bluuebunny/crossref_metadata_2025 huggingface dataset:
Seroprevalence of anti-ganglionic acetylcholine receptor antibodies in patients with functional neurological symptom disorder/conversion disorder
Authors: Nagata Ryusei , Matsuura Eiji , Nozuma Satoshi , Dozono Mika , Noguchi Yutaka , Ando Masahiro , Hiramatsu Yu , Kodama Daisuke , Tanaka Masakazu , Kubota Ryuji , Yamakuchi Munekazu , Higuchi Yujiro , Sakiyama Yusuke , Arata Hitoshi , Higashi Keiko , Hashiguchi Teruto , Nakane Shunya , Takashima Hiroshi
Published: October 2022

Background

Autoimmune autonomic ganglionopathy (AAG) is a rare disorder characterized by autonomic failure associated with the presence of anti-ganglionic acetylcholine receptor (gAChR) antibodies; however, several studies have reported that individuals with anti-gAChR antibodies present with central nervous system (CNS) symptoms such as impaired consciousness and seizures. In the present study, we investigated whether the presence of serum anti-gAChR antibodies correlated with autonomic symptoms in patients with functional neurological symptom disorder/conversion disorder (FNSD/CD).

Methods

Clinical data were collected for 59 patients presenting with neurologically unexplained motor and sensory symptoms at the Department of Neurology and Geriatrics between January 2013 and October 2017 and who were ultimately diagnosed with FNSD/CD according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition. Correlations between serum anti-gAChR antibodies and clinical symptoms and laboratory data were analyzed. Data analysis was conducted in 2021.

Results

Of the 59 patients with FNSD/CD, 52 (88.1%) exhibited autonomic disturbances and 16 (27.1%) were positive for serum anti-gAChR antibodies. Cardiovascular autonomic dysfunction, including orthostatic hypotension, was significantly more prevalent (75.0%vs34.9%,p= 0.008), whereas involuntary movements were significantly less prevalent (31.3%vs69.8%,p= 0.007), among anti-gAChR antibody-positive compared with - negative patients. Anti-gAChR antibody serostatus did not correlate significantly with the frequency of other autonomic, sensory, or motor symptoms analyzed.

Conclusions

An autoimmune mechanism mediated by anti-gAChR antibodies may be involved in the etiology of FNSD/CD in a subgroup of patients.
The Association of Alpha Globin Gene Copy Number with Exhaled Nitric Oxide in a Cross-sectional Study of Healthy Black Adults
Authors: Ruhl A. Parker , Jackson Jarrett M. , Carhuas Carlos J. , Niño de Rivera Jessica G. , Fay Michael P. , Weinberg J. Brice , Que Loretta G. , Ackerman Hans C.
Published: October 2022

Introduction

The genetic determinants of fractional exhalation of nitric oxide (FeNO), a marker of lung inflammation, are understudied in Black individuals. Alpha globin (HBA) restricts nitric oxide signaling in arterial endothelial cells via interactions with nitric oxide synthase (NOS); however, its role in regulating the release of NO from respiratory epithelium is less well understood. We hypothesized that anHBAgene deletion, common among Black individuals, would be associated with higher FeNO.

Methods

Healthy Black adults were enrolled at four study sites in North Carolina from 2005-2008. FeNO was measured in triplicate using a nitric oxide analyzer. The −3.7 kbHBAgene deletion was genotyped using droplet digital PCR on genomic DNA. The association of FeNO withHBAcopy number was evaluated using multivariable linear regression employing a linear effect ofHBAcopy number and adjusting for age, sex, and serum IgE levels. Post-hoc analysis employing a recessive mode of inheritance was performed.

Results

895 individuals were in enrolled in the study and 720 consented for future genetic research; 643 had complete data and were included in this analysis. Median (25th, 75th) FeNO was 20 (13, 31) ppb.HBAgenotypes were: 30 (4.7%) -a/-a, 197 (30.6%) -a/aa, 405 (63%) aa/aa, and 8 (1.2%) aa/aaa. Subjects were 35% male with median age 20 (19, 22) years. Multivariable linear regression analysis revealed no association between FeNO andHBAcopy number (β = −0.005 [95% CI: −0.042, 0.033], p=0.81). In the post-hoc sensitivity analysis, homozygosity for the HBA gene deletion was associated with higher FeNO (β = 0.107 [95% CI 0.003, 0.212]; p = 0.045)

Conclusion

We found no association betweenHBAcopy number and FeNO using a prespecified additive genetic model. However, a post hoc recessive genetic model found FeNO to be higher among subjects homozygous for theHBAdeletion.

KEY MESSAGES

What is already known on this topic– The alpha subunit of hemoglobin restricts the release of nitric oxide from vascular endothelial cells, but alpha globin’s role in restricting exhaled nitric oxide is less well understood.

What this study adds– We examined the association between fractional exhaled nitric oxide and deletion of the alpha globin gene, a frequent genetic polymorphism among people with African or Asian ancestry. We found that healthy Black individuals who were homozygous for the alpha globin gene deletion had higher fractional exhaled nitric oxide, consistent with alpha globin’s role as a nitric oxide restrictor.

How this study might affect research, practice or policy– An alpha globin gene deletion, commonly found among Black individuals, may increase fractional exhaled nitric oxide. Whether this changes the normal range of fractional exhaled nitric oxide for Black individuals or impacts the risk of developing asthma requires further study.
Time trends of mental health indicators in Germany’s adult population before and during the COVID-19 pandemic
Authors: Mauz Elvira , Walther Lena , Junker Stephan , Kersjes Christina , Damerow Stefan , Eicher Sophie , Hölling Heike , Müters Stephan , Peitz Diana , Schnitzer Susanne , Thom Julia
Published: October 2022

Background

Times of crisis such as the COVID-19 pandemic are expected to compromise mental health. Despite a large number of studies, evidence on the development of mental health in general populations during the pandemic is inconclusive. One reason may be that representative data spanning the whole pandemic and allowing for comparisons to pre-pandemic data are scarce.

Methods

We analyzed representative data from telephone surveys of Germany’s adults: “German Health Update (GEDA)” and “COVID-19 vaccination rate monitoring in Germany (COVIMO)”. Three indicators of mental health were observed in approximately 1,000 and later 3,000 randomly sampled participants monthly until June 2022: symptoms of depression (observed since April 2019 using the PHQ-2), symptoms of anxiety (observed since March 2021 using the GAD-2) and self-rated mental health (observed since March 2021 using a single item). We produced time series graphs including estimated three-month moving means and proportions of individuals with a positive screen (PHQ/GAD-2 score ≥ 3) and of those reporting very good/excellent mental health, as well as smoothing curves. We also compared time periods between years. Analyses were stratified by sex, age, and level of education.

Results

While mean depressive symptom scores declined from the first wave of the pandemic to summer 2020, they increased from October 2020 and remained consistently elevated throughout 2021 with another increase between 2021 and 2022. Correspondingly, the proportion of positive screens first decreased from 11.1 % in spring/summer 2019 to 9.3 % in the same period in 2020 and then rose to 13.1 % in 2021 and to 16.9 % in 2022. While depressive symptoms increased in all subgroups at different times, developments among women, the youngest and eldest adults, and the high level of education group stand out. Furthermore, symptoms of anxiety increased while self-rated mental health decreased between 2021 and 2022.

Conclusions

Elevated symptom levels and reduced self-rated mental health at the end of our observation period in June 2022 call for further continuous mental health surveillance. Mental healthcare needs of the population should be monitored closely. Findings should serve to inform policymakers and clinicians of ongoing dynamics to guide health promotion, prevention, and care.
Fast multi-resolution consensus clustering
Authors: van Dongen Stijn
Published: October 2022

Clustering is a key tool for exploring results from large scale data collection efforts. It is especially useful to find clusterings (partitions of data into non-overlapping sets) at different levels of granularity, ranging from detailed to abstract. In order to be consistent such a set of clusterings should be nested, requiring that elements that group together in a given clustering group together in all coarser clusterings. Hierarchical clustering provides a tree for the data and naturally induces nested clusterings, but none of the methods have gained traction to provide such a multi-resolution view. Widely used methods such as Leiden and the Markov Cluster method (MCL) can produce clusterings at different scales controlled by a resolution parameter, but the results are generally not nested. I introduce Restricted Contingency Linkage (RCL), a parameter-free consensus method that uniquely integrates and reconciles a set of flat clusterings with potentially widely varying levels of granularity into a single multi-resolution view. A common starting point in consensus methods is the association matrix A, where Aij tallies the number of co-occurrences of i and j in the same cluster across all clusterings. RCL creates a matrix R where Rij tallies a measure that differentiates i-j pairs with respect to the amount that they co-cluster in pairs of clusterings while taking into account the subset relationship between the clusters involved. The entries in R are fully abstracted from the input data, richly differentiated and uniformly normalised, making it suitable for single linkage clustering. From the resulting tree a limited set of flat clusterings is obtained by varying a resolution criterion along a logarithmic scale. I validate the method using large-scale single-cell transcriptome data from human developing kidneys, along with visualisations and quality control measures of clustering ensembles Marker gene expression is summarised in a heatmap across the multi-level RCL clusters, providing a coherent view of cell type and cell state hierarchies within the tissue. This reveals clusters corresponding to small populations of mast cells, plasma cells and interstitial cells, and shows segregation of cycling cells in small populations across different cell clades. Given an ensemble of input clusterings, RCL rapidly enables these analyses in a parameter-free manner. An RCL reference implementation is provided for clustering ensembles that are associated with a network G, further restricting the RCL matrix to entries that correspond to edges in G. For a network G with m edges this implementation has complexity O(m(p2+log(m))) where p is the number of input clusterings, taking less than a minute on a dataset with N=27k elements, m=1.5M edges and p=24 clusterings. The implementation, including software for QC plots, marker gene heatmaps and other visualisations is available as part of the MCL software package (https://github.com/micans/mcl).
Brief report: Reclassifying SCLC-Y as SMARCA4 deficient malignancies - resolving the controversy
Authors: Ng Jin , Cai Ling , Girard Luc , Prall Owen W.J. , Rajan Neeha , Khoo Christine , Batrouney Ahida , Kersbergen Ariena , Christie Michael , Minna John D. , Burr Marian L. , Sutherland Kate D.
Published: October 2022

Introduction

The classification of small cell lung cancer (SCLC) into distinct molecular subtypes defined by ASCL1, NEUROD1, POU2F3 or YAP1 expression, paves the way for the development of targeted therapeutics. However, the existence of a distinct YAP1-expressing SCLC subtype remains controversial. Here we have undertaken a detailed molecular and histological characterisation of YAP1 expressing SCLC-Y to understand the biology of this proposed subtype.

Methods

The mutational landscape of human SCLC cell lines was interrogated to identify pathogenic genomic alterations unique to SCLC-Y. Xenograft tumours generated from cell lines representing the molecular subtypes of SCLC (SCLC-A, -N, -P and -Y) were evaluated by a panel of pathologists. Diagnoses were validated by transcriptomic analysis of primary tumour and human cell line datasets.

Results

Unexpectedly, pathogenic mutations in SMARCA4 were identified in six of eight SCLC-Y cell lines and correlated with reduced SMARCA4 mRNA and protein expression. Pathologist evaluations revealed that SMARCA4-deficient SCLC-Y tumours exhibited features consistent with thoracic SMARCA4-deficient undifferentiated tumours (SMARCA4-UT). Similarly, the transcriptional profile SMARCA4-mutant SCLC-Y lines more closely resembled primary SMARCA4-UT, or SMARCA4-deficient non-small cell carcinoma, than SCLC. Combining clinical, pathological, transcriptomic, and genetic data we found little evidence to support a diagnosis of SCLC for any of the YAP1-expressing cell lines originally used to define the SCLC-Y subtype.

Conclusions

SCLC-Y cell lines harbour inactivatingSMARCA4mutations and exhibit characteristics consistent with SMARCA4-deficient malignancies rather than SCLC. Our findings suggest that, unlike ASCL1, NEUROD1 and POU2F3, YAP1 is not a subtype defining transcription factor in SCLC.
Knowledge, attitude and practice of primary school teachers toward epilepsy in Khartoum city, Sudan: A cross-sectional Study
Authors: MohamedSharif Abubaker A , Mohammed Isra Bdraldein Salih , Koko Abubaker E.A.
Published: October 2022

Objectives

The aim is to assess the knowledge, attitude and practice of the primary school teachers toward.

Methods

A descriptive cross-sectional study was conducted among primary school teachers in Khartoum using self-administered, closed ended questionnaires.

Results

Almost all teachers have heard about epilepsy before. Most of them believed that epilepsy was due to genetic factors (25.4%). (74.6%) of the participants thought that epilepsy was a contagious disease. Concerning practice, (26.5%) of the teachers who did first aid, they carried out all the steps of management truly.

Conclusion

Teachers generally have some knowledge about epilepsy, but there were also deficiencies in their management measures. Most of them heard about epilepsy from community reflecting the need for training sessions and a national program to raise their awareness and attitude.
Systematic Evaluation of Common Natural Language Processing Techniques to Codify Clinical Notes
Authors: Tavabi Nazgol , Singh Mallika , Pruneski James , Kiapour Ata M.
Published: October 2022

Proper codification of medical diagnoses and procedures is essential for optimized health care management, quality improvement, research, and reimbursement tasks within large healthcare systems. Assignment of diagnostic or procedure codes is a tedious manual process, often prone to human error. Natural Language Processing (NLP) have been suggested to facilitate these manual codification process. Yet, little is known on best practices to utilize NLP for such applications. Here we comprehensively assessed the performance of common NLP techniques to predict current procedural terminology (CPT) from operative notes. CPT codes are commonly used to track surgical procedures and interventions and are the primary means for reimbursement. The direct links between operative notes and CPT codes makes them a perfect vehicle to test the feasibility and performance of NLP for clinical codification. Our analysis of 100 most common musculoskeletal CPT codes suggest that traditional approaches (i.e., TF-IDF) can outperform resource intensive approaches like BERT, in addition to providing interpretability which can be very helpful and even crucial in the clinical domain. We also proposed a complexity measure to quantify the complexity of a classification task and how this measure could influence the effect of dataset size on model’s performance. Finally, we provide preliminary evidence that NLP can help minimize the codification error, including mislabeling due to human error.
Prevalence of diarrheagenicEscherichia coliand impact on child health in Cap-Haitien, Haiti
Authors: Diaz Jenna N. , Iannotti Lora L. , Louis Dulience Sherlie Jean , Vie Sydney , Jiang Xuntian , Grigura Vadim , Boncy Jacques , Marhône Pierre Francesca J. , Kuhlmann F. Matthew
Published: October 2022

Background

Diarrheagenic Escherichiacoli(DEC) are common pathogens infecting children during their growth and development. Determining the epidemiology and the impact of DEC on child anthropometric measures informs prioritization of prevention efforts. These relationships were evaluated in a novel setting, Cap-Haitien, Haiti.

Methods

A case-control study of children 6-36 months of age enrolled 99 cases with diarrhea and 96 asymptomatic controls. Assessments were performed at enrollment and one month follow-up. Established PCR methodologies targeted DEC using fecal swabs. The association between pathogens and anthropometric z-scores was determined using multiple linear regression.

Results

EnterotoxigenicEscherichia coli(ETEC) was identified in 21.9% of cases vs. 16.1% of controls with heat-stable producing ETEC significantly associated with symptomatic disease. EnteroaggregativeE. coli(EAEC) was found in 30.2% of cases vs. 27.3% of controls, and typical enteropathogenicE. coliin 6.3% vs. 4.0% of cases and controls, respectively. Multivariate linear regression demonstrated ETEC and EAEC were significantly associated with reduced weight-age z-score (WAZ) and height-age z-score (HAZ) after adjusting for confounders.

Conclusions

DEC are prevalent in north Haitian children. ETEC, EAEC, household environment, and diet are associated with unfavorable anthropometric measures. Further studies may quantify the contribution of individual pathogens to adverse health outcomes.

Author Summary

Multiple factors contribute to poor child growth and development including infectious diarrhea, malnutrition, and water, sanitation, and hygiene infrastructure. Efforts to improve child development require prioritization based on their cost and expected benefits. This study contributes to prioritization efforts by determining the local burden of disease in an understudied region, Cap-Haitien, Haiti, and associating this burden with measures of child growth. Moreover, it captures data on social determinants contributing to child growth to control for confounding variables. Unlike prior studies in Haiti, we evaluated children with diarrheal disease in the community instead of the hospital setting. Ultimately, we showed that EnterotoxigenicEscherichia coliand EnteroaggregativeE. coliare common and associated with surrogate measures of poor child growth. This result suggests that ETEC vaccination efforts may have a strong effect on improving child health. This work supports the continued investments in the development of ETEC vaccines.
Infection-induced immunity is associated with protection against SARS-CoV-2 infection, but not decreased infectivity during household transmission
Authors: Frutos Aaron M , Kuan Guillermina , Lopez Roger , Ojeda Sergio , Shotwell Abigail , Sanchez Nery , Saborio Saira , Plazaola Miguel , Barilla Carlos , Kenah Eben , Balmaseda Angel , Gordon Aubree
Published: October 2022

Background

Understanding the impact of infection-induced immunity on SARS-CoV-2 transmission will provide insight into the transition of SARS-CoV-2 to endemicity. Here we estimate the effects of prior infection induced immunity and children on SARS-CoV-2 transmission in households.

Methods

We conducted a household cohort study between March 2020-June 2022 in Managua, Nicaragua where when one household member tests positive for SARS-CoV-2, household members are closely monitored for SARS-CoV-2 infection. Using a pairwise survival model, we estimate the association of infection period, age, symptoms, and infection-induced immunity with secondary attack risk.

Results

Overall transmission occurred in 72.4% of households, 42% of household contacts were infected and the secondary attack risk was 13.0% (95% CI: 11.7, 14.6). Prior immunity did not impact the probability of transmitting SARS-CoV-2. However, participants with pre-existing infection-induced immunity were half as likely to be infected compared to naïve individuals (RR 0.53, 95% CI: 0.39, 0.72), but this reduction was not observed in children. Likewise, symptomatic infected individuals were more likely to transmit (RR 24.4, 95% CI: 7.8, 76.1); however, symptom presentation was not associated with infectivity of young children. Young children were less likely to transmit SARS-CoV-2 than adults. During the omicron era, infection-induced immunity remained protective against infection.

Conclusions

Infection-induced immunity is associated with protection against infection for adults and adolescents. While young children are less infectious, prior infection and asymptomatic presentation did not reduce their infectivity as was seen in adults. As SARS-CoV-2 transitions to endemicity, children may become more important in transmission dynamics.

Article summary

Infection-induced immunity protects against SARS-CoV-2 infection for adolescents and adults; however, there was no protection in children. Prior immunity in an infected individual did not impact the probability they will spread SARS-CoV-2 in a household setting.
Prediction of the risk for diabetic neuropathy among diabetes mellitus patients at selected referral hospitals, in Amhara regional state Northwest Ethiopia, January, 2005- December 2021; Development and validation of risk prediction model
Authors: Gelaw Negalgn Byadgie , Muche Achenef Asmamaw , Alem Adugnaw Zeleke , Gebi Nebiyu Bekele , Chekol Yazachew Moges , Tesfie Tigabu Kidie , Tebeje Tsion Mulat
Published: October 2022

Background

Diabetic neuropathy is the most common complication in both Type-1 and Type-2 DM patients with more than one half of all patients developing nerve dysfunction in their lifetime. Although, risk prediction model was developed for diabetic neuropathy in developed countries, It is not applicable in clinical practice, due to poor data, methodological problems, inappropriately analyzed and reported. To date, no risk prediction model developed for diabetic neuropathy among DM in Ethiopia, Therefore, this study aimed prediction the risk of diabetic neuropathy among DM patients, used for guiding in clinical decision making for clinicians

Objective

Prediction of the risk for diabetic neuropathy among diabetes mellitus patients, in selected referral hospitals, Amhara regional state, northwest Ethiopia,2022

Methods

A retrospective follow up study was conducted with a total of 808 DM patients were enrolled from January 1,2005 to December 30,2021 at two selected referral hospitals in Amhara regional state. Multi-stage sampling techniques were used and the data was collected by checklist from medical records by Kobo collect and exported to STATA version-17 for analysis. Lasso method were used to select predictors and entered to multivariable logistic regression with P-value<0.05 was used for nomogram development. Model performance was assessed by AUC and calibration plot. Internal validation was done through bootstrapping method and decision curve analysis was performed to evaluate net benefit of model

Results

The incidence proportion of diabetic neuropathy among DM patients was 21.29 %(95% CI; 18.59, 24.25).In multivariable logistic regression glycemic control, other comorbidities, physical activity, hypertension, alcohol drinking, type of treatment, white blood cells and red blood cells count were statistically significant. Nomogram was developed, has discriminating power AUC; 73.2 %(95% CI; 69.0%, 77.3%) and calibration test (P-value = 0.45). It was internally validated by bootstrapping method with discrimination performance 71.7(95% CI; 67.2 %, 75.9%).It had less optimism coefficient (0.015).To make nomogram accessible, mobile based tool were developed. In machine learning, classification and regression tree has discriminating performance of 70.2 %(95 % CI; 65.8%, 74.6%).The model had high net benefit at different threshold probabilities in both nomogram and classification and regression tree.

Conclusion

The developed nomogram and decision tree, has good level of accuracy and well calibration, easily individualized prediction of diabetic neuropathy. Both models had added net benefit in clinical practice and to be clinically applicable mobile based tool were developed.
kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data
Authors: Dill-McFarland Kimberly A , Mitchell Kiana , Batchu Sashank , Segnitz R Max , Benson Basilin , Janczyk Tomasz , Cox Madison S , Mayanja-Kizza Harriet , Boom W Henry , Benchek Penelope , Stein Catherine M. , Hawn Thomas R , Altman Matthew C
Published: October 2022

We introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling of RNA-seq including covariates, weights, random effects, covariance matrices, and fit metrics. In simulated datasets, kimma detects differentially expressed genes (DEGs) with similar specificity, sensitivity, and computational time as limma unpaired and dream paired models. Unlike other software, kimma supports covariance matrices as well as fit metrics like AIC. Utilizing genetic kinship covariance, kimma revealed that kinship impacts model fit and DEG detection in a related cohort. Thus, kimma equals or outcompetes current DEG pipelines in sensitivity, computational time, and model complexity.
Initiator AUGs are discriminated from elongator AUGs predominantly through mRNA accessibility inC. crescentus
Authors: Ghosh Aishwarya , Bharmal Mohammed-Husain M. , Ghaleb Amar M. , Schrader Jared M.
Published: October 2022

Translation initiation in bacteria is thought to occur upon base-pairing between the Shine-Dalgarno site in the mRNA and anti-Shine-Dalgarno site in the rRNA. However, in many bacterial species, such asCaulobacter crescentus, a minority of mRNAs have Shine-Dalgarno sites. To examine the functional importance of Shine-Dalgarno sites inC. crescentus, we analyzed the transcriptome and found more Shine-Dalgarno sites exist in the coding sequence than preceding start codons. To examine the function of Shine-Dalgarno sites in initiation we designed a series of mutants with altered ribosome accessibility and Shine-Dalgarno content in translation initiation regions (TIRs) and elongator AUG regions (EARs). A lack of mRNA structure content is required for initiation in TIRs, and when introduced into EARs, can stimulate initiation, suggesting that low mRNA structure content is a major feature required for initiation. SD sites appear to stimulate initiation in TIRs, which generally lack structure content, but SD sites only stimulate initiation in EARs if RNA secondary structures are destabilized. Taken together, this suggests that the difference in secondary structure between TIRs and EARs directs ribosomes to start codons where SD base pairing can tune the efficiency of initiation, but SDs in EARs do not stimulate initiation as they are blocked by stable secondary structures. This highlights the importance of studying translation initiation mechanisms in diverse bacterial species.
Smooth Muscle Myosin 2 Filaments Dynamically Assemble and Stabilize During Induced Contractility
Authors: Bennett Margaret A. , Demeulenaere Sasha G. , Wu Huini , Patel Hiral , Sala Stefano , Longtine Elizabeth R. , Oakes Patrick W. , Beach Jordan R.
Published: October 2022

Vascular smooth muscle cells (SMCs) line blood vessels throughout the body, where they dynamically alter vessel diameter to regulate blood pressure, provide structural integrity, and absorb shock on a beat-to-beat timescale. As smooth muscle function fails, profound vascular disease ensues, often with tragic results- even death. Smooth muscle myosin 2 (SM2) is the dominant motor protein that actuates contractility and allows SMCs to perform these vital functions. To function, SM2 monomers dynamically assemble into filaments, which upon SMC activation, associate with filamentous actin to drive contractility. Despite the critical contribution of SM2 to SMC function, foundational aspects of SM2 assembly and dynamics remain unexplored. To remedy this, we expressed EGFP-tagged SM2 in rat aortic smooth muscle cells (A7R5), which retained a cytosolic calcium and contractile response to the acetylcholine agonist carbachol. Using fluorescence recovery after photobleaching (FRAP), we observed rapid polymer exchange kinetics for SM2, more similar to non-muscle myosin 2 (NM2) than striated myosin 2s. Consistently, super-resolution imaging of SM2 and NM2 suggests they form filamentous co-polymers. Using a single cell filament assembly assay, we observed that the majority of SM2 is assembled in filaments at steady-state, but that SMC activation with carbachol rapidly increases SM2 assembly levels. Carbachol also reduced polymer exchange kinetics, suggesting stabilization of filaments during SMC activation. This carbachol-induced increase in SM2 assembly and decrease in exchange kinetics closely parallels the cytosolic calcium and contractility kinetics. Collectively, our data supports an updated model in which highly dynamic SM2 filaments assemble, are stabilized, and are activated to produce cell-scale contractile forces during SMC activation.
Polymorphisms in HIV-1nefare associated with plasma concentration of biomarkers of endothelial activation
Authors: Mezoh Genevieve , Lutchman Nereshni , Cave Eleanor M , Prigge Katherine , Worsley Catherine , Martinson Neil , Mayne Elizabeth , Lambson Bronwen E , Moore Penny L , Crowther Nigel J
Published: October 2022

Infection with HIV is associated with an increased risk of cardiovascular disease (CVD), which may be mediated by the effect of the viral proteins, Nef and Tat, on inflammation and endothelial activation. The viral genes coding for Nef and Tat contain numerous polymorphisms, which we hypothesised may be differentially associated with endothelial activation. Therefore, our aim was to assess the association of these polymorphisms with endothelial activation and inflammation in subjects infected with HIV-1.

The HIV-1nefandtatgenes were sequenced from clinical isolates from 31 and 34 patients, respectively. Plasma concentration of biomarkers of endothelial activation (intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), endothelial leukocyte adhesion molecule-1 (E-selectin), monocyte chemoattractant protein-1 (MCP-1) and von Willebrand factor (vWF)), and biomarkers of inflammation (tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-8 (IL-8)), were measured. Analysis of HIV-1nefgene sequences identified five polymorphisms (V16I, H40Y, T50A,H, S169N and H188Q,S) that were each significantly (p<0.05) associated with ICAM-1 plasma concentration. An additive effect of these variants on plasma ICAM-1 concentration (p=0.004 for trend), was observed. No significant associations were seen between Tat amino acid residues and plasma concentration of markers of endothelial activation and inflammation. These are the first humanin vivodata that support the hypothesis thatnefgene polymorphisms impact endothelial function.

Importance

Cardiovascular disease (CVD) is a leading cause of mortality in adults living with HIV, which may in part be due to endothelial activation and inflammation caused by the viral proteins, Nef and Tat. However, there is no data from humans supporting the CVD-associated Nef and Tat hypothesis, and assays for accurately measuring Nef and Tat plasma concentrations are not currently available. Therefore, we hypothesized that polymorphisms in thenefandtatgenes of clinical viral isolates may be associated with host plasma markers of endothelial activation and inflammation. Our results show that this was the case, with fivenefpolymorphisms showing both individual and additive association with plasma concentration of ICAM-1. The HIV-1Tatgene, however, showed no significant association with plasma concentrations of markers of endothelial activation and inflammation. This is the first human study to directly link Nef to endothelial activation and to provide a possible screening tool i.e.,nefgenotyping, for identifying individuals at high risk of endothelial-based diseases.
The Eyes Absent family members EYA4 and EYA1 promote PLK1 activation and successful mitosis through tyrosine dephosphorylation
Authors: Nelson Christopher B. , Rogers Samuel , Roychoudhury Kaushik , Tan Yaw Sing , Atkinson Caroline J. , Sobinoff Alexander P. , Tomlinson Christopher G. , Hsu Anton , Lu Robert , Dray Eloise , Haber Michelle , Fletcher Jamie I. , Cesare Anthony J. , Hegde Rashmi S. , Pickett Hilda A.
Published: October 2022

The Eyes Absent family of proteins (EYA1-4) are a biochemically unique group of tyrosine phosphatases known to be tumour promoting across a range of cancer types. To date, the molecular targets of EYA phosphatase activity remain largely uncharacterised. Here, we identify Polo-like kinase 1 (PLK1) as a direct interactor and phosphatase substrate of both EYA4 and EYA1, with pY445 on PLK1 being the primary target site. EYA-mediated dephosphorylation of PLK1 in the G2 phase of the cell cycle is required for centrosome maturation, PLK1 localization to centrosomes, and polo-box domain (PBD) dependent interactions between PLK1 and the PLK1-activating proteins BORA and CEP192. Molecular dynamics simulations support the rationale that pY445 confers a structural impairment to PBD-substrate interactions that is relieved by EYA-mediated dephosphorylation. Depletion of EYA4 or EYA1, or chemical inhibition of EYA phosphatase activity, dramatically reduces PLK1 activation, causing mitotic defects and cell death. Overall, we have characterized a novel phosphotyrosine signalling network governing PLK1 and mitosis. This work provides a mechanism of cell killing for EYA phosphatase inhibitors with important therapeutic implications.
The glyoxylate shunt protein ICL-1 protects from mitochondrial superoxide stress through activation of the mitochondrial unfolded protein response
Authors: Wang Guoqiang , Laranjeiro Ricardo , LeValley Stephanie , Van Raamsdonk Jeremy M. , Driscoll Monica
Published: October 2022

Eliminating mitochondrial superoxide dismutase (SOD) causes neonatal lethality in mice and death of flies within 24 hours after eclosion. Deletion of mitochondrialsodgenes inC. elegansimpairs fertility as well, but surprisingly is not detrimental to survival of progeny generated. The comparison of metabolic pathways among mouse, flies and nematodes reveals that mice and flies lack the glyoxylate shunt. Here we show that ICL-1, the only protein of the glyoxylate shunt, is critical for protection against embryonic lethality resulting from elevated levels of mitochondrial superoxide. In exploring the mechanism by which ICL-1 protects against ROS-mediated embryonic lethality, we find that ICL-1 is required for the efficient activation of mitochondrial unfolded protein response (UPRmt) and that the UPRmtis essential to suppress embryonic/neonatal lethality in animals lacking mitochondrial SOD. In sum, we identified a biochemical pathway that highlights a molecular strategy for combating superoxide consequences in cells.
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
Authors: Zvyagin Maxim , Brace Alexander , Hippe Kyle , Deng Yuntian , Zhang Bin , Bohorquez Cindy Orozco , Clyde Austin , Kale Bharat , Perez-Rivera Danilo , Ma Heng , Mann Carla M. , Irvin Michael , Gregory Pauloski J. , Ward Logan , Hayot-Sasson Valerie , Emani Murali , Foreman Sam , Xie Zhen , Lin Diangen , Shukla Maulik , Nie Weili , Romero Josh , Dallago Christian , Vahdat Arash , Xiao Chaowei , Gibbs Thomas , Foster Ian , Davis James J. , Papka Michael E. , Brettin Thomas , Stevens Rick , Anandkumar Anima , Vishwanath Venkatram , Ramanathan Arvind
Published: October 2022

We seek to transform how new and emergent variants of pandemiccausing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLMs) which can learn the evolutionary landscape of SARS-CoV-2 genomes. By pretraining on over 110 million prokaryotic gene sequences and finetuning a SARS-CoV-2-specific model on 1.5 million genomes, we show that GenSLMs can accurately and rapidly identify variants of concern. Thus, to our knowledge, GenSLMs represents one of the first whole genome scale foundation models which can generalize to other prediction tasks. We demonstrate scaling of GenSLMs on GPU-based supercomputers and AI-hardware accelerators utilizing 1.63 Zettaflops in training runs with a sustained performance of 121 PFLOPS in mixed precision and peak of 850 PFLOPS. We present initial scientific insights from examining GenSLMs in tracking evolutionary dynamics of SARS-CoV-2, paving the path to realizing this on large biological data.
Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments
Authors: Khan Nelson , Muge Edward , Mulaa Francis J. , Wamalwa Benson , von Bergen Martin , Jehmlich Nico , Wick Lukas Y.
Published: October 2022

Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equisetiK3) and a co-metabolically HCH-degrading bacterium (Sphingomonassp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using13C-labelled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of13C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1 – 14.2%), labeling ratio (LR, 0.13 – 0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of13C-labeled fungal metabolites into bacterial proteins. Distinct13C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).
A quantitative fluorescence-based approach to study mitochondrial protein import
Authors: Jain Naintara , Gomkale Ridhima , Bernhard Olaf , Rehling Peter , Cruz-Zaragoza Luis Daniel
Published: October 2022

Mitochondria play central roles in cellular energy production and metabolism. Most of the proteins that are required to carry out these functions are synthesized in the cytosol and imported into mitochondria. A growing number of metabolic disorders arising from mitochondrial dysfunction can be traced to errors in mitochondrial protein import. The mechanisms underlying the import of precursor proteins are commonly studied by using radioactively-labeled precursor proteins, which are imported into purified mitochondria. Here, we establish a fluorescence-based import assay to analyze protein import into mitochondria. We show that fluorescently-labeled precursors enable import analysis with similar sensitivity to those using radioactive precursors, yet they provide the advantage of quantifying import with picomole resolution. We adapted the import assay to a 96-well plate format allowing for fast analysis in a screening-compatible format. Moreover, we show that fluorescently labeled precursors can be used to monitor the assembly of the F1F0 ATP-synthase in purified mitochondria. Thus, we provide a sensitive fluorescence-based import assay that enables quantitative and fast-import analysis.
FBXO7/ntc and USP30 antagonistically set the ubiquitination threshold for basal mitophagy and provides a target for Pink1 phosphorylationin vivo
Authors: Sanchez-Martinez Alvaro , Martinez Aitor , Whitworth Alexander J.
Published: October 2022

Functional analyses of genes linked to heritable forms of Parkinson’s disease (PD) have revealed fundamental insights into the biological processes underpinning pathogenic mechanisms. Mutations inPARK15/FBXO7cause autosomal recessive PD and FBXO7 has been shown to regulate mitochondrial homeostasis. We investigated the extent to which FBXO7 and itsDrosophilaorthologue, ntc, share functional homology and explored its role in mitophagyin vivo. We show thatntcmutants partially phenocopyPink1andparkinmutants andntcoverexpression supressesparkinphenotypes. Furthermore, ntc can modulate basal mitophagy in a Pink1- and parkin-independent manner by promoting the ubiquitination of mitochondrial proteins, a mechanism that is opposed by the deubiquitinase USP30. This basal ubiquitination serves as the substrate for Pink1-mediated phosphorylation which triggers stress-induced mitophagy. We propose that FBXO7/ntc works in equilibrium with USP30 to provide a checkpoint for mitochondrial quality control in basal conditionsin vivoand presents a new avenue for therapeutic approaches.
Post-translational modification by the Pgf glycosylation machinery modulatesStreptococcus mutansphysiology and virulence
Authors: de Mojana di Cologna Nicholas , Andresen Silke , Samaddar Sandip , Archer-Hartmann Stephanie , Ganguly Tridib , Kajfasz Jessica K. , Garcia Bruna A. , Saengpet Irene , Peterson Alexandra M. , Azadi Parastoo , Szymanski Christine M. , Lemos José A. , Abranches Jacqueline
Published: October 2022

Streptococcus mutansis a keystone pathogen of dental caries, and the ability to form biofilms is essential for its pathogenicity. We identified a glycosylation machinery (Pgf) inS. mutansthat post-translationally modifies two surface-associated adhesins, Cnm and WapA. The fourpgfgenes (pgfS,pgfM1,pgfE,andpgfM2) are part ofS. mutanscore genome and we hypothesized that the scope of Pgf goes beyond Cnm and WapA. By inactivating eachpgfgene individually or creating a quadruplepgfmutant inS. mutansOMZ175, we showed that the Pgf machinery is important for biofilm formation. Compared to OMZ175, differences in surface charge, membrane stability, and genetic competence were also observed for most mutants. Importantly,in silicoanalyses and tunicamycin MIC assays suggest a functional redundancy between the Pgf machinery and the rhamnose-glucose polysaccharide synthesis pathway. Using a rat oral colonization model, we showed a 10-fold reduction in recovered CFUs for thepgfquadruple mutant compared to OMZ175. Finally, using Cnm as a model, we showed by glycoproteomics analyses that Cnm is heavily modified with N-acetyl hexosamine in OMZ175 whereas phosphorylations were observed for thepgfSmutant. Our findings indicate that the Pgf machinery participates in important aspects ofS. mutanspathobiology.

Graphical Abstract

Abbreviated summary

In this study, we demonstrate that the Pgf glycosylation machinery ofStreptococcus mutans, a keystone pathogen of dental caries, regulates several aspects of bacterial pathophysiology that ultimately contribute toS. mutansfitness in oral colonization experiments. Using the heavily glycosylated Cnm adhesin as a model, we found that inactivation of the glycosyltransferase PgfS results in loss of Cnm glycosylation, but instead, Cnm became heavily phosphorylated, suggesting a crosstalk/competition between these two post-translational modification mechanisms.
A novel image-based approach for soybean seed phenotyping using machine learning techniques
Authors: de Carvalho Miranda Melissa Cristina , Aono Alexandre Hild , Pinheiro José Baldin
Published: October 2022

Soybean is one of the most important sources of protein and vegetable oil in the world. Given its increasing demand, the increment in yield has only been possible due to investments in research and production technology, especially in breeding programs. One of the main factors influencing soybean yield is the seed morphology; however, its analyses are hampered by the lack of efficient computational approaches with not only accurate results, but also a high flexibility to user preferences and needs. In this context, the present work provides a methodological framework for: (i) seed segmentation in soybean images; (ii) seed morphological evaluation; and (iii) image-based prediction of the hundred-seed weight trait. We used genotypes from a partial diallel cross design, which aimed at obtaining genotypes with high agronomic performance. In addition to the measurement of the hundred-seed weight, we collected RGB images of seeds of each plot. For image segmentation, we created an in-house image processing pipeline, which enabled a full morphological seed evaluation. For predicting the hundred-seed weight, we compared different machine learning algorithms using as input the morphological characteristics obtained, and also features from state-of-the-art convolutional neural network (CNN) architectures. The image segmentation methodology showed to be highly efficient, as more than 98% of the seeds in the images were correctly identified. Even if the seeds were close, the segmentation strategy could separate them into independent image components. In addition to supplying a highly accurate decision support system for soybean breeders, we verified the morphological phenotyping adaptability in other plant species, fully assessing the pipeline generalization. We consider the use of this methodology highly advantageous, as the method is entirely based on widely used morphological operations, which results in an easy implementation and low computational costs. Using these morphological measures, we could estimate machine learning models for predicting the hundred-seed weight, achieving considerable predictive accuracy. The same results were observed for CNN-obtained features, showing the efficiency of the morphological measurements as feature extractors. The possibility of obtaining seed morphological characteristics provides a valuable tool for the continuous and efficient development of new soybean cultivars in breeding programs aimed at long-term genetic gain. Additionally, through a faster seed image acquisition workflow, with less chance of errors and low cost, it is also possible to make predictions of important soybean characteristics. The work conducted has the potential to help future research and the industry to develop automated phenotyping tools, incorporating the proposed analytical workflows.
Cropbox: a declarative crop modeling framework
Authors: Yun Kyungdahm , Kim Soo-Hyung
Published: October 2022

Crop models mirror our knowledge on cropsin silico. Therefore, crop modeling inherits common issues of software engineering and often suffers from technical debts. We introduce a new crop modeling framework: Cropbox as a declarative domain-specific language. Recognizing that a crop model is fundamentally an integrated network of generalized state variables, we developed the framework to encapsulate abstract primitives for representing variables, systems, and functions that are essential to crop modeling workflows. With a constrained syntax, high-level model specifications are automatically translated into low-level host code written in Julia programming language. This allows complex crop models to become more accessible and transparent for modelers to build and use. We highlight key capabilities of the Cropbox framework through specific case studies featuring a coupled leaf gas-exchange model and a process-based crop simulation model. We also illustrate potential extensions of the framework to support functional-structural plant modeling (FSPM) using a 3D root architectural model as an example.