bluuebunny/crossref_metadata_2025 huggingface dataset:
How are declarations of interest working? A cross sectional study in declarations of interest in medical practice in Scotland and England in 2020/2021
Authors: McCartney M , Hartman RB , Feldman H , MacDonald R , Sullivan F , Heneghan C , McCutcheon C
Published: March 2022

Objective

To understand arrangements for doctors’ declarations of interest in Scotland and England in the context of current recommendations.

Design

Cross sectional study of a random selection of NHS hospital registers of interest by two independent observers in England, all NHS Boards in Scotland, and a random selection of Clinical Commissioning Groups (CCGs) in England.

Setting

NHS Trusts in England (NHSE), NHS Boards in Scotland, CCGs in England, and private healthcare organisations.

Participants

Registers of declarations of interest published in a random sample of 67 of 217 NHS Trusts, a random sample of 15 CCGs of in England, registers held by all 14 NHS Scotland boards, a purposeful selection of private hospitals/clinics in the UK.

Main Outcome Measures

Adherence to NHSE guidelines on declarations of interests, and comparison in Scotland.

Results

76% of registers published by Trusts did not routinely include all declaration of interest categories recommended by NHS England. In NHS Scotland only 14% of Boards published staff registers of interest. Of these employee registers (most obtained under Freedom of Information), 27% contained substantial retractions. In England, 96% of Clinical Commissioning Groups published a Gifts and Hospitality register, with 67% of CCG staff declaration templates and 53% of governor registers containing full standard NHS England declaration categories. Single organisations often held multiple registers lacking enough information to interpret them. Only 35% of NHS Trust registers were organised to enable searching. None of the private sector organisations studied published a comparable declarations of interest register.

Conclusion

Despite efforts, the current system of declarations frequently lacks ability to meaningfully obtain complete health care professionals’ declaration of interests.
Temporal trends, socio-economic inequalities in obesity and responses by federal government, Nepal: a systematic review of observational studies, policies, strategies and plans, 2005-2019
Authors: Bhurtyal Ashok , Adhikari Dushala
Published: March 2022

Background

Obesity has risen to epidemic proportions in low-income countries such as Nepal whose achievements in reducing maternal and child-undernourishment is well known. However, scientific evidence concerning recent transition towards obesity and corresponding responses by the state remains scanty. This review purported to assess the trends and disparities in obesity prevalence among women and children, and to analyse the governmental policies and programmes.

Methods

We searched PubMed and Google Scholar for articles published between January 1, 2005 and April 10, 2019, and websites of Demographic and Health Survey, Non-Communicable Diseases Risk Factor Survey, and Micronutrient Status Survey. We extracted data on the prevalence of obesity and overweight from the selected studies and synthesised narratively. Overweight and obesity prevalence data from the latest available nationwide surveys were disaggregated by gender, geographical location and household wealth quintile. We retrieved the federal governmental policies, strategies and plans from the websites of Ministry of Health and Population and the National Nutrition and Food Security Secretariat, National Planning Commission.

Results

Twenty studies that reported prevalence of overweight and/or obesity, with data from 79,082 men and women aged 15 years or more and 11,866 children under five years, were included. Obesity or overweight among men and women increased from 20.0% in 2004 to 36.1% in 2016 while obesity alone rose from 5.3% to 7.5%. Prevalence of childhood obesity or overweight remained very low, although doubled between 2006 and 2016, from 0.6% to 1.2%. Prevalences of overweight and obesity were much higher among women, inhabitants of urban areas and central provinces, and the affluent. Governmental policies, strategies and plans on nutrition were primarily designed to control undernutrition, with some direct and indirect implications for preventing obesity.

Conclusions

Prevalence of overweight and obesity increased substantially between 2005 and 2019, disproportionately affecting socio-economic and geographical groups in Nepal. Governmental efforts to contain the obesity epidemic should be reinforced by actions that are more specifically targeted to addressing obesogenic environments.

Systematic review registration

PROSPERO CRD42019132332
High vaccine effectiveness against severe Covid-19 in the elderly in Finland before and after the emergence of Omicron
Authors: Baum Ulrike , Poukka Eero , Leino Tuija , Kilpi Terhi , Nohynek Hanna , Palmu Arto A.
Published: March 2022

Background

The elderly are highly vulnerable to severe Covid-19. Waning immunity and emergence of Omicron have caused concerns about reduced effectiveness of Covid-19 vaccines. The objective was to estimate vaccine effectiveness (VE) against severe Covid-19 among the elderly.

Methods

This nationwide, register-based cohort analysis included all residents aged 70 years and over in Finland. The follow-up started on December 27, 2020, and ended on March 31, 2022. The outcomes of interest were Covid-19-related hospitalization and intensive care unit (ICU) admission timely associated with SARS-CoV-2 infection. VE was estimated as one minus the hazard ratio comparing the vaccinated and unvaccinated and taking into account time since vaccination. Omicron-specific VE was evaluated as the effectiveness observed since January 1, 2022.

Results

The cohort included 896220 individuals. Comirnaty (BioNTech/Pfizer) VE against Covid-19-related hospitalization was 93% (95% CI 89%–95%) and 85% (95% CI 82%–87%) 14–90 and 91–180 days after the second dose; VE increased to 95% (95% CI 94%–96%) 14–60 days after the third dose. VE of other homologous and heterologous three dose series was similar. Protection against severe Covid-19 requiring ICU treatment was even better. Since January 1, 2022, Comirnaty VE was 98% (95% CI 92%–99%) and 92% (95% CI 87%–95%) 14–90 and 91–180 days after the second and 98% (95% CI 95%–99%) 14–60 days after the third dose.

Conclusions

VE against severe Covid-19 is high among the elderly. It waned slightly after two doses, but a third restored the protection. VE against severe Covid-19 remained high even after the emergence of Omicron.
Analysis of immunization time, amplitude, and adverse events of seven different vaccines against SARS-CoV-2 across four different countries
Authors: Romero-Ibarguengoitia Maria Elena , González-Cantú Arnulfo , Pozzi Chiara , Levi Riccardo , Mollura Maximiliano , Sarti Riccardo , Sanz-Sánchez Miguel Angel , Rivera-Salinas Diego , Hernández-Ruíz Yodira Guadalupe , Armendariz-Vázquez Ana Gabriela , Del Rio-Parra Gerardo Francisco , Barco-Flores Irene Antonieta , González-Facio Rosalinda , Azzolini Elena , Barbieri Riccardo , de Azevedo Dias Alessandro Rodrigo , Henriques-Guimaraes Milton , Bastos-Borges Alessandra , Acciardi Cecilia , Paez-Bo Graciela , Teixeira Mauro Martins , Rescigno Maria
Published: March 2022

Background

Scarce information exists in relation to the comparison of seroconversion and adverse events following immunization (AEFI) with different SARS-CoV-2 vaccines. Our aim was to correlate the magnitude of the antibody response to vaccination with previous clinical conditions and AEFI.

Methods

A multicentric comparative study where SARS-CoV-2 spike 1-2 IgG antibodies IgG titers were measured at baseline, 21-28 days after the first and second dose (when applicable) of the following vaccines: BNT162b2 mRNA, mRNA-1273, Gam-COVID-Vac, Coronavac, ChAdOx1-S, Ad5-nCoV and Ad26.COV2. Mixed model and Poisson generalized linear models were performed.

Results

We recruited 1867 subjects [52 (SD 16.8) years old, 52% men]. All vaccines enhanced anti-S1 and anti-S2 IgG antibodies over time (p<0.01). The highest increase after the first and second dose was observed in mRNA-1273 (p<0.001). There was an effect of previous SARS-CoV-2 infection; and an interaction of age with SARS-CoV-2, Gam-COVID-Vac and ChAdOx1-S (p<0.01). There was a negative correlation of Severe or Systemic AEFI (AEs) of naïve SARS-CoV-2 subjects with age and sex (p<0.001); a positive interaction between the delta of antibodies with Gam-COVID-Vac (p=0.002). Coronavac, Gam-COVID-Vac and ChAdOx1-S had less AEs compared to BNT162b (p<0.01). mRNA-1273 had a higher number of AEFIs. The delta of the antibodies showed an association with AEFIs in previously infected individuals (p<0.001).

Conclusions

The magnitude of seroconversion is predicted by age, vaccine type and SARS-CoV-2 exposure. AEs are correlated with age, sex, and vaccine type. The delta of the antibody response is positively correlated with AEs in patients previously exposed to SARS-CoV-2.

Registration number

NCT05228912
Alcohol use and poor sleep quality: a longitudinal twin study across 36 years
Authors: Helaakoski Viola , Kaprio Jaakko , Hublin Christer , Ollila Hanna M. , Latvala Antti
Published: March 2022

Poor sleep is one of the multiple health issues associated with heavy alcohol consumption. While acute effects of alcohol intake on sleep have been widely investigated, the longitudinal associations remain relatively underexplored. The objective of our research was to shed light on cross-sectional and longitudinal associations between alcohol use and insomnia symptoms over time, and to elucidate the role of familial confounding factors in such associations. Using self-report questionnaire data from the Older Finnish Twin Cohort (N=13,851), we examined how alcohol consumption and binge drinking are associated with sleep quality during a period of 36 years. Cross-sectional logistic regression analyses revealed significant associations between poor sleep and alcohol misuse, including heavy and binge drinking, at all four time points (OR range =1.61-3.37, P <0.05), suggesting that higher alcohol intake is associated with poor sleep quality over the years. Longitudinal cross-lagged analyses indicated that moderate, heavy and binge drinking predict poor sleep quality (OR range =1.25-1.76, P <0.05), but not the reverse. Within-pair analyses suggested that the associations between heavy drinking and poor sleep quality were not fully explained by genetic and environmental influences shared by the co-twins. In conclusion, our findings support previous literature in that alcohol use is associated with poor sleep quality, such that alcohol use predicts poor sleep quality later in life, but not vice versa, and that the association is not fully explained by familial factors.
Periodontopathogens in oral cancer: a meta-analysis of bacterial taxa of the oral microbiome associated with risk factors of oral squamous cell carcinoma
Authors: Salam Abdus , Khan Faisal
Published: March 2022

This study aims to investigate the distribution of microbial taxa that are present in abundance in the oral cavity of patients diagnosed with Oral Squamous Cell Carcinoma (OSCC). We begin with a search for relevant literature on the OSCC microbiome in electronic databases (PubMed and Google Scholar). From the identified literature, studies were considered for data extraction based on an inclusion criteria according to PRISMA guidelines. From an initial 1217 published studies, a total of 15 relevant studies were identified that fulfilled the inclusion criteria. These studies were conducted for the detection of microbial taxa in the oral cavities of patients with OSCC by correlation with healthy controls for differential microbial abundance. The data from the selected studies provided evidence on microbial taxa in different anatomical sites of the oral cavity i.e. gingival region, tongue, buccal site and floor of the mouth. The most common method for the detection of microbial flora in the literature was 16s rRNA sequencing. Only those studies from the literature were considered for further analysis that showed the association of risk factors i.e. tobacco smoking and smokeless, betel quid, alcohol and periodontitis with OSCC. Risk factors in the resulting 6 studies showed a strong odd’s ratio (OR) with statistical significance (p-value <0.05). The calculated risk ratio (RR) of these risk factors also demonstrated substantial heterogeneity. These studies showed an increase in the abundance of periodontopathogens belonging to the genusFusobacterium, Capnocytophaga, Prevotella, ParvimonasandPorphyromonas. The microbial taxa associated in abundance with risk factors of OSCC such as smoked or smokeless tobacco, betel quid and alcohol were quite similar to the microbial taxa that cause periodontitis. The detection for abundance of periodontopathogens in OSCC a class of putative biomarkers at early stages of tumor development in OSCC, in individuals exposed to these risk factors.
Surveillance of COVID-19 cases associated with dental settings using routine health data from the East of Scotland with a description of efforts to break chains of transmission from October 2020 to December 2021
Authors: Goldrick Niall Mc , O’Keefe Emma
Published: March 2022

Introduction

Dental settings have been considered high risk setting s for COVID-19. A Dental Public Health Team in South East Scotland have worked to risk assess the situation timeously to break chains of transmission.

Aim

To present routine data produced from a contact tracing service for COVID-19 cases in the dental setting with a focus on transmission.

Design

Observational retrospective analysis of a routine data set of COVID-19 cases associated with a dental setting reported via the national contact tracing system for two health board areas in the east of Scotland.

Methods

COVID-19 cases were confirmed by PCR testing. Descriptive statistics are used to summarise the data collected over a 13-month period (Oct 2020-Dec 2021). A narrative presents themes identified during contact tracing that led to transmission within a dental setting and includes a case study.

Results

A total of 811 incidents are included. No evidence of staff to patient transmission or vice versa was found in this study. Staff to staff transmission occurred in non-clinical areas contributing to 33% of total staff cases.

Conclusion

Transmission of COVID-19 in a dental setting in the context of this study appears to be confined to non-clinical areas. Future pandemic plans should include tools to aid with implementation of guidance in non-clinical areas.

In brief points

Outbreaks of COVID-19 in a dental setting appear to be confined to the non-clinical areas of dental practices.

We have found no evidence of staff to patient transmission or vice versa using our contact tracing methods.

Future pandemic preparedness would benefit from including current quality improvement tools to aid with implementation of new standard operating procedures and other regularly changing guidance.
Association of frailty, age, and biological sex with SARS-CoV-2 mRNA vaccine-induced immunity in older adults
Authors: Shapiro Janna R. , Park Han-Sol , Aytenfisu Tihitina Y. , Caputo Christopher , Lee John , Johnston Trevor S. , Li Huifen , Hauk Pricila , Jacobsen Henning , Li Yukang , Abrams Engle , Kocot Andrew J. , Yang Tianrui , Huang Yushu , Cramer Steven M. , Betenbaugh Michael J. , Debes Amanda K. , Morgan Rosemary , Milstone Aaron M. , Karaba Andrew H. , Leng Sean X. , Klein Sabra L.
Published: March 2022

Background

Male sex and old age are risk factors for severe COVID-19, but the intersection of sex and aging on antibody responses to SARS-CoV-2 vaccines has not been characterized.

Methods

Plasma samples were collected from older adults (75-98 years) before and after three doses of SARS-CoV-2 mRNA vaccination, and from younger adults (18-74 years) post-dose two, for comparison. Antibody binding to SARS-CoV-2 antigens (spike protein [S], S-receptor binding domain [S-RBD], and nucleocapsid [N]) and functional activity against S were measured against the vaccine virus and variants of concern (VOC).

Results

Vaccination induced greater antibody titers in older females than males, with both age and frailty associated with reduced antibody responses to vaccine antigens in males, but not females. ACE2 binding inhibition declined more than anti-S or anti-S-RBD IgG in the six months following the second dose (28-fold vs. 12- and 11-fold decreases in titer). The third dose restored functional antibody responses and eliminated disparities caused by sex, age, and frailty in older adults. Responses to the VOC were significantly reduced relative to the vaccine virus, with older males having lower titers to the VOC than females. Older adults had lower responses to the vaccine and VOC viruses than younger adults, with disparities being greater in males than females.

Conclusion

Older and frail males may be more vulnerable to breakthrough infections due to low antibody responses before receipt of a third vaccine dose. Promoting third dose coverage in older adults, especially males, is crucial to protecting this vulnerable population.

Brief summary

SARS-CoV-2 mRNA vaccination induces greater antibody response in older females than males, and age and frailty reduce responses in males only. These effects are eliminated by a third vaccine dose, highlighting the need for third dose coverage, especially in older males.
“We don’t routinely check vaccination background in adults”: A national qualitative study of barriers and facilitators to vaccine delivery and uptake in adult migrants through UK primary care
Authors: Carter Jessica , Mehrotra Anushka , Knights Felicity , Deal Anna , Crawshaw Alison F , Farah Yasmin , Goldsmith Lucy P , Wurie Fatima , Ciftci Yusuf , Majeed Azeem , Hargreaves Sally
Published: March 2022

Background

The COVID-19 pandemic has highlighted shortfalls in the delivery of vaccine programmes to some adult migrant groups; however, little is known around care pathways and engagement of these older cohorts in routine vaccinations in primary care, including catch-up programmes. Guidelines exist, but the extent to which they are put into practice and prioritised is unclear.

Objectives

To explore the views of primary care professionals around barriers and facilitators to catch-up vaccination in adult migrants (defined as foreign born; over 18 years) with incomplete or uncertain vaccination status and for routine vaccines to inform development of future interventions to improve vaccine uptake in this group and improve coverage.

Design

Qualitative interview study with purposive sampling and thematic analysis

Setting

UK primary care, 50 included practices.

Participants

64 primary care professionals (PCPs): 48 clinical including GPs, Practice Nurses and healthcare assistants (HCAs); 16 administrative staff including practice managers and receptionists (mean age 45 years; 84.4% female; a range of ethnicities).

Results

Participants highlighted direct and indirect barriers to catch-up vaccines in adult migrants who may have missed vaccines as children, missed boosters, and not be aligned with the UK’s vaccine schedule, from both a personal and service-delivery level, with themes including: lack of training and knowledge of guidance around catch-up vaccination among staff; unclear or incomplete vaccine records; and lack of incentivization (including financial reimbursement) and dedicated time and care pathways. Adult migrants were reported as being excluded from many vaccination initiatives, most of which focus exclusively on children. Where delivery models existed they were diverse and fragmented but included a combination of opportunistic and proactive programmes. PCPs noted that migrants expressed to them a range of views around vaccines, from positivity to uncertainty, to refusal, with specific nationality groups reported as more hesitant to get vaccinated with specific vaccines, including MMR.

Conclusions

WHO’s new Immunization Agenda (IA2030) has called for greater focus to be placed on delivering vaccination across the life-course, targeting under-immunised groups for catch-up vaccination at any age, with UK primary care services therefore having a key role to play. Vaccine uptake in adult migrants could be improved through implementing new financial incentives or inclusion of adult migrant vaccination targets in QOF, strengthening care pathways and training, and working directly with local community groups to improve understanding around the benefits of vaccination at all ages.
A robust Reeb graph model of white matter fibers with application to Alzheimer’s disease progression⋆
Authors: Shailja S. , Grafton Scott T. , Manjunath B. S.
Published: March 2022

Tractography generates billions of complex curvilinear fibers (streamlines) in 3D that exhibit the geometry of white matter pathways. Analysis of raw streamlines on such a large scale is time-consuming and intractable. Further, it is well known that tractography computations produce noisy streamlines, and this in turn severely affect their use in structural brain connectivity analysis. Prompted by these challenges, we propose a novel method to model the bundling structures of streamlines using the construct of a Reeb graph. Three key parameters in our method capture the geometry and topology of the streamlines: (i) ϵ – distance between a pair of streamlines in a bundle that defines its sparsity; (ii) α – spatial length of the bundle that introduces persistence; and (iii) δ – the bundle thickness. Together, these parameters control the robustness and granularity of the model to provide a compact signature of the streamlines and their underlying anatomic fiber structure. We validate the robustness of the bundling structure using synthetic and ISMRM datasets. Next, we demonstrate the potential of this approach as a tool for efficient tractogram comparison by quantifying the fiber densities in the progression of Alzheimer’s disease. Our results on ADNI data localize the maximal bundles of various brain regions and show a significant depletion in the fiber density as Alzheimer’s disease progresses. The source code for the implementation is available on GitHub.
IRONMAN interacts with OsHRZ1 and OsHRZ2 to maintain Fe homeostasis
Authors: Peng Feng , Li Chenyang , Lu Chengkai , Li Yang , Xu Peng , Liang Gang
Published: March 2022

IRONMAN is a family of small peptides which positively regulate the Fe deficiency response. However, the molecular mechanism by which OsIMA1 and OsIMA2 regulate Fe homeostasis was unclear. Here, we reveal that OsIMA1 and OsIMA2 interact with the potential Fe sensors, OsHRZ1 and OsHRZ2. OsIMA1 and OsIMA2 contain a conserved 17-amino acid C-terminal region which is responsible for the interactions with OsHRZ1 and OsHRZ2. The OsIMA1 overexpressing plants have the increased seed Fe concentration and the reduced fertility, as observed in the hrz1-2 loss-of-function mutant plants. Moreover, the expression trends of Fe deficiency inducible genes in the OsIMA1 overexpressing plants are the same to those in the hrz1-2. Co-expression assays suggest that OsHRZ1 and OsHRZ2 promote the degradation of OsIMA1 proteins. As the interaction partners of OsHRZ1, the OsPRI proteins also interact with OsHRZ2. The conserved C-terminal region of four OsPRIs contributes to the interactions with OsHRZ1 and OsHRZ2. An artificial IMA (aIMA) derived from the C-terminal of OsPRI1 can be also degraded by OsHRZ1. Moreover, the aIMA overexpressing rice plants accumulate more Fe without reduction of fertility. This work establishes the link between OsIMAs and OsHRZs, and develops a new strategy for Fe fortification in rice.
Combining two Genetic Sexing Strains allows sorting of non-transgenic males forAedesgenetic control
Authors: Lutrat Célia , Burckbuchler Myriam , Olmo Roenick Proveti , Beugnon Rémy , Fontaine Albin , Akbari Omar S. , Argilés-Herrero Rafael , Baldet Thierry , Bouyer Jérémy , Marois Eric
Published: March 2022

Chemical control of disease vectoring mosquitoesAedes albopictusandAedes aegyptiis costly, unsustainable, and increasingly ineffective due to the spread of insecticide resistance. The Sterile Insect Technique is a valuable alternative but is limited by the slow, error-prone, and wasteful sex-separation requirement. Here, we present four Genetic Sexing Strains (two for eachAedesspecies) based on fluorescence markers linked to the m and M sex loci, allowing for the isolation of transgenic males. Furthermore, we demonstrate how combining these sexing strains enables the production of non-transgenic males. Scaling-up would allow the sorting of 100,000 first instar male larvae in under 1.5 hours with an estimated 0.01-0.1% female contamination. Cost-efficiency analyses revealed that using these strains could result in important savings while setting up and running a mass-rearing facility. Altogether, these Genetic Sexing Strains should enable a major upscaling in control programmes against these important vectors.

Graphical abstract
Co-release of histamine and GABA in prefrontal cortex excites fast-spiking interneurons and causes divisive gain change in pyramidal cells; an effect that is enhanced in older mice
Authors: Lucaci Diana , Yu Xiao , Chadderton Paul , Wisden William , Brickley Stephen G
Published: March 2022

We studied how co-release of histamine/GABA from axons originating from the hypothalamic tuberomammillary nucleus (TMN) and projecting to the prefrontal cortex (PFC) influences circuit processing. We opto-stimulated histamine/GABA co-release from genetically defined TMN axons that express the histidine decarboxylase gene (TMNHDC axons). Whole-cell recordings were used to monitor excitability of visually identified PFC neurons in layer 2/3 of prelimbic (PL), anterior cingulate (AC) and infralimbic (IL) regions before and after opto-stimulated histamine/GABA release. We found that histamine-GABA co-release influences the PFC through actions on distinct neuronal types: histamine stimulates fast-spiking interneurons; and co-released GABA enhances tonic (extrasynaptic) inhibition on pyramidal cells (PyrNs). For fast spiking non-accommodating interneurons, opto-stimulation increased excitability, an effect blocked by histamine H1 and H2 receptor antagonists. The excitability of other interneuron types in the PFC was not altered. In contrast, the combined action of histamine and GABA co-release from TMNHDC axons produced predominantly divisive gain changes in PyrNs, increasing their resting input conductance, and decreasing the slope of the input-output relationship. The direct inhibitory effect of TMNHDC axon activation on PyrNs was not blocked by histamine receptor antagonists but was blocked by GABAA receptor antagonists. Across the adult lifespan (from 3 months to over 2 years of age), stimulation of TMNHDC axons in the PFC inhibited PyrN excitability significantly more in older mice. For individuals that maintain cognitive performance into later life, increases in TMNHDC modulation of PyrNs could enhance information processing and be an adaptive mechanism to buttress cognition.
EZH2 endorses cell plasticity to carcinoma cells facilitating mesenchymal to epithelial transition and tumour colonization
Authors: Gallardo Amador , Molina Aldara , Asenjo Helena G , Lopez-Onieva Lourdes , Alvarez-Perez Juan Carlos , Martorell-Marugán Jordi , Cara Francisca E , Espinosa-Martinez Mencia , Carmona-Sáez Pedro , Granados-Principal Sergio , Medina Pedro P , Sanchez-Pozo Antonio , Landeira David
Published: March 2022

Reversible transition between the epithelial and mesenchymal states are key aspects of carcinoma cell dissemination and the metastatic disease, and thus, characterizing the molecular basis of the epithelial to mesenchymal transition (EMT) is crucial to find druggable targets and more effective therapeutic approaches in cancer. Emerging studies suggest that epigenetic regulators might endorse cancer cells with the cell plasticity required to conduct dynamic changes in cell state during EMT. However, epigenetic mechanisms involved remain mostly unknown. Polycomb Repressive Complexes (PRCs) proteins are well-established epigenetic regulators of development and stem cell differentiation, but their role in different cancer systems is inconsistent and sometimes paradoxical. In this study, we have analysed the role of the PRC2 protein EZH2 in lung carcinoma cells. We found that besides its described role in CDKN2A-dependent cell proliferation, EZH2 upholds the epithelial state of cancer cells by repressing the transcription of hundreds of mesenchymal genes. Chemical inhibition or genetic removal of EZH2 promotes the residence of cancer cells in the mesenchymal state during reversible epithelial-mesenchymal transition. In fitting, analysis of human patient samples and tumour xenograft models indicate that EZH2 is required to efficiently repress mesenchymal genes and facilitate tumour colonization in vivo. Overall, this study discloses a novel role of PRC2 as a master regulator of EMT in carcinoma cells. This finding has important implications for the design of therapies based on EZH2 inhibitors in human cancer patients.
Cold-induced [Ca2+]cytelevations function to support osmoregulation in marine diatoms
Authors: Kleiner Friedrich H. , Helliwell Katherine E. , Chrachri Abdul , Hopes Amanda , Parry-Wilson Hannah , Gaikwad Trupti , Mieszkowska Nova , Chrachri Abdul , Mock Thomas , Wheeler Glen L. , Brownlee Colin
Published: March 2022

Diatoms are a group of microalgae that are important primary producers in a range of open ocean, freshwater and intertidal environments. The latter can experience significant long- and short-term variability in temperature, from seasonal variations to rapid temperature shifts caused by tidal immersion and emersion. As temperature is a major determinant in the distribution of diatom species, their temperature sensory and response mechanisms likely have important roles in their ecological success. We have examined the mechanisms diatoms use to sense rapid changes in temperature, such as those experienced in the intertidal zone. We find that the diatomsPhaeodactylum tricornutumandThalassiosira pseudonanaexhibit a transient cytosolic Ca2+([Ca2+]cyt) elevation in response to rapid cooling, similar to those observed in plant and animal cells. However, [Ca2+]cytelevations were not observed in response to rapid warming. The kinetics and magnitude of cold-induced [Ca2+]cytelevations correlate with the rate of temperature decrease. We do not find a role for the [Ca2+]cytelevations in enhancing cold tolerance, but show that cold shock induces a Ca2+-dependent K+efflux and reduces mortality ofP. tricornutumduring a simultaneous hypo-osmotic shock. As inter-tidal diatom species may routinely encounter simultaneous cold and hypo-osmotic shocks during tidal cycles, we propose that cold-induced Ca2+signalling interacts with osmotic signalling pathways to aid in the regulation of cell volume. Our findings provide insight into the nature of temperature perception in diatoms and highlight that cross-talk between signalling pathways may play an important role in their cellular responses to multiple simultaneous stressors.
BrainQCNet: a Deep Learning attention-based model for the automated detection of artifacts in brain structural MRI scans
Authors: Garcia Mélanie , Dosenbach Nico , Kelly Clare
Published: March 2022

Analyses of structural MRI (sMRI) data depend on robust upstream data quality control (QC). It is also crucial that researchers seek to retain maximal amounts of data to ensure reproducible, generalizable models and to avoid wasted effort, including that of participants. The time-consuming and difficult task of manual QC evaluation has prompted the development of tools for the automatic assessment of brain sMRI scans. Existing tools have proved particularly valuable in this age of Big Data; as datasets continue to grow, reducing execution time for QC evaluation will be of considerable benefit. The development of Deep Learning (DL) models for artifact detection in structural MRI scans offers a promising avenue toward fast, accurate QC evaluation. In this study, we trained an interpretable Deep Learning model, ProtoPNet, to classify minimally preprocessed 2D slices of scans that had been manually annotated with a refined quality assessment (ABIDE 1;n= 980 scans). To evaluate the best model, we applied it to 2141 ABCD scans for which gold-standard manual QC annotations were available. We obtained excellent accuracy: 82.4% for good quality scans (Pass), 91.4% for medium to low quality scans (Fail). Further validation using 799 scans from ABIDE 2 and 750 scans from ADHD-200 confirmed the reliability of our model. Accuracy was comparable to or exceeded that of existing ML models, with fast processing and prediction time (1 min per scan, GPU machine, CUDA-compatible). Our attention model also performs better than traditional DL (i.e., convolutional neural network models) in detecting poor quality scans. To facilitate faster and more accurate QC prediction for the neuroimaging community, we have shared the model that returned the most reliable global quality scores as a BIDS-app (https://github.com/garciaml/BrainQCNet).
The rostral medial frontal cortex is crucial for engagement in consummatory behavior
Authors: White Samantha R. , Laubach Mark
Published: March 2022

The medial frontal cortex (MFC) in rodents emits rhythmic activity that is entrained to the animal’s licking cycle during consumption and encodes the value of consumed fluids (Horst and Laubach, 2013; Amarante et al., 2017; Amarante and Laubach, 2021). These signals are especially prominent in the rostral half of the MFC. This region is located above an orbitofrontal region where mu opioid receptors regulate intake (Mena et al., 2011; Castro and Berridge, 2017) and reversible inactivation reduces behavioral measures associated with the incentive value and palatability of liquid sucrose (Parent et al., 2015a). Here, we examined the effects of reversible inactivation and stimulation of mu opioid receptors in rostral MFC on behavior in an incentive contrast licking task. Adult male rats licked to receive access to liquid sucrose, which alternated between high (16%) and low (4%) values over 30 sec periods. Bilateral infusion of muscimol reduced the total number of licks emitted over the 30 min test sessions, the time spent actively consuming sucrose, and the ratio of licks for the higher and lower value fluids. Inactivation did not alter licking frequency or variability or microstructural measures such as the duration of licking bouts that are classically associated with the palatability of a liquid reward. Infusions of DAMGO (1μg/μL) at the same sites had inconsistent behavioral effects across different subjects. Our findings suggest that the rostral MFC has a distinct role in the control of consummatory behavior and contributes to peristent consumption and not to the expression of palatability.

SIGNIFICANCE STATEMENT

The medial frontal cortex (MFC) of rodents has received attention in recent years and is considered as a singular cortical region with a potential unitary function. Increasing evidence suggests that MFC is composed of distinct subregions, with unique roles in the control of behavior. The present study adds to this literature by showing unique effects of reversibly inactivating the most rostral part of the medial frontal cortex and a lack of consistent effects of stimulating mu opioid receptors in the subregion. Findings are in contrast to previous reports on the more ventral orbitofrontal cortex and caudal medial frontal cortex and are important for understanding the general role of the rodent frontal cortex and how opioids may act to control behavior.
The pore-forming protein gasdermin D is a cellular redox sensor
Authors: Devant Pascal , Boršić Elvira , Ngwa Elsy M. , Thiagarajah Jay R. , Hafner-Bratkovič Iva , Evavold Charles L. , Kagan Jonathan C.
Published: March 2022

Reactive oxygen species (ROS) affect inflammation and immunity in a multitude of ways, in particular in the context of the signaling pathways that determine cell fate. Inflammasomes are multiprotein cytoplasmic complexes whose pyroptosis-inducing activities are controlled by ROS. Our knowledge of how ROS mediates inflammasome activities is largely based on studies of the initiating events in these pathways. Herein, we show that ROS controls the terminal events in the pyroptosis pathways. We found that ROS oxidizes the protein gasdermin D (GSDMD) and promotes its assembly into a death-inducing pore forming complex. Mechanistically, ROS enhances GSDMD-mediated pyroptosis in an intrinsic manner, likely through oxidative modification of a specific cysteine residue (C192). Diverse ROS sources promote GSDMD oxidation, ranging from homeostatic control via the Ragulator-Rag complex, to inducible control via diverse microbial products and environmental toxins. These findings expand the steps in the inflammasome pathway that are controlled by ROS and suggest that GSDMD operates as a pyroptosis-inducing redox sensor.
Identification of unusually disulphide-bonded insulin forms using mass spectrometry and thermolysin cleavage
Authors: Jevon Dillon , Moon Kyung-Mee , Foster Leonard J. , Johnson James D.
Published: March 2022

Insulin is an essential hormone made by the pancreatic beta-cells in the islets of Langerhans. Beta-cells produce more insulin protein than virtually all other cellular proteins combined. Dysfunction in the process of insulin synthesis can lead to disease, including rare forms of monogenic diabetes. Specifically, aberrant intra-insulin and inter-insulin disulphide bonds have been implicated in the pathology of type 1 diabetes and type 2 diabetes, respectively. In type 1 diabetes, misprocessed insulin isoforms may be neoepitopes that kick-start and/or exacerbate the auto-immune response. In type 2 diabetes, aberrant disulphides form insulin dimers that can clog the endoplasmic reticulum and contribute to beta cell dysfunction. To facilitate the study of novel and known insulin neoepitopes and dimers, we present an unbiased and rapid technique for identifying insulin disulphide patterns from pancreatic islet extracts. The basis of this method is the cleavage between insulin’s cysteine residues with the metalloprotease, thermolysin, and subsequent identification of cysteine containing fragments and their partner peptides by LC-MS/MS. Using this technique, we identify 6 aberrant disulphide bonded insulin species, including a previously described type 1 diabetes neoepitope, as well as inter-chain disulphide bonded insulin dimers. Furthermore, using the endoplasmic stress inducer, thapsigargin, we observe increased disulphide errors in a patient donor sample. This approach lays foundations to identify the scope and cause of aberrant insulin disulphide formation in health and disease.
Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant Small ORFs and Functional Microproteins
Authors: Martinez Thomas F. , Lyons-Abbott Sally , Bookout Angie L. , Donaldson Cynthia , Vaughan Joan M. , Lau Calvin , Abramov Ariel , Baquero Arian F. , Baquero Karalee , Friedrich Dave , Huard Justin , Davis Ray , Kim Bong , Koch Ty , Mercer Aaron J. , Misquith Ayesha , Murray Sara A. , Perry Sakara , Pino Lindsay K. , Sanford Christina , Simon Alex , Zhang Yu , Zipp Garrett , Shokhirev Maxim N. , Whittle Andrew J. , Searle Brian C. , MacCoss Michael J. , Saghatelian Alan , Barnes Christopher A.
Published: March 2022

The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides such as insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1) in metabolism, microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B as a metabolic regulator and potentially part of the brain-adipose axis. Furthermore, we demonstrated that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 33 from mouse plasma. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that plasma levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.
Assessing cats’ (Felis catus) sensitivity to human pointing gestures
Authors: Mäses Margaret , Wascher Claudia A.F.
Published: March 2022

A wide range of non-human animal species have been shown to be able to respond to human referential signals, such as pointing gestures. The aim of the present study was to replicate previous findings showing cats to be sensitive to human pointing cues (Miklósi et al. 2005). In our study, we presented two types of human pointing gestures - momentary ipsilateral (direct pointing) and momentary cross-body pointing. We tested nine rescue cats in a two-way object choice task. On a group level, the success rate of cats was 74.4 percent. Cats performed significantly above chance level in both the ipsilateral and cross-body pointing condition. Trial number, rewarded side and type of gesture did not significantly affect the cats’ performances in the experiment. On an individual level, 5 out of 7 cats who completed 20 trials, performed significantly above chance level. Two cats only completed 10 trials. One of them succeeded in 8, the other in 6 of these. The results of our study replicate previous findings of cats being responsive to human ipsilateral pointing cues and add additional knowledge about their ability to follow cross-body pointing cues. Our results highlight that a domestic species, socialised in a group setting, may possess heterospecific communication skills. Further research is needed to exclude alternative parsimonious explanations, such as local and stimulus enhancement.
Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery
Authors: Prasad Vidya Mangala , Blijleven Jelle S. , Smit Jolanda M. , Lee Kelly K.
Published: March 2022

Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV’s complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein’s post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.
Regulation of Cardiomyocyte Adhesion and Mechanosignalling Through Distinct Nanoscale Behaviour of Integrin Ligands Mimicking Healthy or Fibrotic ECM
Authors: Hawkes William , Marhuenda Emilie , Reynolds Paul , O’Neill Caoimhe , Pandey Pragati , Samuel Wilson Darren Graham , Freeley Mark , Huang Da , Hu Junquiang , Gondarenko Sasha , Hone James , Gadegaard Nikolaj , Palma Matteo , Iskratsch Thomas
Published: March 2022

The stiffness of the cardiovascular environment changes during ageing and in disease and contributes to disease incidence and progression. Changing collagen expression and crosslinking regulate the rigidity of the cardiac ECM. Additionally, basal lamina glycoproteins, especially laminin and fibronectin regulate cardiomyocyte adhesion formation, mechanics and mechano-signalling. Laminin is abundant in the healthy heart, but fibronectin is increasingly expressed in the fibrotic heart. ECM receptors are co-regulated with the changing ECM. Due to differences in integrin dynamics, clustering, and downstream adhesion formation this is expected to ultimately influence cardiomyocyte mechanosignalling; however details remain elusive. Here we sought to investigate how different cardiomyocyte ligand/integrin combinations are affecting adhesion formation, traction forces and mechanosignalling, using a combination of uniformly coated surfaces with defined stiffness, PDMS nanopillars, micropatterning and specifically designed bionanoarrays for precise ligand presentation. Thereby we find that neonatal rat cardiomyocytes (which express both laminin and fibronectin binding integrins) adhesion nanoscale organisation, signalling and traction force generation are strongly dependent on the integrin/ligand combination. Together our data indicates that the presence of fibronectin in combination with the enhanced stiffness in fibrotic areas will strongly impact on the cardiomyocyte behaviour and influence disease progression.
Helical ultrastructure of the oncogenic metalloprotease meprin α in complex with a small molecule hydroxamate inhibitor
Authors: Bayly-Jones Charles , Lupton Christopher J. , Fritz Claudia , Venugopal Hariprasad , Ramsbeck Daniel , Wermann Michael , Jäger Christian , de Marco Alex , Schilling Stephan , Schlenzig Dagmar , Whisstock James C.
Published: March 2022

The zinc-dependent metalloprotease meprin α is predominantly expressed in the brush border membrane of proximal tubules in the kidney and enterocytes in the small intestine and colon. In normal tissue homeostasis meprin α performs key roles in inflammation, immunity, and extracellular matrix remodelling. The latter activity is furthermore important for driving aggressive metastasis in the context of certain cancers such as colorectal carcinoma. Accordingly, meprin α is the target of drug discovery programs. In contrast to meprin β, meprin α is secreted into the extracellular space, whereupon it oligomerises to form giant assemblies and is the largest extracellular protease identified to date (~6 MDa). Here, using cryo-electron microscopy, we determine the high-resolution structure of the zymogen and mature form of meprin α, as well as the structure of the active form in complex with a prototype small molecule inhibitor and human fetuin-B. Our data reveal that meprin α forms a giant, flexible, left-handed helical assembly of roughly 22 nm in diameter. We find that oligomerisation improves proteolytic and thermal stability but does not impact substrate specificity or enzymatic activity. Furthermore, structural comparison with meprin β reveal unique features of the active site of meprin α, and helical assembly more broadly.