bluuebunny/crossref_metadata_2025 huggingface dataset:
Azithromycin Partially Mitigates Dysregulated Repair of Lung Allograft Small Airway Epithelium
Authors: Ling Kak-Ming , Garratt Luke W. , Banerjee Balarka , Lavender Melanie A. , Wrobel Jeremy P. , Musk Michael , Martinovich Kelly M. , Shaw Nicole C. , Iosifidis Thomas , Looi Kevin , Kicic-Starcevich Elizabeth , Sutanto Erika N. , Yerkovich Stephanie T. , Chambers Daniel C. , Stick Stephen M. , Kicic Anthony
Published: January 2020

Background.

Dysregulated airway epithelial repair following injury is a proposed mechanism driving posttransplant bronchiolitis obliterans (BO), and its clinical correlate bronchiolitis obliterans syndrome (BOS). This study compared gene and cellular characteristics of injury and repair in large (LAEC) and small (SAEC) airway epithelial cells of transplant patients.

Methods.

Subjects were recruited at the time of routine bronchoscopy posttransplantation and included patients with and without BOS. Airway epithelial cells were obtained from bronchial and bronchiolar brushing performed under radiological guidance from these patients. In addition, bronchial brushings were also obtained from healthy control subjects comprising of adolescents admitted for elective surgery for nonrespiratory-related conditions. Primary cultures were established, monolayers wounded, and repair assessed (±) azithromycin (1 µg/mL). In addition, proliferative capacity as well as markers of injury and dysregulated repair were also assessed.

Results.

SAEC had a significantly dysregulated repair process postinjury, despite having a higher proliferative capacity than large airway epithelial cells. Addition of azithromycin significantly induced repair in these cells; however, full restitution was not achieved. Expression of several genes associated with epithelial barrier repair (matrix metalloproteinase 7, matrix metalloproteinase 3, the integrins β6 and β8, and β-catenin) were significantly different in epithelial cells obtained from patients with BOS compared to transplant patients without BOS and controls, suggesting an intrinsic defect.

Conclusions.

Chronic airway injury and dysregulated repair programs are evident in airway epithelium obtained from patients with BOS, particularly with SAEC. We also show that azithromycin partially mitigates this pathology.
Trophic rewilding presents regionally specific opportunities for mitigating climate change
Authors: Sandom Christopher J. , Middleton Owen , Lundgren Erick , Rowan John , Schowanek Simon D. , Svenning Jens-Christian , Faurby Søren
Published: January 2020

Large-bodied mammalian herbivores can influence processes that exacerbate or mitigate climate change. Herbivore impacts are, in turn, influenced by predators that place top-down forcing on prey species within a given body size range. Here, we explore how the functional composition of terrestrial large-herbivore and -carnivore guilds varies between three mammal distribution scenarios: Present-Natural, Current-Day and Extant-Native Trophic (ENT) Rewilding. Considering the effects of herbivore species weakly influenced by top-down forcing, we quantify the relative influence keystone large-herbivore guilds have on methane emissions, woody vegetation expansion, fire dynamics, large-seed dispersal, and nitrogen and phosphorus transport potential. We find strong regional differences in the number of herbivores under weak top-down regulation between our three scenarios, with important implications for how they will influence climate change relevant processes. Under the Present-Natural non-ruminant, megaherbivore, browsers were a particularly important guild across much of the world. Megaherbivore extinction and range contraction and the arrival of livestock mean large, ruminant, grazers have become more dominant. ENT Rewilding can restore the Afrotropics and the Indo-Malay realm to the Present-Natural benchmark, but causes top-down forcing of the largest herbivores to become commonplace elsewhere. ENT Rewilding will reduce methane emissions, but does not maximize natural climate solution potential.

This article is part of the theme issue ‘Climate change and ecosystems: threats, opportunities and solutions'.
National mitigation potential from natural climate solutions in the tropics
Authors: Griscom Bronson W. , Busch Jonah , Cook-Patton Susan C. , Ellis Peter W. , Funk Jason , Leavitt Sara M. , Lomax Guy , Turner Will R. , Chapman Melissa , Engelmann Jens , Gurwick Noel P. , Landis Emily , Lawrence Deborah , Malhi Yadvinder , Schindler Murray Lisa , Navarrete Diego , Roe Stephanie , Scull Sabrina , Smith Pete , Streck Charlotte , Walker Wayne S. , Worthington Thomas
Published: January 2020

Better land stewardship is needed to achieve the Paris Agreement's temperature goal, particularly in the tropics, where greenhouse gas emissions from the destruction of ecosystems are largest, and where the potential for additional land carbon storage is greatest. As countries enhance their nationally determined contributions (NDCs) to the Paris Agreement, confusion persists about the potential contribution of better land stewardship to meeting the Agreement's goal to hold global warming below 2°C. We assess cost-effective tropical country-level potential of natural climate solutions (NCS)—protection, improved management and restoration of ecosystems—to deliver climate mitigation linked with sustainable development goals (SDGs). We identify groups of countries with distinctive NCS portfolios, and we explore factors (governance, financial capacity) influencing the feasibility of unlocking national NCS potential. Cost-effective tropical NCS offers globally significant climate mitigation in the coming decades (6.56 Pg CO
2
e yr
−1
at less than 100 US$ per Mg CO
2
e). In half of the tropical countries, cost-effective NCS could mitigate over half of national emissions. In more than a quarter of tropical countries, cost-effective NCS potential is greater than national emissions. We identify countries where, with international financing and political will, NCS can cost-effectively deliver the majority of enhanced NDCs while transforming national economies and contributing to SDGs.

This article is part of the theme issue ‘Climate change and ecosystems: threats, opportunities and solutions’.
Arthrobacter ulcerisalmonis sp. nov., isolated from an ulcer of a farmed Atlantic salmon (Salmo salar), and emended description of the genus Arthrobacter sensu lato
Authors: Kämpfer Peter , Busse Hans-Jürgen , Schumann Peter , Criscuolo Alexis , Clermont Dominique , Irgang Rute , Poblete-Morales Matías , Glaeser Stefanie P. , Avendaño-Herrera Ruben
Published: January 2020

A Gram-stain positive, pleomorphic, oxidase-negative, non-motile isolate from the ulcer of a farmed Atlantic salmon (Salmo salar), designated strain T11bT, was subjected to a comprehensive taxonomic investigation. A comparative analysis of the 16S rRNA gene sequence showed highest similarities to the type strains of

Pseudarthrobacter siccitolerans

(98.1 %) and

Arthrobacter methylotrophus

and

Pseudarthrobacter phenanthrenivorans

(both 98.0 %). The highest ANI value observed between the assembled genome of T11bT and the publicly available

Pseudarthrobacter

and

Arthrobacter

type strain genomes were 81.15 and 80.99 %, respectively. The major respiratory quinone was menaquinone MK-9(H2). The polyamine pattern contained predominantly spermidine. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol, monogalactosyl-diacylglycerol and dimannosylglyceride. Minor amouts of trimannosyldiacylglycerol and phosphatidylinositol were also detected. The peptidoglycan was of the type A3α l-Lys–l-Ser–l-Thr–l-Ala (A11.23). In the fatty acid profile, anteiso and iso branched fatty acids predominated (anteiso C15 : 0, iso C16 : 0, anteiso C17 : 0). Moderate to low DNA–DNA similarities, physiological traits as well as unique traits in the fatty acid pattern distinguished strain T11bT from the next related species. All these data point to the fact that strain T11bT represents a novel species of the genus

Arthrobacter

for which we propose the name Arthrobacter ulcerisalmonis sp. nov. The type strain is T11bT (=CIP 111621T=CCM 8854T=LMG 30632T=DSM 107127T).
Integrated single cell analysis of human lung fibrosis resolves cellular origins of predictive protein signatures in body fluids
Authors: Mayr Christoph H. , Simon Lukas M. , Leuschner Gabriela , Ansari Meshal , Geyer Philipp E. , Angelidis Ilias , Strunz Maximilian , Singh Pawandeep , Kneidinger Nikolaus , Reichenberger Frank , Silbernagel Edith , Böhm Stephan , Adler Heiko , Hilgendorff Anne , Lindner Michael , Prasse Antje , Behr Jürgen , Mann Matthias , Eickelberg Oliver , Theis Fabian J. , Schiller Herbert B.
Published: January 2020

Single cell genomics enables characterization of disease specific cell states, while improvements in mass spectrometry workflows bring the clinical use of body fluid proteomics within reach. The correspondence of cell state changes in diseased organs to peripheral protein signatures is currently unknown. Here, we leverage single cell RNA-seq and proteomic analysis of large pulmonary fibrosis patient cohorts to identify disease specific changes on the cellular level and their corresponding reflection in body fluid proteomes. We discovered and validated transcriptional changes in 45 cell types across three patient cohorts that translated into distinct changes in the bronchoalveolar lavage fluid and plasma proteome. These protein signatures correlated with diagnosis, lung function, smoking and injury status. Specifically, the altered expression of a novel marker of lung health, CRTAC1, in alveolar epithelium is robustly reflected in patient plasma. Our findings have direct implications for future non-invasive prediction and monitoring of pathological cell state changes in patient organs.

Abstract Figure
Healthcare Cost of Stargardt Disease
Authors: Aziz Kanza , Swenor Bonnielin K. , Canner Joseph K. , Singh Mandeep S.
Published: January 2020

Importance

Stargardt disease (SD) is the most common juvenile macular degeneration and a leading cause of uncorrectable childhood blindness. The progressive and incurable nature of this chronic condition entails a long-term financial burden on affected individuals. The economic costs of SD have not been characterized in detail.

Objective

To estimate the direct healthcare cost of SD.

Design

Cross-sectional analysis of healthcare claims.

Participants

Patients with an ICD-9 diagnosis code of SD, non-exudative age-related macular degeneration (AMD), or bilateral sensorineural hearing loss (SHL).

Methods

Outpatient administrative claims data from the IBM® MarketScan® Commercial Claims and Encounters Database from 2010 to 2014 were analyzed.

Main Outcome Measure

Annual per-patient direct healthcare cost.

Results

A total of 472,428 patients were analyzed (5,015 SD, 369,750 SHL and 97,663 AMD patients respectively). The payment per year of insurance coverage for SD (median: $105.58, IQR: $50.53-$218.71) was higher than that of SHL (median: $51.01, IQR: $25.66-$121.66, p <0.001) and AMD (median: $76.20, IQR: $38.00-$164.86, p <0.001). When adjusted for covariates, the annual payment for SD was $47.83 higher than SHL (p<0.001) and $17.34 higher than AMD (p<0.001).

Conclusions and Relevance

There is a significant direct healthcare cost associated with SD. The annual per-patient cost of SD was higher than SHL, another condition that causes sensory impairment in people of all ages, and nonexudative AMD which causes a similar pattern of visual loss that typically begins later in life. The total lifetime per-patient cost of SD may exceed that of nonexudative AMD.
Genome-wide meta-analysis, fine-mapping, and integrative prioritization identify new Alzheimer’s disease risk genes
Authors: Schwartzentruber Jeremy , Cooper Sarah , Liu Jimmy Z , Barrio-Hernandez Inigo , Bello Erica , Kumasaka Natsuhiko , Johnson Toby , Estrada Karol , Gaffney Daniel J. , Beltrao Pedro , Bassett Andrew
Published: January 2020

Genome-wide association studies (GWAS) have discovered numerous genomic loci associated with Alzheimer’s disease (AD), yet the causal genes and variants remain incompletely identified. We performed an updated genome-wide AD meta-analysis, which identified 37 risk loci, including novel associations near genes CCDC6, TSPAN14, NCK2, and SPRED2. Using three SNP-level fine-mapping methods, we identified 21 SNPs with greater than 50% probability each of being causally involved in AD risk, and others strongly suggested by functional annotation. We followed this with colocalisation analyses across 109 gene expression quantitative trait loci (eQTL) datasets, and prioritization of genes using protein interaction networks and tissue-specific expression. Combining this information into a quantitative score, we find that evidence converges on likely causal genes, including the above four genes, and those at previously discovered AD loci including BIN1, APH1B, PTK2B, PILRA, and CASS4.
The cholinergic system and treatment response in subtypes of Alzheimer’s disease
Authors: Machado Alejandra , Ferreira Daniel , Grothe Michel J. , Eyjolfsdottir Helga , Almqvist Per M. , Cavallin Lena , Lind Göran , Linderoth Bengt , Seiger Åke , Teipel Stefan , Wahlberg Lars U. , Wahlund Lars-Olof , Westman Eric , Eriksdotter Maria ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2020

BACKGROUND

The heterogeneity within Alzheimer’s disease (AD) seriously challenges the development of disease modifying treatments. We investigated volume of the basal forebrain, hippocampus, and precuneus in atrophy subtypes of AD, and explored the relevance of subtype stratification in a clinical trial on encapsulated cell biodelivery (ECB) of nerve growth factor (NGF) to the basal forebrain.

METHODS

Structural MRI data was collected for 90 amyloid-positive patients and 69 amyloid-negative healthy controls at baseline, 6-, 12-, and 24-month follow-up. The effect of the NGF treatment was investigated in 10 biopsy verified AD patients with structural MRI data at baseline and at 6- or 12-months follow-up. Patients were classified as typical, limbic-predominant, hippocampal-sparing, or minimal atrophy AD, using a validated visual assessment method. Volumetric analyses were performed using a region-of-interest approach.

RESULTS

All AD subtypes showed reduced basal forebrain volume as compared with controls. Limbic-predominant subtype showed fastest basal forebrain atrophy rate, whereas minimal atrophy subtype did not show significant volume decline over time. Atrophy rates of hippocampus and precuneus also differed across subtypes. The NGF treatment seemed to slow the rate of atrophy in precuneus and hippocampus, particularly in the hippocampal-sparing AD subtype.

CONCLUSIONS

The cholinergic system is differentially affected in distinct atrophy subtypes of AD, possibly contributing to their differential response to cholinergic treatment. Our findings suggest that future clinical trials should target specific subtypes of AD, or at least report treatment effects stratifying by subtype.

Trial registration

ClinicalTrials.gov identifier: NCT01163825. Registered 14 July 2010 - https://clinicaltrials.gov/ct2/show/NCT01163825
Effects of Metformin compared to Thiazolidinediones on vascular endothelial function in Polycystic Ovary syndrome: A systematic review
Authors: Mazumder Hoimonty , Faizah Farah , Hossain Md. Mahbub
Published: January 2020

Metformin and Thiazolidinediones are insulin sensitizers used as the first-line treatment of PCOS, which are recently being examined for their extensive beneficial impacts at biochemical and molecular level of body function in Polycystic ovary syndrome. Therefore, purpose of this review is to compare the effectiveness of Metformin and Thiazolidinediones on vascular endothelial function in PCOS. MEDLINE (1966- October 2018), CINAHL (1982 to October 2018), Cochrane Central Register of Controlled Trials and Cochrane Menstrual Disorders and Subfertility Group trials register (October 2018) and Google Scholar were searched electronically without language restriction. Three Randomized controlled trials (RCTs) were selected with a total of 90 participants comparing effect of Metformin (Intervention) to Thiazolidinediones (Comparator) with an outcome on endothelial function among women with PCOS. In results, Meta-analysis shows no statistically significant difference on endothelial-dependent vasodilation between Metformin and Thiazolidinedione (p value= 0.59 at 95% CI - 1.31, 0.74).
Umbilical cord blood-derived ILC1-like cells constitute a novel precursor for mature KIR+NKG2A-NK cells
Authors: Bennstein Sabrina Bianca , Weinhold Sandra , Manser Angela Ricarda , Scherenschlich Nadine , Noll Angela , Raba Katharina , Kögler Gesine , Walter Lutz , Uhrberg Markus
Published: January 2020

Despite their identification several years ago, molecular identity and developmental relation between human ILC1 and NK cells, comprising group 1 ILCs, is still elusive. To unravel their connection, thorough transcriptional, epigenetic, and functional characterization was performed from umbilical cord blood (CB). Unexpectedly, ILC1-like cells lacked Tbet expression and failed to produce IFNg. Moreover, in contrast to previously described ILC1 subsets they could be efficiently differentiated into NK cells. These were characterized by highly diversified KIR repertoires including late stage NKG2A-KIR+ effector cells that are commonly not generated from previously known NK cell progenitor sources. This property was dependent on stroma cell-derived Notch ligands. The frequency of the novel ILC1-like NK cell progenitor (NKP) significantly declined in CB from early to late gestational age. The study supports a model in which circulating fetal ILC1-like NKPs travel to secondary lymphoid tissues to initiate the formation of diversified NK cell repertoires after birth.
TMEM184b is necessary for IL-31 induced itch
Authors: Larsen Erik G. , Cho Tiffany S. , McBride Matthew L. , Feng Jing , Manivannan Bhagyashree , Madura Cynthia , Klein Nathaniel E. , Wright Elizabeth B. , Garcia-Verdugo Hector D. , Jarvis Chelsea , Khanna Rajesh , Hu Hongzhen , Largent-Milnes Tally M. , Bhattacharya Martha R.C.
Published: January 2020

Nociceptive and pruriceptive neurons in the dorsal root ganglia (DRG) convey sensations of pain and itch to the spinal cord, respectively. One subtype of mature DRG neurons, comprising about 5% of neurons in the ganglia, is responsible for sensing mediators of acute itch and atopic dermatitis, including the cytokine IL-31. How itch-sensitive (pruriceptive) neurons are specified is unclear. Here we show thatTmem184b, a gene with roles in axon degeneration and nerve terminal maintenance, is required for the expression of a large cohort of itch receptors, including those for IL-31, Leukotriene C4, and Histamine. Male and female mice lackingTmem184bshow reduced responses to IL-31, but maintain normal responses to pain and mechanical force, indicating a specific behavioral defect in pruriception. Calcium imaging experiments indicate that a reduction in IL-31 induced calcium entry is a likely contributor to this phenotype. We identify an early failure of proper Wnt-dependent transcriptional signatures and signaling components in Tmem184b mutant mice that may explain the improper DRG neuronal subtype specification. Accordingly, lentiviral re-expression of Tmem184b in mutant embryonic neurons restores Wnt signatures. Together, these data demonstrate that Tmem184b promotes adult somatosensation through developmental Wnt signaling and promotion of proper pruriceptive gene expression. Our data illuminate a new key regulatory step in the processes controlling the establishment of diversity in the somatosensory system.
Giant magnetoresistive biosensors for real-time quantitative detection of protease activity
Authors: Adem Sandeep , Jain Sonal , Sveiven Michael , Zhou Xiahan , O’Donoghue Anthony J. , Hall Drew A.
Published: January 2020

Proteases are enzymes that cleave proteins and are crucial to physiological processes such as digestion, blood clotting, and wound healing. Unregulated protease activity is a biomarker of several human diseases. Synthetic peptides that are selectively hydrolyzed by a protease of interest can be used as reporter substrates of unregulated protease activity. We developed an activity-based protease sensor by immobilizing magnetic nanoparticles (MNP) to the surface of a giant magnetoresistive spin-valve (GMR SV) sensor using peptides. Cleavage of these peptides by a protease, releases the magnetic nanoparticles resulting in a time-dependent change in the local magnetic field. Using this approach, we detected a significant release of MNPs after 3.5 minutes incubation using just 4 nM of the cysteine protease, papain. In addition, we show that proteases in healthy human urine do not release the MNPs, however addition of 20 nM of papain to the urine samples resulted in a time-dependent change in magnetoresistance. This study lays the foundation for using GMR SV sensors as a platform for real-time quantitative detection of protease activity in biological fluids.
Computationally-guided technology platform for on-demand production of diversified therapeutic phage cocktails
Authors: Mageeney Catherine M. , Sinha Anupama , Mosesso Richard A. , Medlin Douglas L. , Lau Britney Y. , Rokes Alecia B. , Lane Todd W. , Branda Steven S. , Williams Kelly P.
Published: January 2020

New therapies are necessary to combat increasingly antibiotic-resistant bacterial pathogens. We have developed a technology platform of computational, molecular biology, and microbiology tools which together enable on-demand production of phages that target virtually any given bacterial isolate. Two complementary computational tools that identify and precisely map prophages and other integrative genetic elements (IGEs) in bacterial genomes are used to identify prophage-laden bacteria that are close relatives of the target strain. Phage genomes are engineered to disable lysogeny, through use of long amplicon PCR and Gibson assembly. Finally, the engineered phage genomes are introduced into host bacteria for phage production. As an initial demonstration, we used this approach to produce a phage cocktail against the opportunistic pathogenPseudomonas aeruginosaPAO1. Two prophage-ladenP. aeruginosastrains closely related to PAO1 were identified, ATCC 39324 and ATCC 27853. Deep sequencing revealed that mitomycin C treatment of these strains induced seven phages that grow onP. aeruginosaPAO1. The most diverse five of these were engineered for non-lysogeny by deleting the integrase gene (int), which is readily identifiable and typically conveniently located at one end of the prophage. The Δintphages, individually and in cocktails, showed killing ofP. aeruginosaPAO1in vitroas well as in a waxworm (Galleria mellonella) model of infection.

SIGNIFICANCE STATEMENT

The antibiotic-resistance crisis in medicine and agriculture has led to renewed interest in phage therapy as an alternative means of treating infection. However, conventional methods for isolating pathogen-specific phage are slow, labor-intensive, and frequently unsuccessful. We have demonstrated that prophages carried by near-neighbor bacteria can serve as starting material for production of engineered phages that kill the target pathogen. Our approach and technology platform offer new opportunity for rapid development of phage therapies against most, if not all, bacterial pathogens, a foundational advance for use of phage in treating infectious disease.
Investigating resting brain perfusion abnormalities and target-engagement by intranasal oxytocin in women with bulimia nervosa and binge-eating disorder and healthy controls
Authors: Martins Daniel , Leslie Monica , Rodan Sarah , Zelaya Fernando , Treasure Janet , Paloyelis Yannis
Published: January 2020

Advances in the treatment of bulimia nervosa and binge eating disorder (BN/BED) have been marred by our limited understanding of the underpinning neurobiology. Here we measured regional cerebral blood flow (rCBF) to map resting perfusion abnormalities in women with BN/BED compared to healthy controls and investigate if intranasal oxytocin (OT), proposed as a potential treatment, can restore perfusion in disorder-related brain circuits. Twenty-four women with BN/BED and 23 healthy women participated in a randomised, double-blind, crossover, placebo-controlled study. We used arterial spin labelling MRI to measure rCBF and the effects of an acute dose of intranasal OT (40IU) or placebo over 18-26 minutes post-dosing, as we have previously shown robust OT-induced changes in resting rCBF in men 15-36min post-dosing. We tested for effects of treatment, diagnosis and their interaction on extracted rCBF values in anatomical regions-of-interest previously implicated in BN/BED by other neuroimaging modalities, and conducted exploratory whole-brain analyses to investigate previously unidentified brain regions. We demonstrated that women with BN/BED presented increased resting rCBF in key neural circuits previously implicated in BN/BED pathophysiology, namely the medial prefrontal and orbitofrontal cortices, anterior cingulate gyrus, posterior insula and middle/inferior temporal gyri bilaterally. Hyperperfusion in these areas specifically correlated with eating symptoms severity in patients. Our data did not support a normalizing effect of 40IU intranasal OT on perfusion abnormalities in these patients 18-26 minutes post-dosing. Our findings enhance our understanding of resting brain abnormalities in BN/BED and identify resting rCBF as a non-invasive potential biomarker for disease-related changes and treatment monitoring.
The Power of Citizen Science to Quantify Ecological Risks in Cities
Authors: Putman Breanna J. , Williams Riley , Li Enjie , Pauly Gregory B.
Published: January 2020

Urbanization is an extreme form of habitat modification that can alter ecological relationships among organisms, but these can be hard to study because much of the urban landscape is inaccessible private property. We show that citizen science can be a powerful tool to overcome this challenge. We used photo-vouchered observations submitted to the citizen science platform iNaturalist to assess predation and parasitism across urbanization gradients in a secretive yet widespread species, the Southern Alligator Lizard (Elgaria multicarinata), in Southern California, USA. From photographs, we quantified predation risk by assessing tail injuries and quantified parasitism rates by counting tick loads on lizards. We estimated urbanization intensity by determining percent impervious surface around each lizard observation. We found that tail injuries increased with age of the lizard and with urbanization, suggesting that urban areas are riskier habitats, likely because of elevated populations of predators such as outdoor cats. Conversely, parasitism decreased with urbanization likely due to a loss of mammalian hosts and anti-tick medications used on companion animals. Moreover, our citizen science approach allowed us to generate a large dataset on a secretive species extremely rapidly and at an immense spatial scale that facilitated quantitative measures of urbanization (e.g. percent impervious surface cover) as opposed to qualitative measures (e.g. urban vs rural). This study demonstrates that citizen science is allowing researchers to answer ecological questions that otherwise would go unanswered.
High fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imagingin vivo
Authors: Xie Michael E. , Adam Yoav , Fan Linlin Z. , Böhm Urs L. , Kinsella Ian , Zhou Ding , Paninski Liam , Cohen Adam E.
Published: January 2020

The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved high signal to noise ratioin vivowith 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise that present analysis challenges, namely light scattering, out-of-focus sources, motion, and blood flow. We present a novel signal extraction methodology, Spike-Guided Penalized Matrix Decomposition-Nonnegative Matrix Factorization (SGPMD-NMF), which resolves supra- and sub-threshold voltages with high fidelity, even in the presence of correlated noise. The method incorporates biophysical constraints (shared soma profiles for spiking and subthreshold dynamics) and optical constraints (smoother spatial profiles from defocused vs. in-focus sources) to cleave signal from background. We validated the pipeline using simulated and composite datasets with realistic noise properties. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon, mouse cortex expressing SomArchon or Voltron, and zebrafish spine expressing zArchon1.
Robustness testing and scalability of phosphate regulated promoters useful for two-stage autoinduction inE. coli
Authors: Moreb Eirik A. , Ye Zhixia , Efromson John P. , Hennigan Jennifer N. , Menacho-Melgar Romel , Lynch Michael D.
Published: January 2020

A key challenge in synthetic biology is the successful utilization of characterized parts, such as promoters, in different biological contexts. We report the robustness testing of a small library ofE. coliPhoB regulated promoters that enable heterologous protein production in two-stage cultures. Expression levels were measured both in a rich Autoinduction Broth as well as a minimal mineral salts media. Media dependent differences were promoter dependent. 4 out of 16 promoters tested were identified to have tightly controlled expression which was also robust to media formulation. Improved promoter robustness led to more predictable scale up and consistent expression in instrumented bioreactors. This subset of PhoB activated promoters, useful for two-stage autoinduction, highlight the impact of the environment on the performance of biological parts, and the importance of robustness testing in synthetic biology.

Highlights

Characterization of the impact of media on promoter activity

Identification of promoters robust to environmental variables

Identification of promoters whose expression scale from microtiter plates to bioreactors

Abstract Figure

Graphical Abstract
Opposing neural signals of CaV1-encoded peptides are tuned by C-terminus mediated inhibition
Authors: Yang Yaxiong , Liu Min , Liu Nan , Li Wenxiang , Yu Zhen , Hong Weili , Li Ping , Jiang He , Ge Haiyan , Wang Ping , Song Sen , Li Xiaomei , Fan Yubo , Liu Xiaodong
Published: January 2020

L-type calcium (CaV1) channels regulate gene expressions via the cascade of excitation-transcription coupling, or directly as standalone CCAT (Calcium Channel Associated Transcriptional-regulator) peptides encoding distal carboxyl-terminus (DCT) of CaV1, both evidenced in dendritogenesis signaling in neurons. We here discover that DCT peptides opposedly mediate these two sets of transcription signals, all tunable in accordance to C-terminus mediated inhibition (CMI) of Ca2+/CaV1 influx. By electrophysiology, neurite morphology, and FRET 2-hybrid binding analyses, we systematically examined native and derived DCT peptides across CaV1, unveiling that the overall balance between cytosolic inhibitionversusnuclear facilitation is spatially and temporally tuned by CMI of each DCT variant. Our findings not only resolve several controversies existing to DCT variants, but also propose ade novoscheme of CaV1-centric gene regulation: two concurrent routes of transcription signals initiated from either membrane CaV1 channels or nuclear CaV1-encoded peptides are subject to autonomous feedback tuning by peptide/channel interactions.
Detailed surface analysis of V-defects in GaN films on patterned silicon(111) substrates by metal–organic chemical vapour deposition. Corrigendum
Authors: Gao Jiang-Dong , Zhang Jian-Li , Zhu Xin , Wu Xiao-Ming , Mo Chun-Lan , Pan Shuan , Liu Jun-Lin , Jiang Feng-Yi
Published: January 2020

An error in the article by Gao, Zhang, Zhu, Wu, Mo, Pan, Liu & Jiang [J. Appl. Cryst. (2019), 52, 637–642] is corrected.
Challenges in auditing fair value measurement and accounting estimates
Authors: Oyewo Babajide , Emebinah Ebuka , Savage Romeo
Published: January 2020

Purpose

Following the issuance of International Financial Reporting Standard 13 on fair value measurement (which became operational from January 2013), this study aims to investigate post-implementation challenges in the audit of fair value measurement and accounting estimates in the Nigerian context.

Design/methodology/approach

Data-collection was through a structured-questionnaire administered on 400 auditors from diverse backgrounds in terms of audit firm size, international affiliation and global presence.

Findings

Empirical data obtained from 277 auditors were analysed using descriptive statistics, factor analysis, one-way ANOVA, cluster analysis, independent samplet-test and one-way multivariate analysis of co-variance. It was observed that the two highest-ranking and most-prevalent challenges of auditing fair value measurement and accounting estimates are the tendency for managers to manipulate earnings owing to the inability of auditor to effectively test fair value estimates; and the difficulty in testing unobservable inputs due to the application of assumptions and judgement in arriving at estimates by preparers of financial reports.

Originality/value

While there is no significant difference in the perception of auditors on the audit challenges associated with fair value measurement and accounting estimates, there is a significant difference in the magnitude of audit challenges faced in verifying fair value measurements and accounting estimates across industry sectors. Concerned stakeholders (including but not limited to accounting regulators, auditing standard setters, audit firms, researchers) are importuned to come up with robust and pragmatic measures to curtain these challenges, as the inability of auditors to rigorously verify fair value estimates may jeopardize the very essence of fair value measurement which is to elevate financial reporting quality.
Money laundering through banks in Dubai
Authors: Teichmann Fabian Maximilian , Falker Marie-Christin
Published: January 2020

Purpose

The purpose of this paper is to illustrate how illegally obtained funds from Austria, Germany, Liechtenstein and Switzerland are laundered through the banking system in Dubai.

Design/methodology/approach

The study is conducted using a qualitative content analysis of 60 semi-structured expert interviews with both criminals and money laundering prevention experts, and a quantitative survey of 200 financial sector compliance officers.

Findings

Some banks in Dubai are highly suitable for all stages of the money laundering process. However, although certain banks have weak compliance mechanisms, others act in an exemplary manner.

Research limitations/implications

The qualitative findings are based on semi-structured interviews and are limited to the 60 interviewees’ perspectives.

Practical implications

Identification of gaps in anti-money laundering mechanisms provides compliance officers, law enforcement agencies and legislators with valuable insights into how money laundering criminals operate.

Originality/value

The existing literature focuses mainly on organizations and the methods they use to combat money laundering. This paper outlines how money launderers operate to avoid detection. Authentic experiences are illustrated. The reader is provided with valuable insights into the minds of money launderers. Both lawful and criminal perspectives are taken into account.
Consumer engagement in social media: scale comparison analysis
Authors: Ferreira Mateus , Zambaldi Felipe , Guerra Diego de Sousa
Published: January 2020

Purpose

Engagement is a construct that varies according to the subject, object and context; this has been used to justify the coexistence of a variety of construct definitions and scales. Instead of proposing a new scale, this paper aims to create a procedure for comparing scales and to use it to evaluate brand engagement measures in social media.

Design/methodology/approach

This study first defines a procedure for the selection, standardization and comparison of scales; this procedure considers both the classical test theory (CTT) and item response theory (IRT). The authors apply the procedure in a survey of 233 respondents to compare three scales for measuring consumer engagement with brands in social media.

Findings

The establishment of a procedure for scale comparison is useful in assisting researchers to choose specific measures. Results showed that the three scales have similar characteristics, but Vivek et al.’s (2014) scale is recommended when better discrimination between construct dimensions is required, Hollebeek et al.’s (2014) scale could be used as a one-dimensional scale and Dessart et al.’s (2016) reduced scale has better ability to capture information for the affective and cognitive dimensions. None of the scales were very efficient in discriminating weakly and strongly engaged individuals.

Originality/value

This study makes a substantive contribution by proposing a procedure for scale comparison that considers CTT and IRT and shows the advantages, limitations and recommendations for using three different scales of consumer engagement.
Heavy metals concentration and target hazard quotients assessment through the consumption of fish muscle Ctenopharyngodon Idella (Cyprinidae) from markets in Ahvaz province, Iran
Authors: Bahreini Esfahani Nimah , Jafari Maryam , Moravejolahkami Amir Reza
Published: January 2020

Purpose

Heavy metals constitute one of the most hazardous substances that could be accumulated in biota coming from human activities such as agricultural and industrial wastes. This paper aims to study the levels of some of the most common heavy metals in muscles of the fish caught in the Karun River (Ahvaz, Iran) and to assess the health risks associated with their consumption.

Design/methodology/approach

In present study, the concentrations of three heavy metals (Pb, Cd and Cu) in the muscle of highly consumed fish species Ctenopharyngodon Idella (Cyprinidae) collected from three selected markets (Khoram Kooshk, Ahvaz-e Qadim and Padad Shahr; total number of samples was 45) in Ahvaz city and human health risk associated with their consumption were detected by Inductively Coupled Plasma Mass Spectrometry (ICP-MS).

Findings

The results indicated that the highest and lowest accumulated metal concentrations were related to Cu (20.36 ± 0.84) and Cd (0.53 ± 0.02), respectively. In addition, the mean difference for Pb and Cu across two pairwise of sampling sites were significant (Ahvaz-e Qadim and Khoram Kooshk, P for Pb = 0.025, P for Cu = 0.033; Ahvaz-e Qadim and Padad Shahr, p for Pb = 0.018, p for Cu = 0.039). The estimated daily intake of all metals in muscles of fish in this study were below the legal limit, and mean differences were not statistically significant among the sampling sites, except for Cu (Ahvaz-e Qadim and Khoram Kooshk, p = 0.048; Ahvaz-e Qadim and Padad Shahr, p = 0.041). Target hazard quotient values were also all below 1.

Originality/value

It can be concluded that the fishes from Ahvaz city markets are comparatively clean and do not constitute a risk for human health.
Utilization of internal waste fluffy portion of Cucurbita maxima for extraction of ß-carotene pigment
Authors: Sharma Anshu , Dhiman Anju Kumari , Attri Surekha
Published: January 2020

Purpose

Internal fluffy portion along with fibrous strands of ripe pumpkin is considered as waste in processing industries though it contains sufficient amount of ß-carotene pigment. The purpose of this paper is to use the leftover fluffy portion of ripe pumpkin (Cucurbita maxima) after the use of its flesh for the purpose of processing.

Design/methodology/approach

The data were analyzed statistically by following a complete randomized design (CRD). All analysis were performed using the software OPSTAT.

Findings

One hour pre-enzymatic treatment before solvent extraction showed significant improvement in extraction yield in comparison to the isolation of ß-carotene pigment through solvent only. Temperature time combination was optimized as 40°C for 2 h during solvent extraction to obtain maximum yield irrespective of the type of extraction method used.

Practical implications

Extracted carotene pigment can further be used as a natural food colorant in processed food products not only to enhance the color appeal but also it improves the nutritional value of the product as ß-carotene acts as a precursor of vitamin A.

Social implications

Coloring agents of natural origin are becoming famous among society due to their health benefits. Consumers are becoming reluctant to use synthetic colors because of the undesirable allergic reactions caused by them, so carotene bio-pigment produced is a natural coloring compound with wide application in the food sector.

Originality/value

Even though few researchers have worked on the extraction of carotene pigment from pumpkin, but no researcher has reported the use of a waste fluffy portion of C. maxima for extraction of ß-carotene pigment.
Shape recovery characteristics of shape memory cyanate ester/epoxy composite reinforced with calcium sulfate whisker
Authors: Wang Yongkun , Zhang Yuting , Zhang Jinhua , Ye Junjue , Tian Wenchao
Published: January 2020

Purpose

The purpose of this paper is to study the influence of calcium sulfate whiskers (CSWs) on the thermodynamic properties and shape memory properties of epoxy/cyanate ester shape memory composites.

Design/methodology/approach

To improve the mechanical properties of shape memory cyanate ester (CE)/epoxy polymer (EP) resin, high performance CSWs were used to reinforce the thermo-induced shape memory CE/EP composites and the shape memory CSW/CE/EP composites were prepared by molding. The effect of CSW on the mechanical properties and shape memory behavior of shape memory CE/EP composites was investigated.

Findings

After CSW filled the shape memory CE/EP composites, the bending strength of the composites is greatly improved. When the content of CSW is 5 Wt.%, the bending strength of the composite is 107 MPa and the bending strength is increased by 29 per cent compared with bulk CE/EP resin. The glass transition temperature and storage modulus of the composites were improved in CE/EP resin curing system. However, when the content of CSW is more than 10 Wt.%, clusters are easily formed between whiskers and the voids between whiskers and matrix increase, which will lead to the decrease of mechanical properties of composites. The results of shape memory test show that the shape memory recovery time of the composites decreases with the decrease of CSW content at the same temperature. In addition, the shape recovery ratio of the composites decreased slightly with the increase of the number of thermo-induced shape memory cycles.

Research limitations/implications

A simple way for fabricating thermo-activated SMP composites has been developed by using CSW.

Originality/value

The outcome of this study will help to fabricate the SMP composites with high mechanical properties and the shape memory CSW/CE/EP composites are expected to be used in space deployable structures.
Neighbourhood‐dependent root distributions and the consequences on root separation in arid ecosystems
Authors: Chen Bin J. W. , Xu Chi , Liu Mao‐Song , Huang Zheng Y. X. , Zhang Ming‐Juan , Tang Jian , Anten Niels P. R.
Published: January 2020

Interspecific root separation is an important example of spatial niche differentiation that drives species coexistence in many ecosystems. Particularly under water‐stressed conditions, it is believed to be an inevitable outcome of species interactions. However, evidence for and against this idea has been found. So far, studies aiming at reconciling the debate have mainly focused on abiotic determinants. It remains unclear if and to what extent root separation depends on the type and growth form of interacting plants.

We conducted a detailed field study in three adjacently located (with pairwise distances <500 m) arid patchy communities where a common tussock grass species Achnatherum splendens grew in association with either a tree Elaeagnus angustifolia, a shrub Nitraria tangutorum or a perennial forb species Sophora alopecuroides. In each community, roots and soils were sampled along the soil layers from five depths (0–10, 10–30, 30–60, 60–100 and 100–150 cm) in the patches and in the adjacent bare ground outside the patches.

Significant vertical interspecific root separation occurred in the species‐association patches of tree‐grass and forb‐grass communities, but not in the shrub‐grass community. As the neighbour changed going from trees to shrubs and to forbs, rooting profiles of the grass Achnatherum became progressively deeper, with progressively less roots allocated in the upmost 10 cm soil layer and more in the subsequent two layers. After controlling for the differences in soil water and nutrient conditions among the three communities, the effects of neighbour type on grass rooting profiles remained robust.

Synthesis. We found that the root distributions of plants in the dryland strongly depend on the type of neighbour plants, which can, at least partially, determine the extent of interspecific root separation at the community scale. Our work poses new questions about plasticity in root distribution and helps to better understand species interactions and coexistence under stressful conditions.
Scope of occupational therapy practice for adults with both Down syndrome and dementia: A cross‐sectional survey
Authors: Raj Sujatha , Stanley Mandy , Mackintosh Shylie , Fryer Caroline
Published: January 2020

Introduction

Dementia in adults with Down syndrome causes a progressive decline in daily occupations impacting both persons with Down syndrome and their informal caregivers. This study aimed to explore the scope of occupational therapy practice for adults with both Down syndrome and dementia and their informal caregivers living in their homes.

Methods

A survey was conducted with occupational therapists having clinical experience in providing interventions for adults with Down syndrome. A web‐based survey was developed to explore occupational therapy practice for this group of people with Down syndrome and their informal caregivers. Responses to closed‐ended questions were analysed descriptively, and inductive content analysis was used for open‐ended questions.

Results

Forty‐three occupational therapists from Australia, Canada, United Kingdom and the United States of America participated in the survey. Two‐thirds were from the United Kingdom, most of whom were employed in the public sector and had at least 10 years of clinical experience. Over 90% of respondents received one or more referrals in a typical month for adults with Down syndrome having dementia, 68% of which were for a decline in activities of daily living. Home environment and activities of daily living were frequently assessed areas, and the commonest interventions were compensatory strategies and environmental modifications. Only half the respondents provided interventions for informal caregivers. Risk and safety and manual handling were frequently addressed domains for informal caregivers. Collaboration and developing clinical expertise were the two key perceived enablers for providing effective occupational therapy services. Fragmentation of services and a lack of client‐centred care were the common perceived barriers.

Conclusion

Occupational therapists often address decline in activities of daily living for individuals with both Down syndrome and dementia. To support participation in meaningful occupations for these people and support the needs of their informal caregivers, it is essential that services are offered in a collaborative approach.