bluuebunny/crossref_metadata_2025 huggingface dataset:
CLINICAL, MOLECULAR, AND EXOSOMAL MECHANISMS OF CARDIAC AND BRAIN DYSFUNCTION IN SEPSIS
Authors: Morris Daniel C. , Zhang Zheng Gang , Jaehne Anja K. , Zhang Jing , Rivers Emanuel P.
Published: February 2023

Sepsis is a complex disease resulting from a dysregulated inflammatory response to an infection. Initiation of sepsis occurs from a localized infection that disseminates to the bloodstream placing all organ systems at risk. Septic shock is classically observed to manifest itself as systemic hypotension with hyporesponsiveness to vasopressor agents. Myocardial dysfunction occurs resulting in an inability to perfuse major organ systems throughout the body. Most importantly, the brain is hypoperfused creating an ischemic and inflammatory state resulting in the clinical observation of acute mental status changes and cognitive dysfunction commonly known as sepsis-associated encephalopathy. This short review describes the inflammatory molecular mechanisms of myocardial dysfunction, discusses the evidence of the dual roles of the microglia resulting in blood-brain barrier disruption, and suggests that septic-derived exosomes, endosome-derived lipid bilayer spheroids released from living cells, influence cardiac and neurological cellular function.
The Impact of the Patient Role on Medical Student Learning During Peer Simulation
Authors: Rudinsky Sherri L. , Weissbrod Elizabeth , Cole Rebekah
Published: February 2023

Introduction

Simulation-based learning is an effective approach to teaching and assessing medical students. However, there is a lack of research regarding how playing the patient role during peer simulation impacts medical student learning. This study, therefore, examines the experiences of first-year medical students in the patient role during a high-fidelity, multiday peer simulation.

Methods

Using a phenomenological approach to qualitative data analysis, we analyzed 175 student reflection papers assigned to the students at the conclusion of the peer simulation. Our research team individually coded each paper and then came to a consensus on themes and patterns within the data.

Results

We discovered the following 4 themes within the data: (1) communication, (2) empathy, (3) stress, and (4) professional identity. Through observation and peer simulation students learned the importance of team, patient, and nonverbal communication, especially during transitions of care. Next, the students recognized the importance of quality patient care and prioritizing the humanity of their future patients. The students also connected stress and mistakes, teaching them the importance of stress management. Finally, inspired by their peers and looking to their future selves, the students expressed a commitment to continued professional development.

Conclusions

The patient role during peer simulation is an impactful learning experience for first-year medical students. Our study holds important implications for ways in which medical educators can maximize the benefits of simulation-based education for junior medical student learning.
Prevalence and Risk Factors for Urinary Incontinence in Nulliparous Women: A Contemporary, Population-Based Cohort Study
Authors: Kupfer Nathalie , Clancy Aisling , Maguire Finlay , Stairs Jocelyn
Published: February 2023

Importance and Objectives

Epidemiologic studies of incontinence largely focus on parous women, and there are limited data regarding nulliparous women. Our objectives were to evaluate risk factors for urinary incontinence among a nationally representative, contemporary sample of nulliparous women of all ages in the United States and to describe the prevalence and subtypes of urinary incontinence and nocturia in this population.

Study Design

This cross-sectional, population-based study used the National Health and Nutrition Examination Survey cycles 2011–2018 to assemble a sample of nulliparous women 20–80 years old. Crude and adjusted odds ratios were estimated using multivariable logistic regression for the exposures of interest: body mass index (BMI), age, physical activity, prior hysterectomy, and current smoking. Prevalence of urinary incontinence and nocturia were estimated.

Results

Among 1,603 nulliparous women, prevalence of any urinary incontinence was 29.38%. Prevalence of stress, urgency, and mixed urinary incontinence and nocturia, respectively, were 27.68%, 19.64%, 10.57%, and 58.95%. Women with a BMI ≥25 (calculated as weight in kilograms divided by height in meters squared; adjusted odds ratio [aOR], 1.57; 95% confidence interval [CI], 1.11–2.23), at least 45 years (aOR, 3.75; 95% CI, 2.31–5.83), and current smoking (aOR, 1.63; 95% CI, 1.07–2.49) had increased the odds of incontinence compared with women without these risk factors. When stress urinary incontinence (SUI) was considered alone, only women with a BMI ≥25 (aOR, 1.66; 95% CI, 1.20–2.31) and age at least 45 years (aOR, 3.17; 95% CI, 2.01–5.00) had increased odds of SUI compared with women without these risk factors.

Conclusions

Urinary incontinence and nocturia are prevalent in nulliparous women, and age, elevated BMI, and current smoking may represent risk factors for incontinence in this population.
Aripiprazole Used to Treat Capgras Syndrome in an Adolescent Diagnosed With Autism
Authors: Baykal Saliha , Mutlu Caner
Published: February 2023

Objectives

This report discusses the emergence, clinical appearance, and treatment of the rare entity Capgras syndrome (CS) in an adolescent diagnosed with autism.

Methods

After a brief introduction to the CS, we conduct a detailed description of the case and review, after a search on the PubMed database, the known pathophysiology, psychiatric disorders associated with the onset of this syndrome, and the management of CS.

Results

Capgras syndrome generally emerges during the course of delusional disorder, schizophrenia, or mood disorders, and for reasons such as neurological, infectious, or endocrinological diseases, drug intoxications, or deprivation. We encountered no previous reports of CS developing during the course of autism. There are no prospective studies concerning the treatment of the syndrome. However, antipsychotic drug use is primarily recommended in treatment. Antipsychotic drug therapy was therefore planned for the treatment of delusion, a psychotic symptom, in this case. The atypical antipsychotic aripiprazole was used based on the presence of accompanying diagnosis of autism, and the patient's body mass index and age. A relatively high dose of aripiprazole was required for the first psychotic attack in our patient. However, a good level of response was achieved within the expected time frame. In addition, no marked adverse effects were observed.

Conclusions

Aripiprazole seems to be an effective and well-tolerated antipsychotic drug in the treatment of CS accompanying autism.
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes
Authors: Denise Rémi , Babor Jill , Gerlt John A. , de Crécy-Lagard Valérie
Published: February 2023

Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria

Escherichia coli

or

Bacillus subtilis

. Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.
Pre-diagnosis plasma cell-free DNA methylome profiling up to seven years prior to clinical detection reveals early signatures of breast cancer
Authors: Cheng Nicholas , Skead Kimberly , Singhawansa Althaf , Ouellette Tom W. , Elliott Mitchell , Cescon David W. , Bratman Scott V. , De Carvalho Daniel D. , Soave David , Awadalla Philip
Published: February 2023

Profiling of cell-free DNA (cfDNA) has been well demonstrated to be a potential non-invasive screening tool for early cancer detection. However, limited studies have investigated the detectability of cfDNA methylation markers that are predictive of cancers in asymptomatic individuals. We performed cfDNA methylation profiling using cell-free DNA methylation immunoprecipitation sequencing (cfMeDIP-Seq) in blood collected from individuals up to seven years before a breast cancer diagnosis in addition to matched cancer-free controls. We identified differentially methylated cfDNA signatures that discriminated cancer-free controls from pre-diagnosis breast cancer cases in a discovery cohort that is used to build a classification model. We show that predictive models built from pre-diagnosis cfDNA hypermethylated regions can accurately predict early breast cancers in an independent test set (AUC=0.930) and are generalizable to late-stage breast cancers cases at the time of diagnosis (AUC=0.912). Characterizing the top hypermethylated cfDNA regions revealed significant enrichment for hypermethylation in external bulk breast cancer tissues compared to peripheral blood leukocytes and breast normal tissues. Our findings demonstrate that cfDNA methylation markers predictive of breast cancers can be detected in blood among asymptomatic individuals up to six years prior to clinical detection.
Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after Fecal Microbiota Transplant in Inflammatory Bowel Disease
Authors: Zhang Yanjia Jason , Bousvaros Athos , Docktor Michael , Kaplan Abby , Rufo Paul A. , Leier McKenzie , Weatherly Madison , Zimmerman Lori , Tu Nguyen Le Thanh , Barton Brenda , Russell George , Alm Eric J. , Kahn Stacy A.
Published: February 2023

Background

Fecal Microbiota Transplant (FMT) has proven effective in treating recurrentClostridioides difficileinfection (rCDI) and has shown some success in treating inflammatory bowel diseases (IBD). There is emerging evidence that host engraftment of donor taxa is a tenet of successful FMT. However, there is little known regarding predictors of engraftment. We undertook a double-blind, randomized, placebo-controlled pilot study to characterize the response to FMT in children and young adults with mild to moderate active Crohn’s disease (CD) and ulcerative colitis (UC).

Results

Subjects with CD or UC were randomized to receive antibiotics and weekly FMT or placebo in addition to baseline medications. The treatment arm received seven days of antibiotics followed by FMT enema and then capsules weekly for seven weeks. We enrolled four subjects with CD and 11 with UC, ages 14-29 years. Due to weekly stool sampling, we were able to create a time series of alpha diversity, beta diversity and engraftment as they related to clinical response. Subjects exhibited a wide range of microbial diversity and donor engraftment as FMT progressed. Specifically, engraftment ranged from 26% to 90% at week 2 and 3% to 92% at two months. Consistent with the current literature, increases over time of both alpha diversity (p< 0.05) and donor engraftment (p< 0.05) correlated with improved clinical response. Additionally, our weekly time series enabled an investigation into the clinical and microbial correlates of engraftment at various time points. We discovered that the post-antibiotic but pre-FMT time point, often overlooked in FMT trials, was rich in microbial correlates of eventual engraftment. Greater residual alpha diversity after antibiotic treatment was positively correlated with engraftment and subsequent clinical response. Interestingly, a transient rise in the relative abundance of Lactobacillus was also positively correlated with engraftment, a finding that we recapitulated with our analysis of another FMT trial with publicly available weekly sequencing data.

Conclusions

We found that higher residual alpha diversity and Lactobacillus blooms after antibiotic treatment correlated with improved engraftment and clinical response to FMT. Future studies should closely examine the host microbial communities pre-FMT and the impact of antibiotic preconditioning on engraftment and response.
Assessment of human milk samples obtained pre- and post-influenza vaccination reveals a poor boosting of seasonally-relevant, hemagglutinin-specific antibodies
Authors: Yang Xiaoqi , DeCarlo Claire , Fox Alisa , Pineda Nicole , Powell Rebecca L.R.
Published: February 2023

Influenza (flu) vaccination prevented over 100,000 hospitalizations and 7000 deaths from flu over the 2019-2020 season in the USA [1]. Infants <6 months are the most likely to die from flu, though flu vaccines are only licensed for infants >6□months old. Therefore, it is recommended that flu vaccination occur during pregnancy, as this reduces severe complications; however, vaccination rates are suboptimal, and vaccination is also recommended postpartum [2-6]. For breast/chest-fed infants, the vaccine is believed to elicit protective and robust seasonally-specific milk antibody (Ab) [4, 7]. Few comprehensive studies exist examining Ab responses in milk after vaccination, with none measuring secretory Ab (sAb). Determining whether sAbs are elicited is critical, as this Ab class is highly stable in milk and mucosae [8, 9]. In the present study, our aim was to determine to what extent specific Ab titers in the milk of lactating people were boosted after seasonal influenza vaccination. Over the 2019-2020 and 2020-2021 seasons, milk was obtained pre- and post-vaccination and assessed for specific IgA, IgG, and sAb against relevant hemagglutinin (HA) antigens by a Luminex immunoassay. IgA and sAb were not found to be significantly boosted, while only IgG titers against B/Phuket/3073/2013, included in vaccines since 2015, exhibited an increase. Across the 7 immunogens examined, as many as 54% of samples exhibited no sAb boost. No significant differences for IgA, sAb, or IgG boosting were measured between seasonally-matched versus mismatched milk groups, indicating boosting was not seasonally-specific. No correlations between IgA and sAb increases were found for 6/8 HA antigens. No boost in IgG-or IgA-mediated neutralization post vaccination was observed. This study highlights the critical need to redesign influenza vaccines with the lactating population in mind, wherein the aim should be to elicit a potent seasonally-specific sAb response in milk. As such, this population must be included in clinical studies.
An Expert-guided Hierarchical Graph Attention Network for Post-traumatic Stress Disorder Highly-associative Genetic Biomarkers Identification
Authors: Zhang Qi , Han Yang , Lam Jacqueline CK , Bai Ruiqiao , Gozes Illana , Li Victor OK
Published: February 2023

Post-traumatic Stress Disorder (PTSD) is a common debilitating mental disorder, that occurs in some individuals following extremely traumatic events. Traditional identification of Genetic Markers (GM) for PTSD is mainly based on a statistical clinical approach by comparing PTSD patients with normal controls. However, these statistical studies present limitations, often generating inconsistent results. Few studies have yet examined thoroughly the role of somatic mutations, PTSD disease pathways and their relationships. Capitalizing on deep learning techniques, we have developed a novel hierarchical graph attention network to identify highly correlational GM (HGMs) of PTSD. The network presents the following novelties: First, both a hierarchical graph structure and a graph attention mechanism have been integrated into a model to develop a graph attention network (GAtN) model. Second, domain-specific knowledge, including somatic mutations, genes, PTSD pathways and their correlations have been incorporated into the graph structures. Third, 12 somatic mutations having high or moderate impacts on proteins or genes have been identified as the potential HGMs for PTSD. Fourth, our study is carefully guided by prominent PTSD literature or clinical experts of the field; any high saliency HGMs generated from our model are further verified by existing PTSD-related authoritative medical journals. Our study illustrates the utility and significance of a hybrid approach, integrating both AI and expert-guided/domain-specific knowledge for thorough identification of biomarkers of PTSD, while building on the nature of convergence and divergence of PTSD pathways. Our expert-guided AI-driven methodology can be extended to other pathological-based HGM identification studies; it will transform the methodology of biomarker identification for different life-threatening diseases to speed up the complex lengthy procedures of new biomarkers identification.
The emergence of SARS-CoV-2 lineages and associated antibody responses among asymptomatic individuals in a large university community
Authors: Merling Marlena R. , Williams Amanda , Mahfooz Najmus , Ruane-Foster Marisa , Smith Jacob , Jahnes Jeff , Ayers Leona W. , Bazan Jose A. , Norris Alison , Norris Turner Abigail , Oglesbee Michael , Faith Seth A. , Quam Mikkel B. , Robinson Richard T.
Published: February 2023

SARS-CoV-2 (CoV2) infected, asymptomatic individuals are an important contributor to COVID transmission. CoV2-specific immunoglobulin (Ig)—as generated by the immune system following infection or vaccination—has helped limit CoV2 transmission from asymptomatic individuals to susceptible populations (e.g. elderly). Here, we describe the relationships between COVID incidence and CoV2 lineage, viral load, saliva Ig levels (CoV2-specific IgM, IgA and IgG) and inhibitory capacity in asymptomatic individuals between Jan 2021 and May 2022. These data were generated as part of a large university COVID monitoring program and demonstrate that COVID incidence among asymptomatic individuals occurred in waves which mirrored those in surrounding regions, with saliva CoV2 viral loads becoming progressively higher in our community until vaccine mandates were established. Among the unvaccinated, infection with each CoV2 lineage (pre-Omicron) resulted in saliva Spike-specific IgM, IgA and IgG responses, the latter increasing significantly post-infection and being more pronounced than N-specific IgG responses. Vaccination resulted in significantly higher Spike-specific IgG levels compared to unvaccinated infected individuals, and uninfected vaccinees’ saliva was more capable of inhibiting Spike function. Vaccinees with breakthrough Delta infections had Spike-specific IgG levels comparable to those of uninfected vaccinees; however, their ability to inhibit Spike binding was diminished. These data demonstrate that COVID vaccines achieved hoped-for effects in our community, including the generation of mucosal antibodies that inhibit Spike and lower community viral loads, and suggest breakthrough Delta infections were not due to an absence of vaccine-elicited Ig, but instead limited Spike binding activity in the face of high community viral loads.
Does engagement in HIV care affect screening, diagnosis, and control of noncommunicable diseases in sub-Saharan Africa? A systematic review and meta-analysis
Authors: Kileel Emma M , Zheng Amy , Bor Jacob , Fox Matthew P , Crowther Nigel J , George Jaya A , Khoza Siyabonga , Rosen Sydney , Venter Willem DF , Raal Frederick , Hibberd Patricia , Brennan Alana T
Published: February 2023

Objective

Low- and middle-income countries are facing a growing burden of noncommunicable diseases (NCDs). Providing HIV treatment may also provide opportunities to increase access to NCD services in under-resourced environments. We sought to investigate whether reported use of antiretroviral therapy (ART) was associated with increased screening, diagnosis, treatment, and/or control of diabetes, hypertension, chronic kidney disease, or cardiovascular disease among people living with HIV (PLWH) in sub-Saharan Africa (SSA).

Design

Systematic review and meta-analysis.

Methods

We searched 10 electronic literature databases for studies published between 01 January 2011 and 31 December 2022 using a comprehensive search strategy. We sought studies reporting on screening, diagnosis, treatment, and/or control of NCDs of interest by ART use among non-pregnant adults with HIV>16 years of age in SSA. Random effects models were used to calculate summary odds ratios (ORs) of the risk of diagnosis by ART status and corresponding 95% confidence intervals (95% CIs), where appropriate.

Results

Twenty-six studies, describing 13,570 PLWH in SSA, 61% of whom were receiving ART, were included. ART use was associated with a small but imprecise increase in the odds of diabetes diagnosis (OR: 1.07; 95% CI: 0.71, 1.60) and an increase in the odds of hypertension diagnosis (OR: 2.10, 95% CI: 1.42, 3.09). We found minimal data on the association between ART use and screening, treatment, or control of NCDs.

Conclusion

Despite a potentially higher NCD risk among PLWH and regional efforts to integrate NCD and HIV care, evidence to support effective care integration models is lacking.
Association of Inflammation Biomarkers with Food Cravings and Appetite Changes Across the Menstrual Cycle
Authors: Agarwal Khushbu , Franks Alexis T. , Zhang Xuemin , Schisterman Enrique , Mumford Sunni L. , Joseph Paule V.
Published: February 2023

Background

Premenstrual symptoms, including food cravings, are often a regular complaint among menstruating women. However, existing evidence regarding the biological mechanisms by which these food cravings occur remains unclear. Inflammation may play an essential role in the occurence of these food cravings before menstruation.

Purpose

The purpose of the present study was to examine the associations between inflammatory markers and the risk of moderate/severe food cravings while accounting for changes in hormone levels and stress across the menstrual cycle.

Methods

The BioCycle Study followed women (n=259) aged 18-44 for two menstrual cycles. Food cravings (via questionnaire) were assessed up to four times per cycle. Each assessment corresponded to menses and mid-follicular, ovulation, and luteal phases of the menstrual cycle. A wide range of cytokine and chemokine levels (hsCRP, GCSF, GMCSF, IL-4, IL-6, RANTES, MIP1B, etc.) were assessed in blood samples collected at up to 8 visits per cycle, with visits timed using fertility monitors. Cravings for chocolate, sweets, salty, and other foods, and changes in appetite were determined to estimate the odds of moderate or severe cravings. Associations between inflammatory markers and risk of reporting a moderate/severe craving symptom at each cycle visit was determined using weighted generalized linear models (e.g., marginal structural models). Models were adjusted for age, BMI, and race, as well as time-varying covariates such as estradiol, stress, leptin, and total energy intake, and accounted for repeated measures (i.e., multiple cycles per woman). Both inflammatory markers and reports of cravings were modeled to account for variation at each visit.

Results

An association between higher inflammatory biomarkers such as hsCRP, GCSF, GMCSF, IL-4, IL-6, RANTES, MIP1B, and increased risk of moderate/severe cravings were identified across the menstrual cycle |all risk ratio>0.8, all CIs range>0.7-0.9|. hsCRP retained statistical significance after false discovery rate correction with chocolate, sweet, and salty cravings, while GCSF, GMCSF, IL-6, and RANTES retained significance with chocolate and sweet cravings only.

Conclusion

The results suggest a potential role of inflammation in food cravings and appetite changes across the menstrual cycle.
COVID-19 diagnostic testing underestimated cases amongst females in Pakistan
Authors: Ghanchi Najia Karim , Masood Kiran Iqbal , Nasir Asghar , Islam Nazneen , Ansar Zeeshan , Hasan Zahra
Published: February 2023

Objectives

Understanding the impact of COVID-19 largely depended on information from PCR based diagnostic testing of SARS-CoV-2. It was recognized early in the pandemic that testing rates varied greatly between high and low income countries. Whilst total numbers of tests conducted are noted, little attention has been made to differences that may be due to gender and we examined this in the context of Pakistan.

Methods

We conducted a retrospective cross-sectional analysis of respiratory specimens received for SARS-CoV-2 by PCR at Aga Khan University Hospital, Karachi, Pakistan between February 2020 and February 2022. Data was analysed in six monthly intervals; P-I, February to July 2020; P-II, August 2020 to January 2021; P-III, February to July 2021 and August 2021 until February 2022.

Results

A total of 470,047 PCR tests were conducted. The proportion of tests conducted for females was, 35% in P-I; 40% in P-II; 44% in P-III and 46% in P-III. 21% of specimens were positive for SARS-CoV-2, only 9% of these specimens were from females. The greatest numbers of tests were conducted in males aged 31 to 45 years followed by those aged 16-30 years. The fewest tests were conducted in children aged under 15 years. The highest percentage of PCR positive tests was found in those ages 60 years and above. Compared for gender SARS-CoV-2 positivity rates were comparable across the study period.

Conclusions

COVID-19 data from Pakistan indicates that there are larger numbers of males as compared with females who were affected by this disease. Our results show that this may be due to a gender bias in the demographics of testing. This was especially true in the early pandemic period, leading to under-surveillance and -reporting of COVID-19 cases in females especially, in those of younger and older age groups.

Strengths and limitations of this study

we stratified PCR testing based on gender and provide information on diagnostic trends

we found COVID-19 rates were comparable between females and males

Fewer samples from females were received particularly, in 2020 with an increase by 2022

it proposes the importance of examine the total samples tested in any case before drawing conclusions based on results of laboratory reports.

Limitations

This study was from one private healthcare system and cannot completely reflect nationwide trends to limited access to testing and also stigma related to the COVID-19.
DLK-dependent axonal mitochondrial fission drives degeneration following axotomy
Authors: Gómez-Deza Jorge , Nebiyou Matthew , Alkaslasi Mor R. , Nadal-Nicolás Francisco M. , Somasundaran Preethi , Slavutsky Anastasia L. , Ward Michael E. , Li Wei , Watkins Trent A. , Le Pichon Claire E.
Published: February 2023

Currently there are no effective treatments for an array of neurodegenerative disorders to a large part because cell-based models fail to recapitulate disease. Here we developed a reproducible human iPSC-based model where laser axotomy causes retrograde axon degeneration leading to neuronal cell death. Time-lapse confocal imaging revealed that damage triggers an apoptotic wave of mitochondrial fission proceeding from the site of injury to the soma. We demonstrated that this apoptotic wave is locally initiated in the axon by dual leucine zipper kinase (DLK). We found that mitochondrial fission and resultant cell death are entirely dependent on phosphorylation of dynamin related protein 1 (DRP1) downstream of DLK, revealing a new mechanism by which DLK can drive apoptosis. Importantly, we show that CRISPR mediatedDrp1depletion protected mouse retinal ganglion neurons from degeneration after optic nerve crush. Our results provide a powerful platform for studying degeneration of human neurons, pinpoint key early events in damage related neural death and new focus for therapeutic intervention.
Spatially resolved multiomics of human cardiac niches
Authors: Kanemaru Kazumasa , Cranley James , Muraro Daniele , Miranda Antonio M.A. , Pett Jan Patrick , Litvinukova Monika , Kumasaka Natsuhiko , Ho Siew Yen , Polanski Krzysztof , Richardson Laura , Mach Lukas , Dabrowska Monika , Richoz Nathan , Barnett Sam N. , Perera Shani , Wilbrey-Clark Anna , Talavera-López Carlos , Mulas Ilaria , Mahbubani Krishnaa T. , Bolt Liam , Mamanova Lira , Tuck Liz , Wang Lu , Huang Margaret M. , Prete Martin , Pritchard Sophie , Dark John , Saeb-Parsy Kourosh , Patel Minal , Clatworthy Menna R. , Hübner Norbert , Chowdhury Rasheda A. , Noseda Michela , Teichmann Sarah A.
Published: February 2023

A cell’s function is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here, we combine single-cell and spatial transcriptomic data to discover cellular niches within eight regions of the human heart. We map cells to micro-anatomic locations and integrate knowledge-based and unsupervised structural annotations. For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors, and cell interactions using a customCellPhoneDB.orgmodule. We show that the sinoatrial node is compartmentalised, with a core of pacemaker cells, fibroblasts and glial cells supporting paracrine glutamatergic signalling. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions, providing unexpected mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches which may contribute to infection defence. We define a ventricular myocardial-stress niche enriched for activated fibroblasts and stressed cardiomyocytes, cell states that are expanded in cardiomyopathies. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be deployed to other tissues and organs.
Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens
Authors: Attar Sahar , Browning Valentino E. , Liu Yuzhen , Nichols Eva K. , Tsue Ashley F. , Shechner David M. , Shendure Jay , Lieberman Joshua A. , Akilesh Shreeram , Beliveau Brian J.
Published: February 2023

In situhybridization (ISH) is a powerful tool for investigating the spatial arrangement of nucleic acid targets in fixed samples. ISH is typically visualized using fluorophores to allow high sensitivity and multiplexing or with colorimetric labels to facilitate co-visualization with histopathological stains. Both approaches benefit from signal amplification, which makes target detection effective, rapid, and compatible with a broad range of optical systems. Here, we introduce a unified technical platform, termed ‘pSABER’, for the amplification of ISH signals in cell and tissue systems. pSABER decorates thein situtarget with concatemeric binding sites for a horseradish peroxidase-conjugated oligonucleotide which can then catalyze the massive localized deposition of fluorescent or colorimetric substrates. We demonstrate that pSABER effectively labels DNA and RNA targets, works robustly in cultured cells and challenging formalin fixed paraffin embedded (FFPE) specimens. Furthermore, pSABER can achieve 25-fold signal amplification over conventional signal amplification by exchange reaction (SABER) and can be serially multiplexed using solution exchange. Therefore, by linking nucleic acid detection to robust signal amplification capable of diverse readouts, pSABER will have broad utility in research and clinical settings.
Spectral signatures of cross-modal attentional control in the adolescent brain and their link with physical activity and aerobic fitness levels
Authors: Hernández Doris , Kujala Jan , Heinilä Erkka , Ruotsalainen Ilona , Lapinkero Hanna-Maija , Syväoja Heidi , Parkkonen Lauri , Tammelin Tuija H. , Parviainen Tiina
Published: February 2023

Top–down attentional control seems to increase and suppress the activity of sensory cortices for relevant stimuli and to suppress activity for irrelevant ones. Higher physical activity (PA) and aerobic fitness (AF) levels have been associated with improved attention, but most studies have focused on unimodal tasks (e.g., visual stimuli only). The impact of higher PA or AF levels on the ability of developing brains to focus on certain stimuli while ignoring distractions remains unknown. The aim of this study was to examine the neural processes in visual and auditory sensory cortices during a cross-modal attention–allocation task using magnetoencephalography in 13–16-year-old adolescents (n= 51). During continuous and simultaneous visual (15 Hz) and auditory (40 Hz) noise-tagging stimulation, participants attended to either visual or auditory targets appearing on their left or right sides. High and low PA groups were formed based on seven-day accelerometer measurements, and high and low AF groups were determined based on the 20-m shuttle-run test. Steady-state (evoked) responses to the visual stimulus were observed in all the adolescents in the primary visual cortex, but some did not show responses in the primary auditory cortices to the auditory stimulus. The adolescents with auditory-tag-driven signals in the left temporal cortex were older than those who did not show responses. Visual cortices showed enhanced visual-tag-related activity with attention, but there was no cross-modal effect, perhaps due to the developmental effect observed in the temporal areas. The visual-tag-related responses in the occipital cortex were enhanced in the higher-PA group, irrespective of task demands. In summary, sensory cortices are unequally involved in cross-modal attention in the adolescent brain. This involvement seems to be enhanced by attention. Higher PA seems to be associated with a specific visual engagement benefit in the adolescent brain.

Highlights

- Visual and auditory cortices’ engagement differs in cross-modal processing in adolescence.

- Adolescents with responses in the left temporal cortex are older than those without responses.

- Physical activity, but not aerobic fitness, is associated with visual engagement benefits in the adolescent brain.
Production of antigenically stable enterovirus A71 virus-like particles inPichia pastorisas a vaccine candidate
Authors: Kingston Natalie J , Snowden Joseph S , Martyna Agnieszka , Shegdar Mona , Grehan Keith , Tedcastle Alison , Pegg Elaine , Fox Helen , Macadam Andrew J , Martin Javier , Hogle James M , Rowlands David J , Stonehouse Nicola J
Published: February 2023

Enterovirus A71 (EVA71) causes widespread disease in young children with occasional fatal consequences. In common with other picornaviruses, both empty capsids (ECs) and infectious virions are produced during the viral lifecycle. While initially antigenically indistinguishable from virions, ECs readily convert to an expanded conformation at moderate temperatures. In the closely related poliovirus, these conformational changes result in loss of antigenic sites required to elicit protective immune responses. Whether this is true for EVA71 remains to be determined and is the subject of this investigation.

We previously reported the selection of a thermally resistant EVA71 genogroup B2 population using successive rounds of heating and passage. The mutations found in the structural protein-coding region of the selected population conferred increased thermal stability to both virions and naturally produced ECs. Here, we introduced these mutations into a recombinant expression system to produce stabilised virus-like particles (VLPs) inPichia pastoris.

The stabilised VLPs retain the native virion-like antigenic conformation as determined by reactivity with a specific antibody. Structural studies suggest multiple potential mechanisms of antigenic stabilisation, however, unlike poliovirus, both native and expanded EVA71 particles elicited antibodies able to directly neutralise virusin vitro. Therefore, the anti-EVA71 neutralising antibodies are elicited by sites which are not canonically associated with the native conformation, but whether antigenic sites specific to the native conformation provide additional protective responsesin vivoremains unclear. VLPs are likely to provide cheaper and safer alternatives for vaccine production and these data show that VLP vaccines are comparable with inactivated virus vaccines at inducing neutralising antibodies.
ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes
Authors: Zhou Zhichao , Martin Cody , Kosmopoulos James C. , Anantharaman Karthik
Published: February 2023

Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate screening of viruses from enormous sequencing datasets originating from various environments. Though many tools and databases have been developed for advancing the study of viruses from metagenomes, there is a lack of integrated tools enabling a comprehensive workflow and analyses platform encompassing all the diverse segments of virus studies. Here, we developed ViWrap, a modular pipeline written in Python. ViWrap combines the power of multiple tools into a single platform to enable various steps of virus analysis including identification, annotation, genome binning, species- and genus-level clustering, assignment of taxonomy, prediction of hosts, characterization of genome quality, comprehensive summaries, and intuitive visualization of results. Overall, ViWrap enables a standardized and reproducible pipeline for both extensive and stringent characterization of viruses from metagenomes, viromes, and microbial genomes. Our approach has flexibility in using various options for diverse applications and scenarios, and its modular structure can be easily amended with additional functions as necessary. ViWrap is designed to be easily and widely used to study viruses in human and environmental systems. ViWrap is publicly available via GitHub (https://github.com/AnantharamanLab/ViWrap). A detailed description of the software, its usage, and interpretation of results can be found on the website.

Highlights

ViWrap integrates state-of-the-art tools and databases for comprehensive characterization and study of viruses from metagenomes and genomes.

ViWrap offers a highly flexible, modular, customizable, and easy-to-use pipeline with options for various applications and scenarios.

ViWrap enables a standardized and reproducible pipeline for viral metagenomics, genomics, ecology, and evolution.
Metabolomics reveals nucleoside analogs for regulating mucosal-associated invariant T cell responses
Authors: Huang Shouxiong , Sharma Manju , Sallans Larry , Li Chunshun , Kh Zaman , Choubey Divaker , Newburg David , Huaman Moises A. , Hansen Ted , Cao Shugeng
Published: February 2023

Although mucosal-associated invariant T (MAIT) cells recognize riboflavin-like metabolites from Gram-negative bacteria, MAIT cell stimulation by broad bacterial families and mammalian cells suggests the existence of novel ligands from different biological sources. Here we established a comparative platform of functional metabolomics and usedMycobacterium tuberculosisas a model to characterize novel metabolites for MAIT cell activation. We extracted and fractionated small metabolites ofM. tuberculosisusing high-performance liquid chromatography, showing a different MAIT cell stimulation pattern ofM. tuberculosismetabolite fractions in comparison withEscherichia colifractions. Mass profiling predicted multiple nucleoside analogs enriched in a biologically active fraction ofM. tuberculosis. Whereas the synthetic forms of these predictedM. tuberculosisnucleosides were unavailable, structural-based autodocking of analogous nucleosides conserved in mammals supported potential binding with MR1 protein. Indeed, functional assays of these conserved nucleosides demonstrated guanosine as a stimulator and deoxyformyluridine as an inhibitor of MAIT cell activation. Identification of bioactive nucleoside metabolites broadly conserved in bacterial and mammalian systems will facilitate an understanding of the regulatory roles of MAIT cells in infectious and inflammatory conditions.
Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases
Authors: Funabiki Hironori , Wassing Isabel E. , Jia Qingyuan , Luo Ji-Dung , Carroll Thomas
Published: February 2023

5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and thede novoDNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
Diagnostic performance of host protein signatures as a triage test for active pulmonary TB
Authors: Koeppel Lisa , Denkinger Claudia M , Wyss Romain , Broger Tobias , Chegou Novel N , Dunty Jill M , Scott Kerry , Cáceres Tatiana , Dutoit Elloise , Ugarte-Gil Cesar , Nicol Mark , Gotuzzo Eduardo , Corstjens Paul L A M , Geluk Annemieke , Sigal George B , Moreau Emmanuel , Albertini Audrey , Mantsoki Anna , Ongarello Stefano , Walzl Gerhard , Fernandez Suarez Marta
Published: February 2023

The current four symptom screen recommended by the WHO is widely used as screen to initiate diagnostic testing for active pulmonary tuberculosis (TB), yet the performance is poor especially when TB prevalence is low. In contrast, more sensitive molecular tests are less suitable for the placement at primary care level in low resource settings. In order to meet the WHO End TB targets new diagnostic approaches are urgently needed to find the missing undiagnosed cases. Proteomics-derived blood host biomarkers have been explored because protein detection technologies are suitable for the point-of-care setting and could meet cost targets.

This study aims to find a biomarker signature that fulfills WHO’s target product profile (TPP) for a TB screening. 12 blood-based protein biomarkers from three sample populations (Vietnam, Peru, South Africa) are analyzed individually and in combinations via advanced statistical methods and machine learning algorithms. The combination of I-309, SYWC and kallistatin shows the most promising results for TB prediction throughout the datasets meeting the TPP for a triage test in adults from two countries (Peru and South Africa). The top performing individual markers identified at the global level (I-309 and SYWC) were also among the best performing markers at country level in South Africa and Vietnam.

This analysis clearly shows that a host protein biomarker assay is feasible in adults for certain geographical regions based on one or two biomarkers with a performance that meets minimal WHO TPP criteria.

Abstract Importance

Tuberculosis (TB) remains a serious worldwide health problem and diagnosis is hampered by the complexity of tests at primary care level in low resource settings or the low accuracy for screening settings. In order to meet the WHO End TB targets new diagnostic approaches are urgently needed to find the missing undiagnosed cases.

This analysis clearly shows that a host protein biomarker assay is feasible in adults for certain geographical regions. We were able to construct an algorithm through statistical methods and machine learning algorithms whose performance meets the minimum of the WHO target product profile criteria. Thus, further work should be addressed at demonstrating that such as assay can be translated into a practical point-of-care test, and to better understand how to address regional differences in biomarker levels and responses.