odor concentrations, whereas synergy was more prominent at lower odor concentrations. Thus, odor responses are extensively tuned by inhibition, antagonism, and synergy, at the early peripheral stage, contributing to robust odor representations.
Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
Authors: Bawn Matt , Thilliez Gaetan , Kirkwood Mark , Wheeler Nicole , Petrovska Liljana , Dallman Timothy J. , Adriaenssens Evelien M. , Hall Neil , Kingsley Robert A.
Published: October 2019

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and disseminated disease worldwide. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. A robust fully parsimonious phylogenetic tree constructed from recombination purged variation in the whole genome sequence of 131 diverse strains of S. Typhimurium revealed population structure composed of two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β predominantly contained subclades associated with wild avian species, with the notable exception of a subclade containing the DT204/49 complex. The contrasting epidemiology of α and β strains was reflected in a distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification associated with invasiveness of host adapted serotypes. Gene flux was predominantly driven by acquisition, loss or recombination of prophage. The acquisition of large genetic islands (SGI-1 and 4) was limited to two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) in clade α. Together, our data are consistent with the view that a broad host range common ancestor of S. Typhimurium diversified with clade α lineages remained largely associated with multiple domesticated animal species, while clade β spawned multiple lineages that underwent diversifying selection associated with adaptation to various niches, predominantly in wild avian species.
Open-source 3D printed air-jet for generating monodispersed alginate microhydrogels
Authors: Hadley Dustin J. , Campbell Kevin T. , Gabriel Marina H. , Silva Eduardo A.
Published: October 2019

Open-source designs represent an attractive and new tool for research as it provides both affordable and accessible options to the lab environment. In particular, with the advent of new and cheap additive manufacturing technologies, the open-source design of lab hardware enables others to perform research that would be difficult otherwise. This manuscript describes an air-jet system designed to be open-source and simple to produce with 3D printing. The fully 3D printed air-jet was designed for the generation of hydrogel microbeads of a controllable size. Alginate microbeads were used as a working model, given that it has many promising research applications due to their injectability and highly reproducible properties. A fit definitive design of experiments was performed to determine critical factors affecting diameter, index of dispersity, and circularity of microbeads from this air-jet design. By regulating alginate concentration, air pressure, pump speed, and needle diameter could achieve control over microbeads size from 200-800 µm with low variance. Furthermore, we also demonstrate the potential probiotic research applications of the open-source air-jet through the encapsulation of bacteria in alginate microbeads with controllable degradation. The results of this study exhibit an open-source platform for making microscale biomaterials with controllable properties that can be achieved through budget 3D printers.
Efficient and robust coding in heterogeneous recurrent networks
Authors: Zeldenrust Fleur , Gutkin Boris , Denéve Sophie
Published: October 2019

Cortical networks show a large heterogeneity of neuronal properties. However, traditional coding models have focused on homogeneous populations of excitatory and inhibitory neurons. Here, we analytically derive a class of recurrent networks of spiking neurons that close to optimally track a continuously varying input online, based on two assumptions: 1) every spike is decoded linearly and 2) the network aims to reduce the mean-squared error between the input and the estimate. From this we derive a class of predictive coding networks, that unifies encoding and decoding and in which we can investigate the difference between homogeneous networks and heterogeneous networks, in which each neurons represents different features and has different spike-generating properties. We find that in this framework, ‘type 1’ and ‘type 2’ neurons arise naturally and networks consisting of a heterogeneous population of different neuron types are both more efficient and more robust against correlated noise. We make two experimental predictions: 1) we predict that integrators show strong correlations with other integrators and resonators are correlated with resonators, whereas the correlations are much weaker between neurons with different coding properties and 2) that ‘type 2’ neurons are more coherent with the overall network activity than ‘type 1’ neurons.
The LTB4-BLT1 axis regulates actomyosin and β2 integrin dynamics during neutrophil extravasation
Authors: Subramanian Bhagawat C. , Melis Nicolas , Chen Desu , Wang Weiye , Gallardo Devorah , Weigert Roberto , Parent Carole A.
Published: October 2019

The eicosanoid Leukotriene B4(LTB4) relays chemotactic signals to direct neutrophil migration to inflamed sites through its receptor BLT1. However, the mechanisms by which the LTB4-BLT1 axis relays chemotactic signals during intravascular neutrophil response to inflammation remain unclear. Here, we report that LTB4produced by neutrophils acts as an autocrine/paracrine signal to direct the vascular recruitment, arrest and extravasation of neutrophils in a sterile inflammation model in the mouse footpad. Using Intravital Subcellular Microscopy (ISMic), we reveal that LTB4elicits sustained cell polarization and adhesion responses during neutrophil arrestin vivo. Specifically, LTB4signaling coordinates the dynamic redistribution of non-muscle Myosin IIA (NMIIA) and β2-integrin (Itgb2), which facilitate neutrophil arrest and extravasation. Notably, we also found that neutrophils shed extracellular vesicles (EVs) in the vascular lumen, and that inhibition of EV release blocks LTB4-mediated autocrine/paracrine signaling required for neutrophil arrest and extravasation. Overall, we uncover a novel complementary mechanism by which LTB4relays extravasation signals in neutrophils during early inflammation response.

Neutrophils arrest and extravasate from the blood vessels in response to infection and injury. Using intravital subcellular microscopy, Subramanianet al. identify a role for extracellular vesicles-based autocrine/paracrine LTB4-BLT1 signaling in promoting the re-arrangement of actomyosin cytoskeleton and β2-integrin during neutrophil extravasation in live animals.
DNA hydroxymethylation reveals transcription regulation networks and prognostic signatures in multiple myeloma
Authors: Alberge Jean-Baptiste , Magrangeas Florence , Wagner Mirko , Denié Soline , Guérin-Charbonnel Catherine , Campion Loïc , Attal Michel , Avet-Loiseau Hervé , Carell Thomas , Moreau Philippe , Minvielle Stéphane , Sérandour Aurélien A.
Published: October 2019

Multiple myeloma (MM) is a plasma cell malignancy that remains challenging to cure despite a substantially improving median survival. During the last decade, DNA copy number variation and gene expression studies have described the pathology and its heterogeneity among patients. Epigenetic modifications play important roles in MM, but they are rarely associated with clinical aspects of the disease. In this epigenomics study, we produced quantifications of genomic 5-methylcytosine (5mC) and of 5-hydroxymethylcytosine (5hmC) as well as genome-wide maps of hydroxymethylation to analyse myeloma cells taken from a cohort of 40 newly diagnosed and homogeneously treated patients. We found 5hmC to be globally depleted in MM compared to normal plasma cells, as well as being reduced in advanced clinical stages of the disease. From the hydroxymethylome data, we observed that remaining 5hmC is organised in large peak clusters and is associated with well-known disease-related genes. Based on their signal correlation, these 5hmC peak clusters can be gathered in 2 regulation networks involving core transcription factors such as IRF4, MYC, PRDM1 and TCF3. By performing paired hydroxymethylomes at diagnosis and at relapse, we found the disease progression to be heterogeneous and patient-specific. We found that the location of 5hmC at tumor suppressor TP53INP1 is associated with better outcome while global high level of 5hmC tends to be associated with better overall survival. Together, our study suggests that 5hmC provides new biological insights of the disease severity and progression, and can be used for retrospective studies.

Key Points

5hmC is globally depleted in MM and even more in advanced stages of the disease.

5hmC is locally detected at transcriptionally active regions of MM where its presence can be associated with survival.
Structural differences in translation initiation between pathogenic trypanosomatids and their mammalian hosts
Authors: Bochler Anthony , Querido Jailson Brito , Prilepskaja Terezie , Soufari Heddy , Simonetti Angelita , Cistia Mayara Lucia Del , Kuhn Lauriane , Ribeiro Aline Rimoldi , Valášek Leoš Shivaya , Hashem Yaser
Published: October 2019

Canonical mRNA translation in eukaryotes begins with the formation of the 43S pre-initiation complex (PIC). Its assembly requires the binding of several eukaryotic initiation factors (eIF 1, 1A, 2, 3 and 5), Met-tRNAiMet and the small ribosomal subunit (40S). Compared to their mammalian hosts, trypanosomatids present significant structural differences in their 40S suggesting substantial variability in translation initiation. Here we determined the structure of the 43S PIC from Trypanosoma cruzi, the parasite causing the Chagas disease. Our structure shows numerous specific features, such as the variant eIF3 structure and its unique interactions with the large rRNA ESs 9S, 7S and 6S, and the association of a kinetoplastid-specific ~245 kDa DDX60-like helicase. It also revealed the so-far-elusive 40S-binding site of the eIF5 C-terminal domain and the structures of key terminal tails of several conserved eIFs underlying their activities within the PIC. Our results are corroborated by GST-pulldown assays in both human and T. cruzi and mass-spectrometry data.
The STING pathway does not contribute to Pink1/parkin phenotypes in Drosophila
Authors: Lee Juliette J. , Andreazza Simonetta , Whitworth Alexander J.
Published: October 2019

Mutations in PINK1 and Parkin/PRKN cause the degeneration of dopaminergic neurons in familial forms of Parkinson’s disease but the precise pathogenic mechanisms are unknown. The PINK1/Parkin pathway has been described to play a central role in mitochondrial homeostasis by signaling the targeted destruction of damaged mitochondria, however, how disrupting this process leads to neuronal death until recently was unclear. An elegant study in mice revealed that the loss of Pink1 or Prkn coupled with an additional mitochondrial stress resulted in the aberrant activation of the innate immune signaling, mediated via the cGAS/STING pathway, causing degeneration of dopaminergic neurons and motor impairment. Genetic knockout of Sting was sufficient to completely prevent neurodegeneration and accompanying motor deficits. To determine whether Sting plays a conserved role in Pink1/parkin related pathology, we tested for genetic interactions between Sting and Pink1/parkin in Drosophila. Surprisingly, we found that loss of Sting, or its downstream effector Relish, was insufficient to suppress the behavioral deficits or mitochondria disruption in the Pink1/parkin mutants. Thus, we conclude that phenotypes associated with loss of Pink1/parkin are not universally due to aberrant activation of the STING pathway.
Reactive astrocyte-driven epileptogenesis is induced by microglia initially activated following status epilepticus
Authors: Sano Fumikazu , Shigetomi Eiji , Shinozaki Youichi , Tsuzukiyama Haruka , Saito Kozo , Mikoshiba Katsuhiko , Sugita Kanji , Aihara Masao , Koizumi Schuichi
Published: October 2019

Extensive activation of glial cells during a latent period has been well documented in various animal models of epilepsy; however, it remains unknown whether such glial activation is capable of promoting epileptogenesis. Here, we show that temporally distinct activation profiles of microglia and astrocytes collaboratively contribute to epileptogenesis in a drug-induced status epilepticus model. We found that reactive microglia appear first, followed by reactive astrocytes and increased susceptibility to seizures. Pharmacological intervention against microglial activation reduces astrogliosis, aberrant astrocyte Ca2+signaling, and seizure susceptibility. Reactive astrocytes exhibit larger Ca2+signals mediated by IP3R2, whereas deletion of this type of Ca2+signaling reduces seizure susceptibility after status epilepticus. Together, our findings indicate that the sequential activation of glial cells constitutes a cause of epileptogenesis after status epilepticus.
Radiologic Evaluation of the Influence of Cleft Type on Nasal Dorsum Growth
Authors: Pu Lingling , Liu Renkai , Shi Bing , Low David W , Li Chenghao
Published: October 2019

Purpose

The study was designed to evaluate whether intrinsic morphological characteristics of the nasal dorsum are affected by cleft type, specifically cleft lip only (CL) and cleft lip with cleft palate(CL/P).

Methods

576 cleft patients (278 CL only, 298 CL/P), and 333 individuals without orofacial clefts were retrospectively enrolled. Lateral cephalometric radiographs of all individuals were taken to evaluate the nasal length and nasal dorsum height. Dunn’s test was used to analyze the difference (p< 0.001).

Results

In CL and control, the angulation of the nasal bone and nasal dorsum increase by age similarly (5y-18y, p>0.05). In CL, the total dorsal length is significantly shorter (5y-18y,p<0.001). Although the upper nasal dorsum is similar (except in 5y-6y), the lower nasal dorsum is shorter (5y-18y,p<0.001).

In CLP, there is no significant difference in the nasal bone angle compared with controls between 5y-7y. However, it develops insufficiently as children grow (8y-18y,p<0.001). The nasal dorsum angle is notably smaller (5y-18y, p<0.001). Nasal bone length is not significantly different from control at all stages except during ages 11y-13y (p<0.05). Total nasal dorsal length is similar to the control at skeletal maturity (17y-18y,p>0.05), although it is shorter during 8y to 16y (p<0.05). The upper nasal dorsum is overdeveloped (14y-18y,p<0.05), whereas the lower nasal dorsum is underdeveloped (5y-18y,p<0.001).

Conclusion

CL inhibits the growth of nasal dorsum length, leading to short nose deformity. CL/P patients are prone to saddle-nose deformity because of the diminished nasal height (decreased nasal angle).
Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway
Authors: Turnšek Jernej , Brunson John K. , Martinez Viedma Maria del Pilar , Deerinck Thomas J. , Horák Aleš , Oborník Miroslav , Bielinski Vincent A. , Allen Andrew E.
Published: October 2019

Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed, however proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatomPhaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
Niche-inspired synthetic matrices for epithelial organoid culture
Authors: Hernandez-Gordillo Victor , Kassis Timothy , Lampejo Arinola , Choi GiHun , Gamboa Mario E. , Gnecco Juan S. , Breault David T. , Carrier Rebecca , Griffith Linda G.
Published: October 2019

Epithelial organoids are now an important tool in fields ranging from regenerative medicine to drug discovery. Organoid culture requires Matrigel, a complex, tumor-derived, extracellular matrix. An alternative completely synthetic matrix could improve culture reproducibility, clarify mechanistic phenomena, and enable applications involving human implantation. Here, we designed synthetic matrices with tunable biomolecular and biophysical properties that allowed us to identify critical gel parameters in organoid formation. Inspired by known epithelial integrin expression in the proliferative niche of the human intestine, we identified an α2β1 integrin-binding peptide as a critical component of the synthetic matrix that supports human duodenal colon and endometrial organoid propagation. We show that organoids emerge from single cells, retain their proliferative capacity, are functionally responsive to basolateral stimulation and have correct apicobasal polarity upon induction of differentiation. The local biophysical presentation of the cues, rather than bulk mechanical properties, appears to be the dominant parameter governing epithelial cell proliferation and organoid formation in the synthetic matrix.
Cannabis use is associated with increased levels of soluble gp130 in schizophrenia but not in bipolar disorder
Authors: Szabo Attila , Akkouh Ibrahim A. , Ueland Thor , Lagerberg Trine Vik , Dieset Ingrid , Bjella Thomas , Aukrust Pål , Le Hellard Stephanie , Stavrum Anne-Kristin , Melle Ingrid , Andreassen Ole A. , Djurovic Srdjan
Published: October 2019

The complex effects of plant cannabinoids on human physiology is not yet fully understood, but include a wide spectrum of effects on immune modulation. The immune system and its inflammatory effector pathways are recently emerging as possible causative factors in psychotic disorders. The present study aimed to investigate whether self-administered cannabis use was associated with changes in circulating immune and neuroendocrine markers in schizophrenia (SCZ, n=401) and bipolar disorder patients (BD, n=242). A screening of 13 plasma markers reflecting different inflammatory pathways was performed in SCZ and BD patients after subdividing each group into cannabis user and non-user subgroups. We found that i) soluble gp130 (sgp130) concentrations were significantly elevated among cannabis users in the SCZ group (p=0.002) after multiple testing correction, but not in BD. ii) Nominally significant differences were observed in the levels of IL-1RA (p=0.0059), YKL40 (p=0.0069), CatS (p=0.013), sTNFR1 (p=0.031), and BDNF (p=0.020), where these factors exhibited higher plasma levels in cannabis user SCZ patients than in non-users. iii) These differences in systemic levels were not reflected by altered mRNA expression of genes encoding sgp130, IL-1RA, YKL40, CatS, sTNFR1, and BDNF in whole blood. In sum, our results show that cannabis self-administration is associated with markedly higher sgp130 levels in SCZ, but not in BD, and that this phenomenon is independent of the modulation of peripheral immune cells. These findings warrant further investigation into the potential neuroimmune, anti-inflammatory, and biobehavioral-cognitive effects of cannabis use in SCZ.
Coding and noncoding somatic mutations in basal cell carcinoma
Authors: Maturo Maria Giovanna , Rachakonda Sivaramakrishna , Heidenreich Barbara , Pellegrini Cristina , Srinivas Nalini , Requena Celia , Serra-Guillen Carlos , Llombart Beatriz , Sanmartin Onofre , Guillen Carlos , Nardo Lucia Di , Peris Ketty , Fargnoli Maria Concetta , Nagore Eduardo , Kumar Rajiv
Published: October 2019

Basal cell carcinoma (BCC) represents the most commonly diagnosed human cancer among persons of European ancestry with etiology mainly attributed to sun-exposure. In this study we investigated mutations in coding and flanking regions of the PTCH1 and TP53 genes and noncoding alterations in the TERT and DPH3 promoters in 191 BCC tumors. In addition, we measured CpG methylation within the TERT hypermethylated oncological region (THOR) and transcriptions levels of the reverse transcriptase subunit. We observed mutations in PTCH1 in 59% and TP53 in 31% of the tumors. Noncoding mutations in TERT and DPH3 promoters were detected in 59% and 38% of the tumors, respectively. We observed a statistically significant co-occurrence of mutations at the four investigated loci. While PTCH1 mutations tended to associate with decreased patient age at diagnosis; TP53 mutations were associated with light skin color and increased number of nevi; TERT and DPH3 promoter with history of cutaneous neoplasms in BCC patients. TERT promoter mutations but not THOR methylation associated with an increased expression of the reverse transcriptase subunit. Our study signifies, in addition to the protein altering mutations in the PTCH1 and TP53 genes, the importance of noncoding mutations in BCC, particularly functional alterations in the TERT promoter.
Performance of nearly fixed offset asymmetric channel-cut crystals for X-ray monochromators
Authors: Frahm Ronald , Diao Qianshun , Murzin Vadim , Bornmann Benjamin , Lützenkirchen-Hecht Dirk , Hong Zhen , Li Tang
Published: October 2019

X-ray double-crystal monochromators face a shift of the exit beam when the Bragg angle and thus the transmitted photon energy changes. This can be compensated for by moving one or both crystals accordingly. In the case of monolithic channel-cut crystals, which exhibit utmost stability, the shift of the monochromated beam is inevitable. Here we report performance tests of novel, asymmetrically cut, channel-cut crystals which reduce the beam movements by more than a factor of 20 relative to the symmetric case over the typical energy range of an EXAFS spectrum at the Cu K-edge. In addition, the presented formulas for the beam offset including the asymmetry angle directly indicate the importance of this value, which has been commonly neglected so far in the operation of double-crystal monochromators.
R3c-type LnNiO3(Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) half-metals with multiple Dirac cones: a potential class of advanced spintronic materials
Authors: Wang Xiaotian , Ding Guangqian , Cheng Zhenxiang , Yuan Hongkuan , Wang Xiao-Lin , Yang Tie , Khenata Rabah , Wang Wenhong
Published: October 2019

In the past three years, Dirac half-metals (DHMs) have attracted considerable attention and become a high-profile topic in spintronics becuase of their excellent physical properties such as 100% spin polarization and massless Dirac fermions. Two-dimensional DHMs proposed recently have not yet been experimentally synthesized and thus remain theoretical. As a result, their characteristics cannot be experimentally confirmed. In addition, many theoretically predicted Dirac materials have only a single cone, resulting in a nonlinear electromagnetic response with insufficient intensity and inadequate transport carrier efficiency near the Fermi level. Therefore, after several attempts, we have focused on a novel class of DHMs with multiple Dirac crossings to address the above limitations. In particular, we direct our attention to three-dimensional bulk materials. In this study, the discovery via first principles of an experimentally synthesized DHM LaNiO3with many Dirac cones and complete spin polarization near the Fermi level is reported. It is also shown that the crystal structures of these materials are strongly correlated with their physical properties. The results indicate that many rhombohedral materials with the general formula LnNiO3(Ln = La, Ce, Nd, Pm, Gd, Tb, Dy, Ho, Er, Lu) in the space groupR3care potential DHMs with multiple Dirac cones.
Mutagenesis facilitated crystallization of GLP-1R
Authors: Xu Yueming , Wang Yuxia , Wang Yang , Liu Kaiwen , Peng Yao , Yao Deqiang , Tao Houchao , Liu Haiguang , Song Gaojie
Published: October 2019

The class B family of G-protein-coupled receptors (GPCRs) has long been a paradigm for peptide hormone recognition and signal transduction. One class B GPCR, the glucagon-like peptide-1 receptor (GLP-1R), has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease. The previously determined structures of inactive GLP-1R in complex with two negative allosteric modulators include ten thermal-stabilizing mutations that were selected from a total of 98 designed mutations. Here we systematically summarize all 98 mutations we have tested and the results suggest that the mutagenesis strategy that strengthens inter-helical hydrophobic interactions shows the highest success rate. We further investigate four back mutations by thermal-shift assay, crystallization and molecular dynamic simulations, and conclude that mutation I1962.66bF increases thermal stability intrinsically and that mutation S2714.47bA decreases crystal packing entropy extrinsically, while mutations S1932.63bC and M2333.36bC may be dispensable since these two cysteines are not disulfide-linked. Our results indicate intrinsic connections between different regions of GPCR transmembrane helices and the current data suggest a general mutagenesis principle for structural determination of GPCRs and other membrane proteins.
Project-specific constraints influencing productivity of tradespeople in the Nigerian construction industry
Authors: Ugulu Rex Asibuodu , Arewa Andrew , Allen Stephen
Published: October 2019

Purpose

The purpose of this paper is to establish the perception of tradespeople about project-specific constraints (PSCs) influencing construction productivity in Nigeria.

Design/methodology/approach

Using a qualitative descriptive survey comprising face-to-face semi-structured interviews and a purposive sampling method, views of eight groups of tradespeople and seven project managers on live construction projects in Nigeria were collected. The study used conventional content analysis with the aid of NVivo 12 pro computer software for the analysis.

Findings

The research evaluated the PSCs and their effect on construction productivity of tradespeople. The findings identified five key PSCs, namely: lack of promotions/reward system, unsafe/poor health condition of workers, delay in material availability, inadequate site amenities and an ageing workforce. These results support earlier research on constraints influencing labour productivity, however, the poor health condition of workers and material unavailability appear to be more unique when compared to other previous studies.

Research limitations/implications

The study focussed on the Federal Capital Territory Abuja and the Lagos State of Nigeria. It provides insight into the PSCs influencing the productivity of tradespeople in the Nigerian construction industry. Further research to identify the PSCs in depth, in the Eastern part of Nigeria is necessary.

Practical implications

The PSCs influencing tradespeople’s productivity was identified. The level of the relative impact of the PSCs is expected to guide the project team in addressing the PSCs in a method that is cost effective.

Originality/value

This study is original research that has underlined some areas of improvement in construction project performance.
Assessing building information modeling implementation readiness in building projects in Singapore
Authors: Liao Longhui , Teo Ai Lin Evelyn , Low Sui Pheng
Published: October 2019

Purpose

The purpose of this paper is to identify critical non-value adding (NVA) building information modeling (BIM) implementation activities in current building project delivery process, develop a BIM implementation readiness (BIMIR) evaluation model, and assess BIMIR statuses in building projects in Singapore.

Design/methodology/approach

A questionnaire survey and four post-survey interviews were conducted in Singapore. A fuzzy synthetic evaluation approach was adopted in the model development.

Findings

In total, 38 out of 44 NVA BIM implementation activities were deemed critical and used in the proposed model, among which “lack of involvement by contractors to contribute site knowledge” in the design development phase was ranked top. This model was validated in five projects. It was found that most of 73 surveyed building projects were in a low BIMIR status and the assessment results were consistent with current industry practices of BIM implementation in Singapore.

Research limitations/implications

There may be geographical limitation on the identification of the critical NVA BIM implementation activities. However, because BIM mandate spreads globally, the findings can help overseas project teams customize their own NVA activities and evaluation models.

Practical implications

As BIM implementation is mandated in Singapore, BIMIR evaluation helps local project teams identify weak areas of their BIM implementation activities and prioritize resources to enhance those areas.

Originality/value

No tool has been developed for evaluating BIMIR at the project level in the construction industry in Singapore or at large in Asia. Four BIMIR statuses are defined, which are consistent with Singapore’s BIM guidelines and standards.
Is the rest of the EU missing out on REITs?
Authors: Grybauskas Andrius , Pilinkiene Vaida
Published: October 2019

Purpose

The purpose of this paper is to investigate whether real estate investment trusts (REITs) have any significant cost-efficiency advantages over real estate operating companies (REOCs).

Design/methodology/approach

The data for listed companies were extracted from the Bloomberg terminal. The authors analyzed financial ratios and conducted a non-parametric data envelope analysis (DEA) for 534 firms in the USA, Canada and some EU member states.

Findings

The results suggest that REITs were much more cost-efficient than REOCs by all the parameters in the DEA model during the entire three-year period under consideration. Although the debt-to-equity levels were similar, REOCs were more relying on short-term than long-term maturities, which made them more vulnerable against market corrections or shocks. Being larger in asset size did not necessarily guarantee greater economies of scale. Both – the cases of increasing economies of scale and diseconomies – were detected. The time period 2015–2017 showed the general trend of decreasing efficiency.

Originality/value

Very few papers on the topic of REITs have attempted to find out whether a different firm structure displays any differences in efficiency. Because the question of REITs and sustainable growth of the real estate market has become a prominent issue, this research can help EU countries to consider the option of adopting a REIT system. If this system were successfully implemented, the EU member states could benefit from a more sustainable and more rapid growth of their real estate markets.
Green and grey infrastructures approaches in flood reduction
Authors: Pamungkas Adjie , Purwitaningsih Santika
Published: October 2019

Purpose

This paper aims to advance the idea of sustainable flood reduction. Flood reduction through the use of the drainage system is considered an unsustainable approach that decreases the use of water. In contrast, the Water Sensitive City is a sustainable concept aimed at increasing the value of water for human needs and reduce flooding.

Design/methodology/approach

The current approach of relying on drainage systems is ineffective and must be combined with green infrastructures to reduce flooding. Green infrastructures can increase infiltration rates or facilitate rain harvesting. The study developed four scenarios that combine green and grey infrastructures and used the Soil and Water Assessment Tool (SWAT) model to select the most effective scenario based on the remaining amount of flood volume in every scenario.

Findings

Green infrastructures that are related to increased infiltration and rain-harvesting instruments reduced flooding by 22.3 and 27.7 per cent, respectively. Furthermore, a combination of the two types of green infrastructures reduced flooding up to 45.5 per cent. Conversely, applying only grey infrastructures (by increasing drainage capacity) to reduce the flooding to zero is unfeasible, as this requires more than double the current capacity. Therefore, a combination of green and grey infrastructures can significantly reduce flooding in a water sensitive and feasible manner.

Originality/value

Applying a combination of green and grey infrastructures is a new and effective approach to reduce flooding in the Kedurus Catchment Area.
Spatial proximity and SME strategy in local networks
Authors: Eiriz Vasco
Published: October 2019

Purpose

Local networks of small- and medium-sized enterprises (SMEs) are founded both on collaborative and competitive inter-organizational relationships within the same network characterised by spatial proximity between firms. This paper aims to propose an original analytical framework to understand how spatial proximity between firms within local networks influences strategy of SMEs.

Design/methodology/approach

Theories and the existing knowledge were used to develop a preliminary conceptual framework. This preliminary framework was then developed as data collection and analysis were carried out. That is, in the more advanced stages of the research, both the literature and data allowed the design of a more specific analytical framework with the development of theoretical propositions. The data supporting the findings was derived from extensive content analysis of secondary documents from manufacturers, channel agents, industry organisations, public agencies and statistical sources. These data were also used as background briefing for 52 in-depth interviews with 36 senior managers within the sector.

Findings

An extensive qualitative research carried out in two major local networks of footwear production in Portugal shows that spatial proximity influences the following major variables of SME strategy: offer specialization, market specialization, competitive behaviour and collaborative behaviour. This paper examines the strong subcontracting relationships among manufacturers within each local network, discusses the competitive and collaborative behaviour of firms within their local networks of subcontracting and explains the nature of interaction between them contributing for a better understanding on the impact of spatial proximity on strategy.

Practical implications

Some management implications can be drawn from this research at the level of the network and of the firm, although both levels are profoundly intertwined. The paper discusses both these implications.

Originality/value

This research clarifies the relationship between spatial proximity and strategy of SMEs immersed in local networks. In particular, the findings show that, in the context of local networks of footwear production, SME strategy is influenced by spatial proximity between firms in the following characteristics of strategy: offer specialization, market specialization, competitive behaviour and collaborative behaviour. As it was discussed and empirically supported, spatial proximity between firms favour resource mobility, firms' interaction and reduction of transaction costs, which, in turn, impact strategy.
The dynamics of bond market development, stock market development and economic growth
Authors: Pradhan Rudra P. , Arvin Mak B. , Norman Neville R. , Bahmani Sahar
Published: October 2019

Purpose

The paper investigates whether Granger causal relationships exist between bond market development, stock market development, economic growth and two other macroeconomic variables, namely, inflation rate and real interest rate. The study aims to expand the domain of economic growth by including a more in-depth analysis of the possible impact that bond market and stock market development has on economic growth than is normally found in the literature.

Design/methodology/approach

This paper uses a panel data set of the G-20 countries for the period 1991-2016. It uses a panel vector auto-regression model to reveal the nature of any Granger causality among the five variables.

Findings

The paper provides empirical insights that both bond market development and stock market development are cointegrated with economic growth, inflation rate and real interest rate. The most robust result from the panel Granger causality test is that bond market development, stock market development, inflation rate and real interest rate are demonstrable drivers of economic growth in the long run.

Research limitations/implications

Because of the chosen research approach, the research results may lack theoretical foundations. Therefore, perhaps the more fully grounded interactive findings of this study can inspire theorists to fill the missing gap.

Practical implications

This paper includes lessons for policymakers in the G-20 countries seeking to stimulate economic growth in the long run and how they need to ensure greater stability of the interest rate and inflation rate as well as fully developing their financial markets, as both bond markets and stock markets are obvious drivers of economic growth.

Originality/value

This paper fulfills an identified need to study causal relationships between bond market development, stock market development, economic growth and two other macroeconomic variables, i.e. inflation rate and real interest rate.
The associations between stock prices, inflation rates, interest rates are still persistent
Authors: Eldomiaty Tarek , Saeed Yasmeen , Hammam Rasha , AboulSoud Salma
Published: October 2019

Purpose

This paper aims to examine the effect of both inflation rate and interest rate on stock prices using quarterly data on non-financial firms listed in DJIA30 and NASDAQ100 for the period 1999-2016. The stock duration model is used to measure the sensitivity in variations in inflation rates and interest rates on stock prices.

Design/methodology/approach

The authors use standard statistical tools that include Johansen cointegration test, linearity, normality tests, cointegration regression, Granger causality and vector error correction model.

Findings

The results of panel Johansen cointegration analysis show that cointegration exists between the stock prices, the changes in stock prices due to inflation rates and the changes in stock prices due to real interest rates. The results of cointegration regression show that inflation rates are negatively associated with stock prices, the real interest rates and stock prices are positively associated, changes in real interest rates and inflation rates Granger cause significant changes in stock prices, significant speed of adjustment to long run equilibrium between observed stock prices and real interest rates and significant speed of adjustment to long run equilibrium between changes in stock prices due to real interest rates and changes in inflation rates.

Originality/value

This paper contributes to the empirical literature in three ways. The paper examines the effects of inflation and interest rates on stock prices differently from other related studies by separating inflation from real interest rates. The paper examines the causality between stock prices, interest and inflation rates. This paper offers significant updated validity to extended literature that a negative association exists between stock prices and inflation rates. This validity can be considered as an existence a theory of stock prices, inflation rates and interest rates.
The impact of market sectors and rating agencies on credit ratings: global evidence
Authors: Lopatta Kerstin , Tchikov Magdalena , Körner Finn Marten
Published: October 2019

Purpose

A credit rating, as a single indicator on one consistent scale, is designed as an objective and comparable measure within a credit rating agency (CRA). While research focuses mainly on the comparability of ratings between agencies, this paper additionally questions empirically how CRAs meet their promise of providing a consistent assessment of credit risk for issuers within and between market segments of the same agency.

Design/methodology/approach

Exhaustive and robust regression analyses are run to assess the impact of market sectors and rating agencies on credit ratings. The examinations consider the rating level, as well as rating downgrades as a further measure of empirical credit risk. Data stems from a large global sample of Bloomberg ratings from 11 market sectors for the period 2010-2018.

Findings

The analyses show differing effects of sectors and agencies on issuer ratings and downgrade probabilities. Empirical results on credit ratings and rating downgrades can then be attributed to investment grade and non-investment grade ratings.

Originality/value

The paper contributes to current finance research and practice by examining the credit rating differences between sectors and agencies and providing assistance to investors and other stakeholders, as well as researchers, how issuers’ sector and rating agency affiliations act as relative metrics.