bluuebunny/crossref_metadata_2025 huggingface dataset:
Finding the elusive trauma denominator: Feasibility of combining data sets to quantify the true burden of firearm trauma
Authors: Carmichael Heather , Samuels Jason M. , Jamison Ethan C. , Bol Kirk A. , Coleman Jamie J. , Campion Eric M. , Velopulos Catherine G.
Published: October 2020

BACKGROUND

Evidence guiding firearm injury prevention is limited by current data collection infrastructure. Trauma registries (TR) omit prehospital deaths and underestimate the burden of injury. In contrast, the National Violent Death Reporting System (NVDRS) tracks all firearm deaths including prehospital fatalities, excluding survivors. This is a feasibility study to link these data sets through collaboration with our state public health department, aiming to better estimate the burden of firearm injury and assess comparability of data.

METHODS

We reviewed all firearm injuries in our Level I TR from 2011 to 2017. We provided the public health department with in-hospital deaths, which they linked to NVDRS using patient identifiers and time of injury/death. The NVDRS collates information about circumstances, incident type, and wounding patterns from multiple sources including death certificates, autopsy records, and legal proceedings. We considered only subjects with injury location in a single urban county to best estimate in-hospital and prehospital mortality.

RESULTS

Of 168 TR deaths, 166 (99%) matched to NVDRS records. Based on data linkages, we estimate 320 prehospital deaths, 184 in-hospital deaths, and 453 survivors for a total of 957 firearm injuries. For the matched patients, there was near-complete agreement regarding simple demographic variables (e.g., age and sex) and good concordance between incident types (suicide, homicide, etc.). However, agreement in wounding patterns between NVDRS and TR varied.

CONCLUSION

We demonstrate the feasibility of linking TR and NVDRS data with good concordance for many variables, allowing for good estimation of the trauma denominator. Standardized data collection methods in one data set could improve methods used by the other, for example, training NVDRS abstractors to utilize Abbreviated Injury Scale designations for injury patterns. Such data integration holds immediate promise for guiding prevention strategies.

LEVEL OF EVIDENCE

Epidemiological study, level IV.
Interocular Difference in Retinal Nerve Fiber Layer Thickness Predicts Optic Neuritis in Pediatric-Onset Multiple Sclerosis
Authors: Waldman Amy T. , Benson Leslie , Sollee John R. , Lavery Amy M. , Liu Geraldine W. , Green Ari J. , Waubant Emmanuelle , Heidary Gena , Conger Darrel , Graves Jennifer , Greenberg Benjamin
Published: October 2020

Background:

Optical coherence tomography (OCT) is capable of quantifying retinal damage. Defining the extent of anterior visual pathway injury is important in multiple sclerosis (MS) as a way to document evidence of prior disease, including subclinical injury, and setting a baseline for patients early in the course of disease. Retinal nerve fiber layer (RNFL) thickness is typically classified as low if values fall outside of a predefined range for a healthy population. In adults, an interocular difference (IOD) in RNFL thickness greater than 5 μm identified a history of unilateral optic neuritis (ON). Through our PERCEPTION (PEdiatric Research Collaboration ExPloring Tests in Ocular Neuroimmunology) study, we explored whether RNFL IOD informs on remote ON in a multicenter pediatric-onset MS (POMS) cohort.

Methods:

POMS (defined using consensus criteria and first attack <18 years) patients were recruited from 4 academic centers. A clinical history of ON (>6 months prior to an OCT scan) was confirmed by medical record review. RNFL thickness was measured on Spectralis machines (Heidelberg, Germany). Using a cohort of healthy controls from our centers tested on the same machines, RNFL thickness <86 μm (<2 SDs below the mean) was defined as abnormal. Based on previously published findings in adults, an RNFL IOD >5 μm was defined as abnormal. The proportions of POMS participants with RNFL thinning (<86 μm) and abnormal IOD (>5 μm) were calculated. Logistic regression was used to determine whether IOD was associated with remote ON.

Results:

A total of 157 participants with POMS (mean age 15.2 years, SD 3.2; 67 [43%] with remote ON) were enrolled. RNFL thinning occurred in 45 of 90 (50%) ON eyes and 24 of 224 (11%) non-ON eyes. An IOD >5 μm was associated with a history of remote ON (P < 0.001). An IOD >5 μm occurred in 62 participants, 40 (65%) with remote ON. Among 33 participants with remote ON but normal RNFL values (≥86 μm in both eyes), 14 (42%) were confirmed to have ON by IOD criteria (>5 μm).

Conclusions:

In POMS, the diagnostic yield of OCT in confirming remote ON is enhanced by considering RNFL IOD, especially for those patients with RNFL thickness for each eye in the normal range. An IOD >5 μm in patients with previous visual symptoms suggests a history of remote ON.
Measuring resilience in children: a review of recent literature and recommendations for future research
Authors: King Leonora , Jolicoeur-Martineau Alexia , Laplante David P. , Szekely Eszter , Levitan Robert , Wazana Ashley
Published: October 2020

Purpose of review

Understanding variability in developmental outcomes following exposure to early life adversity (ELA) has been an area of increasing interest in psychiatry, as resilient outcomes are just as prevalent as negative ones. However, resilient individuals are understudied in most cohorts and even when studied, resilience is typically defined as an absence of psychopathology. This review examines current approaches to resilience and proposes more comprehensive and objective ways of defining resilience.

Recent findings

Of the 36 studies reviewed, the most commonly used measure was the Strengths and Difficulties Questionnaire (n = 6), followed by the Child Behavior Checklist (n = 5), the Resilience Scale for Chinese Adolescents (n = 5), the Rosenberg Self-Esteem Scale (n = 4), and the Child and Youth Resilience Scale (n = 3).

This review reveals that studies tend to rely on self-report methods to capture resilience which poses some challenges. We propose a complementary measure of child resilience that relies on more proactive behavioral and observational indicators; some of our preliminary findings are presented. Additionally, concerns about the way ELA is characterized as well as the influence of genetics on resilient outcomes prompts further considerations about how to proceed with resiliency research.
Analysis of complex, beam-sensitive materials by transmission electron microscopy and associated techniques
Authors: Ilett Martha , S'ari Mark , Freeman Helen , Aslam Zabeada , Koniuch Natalia , Afzali Maryam , Cattle James , Hooley Robert , Roncal-Herrero Teresa , Collins Sean M. , Hondow Nicole , Brown Andy , Brydson Rik
Published: October 2020

We review the use of transmission electron microscopy (TEM) and associated techniques for the analysis of beam-sensitive materials and complex, multiphase systems
in-situ
or close to their native state. We focus on materials prone to damage by radiolysis and explain that this process cannot be eliminated or switched off, requiring TEM analysis to be done within a dose budget to achieve an optimum dose-limited resolution. We highlight the importance of determining the damage sensitivity of a particular system in terms of characteristic changes that occur on irradiation under both an electron fluence and flux by presenting results from a series of molecular crystals. We discuss the choice of electron beam accelerating voltage and detectors for optimizing resolution and outline the different strategies employed for low-dose microscopy in relation to the damage processes in operation. In particular, we discuss the use of scanning TEM (STEM) techniques for maximizing information content from high-resolution imaging and spectroscopy of minerals and molecular crystals. We suggest how this understanding can then be carried forward for
in-situ
analysis of samples interacting with liquids and gases, provided any electron beam-induced alteration of a specimen is controlled or used to drive a chosen reaction. Finally, we demonstrate that cryo-TEM of nanoparticle samples snap-frozen in vitreous ice can play a significant role in benchmarking dynamic processes at higher resolution.

This article is part of a discussion meeting issue ‘Dynamic
in situ
microscopy relating structure and function’.
Progress in environmental high-voltage transmission electron microscopy for nanomaterials
Authors: Tanaka Nobuo , Fujita Takeshi , Takahashi Yoshimasa , Yamasaki Jun , Murata Kazuyoshi , Arai Shigeo
Published: October 2020

A new environmental high-voltage transmission electron microscope (E-HVEM) was developed by Nagoya University in collaboration with JEOL Ltd. An open-type environmental cell was employed to enable in-situ observations of chemical reactions on catalyst particles as well as mechanical deformation in gaseous conditions. One of the reasons for success was the application of high-voltage transmission electron microscopy to environmental (in-situ) observations in the gas atmosphere because of high transmission of electrons through gas layers and thick samples. Knock-on damages to samples by high-energy electrons were carefully considered. In this paper, we describe the detailed design of the E-HVEM, recent developments and various applications.

This article is part of a discussion meeting issue ‘Dynamic
in situ
microscopy relating structure and function'.
Study of diffusionless and diffusional transformations usingin situcooling and heating techniques in a scanning electron microscope
Authors: Kumar Deepak , Sarkar Rajdeep , Singh Vajinder , Kumar Suraj , Mondal Chandan , Ghosal P.
Published: October 2020

In situelectron microscopy can be an effective tool to investigate the underlying science of many transformation mechanisms in materials science. Useful utilization of these experimentations will provide greater insight into many of the existing theories, as microstructural changes can be visualized in real time under some applied constraints. In this study, we have investigated two basic phase transformation phenomena: diffusionless and diffusional mechanisms with the help ofin situcooling and heating techniques in scanning electron microscope (SEM).In situcooling experiments have been carried out on secondary hardening ultra-high-strength steels to understand the diffusionless transformation of austenite to martensite. Nucleation and growth of the martensites have been observed with cooling in different steps to −194°C. Details of the formation of different variants of martensites in steel were studied with the help of orientation imaging microscopy. Diffusional transformations were studied in terms of oxidation of pure copper in SEM usingin situheating technique. Different heating cycles were adopted for different samples byin situheating to a maximum temperature of 950°C for the oxidation study. Nucleation of copper oxides and subsequent growth of the copper oxides at different temperatures were studied systematically. Raman spectroscopy and orientation imaging were done to confirm the formation of oxides and their orientations. The thermal cycling phenomenon was replicated inside SEM with heating and cooling and it has been demonstrated how the nature of copper and its oxides changes with the thermal cycle.

This article is part of a discussion meeting issue ‘Dynamicin situmicroscopy relating structure and function’.
Five Year Pediatric Use of a Digital Wearable Fitness Device: Lessons from a Pilot Case Study
Authors: Butte Kimayani D. , Bahmani Amir , Butte Atul J. , Li Xiao , Snyder Michael P.
Published: October 2020

Objectives

Wearable fitness devices are increasingly used by the general population, with new applications being proposed and designed for healthy adults as well as adults with chronic diseases. Fewer, if any, studies of these devices have been conducted in healthy adolescents and teenagers, especially over a long period of time. The goal of this work was to document the successes and challenges involved in 5 years of a wearable fitness device use in a pediatric case study.

Materials and Methods

Comparison of five years of step counts and minutes asleep from a teenaged girl and her father.

Results

At 60 months, this may be the longest reported pediatric study involving a wearable fitness device, and the first simultaneously involving a parent and a child. We find step counts to be significantly higher for both the adult and teen on school/work days, along with less sleep. The teen walked significantly less towards the end of the 5 year study. Surprisingly, many of the adult’s and teen’s sleeping and step counts were correlated, possibly due to coordinated behaviors.

Discussion

We end with several recommendations for pediatricians and device manufacturers, including the need for constant adjustments of stride length and calorie counts as teens are growing.

Conclusion

With periodic adjustments for growth, this pilot study shows these devices can be used for more accurate and consistent measurements in adolescents and teenagers over longer periods of time, to potentially promote healthy behaviors.
Microbiota compositions from infertile couples seeking in vitro fertilization (IVF), using 16S rRNA gene sequencing methods: any correlation to clinical outcomes?
Authors: Okwelogu Somadina I , Ikechebelu Joseph I , Agbakoba Nneka R , Anukam Kingsley C
Published: October 2020

Bacterial infections are usually suspected in infertile couples seeking IVF with no clear understanding of the microbial compositions present in the seminal fluids and vaginal swabs of the patients. We used next-generation sequencing technology to correlate microbiota compositions with IVF clinical outcomes. Thirty-six couples were recruited to provide seminal fluids and vaginal swabs. Seminal fluid microbiota compositions had lower bacterial concentrations compared with the vagina, but species diversity was significantly higher in seminal fluid samples. Azoospermic subjects had more relative abundance of Mycoplasma and Ureaplasma. In Normospermic semen Lactobacillus (43.86%) was the most abundant, followed by Gardnerella (25.45%), while the corresponding vaginal samples, Lactobacillus (61.74%) was the most abundant, followed by Prevotella (6.07%), and Gardnerella (5.86%). Semen samples with positive IVF were significantly colonized by Lactobacillus jensenii (P=0.002), Faecalibacterium (P=0.042) and significantly less colonized by Proteobacteria, Prevotella, Bacteroides and lower Firmicutes/Bacteroidetes ratio compared with semen samples with negative IVF. Vaginal samples with positive IVF clinical outcome were significantly colonized by Lactobacillus gasseri, less colonized by Bacteroides, and Lactobacillus iners. This study has opened a window of possibility for Lactobacillus replenishments in men and women prior to IVF treatment.
Revisiting the UK Genetic Severity Score for NF2: a proposal for adding functional information
Authors: Catasús N. , García B. , Galvan I. , Plana A. , Negro A. , Rosas I. , Ros A. , Amilibia E. , Becerra JL. , Hostalot C. , Roca-Ribas F. , Bielsa I. , Lazaro C. , de Cid R. , Serra E. , Blanco I. , Castellanos E.
Published: October 2020

Background

Neurofibromatosis Type 2 (NF2) is an autosomal dominant disorder characterized by the development of multiple schwannomas, particularly at vestibular nerves, and meningiomas. The UK NF2 Genetic Severity Score (GSS) helps predicting the disease course from germline NF2 pathogenic variants, optimizing the clinical follow-up and the genetic counselling offered to affected families.

Methods

Spanish Reference Center patients were classified following the GSS and patients’ clinical severity was measured and compared between GSS groups. The GSS was reviewed considering phenotype quantification, genetic variant classification and functional assays of Merlin and its downstream pathways, studied by western blot in patient’s primary fibroblast. Principal component analysis and regression models were considered to evaluate the differences between severity and NF2 germline mutations.

Results

The GSS was validated in the Spanish NF2 cohort. However, for some patients harboring mutations associated to mild and moderate phenotypes, GSS did not perform as well in predicting clinical outcomes as for pathogenic variants associated to severe phenotypes. We studied the possibility of modifying the mutation classification in GSS adding functional assays to evaluate the impact of pathogenic mutations on Merlin’s function. This revision help reducing variability within NF2 mutation classes and moderately enhances the correlation between patients’ phenotype and the different prognosis parameters analyzed.

Conclusions

We validated the UK NF2 GSS in a Spanish NF2 cohort although a significant phenotypic variability was identified. The revision of the GSS, named FGSS, could be an added value to the classification of mosaic patients and patients showing mild and moderate phenotypes.
Predictors of Anxiety in a Sample of Preschoolers with ASD
Authors: Behzadpoor Samaneh , Pouretemad Hamidreza , zardkhaneh Saeed Akbari
Published: October 2020

Objective

Anxiety is one of the most prevalent comorbid disorders in children with autism spectrum disorder (ASD). However, there is inconsistency in research investigating the predictors of anxiety in children with ASD. Also, most studies have focused on school-age children so research on anxiety in preschoolers with ASD has been somewhat neglected. Thus, the aim of this study was to investigate age, gender, ASD symptom severity, and functional language use as potential risk factors for developing anxiety in this sample.

Method

In total, 95 children with ASD and their caregivers participated in this study. The Gilliam Autism Rating Scale–Second Edition (GARS-2), and The Preschool Anxiety Scale (PAS) were used to gather data. Data were analyzed by Independent sample t-tests, MANOVA, Pearson’s r correlations, the point biserial correlation coefficient, and multiple regression analysis with the stepwise procedure.

Results

The findings indicated that anxiety was positively correlated with age and functional language use and negatively with ASD symptom severity. There wasn’t a significant relationship between anxiety and gender.

Conclusion

The findings suggest age and ASD symptom severity were significant predictors of anxiety in this sample. In other words, older children and cases with lower symptom severity are more likely to experience anxiety. It is also implied to examine the role of cognitive deficits in the development of anxiety in autism.
Lockdown related travel behavior undermines the containment of SARS-CoV-2
Authors: Kishore Nishant , Kahn Rebecca , Martinez Pamela P. , De Salazar Pablo M. , Mahmud Ayesha S. , Buckee Caroline O.
Published: October 2020

In response to the SARS-CoV-2 pandemic, unprecedented policies of travel restrictions and stay-at-home orders were enacted around the world. Ultimately, the public’s response to announcements of lockdowns - defined here as restrictions on both local movement or long distance travel - will determine how effective these kinds of interventions are. Here, we measure the impact of the announcement and implementation of lockdowns on human mobility patterns by analyzing aggregated mobility data from mobile phones. We find that following the announcement of lockdowns, both local and long distance movement increased. To examine how these behavioral responses to lockdown policies may contribute to epidemic spread, we developed a simple agent-based spatial model. We find that travel surges following announcements of lockdowns can increase seeding of the epidemic in rural areas, undermining the goal of the lockdown of preventing disease spread. Appropriate messaging surrounding the announcement of lockdowns and measures to decrease unnecessary travel are important for preventing these unintended consequences of lockdowns.
RNF5 Regulation of RBBP4 Defines Acute Myeloid Leukemia Growth and Susceptibility to Histone Deacetylase Inhibitors
Authors: Khateb Ali , Deshpande Anagha , Feng Yongmei , Lee Joo Sang , Lazar Ikrame , Fabre Bertrand , Li Yan , Finlay Darren , Fujita Yu , Zhang Tongwu , Yin Jun , Pass Ian , Livneh Ido , Burian Carol , Mason James R. , Almog Ronit , Horesh Nurit , Ofran Yishai , Brown Kevin , Vuori Kristiina , Jackson Michael , Ruppin Eytan , Deshpande Aniruddha J. , Ronai Ze’ev A.
Published: October 2020

Acute myeloid leukemia (AML) remains incurable, largely due to its resistance to conventional treatments. Here, we found that increased expression and abundance of the ubiquitin ligase RNF5 contributes to AML development and survival. High RNF5 expression in AML patients correlated with poor prognosis. RNF5 inhibition decreased AML cell growth in culture andin vivo, and blocked development of MLL-AF9–driven leukemogenesis in mice, prolonging their survival. RNF5 inhibition led to transcriptional changes that overlapped with those seen upon HDAC1 inhibition. RNF5 induced the formation of K29 ubiquitin chains on the histone-binding protein RBBP4, promoting its recruitment and subsequent epigenetic regulation of genes involved in AML development and maintenance. Correspondingly, RNF5 or RBBP4 knockdown enhanced the sensitivity of AML cells to histone deacetylase (HDAC) inhibitors. Notably, low expression ofRNF5andHDACcoincided with a favorable prognosis. Our studies identified ERAD-independent role for RNF5, demonstrating that its control of RBBP4 constitutes an epigenetic pathway that drives AML while highlighting RNF5/RBBP4 as markers to stratify patients for treatment with HDAC inhibitors.
Label-free composition determination for biomolecular condensates with an arbitrarily large number of components
Authors: McCall Patrick M. , Kim Kyoohyun , Ruer-Gruß Martine , Peychl Jan , Guck Jochen , Hyman Anthony A. , Brugués Jan
Published: October 2020

Biomolecular condensates are membrane-less organelles made of multiple components, often including several distinct proteins and nucleic acids. However, current tools to measure condensate composition are limited and cannot capture this complexity quantitatively, as they either require fluorescent labels, which we show can perturb composition, or can distinguish only 1-2 components. Here, we describe a label-free method based on quantitative phase microscopy to measure the composition of condensates with an arbitrarily large number of components. We first validate the method empirically in binary mixtures, revealing sequence-encoded density variation and complex aging dynamics for condensates composed of full-length proteins. In simplified multi-component protein/RNA condensates, we uncover a regime of constant condensate density and a large range of protein:RNA stoichiometry when varying average composition. The unexpected decoupling of density and composition highlights the need to determine molecular stoichiometry in multi-component condensates. We foresee this approach enabling the study of compositional regulation of condensate properties and function.
Loss of KHSRP Increases Neuronal Growth and Synaptic Transmission and Alters Memory Consolidation Through RNA Stabilization
Authors: Olguin Sarah L. , Patel Priyanka , Dell’Orco Michela , Gardiner Amy S. , Cole Robert , Buchanan Courtney , Sundara Anitha , Mudge Joann , Allan Andrea M. , Ortinski Pavel , Brigman Jonathan L. , Twiss Jeffery L. , Perrone-Bizzozero Nora I.
Published: October 2020

The KH-type splicing regulatory protein (KHSRP) is an RNA-binding protein linked to decay of AU-rich element containing mRNAs. We have previously shown that KHSRP destabilizes the mRNA encoding the growth-associated protein GAP-43 and decreases neurite growth in cultured embryonic neurons. In contrast, loss of KHSRP stabilizesGap43mRNA and increases neurite growth. Here, we have tested functions of neural KHSRPin vivo. We find upregulation of 1460 mRNAs in the neocortex of adultKhsrp−/−mice, of which 527 bind to KHSRP with high specificity. These KHSRP targets are involved in pathways for neuronal morphology, axon guidance, neurotransmission and long-term memory. Neocortical neurons show increased axon growth and dendritic spine density inKhsrp−/−mice. Analyses of neuronal cultures from embryonicKhsrp−/−mice point to a neuron-intrinsic alteration in axonal and dendritic growth and elevations in KHSRP-target mRNAs, including subcellularly localized mRNAs. Hippocampus and infralimbic cortex ofKhsrp−/−mice show presynaptic elevations in neurotransmission. TheKhsrp−/−mice have significant deficits in both trace conditioning and attention set-shifting tasks comparedKhsrp+/+mice, indicating impaired prefrontal- and hippocampal-dependent memory consolidation with loss of KHSRP. Overall, our results indicate that prenatal deletion of KHSRP impairs neuronal development resulting in alterations in neuronal morphology and function by changing post-transcriptional control of neuronal gene expression.
Trade-off between plasticity and velocity in mycelial growth
Authors: Fukuda Sayumi , Yamamoto Riho , Yanagisawa Naoki , Takaya Naoki , Sato Yoshikatsu , Riquelme Meritxell , Takeshita Norio
Published: October 2020

Tip-growing fungal cells maintain the cell polarity at the apical regions and elongate by de novo synthesis of cell wall. Cell polarity and growth rate affect the mycelial morphogenesis, however, it remains unclear how they act cooperatively to determine cell shape. Here we investigated their relationship by analyzing hyphal tip growth of filamentous fungi growing inside extremely narrow 1 μm-width channels of microfluidic devices. Since the channels are much narrower than the diameter of hyphae, the hyphae must change its morphology when they grow through the channels. Live imaging analysis revealed that hyphae of some species continued growing through the channels, whereas hyphae of other species often ceased growing when passing through the channels or lost the cell polarity after emerging from the channels. Fluorescence live imaging analysis of the Spitzenkörper, a collection of secretory vesicles and polarity-related proteins at hyphal tips, inNeurospora crassahyphae indicates that hyphal tip growth requires a very delicate balance of ordered exocytosis to maintain polarity in spatially confined environments. We analyzed the mycelial growth of seven fungal species from different lineages, which also include phytopathogenic fungi. This comparative cell biology showed that the growth defects in the channels were not correlated with their taxonomic classification nor with the width of hyphae, but, correlated with the hyphal elongation rate. This is the first report indicating a trade-off between plasticity and velocity in mycelial growth, and serves to understand fungal invasive growth into substrates or plant/animal cells, with direct impact on fungal biotechnology, ecology and pathogenicity.
Reversible coating of cells with synthetic polymers for mechanochemical regulation of cell adhesion
Authors: Kaizuka Yoshihisa , Machida Rika
Published: October 2020

The chemical control of cell–cell interactions using synthetic materials is useful for a wide range of biomedical applications. Herein, we report a method to regulate cell adhesion and dispersion by introducing repulsive forces to live cell membranes. To induce repulsion, we tethered amphiphilic polymers, such as cholesterol-modified polyethylene glycol (PEG-CLS) to cell membranes. These amphiphilic polymers both bind to and dissociate rapidly from membranes and thus, enable the reversible coating of cells by mixing and washout without requiring genetic manipulation or chemical synthesis in the cells. We found that the repulsive forces introduced by these tethered polymers can induce cell detachment from a substrate and allow cell dispersion in a suspension, modulate the speed of cell migration, and improve the separation of cells from tissues. Our analyses showed that coating the cells with tethered polymers most likely generated two distinct repulsive forces, lateral tension and steric repulsion, on the surface, which can be tuned by altering the polymer size and density. We also modeled how these two forces can be generated in kinetically distinctive manners to explain the various responses of cells to the coating. Collectively, our observations and analyses show how we can mechanochemically regulate cell adhesion and dispersion and may contribute to the optimization of chemical coating strategies for regulating various types of cell–cell interacting systems.
The Arabidopsis E3 ubiquitin ligase PUB4 regulates BIK1 homeostasis and is targeted by a bacterial type-III effector
Authors: Derkacheva Maria , Yu Gang , Rufian Jose S. , Jiang Shushu , Derbyshire Paul , Morcillo Rafael J. L. , Stransfeld Lena , Wei Yali , Menke Frank L.H. , Zipfel Cyril , Macho Alberto P.
Published: October 2020

Plant immunity is tightly controlled by a complex and dynamic regulatory network, which ensures optimal activation upon detection of potential pathogens. Accordingly, each component of this network is a potential target for manipulation by pathogens. Here, we report that RipAC, a type III-secreted effector from the bacterial pathogenRalstonia solanacearum, targets the plant E3 ubiquitin ligase PUB4 to inhibit pattern-triggered immunity (PTI). PUB4 plays a positive role in PTI by regulating the homeostasis of the central immune kinase BIK1. Before PAMP perception, PUB4 promotes the degradation of non-activated BIK1, while, after PAMP perception, PUB4 contributes to the accumulation of activated BIK1. RipAC leads to BIK1 degradation, which correlates with its PTI-inhibitory activity. RipAC causes a reduction in pathogen-associated molecular pattern (PAMP)-induced PUB4 accumulation and phosphorylation. Our results shed light on the role played by PUB4 in immune regulation, and illustrate an indirect targeting of the immune signalling hub BIK1 by a bacterial effector.
Disruption of a GATA2, TAL1, ERG regulatory circuit promotes erythroid transition in healthy and leukemic stem cells
Authors: Thoms Julie A. I , Knezevic Kathy , Harvey Gregory , Huang Yizhou , Seneviratne Janith A. , Carter Daniel R. , Subramanian Shruthi , Skhinas Joanna , Chacon Diego , Shah Anushi , de Jong Ineke , Beck Dominik , Göttgens Berthold , Larsson Jonas , Wong Jason W. H. , Zanini Fabio , Pimanda John E.
Published: October 2020

Changes in gene regulation and expression govern orderly transitions from hematopoietic stem cells to terminally differentiated blood cell types. These transitions are disrupted during leukemic transformation but knowledge of the gene regulatory changes underpinning this process is elusive. We hypothesised that identifying core gene regulatory networks in healthy hematopoietic and leukemic cells could provide insights into network alterations that perturb cell state transitions. A heptad of transcription factors (LYL1, TAL1, LMO2, FLI1, ERG, GATA2, RUNX1) bind key hematopoietic genes in human CD34+ haematopoietic stem and progenitor cells (HSPCs) and have prognostic significance in acute myeloid leukemia (AML). These factors also form a densely interconnected circuit by binding combinatorially at their own, and each other’s, regulatory elements. However, their mutual regulation during normal haematopoiesis and in AML cells, and how perturbation of their expression levels influences cell fate decisions remains unclear. Here, we integrated bulk and single cell data and found that the fully connected heptad circuit identified in healthy HSPCs persists with only minor alterations in AML, and that chromatin accessibility at key heptad regulatory elements was predictive of cell identity in both healthy progenitors and in leukemic cells. The heptad factors GATA2, TAL1 and ERG formed an integrated sub-circuit that regulates stem cell to erythroid transition in both healthy and leukemic cells. Components of this triad could be manipulated to facilitate erythroid transition providing a proof of concept that such regulatory circuits could be harnessed to promote specific cell type transitions and overcome dysregulated haematopoiesis.
A novel dual-domain clustering algorithm for inhomogeneous spatial point event
Authors: Zhu Jie , Yang Jing , Di Shaoning , Zheng Jiazhu , Zhang Leying
Published: October 2020

Purpose

The spatial and non-spatial attributes are the two important characteristics of a spatial point, which belong to the two different attribute domains in many Geographic Information Systems applications. The dual clustering algorithms take into account both spatial and non-spatial attributes, where a cluster has not only high proximity in spatial domain but also high similarity in non-spatial domain. In a geographical dataset, traditional dual spatial clustering algorithms discover homogeneous spatially adjacent clusters suffering from the between-cluster inhomogeneity where those spatial points are described in non-spatial domain. To overcome this limitation, a novel dual-domain clustering algorithm (DDCA) is proposed by considering both spatial proximity and attribute similarity with the presence of inhomogeneity.

Design/methodology/approach

In this algorithm, Delaunay triangulation with edge length constraints is first employed to construct spatial proximity relationships amongst objects. Then, a clustering strategy based on statistical change detection is designed to obtain clusters with similar attributes.

Findings

The effectiveness and practicability of the proposed algorithm are illustrated by experiments on both simulated datasets and real spatial events. It is found that the proposed algorithm can adaptively and accurately detect clusters with spatial proximity and similar non-spatial attributes under the consideration of inhomogeneity.

Originality/value

Traditional dual spatial clustering algorithms discover homogeneous spatially adjacent clusters suffering from the between-cluster inhomogeneity where those spatial points are described in non-spatial domain. The research here is a contribution to developing a dual spatial clustering method considering both spatial proximity and attribute similarity with the presence of inhomogeneity. The detection of these clusters is useful to understand the local patterns of geographical phenomena, such as land use classification, spatial patterns research and big geo-data analysis.
A quartic trigonometric tension b-spline algorithm for nonlinear partial differential equation system
Authors: Ersoy Hepson Özlem
Published: October 2020

Purpose

The purpose of this study is to construct quartic trigonometric tension (QTT) B-spline collocation algorithms for the numerical solutions of the Coupled Burgers’ equation.

Design/methodology/approach

The finite elements method (FEM) is a numerical method for obtaining an approximate solution of partial differential equations (PDEs). The development of high-speed computers enables to development FEM to solve PDEs on both complex domain and complicated boundary conditions. It also provides higher-order approximation which consists of a vector of coefficients multiplied by a set of basis functions. FEM with the B-splines is efficient due both to giving a smaller system of algebraic equations that has lower computational complexity and providing higher-order continuous approximation depending on using the B-splines of high degree.

Findings

The result of the test problems indicates the reliability of the method to get solutions to the CBE. QTT B-spline collocation approach has convergence order 3 in space and order 1 in time. So that nonpolynomial splines provide smooth solutions during the run of the program.

Originality/value

There are few numerical methods build-up using the trigonometric tension spline for solving differential equations. The tension B-spline collocation method is used for finding the solution of Coupled Burgers’ equation.
Examination of sustainable features of stadiums as an integral part of sustainable urban development: the case of Turkey
Authors: Yüce Arif , Katırcı Hakan , Gökce Yüce Sevda
Published: October 2020

Purpose

The purpose of this study is to examine the stadiums in Turkey within the scope of sustainability and evaluate their impact on sustainable urban development.

Design/methodology/approach

In the study, at first, the “Sustainable Stadium Assessment Tool”, where the final score ranges from 0 to 100 and the evaluation is made as bronze, silver, gold and platinum according to the score ranges, is developed. With this assessment tool, a total of 20 stadiums built or renovated/restored between 2008 and 2018 in Turkey is examined in social, environmental, economic dimensions within the scope of sustainability, and the current situation is revealed within the frame of sustainable urban development.

Findings

As a result of the study, it was determined that among the stadiums evaluated, only two stadiums have sustainability properties at platinum level, three stadiums at gold level while the remaining stadiums mainly at silver level.

Originality/value

To date, no assessment tool has been created in the field of sports management that can assess the sustainable properties of stadiums. Therefore, the “Sustainable Stadium Assessment Tool” created within the scope of the study is the foremost in the field of sports sciences and sports management with its different qualities in national and international terms. In addition, the examination of the stadiums in the social, environmental, economic dimensions within the scope of sustainability and revealed the current situation is also the first, and it contains information that will make very significant scientific contributions to the relevant field.
Sustainability reporting adoption in developing countries: managerial perception-based determinants evidence from Uganda
Authors: Tauringana Venancio
Published: October 2020

Purpose

The aim of the study is to investigate managerial perception-based determinants of the adoption of sustainability reporting (SR) by companies in Uganda.

Design/methodology/approach

This study is cross-sectional. Data were collected through a questionnaire survey of 194 companies belonging to the Uganda Manufacturers Association (UMA) and were analysed using multiple regression analysis.

Findings

The findings suggest that lack of expertise, lack of training and negative attitudes/beliefs towards SR are significant and negative determinants of the adoption of SR. The results also show that resources, free training and support and positive attitudes/beliefs towards SR are significantly and positively associated with the likelihood of the adoption of SR. Lack of time, lack of legal requirements and lack of stakeholder pressure are not significant determinants of the adoption of SR.

Research limitations/implications

Since the results are based on a questionnaire survey, they may suffer from issues associated with self-reporting data such as consistency seeking, self-enhancement and self-presentation, which may affect the reliability of the data. Nonetheless, the findings imply that there is a need to sensitise, provide free training and support for companies to engage with SR.

Practical implications

There is a need to sensitise, train and provide support for free to encourage companies to engage with SR.

Originality/value

This study contributes to the literature on managerial perception-based determinants of the adoption of SR by extending the analyses using a multivariate approach. This enhances our understanding of how the determinants interact to explain the adoption of SR by companies in developing countries.
Will Evolving Climate Conditions Increase the Risk of Floods of the Large U.S.‐Canada Transboundary Richelieu River Basin?
Authors: Lucas‐Picher Philippe , Lachance‐Cloutier Simon , Arsenault Richard , Poulin Annie , Ricard Simon , Turcotte Richard , Brissette François
Published: October 2020

In spring 2011, an unprecedented flood hit the complex eastern United States (U.S.)–Canada transboundary Lake Champlain–Richelieu River (LCRR) Basin, destructing properties and inducing negative impacts on agriculture and fish habitats. The damages, covered by the Governments of Canada and the U.S., were estimated to C$90M. This natural disaster motivated the study of mitigation measures to prevent such disasters from reoccurring. When evaluating flood risks, long‐term evolving climate change should be taken into account to adopt mitigation measures that will remain relevant in the future. To assess the impacts of climate change on flood risks of the LCRR basin, three bias‐corrected multi‐resolution ensembles of climate projections for two greenhouse gas concentration scenarios were used to force a state‐of‐the‐art, high‐resolution, distributed hydrological model. The analysis of the hydrological simulations indicates that the 20‐year return period flood (corresponding to a medium flood) should decrease between 8% and 35% for the end of the 21st Century (2070–2099) time horizon and for the high‐emission scenario representative concentration pathway (RCP) 8.5. The reduction in flood risks is explained by a decrease in snow accumulation and an increase in evapotranspiration expected with the future warming of the region. Nevertheless, due to the large climate inter‐annual variability, short‐term flood probabilities should remain similar to those experienced in the recent past.
Spatial and Temporal Patterns of Low Streamflow and Precipitation Changes in the Chesapeake Bay Watershed
Authors: Fleming B.J. , Archfield S.A. , Hirsch R.M. , Kiang J.E. , Wolock D.M.
Published: October 2020

Spatial and temporal patterns in low streamflows were investigated for 183 streamgages located in the Chesapeake Bay Watershed for the period 1939–2013. Metrics that represent different aspects of the frequency and magnitude of low streamflows were examined for trends: (1) the annual time series of seven‐day average minimum streamflow, (2) the scaled average deficit at or below the 2% mean daily streamflow value relative to a base period between 1939 and 1970, and (3) the annual number of days below the 2% threshold. Trends in these statistics showed spatial cohesion, with increasing low streamflow volume at streamgages located in the northern uplands of the Chesapeake Bay Watershed and decreasing low streamflow volume at streamgages in the southern part of the watershed. For a small subset of streamgages (12%), conflicting trend patterns were observed between the seven‐day average minimum streamflow and the below‐threshold time series and these appear to be related to upstream diversions or the influence of reservoir‐influenced streamflows in their contributing watersheds. Using multivariate classification techniques, mean annual precipitation and fraction of precipitation falling as snow appear to be broad controls of increasing and decreasing low‐flow trends. Further investigation of seasonal precipitation patterns shows summer rainfall patterns, driven by the Atlantic Multidecadal Oscillation, as the main driver of low streamflows in the Chesapeake Bay Watershed.
Genetic differences and longevity‐related phenotypes influence lifespan and lifespan variation in a sex‐specific manner in mice
Authors: Yuan Rong , Musters C. J. M. , Zhu Yun , Evans Tracy R. , Sun Yujie , Chesler Elissa J. , Peters Luanne L. , Harrison David E. , Bartke Andrzej
Published: October 2020

Epidemiological studies of human longevity found two interesting features, robust advantage of female lifespan and consistent reduction of lifespan variation. To help understand the genetic aspects of these phenomena, the current study examined sex differences and variation of longevity using previously published mouse data sets including data on lifespan, age of puberty, and circulating insulin‐like growth factor 1 (IGF1) levels in 31 inbred strains, data from colonies of nuclear‐receptor‐interacting protein 1 (Nrip1) knockout mice, and a congenic strain, B6.C3H‐Igf1. Looking at the overall data for all inbred strains, the results show no significant difference in lifespan and lifespan variation between sexes; however, considerable differences were found among and within strains. Across strains, lifespan variations of female and male mice are significantly correlated. Strikingly, between sexes, IGF1 levels correlate with the lifespan variation and maximum lifespan in different directions. Female mice with low IGF1 levels have higher variation and extended maximum lifespan. The opposite is detected in males. Compared to domesticated inbred strains, wild‐derived inbred strains have elevated lifespan variation due to increased early deaths in both sexes and extended maximum lifespan in female mice. Intriguingly, the sex differences in survival curves of inbred strains negatively associated with age of female puberty, which is significantly accelerated in domesticated inbred strains compared to wild‐derived strains. In conclusion, this study suggests that genetic factors are involved in the regulation of sexual disparities in lifespan and lifespan variation, and dissecting the mouse genome may provide novel insight into the underlying genetic mechanisms.
“You Never Know What Will Happen”: Youth, Affect, and the Eventfulness of Tourism Encounters
Authors: Frohlick Susan , Zamora Carolina Meneses
Published: October 2020

In a small town in the Caribbean region of Costa Rica, affective tourism economies shape the ways that the future is imagined and played out for racialized local youth. We tell a story of one interlocutor, Fred, a sanguine young man with a troubled childhood, to explore how intensities and emotions in his encounters with a wealthy tourist during his late teen years generated possibilities. Events unfolded to become eventfulness that made the future something. For youth like Fred, affective encounters with tourists instantiated the future, or rather, moved the future along, in indeterminate rather than predetermined or inevitable ways. Nevertheless, the hopefulness felt by Fred about the next tourist encounter that lay before him was tempered by his devaluation vis‐à‐vis a well‐off expat patrona (boss), who both stirred and deterred his dreams for “a” future.
Seasonality and interspecific competition shape individual niche variation in co‐occurring tetra fish in Neotropical streams
Authors: Neves Mayara Pereira , Costa‐Pereira Raul , Delariva Rosilene Luciana , Fialho Clarice Bernhardt
Published: October 2020

The drivers of intraspecific niche variation and its effects on species interactions are still unclear, especially in species‐rich Neotropical environments. Here, we investigated how ecological opportunity and interspecific competition affect the degree of individual trophic specialization and the population niche breadth in tetra fish. We studied the four ecologically similar species (Psalidodon aff. gymnodontus, P. aff. paranae, P. bifasciatus, and Bryconamericus ikaa) in subtropical headwater streams (three sites with two co‐occurring species and three sites with only one species). We sampled fish in two contrasting seasons (winter/dry and summer/wet) and quantified their trophic niches using gut content analysis. Psalidodon bifasciatus was the only species distributed over all the sampled streams. We observed seasonal differences in population trophic niche breadth of P. bifasciatus just when this species co‐occurred with P. aff. gymnodontus. These findings confirm the complex nature of the effects of interspecific competition, depending, for instance, on the identity of the competitor. The degree of individual specialization of P. bifasciatus was higher in the winter, and it was not influenced by the presence of another species. Conversely, the other two Psalidodon species studied presented greater individual specialization in the summer, when fish consumed a higher proportion of allochthonous items (terrestrial insects and seeds), and there were no effects only for B. ikaa. Herein, our results suggest that seasonality in food‐resource availability is a major driver of niche variation and it has the potential to play an important role in how these similar tetra species interact and coexist.

Abstract in Portuguese is available with online material.