bluuebunny/crossref_metadata_2025 huggingface dataset:
Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand
Authors: Booncharoen Auttaporn , Visessanguan Wonnop , Kuncharoen Nattakorn , Yiamsombut Supalurk , Santiyanont Pannita , Mhuantong Wuttichai , Rojsitthisak Pornchai , Tanasupawat Somboon
Published: November 2021

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus

Halobacillus

and was most closely related to

Halobacillus salinus

JCM 11546T (98.6 %),

Halobacillus locisalis

KCTC 3788T (98.6 %) and

Halobacillus yeomjeoni

KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T and its related species were 18.2–19.3 % and 69.84–84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30–40 °C, at pH 7.0 and with 10–15 % (w/v) NaCl. It contained l-Orn–d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA–DNA relatedness and ANI values, strain SKP4-6T represents a novel species of the genus

Halobacillus

, for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).
SARS-CoV-2 vaccination predicts COVID-19 progression and outcomes in hospitalized patients
Authors: Padovani Alessandro , Cristillo Viviana , Tomasoni Daniela , Gipponi Stefano , Pilotto Andrea
Published: November 2021

Background

SARS-CoV-2 vaccination might impact on clinical progression of cases with breakthrough COVID-19 disease.

Objective

to evaluate the impact of SARS-CoV-2 vaccination on disease progression in COVID-19 hospitalized patient

Methods and Findings

Two-hundred eighty-four consecutive COVID-19 hospitalized patients, including 50 vaccinated cases entered the study. Compared to unvaccinated cases, vaccinated patients were older, exhibited more comorbidities and did not differ for COVID-19 severity at admission. During hospitalisation, unvaccinated patients showed worse disease progression, including higher need of oxygen and higher risk of death compared to vaccinated patients (OR 3.3; 1.05-10.7 95% CI in the whole cohort and OR 54.8; 3.5-852 in the ventilated cases).

Discussion

These findings argue for an important reduction in severity among vaccine breakthrough infection compared to unvaccinated cases in COVID-19 disease.
Delay of TB patients in diagnosis in a conflict setting of Mogadishu, Somalia - a cross-sectional study
Authors: Sheikh Naima Said , Salad Abdulwahab M. , Gele Abdi A.
Published: November 2021

Background

The TB case detection rate in Somalia is 42%, which is much lower than the WHO target of detecting 70% of new TB cases. Understanding the factors contributing to the delay of TB patients in the diagnosis, and reducing the time between the onset of TB symptoms to diagnosis, is a prerequisite to increase the case detection rate and to ultimately bring the TB epidemic in Somalia under control. The aim of this study is to examine the duration of delay, and factors associated with the delay among patients in TB management centers in Mogadishu, Somalia.

Methods

An institution-based, cross-sectional study was conducted in TB management clinics providing directly observed treatments (DOTS) programs in Mogadishu. A total of 276 patients were interviewed using a structured questionnaire from June-October 2018. We analyzed data using descriptive statistics and different logistic regression models.

Results

Approximately 78% of study participants were male. Nearly a third (36.5%) came from a household of nine individuals or more, while 73% were unemployed. The median patient and provider delays were 50 days and one day, respectively. The median total delay was 55 days, with an inter-quartile range of 119 days. Patients who had a poor knowledge of the symptoms of TB had 3.16 times higher odds of delay over 50 days than their counterparts. Furthermore, a poor knowledge of the symptoms of TB (aOR 4.22, CI 2.13-8.40), not making one’s own decisions in seeking TB treatment (aOR 2.43, CI 1.22-4.86) and a poor understanding of the fact that TB can be treated with biomedical treatment, as opposed to traditional treatment (aOR 2.07, CI 1.02-4.16), were predictors of a patient delay over 120 days.

Conclusions

The duration in the delay of TB patients under diagnosis in Mogadishu is one of the highest reported in developing countries, exceeding two years in some patients. Training local community health workers to detect suspected TB cases, and referring the cases of prolonged cough over three weeks for TB care centers for diagnosis, is imperative to help break the transmission and reduce the infectious pool in the population of Mogadishu. This may not only increase the community awareness of TB disease, but it may also facilitate the early referral of TB patients to diagnostic and treatment care centers.
Natural Language Model for Automatic Identification of Intimate Partner Violence Reports from Twitter
Authors: Al-Garadi Mohammed Ali , Kim Sangmi , Guo Yuting , Warren Elise , Yang Yuan-Chi , Lakamana Sahithi , Sarker Abeed
Published: November 2021

Background

Intimate partner violence (IPV) is a preventable public health issue that affects millions of people worldwide. Approximately one in four women are estimated to be or have been victims of severe violence at some point in their lives, irrespective of their age, ethnicity, and economic status. Victims often report IPV experiences on social media, and automatic detection of such reports via machine learning may enable the proactive and targeted distribution of support and/or interventions for those in need.

Methods

We collected posts from Twitter using a list of keywords related to IPV. We manually reviewed subsets of retrieved posts, and prepared annotation guidelines to categorize tweets into IPV-report or non-IPV-report. We manually annotated a random subset of the collected tweets according to the guidelines, and used them to train and evaluate multiple supervised classification models. For the best classification strategy, we examined the model errors, bias, and trustworthiness through manual and automated content analysis.

Results

We annotated a total of 6,348 tweets, with inter-annotator agreement (IAA) of 0.86 (Cohen’s kappa) among 1,834 double-annotated tweets. The dataset had substantial class imbalance, with only 668 (∼11%) tweets representing IPV-reports. The RoBERTa model achieved the best classification performance (accuracy: 95%; IPV-report F1-score 0.76; non-IPV-report F1-score 0.97). Content analysis of the tweets revealed that the RoBERTa model sometimes misclassified as it focused on IPV-irrelevant words or symbols during decision making. Classification outcome and word importance analyses showed that our developed model is not biased toward gender or ethnicity while making classification decisions.

Conclusion

Our study developed an effective NLP model to identify IPV-reporting tweets automatically and in real time. The developed model can be an essential component for providing proactive social media based intervention and support for victims. It may also be used for population-level surveillance and conducting large-scale cohort studies.
Anatomy of the first six months of COVID-19 Vaccination Campaign in Italy
Authors: Gozzi Nicolò , Chinazzi Matteo , Davis Jessica T. , Mu Kunpeng , y Piontti Ana Pastore , Ajelli Marco , Perra Nicola , Vespignani Alessandro
Published: November 2021

We analyze the effectiveness of the first six months of vaccination campaign against SARS-CoV-2 in Italy by using a computational epidemic model which takes into account demographic, mobility, vaccines, as well as estimates of the introduction and spreading of the more transmissible Alpha variant. We consider six sub-national regions and study the effect of vaccines in terms of number of averted deaths, infections, and reduction in the Infection Fatality Rate (IFR) with respect to counterfactual scenarios with the actual non-pharmaceuticals interventions but no vaccine administration. Furthermore, we compare the effectiveness in counterfactual scenarios with different vaccines allocation strategies and vaccination rates. Our results show that, as of 2021/07/05, vaccines averted 29, 350 (IQR: [16, 454 − 42, 826]) deaths and 4, 256, 332 (IQR: [1, 675, 564 − 6, 980, 070]) infections and a new pandemic wave in the country. During the same period, they achieved a −22.2% (IQR: [−31.4%; −13.9%]) reduction in the IFR. We show that a campaign that would have strictly prioritized age groups at higher risk of dying from COVID-19, besides frontline workers, would have implied additional benefits both in terms of avoided fatalities and reduction in the IFR. Strategies targeting the most active age groups would have prevented a higher number of infections but would have been associated with more deaths. Finally, we study the effects of different vaccination intake scenarios by rescaling the number of available doses in the time period under study to those administered in other countries of reference. The modeling framework can be applied to other countries to provide a mechanistic characterization of vaccination campaigns worldwide.
Neurology in a Changing Climate: A Scoping Review
Authors: Louis Shreya , Carlson Alise , Suresh Abhilash , Rim Joshua , Mays MaryAnn , Ontaneda Daniel , Dhawan Andrew
Published: November 2021

Importance

Although the international community collectively seeks to reduce global temperature rise to less than 1.5ºC, there are already irreversible environmental changes that have occurred, and currently available evidence suggests these changes will continue to occur. As we begin to witness the effects of a warming planet on human health, it is imperative that as neurologists we anticipate the ways in which the epidemiology and incidence of neurologic disease may be affected.

Objective

In this review, we organize our analysis around three key themes related to climate change and neurologic health: extreme weather events and temperature fluctuations, emerging neuro-infectious diseases, and pollutant impacts. Across each of these key themes, we appraise and review recent literature relevant to neurological disease and the practice of neurology.

Evidence Review

Studies were identified using a set of relevant search terms relating to climate change and neurologic diseases in the PubMed repository for publications between 1990 and 2021. Studies were included if they pertained to human incidence or prevalence of disease, were in the English language, and were relevant to neurologic disease.

Findings

We identified a total of 136 articles, grouped into the three key themes of our study; extreme weather events and temperature fluctuations (23 studies), emerging neuro-infectious diseases (42 studies), and pollutant impacts (71 studies). Broadly, the studies included highlighted the relationships between neurologic symptom exacerbation and temperature variability, tick-borne infections and warming climates, and airborne pollutants and cerebrovascular disease incidence and severity.

Conclusions and Relevance

Our work highlights three key priorities for further work; namely, neuro-infectious disease risk mitigation, an understanding of the pathophysiology of airborne pollutants on the nervous system, and research into how to improve delivery of neurologic care in the face of climate-related disruptions.

Key Points

Question

How does climate change impact neurological disease?

Findings

136 articles were identified relating neurologic disease to climate change. Articles were grouped into three key themes, highlighting evidence linking neurologic disease exacerbation to temperature fluctuation, tick-borne infections with climate change, and airborne pollutants to cerebrovascular disease.

Meaning

A substantial body of literature suggests that neurologic disease incidence, morbidity, and mortality is directly impacted by climate change and its sequelae, but much remains to be uncovered.
A continuous indicator of food environment nutritional quality
Authors: Liu Iris C. , de la Haye Kayla , Abeliuk Andrés , Horn Abigail L.
Published: November 2021

Food environments can profoundly impact diet and related diseases. Effective, robust measures of food environment nutritional quality are required by researchers and policymakers investigating their effects on individual dietary behavior and designing targeted public health interventions. The most commonly used indicators of food environment nutritional quality are limited to measuring the binary presence or absence of entire categories of food outlet type, such as ‘fast-food’ outlets, which can range from burger joints to salad chains. This work introduces a summarizing indicator of restaurant nutritional quality that exists along a continuum, and which can be applied at scale to make distinctions between diverse restaurants within and across categories of food outlets. Verified nutrient data for a set of over 500 chain restaurants is used as ground-truth data to validate the approach. We illustrate the use of the validated indicator to characterize food environments at the scale of an entire jurisdiction, demonstrating how making distinctions between different shades of nutritiousness can help to uncover hidden patterns of disparities in access to high nutritional quality food.

CCS CONCEPTS

Applied computing → Life and medical sciences.
Pan-tissue and -cancer analysis of ROR1 and ROR2 transcript variants identify novel functional significance for an alternative splice variant of ROR1
Authors: John M. , Ford C.
Published: November 2021

Background

ROR1/2 are putative druggable targets increasing in significance in translational oncology. Expression of ROR1/2 mRNA and transcript variants has not been systematically examined thus far.

Methods

ROR1/2 transcript variant sequences, signal peptides for cell surface localisation, and mRNA and transcript variant expression were examined in 34 transcriptomic datasets including 33 cancer types and 54 non-diseased human tissues.

Results

ROR1/2 have four and eight transcript variants respectively. ROR1/2 mRNA and transcript variant expression was detected in various non-diseased tissues. Our analysis identifies predominant expression of ROR1 transcript variant ENST00000545203, which lacks a signal peptide for cell surface localisation, rather than the predicted principal variant ENST00000371079. ENST00000375708 is the predominantly expressed transcript variant of ROR2.

Conclusion

ROR1/2 expression in healthy human tissues should be carefully considered for safety assessment of targeted therapy. Studies exploring the function and significance of the predominantly expressed ROR1 transcript variant ENST00000545203 are warranted.
Heterogeneity of circulating epithelial cells in breast cancer at single-cell resolution: identifying tumor and hybrid cells
Authors: Menyailo Maxim E. , Zainullina Viktoria R. , Tashireva Liubov A. , Zolotareva Sofia Yu. , Gerashchenko Tatiana S. , Alifanov Vladimir V. , Savelieva Olga E. , Grigoryeva Evgeniya S. , Tarabanovskaya Nataliya A. , Popova Nataliya O. , Khozyainova Anna A. , Choinzonov Evgeny L. , Cherdyntseva Nadezhda V. , Perelmuter Vladimir M. , Denisov Evgeny V.
Published: November 2021

Circulating tumor cells and hybrid cells formed by the fusion of tumor cells with normal cells are leading players in metastasis and have prognostic relevance. Circulating tumor cells and hybrid cells are identified as CD45-negative and CD45-positive epithelial cells. However, such an approach is challenging because epithelial cells are observed in the blood of healthy individuals. In this study, we applied single-cell RNA sequencing to profile CD45-negative and CD45-positive circulating epithelial cells (CECs) in 20 breast cancer patients and one healthy donor. DNA ploidy analysis was used to identify the tumor and hybrid cells among CD45─and CD45+CECs in patients, respectively. Functional enrichment analysis was applied to characterize aneuploid and diploid cells. Diploid cells were also annotated to generate cell-type candidates and analyzed for copy-number aberrations (CNAs) to confirm or refute their tumor origin. CD45─and CD45+CECs were found in cancer patients (25.5 (range 0-404) and median 6.5 (0-147)) and the healthy donor (8 and 11 cells) and divided into three clusters. Two CD45─CEC clusters were predominantly aneuploid (97% and 98%), but one cluster contained more diploid (59%) than aneuploid cells. CD45+CECs were mostly diploid: only clusters 1 and 2 had aneuploid cells (16% and 2%). Diploid CD45─and CD45+CECs were annotated as different immune cells and surprisingly harbored many CNAs. Cancer-associated signaling pathways were found only in aneuploid cells of CD45─CEC cluster 1 and diploid cells of CD45+CEC cluster 1. Thus, our findings suggest that CECs in breast cancer patients are a highly heterogeneous population comprising aneuploid (tumor and hybrid) and diploid (normal) cells. DNA ploidy analysis is an effective instrument for identifying tumor and hybrid cells among CD45─and CD45+CECs, respectively.
Altered reward network responses to social touch in major depression
Authors: Mielacher Clemens , Scheele Dirk , Kiebs Maximilian , Schmitt Laura , Dellert Torge , Philipsen Alexandra , Lamm Claus , Hurlemann René
Published: November 2021

Introduction

Affective touch is highly rewarding and an integral part of social relationships. Major depressive disorder (MDD) is characterized by severe impairments in reward processing, but the neural effects of social touch in MDD are still elusive.

Objective

We aimed to determine whether the neural processing of social touch is impaired in MDD and to assess the impact of antidepressant therapy.

Methods

Before and after antidepressant treatment, 53 MDD patients and 41 healthy controls underwent functional magnetic resonance imaging (fMRI) while receiving social touch. We compared neural responses to social touch in the reward network, behavioral ratings of touch comfort and general aversion to interpersonal touch in MDD patients to controls. Additionally, we examined the effect of treatment response on those measures.

Results

Clinical symptoms decreased after treatment and 43.4% of patients were classified as responders. Patients reported higher aversion to social touch and lower comfort ratings during the fMRI paradigm than controls. Patients showed reduced responses to social touch in the nucleus accumbens, caudate nucleus and putamen than controls, both before and after treatment. Non-responders exhibited blunted response in the caudate nucleus and the insula compared to responders, again irrespective of treatment.

Conclusions

These findings confirm our hypothesis that interpersonal touch as an indicator of social reward processing is impaired in MDD. Persistent dysfunctional processing of social touch despite clinical improvements may constitute a latent risk factor for social withdrawal and isolation. New treatment approaches are necessary to specifically target social reward processing and disturbed body awareness in MDD.
High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine
Authors: Hickey John W. , Becker Winston R. , Nevins Stephanie A. , Horning Aaron , Perez Almudena Espin , Chiu Roxanne , Chen Derek C. , Cotter Daniel , Esplin Edward D. , Weimer Annika K. , Caraccio Chiara , Venkataraaman Vishal , Schürch Christian M. , Black Sarah , Brbić Maria , Cao Kaidi , Leskovec Jure , Zhang Zhengyan , Lin Shin , Longacre Teri , Plevitis Sylvia K. , Lin Yiing , Nolan Garry P. , Greenleaf William J. , Snyder Michael
Published: November 2021

The colon is a complex organ that promotes digestion, extracts nutrients, participates in immune surveillance, maintains critical symbiotic relationships with microbiota, and affects overall health. To better understand its organization, functions, and its regulation at a single cell level, we performed CODEX multiplexed imaging, as well as single nuclear RNA and open chromatin assays across eight different intestinal sites of four donors. Through systematic analyses we find cell compositions differ dramatically across regions of the intestine, demonstrate the complexity of epithelial subtypes, and find that the same cell types are organized into distinct neighborhoods and communities highlighting distinct immunological niches present in the intestine. We also map gene regulatory differences in these cells suggestive of a regulatory differentiation cascade, and associate intestinal disease heritability with specific cell types. These results describe the complexity of the cell composition, regulation, and organization for this organ, and serve as an important reference map for understanding human biology and disease.
Centripetal nuclear shape fluctuations associate with chromatin condensation towards mitosis
Authors: Introini Viola , Kidiyoor Gururaj Rao , Porcella Giancarlo , Foiani Marco , Cicuta Pietro , Lagomarsino Marco Cosentino
Published: November 2021

The cell nucleus plays a central role in several key cellular processes, including chromosome organisation, replication and transcription. Recent work intriguingly suggests an association between nuclear mechanics and cell-cycle progression, but many aspects of this connection remain unexplored. Here, by monitoring nuclear shape fluctuations at different cell cycle stages, we uncover increasing inward fluctuations in late G2 and early mitosis, which are initially transient, but develop into instabilities that culminate into nuclear-envelope breakdown in mitosis. Perturbation experiments and correlation analysis reveal an association of these processes with chromatin condensation. We propose that the contrasting forces between an extensile stress and centripetal pulling from chromatin condensation could link mechanically chromosome condensation and nuclear- envelope breakdown, the two main nuclear processes during mitosis.

Significance Statement

The nucleus was recently shown to exhibit shape fluctuations that vary with cell-cycle stage, but we know very little about the possible links between nuclear mechanics and cell cycle- progression. Through flickering analysis, this study monitors radius and nuclear envelope fluctuations across the cell cycle. The authors discover that as the cell cycle progresses towards mitosis, localised inward invaginations of the nuclear shape form initially transiently and gradually increasing their amplitude, in association with chromatin condensation. This phenomenon develops into nuclear envelope breakdown, suggesting a novel link between cell cycle, chromatin mechanics and nuclear shape fluctuations.
Systemic LSD1 inhibition prevents aberrant remodeling of metabolism in obesity
Authors: Ramms Bastian , Pollow Dennis P. , Zhu Han , Nora Chelsea , Harrington Austin R. , Omar Ibrahim , Gordts Philip L.S.M. , Wortham Matthew , Sander Maike
Published: November 2021

The transition from lean to obese states involves systemic metabolic remodeling that impacts insulin sensitivity, lipid partitioning, inflammation, and glycemic control. Here, we have taken a pharmacological approach to test the role of a nutrient-regulated chromatin modifier, lysine-specific demethylase (LSD1), in obesity-associated metabolic reprogramming. We show that systemic administration of an LSD1 inhibitor (GSK-LSD1) reduces food intake and body weight, ameliorates non-alcoholic fatty liver disease (NAFLD), and improves insulin sensitivity and glycemic control in mouse models of obesity. GSK-LSD1 has little effect on systemic metabolism of lean mice, suggesting LSD1 has a context-dependent role in promoting maladaptive changes in obesity. Analysis of insulin target tissues identified white adipose tissue as the major site of insulin sensitization by GSK-LSD1, where it reduces adipocyte inflammation and lipolysis. We demonstrate that GSK-LSD1 reverses NAFLD in a non-hepatocyte-autonomous manner, suggesting an indirect mechanism via inhibition of adipocyte lipolysis and subsequent effects on lipid partitioning. Pair-feeding experiments further revealed that effects of GSK-LSD1 on hyperglycemia and NAFLD are not a consequence of reduced food intake and weight loss. These findings suggest that targeting LSD1 could be a strategy for treatment of obesity and its associated complications including type 2 diabetes and NAFLD.
A LRRK2/dLRRK-mediated lysosomal pathway that contributes to glial cell death and DA neuron survival
Authors: Wang Linfang , Wang Honglei , Ho Margaret S.
Published: November 2021

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial and sporadic Parkinson’s disease (PD). A plethora of evidence has indicated a role for LRRK2 in endolysosomal trafficking in neurons, while LRRK2 function in glia, although highly expressed, remains largely unknown. Here we present evidence that LRRK2/dLRRK mediates a glial lysosomal pathway that contributes to the mechanism of PD. Independent of its kinase activity, glial LRRK2/dLRRK knockdown in the immortalized microglial cells or flies results in enlarged and swelling lysosomes fewer in number. These lysosomes are less mobile, wrongly acidified, and exhibit defective membrane permeability and reduced activity of the lysosome hydrolase cathespin B. In addition, microglial LRRK2 depletion causes increased Caspase 3 levels, leading to glial apoptosis, dopaminergic neurodegeneration, and locomotor deficits in an age-dependent manner. Taken together, these findings demonstrate a functional role of LRRK2/dLRRK in regulating the glial lysosomal pathway; deficits in lysosomal biogenesis and function linking to glial apoptosis potentially underlie the mechanism of DA neurodegeneration, contributing to the progression of PD.
Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae
Authors: Brothers Molly , Rine Jasper
Published: November 2021

The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. We developed a method to study these two processes at single base-pair resolution. Using a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, we mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein. A silencing-deficient mutant of Sir3 lacking its Bromo-Adjacent Homology (BAH) domain, sir3-bahΔ, was still recruited to HML, HMR, and telomeres. However, in the absence of the BAH domain, it was unable to spread away from those recruitment sites. Overexpression of Sir3 did not lead to further spreading at HML, HMR, and most telomeres. A few exceptional telomeres, like 6R, exhibited a small amount of Sir3 spreading, suggesting that boundaries at telomeres responded variably to Sir3 overexpression. Finally, by using a temperature-sensitive allele of SIR3 fused to M.ECOGII, we tracked the positions first methylated after induction and found that repression of genes at HML and HMR began before Sir3 occupied the entire locus.
Larval densities of the protected Striped lychnis moth Shargacucullia lychnis (Lepidoptera: Noctuidae) in Buckinghamshire
Authors: Morimoto Juliano , Kerr Lucy
Published: November 2021

Natural history information is essential for ecologically-relevant inferences about (adaptive) responses in organismal biology. Yet, natural history data can be difficult to obtain, particularly for the developmental stages of holometabolous insects. This gap can compromise our ability to design controlled experiments that provide useful understanding of insect responses to changing environments and precludes our ability to understand how natural populations may respond to unpredictable climatic changes in their natural environment. In this study, we collated data from previous reports from the Butterfly Conservation Upper Thames Branch on the larval population density of Shargacucullia lychnis (Lepidoptera: Noctuidae) in Buckinghamshire. In the UK, S. lychnis is a protected species, for which natural history information can be invaluable for its effective conservation. We report here that the natural range of larval densities observed for S. lychnis across locations and years is 0.001 to 6.417 larvae per spike. More importantly, S. lychnis larval density has overall declined from 1996 to 2020, which could support previous reports of a contraction in population range for this species. Overall, this study provides invaluable information about larval population density for an important protected Lepidopteran species of the UK.
The structure of the enigmatic ripple phase in saturated bilayers resolved: Machine learning reveals four lipid populations
Authors: Davies Matthew , Reyes-Figueroa A. D. , Gurtovenko Andrey A. , Frankel Daniel , Karttunen Mikko
Published: November 2021

A new mixed radial-angular, three-particle correlation function method in combination with unsupervised machine learning (ML) was applied to examine the emergence of the ripple phase in dipalmitoyphosphatidylcholine (DPPC) lipid bilayers using data from atomistic molecular dynamics (MD) simulations of system sizes ranging from 128 to 4,096 lipids. Based on the acyl tail conformations, the analysis revealed the presence of four distinct conformational populations of lipids in the ripple phases of the DPPC lipid bilayers. The expected gel- (ordered; Lo) and fluid-like (disordered; Ld) lipids are found along with their splayed tail equivalents (Lo,s and Ld,s). These lipids differ based on their gauche distribution and tail packing. The disordered (Ld) and disordered splayed (Ld,s) lipids spatially cluster in the ripple in the groove side, that is, in an asymmetric manner across the bilayer leaflets. The ripple phase does not contain large numbers of Ld lipids, instead they only exist on the interface of the groove side of the undulation. The bulk of the groove side is a complex coexistence of Lo, Lo,s and Ld,s lipids. The convex side of the undulation contains predominantly Lo lipids. Thus, the structure of the ripple phase is neither a simple coexistence of ordered and disordered lipids nor a coexistence of ordered interdigitating gel-like (Lo) and ordered splayed (Lo,s) lipids, but instead a coexistence of an ordered phase and a complex mixed phase. Principal component analysis (PCA) further confirmed the existence of the four lipid groups.
Dysregulated Transferrin Receptor Disrupts T Cell Iron Homeostasis to Drive Inflammation in Systemic Lupus Erythematosus
Authors: Voss Kelsey , Young Arissa C. , Gibson-Corley Katherine N. , Sewell Allison E. , Krystofiak Evan S. , Bashum Jacob H. , Beavers William N. , Sugiura Ayaka , Skaar Eric P. , Ormseth Michelle J. , Major Amy S. , Rathmell Jeffrey C.
Published: November 2021

T cells in systemic lupus erythematosus (SLE) exhibit mitochondrial abnormalities including elevated oxidative stress. Because excess iron can promote these phenotypes, we tested iron regulation of SLE T cells. A CRISPR screen identified Transferrin Receptor (CD71) as important for Th1 cells but detrimental for induced regulatory T cells (iTreg). Activated T cells induce CD71 to increase iron uptake, but this was exaggerated in T cells from SLE-prone mice which accumulated iron. Treatment of T cells from SLE-prone mice with CD71 blocking antibody reduced intracellular iron and mTORC1 signaling and restored mitochondrial physiology. While Th1 cells were inhibited, CD71 blockade enhanced iTreg.In vivothis treatment reduced pathology and increased IL-10 in SLE-prone mice. Importantly, disease severity correlated with CD71 expression on SLE patient T cells and blocking CD71 enhanced IL-10 secretion. Excess T cell iron uptake thus contributes to T cell dysfunction and can be targeted to correct SLE-associated pathology.
Evolution of Human-specific Alleles Protecting Cognitive Function of Grandmothers
Authors: Saha Sudeshna , Khan Naazneen , Comi Troy , Verhagen Andrea , Sasmal Aniruddha , Diaz Sandra , Yu Hai , Chen Xi , Akey Joshua M. , Frank Martin , Gagneux Pascal , Varki Ajit
Published: November 2021

Late-onset Alzheimer’s Disease (LOAD) pathology is rare in our closest living evolutionary relatives (chimpanzees), which also express much lower microglial levels of CD33(Siglec-3)–a myelomonocytic receptor inhibiting innate immune reactivity by extracellular V-set domain recognition of sialic acid(Sia)-containing “self-associated molecular patterns” (SAMPs). We earlier showed that V-set domain-deficient CD33-variant allele, protective against LOAD, is derived and specific to hominin-lineage. We now report that CD33 also harbors multiple hominin-specific V-set domain mutations and explore selection forces that may have favored such genomic changes. N-glycolylneuraminic acid (Neu5Gc), the preferred Sia-ligand of ancestral CD33 is absent in humans, due to hominin-specific, fixed loss-of-function mutation in CMAH, which generates CMP-Neu5Gc from its precursor, CMP-N-acetylneuraminic acid (Neu5Ac). Extensive mutational analysis and MD-simulations indicate that fixed change in amino acid 21 of hominin V-set domain and conformational changes related to His45 corrected for Neu5Gc-loss by switching to Neu5Ac-recognition. Considering immune-evasive “molecular mimicry” of SAMPs by pathogens, we found that human-specific pathogens Neisseria gonorrhoeae and Group B Streptococcus (affecting fertility and fetuses/neonates respectively) selectively bind huCD33 and this binding is significantly impacted by amino acid 21 modification. Alongside LOAD-protective CD33 alleles, humans harbor additional, derived, population-universal, cognition-protective variants absent in “great ape” genomes. Interestingly, 11 of 13 SNPs in these human genes (including CD33), that protect the cognitive health of elderly populations, are not shared by genomes of archaic hominins: Neanderthals and Denisovans. Finally, we present a plausible evolutionary scenario to compile, correlate and comprehend existing knowledge about huCD33 evolution and suggest that grandmothering emerged in humans.
Impact of COVID-19 pandemic on the economy of oil palm smallholder's household income
Authors: Irawan Andi , Saefudin Saefudin , Suryanty Melli , Yuliarso M. Zulkarnain
Published: November 2021

Purpose

This study aimed to determine the impact of the COVID-19 pandemic on the oil palm smallholders' income, which includes both on-farm and off-farm resources.

Design/methodology/approach

This study used a simultaneous equations system for arranging the oil palm household economic model.

Findings

The results showed that the negative effect of demand disruption (decreasing of household income) is more than supply disruption (production declining). Declining household income due to COVID-19 caused farmer households to have no access to both basic need and other goods.

Research limitations/implications

The samples for before-pandemic data differed from the situation during COVID-19 in both the location and the person due to technical constraints in research sites.

Originality/value

The main contribution of this study was providing an empirical understanding of how the COVID-19 pandemic influences the economic behavior of the most vulnerable entities in the Indonesian palm oil industry (oil palm smallholder farmers' households). This study would provide baseline information on the impact of the COVID-19 pandemic on the economy of oil palm smallholder's household income.
Exploring participatory heritage governance after the EU Faro Convention
Authors: Colomer Laia
Published: November 2021

Purpose

This paper aims to analyse the key Faro notions of “heritage community” and “democratic participation” as defined in the Faro Convention, and how they challenge core notions of authority and expertise in the discipline and professional practice of cultural heritage.

Design/methodology/approach

This paper examines notions of “heritage community” and “democratic participation” as they are framed in the Faro Convention, and it briefly introduces two cases (Finland and Marseille) to explore their application. It then focusses on the implications of these two notions for heritage administration (expertise) in terms of citizen agency, co-creation of knowledge and forms of decision-making processes.

Findings

The Faro Convention favours an innovative approach to social, politic and economic problems using cultural heritage. To accomplish this, it empowers citizens as actors in developing heritage-based approaches. This model transforms heritage into a means for achieving socioeconomic goals and attributes to the public the ability to undertake heritage initiatives, leaving the administration and expert bodies as mediators in this process. To bring about this shift, Faro institutes the notion of “heritage communities” and fosters participative governance. However, how heritage communities practise participation may follow different paths and result in different experiences due to local and national political circumstances.

Originality/value

The Faro Convention opens up a window by framing cultural heritage within the realm of social and democratic instrumentality, above and beyond the heritage per se. But it also poses some questions regarding the rationale of heritage management (authority in governability), at least as understood traditionally under official heritage management discourses.
Keep fighting or give up? An investigation of consumer regret over repetitive failures in weight loss services
Authors: Liu Yi-Fen , Ling I-Ling
Published: November 2021

Purpose

Weight loss services feature high consumer involvement that is sometimes marked by repetitive failures. These features can affect regret and its associated factors differently from the way that discrete failure can. The purpose of this study is to investigate consumer regret over repetitive failures in weight loss services as well as its antecedents (overeating and insufficient exercise), consequences (rumination and reflection) and moderators (failure experiences and required effort). This study also investigates how rumination and reflection affect persistence intention.

Design/methodology/approach

A total of 318 samples were collected through three surveys, one of which contained a scenario, provided to consumers who experienced repetitive failures in weight loss. The proposed relationships were tested using structural equation modeling, dominance analysis and PROCESS modeling.

Findings

The results of this study reveal that overeating contributes to regret more saliently than does insufficient exercise. The effect of regret on rumination (thoughts about continuing to blame oneself and giving up the pursuit of goals) is stronger than on reflection (thoughts about learning from prior failures and willingness to try again), and greater reflection results in higher persistence intention. Moreover, the effect of insufficient exercise on regret and the effect of regret on rumination are augmented with cumulative failure experiences, whereas required effort enhances the impact of regret on reflection.

Originality/value

This study is the first to focus on regret over repetitive failures in weight loss. It advances the literature by clarifying the antecedents and consequences of regret, showing how failure experiences influence the relationships between regret and its associated factors as well as identifying interventions that benefit from regret.
AI and libraries: trends and projections
Authors: Oyelude Adetoun A.
Published: November 2021

Purpose

This paper aims to focus on the trends and projection for future use of artificial intelligence (AI) in libraries. AI technologies is the latest among the technologies being used in libraries. The technology has systems that have natural language processing, machine learning and pattern recognition capabilities that make service provision easier for libraries.

Design/methodology/approach

Systematic literature review is done, exploring blogs and wikis, to collect information on the ways in which AI is used and can be futuristically used in libraries.

Findings

This paper found that uses of AI in libraries entailed enhanced services such as content indexing, document matching, content mapping content summarization and many others. AI possibilities were also found to include improving the technology of gripping, localizing and human–robot interaction and also having artificial superintelligence, the hypothetical AI that surpasses human intelligence and abilities.

Originality/value

It is concluded that advanced technologies that AI are, will help librarians to open up new horizons and solve challenges that crop up in library service delivery.
Social media and CSR communication in European ports: the case of Twitter at the Port of Rotterdam
Authors: Vitellaro Francesco , Satta Giovanni , Parola Francesco , Buratti Nicoletta
Published: November 2021

Purpose

The research objective of the paper is twofold. First, it scrutinises the current state of the art concerning adopting the most popular social media by European port managing bodies (PMBs). Second, it investigates the use of social media in the corporate social responsibility (CSR) communication strategies of European PMBs.

Design/methodology/approach

The paper carries out online field research on the use of social media by the top-25 European ports. Then, it provides an in-depth case study of the use of Twitter by the Port of Rotterdam for CSR communication. Finally, a content analysis of the tweets published in the 2017–2019 timeframe is performed.

Findings

Empirical results demonstrate the extensive use of social media by European PMBs to reach a wider array of stakeholders. Uneven approaches emerge considering port sizes and cultural clusters. The content analysis shows that one-third of tweets published by the Twitter account of the Port of Rotterdam address CSR issues, especially green initiatives, advocating the use of social media to communicate CSR.

Research limitations/implications

The study focuses on the European domain. A broader sample of ports worldwide should be examined to further investigate the drivers affecting PMBs' strategic adoption and use of social media, mainly to communicate CSR.

Practical implications

The paper provides port managers with insights to strengthen CSR communication. Given the increasing pressure of the public opinion on environmental and social issues, the ability of European PMBs to communicate their CSR commitment through social media represents a key driver when searching for consensus of stakeholders and “licence to operate”.

Originality/value

The paper adds to the existing maritime logistics literature by introducing a promising field of research.
Loss of fungal symbionts at the arid limit of the distribution range in a native Patagonian grass—Resource eco‐physiological relations
Authors: Casas Cecilia , Gundel Pedro E. , Deliens Eluney , Iannone Leopoldo J. , García Martinez Guillermo , Vignale María V. , Schnyder Hans
Published: November 2021

Crucial to our understanding of plant ecology is the consideration of the eco‐physiological responses and constraints of plant–fungal symbioses throughout the native distribution range of their host.

We examined key eco‐physiological roles of two co‐occurring fungal symbionts [Epichloë endophytes and arbuscular mycorrhizal fungi (AMF)] in the endemic grass Hordeum comosum across a wide bioclimatic gradient and contrasting grazing severity. We sampled H. comosum plants along four humid‐to‐arid transects in Patagonia, Argentina, covering its entire distribution range and determined Epichloë presence, AMF root colonization, nitrogen and phosphorus concentration, intrinsic water‐use efficiency (iWUE, the ratio of photosynthesis to stomatal conductance) and 18O‐enrichment of cellulose in shoots.

Root colonization by AMF increased with Epichloë presence. All plants hosted Epichloë in the humid range of the gradient, but symbioses occurrence decreased towards arid sites which also displayed severe grazing symptoms at site level.

Symbiosis with Epichloë correlated positively with shoot nitrogen concentration in the centre of the distribution range, and with shoot phosphorus concentration across the entire distribution range.

The site‐level relationship of AMF colonization with 18O‐enrichment and iWUE suggested that mycorrhiza boosted stomatal conductance in humid environments but curbed it in arid environments.

While the interpretation of interactions and potential causalities from observational studies should be done with caution, this study demonstrates distinct correlations between plant–fungal symbiont associations and key resource parameters (phosphorus, nitrogen and iWUE vs. 18O‐enrichment). Such correlations may suggest particular functional roles for these symbionts in the ecology of their host plant.

A free Plain Language Summary can be found within the Supporting Information of this article.
Assistance dogs in occupational therapy practice: A survey of Australian occupational therapists' experiences and recommendations
Authors: Chan Kar Wei , Young Janette , Williams Lindy J. , Nottle Carmel
Published: November 2021

Introduction

Assistance dogs perform multiple tasks to support people with disabilities and bring various benefits. Occupational therapists play a key role in assessing or referring clients for assistive technology, which includes assistance dogs. However, little is known about Australian occupational therapists' experiences with assistance dogs and how they perceive their roles in this area of practice.

Methods

A cross‐sectional online survey was developed and distributed nationally to Australian occupational therapists to glean their experiences and perceptions of assistance dogs and their recommendations to support future practice.

Results

A total of 220 completed surveys were received with all perceiving assistance dogs as beneficial for clients with disabilities. Over 60% agreed it was within their scope to assess or refer clients for assistance dogs, but more than two thirds had not had the occasion to do so and/or lacked relevant education and training. Common difficulties experienced in the referral or assessment process include challenges with accessing and navigating funding, lack of resources and/or assistance dogs, and perceived insufficient evidence to support the use of assistance dogs.

Conclusion

Findings indicate that occupational therapists' lack experience and knowledge of assistance dogs although they perceive assistance dogs as within the scope of occupational therapy practice. This study highlights a need for increasing professional development opportunities for occupational therapists regarding assistance dogs, including assessment and referral processes. This will be steadily more important given the increasing profile and expanding application of assistance dogs, and funding organisation requests for occupational therapists in assessing clients for assistance dogs.