bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of VEGF and KDR polymorphisms with the development of schizophrenia
Authors: Saoud Hana , Aflouk Youssef , Ben Afia Amira , Gaha Lotfi , Bel Hadj Jrad Besma
Published: August 2021

Aim

Several approaches indicate different blood flow disturbances in schizophrenia (Scz). Vascular endothelial growth factor (VEGF) is widely recognized as one of the key molecules implicated in the angiogenesis process through mainly its receptor KDR. The current work was designed to investigate the potential association between three polymorphisms (rs699947; rs833061 and rs3025039) in VEGF gene and two SNPs (rs2305948 and rs1870377) within KDR gene and predisposition to Scz among the Tunisian population.

Methods

We carried-out a case-control study composed of 200 schizophrenic patients and 200 healthy subjects using RFLP-PCR.

Results

Of all analyzed polymorphisms, only rs3025039, rs833061 and rs1870377 showed a significant risk for Scz. Following the stratified analysis, rs833061 was more prevalent among undifferentiated form. Yet, rs1870377 was especially correlated with paranoid subtype. We found also that rs699947 and rs833061 had an impact on patients’ symptomatology. Haplotype analysis unveiled a strong LD between rs833061 and rs3025039 only for undifferentiated patients. Moreover, the -2578/-460/+936 CTT haplotype, with only one mutated allele +936T, conferred a high risk to Scz and, in particular, to undifferentiated and paranoid forms. Among the last-mentioned subgroup, we noticed another overrepresented haplotype (ATT). Furthermore, the +1192/+1719 GT haplotype carrying the minor allele +1719T displayed increased frequencies in schizophrenics as well as in paranoid patients.

Conclusion

Our results show that all SNPs associated with the development or the severity of schizophrenia, were subsequently correlated with a decrease in the VEGF levels or influence VEGFR-2 binding affinity. Nevertheless, these data need to be strengthened by further independent analyses.
The Impact of Climate Change on the Prevalence of Mental Illness Symptoms
Authors: Monsour Molly , Clarke-Rubright Emily , Lieberman-Cribbin Wil , Timmins Christopher , Taioli Emanuela , Schwartz Rebecca M. , Corley Samantha S. , Laucis Anna M. , Morey Rajendra A.
Published: August 2021

Background

The repercussions of climate change threaten the population with an increased prevalence of extreme climate events. We explored the impact of climate change induced sea level rise (SLR) and tropical cyclone (TC) exposure on mental illness symptom prevalence.

Methods

Using three datasets, TC exposure scores were calculated for each subject to determine how exposure affects posttraumatic stress disorder (PTSD), anxiety, and major depressive disorder (MDD) symptom prevalence. Inundation mapping of various SLR and storm surge (SS) scenarios were performed for the susceptible region of Miami-Dade and Broward counties to determine the population impact of flooding.

Results

We found an elevated risk of mental illness symptoms from exposure to more high-intensity TCs and identified demographic variables that may contribute to this risk. Furthermore, inundation mapping demonstrated severe and widespread impact of SLR and SS on the mental health of communities.

Limitations

This study did not include data directly measuring comorbidity, resilience, preparedness, or ability to adapt to climate change. Also, multiple imputation using chained equations may have been imperfect. Finally, when conducting inundation mapping, static mapping may overestimate flooding severity.

Conclusion

The impacts of climate change have been frequently studied in terms of physical health, natural disaster prevalence, and economic impacts, but rarely on mental health burden. However, it is vital that national, state, and local governments develop and deploy plans to address mental health needs along with expenditures for protecting infrastructure, the economy, and physical health from the combined effects of SLR and climate change-induced natural disasters.
Data science competition for cross-site delineation and classification of individual trees from airborne remote sensing data
Authors: Graves Sarah Jane , Marconi Sergio , Stewart Dylan , Harmon Ira , Weinstein Ben G. , Kanazawa Yuzi , Scholl Victoria M , Joseph Maxwell B , McClinchy Joseph , Browne Luke , Sullivan Megan K , Estrada-Villegas Sergio , Tusa Eduardo , Wang Daisy Zhe , Singh Aditya , Bohlman Stephanie A , Zare Alina , White Ethan P.
Published: August 2021

Delineating and classifying individual trees in remote sensing data is challenging. Many tree crown delineation methods have difficulty in closed-canopy forests and do not leverage multiple datasets. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for delineation of individual crowns and classification to determine species identity. This competition included data from multiple sites to assess the methods’ ability to generalize learning across multiple sites simultaneously, and transfer learning to novel sites where the methods were not trained. Six teams, representing 4 countries and 9 individual participants, submitted predictions. Methods from a previous competition were also applied and used as the baseline to understand whether the methods are changing and improving over time. The best delineation method was based on an instance segmentation pipeline, closely followed by a Faster R-CNN pipeline, both of which outperformed the baseline method. However, the baseline (based on a growing region algorithm) still performed well as did the Faster R-CNN. All delineation methods generalized well and transferred to novel forests effectively. The best species classification method was based on a two-stage fully connected neural network, which significantly outperformed the baseline (a random forest and Gradient boosting ensemble). The classification methods generalized well, with all teams training their models using multiple sites simultaneously, but the predictions from these trained models generally failed to transfer effectively to a novel site. Classification performance was strongly influenced by the number of field-based species IDs available for training the models, with most methods predicting common species well at the training sites. Classification errors (i.e., species misidentification) were most common between similar species in the same genus and different species that occur in the same habitat. The best methods handled class imbalance well and learned unique spectral features even with limited data. Most methods performed better than baseline in detecting new (untrained) species, especially in the site with no training data. Our experience further shows that data science competitions are useful for comparing different methods through the use of a standardized dataset and set of evaluation criteria, which highlights promising approaches and common challenges, and therefore advances the ecological and remote sensing field as a whole.
A flexible summary-based colocalization method with application to the mucin Cystic Fibrosis lung disease modifier locus
Authors: Wang Fan , Panjwani Naim , Wang Cheng , Sun Lei , Strug Lisa J
Published: August 2021

Mucus obstruction is a central feature in the Cystic Fibrosis (CF) airways. A genome-wide association study (GWAS) of lung disease by the CF Gene Modifier Consortium (CFGMC) identified a significant locus containing two mucin genes, MUC20 and MUC4. Expression quantitative trait locus (eQTL) analysis using human nasal epithelial (HNE) from 94 CF Canadians in the CFGMC demonstrated MUC4 eQTLs that mirrored the lung association pattern in the region, suggesting that MUC4 expression may mediate CF lung disease. Complications arose, however, with colocalization testing using existing methods: the locus is complex and the associated SNPs span a 0.2Mb region with high linkage disequilibrium and evidence of eQTLs for multiple genes and tissues (heterogeneity). We previously developed the Simple Sum (SS), a powerful colocalization test in regions with heterogeneity, but SS assumed eQTLs to be present to achieve type I error control. Here we propose a two-stage SS (SS2) colocalization test that avoids a prior eQTL assumptions, accounts for multiple hypothesis testing and the composite null hypothesis and enables meta-analysis. We compare SS2 to published approaches through simulation and demonstrate type I error control for all settings with the greatest power in the presence of high LD and heterogeneity. Applying SS2 to the MUC20/MUC4 CF lung disease locus with eQTLs from CF HNE revealed significant colocalization with MUC4 (p = 1.71×10−5) rather than MUC20. The SS2 is a powerful method to inform the responsible gene(s) at a locus and guide future functional studies. SS2 has been implemented in the application LocusFocus (locusfocus.research.sickkids.ca).
A kinetic error filtering mechanism for enzyme-free copying of nucleic acid sequences
Authors: Göppel Tobias , Obermayer Benedikt , Chen Irene A. , Gerland Ulrich
Published: August 2021

Accurate copying of nucleic acid sequences is essential for self-replicating systems. Modern cells achieve error ratios as low as 10-9with sophisticated enzymes capable of kinetic proofreading. In contrast, experiments probing enzyme-free copying of RNA and DNA as potential prebiotic replication processes find error ratios on the order of 10%. Given this low intrinsic copying fidelity, plausible scenarios for the spontaneous emergence of molecular evolution require an accuracy-enhancing mechanism. Here, we study a ‘kinetic error filtering’ scenario that dramatically boosts the likelihood of producing exact copies of nucleic acid sequences. The mechanism exploits the observation that initial errors in template-directed polymerization of both DNA and RNA are likely to trigger a cascade of consecutive errors and significantly stall downstream extension. We incorporate these characteristics into a mathematical model with experimentally estimated parameters, and leverage this model to probe to what extent accurate and faulty polymerization products can be kinetically discriminated. While limiting the time window for polymerization prevents completion of erroneous strands, resulting in a pool in which full-length products show an enhanced accuracy, this comes at the price of a concomitant reduction in yield. We show that this fidelity-yield trade-off can be circumvented via repeated copying attempts in cyclically varying environments such as the temperature cycles occurring naturally in the vicinity of hydrothermal systems. This setting could produce exact copies of sequences as long as 50mers within their lifetime, facilitating the emergence and maintenance of catalytically active oligonucleotides.
Identifying Meta-QTLs for Stay-Green in Sorghum
Authors: Aquib Ahmed , Nafis Shadma
Published: August 2021

To develop resilient crops it is necessary to understand the underlying genetics of climatic response. A strong association between stay-green and post-flowering drought tolerance in Sorghum has been established. Being a complex quantitative trait, Quantitative Trait Loci (QTL) mapping experiments of stay-green in Sorghum have been frequently performed. The objective of the current study was to find consensus genomic regions that control stay-green by integrating the QTLs mapped in previous studies. Meta-QTL analysis was performed to summarize 115 QTLs projected on the consensus map. The analysis generated 32 Meta-QTL regions within which candidate gene (CG) identification was undertaken. 7 candidate genes were identified using the markers tightly linked to the Meta-QTLs. The results from this study will facilitate future attempts aiming to improve and understand drought tolerance in Sorghum.
SIRPα sequesters SHP-2 to promote IL-4/13 signaling and alternative activation of macrophages
Authors: Shi Lei , Kidder Koby , Bian Zhen , Chiang Samantha Kuon Ting , Ouellette Corbett , Liu Yuan
Published: August 2021

The Th2 cytokines IL-4 and IL-13 through activation of their shared receptor IL-4Rα direct macrophage alternative activation to promote immunosuppression and wound healing. However, the mechanisms that control macrophage responses to IL-4/13 are not fully understood. Apart from driving JAK-STAT and PI3K-Akt pathways to polarize macrophages toward the alternative phenotype, the activated IL-4/13 receptors recruit negative regulators SHP-1 and SHP-2, which dephosphorylate IL-4Rα and decrease its signaling. Here we report that SIRPα spatially restricts SHP-2 and, by such, promotes IL-4/13 signaling and macrophage alternative activation. SIRPα executes this regulation via its cytoplasmic ITIMs/ITSMs that undergo phosphorylation by IL-4/13-induced, Src kinase-activated Bruton’s tyrosine kinase (Btk), resulting in recruitment of SHP-2 and preclusion of SHP-2 from binding to and inhibiting IL-4/13 receptors. Despite that this regulation occurs independent of CD47, extracellular CD47 ligation of SIRPα facilitates its cytoplasmic phosphorylation and SHP-2 sequestration, leading to stronger IL-4/13 signaling and enhanced macrophage expression of IL-10, TGFβ, CD206, arginase-1, etc. Conversely, deficiency of SIRPα allows SHP-2 to freely bind to γC or IL-13Rα1 and through which dephosphorylate IL-4Rα, dampening its signaling. Consistent with these findings, impaired wound healing in Sirpα−/−mice under experimental colitis correlated with a deficit of immunosuppressive macrophages in the colon, a condition that was corrected by transfusion of ex vivo-produced SIRPαhighalternatively activated macrophages.
High genetic barrier to escape from human polyclonal SARS-CoV-2 neutralizing antibodies
Authors: Schmidt Fabian , Weisblum Yiska , Rutkowska Magdalena , Poston Daniel , Silva Justin Da , Zhang Fengwen , Bednarski Eva , Cho Alice , Schaefer-Babajew Dennis J. , Gaebler Christian , Caskey Marina , Nussenzweig Michel C. , Hatziioannou Theodora , Bieniasz Paul D.
Published: August 2021

The number and variability of the neutralizing epitopes targeted by polyclonal antibodies in SARS-CoV-2 convalescent and vaccinated individuals are key determinants of neutralization breadth and, consequently, the genetic barrier to viral escape. Using chimeric viruses and antibody-selected viral mutants, we show that multiple neutralizing epitopes, within and outside the viral receptor binding domain (RBD), are variably targeted by polyclonal plasma antibodies and coincide with sequences that are enriched for diversity in natural SARS-CoV-2 populations. By combining plasma-selected spike substitutions, we generated synthetic ‘polymutant’ spike proteins that resisted polyclonal antibody neutralization to a similar degree as currently circulating variants of concern (VOC). Importantly, by aggregating VOC-associated and plasma-selected spike substitutions into a single polymutant spike protein, we show that 20 naturally occurring mutations in SARS-CoV-2 spike are sufficient to confer near-complete resistance to the polyclonal neutralizing antibodies generated by convalescents and mRNA vaccine recipients. Strikingly however, plasma from individuals who had been infected and subsequently received mRNA vaccination, neutralized this highly resistant SARS-CoV-2 polymutant, and also neutralized diverse sarbecoviruses. Thus, optimally elicited human polyclonal antibodies against SARS-CoV-2 should be resilient to substantial future SARS-CoV-2 variation and may confer protection against future sarbecovirus pandemics.
SARS-CoV-2 vaccine effectiveness in immunosuppressed kidney transplant recipients
Authors: Chemaitelly Hiam , AlMukdad Sawsan , Joy Jobin Paravila , Ayoub Houssein H. , Yassine Hadi M. , Benslimane Fatiha M. , Al Khatib Hebah A. , Tang Patrick , Hasan Mohammad R. , Coyle Peter , Al Kanaani Zaina , Al Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Nasrallah Gheyath K. , Al Kuwari Mohamed Ghaith , Butt Adeel A. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Alkadi Mohamad M. , Ali Omar , Al-Maslamani Muna , Bertollini Roberto , Al Malki Hassan , Almaslamani Yousuf , Abu-Raddad Laith J. , Al Khal Abdullatif
Published: August 2021

COVID-19 vaccine protection against infection in immunosuppressed solid organ transplant recipients is unknown but possibly weak with the low proportion of these patients mounting a robust humoral and cellular immune response after vaccination. Using a retrospective cohort study design with cross-over, we assessed vaccine effectiveness among 782 kidney transplant recipients registered at Hamad Medical Corporation, the national public healthcare provider in Qatar, where the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines have been used in the national immunization campaign. Vaccine effectiveness against any SARS-CoV-2 infection was estimated at 46.6% (95% CI: 0.0-73.7%) ≥14 days after the second dose, 66.0% (95% CI: 21.3-85.3%) ≥42 days after the second dose, and 73.9% (95% CI: 33.0-89.9%) ≥56 days after the second dose. Vaccine effectiveness against any severe, critical, or fatal COVID-19 disease was estimated at 72.3% (95% CI: 0.0-90.9%) ≥14 days after the second dose, 85.0% (95% CI: 35.7-96.5%) ≥42 days after the second dose, and 83.8% (95% CI: 31.3-96.2%) ≥56 days after the second dose. Most vaccine breakthrough infections occurred in the first few weeks after receiving the first and/or second dose. Vaccine effectiveness reached considerable levels in kidney transplant recipients, but vaccine protection mounted slowly and did not reach a high level until several weeks after the second dose.
MAVS expression in alveolar macrophages is essential for host resistance against Aspergillus fumigatus
Authors: Wang Xi , Cunha Cristina , Grau Madeleine S. , Robertson Shelly J. , Lacerda João F. , Campos António , Lagrou Katrien , Maertens Johan , Best Sonja M. , Carvalho Agostinho , Obar Joshua J.
Published: August 2021

Our recent data demonstrates a critical role of the RIG-I-like receptor (RLR) family in regulating antifungal immunity against Aspergillus fumigatus in a murine model. However, the importance of this pathway in humans and the cell type(s) which utilize this innate immune receptor to detect A. fumigatus remains unresolved. Here using patients who underwent hematopoietic stem cell transplantation (HSCT), we demonstrate that a polymorphism in human MAVS present in the donor genome was associated with the incidence of invasive pulmonary aspergillosis (IPA). Moreover, in a separate cohort of confirmed IPA patients, polymorphisms in the IFIH1 gene alter the inflammatory response, including interferon-responsive chemokines. Returning to our murine model, we now demonstrate that CD11c+ SiglecF+ alveolar macrophages require Mavs expression to maintain host resistance against A. fumigatus. Our data support the role of MAVS signaling in mediating antifungal immunity in both mice and human at least in part through the role of MAVS-dependent signaling in alveolar macrophages.
Classifying Radiology Abstracts with Deep Learning
Authors: Chen Hongyu , Shih George
Published: August 2021

Background

The Radiological Society of North America (RSNA) receives more than 8000 abstracts yearly for scientific presentations, scientific posters, and scientific papers. Each abstract is assigned manually one of 16 top-level categories (e.g. “Breast Imaging”) for workflow purposes. Additionally, each abstract receives a grade from 1-10 based on a variety of subjective factors such as style and perceived writing quality. Using machine learning to automate, at least partially, the categorization of abstract submissions can result in saving many hours of manual labor.

Methods

A total of 45527 RSNA abstract submissions from 2014 through 2019 were ingested, tokenized, and pre-processed with a standard natural language programming protocol. A bag-of-words (BOW) model was used as a baseline to evaluate two more sophisticated models, convolutional neural networks and recurrent neural networks, and also evaluate an ensemble model featuring all three neural networks.

Results

ensemble model was able to achieve 73% testing accuracy for classifying the 16 top-level categories, outperforming all other models. The top model for classifying abstract grade was also an ensemble model, achieving a mean average error (MAE) of 1.01.

Conclusion

While the baseline BOW model was the highest performing individual classifier, ensemble models that included state-of-the-art neural networks were able to outperform it. Our research shows that machine learning techniques can, to a reasonable degree of accuracy, predict both objective factors such as abstract category as well as subjective factors such as abstract grade. This work builds upon previous research involving using natural language processing on scientific abstracts to make useful inferences that address a meaningful problem.
Speeding and Traffic-Related Injuries and Fatalities during the 2020 COVID-19 Pandemic: The Cases of Seattle and New York City
Authors: Liao Felix Haifeng , Lowry Michael
Published: August 2021

Despite fewer cars on roads during the COVID-19 pandemic, deaths associated with motor vehicle collisions in New York City and Seattle remained largely unchanged in 2020. Using police data on weekly counts of collisions, we compared trends in 2020 with those of 2019, while controlling for the reduction of traffic volumes and seasonal weather conditions. Results of difference-in-differences estimation suggest that during the early months of the pandemic, or March-May, the incidence rates of severe or fatal injury crashes related to speeding increased by nearly 8 times in Seattle and more than 4 times in New York City. In the rest of 2020, they were still significantly higher than what would be expected in the absence of the pandemic. This research suggests that in similar situations that depress travel demand (e.g., another pandemic), policymakers should formulate plans to reduce speeding which may prevent an upswing in severe injuries and fatalities.
T cell responses to SARS-CoV-2 in people with and without neurologic symptoms of long COVID
Authors: Visvabharathy Lavanya , Hanson Barbara A. , Orban Zachary S. , Lim Patrick H. , Palacio Nicole M. , Jimenez Millenia , Clark Jeffrey R. , Graham Edith L. , Liotta Eric M. , Tachas George , Penaloza-MacMaster Pablo , Koralnik Igor J.
Published: August 2021

Many people experiencing long COVID syndrome, or post-acute sequelae of SARS-CoV-2 infection (PASC), suffer from debilitating neurologic symptoms (Neuro-PASC). However, whether virus-specific adaptive immunity is affected in Neuro-PASC patients remains poorly understood. We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated humoral and cellular responses toward SARS-CoV-2 Nucleocapsid protein at an average of 6 months post-infection compared to healthy COVID convalescents. Neuro-PASC patients also had enhanced virus-specific production of IL-6 from and diminished activation of CD8+T cells. Furthermore, the severity of cognitive deficits or quality of life disturbances in Neuro-PASC patients were associated with a reduced diversity of effector molecule expression in T cells but elevated IFN-γ production to the C-terminal domain of Nucleocapsid protein. Proteomics analysis showed enhanced plasma immunoregulatory proteins and reduced pro-inflammatory and antiviral response proteins in Neuro-PASC patients compared with healthy COVID convalescents, which were also correlated with worse neurocognitive dysfunction. These data provide new insight into the pathogenesis of long COVID syndrome and a framework for the rational design of predictive biomarkers and therapeutic interventions.

One Sentence Summary

Adaptive immunity is altered in patients with neurologic manifestations of long COVID.
Tankyrase interacts with the allosteric site of glucokinase and inhibits its glucose-sensing function in the beta cell
Authors: Chi Nai-Wen , Eisemann Travis , Yeh Tsung-Yin J. , Roy Swati , Chi Tyler J. , Lu Sunny H. , Pascal John M. , Osborn Olivia
Published: August 2021

Insulin secretion in the pancreatic beta cell is rate-limited by glucokinase (GCK), the glucose sensor that catalyzes the first step of glucose metabolism. GCK consists of two lobes connected by a flexible hinge that allows the kinase to exhibit a spectrum of conformations ranging from the active, closed form to several inactive, less-compact forms. Activating GCK mutations can cause hyperinsulinemia and hypoglycemia in infants. A similar phenotype exhibited by tankyrase (TNKS)-deficient mice prompted us to investigate whether TNKS might modulate the glucose-sensing function of GCK. We found that TNKS colocalizes and directly interacts with GCK. Their interaction is mediated by two ankyrin-repeat clusters (ARC-2 and −5) in TNKS and a tankyrase-binding motif (TBM, aa 63-68) in the GCK hinge. This interaction is conformation sensitive, human GCK variants that cause hyperglycemia (V62M) or hypoglycemia (S64Y) enhance or diminish the interaction respectively, even though they have no impact on TNKS interaction in the context of a GCK peptide (V62M) or a peptide library (S64Y). Moreover, the TNKS-GCK interaction is inhibited by high glucose concentrations, which are known to stabilize GCK in the active (closed, glucose-avid) conformation. Conversely, glucose phosphorylation by GCK in vitro is inhibited by TNKS. To study this in vitro inhibitory effect in the MIN6 beta cells, we showed that glucose-stimulated insulin secretion is suppressed upon stabilization of the TNKS protein and is conversely enhanced upon TNKS knockdown. Based on these findings as well as by contrasting with hexokinase-2, we propose that TNKS is a physiological GCK inhibitor in pancreatic beta cells that acts by trapping the kinase in the open (inactive) conformation.
Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia
Authors: Thomas L , Underwood JN , Rose NH , Fuller ZL , Richards ZT , Dugal L , Grimaldi C , Cooke IR , Palumbi SR , Gilmour JP
Published: August 2021

Understanding the mechanisms driving phenotypic variation in traits facing intensified selection from climate change is a crucial step in developing effective conservation and restoration initiatives. This is particularly true for reef-building corals, which are among the most vulnerable to climate change and are in dramatic decline globally. At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterising the mechanisms that control phenotypic responses to different environments. We combined whole genome re-sequencing, common garden heat stress experiments, transcriptome-wide gene expression analyses, and symbiont metabarcoding to explore the mechanisms that facilitate survival in contrasting habitat conditions. Our data show that, despite high gene flow between habitats, spatially varying selection drives subtle shifts in allele frequencies at hundreds of loci. These changes were concentrated into several islands of divergence spanning hundreds of SNPs that showed strong linkage disequilibrium and were associated with a coordinated increase in minor allele frequencies in corals taken from the lagoon habitat, where the range of environmental conditions is greatest. Common garden heat stress assays showed individuals from the lagoon exhibited higher bleaching resistance than colonies from the reef slope, and RNAseq identified pronounced physiological differences between the corals from the two habitats, primarily associated with molecular pathways including cell signalling, ion transport and metabolism. Despite the pronounced physioloigical and environmental differences between habitats, metabarcoding of theSymbiodiniaceaeITS2 region revealed all colonies to be associated exclusively with the genusCladocopium, with no detectable differences between habitats. This study contributes to the growing number of studies documenting the complex mechanisms that facilitate coral survival in extreme environments, and showcases the utility of combining multiple sequencing techniques to unravel complex climate-related traits.
Extent and complexity of RNA processing in the development of honey bee queen and worker castes revealed by Nanopore direct RNA sequencing
Authors: He Xu Jiang , Barron Andrew B. , Yang Liu , Chen Hu , He Yu Zhu , Zhang Li Zhen , Huang Qiang , Wang Zi Long , Wu Xiao Bo , Yan Wei Yu , Zeng Zhi Jiang
Published: August 2021

The distinct honey bee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity. Prior studies have explored differences in gene expression and methylation during development of the two castes, but thus far no study has performed a genome-wide analysis of differences in RNA processing. To address this here we performed a Nanopore-based direct RNA sequencing with exceptionally long reads to compare the mRNA transcripts between honey bee queen and workers at three points during their larval development. We found thousands of significantly differentially expressed isoforms (DEIs) between queen and worker larvae. Most DEIs contained alternative splicing, and many of them contained at least two types of alternative splicing patterns, indicating complex RNA processing in honey bee caste differentiation. We found a negative correlation between poly(A) length and DEI expression, suggesting that poly(A) tails participate in the regulation of isoform expression. Hundreds of isoforms uniquely expressed in either queens or workers during their larval development, and isoforms were expressed at different points in queen and worker larval development demonstrating a dynamic relationship between isoform expression and developmental mechanisms. These findings show the full complexity of RNA processing and transcript expression in honey bee phenotypic plasticity.
Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation
Authors: Williams Ruth M , Lukoseviciute Martyna , Sauka-Spengler Tatjana , Bronner Marianne E
Published: August 2021

The epiblast of vertebrate embryos is comprised of neural and non-neural ectoderm, with the border territory at their intersection harbouring neural crest and cranial placode progenitors. Here we profile avian epiblast cells as a function of time using single-cell RNA-seq to define transcriptional changes in the emerging ‘neural plate border’. The results reveal gradual establishment of heterogeneous neural plate border signatures, including novel genes that we validate by fluorescent in situ hybridisation. Developmental trajectory analysis shows that segregation of neural plate border lineages only commences at early neurulation, rather than at gastrulation as previously predicted. We find that cells expressing the prospective neural crest marker Pax7 contribute to multiple lineages, and a subset of premigratory neural crest cells shares a transcriptional signature with their border precursors. Together, our results suggest that cells at the neural plate border remain heterogeneous until early neurulation, at which time progenitors become progressively allocated toward defined lineages.
Activation of T cell checkpoint pathways during β-cell antigen presentation by engineered dendritic cells promotes protection of non-obese diabetic mice from type 1 diabetes
Authors: Gudi Radhika R. , Perez Nicolas , Karumuthil-Melethil Subha , Li Gongbo , Vasu Chenthamarakshan
Published: August 2021

Defective immune regulation has been recognized in type 1 diabetes (T1D). Immune regulatory T cell check-point receptors, which are generally upregulated on activated T cells, have been the molecules of attention as therapeutic targets for enhancing immune response in tumor therapy. We reported that dendritic cells (DCs) that are engineered to express selective ligands for checkpoint receptors can induce effective T cell tolerance in antigen-immunization models. Here, we show that pancreatic β -cell antigen (BcAg) presentation by engineered tolerogenic-DCs (tDCs) that express CTLA4 selective ligand (B7.1wa) or a combination of CTLA4, PD1 and BTLA selective ligands (B7.1wa, PD-L1, and HVEM-CRD1 respectively; multiligand-DCs) causes an increase in regulatory cytokine and T cell (Treg) responses and suppression of the effector T cell function as compared to engineered control-DCs. Non-obese diabetic (NOD) mice treated with BcAg-pulsed CTLA4-ligand-DCs and multiligand-DCs at pre-diabetic and early-hyperglycmic stages showed significantly lower degree of insulitis, higher frequencies of insulin-positive islets, profound delay in, and reversal of, hyperglycemia for a significant duration. Immune cells from the tDC treated mice not only produced lower amounts of IFNγ and higher amounts of IL10 and TGFβ1 upon BcAg challenge, but also failed to induce hyperglycemia upon adoptive transfer. While both CTLA4-ligand-DCs and multiligand-DCs were effective in inducing tolerance, multiligand-DC treatment produced an overall higher suppressive effect on effector T cell function and disease outcome. These studies show that enhanced engagement of T cell checkpoint receptors during BcAg presentation can modulate T cell function and suppress autoimmunity and progression of the disease in T1D.
Single molecule fingerprinting reveals different amplification properties of α-synuclein oligomers and preformed fibrils in seeding assay
Authors: Lau Derrick , Magnan Chloé , Hill Kathryn , Cooper Antony , Gambin Yann , Sierecki Emma
Published: August 2021

The quantification of α-synuclein (α-syn) aggregates has emerged as a promising biomarker for synucleinopathies. Assays that amplify and detect such aggregates have revealed the presence of seeding-competent species in biosamples of patients diagnosed with Parkinson’s disease. However, multiple species such as oligomers and amyloid fibrils, are formed during the aggregation of α-synuclein and these species are likely to co-exist in biological samples and thus it remains unclear which species(s) are contributing to the signal detected in seeding assays. To identify which species can be detected in seeding assays, recombinant oligomers and preformed fibrils were produced and purified to characterise their individual biochemical and seeding potential. Here, we used single molecule spectroscopy to track the formation and purification of oligomers and fibrils at the single particle level and compare their respective seeding potential in an amplification assay. Single molecule detection validates that size-exclusion chromatography efficiently separates oligomers from fibrils. Oligomers were found to be seeding-competent but our results reveal that their seeding behaviour is very different compared to preformed fibrils in our amplification assay. Overall, our data suggest that even a low number of preformed fibrils present in biosamples are likely to dominate the response in seeding assays.
Numerical evaluation of the exhaust-direction effects on plume flow and helicopter infrared radiation under hover and cruise statuses
Authors: Yang Zongyao , Shan Yong , Zhang Jingzhou
Published: August 2021

Purpose

This study aims to investigate the effects of exhaust direction on exhaust plume and helicopter infrared radiation in hover and cruise status.

Design/methodology/approach

Four exhaust modes are concerned, and the external flow field and fuselage temperature field are calculated by numerical simulation. The infrared radiation intensity distributions of the four models in hovering and cruising states are computed by the ray-tracing method.

Findings

Under the hover status, the exhaust plume is deflected to flow downward after it exhausts from the nozzle exit, upon the impact of the main-rotor downwash. Besides, the exhaust plume shows a “swirling” movement following the main-rotor rotational direction. The forward-flight flow helps prevent the hot exhaust plume from a collision with the helicopter fuselage generally for the cruise status. In general, the oblique-upward exhaust mode provides moderate infrared radiation intensities in all of the viewing directions, either under the hover or the cruise status. Compared with the hover status, the infrared radiation intensity distribution alters somewhat in cruise.

Originality/value

Illustrating the influences of exhaust direction on plume flow and helicopter infrared radiation and the differences of helicopter infrared radiation under hover and cruise statuses are identified. Finally, an appropriate exhaust mode is proposed to provide a better IR signature distribution.
Determination of airports’ atmospheric mixing height boundaries using operational data
Authors: Dalkıran Alper
Published: August 2021

Purpose

This study aims to determine the distance and duration to reach airports mixing height of 3,000 feet limit. Airport operations significantly contribute to the aircraft landing and take-off (LTO) cycle. Eurocontrol’s SO6 data sets comprise several abutted segment data to analyse the duration and distance for specific flights.

Design/methodology/approach

Two consequential methods have been used to calculate the distance and destination from the SO6 databases. First, SQL filtering and pivot tables were formed for the required data. Second, over 583,000 data lines for a year of Boeing 747–400 aircraft routes were calculated and filtered for the monthly assessments.

Findings

LTO cycles’ durations have deviated −24% to 76% from the ICAO assumptions. Distance facts determined for specific airports as 2.57 to 3.66 nm for take-off and 5.02 to 23.25 nm for the landing. The average duration of the aircraft’s in mentioned airport take-off are 66 to 74 s and 40 to 50 s; averages have been calculated as 70 to 44 s. Landing durations have been calculated for four different airports as 173 to 476 s.

Practical implications

This study provides a re-evaluation chance for the current assumptions and helps for better assessments. Each airport and aircraft combinations have their duration and distance figures.

Originality/value

This study has calculated the first LTO distances in the literature for the aerodrome. This method applies to all airports, airline fleets and aircraft if the segmented SO6 data are available.
Connectivity is key: holistic sustainability assessment and reporting from the perspective of food manufacturers
Authors: Küchler Rebekka , Herzig Christian
Published: August 2021

Purpose

As members of the food supply chain, food manufacturers acquire power and hold responsibility for the sustainable transformation of our food systems. Sustainability assessment and reporting frameworks function as instruments to shape sustainable transformation processes. The purpose of the paper is to investigate the suitability for food manufacturing companies and their connectivity with the up- and downstream food supply chain.

Design/methodology/approach

The first section of the study explores the need for holistic, company-based sustainability frameworks in the food manufacturing sector from the literature. The second part compares seven frameworks, in terms of content and supply chain connectivity.

Findings

Food sector specificity demands the inclusion of topics specific to food systems. Furthermore, none of the investigated frameworks fulfil both food sector specificity and full connectivity with the up- and downstream supply chain.

Research limitations/implications

As a limitation to this work, comparison of the frameworks at topic level instead of indicator level is considered. The findings call for more harmonised and integrated sustainability assessment throughout the food supply chain.

Practical implications

The framework a food manufacturer should apply depends on their motivation behind conducting the sustainability assessment and reporting. Evidence is provided from various perspectives and with regard to key issues such as content, certification and communication.

Originality/value

No comparison between sustainability frameworks has been made yet from the supply chain perspective of food manufacturers.
Strategic fit of mergers and acquisitions in Latin American airlines: a two-stage DEA approach
Authors: Wanke Peter , Antunes Jorge Junio Moreira , Correa Henrique Luiz , Tan Yong
Published: August 2021

Purpose

The purpose of this paper is to assess the efficiency determinants of mergers and acquisitions (M&A) in the context of Latin American airlines based on business-related variables commonly found in the literature. The idea is to identify preferable potential airline matches in light of fleet mix, ownership structure and geographical proximity.

Design/methodology/approach

In order to achieve the objective, all possible combinations of M&A pairs are considered in the analysis, which is developed in a two-stage approach. First, the M&A Data Envelopment Analysis model efficiency and returns-to-scale estimates are computed. Then, robust regression and multinomial logistic regression are respectively used to discriminate these estimates in terms of such business-related variables.

Findings

The results reveal that these different contextual variables significantly impact virtual efficiency and returns-to-scale levels. Private ownership, passenger focus and a better match between aircraft size and demand for flights appear to be key drivers for merged airline efficiency.

Research limitations/implications

The study makes theoretical contributions, though limited to analyzing Latin American airlines only. The use of bootstrapped robust/multinominal logistic regression, compared to the methods adopted by previous literature studies, generates more accurate and robust results related to the efficiency drivers due to its special feature and ability to allow the discrimination of increasing, decreasing, and constant returns to scale in light of a given set of contextual variables.

Practical implications

This study examines the pure effect of the merging activity on efficiency gains. Not only private ownership but also a hybrid public–private ownership has a positive influence on virtual efficiency, suggesting an important governmental role in promoting M&A in the airline industry.

Originality/value

The authors present an original take on the issue of airline mergers by exploring what are the major drivers possibly involved in efficiency gains of potentially merged (virtual) airlines. The authors identify preferable potential airline matches where efficiency gains would be positive in light of business-related variables such as fleet mix, ownership structure and geographical proximity. The analysis also includes an assessment of the impact of contextual variables such as cargo type, ownership structure and geographical proximity in relation to the strategic fit of mergers considering the resulting efficiency and returns-to-scale scores of virtually merged airlines. To the authors’ knowledge, no previous research has addressed these issues in Latin American airlines. Further research directions for this industry are also discussed.
Design of bilayer graphene nanoribbon tunnel field effect transistor
Authors: Vobulapuram Ramesh Kumar , Shaik Javid Basha , P. Venkatramana , Mekala Durga Prasad , Lingayath Ujwala
Published: August 2021

Purpose

The purpose of this paper is to design novel tunnel field effect transistor (TFET) using graphene nanoribbons (GNRs).

Design/methodology/approach

To design the proposed TFET, the bilayer GNRs (BLGNRs) have been used as the channel material. The BLGNR-TFET is designed in QuantumATK, depending on 2-D Poisson’s equation and non-equilibrium Green’s function (NEGF) formalism.

Findings

The performance of the proposed BLGNR-TFET is investigated in terms of current and voltage (I-V) characteristics and transconductance. Moreover, the proposed device performance is compared with the monolayer GNR-TFET (MLGNR-TFET). From the simulation results, it is investigated that the BLGNR-TFET shows high current and gain over the MLGNR-TFET.

Originality/value

This paper presents a new technique to design GNR-based TFET for future low power very large-scale integration (VLSI) devices.
Producing work-ready commercial art graduates: stakeholders' perceptions
Authors: Sarpong-Nyantakyi Josephine , Osei-Poku Patrick , Eshun Eric Francis
Published: August 2021

Purpose

Graduate unemployment is widely reported not only in Ghana but also across the globe. The purpose of this study is to examine the relevance of the HND Commercial Art Programme, Graphic Design (CAPGD) option, to the graphic art industry and to determine the work readiness of graduates of HND CAPGD at the world of work.

Design/methodology/approach

A qualitative, evaluative case study research design was adopted to examine the perspectives of stakeholders of CAPGD. It was a multiple case study, which involved faculty members, graduates and industry-based supervisors. The study was conducted using in-depth semi-structured interviews and focus group discussions to obtain in-depth interpretations and conclusions that reflected the perceptions of the stakeholders.

Findings

The qualitative results indicate that the existing curriculum, based on the old polytechnic educational system, does not provide adequate practical approach to teaching and learning processes. Hence the majority of graduates lack competencies to meet industry's expectations.

Research limitations/implications

The key limitation is lack of database on the HND Graphic Design graduates at Takoradi Technical University. This affected the data collection process as the HND Graphic Design graduate participants were not easily accessible, and, as such, much effort and risk were required to contact them. Considering the implication for education policy, the findings propose stakeholders' collaboration to ensure cross fertilization of ideas (Nwajiuba et al., 2020). Hence, a compilation of database could engender further study in this area and thus form the bases of a mixed method approach resulting in in-depth analysis for fresh insights into the study.

Originality/value

The findings provide unique insights into work readiness of Commercial Art graduates, specifically in Ghana, as it seeks to bridge a gap in literature.