bluuebunny/crossref_metadata_2025 huggingface dataset:
Silent progressive bilateral papillitis after COVID-19 vaccination: A case report
Authors: Lee Geun Woo , Park Hyeong Seok , Lee Donghun
Published: October 2022

Rationale:

We report the case of a patient who developed asymptomatic bilateral papillitis after coronavirus disease 2019 (COVID-19) vaccination.

Patient concerns:

A 61-year-old man presented to our tertiary clinic with bilateral optic disc edema, which was incidentally detected during his visit to a primary ophthalmology clinic. He had received an adenovirus-vectored COVID-19 vaccine 2 weeks before the optic disc edema was detected and had experienced no ocular discomfort, except for a floater in his right eye. Although his visual acuity was normal and he had no color vision deficiencies or marked visual field defects, the optic disc edema worsened over several days. Orbital magnetic resonance imaging showed no optic tract enhancement, and lumbar puncture revealed normal cerebrospinal fluid pressure. The patient tested negative for aquaporin-4 and myelin oligodendrocyte glycoprotein antibodies and Leber hereditary optic neuropathy-associated gene mutations.

Diagnosis:

The patient was diagnosed with bilateral papillitis, possibly induced by the COVID-19 vaccination.

Interventions:

The patient received steroid pulse therapy with methylprednisolone (500 mg/day) for 3 days followed by an oral prednisolone taper for 3 weeks.

Outcomes:

The patient’s papillitis started to subside 3 weeks after he received systemic steroid therapy and completely resolved without any sequelae 2 months later. A year after the diagnosis, the fundus remained stable without disease recurrence or optic disc atrophy.

Lessons:

Healthy individuals receiving COVID-19 vaccines may present with various manifestations of optic neuritis. In the present case, the patient presented with asymptomatic progressive bilateral optic disc edema and had a favorable long-term course after receiving steroid therapy.
Increased incidence of dementia following herpesvirus infection in the Korean population
Authors: Shim YongSoo , Park Minae , Kim JaeYoung
Published: October 2022

Herpesviruses affect the development of dementia. We investigated the association between herpes infection and subsequent diagnoses of dementia. Data from the National Health Insurance Service of South Korea were used. Patients aged ≥50 years with the relevant diagnostic codes in the reference year 2009 were included and prospectively reviewed from January 2010 to December 2018. All study participants were followed from the index date until the onset of dementia, death, or the study endpoint. The three cohorts comprised 92,095 patients with herpes simplex virus (HSV) infections, 97,323 patients with varicella-zoster virus (VZV) infections, and 183,779 controls. During the follow-up period, 15,831 (17.19%) subjects with HSV infection and 17,082 (17.55%) VZV-infected subjects, compared to 27,028 (14.17%) control subjects, were subsequently diagnosed with dementia (all, P < .001). The adjusted hazard ratio for developing dementia was found to be 1.18 (95% confidence interval [CI]; 1.16–1.20) in HSV and 1.09 (95% CI; 1.07–1.11) in VZV patients (all, P < .001). HSV1 infections such as oral or ocular subtypes, but not HSV2, anogenital subtype, were associated with dementia, including several subtypes such as Alzheimer’s disease (AD), vascular dementia, and dementia with Lewy bodies. VZV infection is also associated with AD. In this Korean nationwide population-based cohort study, both HSV and VZV infections were associated with a higher risk of dementia, particularly AD. Among the subtypes of HSV infection, HSV1 is associated with a risk of dementia. Further studies including appropriate public health interventions could evaluate the causality of these relationships.
Assessing the psychological impact of Beirut Port blast: A cross-sectional study
Authors: Al Hariri Moustafa , Zgheib Hady , Abi Chebl Karen , Azar Maria , Hitti Eveline , Bizri Maya , Rizk Jennifer , Kobeissy Firas , Mufarrij Afif
Published: October 2022

Beirut Port blast’s magnitude is considered the third after Hiroshima and Nagasaki atomic bombings. This blast occurred in the densely populated section of Beirut, leaving more than six thousand injured patients. The psychological disturbances were assessed in the blast survivors who presented to the Emergency Department (ED) at the American University of Beirut Medical Center (AUBMC). This was a cross-sectional study at the ED of AUBMC. Identified patients were contacted and consented to participate in the study. Post-Traumatic Stress Disorder (PTSD) was selected as an outcome. Depression, PTSD, and concussion were assessed using patient health questionnaire (PHQ)-9, PTSD checklist for DSM-5 (PCL5), and brain injury symptoms (BISx) tools, respectively. The association of patients and injury characteristics with the study outcome was assessed using logistic regression. 145 participants completed the study procedures. The participants’ average age was 39.8 ± 15.4 years, and 60% were males. Almost half of the participants showed depression on PHQ, and 2-thirds had PTSD. The participant’s age was negatively associated with PTSD, whereas being a female, having depression, and having a concussion were positively associated with PTSD. The results of this study were in line with the previous literature report except for the association between younger age and PTSD, which warrants further investigations to delineate the reasons.
Regional gastrointestinal transit times in patients with chronic pancreatitis
Authors: Larsen Isabelle M. , Holten-Rossing Sidse , Mark Esben Bolvig , Poulsen Jakob Lykke , Krogh Klaus , Scott S. Mark , Olesen Søren Schou , Drewes Asbjørn Mohr
Published: October 2022

The mechanisms behind disrupted gastrointestinal (GI) motor function in patients with chronic pancreatitis (CP) have not been fully elucidated. We compared regional transit times in patients with CP to those in healthy controls, and investigated whether they were associated with diabetes mellitus, exocrine dysfunction, opioid treatment or quality of life. Twenty-eight patients with CP and 28 age- and gender-matched healthy controls were included. Regional GI transit times were determined using the 3D-Transit system, which consists of an ingestible electromagnetic capsule and a detector worn in an abdominal belt for 5 days. Exocrine function was assessed using the fecal elastase-1 test, and quality of life was assessed using the European Organization for Research and Treatment of Cancer questionnaire. Transit times were analyzed for associations with diabetes mellitus, exocrine pancreatic insufficiency (EPI), opioid treatment and quality of life. Compared with healthy controls, patients with CP had prolonged transit times in the small intestine (6.6 ± 1.8 vs 4.8 ± 2.2 hours, P = .006), colon (40 ± 23 vs 28 ± 26 hours, P = .02), and total GI tract (52 ± 26 vs 36 ± 26 hours, P = .02). There was no difference in gastric emptying time (4.8 ± 5.2 vs 3.1 ± 1.3 hours, P = .9). No associations between transit times and diabetes, EPI, or opioid consumption were found (all P > .05). Quality of life and associated functional and symptom subscales were not associated with transit times, except for diarrhea (P = .03). Patients with CP have prolonged small intestinal and colonic transit times. However, these alterations do not seem to be mediated by diabetes, EPI, or opioid consumption.
High expression of PYK2 is associated with poor prognosis and cancer progression in early-stage cervical carcinoma
Authors: Zhang Can , Zhu Xinghua , Li Yong , Shao Jia , Xu Haibo , Chen Lei , Dan Youli , Jin Hua , He Aiqin
Published: October 2022

Proline-rich tyrosine kinase-2 (PYK2), also known as calcium dependent tyrosine kinase, regulates different signal transduction cascades that control cell proliferation, migration, and invasion. However, the role of PYK2 in cervical cancer remains to be elucidated. The current study retrospectively included 134 patients with cervical cancer from December 2007 to September 2014. PYK2 expression was detected in tissue microarray and cervical cancer cell lines. Statistical analysis was performed to evaluate its clinicopathological significance. Small interfering RNA (siRNA) was employed to suppress endogenous PYK2 expression in cervical cancer cells to observe the biological function. PYK2 expression was up-regulated in cervical cancer specimens compared with paired adjacent normal cervical tissue samples. Statistical analyses indicated that PYK2 expression might be an independent prognostic indicator for patients with early-stage cervical cancer. A nomogram model was constructed based on PYK2 expression and other clinicopathological risk factors, and it performed well in predicting patients survival. In cellular studies, down-regulation of PYK2 remarkably inhibited cellular proliferation, migration and invasion. PYK2 expression possessed the potential to serve as a novel prognostic marker in cervical cancer patients.
Factors related to Japanese nurses’ desire to quit their jobs during the COVID-19 pandemic: A cross-sectional study
Authors: Nakai Hisao , Kitamura Yoshiko , Teranishi Keiko
Published: October 2022

The purpose of this study was to investigate the factors related to Japanese nurses’ desire to quit their jobs during the Omicron wave of the coronavirus disease 2019 pandemic. We distributed an original, self-administered questionnaire to nurses at 3 facilities that accepted patients with coronavirus disease 2019 in Ishikawa Prefecture, Japan. Of the 625 nurses, 152 responded (24.3%); after excluding 3 men to rule out the effects of sex, responses for 81 (53.3%) nurses were analyzed. In total, 49 (60.5%) nurses expressed a desire to quit their current job. After controlling for the effects of age and years of experience, factors related to the desire to quit the current job included having fewer than 2 years of experience (odds ratio [OR] 9.08, 95% confidence interval [CI] 1.69–48.87), feeling anxiety at work (OR 4.59, 95% CI 1.01–20.81), being afraid to go to work (OR 4.10, 95% CI 1.20–21.69), and experiencing difficulty talking to people (OR 10.26, 95% CI 1.48–70.99). Nurse managers should regularly screen nurses who have fewer than 2 years of experience, feel anxiety at work, are afraid to go to work, and find it difficult to talk to people. Early action may prevent the turnover of nurses during a public health emergency.
Mediterranean Diet and Prevention of Cardiovascular Disease
Authors: García-Pérez-de-Sevilla Guillermo , Sánchez-Pinto Pinto Beatriz
Published: October 2022

The adherence to the Mediterranean diet involves a relatively large intake of monounsaturated and polyunsaturated fatty acids, antioxidants, fiber, and potassium, and a low intake of saturated fat and sodium. It seems to be associated with decreased blood pressure, improved lipid profile, less inflammation, better endothelial function, and, therefore, a reduction in cardiovascular risk. To achieve these goals, the Mediterranean plan involves eating 3 servings of fish or shellfish a week, 2 servings of vegetables a day, 3 servings of fruit a day, and 90 g of nuts per week, and using olive oil as the main culinary fat. In addition, the consumption of red meat, salt, sweet and pastries, sweet beverages, and butter should be limited. It is advisable to evaluate adherence to the Mediterranean diet of the patients using the Mediterranean Diet Adherence Screener (MEDAS) questionnaire, considering an optimal adherence score equal to or higher than 10, to give proper advice.
From Darkness Into…Darkness
Authors: Rowe Sylvia , Alexander Nick
Published: October 2022

The last 2 years have wrought profound changes in the science communication landscape, especially as it concerns health and related issues. In 2 previous articles, the present authors have analyzed risk and crisis communication in the COVID-19 environment—what mistakes may have been made and how communicators can improve message dissemination in future crisis situations. However, the effects of the past 2 years on current science communication do not end there. The recent enhanced focus on social media's possible role in spreading not only misinformation or disinformation but also actual harmful assaultive messaging has raised the communication stakes significantly. Given increasing public claims of widespread censorship and complaints about efforts to “manage” robust expression of both scientific and other ideas, communicators face unprecedented new challenges in their work. The present article offers perspective on the current state of affairs in health and science communications in historical context. The authors offer their guidance for delivering trustworthy information transparently.
Prescription of Steroids in General Pediatric Intensive Care Patients—A Two-Center Retrospective Observational Study
Authors: Mitting Rebecca , Fitchett Elizabeth J. A. , Peters Mark J. , Ray Samiran
Published: October 2022

OBJECTIVES:

Designing randomized trials to determine utility, dose, and timing of steroid administration in the management of critically unwell children may be difficult owing to a high proportion of patients who receive steroid as part of current care. We aimed to describe steroid use among all patients on two general PICUs.

DESIGN:

Retrospective observational study using a multilevel logistic regression model.

SETTING:

Two tertiary, general mixed medical and surgical PICUs.

PATIENTS:

All admissions between 2016 and 2019. All parenteral or enteral steroid prescriptions were identified, and steroid type, frequency, timing, and peak daily doses were recorded. The outcome measure was mortality prior to PICU discharge.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

There were 5,483 admissions during the study period, and 1,804 (33%) of these involved prescription of at least one steroid. Among patients prescribed steroids, the median peak daily dose when steroids were prescribed was 2.4 mg/kg/d prednisolone equivalent (interquartile range, 1.6–3.6), and the median time to peak steroid doses was 2 days (1–5 d). Administration of steroid was associated with increased risk-adjusted mortality odds ratio (OR) of 1.37 (95% CI, 1.04–1.79). Steroids were prescribed in 42.3% of admissions, in which the child did not survive to PICU discharge. Among children who were prescribed steroids, use of hydrocortisone (OR, 6.75; 95% CI, 3.79–12.27) and methylprednisolone (OR, 7.85; 95% CI, 4.21–14.56), or starting steroids later than 2 days after PICU admission were associated with an increased mortality (OR, 1.93; 95% CI, 1.15–3.25).

CONCLUSIONS:

Steroids are widely used in pediatric critical illness and nonsurvival associated with increased frequency of use. This association appears to be related to steroid class and timing of dose, both likely to reflect indication for steroid prescription. Prospective trials are required to estimate these complex risks and benefits, and study design will need to consider these patterns.
Sporadic Cerebellar Hemangioblastoma With Strong SSTR Expression on 68Ga-DOTANOC PET/CT
Authors: Dev Indraja D. , Rangarajan Venkatesh , Puranik Ameya D. , Agrawal Archi , Shah Sneha , Sahay Ayushi , Purandare Nilendu C.
Published: October 2022

Sporadic cerebellar hemangioblastomas are rare with majority of these tumors presenting as a part of von Hippel–Lindau syndrome. We demonstrate an unusual case of a symptomatic sporadic cerebellar hemangioblastoma mimicking a meningioma on MRI and 68Ga-DOTANOC PET imaging.
The Role of Dynamic DNA Methylation in Liver Transplant Rejection in Children
Authors: Ningappa Mylarappa , Shao Xiaojian , Ashokkumar Chethan , Xu Qingyong , Zeevi Adriana , Grundberg Elin , Pastinen Tomi , Sindhi Rakesh
Published: October 2022

Background.

Transcriptional regulation of liver transplant (LT) rejection may reveal novel predictive and therapeutic targets. The purpose of this article is to test the role of differential DNA methylation in children with biopsy-proven acute cellular rejection after LT.

Methods.

Paired peripheral blood DNA samples were obtained before and after LT from 17 children, including 4 rejectors (Rs) and 13 nonrejectors (NRs), and assayed with MethylC capture sequencing approach covering 5 million CpGs in immune-cell–specific regulatory elements. Differentially methylated CpGs (DMCs) were identified using generalized linear regression models adjusting for sex and age and merged into differentially methylated regions (DMRs) comprising 3 or more DMCs.

Results.

Contrasting Rs versus NRs, we identified 2238 DMCs in post-LT and 2620 DMCs in pre-LT samples, which clustered in 216 and 282 DMRs, respectively. DMCs associated with R were enriched in enhancers and depleted in promoters. Among DMRs, the proportion of hypomethylated DMRs increased from 61/282 (22%) in pre-LT to 103/216 (48%, P < 0.0001) in post-LT samples. The highest-ranked biological processes enriched in post-LT DMCs were antigen processing and presentation via major histocompatibility complex (MHC) class I, MHC class I complex, and peptide binding (P < 7.92 × 10−17), respectively. Top-ranked DMRs mapped to genes that mediate B-cell receptor signaling (ADAP1) or regulate several immune cells (ARRB2) (P < 3.75 × 10−08). DMRs in MHC class I genes were enriched for single nucleotide polymorphisms (SNPs), which bind transcription factors, affect gene expression and splicing, or alter peptide-binding amino acid sequences.

Conclusions.

Dynamic methylation in distal regulatory regions reveals known transplant-relevant MHC-dependent rejection pathways and identifies novel loci for future mechanistic evaluations in pediatric transplant subcohorts.
The big six: key principles for effective use of Behavior substitution in interventions to de-implement low-value care
Authors: Patey Andrea M. , Grimshaw Jeremy M. , Francis Jill J.
Published: October 2022

Healthcare professionals provide care to help patients; however, sometimes that care is of low value – at best ineffective and at worst harmful. To address this, recent frameworks provide guidance for developing and investigating de-implementation interventions; yet little attention has been devoted to identifying what strategies are most effective for de-implementation. In this paper, we discuss Behavior substitution, a strategy whereby an unwanted behavior is replaced with a wanted behavior, thereby making it hypothetically easier to reduce or stop the unwanted behavior. We discuss why Behavior substitution may be a useful de-implementation strategy, and why it may not be suitable for all circumstances. On the basis of the body of knowledge in behavioral science, we propose a list of principles to consider when selecting a substitute behavior for a de-implementation intervention. Applying these principles should increase the likelihood that this technique will be effective in reducing low-value care.
Improving HIV Pre Exposure Prophylaxis (PrEP) uptake and initiation: process evaluation and recommendation development from a national PrEP programme
Authors: Estcourt Claudia S , MacDonald Jen , Saunders John , Nandwani Rak , Young Ingrid , Frankis Jamie , Clutterbuck Dan , Steedman Nicola , McDaid Lisa , Dalrymple Jenny , Flowers Paul
Published: October 2022

Background

HIV pre-exposure prophylaxis (PrEP) is key to HIV transmission elimination but implementation is challenging and under-researched. We undertook a process evaluation of the first two years of a national PrEP programme to explore barriers and facilitators to implementation and to develop recommendations to improve implementation, focussing on PrEP uptake and initiation.

Methods

Stage 1 involved semi-structured telephone interviews and focus groups (09/2018-07/2019) with geographically and demographically diverse patients seeking/using/declining/stopping PrEP (n=39), sexual healthcare professionals (n= 54), community-based organisation service users (n=9) and staff (n=15) across Scotland. We used deductive thematic analysis, to derive and then map key barriers and facilitators to priority areas that experts agreed would enhance initiation and uptake. In Stage 2 we used analytic tools from implementation science to systematically generate evidence-based, theoretically-informed recommendations to enhance uptake and initiation of PrEP.

Results

Barriers and facilitators were multi-levelled and interdependent. Barriers included the rapid pace of implementation without additional resource, and a lack of familiarity with PrEP prescribing. Facilitators included opportunities for acquisition of practice-based knowledge and normalisation of initiation activities. We refined our 68 “long-list” recommendations to 41 using expert input and the APEASE criteria. Examples include: provision of PrEP in diverse settings to reach all in need; co-produced, culturally sensitive training resources for healthcare professionals, with focused content on non-daily dosing; meaningful collaborative working across all stakeholders.

Conclusions

These evidence-based, theory informed recommendations provide a robust framework for optimising PrEP uptake and initiation in diverse settings to ensure PrEP reaches all who may benefit.

Summary for table of contents

Zero new HIV infections could become a reality if HIV pre-exposure prophylaxis (PrEP) programmes are successfully implemented but the World Health Organisation recognizes that large scale roll out is challenging.

We used implementation science research tools in novel ways to evaluate one of the world’s first national PrEP programmes, to develop evidence-based recommendations for use across a range of settings to improve PrEP uptake and initiation.

Adopting these recommendations could enable governments and societies to better address HIV prevention goals.
Understanding mental health trends during COVID-19 pandemic in the United States using network analysis
Authors: Kobayashi Hiroko , Saenz-Escarcega Raul , Fulk Alexander , Agusto Folashade B.
Published: October 2022

The emergence of COVID-19 in the United States resulted in a series of federal and state-level lock-downs and COVID-19 related health mandates to manage the spread of the virus. These policies may negatively impact the mental health state of the population. This study focused on the trends in mental health indicators following the COVID-19 pandemic amongst four United States geographical regions, and political party preferences. Indicators of interest included feeling anxious, feeling depressed, and worried about finances. Survey data from Delphi Group in Carnegie Mellon University were analyzed using clustering algorithms and dynamic connectome obtained from sliding window analysis. United States maps were generated to observe spatial trends and identify communities with similar mental health and COVID-19 trends. Between March 3rd, 2021 and January 10th, 2022, states in the south geographic region showed similar trends for reported values of feeling anxious and worried about finances. There were no identifiable communities resembling geographical regions or political party affiliation for the feeling depressed indicator. We observed a high degree of correlation among southern states as well as within republican states, where the highest correlation values from the dynamic connectome analysis for feeling anxious and feeling depressed variables seemingly overlapped with an increase in COVID-19 related cases, deaths, hospitalizations, and rapid spread of the COVID-19 Delta variant.
A neural mechanism underlying predictive visual motion processing in patients with schizophrenia
Authors: Scheliga Sebastian , Schwank Rosalie , Scholle Ruben , Habel Ute , Kellermann Thilo
Published: October 2022

Psychotic symptoms may be traced back to sensory sensitivity. Thereby, visual motion (VM) processing particularly has been suggested to be impaired in schizophrenia (SCZ). In healthy brains, VM underlies predictive processing within hierarchically structured systems. However, less is known about predictive VM processing in SCZ. Therefore, we performed fMRI during a VM paradigm with three conditions of varying predictability, i.e., predictable-, random-, and arbitrary motion. The study sample comprised 17 SCZ patients and 23 healthy controls. We calculated general linear model (GLM) analysis to assess group differences in VM processing across motion conditions. Here, we identified significantly lower activity in right temporoparietal junction (TPJ) for SCZ patients. Therefore, right TPJ was set as seed for connectivity analyses. For patients, across conditions we identified increased connections to higher regions, namely medial prefrontal cortex, or paracingulate gyrus. Healthy subjects activated sensory regions as area V5, or superior parietal lobule. Since TPJ operates as hub modulating network shifts, aberrant functional connectivity with higher structures may thus reflect a compensatory mechanism co-occurring to impaired TPJ activity in SCZ. In sum, these altered neural patterns provide a framework for future studies focusing on predictive VM processing to identify potential biomarkers of psychosis.
Effect of behavioral conditions on silk characteristics in the Indian meal moth (Plodia interpunctella)
Authors: Barve Toshita V. , Godfrey R. Keating , Storer Caroline G. , Kawahara Akito Y.
Published: October 2022

Lepidopteran silks are produced during the larval stage and are used for mobility and protection from predators, parasitoids, and pathogens. Our knowledge of silk structure and production in Lepidoptera is based largely on the biology of the domestic silk moth (Bombyx mori), but recent comparative evidence suggests that silk production and structure vary widely across moth taxa. Some species like the Indian meal moth (Plodia interpunctella) are becoming important biological models to study silk for its potential application to materials science and medicine, but many aspects of silk production in this species remain unknown. Here we characterize the silk ofP. interpunctellaby measuring the width of wandering and pupal silk strands and find that pupal silk is significantly thicker than the latter. We then report individual variation in pupal silk production in our lab-reared colony with a very small number of individuals forgoing pupal silk (< 4%) and find that overcrowding had no effect on this, whereas exposure to elevated temperatures reduced rates of pupal silk production.
Data Descriptor: Human whole exome genotype data for Alzheimer’s Disease
Authors: Leung Yuk Yee , Naj Adam C , Chou Yi-Fan , Valladares Otto , Wheeler Nicholas , Lin Honghuang , Gangadharan Prabhakaran , Qu Liming , Clark Kaylyn , Cantwell Laura , Issen Heather ,   the Alzheimer’s Disease Sequencing Project, Seshadri Sudha , Brkanac Zoran , Cruchaga Carlos , Pericak-Vance Margaret , Mayeux Richard P. , Kuzma Amanda B , Lee Wan-Ping , Bush William S. , Destefano Anita , Martin Eden , Schellenberg Gerard D. , Wang Li-San
Published: October 2022

Bigger sample size can help to identify new genetic variants contributing to an increased risk of developing Alzheimer’s disease. However, the heterogeneity of the whole-exome sequencing (WES) data generation methods presents a challenge to a joint analysis. Here we present a bioinformatics strategy for joint calling 20,504 WES samples collected across nine studies and sequenced using ten different capture kits in fourteen sequencing centers in the Alzheimer’s Disease Sequencing Project. gVCFs of samples were joint-called by the Genome Center for Alzheimer’s Disease into a single VCF, containing only positions within the union of capture kits. The VCF was then processed using specific strategies to account for the batch effects arising from the use of different capture kits from different studies.

We identified 8.2 million autosomal variants. 96.82% of the variants are high-quality, and are located in 28,579 Ensembl transcripts. 41% of the variants are intronic and 15% are missense variants. 1.8% of the variants are with CADD>30.

Our new strategy for processing these diversely generated WES samples has shown to generate high-quality data. The improved ability to combine data sequenced in different batches benefits the whole genomics research community. The WES data are accessible to the scientific community viahttps://dss.niagads.org/.
Fully Automated Point Spread Function Analysis Using Pycalibrate
Authors: Metz J , Gintoli M , Corbett AD
Published: October 2022

Reproducibility is severely limited if instrument performance is assumed rather than measured. Within optical microscopy, instrument performance is typically measured using sub-resolution fluorescent beads. However, the process is performed infrequently as it is requires time and suitably trained staff to acquire and then process the bead images. Analysis software still requires the manual entry of imaging parameters. Human error from repeatedly typing these parameters can significantly affect the outcome of the analysis, rendering the results less reproducibile. To avoid this issue, PyCalibrate has been developed to fully automate the analysis of bead images. PyCalibrate can be accessed either by executing the Python code locally or via a user-friendly web portal to further improve accessibility when moving between locations and machines. PyCalibrate interfaces with the BioFormats library to make it compatible with a wide range of proprietary image formats. In this study, PyCalibrate analysis performance is directly compared with alternative free-access analysis software PSFj, MetroloJ QC and DayBook3 and is demonstrated to have equivalent performance but without the need for user supervision.
Immune-modulatory effects of low dose γ-radiation on wax moth (Galleria mellonella) larvae
Authors: Copplestone David , Coates Christopher J , Lim Jenson
Published: October 2022

Larvae of the greater wax mothGalleria mellonellaare common pests of beehives and commercial apiaries, and in more applied settings, these insects act as alternativein vivobioassays to rodents for studying microbial virulence, antibiotic development, and toxicology. In the current study, our overall aim was to assess the putative adverse effects of background gamma radiation levels onG. mellonella. To achieve this, we exposed larvae to low (0.014 mGy/h), medium (0.056 mGy/h), and high (1.33 mGy/h) doses of caesium-137 and measured larval pupation events, weight, faecal discharge, susceptibility to bacterial and fungal challenges, immune cell counts, activity, and viability (i.e., haemocyte encapsulation) and melanisation levels. The effects of low and medium levels of radiation were distinguishable from the highest dose rates used – the latter insects weighed the least and pupated earlier. In general, radiation exposure modulated cellular and humoral immunity over time, with larvae showing heighted encapsulation/melanisation levels at the higher dose rates but were more susceptible to bacterial (Photorhabdus luminescens) infection. There were few signs of radiation impacts after 7 days exposure, whereas marked changes were recorded between 14 and 28 days. Our data suggest thatG. mellonellademonstrates plasticity at the whole organism and cellular levels when irradiated and offers insight into how such animals may cope in radiologically contaminated environments.
Dynamic map illuminates Hippo to cMyc module crosstalk driving cardiomyocyte proliferation
Authors: Harris Bryana N. , Woo Laura A. , Perry R. Noah , Civelek Mete , Wolf Matthew J. , Saucerman Jeffrey J.
Published: October 2022

Cardiac diseases are characterized by the inability of adult mammalian hearts to overcome the loss of cardiomyocytes (CMs). Current knowledge in cardiac regeneration lacks a clear understanding of the molecular systems determining whether CMs will progress through the cell cycle to proliferate. Here, we developed a computational model of cardiac proliferation signaling that identifies key regulators and provides a systems-level understanding of the cardiomyocyte proliferation regulatory network. This model defines five regulatory networks (DNA replication, mitosis, cytokinesis, growth factor, hippo pathway) of cardiomyocyte proliferation, which integrates 72 nodes and 88 reactions. The model correctly predicts 72 of 76 (94.7%) independent experiments from the literature. Network analysis predicted key signaling regulators of DNA replication (e.g., AKT, CDC25A, Cyclin D/CDK4, E2F), mitosis (e.g., Cyclin B/CDK2, CDC25B/C, PLK1), and cytokinesis, whose functions varied depending on the environmental context. Regulators of DNA replication were found to be highly context-dependent, while regulators of mitosis and cytokinesis were context-independent. We also predicted that in response to the YAP-activating compound TT-10, the Hippo module crosstalks with the growth factor module via PI3K, cMyc, and FoxM1 to drive proliferation. This prediction was validated with inhibitor experiments in primary rat cardiomyocytes and further supported by re-analysis of published data on YAP-stimulated mRNA and open chromatin of Myc from mouse hearts. This study contributes a systems framework for understanding cardiomyocyte proliferation and identifies potential therapeutic regulators that induce cardiomyocyte proliferation.
Chemical modification of human decellularized extracellular matrix for incorporation into phototunable hybrid-hydrogel models of tissue fibrosis
Authors: Hewawasam Rukshika S. , Šerbedžija Predrag , Blomberg Rachel , Magin Chelsea M.
Published: October 2022

Tissue fibrosis remains a serious health condition with high morbidity and mortality rates. There is a critical need to engineer model systems that better recapitulate the spatial and temporal changes in the fibrotic extracellular microenvironment and enable study of the cellular and molecular alterations that occur during pathogenesis. Here, we present a process for chemically modifying human decellularized extracellular matrix (dECM) and incorporating it into a dynamically tunable hybrid-hydrogel system containing a poly(ethylene glycol)-alpha methacrylate (PEGαMA) backbone. Following modification and characterization, an off-stoichiometry thiol-ene Michael addition reaction resulted in hybrid-hydrogels with mechanical properties that could be tuned to recapitulate many healthy tissue types. Next, photoinitiated, free-radical homopolymerization of excess α-methacrylates increased crosslinking density and hybrid-hydrogel elastic modulus to mimic a fibrotic microenvironment. The incorporation of dECM into the PEGαMAhydrogel decreased the elastic modulus and, relative to fully synthetic hydrogels, increased the swelling ratio, the average molecular weight between crosslinks, and the mesh size of hybrid-hydrogel networks. These changes were proportional to the amount of dECM incorporated into the network. Dynamic stiffening increased the elastic modulus and decreased the swelling ratio, average molecular weight between crosslinks, and the mesh size of hybrid-hydrogels, as expected. Stiffening also activated human fibroblasts, as measured by increases in average cellular aspect ratio (1.59 ± 0.02 to 2.98 ± 0.20) and expression of α-smooth muscle actin (αSMA). Fibroblasts expressing αSMA increased from 24.4% to 51.8% upon dynamic stiffening, demonstrating that hybrid-hydrogels containing human dECM support investigation of dynamic mechanosensing. These results improve our understanding of the biomolecular networks formed within hybrid-hydrogels: this fully human phototunable hybrid-hydrogel system will enable researchers to control and decouple the biochemical changes that occur during fibrotic pathogenesis from the resulting increases in stiffness to study the dynamic cell-matrix interactions that perpetuate fibrotic diseases.
Serotonin signaling in the enteric nervous system and connection to autism spectrum disorder: a translational mathematical model
Authors: Kareva Irina
Published: October 2022

While the causes of autism spectrum disorder (ASD) remain unclear, some studies have shown that serotonin-mediated effects on enteric nervous system (ENT) correlate with ASD-like behavioral phenotype in mice. Introduced here is a mathematical model of interactions between gut serotonin and its impact on ENT. The model was used to identify three key factors that affect ENT size, namely, serotonin production, its clearance, and its ability to act as a growth factor on ENT. The model was used to reproduce experimentally reported results from a mouse model by Margolis et al. (2016), which connected serotonin-mediated ENT hypoplasia to an ASD phenotype. The proposed mathematical model was used to scale the quantified relationship from mice to humans to show how the combination of these three factors can translate to a quantifiable metric that could potentially be correlated to ASD spectrum. A detailed discussion of how ENT hypoplasia could mechanistically affect CNS activity concludes this paper.
Neuropathology-basedAPOEgenetic risk score better quantifies Alzheimer’s risk
Authors: Deming Yuetiva , Vasiljevic Eva , Morrow Autumn , Miao Jiacheng , Van Hulle Carol , Jonaitis Erin , Ma Yue , Whitenack Vanessa , Kollmorgen Gwendlyn , Wild Norbert , Suridjan Ivonne , Shaw Leslie M. , Asthana Sanjay , Carlsson Cynthia M. , Johnson Sterling C. , Zetterberg Henrik , Blennow Kaj , Bendlin Barbara B. , Lu Qiongshi , Engelman Corinne D. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: October 2022

INTRODUCTION

APOE ε4-carrier status orε4allele count are included in analyses to account for theAPOEgenetic effect on Alzheimer’s disease (AD); however, this does not account for protective effects ofAPOE ε2or heterogeneous effect ofε2, ε3, ε4haplotypes.

METHODS

We leveraged results from an autopsy-confirmed AD study to generate a weighted risk score forAPOE(APOE-npscore). We regressed cerebrospinal fluid (CSF) amyloid and tau biomarkers onAPOEvariables from the Wisconsin Registry for Alzheimer’s Prevention, Wisconsin Alzheimer’s Disease Research Center, and Alzheimer’s Disease Neuroimaging Initiative (ADNI).

RESULTS

TheAPOE-npscore explained more variance and provided a better model fit for all three CSF measures thanAPOE ε4-carrier status andε4allele count. These findings were replicated in ADNI and observed in subsets of cognitively unimpaired participants.

DISCUSSION

TheAPOE-npscore reflects the genetic effect on neuropathology and provides an improved method to account forAPOEin AD-related analyses.
Mutational Analysis and Deep Learning Classification of Uterine and Cervical Cancers
Authors: Gomez Paul
Published: October 2022

We analyzed tumor mutations of 7 uterine and 2 cervical cancers with the goal of developing a Deep Learning (DL) software tool that can automatically classify tumors based on their somatic mutations. The data were obtained from the AACR Genie Project [1], that has a collection of more than 120,000 tumor samples for more than 750 cancer types. We performed a thorough analysis of the mutational data of tumors of the uterus and uterine cervix, selecting tumors with 3 or more mutations and cancer types with more than 15 cases. For each cancer type we then selected the top 12 most mutated genes among their neoplasms. In the introduction section we summarize our analysis of these nine diseases and in the deep learning section we present a convolutional neural network (CNN) [2] that yields an overall classification accuracy of 94.3% and 89.2% on the train and test datasets, respectively. We hope that this tool can be added to the existing arsenal of histological and immunohistochemical techniques in cases when a precise diagnosis cannot be clearly determined. Each cancer type has a unique somatic mutational profile that can be used to disambiguate two candidate malignancies with similar histologic features.
IS200/IS605 Family-Associated TnpB Increases Transposon Activity and Retention
Authors: Kaur Davneet , Kuhlman Thomas E.
Published: October 2022

The IS200/IS605 family of insertion sequences are abundant mobile elements associated with one of the most numerous genes found in nature,tnpB1–3. Previous studies suggest that TnpB protein may be an evolutionary precursor to CRISPR Cas enzymes, and TnpB has received renewed interest having itself been shown to function as a Cas-like RNA-guided DNA endonuclease3,4. However, interpretation of the fundamental role of TnpB in transposition and how it contributes to genome dynamics5remains controversial without direct, real-time measurement in live cells. Here, using a suite of fluorescent reporters coupled to transposition in liveEscherichia coli, we show that IS608-TnpB causes increased transposon activity, and assists in preventing transposon loss from host genomes. Analyzing our results through a mathematical model of transposon dynamics, we discuss the multifaceted roles it may play in transposon regulation. The mutually beneficial transposon-TnpB interaction may explain the prevalence oftnpB, creating conditions for the appropriation of TnpB’s RNA-guided endonuclease activity for adaptive immunity.

SIGNIFICANCE STATEMENT

Phylogenetic evidence suggests thattnpB, one of the most numerous genes found in nature, is the ancestral form of CRISPR-Cas enzymes and played a critical role in the evolution of adaptive immunity. However, the role TnpB plays in transposition that has contributed to its wide distribution remains unclear. Here, we use a unique approach that couples fluorescent reporters to transposition to non-perturbatively quantify transpositional dynamics in live cells. In contrast to previous indirect methods suggesting that TnpB suppresses transposition, our results instead clearly demonstrate that TnpB significantly increases transposition rates and enhances transposon retention within the host genome, resulting in a mutually beneficial interaction between transposons and TnpB that can account for its wide distribution.
Use of high-plex data reveals novel insights into the tumour microenvironment of clear cell renal cell carcinoma
Authors: De Filippis Raffaele , Wölflein Georg , Um In Hwa , Caie Peter D , Warren Sarah , White Andrew , Suen Elizabeth , To Emily , Arandjelović Ognjen , Harrison David J
Published: October 2022

Although Immune Checkpoint Inhibitors (ICIs) have significantly improved Clear Cell Renal Cell Carcinoma (ccRCC) prognosis, about one third of patients experience recurrence. Current prognostic algorithms like the Leibovich Score (LS) rely on morphological features manually assessed by pathologists, and are therefore subject to bias. Moreover, these tools do not consider the heterogeneous molecular milieu present in the Tumour Microenvironment (TME), which may have prognostic value. We systematically developed a semi-automated method to investigate 62 markers and their combinations in 150 primary ccRCCs using multiplex Immunofluorescence (mIF), NanoString GeoMx®Digital Spatial Profiling (DSP) and Artificial Intelligence (AI)-assisted image analysis in order to find novel prognostic signatures and investigate their spatial relationship. We found that coexpression of Cancer Stem Cell (CSC) and Epithelial-to-Mesenchymal Transition (EMT) markers such as OCT4 and ZEB1 are indicative of poor outcome. OCT4 and the immune markers CD8, CD34 and CD163 significantly stratified patients at intermediate LS. Furthermore, augmenting the LS with OCT4 and CD34 improved patient stratification by outcome. Our results support the hypothesis that combining molecular markers has prognostic value and can be integrated with morphological features to improve risk stratification and personalised therapy. To conclude, GeoMx®DSP and AI image analysis are complementary tools providing high multiplexing capability required to investigate the TME of ccRCC, while reducing observer bias.

Simple Summary

Cancer is a complex ensemble of morphological and molecular features whose role is still unclear. Moreover, their role may change in different areas of the same tumour. Artificial intelligence (AI) allows pathologists to go beyond human perception and bias, and may help better understand how these features influence disease progression. Furthermore, by capturing variation intrinsic to the tumour, AI may improve the accuracy of current prognostic tools, such as Leibovich Score (LS), in predicting patient outcome and response to therapy. For these reasons, we studied in clear cell renal cell carcinoma (ccRCC) tissue, in which molecular features and their coexpression in the same cell were quantified and mapped using AI-based image analysis software. We demonstrated a novel approach for investigating ccRCC and revealed new potential biomarkers of prognosis which may also be able to direct patients towards the most appropriate personalised therapy.
Non-Culprit Left Main Coronary Artery Disease in Acute Myocardial Infarction Complicated by Cardiogenic Shock
Authors: Park Ik Hyun , Jang Woo Jin , Oh Ju Hyeon , Yang Jeong Hoon , Song Young Bin , Hahn Joo-Yong , Choi Seung-Hyuk , Gwon Hyeon-Cheol , Ahn Chul-Min , Yu Cheol Woong , Kim Hyun-Joong , Bae Jang-Whan , Kwon Sung Uk , Lee Hyun-Jong , Lee Wang Soo , Jeong Jin-Ok , Park Sang-Don
Published: October 2022

Objectives

We evaluated the clinical impact of residual non-culprit left main coronary artery disease (LMCAD) on prognosis in patients undergoing emergent percutaneous coronary intervention (PCI) for acute myocardial infarction (AMI) complicated by cardiogenic shock (CS).

Methods

A total of 429 patients who underwent PCI for AMI complicated by CS was enrolled from 12 centers in the Republic of Korea. The patients were divided into two groups according to presence of non-culprit LMCAD or not: the LMCAD non-culprit group (n = 43) and the no LMCAD group (n = 386). Primary outcome was major adverse cardiac event (MACE, defined as a composite of cardiac death, myocardial infarction, or repeat revascularization). Propensity score matching analysis was performed to reduce selection bias and potential confounding factors.

Results

During a 12-month follow-up, a total of 168 MACEs occurred (LMCAD non-culprit group, 17 [39.5%] vs. no LMCAD group, 151 [39.1%]). Multivariate analysis revealed no significant difference in the incidence of MACE at 12 months between the LMCAD non-culprit and no LMCAD groups (adjusted hazard ratio [HR] 0.94, 95% confidence interval [CI] 0.56 to 1.58,p= 0.817). After propensity score matching, the incidence of MACE was still similar between the two groups(HR 1.07; 95% CI 0.49 to 2.36;p= 0.857). The similarity of MACEs between the two groups was consistent across a variety of subgroups.

Conclusions

After adjusting for baseline differences, residual non-culprit LMCAD does not appear to increase the risk of MACEs at 12 months in patients undergoing emergent PCI for AMI complicated by CS.