bluuebunny/crossref_metadata_2025 huggingface dataset:
Community and health system factors influencing snake envenomation management practices in three districts of Ghana: a qualitative inquiry from health stakeholders and snakebite victims
Authors: Dzenu Mabel Worlasi , Agani Afaya , Ayanore Martin
Published: February 2023

Introduction

Snakebite is a neglected public health issue affecting individuals of all ages in many tropical countries. Venom from snakebite is a potentially life-threatening disease associated with severe morbidities and mortalities. However, literature on snakebite envenoms management practices remains understudied. This study sought to explore community and health system factors influencing snake envenomation management practices in three districts in the Oti region of Ghana. Also, we assessed the current adherence to snakebite treatment protocols to the national and World Health Organization (WHO) recommended protocols.

Methods

The study adopted an exploratory descriptive qualitative study design. Purposive sampling technique was used to recruit participants for the study. The participants included snakebite victims, traditional healers, and health professionals. In-depth interviews and focused group discussions were used to collect data from the participants. All the interviews were audio recorded and transcribed verbatim and exported to Atlas Ti for data management and analyses. The transcribed data were analyzed using the content analysis method to develop the categories for the study findings

Findings

Twenty-six (26) participants were recruited including 16 males and 10 females. The study found three main factors that influenced snake envenomation management practices. These factors included health system factors, community-level factors, and adherence to national and WHO-recommended protocols. The health system factors included the unavailability of anti-snake venom, high-cost ASV, and inadequate or no supply of ASV from Ghana Health Service. The community factors included delay in seeking treatment, transportation, and accessibility challenges, and non-community acceptance facility treatment of snakebites. Almost all the health care professional who provide care for snakebite victims adhered to the WHO recommendations.

Conclusion

The evidence adduced from this study could be used by public health practitioners to empower the community by increasing awareness of the prevention of snakebites, first aid, and appropriate treatment-seeking behavior. Culturally appropriate interventions that seek to increase awareness to improve the acceptability of hospital management and sensitize the community for early referral of snakebite victims to the nearest health facility having anti-venom treatment.

Authors summary

The negative responses by the community’s acceptance of the kind of treatment given in the health facilities and the unavailability of Anti-snake Venom (ASV) in the study districts’ health facilities inhibit the management of snakebites.
Emergency and Sequalae Management of Traumatic Dental Injuries: A Quality Assessment of Clinical Practice Guidelines
Authors: Zaror Carlos , Seiffert Andrea , Deana Naira Figueiredo , Espinoza-Espinoza Gerardo , Ata-la-Acevedo Claudia , Diaz Rodrigo , Carrasco-Labra Alonso
Published: February 2023

The prevalence and consequences of traumatic dental injuries (TDI) make them a public health problem. Trustworthy TDI Clinical Practice Guidelines (CPGs) can assist clinicians in making a proper diagnosis, and guide them to the most appropriate therapy for every case. The aim of this study was to identify and evaluate the quality of CPGs for the diagnosis, emergency management and follow-up of TDIs. A systematic search was carried out in MEDLINE, EMBASE, Epistemonikos, Trip database, CPG’ websites, and dental societies to identify documents providing recommendations for the emergency and sequelae management of TDIs. Reviewers assessed the included guidelines independently and in duplicate, using the AGREE II instrument. T-student or ANOVA tests were used to determine the attributes of CPGs associated with the total score in AGREE II. Ten CPGs published between 2010 and 2020 were included, mostly from Europe (n=6). The overall agreement between reviewers was very good (0.94; 95%CI 0.91-0.97). The mean scores for each domain were as follows: Scope and purpose 78.0 ± 18.9%; Stakeholder involvement 46.9 ± 29.6%; Rigour of development 41.8 ± 26.7%; Clarity of presentation 75.8 ± 17.6%; Applicability 15.3 ± 18.8% and Editorial independence 41.7 ± 41.7%. The overall mean rate was 4 ± 1.3 out of a maximum score of 7. Only two guidelines were recommended by the reviewers and rated as high quality. The CPGs developed by governments showed a significantly higher overall score. The overall quality of CPGs on TDI was suboptimal. Therefore, the CPGs developers need to use a methodology that allows them to formulate recommendations in a structured, transparent, and explicit way.
Computed tomography perfusion parameters predictive of symptomatic intracranial hemorrhage after mechanical thrombectomy in patients with cerebral large vessel occlusion
Authors: Abe Soichiro , Inoue Manabu , Shirakawa Manabu , Uchida Kazutaka , Yamada Kiyofumi , Kuramoto Yoji , Namitome Satoshi , Shindo Seigo , Sakakibara Fumihiro , Kouno Junichi , Tatebayashi Kotaro , Kinjo Norito , Tsuji Shoichiro , Tanada Shuichi , Beppu Mikiya , Matsukawa Hidetoshi , Ihara Masafumi , Yoshimura Shinichi
Published: February 2023

Background

Hemorrhagic transformation (HT) after recanalization is a severe complication in patients with a large ischemic core due to cerebral large vessel occlusion. Risk assessment using perfusion imaging to predict hemorrhagic infarction has not been established. Thus, we aimed to investigate the association between perfusion imaging findings and HT in patients with acute cerebral large vessel occlusion who had undergone preoperative perfusion imaging evaluation and mechanical thrombectomy.

Methods

We enrolled consecutive patients who received mechanical thrombectomy (MT) after undergoing perfusion imaging for anterior large vessel occlusion from May 2019 to March 2022. The patients in whom recanalization was not achieved and who experienced procedure-related bleeding were excluded. We investigated the predictors of symptomatic intracranial hemorrhage (sICH) by exploring preoperative perfusion imaging parameters [relative cerebral blood flow, relative cerebral blood volume (rCBV), time of maximum concentration, hypoperfusion index ratio].

Results

Among the 167 patients (median age 79 years, 47% female) enrolled, 63 (38%) and 14 (8%) patients had any intracranial hemorrhage and sICH (sICH group), respectively. The sICH group had a shorter puncture-recanalization time than the non-sICH group (median [interquartile range (IQR)]; 43 [34–55] vs. 61 [37–88], p = 0.046), whereas the modified Rankin Scale at 90 days showed a worse prognosis (median [IQR]; 5 [5–6] vs 3 [1–4], p<0.01). All perfusion imaging parameters were significantly predicting the sICH group in multiple logistic regression analysis. The value of rCBV was the parameter most strongly associated with sICH in receiver operating characteristic curve analysis (area under the curve = 0.90, 95% confidence interval [0.83–0.98]; cutoff 43 ml; sensitivity, 86 %; specificity, 87%).

Conclusion

Among perfusion CT parameters, rCBV is highly associated with sICH after MT for cerebral large vessel occlusion. In patients with low rCBV regions, the indication of mechanical thrombectomy should be carefully considered for postoperative intracranial hemorrhage.

Clinical perspective

Of the various parameters assessed via perfusion CT, the value of rCBV demonstrates a strong correlation with the occurrence of symptomatic intracranial hemorrhage following mechanical thrombectomy for cerebral anterior large vessel occlusion.

When treating patients with regions of large low-rCBV, it is important to carefully determine the indication of mechanical due to the potential risk of postoperative intracranial hemorrhage.
Prediction of plasma volume and total hemoglobin mass with machine learning
Authors: Moreillon B. , Krumm B. , Saugy J.J. , Saugy M. , Botrè F. , Vesin J.-M. , Faiss R.
Published: February 2023

Anemia is a widespread disease commonly diagnosed through hemoglobin concentration ([Hb]) thresholds set by the World Health Organization (WHO). However, [Hb] is subject to significant variations mainly due to shifts in plasma volume (PV) which impair the diagnosis of anemia and other medical conditions. The aim of this study was to develop a model able to accurately predict total hemoglobin mass (Hbmass) and PV based on anthropometric and complete blood count (CBC) analyses. 769 CBC coupled to measures of Hbmass and PV using the CO-rebreathing method were used with a machine learning tool in a numeric computing platform (MATLAB regression learner app) to calculate the model. For the predicted values, root mean square error (RMSE) was of 37.9 g and 50.0 g for Hbmass, and 194 ml and 268 ml for PV, in women and men, respectively. Measured and predicted data were significantly correlated (p<0.001) with the coefficient of determination (R2) ranging from 0.73 to 0.81 for Hbmass, and PV, in both women and men. The bland-altman bias between estimated and measured variables was in average of -0.69 for Hbmass and 0.73 for PV. This study proposes a valid model with a high prediction potential for Hbmass and PV, providing relevant complementary data in numerous contexts. This method can notably bring information applicable to the epidemiology of anemia, particularly in countries with high prevalence or in specific population such as high-altitude communities.
Tempo-spatial dynamics of COVID-19 in Germany – A phase model based on a pandemic severity indicator
Authors: Stabler Martin , Kuebart Andreas
Published: February 2023

While pandemic waves are often analyzed on the national scale, they typically are not distributed evenly in space. This working paper employs a novel approach to analyze the tempo-spatial dynamics of the COVID-19 pandemic for the case of Germany. First, we base the analysis not just on the incidence of cases or mortality but employ a composite indicator of pandemic severity to gain a more robust understanding of the temporal dynamics of the pandemic. Second, we subdivide the pandemic during the years 0f 2020 and 2021 into fifteen phases, each with a coherent trend of pandemic severity. Third, we analyze the spatial patterns predominating in each phase. The resulting tempo-spatial phase model is used to identify explanatory factors for the tempo-spatial patterns identified in the analysis.

Disclosures

This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) with a research grant for the project Socio-spatial diffusion of COVID-19 in Germany. - 492338717
Detection of HypervirulentKlebsiella pneumoniaefrom Clinical Samples in Tamil Nadu
Authors: Shanthini Thamaraiselvan , Manohar Prasanth , Hua Xiaoting , Leptihn Sebastian , Nachimuthu Ramesh
Published: February 2023

Klebsiellapneumoniae is one of the significant opportunistic pathogens which cause both nosocomial and community-acquired infections. This study focuses on the molecular characterization of hypervirulentK. pneumoniaeisolated from clinical samples in Tamil Nadu. A total of 30 clinicalK. pneumoniaeisolates were collected from the diagnostic centres located in Trichy, Madurai, and Chennai. On subjected to the antibiotic susceptibility testing, it was found that 73% were multi-drug resistant. The string test showed that 46.6% of the isolates were hypermucoviscous (HMV). Molecular studies revealed the absence ofmcr (1-5)genes. The isolates belonging to capsular types K1 (n=5), K2 (n=6) and K5 (n=2) were detected. Virulence genes namelyrmpA(n=5), aerobactin (n=8), andKfuBC(n=8) were identified using multiplex polymerase chain reaction. Through molecular studies, 22 isolates were found to be classicalK. pneumoniae(cKP) and 8 were hypervirulentK. pneumoniae(hvKP). The genome sequencing of five isolates revealed that the strains belong to ST86 and ST23.In vivostudies usingGalleria mellonellashowed that HMV-hvKP strains were highly pathogenic among the hvKP strains and the non-K1/K2 and K2 strains were pathogenic among the cKP strains. Our data revealed the emergence of colistin-resistant hvKP strains in Tamil Nadu, India.
Spatially Aware Transformer Networks for Contextual Prediction of Diabetic Nephropathy Progression from Whole Slide Images
Authors: Shickel Benjamin , Lucarelli Nicholas , Rao Adish S. , Yun Donghwan , Moon Kyung Chul , Han Seung Seok , Sarder Pinaki
Published: February 2023

Diabetic nephropathy (DN) in the context of type 2 diabetes is the leading cause of end-stage renal disease (ESRD) in the United States. DN is graded based on glomerular morphology and has a spatially heterogeneous presentation in kidney biopsies that complicates pathologists’ predictions of disease progression. Artificial intelligence and deep learning methods for pathology have shown promise for quantitative pathological evaluation and clinical trajectory estimation; but, they often fail to capture large-scale spatial anatomy and relationships found in whole slide images (WSIs). In this study, we present a transformer-based, multi-stage ESRD prediction framework built upon nonlinear dimensionality reduction, relative Euclidean pixel distance embeddings between every pair of observable glomeruli, and a corresponding spatial self-attention mechanism for a robust contextual representation. We developed a deep transformer network for encoding WSI and predicting future ESRD using a dataset of 56 kidney biopsy WSIs from DN patients at Seoul National University Hospital. Using a leave-one-out cross-validation scheme, our modified transformer framework outperformed RNNs, XGBoost, and logistic regression baseline models, and resulted in an area under the receiver operating characteristic curve (AUC) of 0.97 (95% CI: 0.90-1.00) for predicting two-year ESRD, compared with an AUC of 0.86 (95% CI: 0.66-0.99) without our relative distance embedding, and an AUC of 0.76 (95% CI: 0.59-0.92) without a denoising autoencoder module. While the variability and generalizability induced by smaller sample sizes are challenging, our distance-based embedding approach and overfitting mitigation techniques yielded results that suggest opportunities for future spatially aware WSI research using limited pathology datasets.
Assessing the Value of ChatGPT for Clinical Decision Support Optimization
Authors: Liu Siru , Wright Aileen P. , Patterson Barron L. , Wanderer Jonathan P. , Turer Robert W. , Nelson Scott D. , McCoy Allison B. , Sittig Dean F. , Wright Adam
Published: February 2023

Objective

To determine if ChatGPT can generate useful suggestions for improving clinical decision support (CDS) logic and to assess noninferiority compared to human-generated suggestions.

Methods

We supplied summaries of CDS logic to ChatGPT, an artificial intelligence (AI) tool for question answering that uses a large language model, and asked it to generate suggestions. We asked human clinician reviewers to review the AI-generated suggestions as well as human-generated suggestions for improving the same CDS alerts, and rate the suggestions for their usefulness, acceptance, relevance, understanding, workflow, bias, inversion, and redundancy.

Results

Five clinicians analyzed 36 AI-generated suggestions and 29 human-generated suggestions for 7 alerts. Of the 20 suggestions that scored highest in the survey, 9 were generated by ChatGPT. The suggestions generated by AI were found to offer unique perspectives and were evaluated as highly understandable and relevant, with moderate usefulness, low acceptance, bias, inversion, redundancy.

Conclusion

AI-generated suggestions could be an important complementary part of optimizing CDS alerts, can identify potential improvements to alert logic and support their implementation, and may even be able to assist experts in formulating their own suggestions for CDS improvement. ChatGPT shows great potential for using large language models and reinforcement learning from human feedback to improve CDS alert logic and potentially other medical areas involving complex, clinical logic, a key step in the development of an advanced learning health system.
The allotetraploidNicotiana tabacumgenome and GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits
Authors: Zan Yanjun , Chen Shuai , Ren Min , Liu Guoxiang , Liu Yutong , Si Huan , Liu Zhengwen , Liu Dan , Zhang Xingwei , Tong Ying , Li Yuan , Jiang Caihong , Wen Liuying , Xiao Zhiliang , Sun Yangyang , Geng Ruimei , Feng Quanfu , Wang Yuanying , Ye Guoyou , Fang Lingzhao , Chen Yong , Cheng Lirui , Yang Aiguo
Published: February 2023

Nicotiana tabacumis a model organism in plant molecular and pathogenic research and has significant potential in the production of biofuels and active pharmaceutical compounds in synthetic biology. Because of the large allotetraploid genome of tobacco, its genomic features, genetic diversity and genetic regulation of many complex traits remain unknown. In this study, we present a nearly complete chromosome-scale assembly ofN. tabacumand provide evidence that homoeologous exchange between subgenomes and epigenetic remodelling are likely mechanisms of genome stabilization and subgenome coordination following polyploidization. By leveraging GenBank-scale sequencing and phenotyping data from 5196 lines, geography at the continent scale, rather than types assigned on the basis of curing crop practices, was found to be the most important correlate of genetic structure. Using 178 marker□trait associations detected in genome-wide association analysis, a reference genotype-to-phenotype map was built for 39 morphological, developmental, and disease-resistance traits. A novel gene, auxin response factor 9 (Arf9), associated with wider leaves after being knocked out, was fine-mapped to a single nucleotide polymorphism (SNP). This point mutation alters the translated amino acid from Ala203to Pro203, likely preventing homodimer formation during DNA binding. Our analysis also revealed signatures of positive and polygenic selection for multiple traits during the process of selective breeding. Overall, this study demonstrated the power of leveraging GenBank genomics to gain insights into the genomic features, genetic diversity, and regulation of complex traits inN. tabacum, laying a foundation for future research on plant functional genomics, crop breeding, and the production of biopharmaceuticals and biofuels.
The clinical impact of serious respiratory disease in children under the age of two during the 2021-2022 bronchiolitis season in the United Kingdom and Ireland
Authors: Williams Thomas C. , Marlow Robin , Hardelid Pia , Lyttle Mark D. , Lewis Kate M. , Mpamhanga Chengetai D. ,   PERUKI, Cunningham Steve , Roland Damian
Published: February 2023

Background

Interventions introduced in 2020 to reduce the spread of SARS-CoV-2 led to a widespread reduction in childhood infections, including respiratory syncytial virus (RSV), in the subsequent year. However, from the spring of 2021 onwards the United Kingdom and Ireland began to experience an unusual out of season epidemic of childhood respiratory disease.

Methods

We conducted a prospective observational cohort study (BronchStart), enrolling children aged 0-23 months presenting with clinician-diagnosed bronchiolitis, lower respiratory tract infection or first episode of wheeze in 59 Emergency Departments (ED) across England, Scotland and Ireland from 1 May 2021 to 30 April 2022. We collected baseline data on patient demographics and clinical presentation, and follow-up data at 7 days. We used high-granularity BronchStart clinical data together with national English and Scottish admission datasets to infer the impact of RSV disease in a typical year before the Covid-19 pandemic, and to provide an up-to-date estimate of the annual impact of disease to inform implementation of anti-RSV interventions.

Findings

The BronchStart study collected data on 17,899 ED presentations for 17,179 children. Of these, 6,825 (38.1%) were admitted to hospital for further observation or treatment, 458 (2.6%) required care in a high dependency unit (HDU), and 154 (0.9%) were admitted to a paediatric intensive care unit (PICU). Of the 5,788 children admitted and tested for RSV, 41.8% of the overall study cohort, and 48.7% of those 0-11 months of age, were positive. Risk factors for hospital admission included prematurity and congenital cardiac disease. Patients with these risk factors were also more likely to receive oxygen therapy, or be admitted to a HDU or PICU. However, 84.5% of those admitted to an observation unit, 78.1% of those admitted to a ward, 67.7% of those admitted to HDU and 50.0 % of those admitted to PICU had no identified comorbidity. Using admissions data for England and Scotland we estimate that every year 12,167 infants with RSV infection receive low flow oxygen, 4,998 high flow oxygen and 6,198 a course of antibiotic therapy in secondary care.

Interpretation

Although RSV was the major pathogen in this cohort, 51.3% of admissions for serious respiratory viral infections in those aged <1 year of age were not associated with the virus. Whilst prematurity and congenital cardiac disease were risk factors for admission to hospital, HDU and PICU, the majority of these admissions, for all levels of care except PICU, were in previously healthy term born infants.
Stress in autism (STREAM): A study protocol on the role of circadian activity, sleep quality and sensory reactivity
Authors: Gernert Clara C. , Falter-Wagner Christine M. , Noreika Valdas , Jachs Barbara , Jassim Nazia , Gibbs Kathryn , Streicher Joaquim , Betts Hannah , Bekinschtein Tristan A.
Published: February 2023

Mental health issues are markedly increased in individuals with autism, making it the number one research priority by stakeholders. There is a crucial need to use personalized approaches to understand the underpinnings of mental illness in autism and consequently, to address individual needs. Based on the risk factors identified in typical mental research, we propose the following themes central to mental health issues in autism: sleep difficulties and stress. Indeed, the prevalence of manifold circadian disruptions and sleep difficulties in autism, alongside stress related to sensory overload, forms an integral part of autistic symptomatology.

This proof-of-concept study protocol outlines an innovative, individualised approach towards investigating the interrelationships between stress indices, sleep and circadian activation patterns, and sensory sensitivity in autism. Embracing an individualized methodology, we aim to collect 14 days of data per participant from 20 individuals with autism diagnoses and 20 without. Participants’ sleep will be monitored using wearable EEG headbands and a sleep diary. Diurnal tracking of heart rate and electrodermal activity through wearables will serve as proxies of stress. Those objective data will be synchronized with subjective experience traces collected throughout the day using the Temporal Experience Tracing (TET) method. TET facilitates the quantification of relevant aspects of individual experience states, such as stress or sensory sensitivities, by providing a continuous multidimensional description of subjective experiences. Capturing the dynamics of subjective experiences phase-locked to neural and physiological proxies both between and within individuals, this approach has the potential to contribute to our understanding of critical issues in autism, including sleep problems, sensory reactivity and stress. The planned strives to provide a pathway towards developing a more nuanced and individualized approach to addressing mental health in autism.
Intensive Systolic Blood Pressure Treatment Remodels Brain Perivascular Spaces: A Secondary Analysis of SPRINT
Authors: Kern Kyle C. , Nasrallah Ilya M. , Bryan Robert Nick , Reboussin David M. , Wright Clinton B.
Published: February 2023

Background

Brain perivascular spaces (PVS) are part of the glymphatic system and facilitate clearance of metabolic byproducts. Since enlarged PVS are associated with vascular health, we tested whether intensive systolic blood pressure (SBP) treatment affects PVS structure.

Methods

This is a secondary analysis of the Systolic PRessure INTervention (SPRINT) Trial MRI Substudy: a randomized trial of intensive SBP treatment to goal < 120 mm Hg vs. < 140 mm Hg. Participants had increased cardiovascular risk, pre-treatment SBP 130-180, and no clinical stroke, dementia, or diabetes. Brain MRIs acquired at baseline and follow-up were used to automatically segment PVS in the supratentorial white matter and basal ganglia using a Frangi filtering method. PVS volumes were quantified as a fraction of the total tissue volume. The effects of SBP treatment group and major antihypertensive classes on PVS volume fraction were separately tested using linear mixed-effects models while covarying for MRI site, age, sex, black race, baseline SBP, history of cardiovascular disease (CVD), chronic kidney disease, and white matter hyperintensities (WMH).

Results

For 610 participants with sufficient quality MRI at baseline (mean age 67±8, 40% female, 32% black), greater PVS volume fraction was associated with older age, male sex, non-Black race, concurrent CVD, WMH, and brain atrophy. For 381 participants with MRI at baseline and at follow-up (median = 3.9 years), intensive treatment was associated with decreased PVS volume fraction relative to standard treatment (interaction coefficient: -0.029 [-0.055 to -0.0029] p=0.029). Reduced PVS volume fraction was also associated with exposure to calcium channel blockers (CCB) and diuretics.

Conclusions

Intensive SBP lowering partially reverses PVS enlargement. The effects of CCB use suggests that improved vascular compliance may be partly responsible. Improved vascular health may facilitate glymphatic clearance.

Clincaltrials.gov:NCT01206062
Macroscopic waves, biological clocks and morphogenesis driven by light in a giant unicellular green alga
Authors: Afik Eldad , Liu Toni J.B. , Meyerowitz Elliot M.
Published: February 2023

A hallmark of self-organisation in living systems is their capacity to stabilise their own dynamics, often appearing to anticipate and act upon potential outcomes.Caulerpa brachypusis a marine green alga consisting of differentiated organs resembling leaves, stems and roots. While an individual can exceed a metre in size, it is a single multinucleated giant cell. ThusCaulerpapresents the mystery of morphogenesis on macroscopic scales in the absence of cellularization. The experiments reported here reveal self-organised waves of greenness — chloroplasts — that propagate throughout the alga in anticipation of the day-night light cycle. Using dynamical systems analysis we show that these waves are coupled to a self-sustained oscillator, and demonstrate their entrainment to light. Under constant conditions light intensity affects the natural period and drives transition to temporal disorder. Moreover, we find distinct morphologies depending on light temporal patterns, suggesting waves of chlorophyll could link biological oscillators to metabolism and morphogenesis in this giant single-celled organism.
The balance between growth and resistance is shifted to the latter by over-accumulation of chloroplast-nucleus located WHIRLY1 in barley
Authors: Nia Monireh Saeid , Frank Susann , Schäfer Anke , Desel Christine , Mulisch Maria , Voigt Ulrike , Nowara Daniela , Tandron Moya Yudelsy Antonia , Bilger Wolfgang , Wiren Nicolaus von , Hensel Götz , Krupinska Karin
Published: February 2023

WHIRLY1 is a chloroplast-nucleus located DNA/RNA-binding protein with functions in development and stress tolerance. By overexpression ofHvWHIRLY1in barley, lines with a 10-and two lines with a 50-fold accumulation of the protein were obtained. In these lines, the relative abundance of the nuclear form exceeded that of the chloroplast form indicating that over-accumulating WHIRLY1 exceeded the amount that chloroplasts can sequester. Growth of the plants was shown to be compromised in a WHIRLY1 abundance-dependent manner. Over-accumulation of WHIRLY1 in chloroplasts had neither an evident impact on nucleoid morphology nor on the composition of the photosynthetic apparatus. Nevertheless, oeW1 plants were found to be compromised in the efficiency of photosynthesis. The reduction in growth and photosynthesis was shown to be accompanied by a decrease in the levels of cytokinins and an increase in the level of jasmonic acid. Gene expression analyses revealed that already in non-stress conditions the oeW1 plants had enhanced levels of pathogen response (PR) gene expression indicating activation of constitutive defense. During growth in continuous light of high irradiance,PR1expression further increased in addition to an increase in the expression ofPR10and of the gene encoding phenylalanine lyase (PAL), the key enzyme of salicylic acid biosynthesis in barley. The activation of defense gene expression in oeW1 plants coincided with an enhanced resistance towards powdery mildew, which in barley is independent of salicylic acid. Taken together, the results show that over-accumulation of WHIRLY1 in barley to levels of 10 or more, amplified the tradeoff between growth and stress resistance.
A NovelC. elegansMemory Type Mediated by an Insulin/Phospholipase C Pathway
Authors: Merritt Daniel M. , Udachina Alexandra , Freidel Ninon , Almeida Sylvia M. T. , Anson Lau Yan Ming , Lee Matthew , van der Kooy Derek
Published: February 2023

Memories are often categorized into types, reflecting their behavioral, anatomical and molecular diversity: these classifications both aid understanding of the differences among varieties of memory and help delineate the unifying cross-species principles underlying them. In the nematode wormCaenorhabditis elegans,we find that an associative memory of the pairing of the normally attractive odorant benzaldehyde and starvation depends onde novotranslation, is independent of CREB, and is produced by massed training: a pattern which does not correspond to any of the well-characterized molecular categories of invertebrate memory. Further, as has been shown for many memories in vertebrates, but not previously in nematodes, we find that formation of this memory continues after removal of the stimuli initially causing it, and that it is labile to disruption through protein synthesis inhibition following training, but that inhibition of proteasomal activity does not extend the duration of the memory. Previous findings have implicated insulin pathway signaling, which canonically regulates the transcription factor DAF- 16, as a key component of this benzaldehyde/starvation memory, however our results suggest that transcriptional inhibition has, at most, only moderate effects on memory formation. We find that insulin signaling instead acts to regulate phospholipase C, which in turn regulates memory through diacylglycerol signaling. These findings better characterize this model associative memory in relation to other invertebrate memory types and identify ways in which it both shares their traits and differs from them, as well as revealing a more complete picture of the molecular pathway underlying it.
Functional traits shape plant-plant interactions and recruitment in a hotspot of woody plant diversity
Authors: Cooksley Huw , Dreyling Lukas , Esler Karen J. , Griebenow Stian , Neumann Günter , Valentine Alex , Schleuning Matthias , Schurr Frank M.
Published: February 2023

Understanding and predicting recruitment in species-rich plant communities requires identifying the functional determinants of both density-independent performance and interactions.

In a common-garden field experiment with 25 species of the woody plant genusProtea, we varied the initial spatial and taxonomic arrangement of seedlings and followed their survival and growth during recruitment. Neighbourhood models quantified how six key functional traits affect density-independent performance, interaction effects and responses.

Trait-based neighbourhood models accurately predicted individual survival and growth from the initial spatial and functional composition of species-rich experimental communities. Functional variation among species caused substantial variation in density-independent survival and growth that was not correlated with interaction effects and responses. Interactions were spatially-restricted but had important, predominantly competitive, effects on recruitment. Traits increasing the acquisition of limiting resources (water for survival, soil P for growth) mediated a trade-off between competitive effects and responses. Moreover, resprouting species had higher survival but reduced growth, likely reinforcing the survival-growth trade-off in adult plants.

The combination of field experiments and trait-based neighbourhood analyses holds substantial potential for community ecology. It permits the identification of traits that mediate performance trade-offs promoting coexistence in species-rich communities and contributes key knowledge to guide conservation and restoration of biodiversity hotspots.
Error-corrected Duplex Sequencing enables direct detection and quantification of mutations in human TK6 cells with remarkable inter-laboratory consistency
Authors: Cho Eunnara , Swartz Carol D. , Williams Andrew , Rivas Miriam , Recio Leslie , Witt Kristine L. , Schmidt Elizabeth K. , Yaplee Jeffry , Smith Thomas H. , Van Phu , Lo Fang Yin , Valentine Charles C. , Salk Jesse J. , Marchetti Francesco , Smith-Roe Stephanie L. , Yauk Carole L.
Published: February 2023

Error-corrected Duplex Sequencing (DuplexSeq) enables direct quantification of low-frequency mutations and offers tremendous potential for chemical mutagenicity assessment. We investigated the utility of DuplexSeq to quantify induced mutation frequency (MF) and spectrum in human lymphoblastoid TK6 cells exposed to a prototypical DNA alkylating agent,N-ethyl-N-nitrosourea (ENU). Furthermore, we explored appropriate experimental parameters for this application, and assessed inter-laboratory reproducibility. In two independent experiments in two laboratories, TK6 cells were exposed to ENU (25-200 µM) and DNA was sequenced 48, 72, and 96 h post-exposure. A DuplexSeq mutagenicity panel targeting twenty 2.4-kb regions distributed across the genome was used to sample diverse, genome-representative sequence contexts. A robust increase in MF that was unaffected by time was observed in both laboratories. Concentration-response in the MF from the two laboratories was strongly positively correlated (R2=0.95). C:G>T:A, T:A>C:G, T:A>A:T, and T:A>G:C mutations increased in consistent, concentration-dependent manners in both laboratories, with high proportions of C:G>T:A at all time points. The target sites responded similarly between the two laboratories and revealed a higher average MF in intergenic regions. These results, demonstrating remarkable reproducibility across time and laboratory for both MF and spectrum, support the high value of DuplexSeq for characterizing chemical mutagenicity in both research and regulatory evaluation.
Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries
Authors: Weile Jochen , Ferra Gabrielle , Boyle Gabriel , Pendyala Sriram , Amorosi Clara , Yeh Chiann-Ling , Cote Atina G. , Kishore Nishka , Tabet Daniel , van Loggerenberg Warren , Rayhan Ashyad , Fowler Douglas M , Dunham Maitreya J. , Roth Frederick P
Published: February 2023

Long read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.

Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or non-unique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.

Availability and Implementation

Pacybara, freely available athttps://github.com/rothlab/pacybara, is implemented using R, Python and bash for Linux. It has both a single-threaded implementation and, for GNU/Linux clusters that use Slurm, PBS, or GridEngine schedulers, a multi-node version.

Supplementary Material

Supplementary materials are available at Bioinformatics online.
Single neurons in the human medial temporal lobe flexibly shift representations across spatial and memory tasks
Authors: Donoghue Thomas , Cao Runnan , Han Claire Z , Holman Cameron M , Brandmeir Nicholas J , Wang Shuo , Jacobs Joshua
Published: February 2023

Investigations into how individual neurons encode behavioral variables of interest have revealed specific representations in single neurons, such as place and object cells, as well as a wide range of cells with conjunctive encodings or mixed selectivity. However, as most experiments examine neural activity within individual tasks, it is currently unclear if and how neural representations change across different task contexts. Within this discussion, the medial temporal lobe is particularly salient, as it is known to be important for multiple behaviors including spatial navigation and memory, however the relationship between these functions is currently unclear. Here, to investigate how representations in single neurons vary across different task contexts in the MTL, we collected and analyzed single-neuron activity from human participants as they completed a paired-task session consisting of a passive-viewing visual working memory and a spatial navigation and memory task. Five patients contributed 22 paired-task sessions, which were spike sorted together to allow for the same putative single neurons to be compared between the different tasks. Within each task, we replicated concept-related activations in the working memory task, as well as target-location and serial-position responsive cells in the navigation task. When comparing neuronal activity between tasks, we first established that a significant number of neurons maintained the same kind of representation, responding to stimuli presentations across tasks. Further, we found cells that changed the nature of their representation across tasks, including a significant number of cells that were stimulus responsive in the working memory task that responded to serial position in the spatial task. Overall, our results support a flexible encoding of multiple, distinct aspects of different tasks by single neurons in the human MTL, whereby some individual neurons change the nature of their feature coding between task contexts.
Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions
Authors: Newman Nolan K. , Macovsky Matthew , Rodrigues Richard R. , Bruce Amanda M. , Pederson Jacob W. , Patil Sankalp S , Padiadpu Jyothi , Dzutsev Amiran K. , Shulzhenko Natalia , Trinchieri Giorgio , Brown Kevin , Morgun Andrey
Published: February 2023

Technological advances have generated tremendous amounts of high-throughput omics data. Integrating data from multiple cohorts and diverse omics types from new and previously published studies can offer a holistic view of a biological system and aid in deciphering its critical players and key mechanisms. In this protocol, we describe how to use Transkingdom Network Analysis (TkNA), a unique causal-inference analytical framework that can perform meta-analysis of cohorts and detect master regulators among measured parameters that govern pathological or physiological responses of host-microbiota (or any multi-omic data) interactions in a particular condition or disease.

TkNA first reconstructs the network that represents a statistical model capturing the complex relationships between the different omics of the biological system. Here, it selects differential features and their per-group correlations by identifying robust and reproducible patterns of fold change direction and sign of correlation across several cohorts. Next, a causality-sensitive metric, statistical thresholds, and a set of topological criteria are used to select the final edges that form the transkingdom network. The second part of the analysis involves interrogating the network. Using the network’s local and global topology metrics, it detects nodes that are responsible for control of given subnetwork or control of communication between kingdoms and/or subnetworks.

The underlying basis of the TkNA approach involves fundamental principles including laws of causality, graph theory and information theory. Hence, TkNA can be used for causal inference via network analysis of any host and/or microbiota multi-omics data. This quick and easy-to-run protocol requires very basic familiarity with the Unix command-line environment.
Defining Early Steps inB. subtilisBiofilm Biosynthesis
Authors: Arbour Christine A. , Nagar Rupa , Bernstein Hannah M. , Ghosh Soumi , Al-Sammarraie Yusra , Dorfmueller Helge C. , Ferguson Michael A. J. , Stanley-Wall Nicola R. , Imperiali Barbara
Published: February 2023

TheBacillus subtilisextracellular biofilm matrix includes an exopolysaccharide that is critical for the architecture and function of the community. To date, our understanding of the biosynthetic machinery and the molecular composition of the exopolysaccharide ofB. subtilisremains unclear and incomplete. This report presents synergistic biochemical and genetic studies built from a foundation of comparative sequence analyses targeted at elucidating the activities of the first two membrane-committed steps in the exopolysaccharide biosynthetic pathway. By taking this approach, we determined the nucleotide sugar donor and lipid-linked acceptor substrates for the first two enzymes in theB. subtilisbiofilm exopolysaccharide biosynthetic pathway. EpsL catalyzes the first phosphoglycosyl transferase step using UDP-di-N-acetyl bacillosamine as phospho-sugar donor. EpsD is a GT-B fold glycosyl transferase that facilitates the second step in the pathway that utilizes the product of EpsL as an acceptor substrate and UDP-N-acetyl glucosamine as the sugar donor. Thus, the study defines the first two monosaccharides at the reducing end of the growing exopolysaccharide unit. In doing so we provide the first evidence of the presence of bacillosamine in an exopolysaccharide synthesized by a Gram-positive bacterium.

IMPORTANCE

Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here we identify the first two essential steps in theBacillus subtilisbiofilm matrix exopolysaccharide synthesis pathway. Together our studies and approaches provide the foundation for the sequential characterization of the steps in exopolysaccharide biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenol diphosphate-linked glycan substrates.
Novel Fas-TNFR chimeras that prevents Fas ligand-mediated kill and signals synergistically to enhance CAR T-cell efficacy
Authors: McKenzie Callum , El-Kholy Mohamed , Parekh Farhaan , Robson Mathew , Lamb Katarina , Allen Christopher , Sillibourne James , Cordoba Shaun , Thomas Simon , Pule Martin
Published: February 2023

The hostile tumour microenvironment limits the efficacy of adoptive cell therapies. Activation of the Fas death receptor initiates apoptosis and disrupting these receptors could be key to increase CAR T-cell efficacy. We screened a library of Fas-TNFR proteins identifying several novel chimeras that not only prevented Fas ligand-mediated kill, but also enhanced CAR T-cell efficacy by signalling synergistically with the CAR. Upon binding Fas ligand, Fas-CD40 activated the NF-κB pathway, inducing greatest proliferation and IFNγ release out of all Fas-TNFRs tested. Fas-CD40 induced profound transcriptional modifications, particularly genes relating to the cell cycle, metabolism, and chemokine signalling. Co-expression of Fas-CD40 with either 4-1BB- or CD28-containing CARs increasedin vitroefficacy by eliciting maximal CAR T-cell proliferation and cancer target cytotoxicity, and enhanced tumour killing and overall mouse survivalin vivo. Functional activity of the Fas-TNFRs were dependent on the co-stimulatory domain within the CAR, highlighting crosstalk between signalling pathways. Furthermore, we show that a major source for Fas-TNFR activation derives from CAR T cells themselves via activation-induced Fas ligand upregulation, highlighting a universal role of Fas-TNFRs in augmenting CAR T-cell responses. We have identified Fas-CD40 as the optimal chimera for overcoming Fas ligand-mediated kill and enhancing CAR T-cell efficacy.
HELZ2: a new, interferon-regulated, human 3’-5’ exoribonuclease of the RNB family is expressed from a non-canonical initiation codon
Authors: Huntzinger Eric , Sinteff Jordan , Morlet Bastien , Seraphin Bertrand
Published: February 2023

Proteins containing a RNB domain, originally identified inE. coliRNase II, are widely present throughout the tree of life. Many RNB proteins are endowed with 3’-5’ exoribonucleolytic activity but some have lost catalytic function during evolution. Database searches identified a new RNB domain containing protein in human: HELZ2. Analysis of genomic and expression data with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 harbors also two RNA helicase domains and several zinc-fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3’-5’ ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.