bluuebunny/crossref_metadata_2025 huggingface dataset:
Knowledge Attitude and Practice towards Cutaneous Leishmaniasis in Sodo District Southern Ethiopia
Authors: Gazu Lina , Nkosi Zerish Zethu , Kebede Nigatu
Published: September 2022

Background

In Ethiopia, Cutaneous Leishmaniasis (CL) is a common infectious disease. However, existing knowledge on community awareness is scarce.

Objective

Objectives is to access knowledge, attitude, and practices about CL in Sodo District.

Methods

Primary quantitative method using a cross-sectional descriptive approach was applied. Data were collected from face-to-face interviews held with 423 households between January to April 2018. Knowledge, attitude, and practice scores were obtained by aggregating responses to questions. Levels of these outcomes were determined by dichotomizing the generated scores using their mean vales. Percentages, frequency and mean values were used to descriptively understand the data. Logistic regression was used to model the binary outcomes. R Package Version 3.02 was used to conduct the statistical analysis.

Results

Of 423 participants 263 (61.9%), 226 (53.4%), and 213 (50.4%) have satisfactory knowledge, favourable attitude, and good practice about leishmaniasis. Majority are unable to identify leishmaniasis and unaware of its cause and transmission. Sandfly is considered “important biting and blood-sucking insect” by 210 (49.6%) but knowledge on biting time and breeding place was unsatisfactory. Most believed CL can be treated, is a serious problem and have a disfiguring outcome. However, most (59.3%, n=251) prefer use of traditional medication. Concerning practice, 288 (68.1%) have bed nets but personal protective measures are rarely used.

Conclusion

The level of overall knowledge and attitudes and practice in the current study was not adequate. This finding implies that there is a need for intensified education regarding CL.
The Natural History of Untreated Pulmonary Tuberculosis in Adults: A Systematic Review and Meta-Analysis
Authors: Sossen Bianca , Richards Alexandra , Heinsohn Torben , Frascella Beatrice , Balzarini Federica , Oradini-Alacreu Aurea , Odone Anna , Rogozińska Ewelina , Häcker Brit , Cobelens Frank , Kranzer Katharina , Houben Rein MGJ , Esmail Hanif
Published: September 2022

BACKGROUND

Key stages in TB disease can be delineated by radiology, microbiology and symptoms, but transition between relevant stages remains unclear. We sought to quantify progression and regression across the spectrum of TB disease by systematically reviewing studies of individuals with untreated TB undergoing follow up.

METHODS

We searched PubMED, EMBASE and Web of Science until December 31st 1960, the Index Medicus between 1895 and 1945, and extensive investigator collections without date restriction - in English and German. Eligible studies were observational cohorts and clinical trials, presenting adults/adolescents with TB or recent TB exposure, undergoing follow-up for at least 12 months without therapeutic intervention. Two authors independently reviewed titles/abstracts and full texts for inclusion. Quality was assessed with a modified Newcastle-Ottawa Score, excluding highly biased studies. Summary estimates were extracted to align with TB disease transitions in a conceptual model, and we used meta-analysis of proportions with random-effects to synthesise the extracted data. This study is registered with PROSPERO (CRD42019152585).

FINDINGS

10477 titles were screened and 1648 full texts reviewed. 223 met inclusion criteria. 109 were excluded for high risk of bias and 90 did not have extractable data. 24 studies (34 cohorts) were included. Progression from microbiologically negative to positive disease in those with radiographic TB evidence occurred at an annualized rate of 9.71% (95% CI:6.17-13.34) with “active” TB imaging, and 1.06% (95% CI:0.31-1.82) with “inactive” TB imaging. Reversion from microbiologically-positive to -undetectable in prospective cohorts occurred at an annualized rate of 12.40% (95% CI: 6.81-17.99). Studies reported symptoms poorly not allowing for direct estimation of transitions for subclinical (asymptomatic, culture positive) disease.

INTERPRETATION

We present the risk of progression in those with radiographic evidence of disease and the rate of self-cure for microbiologically positive disease to inform global disease burden estimates, clinical guidelines and policy decisions.
Polygenic risk scores for asthma and allergic disease associate with COVID-19 severity in 9/11 responders
Authors: Waszczuk Monika A. , Morozova Olga , Lhuillier Elizabeth , Docherty Anna R. , Shabalin Andrey A. , Yang Xiaohua , Carr Melissa A. , Clouston Sean A. P. , Kotov Roman , Luft Benjamin J.
Published: September 2022

Background

Genetic factors contribute to individual differences in the severity of coronavirus disease 2019 (COVID-19). A portion of genetic predisposition can be captured using polygenic risk scores (PRS). Relatively little is known about the associations between PRS and COVID-19 severity or post-acute COVID-19 in community-dwelling individuals.

Methods

Participants in this study were 983 World Trade Center responders infected for the first time with SARS-CoV-2 (mean age at infection=56.06; 93.4% male; 82.7% European ancestry). Seventy-five (7.6%) responders were in the severe COVID-19 category; 306 (31.1%) reported at least one post-acute COVID-19 symptom at 4-week follow-up. Analyses were adjusted for population stratification and demographic covariates.

Findings

The asthma PRS was associated with severe COVID-19 category (odds ratio [OR]=1.61, 95% confidence interval: 1.17-2.21) and more severe COVID-19 symptomatology (β=.09,p=.01), independently of respiratory disease diagnosis. Severe COVID-19 category was also associated with the allergic disease PRS (OR=1.97, [1.26-3.07]) and the PRS for COVID-19 hospitalization (OR=1.35, [1.01-1.82]). PRS for coronary artery disease and type II diabetes were not associated with COVID-19 severity.

Conclusion

Recently developed polygenic biomarkers for asthma, allergic disease, and COVID-19 hospitalization capture some of the individual differences in severity and clinical course of COVID-19 illness in a community population.
Long-term spatial patterns in COVID-19 booster vaccine uptake
Authors: Wood A.J. , MacKintosh A.M. , Stead M. , Kao R.R.
Published: September 2022

Vaccination is a critical tool for controlling infectious diseases, with its use to protect against COVID-19 being a prime example. Where a disease is highly transmissible, even a small proportion of unprotected individuals can have substantial implications for disease burdens and compromise disease control. As socio-demographic factors such as deprivation and ethnicity have been shown to influence uptake rates, identifying how uptake varies with socio-demographic indicators is a critical step for reducing hesitancy and issues of access, and identifying plausible future uptake patterns.

Here, we analyse the numbers of COVID-19 booster vaccinations subdivided by age, sex, dose and location. We use publicly available socio-demographic data, and use Random Forest models to capture patterns of first booster uptake at high spatial resolution, with systematic variation restricted to∼1km in urban areas. We introduce a novel method to predict future distributions using our first booster model, assuming existing trends with respect to deprivation will persist. This provides a quantitative estimate of the impact of changing motivations and efforts to increase uptake.

While age and sex have the greatest impact on the model fit, there is a substantial influence of community deprivation and the proportion of residents belonging to a black or minority ethnicity. Changes in patterns from first to second boosters suggest in the longer-term that the impact of deprivation is likely to increase, furthering the disproportionate impact of COVID-19 on deprived communities. Our analysis is based solely on publicly available socio-demographic data and readily recorded vaccination data, and would be easily adaptable to uptake data from countries where data recording is similar, and for aiding vaccination campaigns against other infectious diseases.
Data augmentation for imbalanced blood cell image classification
Authors: Rana Priyanka , Sowmya Arcot , Meijering Erik , Song Yang
Published: September 2022

Due to progression in cell-cycle or duration of storage, classification of morphological changes in human blood cells is important for correct and effective clinical decisions. Automated classification systems help avoid subjective outcomes and are more efficient. Deep learning and more specifically Convolutional Neural Networks have achieved state-of-the-art performance on various biomedical image classification problems. However, real-world data often suffers from the data imbalance problem, owing to which the trained classifier is biased towards the majority classes and does not perform well on the minority classes. This study presents an imbalanced blood cells classification method that utilises Wasserstein divergence GAN, mixup and novel nonlinear mixup for data augmentation to achieve oversampling of the minority classes. We also present a minority class focussed sampling strategy, which allows effective representation of minority class samples produced by all three data augmentation techniques and contributes to the classification performance. The method was evaluated on two publicly available datasets of immortalised human T-lymphocyte cells and Red Blood Cells. Classification performance evaluated using F1-score shows that our proposed approach outperforms existing methods on the same datasets.
Profound lipid dysregulation in mutant TDP-43 mice is ameliorated by the glucocerebrosidase 2 inhibitor ambroxol
Authors: Luikinga Sophia , Henriques Alexandre , Ngo Shyuan T. , Rapasinghe Thusi , Loeffler Jean-Philippe , Spedding Michael , Turner Bradley J.
Published: September 2022

The importance of dyslipidemia in amyotrophic lateral sclerosis (ALS) patients is increasingly recognised as a potential key mechanism driving disease onset, progression and survival. Evidence in familial ALS models suggests that lipid composition is significantly affected, however clinically relevant models have yet to be investigated. Using a powerful lipidomic approach, we uncover significant dysregulation of glycosphingolipid (GSL) metabolism in both the spinal cord and skeletal muscles of transgenic TDP-43Q331K mice. Treatment with the selective glucocerebrosidase 2 (GBA2) inhibitor ambroxol at symptom onset significantly improved motor and gait functions in TDP-43Q331K mice. Ambroxol treatment preserved motor neurons and neuromuscular junctions which was associated with modulation of GSL metabolism. Our study establishes significant lipid dysregulation in a clinically relevant model of ALS. Importantly, we show positive therapeutic outcomes in a mouse model of TDP-43 proteinopathy, suggesting that ambroxol may be a promising candidate to treat underlying dyslipidemia and symptoms of ALS.
ACAT1/SOAT1 Blockade Suppresses LPS-Mediated Neuroinflammation by Modulating the Fate of Toll-Like Receptor 4 in Microglia
Authors: Li Haibo , Huynh Thao N. , Duong Michael Tran , Gow James G. , Chang Catherine C.Y. , Chang Ta-Yuan
Published: September 2022

Background

Cholesterol is essential for growth and maintenance of mammalian cells. It is stored as cholesteryl esters by the enzymes acyl-CoA:cholesterol acyltransferases 1 & 2 (ACAT 1 & 2) (Sterol O-acyltransferase 1 & 2; SOATs in GenBank). ACAT1 blockade (A1B) in macrophages ameliorates various pro-inflammatory responses elicited by lipopolysaccharides (LPS) or by cholesterol loading. In mouse and human brains, Acat1 expression dominates over Acat2 and Acat1 is elevated in many neurodegenerative diseases and in acute neuroinflammation. However, the possible effects of ACAT1 blockade in neuroinflammation, regulated by mediators such as Toll-Like Receptor 4 (TLR4), has not been studied.

Methods

We conducted LPS-induced acute neuroinflammation experiments in control vs myeloid specific or neuron specific Acat1 knockout (KO) mice. Furthermore, we evaluated LPS-induced neuroinflammation in the microglial cell line N9 with or without pre-treatment of the small molecule ACAT1-specific inhibitor K-604. Biochemical and microscopy assays were used to monitor inflammatory responses and the fate of TLR4.

Results

In vivo studies revealed that Acat1 inactivation in myeloid cell lineage, but not in neurons, markedly attenuated LPS-induced activation of various pro-inflammatory response genes in hippocampus and cortex. Studies in cell culture showed that pre-incubating cells with K-604 significantly ameliorated the pro-inflammatory responses induced by LPS. In cells acutely treated with LPS (for 30 min), pre-incubation with K-604 significantly increased the endocytosis of TLR4, the major transmembrane signaling receptor that mediates LPS-dependent acute neuroinflammation. In cells chronically treated with LPS (for 24-48 hrs), pre-incubation with K-604 significantly decreased the total TLR4 protein content, presumably due to enhanced trafficking of TLR4 to the lysosomes for degradation. For ex vivo evidence, we isolated microglia from adult mice, and found that in mice without LPS stimulation, myeloid Acat1 inactivation altered cellular distribution of TLR4; in mice with LPS stimulation, myeloid Acat1 inactivation decreased the cellular content of TLR4.

Conclusion

Blocking ACAT1 in mouse microglia alters the fate of TLR4 and suppresses its ability to participate in pro-inflammatory signaling cascade in response to LPS.
Spatial analysis of the metastatic brain tumor immune and extracellular matrix microenvironment
Authors: Widodo Samuel S. , Dinevska Marija , Cuzcano Lucero , Papanicolaou Michael , Cox Thomas R. , Stylli Stanley S. , Mantamadiotis Theo
Published: September 2022

Metastatic cancer is responsible for the overwhelming majority of cancer-related deaths with metastatic tumors being the most common neoplasms affecting the central nervous system. One of the major factors regulating tumor biology is the tumor microenvironment. However, little is known about the cellular and non-cellular composition of metastatic brain tumors and how tumor cell ontogeny influences the metastatic brain tumor microenvironment. By integrating multiplex immunohistochemistry and histopathological analysis to investigate composition and the spatial relationship between neoplastic cells, infiltrating and brain resident immune cells and the extracellular matrix, we demonstrate that metastatic brain tumors exhibit differences in ECM deposition, compared with the most common primary brain tumor type, glioblastoma, and that the dominant immune cell types in metastatic brain tumors are immunosuppressive macrophages, which preferentially localize to ECM-rich stromal regions.
COVID-19 disruptions of food systems and nutrition services in Ethiopia: Evidence of the impacts and policy responses
Authors: McCann Juliet , Sinno Lea , Ramadhan Eki , Assefa Nega , Berhane Hanna Y. , Madzorera Isabel , Fawzi Wafaie
Published: September 2022

Background

Since its first case of COVID-19 on March 13, 2020 and Ethiopia has exerted efforts to curb the spread of the Coronavirus disease 2019 (COVID-19) without imposing a nationwide lockdown. Globally, COVID-19 related disruptions and mitigation measures have impacted livelihoods and food systems, nutrition, as well as access and use of health services.

Objective

To develop a comprehensive understanding of the impacts of the COVID-19 pandemic on food security and maternal and child nutrition and health services and to synthesize lessons from policy responses to the COVID-19 pandemic in Ethiopia.

Methods

We conducted a review of literature and 8 key informant interviews across government agencies, donors, and non-governmental organizations (NGOs), to map the impacts of the COVID-19 pandemic on the food and health systems in Ethiopia. We summarized policy responses and identified recommendations for future actions related to the COVID-19 pandemic and other future emergencies.

Results

The impacts of the COVID-19 pandemic were felt across the food system. Disruptions were noted in inputs supply due to travel restrictions and closed borders restricting trade, reduced in-person support by agriculture extension workers, income losses, increases in food prices, and the reduction in food security and consumption of less diverse diets. Maternal and child health services were disrupted due to fear of contacting COVID-19, diversion of resources, and lack of personal protective equipment. Disruptions eased over time due to the expansion of social protection, through the Productive Safety Net Program, and the increased outreach and home service provision by the health extension workers.

Conclusion

Ethiopia experienced disruptions to food systems and expanded existing social protection and public health infrastructure and leveraged partnerships with non-state actors. Nevertheless, vulnerabilities and gaps remain and there is a need for a long-term strategy that considers the cyclical nature of COVID-19 cases.
A clinical stage LMW-DS drug inhibits infection of human cells by Dengue, Zika and Yellow Fever viruses
Authors: Logan Ann , Mazzon Michela , Bruce Lars , Barnes Nicholas M.
Published: September 2022

The flavivirus family are responsible for the most abundant arboviral diseases of humans in terms of geographical distribution, morbidity and mortality; at least 2.5 billion people are at risk with, for example, an estimated 100-400 million Dengue infections a year. However, for infections by Dengue, Zika or Yellow Fever virus there are no effective anti-infective drug treatments nor for Dengue or Zika virus a safe effective vaccine and prevention at present focusses on vector (mosquito) control. Whilst symptoms from Dengue, Zika and Yellow Fever virus infection may be mild for some, they are very serious and life threatening for others. For instance, severe Dengue is a leading cause of hospitalisation and death among children and adults in Asian and Latin American countries. Likewise, Zika infection can have catastrophic consequences for pregnant women following the passing of the virus to their foetus with arising miscarriage or birth defects including microcephaly that can be fatal. The aim of the present study was to evaluate the potential of a unique low molecular weight dextran sulphate (LMW-DS) clinical stage drug, ILB®, to inhibit infection of human cells by four serotypes of Dengue virus (DENV1-4), two strains of Zika virus (African and Asian) and Yellow Fever virus (vaccine strain YF17D) assessed by immunofluorescence of viral particles. ILB® potently inhibited infection by all the strains of Dengue, Zika and Yellow Fever virus in a concentration-dependent manner with IC50 for ILB® ranging from 31 to 343 μg/ml. In conclusion, given the safety profile of ILB® established in a number of Phase I and Phase II clinical trials, these results highlight the potential of ILB® to treat patients infected with Dengue, Zika or Yellow Fever virus with the opportunity to translate the findings quickly by clinical investigation.
Multimodal Object Representations Rely on Integrative Coding
Authors: Li Aedan Y. , Ladyka-Wojcik Natalia , Qazilbash Heba , Golestani Ali , Walther Dirk B. , Martin Chris B. , Barense Morgan D.
Published: September 2022

Combining information from multiple senses is essential to object recognition. Yet how the mind combines sensory input into coherent multimodal representations – the multimodal binding problem – remains poorly understood. Here, we applied multi-echo fMRI across a four-day paradigm, in which participants learned 3-dimensional multimodal object representations created from well-characterized visual shape and sound features. Our novel paradigm decoupled the learned multimodal object representations from their baseline unimodal shape and sound features, thus tracking the emergence of multimodal concepts as they were learned by healthy adults. Critically, the representation for the whole object was different from the combined representation of its individual parts, with evidence of an integrative object code in anterior temporal lobe structures. Intriguingly, the perirhinal cortex – an anterior temporal lobe structure – was by default biased towards visual shape, but this initial shape bias was attenuated with learning. Pattern similarity analyses suggest that after learning the perirhinal cortex orthogonalized combinations of visual shape and sound features, transforming overlapping feature input into distinct multimodal object representations. These results provide evidence of integrative coding in the anterior temporal lobes that is distinct from the distributed sensory features, advancing the age-old question of how the mind constructs multimodal objects from their component features.
An RNA sequence that reprograms ribosomes to bypass a 50 nucleotide coding gap is encoded by a mobile element whose sequence conservation illuminates its bypass mechanisms
Authors: Manning Gerard , Atkins John F
Published: September 2022

Background

A remarkable sequence in phage T4 causes ribosomes to skip over a 50 nucleotide insert within a topoisomerase subunit gene, and resume correct synthesis of the protein at a high efficiency. Its mechanism has been extensively studied but it remained an isolated phenomenon whose origin and full function are still a mystery.

Results

We have found dozens of homologous cases in genomic and metagenomic sequences, all part of a mobile DNA element that repeatedly inserts in topoisomerase genes of Myoviridae phages. These have substantial sequence diversity, with selective conservation that specify the elaborate set of mechanisms found experimentally to underlie this extreme case of translational recoding. These sequences provide new variations on these mechanisms, and introduce additional features that may also be important for bypassing. These include a series of RNA secondary structures, a conserved stop codon or rare ‘hungry’ codon at the start of the bypass, a Shine-Dalgarno sequence flanked by AU-rich sequence, and residues in the nascent peptide that prime the ribosome for bypassing.

Conclusions

These data provide an evolutionary foundation for the experimentally derived mechanisms, highlight several new features of the sequence, and provide substantial new variations on the bypass theme that will allow further experimental exploration of biologically meaningful variants.
Glioblastoma disrupts cortical network activity at multiple spatial and temporal scales
Authors: Meyer Jochen , Yu Kwanha , Luna-Figueroa Estefania , Deneen Ben , Noebels Jeffrey
Published: September 2022

The emergence of glioblastoma in cortical tissue initiates early and persistent neural hyperexcitability with signs ranging from mild cognitive impairment to convulsive seizures. The influence of peritumoral synaptic density, growth dynamics, and spatial contours of excess glutamate upon higher order neuronal network modularity is unknown. We combined cellular and widefield imaging of calcium and glutamate fluorescent reporters in two GBM mouse models with distinct synaptic microenvironments and growth profiles. Functional metrics of neural ensembles are dysregulated during tumor invasion depending on the stage of malignant progression and tumor cell proximity. Neural activity is significantly elevated during periods of accelerated tumor growth. Abnormal glutamate accumulation precedes and outpaces the spatial extent of baseline neuronal calcium signaling, indicating these processes are uncoupled in tumor cortex. Distinctive excitability homeostasis patterns and functional connectivity of local and remote neuronal populations support the promise of precision genetic diagnosis and management of this devastating brain disease.
Complex aneuploidy triggers autophagy and p53-mediated apoptosis and impairs the second lineage segregation in human preimplantation embryos
Authors: Regin Marius , Lei Yingnan , De Deckersberg Edouard Couvreu , Janssens Charlotte , Huyghebaert Anfien , Guns Yves , Verdyck Pieter , Verheyen Greta , Van de Velde Hilde , Sermon Karen , Spits Claudia
Published: September 2022

About 70% of human cleavage stage embryos show chromosomal mosaicism, falling to 20% in blastocysts. Chromosomally mosaic human blastocysts can implant and lead to healthy new-borns with normal karyotypes. Studies in mouse embryos and human gastruloids have shown that aneuploid cells show proteotoxic stress, autophagy and p53 activation and that they are eliminated from the epiblast by apoptosis while being tolerated in the trophectoderm. These observations suggest a selective loss of aneuploid cells from human embryos, but the underlying mechanisms are not yet fully understood. In this study we investigated the cellular consequences of aneuploidy in a total of 125 human blastocysts. RNA-sequencing of trophectoderm cells showed transcriptional signatures of activated p53 pathway and apoptosis, which was proportionate to the level of chromosomal imbalance. Immunostaining corroborated that aneuploidy triggers proteotoxic stress, autophagy, p53-signalling, and apoptosis independent from DNA damage. Total cell numbers were lower in aneuploid embryos, due to a decline both in trophectoderm and in epiblast/primitive endoderm cell numbers. While lower cell numbers in trophectoderm may be attributed to apoptosis, it appeared that aneuploidy impaired the second lineage segregation, particularly primitive endoderm formation. This might be reinforced by retention of NANOG in aneuploid embryos. Our findings might explain why fully aneuploid embryos fail to further develop and we hypothesize that the same mechanisms lead to removal of aneuploid cells from mosaic embryos. This hypothesis needs further study as we did not analyze chromosomal mosaic embryos. Finally, we demonstrated a few differences with previous findings in the mouse, emphasizing the need for human embryo research to understand the consequences of aneuploidy.
Transcriptome profiling of tendon fibroblasts at the onset of embryonic muscle contraction reveals novel force-responsive genes
Authors: Nayak Pavan K , Subramanian Arul , Schilling Thomas F
Published: September 2022

Mechanical forces play a critical role in tendon development and function, influencing cell behavior through mechanotransduction signaling pathways and subsequent extracellular matrix (ECM) remodeling. Here we investigate the molecular mechanisms by which tenocytes in developing zebrafish embryos respond to muscle contraction forces during the onset of swimming and cranial muscle activity. Using genome-wide bulk RNA sequencing of FAC-sorted tenocytes we identify novel tenocyte markers and genes involved in tendon mechanotransduction. Embryonic tendons show dramatic changes in expression of Matrix Remodeling Associated 5b (mxra5b), Matrilin 1 (matn1), and the transcription factor Kruppel-like factor 2a (klf2a), as muscles start to contract. Using embryos paralyzed either by loss of muscle contractility or neuromuscular stimulation we confirm that muscle contractile forces influence the spatial and temporal expression patterns of all three genes. Quantification of these gene expression changes across tenocytes at multiple tendon entheses and myotendinous junctions reveals that their responses depend on force intensity, duration and tissue stiffness. These force-dependent feedback mechanisms in tendons, particularly in the ECM, have important implications for improved treatments of tendon injuries and atrophy.
Growth hormone receptor (GHR) in AgRP neurons regulates thermogenesis in aged mice in a sex-specific manner
Authors: Stilgenbauer Lukas , de Lima Juliana Bezerra Medeiros , Debarba Lucas Kniess , Khan Manal , Koshko Lisa , Kopchick John J. , Bartke Andrzej , Schneider Augusto , Sadagurski Marianna
Published: September 2022

Evidence for hypothalamic regulation of energy homeostasis and thermoregulation in brown adipose tissue (BAT) during aging has been well recognized, yet the central molecular mediators involved in this process are poorly understood. The arcuate hypothalamus (ARC), orexigenic agouti-related peptide (AgRP) neurons control nutrient intake, energy homeostasis, and BAT thermogenesis. To determine the roles of growth hormone receptor (GHR) signaling in the AgRP neurons we used mice with the AgRP-specific GHR deletion (AgRPΔGHR). We found that female AgRPΔGHRmice were resistant to temperature adaptation, and their body core temperature remained significantly lower when held at 10°C, 22°C, or 30°C, compared to control mice. Low body core temperature in female AgRPΔGHRmice has been associated with significant reductions inUcp1andPgc1αexpression in the BAT. Further, neuronal activity in AgRP in response to cold exposure was blunted in AgRPΔGHRfemales, while the number of Fos+AgRP neurons was increased in control females exposed to cold. Global transcriptome from BAT identified increased expression of genes related to immune responses and chemokine activity and decreased expression of genes involved in triglycerides synthesis and metabolic pathways in AgRPΔGHRfemales. Importantly, these were the same genes that are downregulated by thermoneutrality in control mice but not in the AgRPΔGHRanimals. Collectively, these data demonstrate a novel circuit of thermal regulation between the hypothalamic AgRP-GHR and BAT and provide insight into the brain systems that are critical for the thermogenic vitality of the elderly.
An automatic entropy method to efficiently mask histology whole-slide images
Authors: Song Yipei , Cisternino Francesco , Mekke Joost M. , de Borst Gert J. , de Kleijn Dominique P.V. , Pasterkamp Gerard , Vink Aryan , Glastonbury Craig A. , van der Laan Sander W. , Miller Clint L.
Published: September 2022

Background

Tissue segmentation of histology whole-slide images (WSI) remains a critical task in automated digital pathology workflows for both accurate disease diagnosis and deep phenotyping for research purposes. This is especially challenging when the tissue structure of biospecimens is relatively porous and heterogeneous, such as for atherosclerotic plaques.

Methods

In this study, we developed a unique approach called EntropyMasker based on image entropy to tackle the fore- and background segmentation (masking) task in histology WSI. We evaluated our method on 97 high-resolution WSI of human carotid atherosclerotic plaques in the Athero-Express Biobank Study, constituting hematoxylin and eosin (H&E) and 8 other staining types.

Results and Conclusion

Using multiple benchmarking metrics, we compared our method with four widely used segmentation methods: Otsu’s method, Adaptive mean, Adaptive Gaussian and slideMask and observed that our method had the highest sensitivity and Jaccard similarity index. We envision EntropyMasker to fill an important gap in WSI preprocessing and deep learning image analysis pipelines and enable disease phenotyping beyond the field of atherosclerosis.
Criteria to Achieve Safe Antimicrobial Intravenous-to-Oral Switch in Hospitalised Adult Populations: A Systematic Rapid Review
Authors: Harvey Eleanor J , McLeod Monsey , De Brún Caroline , Ashiru-Oredope Diane
Published: September 2022

Introduction

Antimicrobial stewardship and patient safety strategies include early intravenous-to-oral switch (IVOS) for antimicrobials.

Aim

This rapid review aimed to assess and collate IVOS criteria from the literature to achieve safe and effective antimicrobial IVOS in the hospital inpatient adult population.

Method

The rapid review follows the PRISMA statement and is registered with PROSPERO. Systematic literature searches were conducted. Articles of adult populations published between 2017-2021 were included. IVOS criteria from UK hospital IVOS policies were categorised to inform the framework synthesis of the literature criteria.

Results

IVOS criteria from 45/164 (27%) UK IVOS policies were categorised into a 5-section framework: 1-Timing of IV antimicrobial review, 2-Clinical signs and symptoms, 3-Infection markers, 4-Enteral route, and 5-Infection exclusions. The literature search identified 477 papers, of which 16 were included. The most common timing for review was 48-72 hours from initiation of intravenous antimicrobial (n=5, 30%). Nine studies (56%) stated clinical signs and symptoms must be improving. Temperature was the most frequently mentioned infection marker (n=14, 88%). Endocarditis had the highest mention as an infection exclusion (n=12, 75%). Overall, 33 IVOS criteria were identified to go forward into the Delphi process.

Conclusion

Through the rapid review, 33 IVOS criteria were collated and presented within 5 distinct and comprehensive sections. The literature highlighted the possibility of reviewing IVOS before 48-72 hours, and of presenting HR, BP and RR as a combination early warning score criterion. The criteria identified can serve as a starting point of IVOS criteria review for any institution globally, as no country or region limits were applied. Further research is required to achieve consensus on IVOS criteria from healthcare professionals that manage patients with infections.

What is already known on this topic

Antimicrobial intravenous-to-oral switch has benefits such as decreased risk of catheter-related infections, reduced equipment costs and increased patient mobility and comfort. Acute hospitals often develop and implement individualised IVOS policies with varying levels of evidence base.

What this study adds

This study provides evidence-based IVOS criteria to standardise practice in hospital settings.

How this study might affect research, practice or policy

IVOS criteria can be taken forward through a consensus process with healthcare professionals providing the care for hospitalised adult patients and making the decisions regarding infection management. In the acute hospital setting, IVOS criteria can be operationalised to promote best practice. The criteria can also be considered as part of organisation-wide audits and quality/policy incentives.
Childhood obesity is linked to putative neuroinflammation in brain white matter, hypothalamus, and striatum
Authors: Li Zhaolong , Samara Amjad , Ray Mary Katherine , Rutlin Jerrel , Raji Cyrus A. , Shimony Joshua S. , Sun Peng , Song Sheng-Kwei , Hershey Tamara , Eisenstein Sarah A.
Published: September 2022

Neuroinflammation is both a consequence and driver of overfeeding and weight gain in rodent obesity models. Advances in magnetic resonance imaging (MRI) enable investigations of brain microstructure that suggests neuroinflammation in human obesity. To assess the convergent validity across MRI techniques and extend previous findings, we used diffusion basis spectrum imaging (DBSI) to characterize obesity-associated alterations in brain microstructure in 601 children (age 9-11 years) from the Adolescent Brain Cognitive DevelopmentSMStudy. Compared to children with normal-weight, greater DBSI restricted fraction (RF), reflecting neuroinflammation-related cellularity, was seen in widespread white matter in children with overweight and obesity. Greater DBSI-RF in hypothalamus, caudate nucleus, putamen, and, in particular, nucleus accumbens, correlated with higher baseline body mass index (BMI) and related anthropometrics. Comparable findings were seen in the striatum with a previously reported restriction spectrum imaging (RSI) model. Gain in waist circumference over one and two years related, at nominal significance, to greater baseline RSI-assessed restricted diffusion in nucleus accumbens and caudate nucleus, and DBSI-RF in hypothalamus, respectively. Here we demonstrate that childhood obesity is associated with microstructural alterations in white matter, hypothalamus, and striatum. Our results also support the reproducibility, across MRI methods, of findings of obesity-related putative neuroinflammation in children.
A MAD7-based genome editing system for E. coli
Authors: Mund Markus , Weber Wadim , Degreif Daniel , Schiklenk Christoph
Published: September 2022

A broad variety of biomolecules is industrially produced in bacteria and yeasts. These microbial expression hosts can be optimized through genomic engineering using CRISPR tools. Here, we designed and characterized such a modular genome editing system based on the Cas12a-like RNA guided nuclease MAD7 in E. coli. Our system enables the efficient generation of single nucleotide polymorphisms (SNPs) or gene deletions and can directly be used with donor DNA from benchtop DNA assembly to increase throughput. We combined multiple edits to engineer an E. coli strain with reduced overflow metabolism and increased plasmid yield, highlighting the versatility and industrial applicability of our approach.
Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assembly prior to nuclear dissolution
Authors: Rocha Helder , Simões Patrícia A. , Budrewicz Jacqueline , Lara-Gonzalez Pablo , Carvalho Ana Xavier , Dumont Julien , Desai Arshad , Gassmann Reto
Published: September 2022

A landmark event in the transition from interphase to mitosis in metazoans is nuclear envelope breakdown (NEBD). Many events important for mitosis occur prior to NEBD, including condensation of replicated chromosomes and assembly of kinetochores to rapidly engage spindle microtubules. Here we show that nuclear-enriched protein phosphatase 4 (PP4) ensures robust assembly of the microtubule-coupling outer kinetochore prior to NEBD. In the absence of PP4, chromosomes exhibit extended monopolar orientation after NEBD and subsequently mis-segregate. A secondary consequence of diminished outer kinetochore assembly is defective sister chromatid resolution. After NEBD, a cytoplasmic activity compensates for PP4 loss, leading to outer kinetochore assembly and recovery of chromosomes from monopolar orientation to significant biorientation. The Ndc80-Ska microtubule-binding module of the outer kinetochore is required for this recovery. PP4 associates with the inner kinetochore protein CENP-C; however, disrupting the PP4–CENP-C interaction does not perturb chromosome segregation. These results establish that PP4-dependent outer kinetochore assembly prior to NEBD is critical for timely and proper engagement of chromosomes with spindle microtubules.
High-grade serous ovarian carcinoma organoids as models of chromosomal instability
Authors: Vias Maria , Morrill Gavarró Lena , Sauer Carolin M. , Sanders Debbie , Piskorz Anna M. , Couturier Dominique-Laurent , Ballereau Stéphane , Hernando Barbara , Hall James , Correia-Martins Filipe , Markowetz Florian , Macintyre Geoff , Brenton James D.
Published: September 2022

High-grade serous ovarian carcinoma (HGSOC) is the most genomically complex cancer, characterised by ubiquitous TP53 mutation, profound chromosomal instability and heterogeneity. The mutational processes driving chromosomal instability in HGSOC can be distinguished by specific copy number signatures. To develop clinically relevant models of these mutational processes we derived 15 continuous HGSOC patient-derived organoids (PDOs). We carried out detailed bulk transcriptomic, bulk genomic, single cell genomic, and drug sensitivity characterisation of the organoids. We show that PDOs comprise communities of different clonal populations and represent models of different causes of chromosomal instability including homologous recombination deficiency, chromothripsis, tandem-duplicator phenotype and whole genome duplication. We also show that these PDOs can be used as exploratory tools to study transcriptional effects of copy number alterations as well as compound-sensitivity tests. In summary, HGSOC PDO cultures provide a genomic tool for studies of specific mutational processes and precision therapeutics.
Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders
Authors: van Hilten Niek , Methorst Jeroen , Verwei Nino , Risselada Herre Jelger
Published: September 2022

Proteins can specifically bind to curved membranes through curvature-induced hydrophobic lipid packing defects. The chemical diversity among such curvature ‘sensors’ challenges our understanding of how they differ from general membrane ‘binders’, that bind without curvature selectivity. Here, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations (Evo-MD) to resolve the peptide sequences that optimally recognize the curvature of lipid membranes. We subsequently demonstrate how a synergy between Evo-MD and a neural network (NN) can enhance the identification and discovery of curvature sensing peptides and proteins. To this aim, we benchmark a physics-trained NN model against experimental data and show that we can correctly identify known ‘sensors’ and ‘binders’. We illustrate that sensing and binding are in fact phenomena that lie on the same thermodynamic continuum, with only subtle but explainable differences in membrane binding free energy, consistent with the serendipitous discovery of sensors.

Teaser

AI-based design helps explain curvature-selective membrane binding behavior.
LGR5 targeting molecules as therapeutic agents for multiple cancer types
Authors: Chen Hung-Chang , Mueller Nico , Stott Katherine , Rivers Eilidh , Kapeni Chrysa , Sauer Carolin M , Beke Flavio , Walsh Stephen , Ashman Nicola , O’Brien Louise , Fard Amir Rafati , Godsinia Arman , Joud Fadwa , Giger Olivier , Zlobec Inti , Olan Ioana , Aitken Sarah J. , Hoare Matthew , Mair Richard , Serrao Eva , Brenton James D , Garcia-Gimenez Alicia , Richardson Simon E. , Huntly Brian , Spring David R. , Skjødt Mikkel-Ole , Skjødt Karsten , de la Roche Marc , de la Roche Maike
Published: September 2022

Leucine-rich repeat-containing G-protein receptor 5 (LGR5) has been characterised as a stem cell and cancer stem cell marker. Previous analyses of LGR5 transcript levels indicate high level expression discriminates malignancies such as colorectal cancer (CRC) and pre-B acute lymphoblastic leukaemia (pre-B ALL) from healthy tissues suggesting LGR5 protein expression may provide a molecular handle for prognosis and treatment.

We have developed highly specific, high affinity antibodies to the extracellular domain of human LGR5 (α-LGR5) that detect high LGR5 protein levels in colorectal cancer (CRC), hepatocellular carcinoma (HCC), and pre-B ALL. In contrast, there is low to undetectable levels of LGR5 protein in normal colon and rectal epithelia, liver, ovarian tissues, brain and immune cell types.

LGR5 is rapidly internalised from the plasma membrane and trafficked to intracellular vesicular compartments including lysosomes. Treatment of high LGR5-expressing CRC and pre-B ALL cancer cell lines with an antibody-drug conjugate version of α-LGR5 (α-LGR5-ADC) lead to effective cell killing at nanomolar concentrations. Interventional treatment of pre-B ALL tumours with α-LGR5-ADC in vivo led to rapid tumour attrition. We further demonstrated the therapeutic utility of humanised α-LGR5 by using the corresponding scFv fragment for the generation of α-LGR5 chimeric antigen receptors (CARs) and a Bispecific T cell Engager (BiTE). α-LGR5-CAR-NK cells were effective at killing LGR5-expressing cells while α-LGR5/α-CD3 BiTEs induce T cell activation and killing of NALM6 cells by cytotoxic CD8+ T cells.

Taken together, this study establishes α-LGR5-based therapeutic modalities that effectively discriminate and target CRC, HCC and pre-B ALL tumour cells.

One Sentence Summary

We generated novel antibodies against the cancer cell marker LGR5, validated diagnostic use in prioritizing specific cancer types for targeting, and developed antibody-based therapeutics.
Rapid intralacustrine evolution of an invasive pelagic three-spined stickleback (Gasterosteus aculeatus) ecotype in Lake Constance
Authors: Dahms Carolin , Roch Samuel , Elmer Kathryn R. , Ros Albert , Brinker Alexander , Jacobs Arne
Published: September 2022

The rapid invasion of the pelagic zone in Lake Constance by three-spined sticklebacks (Gasterosteus aculeatus) since 2012 and their subsequent drastic population growth has had stark ecosystem-wide effects, such as food-web shifts and declines in native biodiversity, including commercially important fish species. Yet, the origin of this invasive pelagic ecotype remains unclear. This study aims to determine if the pelagic ecotype arosein situfrom the existing littoral population or following external colonisation, identify potential phenotypic differences between individuals from different habitats, and assess genomic signals of selection. Integrating RAD-sequencing of Lake Constance individuals and whole-genome sequence data for European outgroup populations, this study shows that the pelagic Lake Constance population likely arose recently within the lake from the littoral population, with only weak genome-wide differentiation between individuals from different habitats. This is further supported by minimal differences in meristic and morphometric traits, with shape differences only found between pelagic/inflow sticklebacks and littoral sticklebacks. Using genome scans, we identified multiple outlier loci between littoral and pelagic ecotypes across the genome, potentially suggesting early signs of sympatric speciation despite high connectivity. Furthermore, increased differentiation between pelagic and littoral sticklebacks for body shape-associated loci and the overlap of outlier loci with quantitative trait loci for ecologically relevant traits points toward a driving role of selection in this pelagic invasion. This study provides an important example of rapid ecological diversification from standing genetic variation and a rare case of littoral-pelagic ecotype divergence under high gene flow in a large oligotrophic lake. Ultimately, the results of this study will have major implications for the management of the invasive pelagic ecotype, and the entire stickleback population as a whole.
Human cellular model systems of β-thalassemia enable in-depth analysis of disease phenotype
Authors: Daniels Deborah E , Ferrer-Vicens Ivan , Hawksworth J , Andrienko Tatyana N , Finnie Elizabeth M , Ferguson Daniel C J , Oliveira A. Sofia F. , Szeto Jenn-Yeu A. , Wilson Marieangela C , Frayne Jan
Published: September 2022

β-thalassemia is a prevalent genetic disorder causing severe anemia due to defective erythropoiesis, with few treatment options. Studying the underlying molecular defects is impeded by paucity of suitable patient material. In this study we created human disease cellular model systems for β-thalassemia, which accurately recapitulate the phenotype of patient erythroid cells. We also developed a high throughput compatible fluorometric-based assay for evaluating severity of disease phenotype and utilised the assay to demonstrate positive response of lines to verified reagents, providing validation for such applications.

TMT-based comparative proteomics confirmed the same profile of proteins previously reported, whilst providing new insights into the altered molecular mechanisms in β-thalassemia erythroid cells, with upregulation of a wide range of biological pathways and processes observed.

Overall, the lines provide a sustainable supply of disease cells as novel research tools, for identifying new therapeutic targets, and as screening platforms for novel drugs and therapeutic reagents.