bluuebunny/crossref_metadata_2025 huggingface dataset:
A Computational Framework for Intraoperative Pupil Analysis in Cataract Surgery
Authors: Giap Binh Duong , Srinivasan Karthik , Mahmoud Ossama , Ballouz Dena , Lustre Jefferson , Likosky Keely , Mian Shahzad I. , Tannen Bradford L. , Nallasamy Nambi
Published: March 2024

Purpose

Pupillary instability is a known risk factor for complications in cataract surgery. This study aims to develop and validate an innovative and reliable computational framework for the automated assessment of pupil morphologic changes during the various phases of cataract surgery.

Design

Retrospective surgical video analysis.

Subjects

Two hundred forty complete surgical video recordings, among which 190 surgeries were conducted without the use of pupil expansion devices and 50 were performed with the use of a pupil expansion device.

Methods

The proposed framework consists of three stages: feature extraction, deep learning (DL)-based anatomy recognition, and obstruction detection/compensation. In the first stage, surgical video frames undergo noise reduction using a tensor-based wavelet feature extraction method. In the second stage, DL-based segmentation models are trained and employed to segment the pupil, limbus, and palpebral fissure. In the third stage, obstructed visualization of the pupil is detected and compensated for using a DL-based algorithm. A dataset of 5,700 intraoperative video frames across 190 cataract surgeries in the BigCat database was collected for validating algorithm performance.

Main Outcome Measures

The pupil analysis framework was assessed on the basis of segmentation performance for both obstructed and unobstructed pupils. Classification performance of models utilizing the segmented pupil time series to predict surgeon use of a pupil expansion device was also assessed.

Results

An architecture based on the FPN model with VGG16 backbone integrated with the AWTFE feature extraction method demonstrated the highest performance in anatomy segmentation, with Dice coefficient of 96.52%. Incorporation of an obstruction compensation algorithm improved performance further (Dice 96.82%). Downstream analysis of framework output enabled the development of an SVM-based classifier that could predict surgeon usage of a pupil expansion device prior to its placement with 96.67% accuracy and AUC of 99.44%.

Conclusions

The experimental results demonstrate that the proposed framework 1) provides high accuracy in pupil analysis compared to human-annotated ground truth, 2) substantially outperforms isolated use of a DL segmentation model, and 3) can enable downstream analytics with clinically valuable predictive capacity.
Feasibility of a Cluster Randomised Trial on the Effect of Trauma Life Support Training: A Pilot Study
Authors:   Trauma life support training Effectiveness Research Network (TERN) collaborators, Gerdin Wärnberg Martin , Basak Debojit , Berg Johanna , Chatterjee Shamita , Felländer-Tsai Li , Ghag Geeta , Khajanchi Monty , Khan Tamal , Juillard Catherine , Nandu Vipul , Roy Nobhojit , Singh Rajdeep , Dev Soni Kapil , Strömmer Lovisa
Published: March 2024

Importance

There is no high-quality evidence to show that trauma life support training programmes improve patient outcomes.

Objective

To assess the feasibility of conducting a cluster randomised controlled trial comparing the effect of Advanced Trauma Life Support®(ATLS®) and Primary Trauma Care (PTC) with standard care on patient outcomes, and to estimate probable effect sizes and other measures needed for the sample size calculations of a full-scale trial.

Design

A pilot pragmatic three-armed parallel, cluster randomised, controlled trial between April 2022 and February 2023. Patient follow up was 30 days.

Setting

Tertiary care hospitals across metropolitan areas in India.

Participants

Adult trauma patients and residents managing these patients.

Interventions

ATLS®or PTC training for residents in the intervention arms.

Main Outcomes and Measures

The outcomes were consent rate, lost to follow up rate, pass rate, missing data rates, differences in distribution between observed and data extracted from medical records as well as all cause and in-hospital mortality at 30 days from the time of arrival to the emergency department.

Results

Two hospitals were randomised to ATLS®, two to PTC, and three to standard care. We included 376 patients and 22 residents. The percentage of patients who consented to follow up was 77% and the percentage of residents who consented to training was 100%. The lost to follow up rate was 14%. The pass rate was 100%. The missing data was overall low for key variables. Data collected through observations were similar to data extracted from medical records, but there was more missing data in the extracted data. Twenty-two (16%) patients died within 30 days in the standard care arm, one (4%) patient in the ATLS®arm, and three (5%) patients in the PTC arm.

Conclusions and Relevance

Conducting a full-scale cluster randomised controlled trial comparing the effects of ATLS®, PTC, and standard care on patient outcomes will be feasible, especially if such a trial would use data and outcomes available in medical records.

Key Points

Question

Is it feasible to conduct a cluster randomised trial comparing trauma life support training with standard care?

Findings

In this pilot cluster randomized trial that included 376 patients and 22 residents from seven hospitals, we found high consent rates, low lost to follow up rates, and low missing data for key variables.

Meaning

Conducting a full-scale cluster cluster trial comparing the effects of trauma life support training with standard care on patient outcomes will be feasible, especially if such a trial would use data and outcomes available in medical records.
Developing a Motherhood regret scale: An examination of reliability, validity, and association with basic attributes
Authors: Haruyama Ranno , Wakashima Koubun , Koiwa Kohei
Published: March 2024

The first objective of this study was to develop a scale that measures the level of regret of becoming a mother among women at various stages of motherhood (child age ranging from unborn to 29 years old) and examine its reliability and validity. The second objective was to explore the effects of participants’ basic attributes on the regret of becoming a mother. The study recruited mothers who were pregnant (before birth), mothers of infants (age 0–1), young children (age 2–6), primary school-aged children (age 7–12), and adolescents and young adults (age 13–29). In all, responses from 462 participants (458 women, 4 others; mean age = 37.77 [SD= 7.03]; age range = 20–59) were analyzed. As a result, the unidimensional nine-item scale showed an acceptable value for goodness of fit and high reliability (α = .96). In addition, we determined the cut-off score to categorize the regret group. Among the participants in the present study (N= 462), 31 were classified as the regret group, and they represented the scores at the top 7%. Moreover, regarding the association between the participants’ basic attributes and level of regret, we found that “having many children” had a significant negative effect on the predicted level of regret (β = –.19,p< .001) while “being a single mother” had a significant positive effect (β = .11,p< .05). Based on these results, we discuss the structure of the scale that was developed and the effect of a mother’s attributes on the level of regret to provide insights on the attributes of respondents classified into the regret group.
Rust Fungus Red Data List and Census Catalogue for Wales
Authors: Woods Ray G. , Stringer R. Nigel , Evans Debbie A. , Chater Arthur O.
Published: March 2024

The rust fungi are a group of specialised plant pathogens. Conserving them seems to fly in the face of reason. Yet as our population grows and food supplies become more precarious, controlling pathogens of crop plants becomes more imperative. Breeding resistance genes into such plants has proved to be the most cost effective solution. Such resistance genes evolve only in plants challenged by pathogens. We hope this report will assist in prioritising the conservation of natural ecosystems and traditional agro-ecosystems that are likely to be the richest sources of resistance genes. Despite its small size (11% of mainland Britain) Wales has supported 225 rust fungi taxa (including 199 species) representing 78% of the total British mainland rust species. For the first time using widely accepted international criteria and data collected from a number of mycologists and institutions, a Welsh regional threat status is offered for all native Welsh rust taxa. The results are compared with other published Red Lists for Wales. Information is also supplied in the form of a census catalogue, detailing the rust taxa recorded from each of the 13 Welsh vice-counties.

Of the 225 rust taxa so far recorded from Wales 7 are probably extinct (3% of the total), and 39 (18%) are threatened with extinction. Of this latter total 13 taxa (6%) are considered to be Critically Endangered, 15 (7%) to be Endangered and 13 (6%) to be Vulnerable. A further 20 taxa (9%) are Near Threatened, whilst 15 taxa (7%) lacked sufficient data to permit evaluation.

Just over a third of Welsh rust fungi taxa require some form of action, either to better understand their status, or reverse known ongoing declines. This is a similar figure to those presented elsewhere for bryophytes and lichens but higher than the 19% of vascular plants requiring action.
Proofreading and single-molecule sensitivity in T-cell receptor signaling by condensate nucleation
Authors: White William L , Baker David , Groves Jay T , Baker David , Ben-sasson Ariel Jaques , Kueh Hao Yuan
Published: March 2024

T-cells display the remarkable ability to detect single foreign peptides displayed on target cells, while ignoring highly abundant self peptides. This selectivity has been explained by kinetic proofreading in the T-cell receptor (TCR) signaling pathway, which prevents responses to short-lived binding events regardless of their abundance. However, the biochemical mechanisms that drive kinetic proofreading have remained unclear. Here, using computational modeling, we show that these key signaling properties of the TCR pathway can emerge from the dynamics of LAT phosphorylation, diffusion, and condensation following TCR-pMHC binding. In this model, time delays in LAT condensate nucleation underlie kinetic proofreading, enabling selective signaling responses to high-affinity pMHC ligands. The cooperativity in the nucleation and growth of LAT condensates also provides a mechanism to amplify weak signals from single foreign peptides and for condensates to grow with increasing antigen numbers. In contrast to other models, condensate-nucleation proofreading predicts a dependence of signal strength on pMHC spacing at fixed number, a prediction we validated experimentally using a protein scaffold to present pMHCs at defined intervals. Our results suggest that nucleation-condensation proofreading underlies the remarkable antigen detection capabilities of the TCR signaling pathway.
A regulatory B cell subpopulation expressing CD301b lectin promotes breast cancer growth
Authors: Paschall Amy V. , Nawaz Zahra , Avci Fikri Y
Published: March 2024

Tumor-associated carbohydrate antigens (TACAs) can promote tumor growth by regulating the anti-tumor immune response. The accumulation of immune suppressor cells within the tumor in response to TACAs suggests a critical pathway to suppress immune targeting of the tumor. Employing murine breast cancer models, we isolated a regulatory B cell subpopulation in the breast tumor microenvironment that displays an immune suppressive phenotype through its Tn TACA-binding lectin, CD301b. We then demonstrated that depleting CD301b+cells facilitated tumor control and mouse survival, whereas increasing Tn antigen expression decreased mouse survival. As tumor cells use Tn expression to overcome immune targeting, interfering with or blocking the Tn-CD301 axis may unleash the immune system, specifically within the aberrantly glycosylated tumor microenvironment, offering new immunotherapy for breast and other cancers.
Insights Into Ribosomal DNA (rDNA) Dominance and Magnification Through Characterization of Isogenic Deletion Alleles
Authors: Kindelay Selina M. , Maggert Keith A.
Published: March 2024

The major loci for the large primary ribosomal RNA genes (35S rRNAs) exist as hundreds to thousands of tandem repeats in all organisms, and dozens to hundreds in Drosophila. The highly repetitive nature of the rDNA makes it intrinsically unstable, and many conditions arise from the reduction or magnification of copy number, but the conditions under which it does so remains unknown. By targeted DNA damage to the rDNA of the Y chromosome, we created and investigated a series of rDNA alleles. We found that complete loss of rDNA leads to lethality after the completion of embryogenesis, blocking larval molting and metamorphosis. We find that the resident retrotransposons – R1 and R2 – are regulated by active rDNA such that reduction in copy number derepresses these elements. Their expression is highest during the early 1stinstar, when loss of rDNA is lethal. Regulation of R1 and R2 may be related to their structural arrangement within the rDNA, as we find they are clustered in the flanks of the Nucleolus Organizing Region (NOR; the cytological appearance of the rDNA). We assessed the complex nucleolar dominance relationship between X- and Y-linked rDNA using a Histone H3.3-GFP reporter construct and incorporation at the NOR, and found that dominance is controlled by rDNA copy number as at high multiplicity the Y-linked array is dominant, but at low multiplicity the X-linked array becomes derepressed. Finally, we found that multiple conditions that disrupt nucleolar dominance lead to increased rDNA magnification, suggesting that the phenomena of dominance and magnification are related, and a single mechanism may underly and unify these two longstanding observations in Drosophila.
Dynamic fibroblast-immune interactions shape wound healing after brain injury
Authors: Ewing-Crystal Nathan A. , Mroz Nicholas M. , Chang Anthony A. , Merrill Eric Dean , Caryotakis Sofia E. , Teo Leon , Larpthaveesarp Amara , Tsukui Tatsuya , Katewa Aditya , Pennington Remy , McKinsey Gabriel L. , Nelson Sophia , Ciesielska Agnieszka , Dahlgren Madelene W. , Paidassi Helena , Jain Saket , Aghi Manish K. , Bourne James A. , Paz Jeanne T. , Gonzalez Fernando F. , Sheppard Dean , Molofsky Anna V. , Arnold Thomas D. , Molofsky Ari B.
Published: March 2024

Fibroblasts coordinate the response to tissue injury, directing organ regeneration versus scarring. In the central nervous system (CNS), fibroblasts are uncommon cells enriched at tissue borders, and their molecular, cellular, and functional interactions after brain injury are poorly understood. Here we define the fibroblast response to sterile brain damage across time and space. Early pro-fibrotic myofibroblasts infiltrated CNS lesions and were functionally and spatially organized by fibroblast TGFβsignaling, pro-fibrotic macrophages and microglia, and perilesional brain glia that activated TGFβvia integrinαvβ8. Early myofibroblasts subsequently transitioned into a variety of late states, including meningeal and lymphocyte-interactive fibroblasts that persisted long term. Interruption of this dynamic fibroblast-macrophage-glial coordination impaired brain wound healing and the resolution of neuroinflammation, disrupted generation of latede novoCNS lymphocyte niches, and increased mortality in a stroke model. This work highlights an unexpected role of fibroblasts as coordinate regulators of CNS healing and neuroinflammation after brain injury.
Identification of candidate causalcis-regulatory variants underlying electrocardiographic QT interval GWAS loci
Authors: Kadagandla Supraja , Kapoor Ashish
Published: March 2024

Identifying causal variants among tens or hundreds of associated variants at each locus mapped by genome-wide association studies (GWAS) of complex traits is a challenge. As vast majority of GWAS variants are noncoding, sequence variation atcis-regulatory elements affecting transcriptional expression of specific genes is a widely accepted molecular hypothesis. Following thiscis-regulatory hypothesis and combining it with the observation that nucleosome-free open chromatin is a universal hallmark of all types ofcis-regulatory elements, we aimed to identify candidate causal regulatory variants underlying electrocardiographic QT interval GWAS loci. At a dozen loci, selected for higher effect sizes and a better understanding of the likely causal gene, we identified and included all common variants in high linkage disequilibrium with the GWAS variants as candidate variants. Using ENCODE DNase-seq and ATAC-seq from multiple human adult cardiac left ventricle tissue samples, we generated genome-wide maps of open chromatin regions marking putative regulatory elements. QT interval associated candidate variants were filtered for overlap with cardiac left ventricle open chromatin regions to identify candidate causalcis-regulatory variants, which were further assessed for colocalizing with a known cardiac GTEx expression quantitative trait locus variant as additional evidence for their causal role. Together, these efforts have generated a comprehensive set of candidate causal variants that are expected to be enriched forcis-regulatory potential and thereby, explaining the observed genetic associations.
Urinary Clusterin is a biomarker of renal epithelial senescence and predicts human kidney disease progression
Authors: Baird David , Reck Maximillian , Campbell Ross , Docherty Marie-Helena , Vermeren Matthieu , Nam Andy , Yang Wei , Schurman Nathan , Williams Claire , Traynor Jamie P. , Mark Patrick B. , Mylonas Katie , Hughes Jeremy , Denby Laura , Conway Bryan , Ferenbach David A
Published: March 2024

Cellular senescence drives organ fibrosis and ageing, and accumulating evidence supports the ability of senescence-depleting drugs to improve outcomes in experimental models of disease. The lack of non-invasive biomarkers represents a major obstacle to the design of human trials of candidate senolytics. On samples from 51 patients with chronic kidney disease (CKD), we performed liquid chromatography mass spectrometry (LC-MS) analysis of urine samples alongside immunofluorescence staining of paired kidney biopsies for p21, Ki67, and CD10+Pancytokeratin as senescence, proliferation and pan-epithelial cell markers respectively. Only Urinary Clusterin (uClusterin) correlated tightly with p21+ epithelial senescencein vivo(rho >0.5, p<0.001) and was upregulated in thein vitroSASP atlas. This was validated in a second cohort of matched urine and kidney samples from n=53 participants, with uClusterin predicting levels of senescence after adjusting for renal function, age and albuminuria. In spatial transcriptomic data from n=13 CKD patients, Clusterin colocalised with senescence marker CDKN1A. In a larger cohort of n=322 participants, elevated levels of uClusterin predicted CKD progression (defined as reaching ESKD or >40% reduction in renal function) after adjusting for baseline eGFR, albuminuria, age, systolic blood pressure (SBP) and sex. uClusterin levels represents a surrogate for histological quantification of p21+Ki67- senescent renal epithelia and predicts outcomes in human kidney disease independent of existing clinical risk factors.
Everolimus and mycophenolate mofetil effectively prevent GvHD in children with severe acute kidney injury undergoing allogeneic HSCT
Authors: Zirngibl Felix , Gebert Pimrapat , Materne Bianca , Launspach Michael , Künkele Annette , Hundsdoerfer Patrick , Cyrull Sandra , Deubzer Hedwig E , Kühl Jörn-Sven , Eggert Angelika , Lang Peter , Oevermann Lena , von Stackelberg Arend , Schulte Johannes H
Published: March 2024

Allogeneic hematopoietic stem cell transplantation (HSCT) serves as a therapeutic intervention for various pediatric diseases. Acute kidney injury afflicts 21-84% of pediatric HSCT cases, significantly compromising clinical outcomes. This retrospective single-institution analysis scrutinized the practice of substituting nephrotoxic ciclosporin A with the everolimus/mycophenolate mofetil combination as graft-versus-host disease (GVHD) prophylaxis in 57 patients following first allogeneic matched donor HSCT. The control cohort comprised 74 patients not receiving everolimus during the same timeframe. Study endpoints encompassed the emergence of retention parameters subsequent to the switch to everolimus, overall survival, relapse incidence of the underlying disease and acute and chronic GVHD in both treatment groups. Our findings reveal a significant improvement in renal function, evidenced by reduced creatinine and cystatin C levels 14 days after ceasing ciclosporin A and initiating everolimus treatment. Crucially, the transition to everolimus did not adversely affect overall survival post-HSCT (HR 1.4; 95% CI: 0.64 – 3.1; p=0.39). Comparable incidences of grade 2-4 and grade 3-4 acute GVHD as well as severe chronic GVHD were observed in both groups. Patients with an underlying malignant disease exhibited similar event-free survival in both treatment arms (HR 0.87, 95% CI: 0.39 – 1.9, p=0.73). This study provides compelling real-world clinical evidence supporting the feasibility of replacing CsA with everolimus and for the use of the everolimus/mycophenolate mofetil combination to manage acute kidney injury following HSCT in children.

KEY POINTS

Everolimus with or without MMF restores kidney function in children with acute kidney injury after allogeneic HSCT.

Everolimus with or without MMF effectively prevent acute and chronic GvHD and leads to similar overall survival compared to standard therapy.
Test-retest reliability of intrahemispheric dorsal premotor and primary motor cortex dual-site TMS connectivity measures
Authors: Heemels Robin E. , Ademi Sian , Hehl Melina
Published: March 2024

Objective

Investigating the optimal interstimulus interval (ISI) and the 24-hour test-retest reliability for intrahemispheric dorsal premotor cortex (PMd) – primary motor cortex (M1) connectivity using dual-site transcranial magnetic stimulation (dsTMS).

Methods

In 21 right-handed adults, left intrahemispheric PMd–M1 connectivity has been investigated with a stacked-coil dsTMS setup (conditioning stimulus: 75% of resting motor threshold; test stimulus: eliciting MEPs of 1–1.5 mV) at ISIs of 3, 5–8, and 10 ms. Additionally, M1–M1 short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) were investigated to assess comparability to standard paired-pulse setups.

Results

Conditioning PMd led to significant inhibition of M1 output at ISIs of 3 and 5 ms, whereas 10 ms resulted in facilitation (all, p < 0.001), with a fair test-retest reliability for 3 (ICC: 0.47) and 6 ms (ICC: 0.44) ISIs. Replication of SICI (p < 0.001) and ICF (p = 0.017) was successful, with excellent test-retest reliability for SICI (ICC: 0.81).

Conclusion

This dsTMS setup can probe the inhibitory and facilitatory PMd–M1 connections, as well as reliably replicate SICI and ICF paradigms.

Significance

The stacked-coil dsTMS setup for investigating intrahemispheric PMd–M1 connectivity offers promising possibilities to better understand motor control.
Rethinking the Impact of Pretransplant Malignancy (Pre-TM) on Double Lung Transplantation (DLT) Eligibility: An Analysis of 23,291 DLT Recipients
Authors: Woo Wongi , Kim Hye Sung , Bharat Ankit , Chae Young Kwang
Published: March 2024

Background

Given the increasing need for lung transplants among older patients with a history of cancer, this study analyzed database registry to assess outcomes for DLT recipients with Pre-TM.

Methods

This study evaluated the United Network for Organ Sharing (UNOS) registry for adult DLT performed between 2005 and 2023. Patients with a history of previous or multi-organ transplants, and those with donors who had cancer history, were excluded. Propensity-score matching was used to compare patients with or without Pre-TM. Overall and Post-TM-free survival were analyzed.

Results

Among the 23,291 recipients of DLT, 8.0%(1,870) had Pre-TM. Compared to those without Pre-TM, patients with Pre-TM had worse overall (hazard ratio[HR] 1.20, 95% confidence interval[CI] 1.12-1.29, p<0.001) and Post-TM-free survival (HR 1.32, 95% CI 1.24-1.41, p<0.001). However, after adjusting for age, sex, and race through propensity-score matching, the survival difference between the groups became non-significant (HR 1.05, 95% CI 0.97-1.13, p=0.229). While the Pre-TM group still had worse Post-TM-free survival, this difference diminished after excluding cutaneous Post-TM (HR 1.06, 95% CI 0.99-1.15, p=0.116). Additionally, the recurrence rate of Pre-TM after transplant wasn’t higher than de novo cancers in patients without Pre-TM.

Conclusion

Patients with Pre-TM had similar overall survival rates after DLT as those without Pre-TM. Importantly, there is no increased risk of the primary Pre-TM type recurring post-transplant compared to patients without Pre-TM. These findings highlight the necessity for a more nuanced evaluation of transplant candidacy to prevent premature exclusion of Pre-TM patients from life-saving surgeries.
COVID-19 mortality in the Philippines: a province-level analysis, 2020-2023
Authors: Celeste Jimuel , Sevilleja Jesus Emmanuel , Bongolan Vena Pearl , Rivera Roselle Leah , Caoili Salvador Eugenio , de Castro Romulo
Published: March 2024

Objective

To investigate the COVID-19 mortality in Philippine provinces from 2020 to 2023.

Methods

We calculated the crude (CMR) and age-standardised mortality rates (ASMR) of the Philippine provinces from the national COVID-19 surveillance data from January 18, 2020 to May 9, 2023. With Spearman’s method, we then performed a correlation analysis between the rates and four independent variables, namely, poverty incidence, population density, hospital beds per 100 000 population and proportion of elderly population (≥ 65).

Results

The province with the highest ASMR is Benguet with 207.83 deaths per 100 000 population, followed by Cagayan, Bataan, Nueva Vizcaya, Quirino, National Capital Region, Isabela, Cebu, Aurora and Davao del Sur. Meanwhile, the province with the lowest ASMR is Tawi-Tawi with 2.22 deaths per 100 000 population, followed by Sulu, Masbate, Misamis Occidental, Camarines Norte, Sarangani, Camiguin, Sultan Kudarat, Southern Leyte, Catanduanes and Batanes. Among the independent variables, poverty incidence and hospital beds per 100 000 population were found to independently predict CMR and ASMR.

Discussion

The results of this analysis provides a starting point for the investigation of COVID-19 mortality in Philippine provinces. The ranking of provinces by ASMR reveals the provinces with the highest and lowest rates, while the results of the correlation analysis, linked with findings from previous studies, explain the ranking, including surveillance issues that are related to health-care access and health-seeking behaviour. Our study paves the way for investigating factors that need to be considered and more closely investigated to get a clearer picture to inform decision-making, which affects millions of lives in communities across the Philippines’ provinces.
Cardiovascular Disease Risk Factor Control Following Release from Carceral Facilities
Authors: Aminawung JA , Puglisi LB , Roy B. , Horton N , Elumn JE , Lin H. , Bibbins-Domingo K , Krumholz H. , Wang EA
Published: March 2024

Background

Incarceration is a social determinant of cardiovascular health but is rarely addressed in clinical settings or public health prevention efforts. People who have been incarcerated are more likely to develop cardiovascular disease (CVD) at younger ages and have worse cardiovascular outcomes compared with the general population, even after controlling for traditional risk factors. This study aims to identify incarceration-specific factors that are associated with uncontrolled CVD risk factors to identify potential targets for prevention.

Methods

Using data from Justice-Involved Individuals Cardiovascular Disease Epidemiology (JUSTICE), a prospective cohort study of individuals released from incarceration with CVD risk factors, we examine the unique association between incarceration-specific factors and CVD risk factor control, including systolic blood pressure (SBP≥140 mmHg, diastolic blood pressure (DBP)≥90, body mass index (BMI)≥40, glycosylated hemoglobin (HbA1c) ≥8%, and low-density lipoprotein cholesterol (LDL-c)≥ 160). Incarceration-specific factors include the conditions of confinement (jail vs. prison, time in solitary confinement), and collateral sanctions following release (barriers to housing, food, employment due to criminal record). Variables associated with uncontrolled CVD risk factors were included in the multivariate model to examine the unique contribution of each risk factor with uncontrolled CVD risk factors.

Results

Participants (N=471), mean age of 45.0 ±SD 10.8 years were disproportionately men (89%), from racially minoritized groups (79%), and poor (91% below the 100% federal poverty level). Over half (54%) had at least one uncontrolled CVD risk factor at baseline. People released from jail, compared with prison, had lower Life’s Essential 8 scores for blood pressure and smoking. Having been incarcerated in jail, as compared with prison, was associated with an increased odds of having an uncontrolled CVD risk factor, even after adjusting for age, race and ethnicity, gender, perceived stress, and life adversity score (AOR 1.62, 95% CI 1.02-2.57).

Discussion

Release from jail is associated with poor CVD risk factor control and requires tailored intervention, which is informative as states design and implement the Centers of Medicare & Medicaid Services Reentry 1115 waiver, which allows Medicaid to cover services prior to release from correctional facilities.
de NovoSequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination
Authors: Le Bihan Thierry , Nunez de Villavicencio Diaz Teressa , Reitzel Chelsea , Lange Victoria , Park Minyoung , Beadle Emma , Wu Lin , Jovic Marko , Dubois Rosalin M. , Couzens Amber L. , Duan Jin , Han Xiaobing , Liu Qixin , Ma Bin
Published: March 2024

We present a method for sequencing polyclonal IgG enriched from human plasma, employing a combination ofde novosequencing, proteomics, bioinformatics, protein separation, sequencing, and peptide separations. Our study analyzes a single patient’s IgG antibody response triggered by the Moderna Spikevax mRNA COVID-19 vaccine. From the sequencing data of the natural polyclonal response to vaccination, we generated 12 recombinant antibodies. Six derived recombinant antibodies, including four generated withde novosequencing, exhibited similar or higher binding affinities than the original natural polyclonal antibody. Our neutralization tests revealed that the six antibodies possess neutralizing capabilities against the target antigen. This research provides insights into sequencing polyclonal IgG antibodies while highlighting the effectiveness and potential of our approach in generating recombinant antibodies with robust binding affinity and neutralization capabilities. Our proposed approach is an advancement in characterizing the IgG response by directly investigating the circulating pool of IgG without relying exclusively on the B-cell repertoire or population. This is crucial as the B-cell analysis may not accurately represent the circulating antibodies. Interestingly, a large proportion (80 to 90%) of the human antibody sequences generated against SARS-CoV-2 in the literature have been derived solely from B-cell analysis. Therefore, the ability to offer a different perspective is crucial in gaining a comprehensive understanding of the IgG response.

Significance Statement

We investigate human IgG targeting the receptor binding domain usingde novoproteomics. The peripheral B-cell repertoire may not adequately cover all the circulating IgG for human IgG sequencing. Our approach overcomes this limitation by using ade novoprotein sequencing on top of standard proteomics. We obtained distinctde novosequences, showcasing our method’s potential. The recombinant proteins we generate possess traits comparable to or surpassing the naturally occurring polyclonal antibodies (pAbs). This study highlights similarities and differences between IgG populations in blood and circulating B-cells, which is crucial for future biologics development.
Arrayed CRISPRi library to suppress genes required forSchizosaccharomyces pombeviability
Authors: Ishikawa Ken , Soejima Saeko , Nishimura Takashi , Saitoh Shigeaki
Published: March 2024

The fission yeast,Schizosaccharomyces pombe,is an excellent eukaryote model organism to study essential biological processes. Its genome contains ∼1200 genes essential for cell viability, most of which are evolutionarily conserved. To study these essential genes, resources enabling conditional perturbation of target genes are required. Here, we constructed comprehensive arrayed libraries of plasmids and strains to knock down essential genes inS. pombe, using a dCas9-mediated CRISPRi. These libraries cover ∼98% of all essential genes in fission yeast. We estimate that in ∼60% of the strains in the library, transcription of a target gene was repressed so efficiently that cell proliferation was significantly inhibited. To demonstrate usefulness of these libraries, we performed metabolic analyses with knockdown strains and revealed a flexible interaction among metabolic pathways. Libraries established in this study enable comprehensive functional analyses of essential genes inS. pombeand will facilitate understanding of essential biological processes in eukaryotes.
The host genotype actively shapes its microbiome across generations in laboratory mice
Authors: Benga Laurentiu , Rehm Anna , Gougoula Christina , Westhoff Philipp , Wachtmeister Thorsten , Benten W. Peter M. , Engelhardt Eva , Weber Andreas P.M. , Köhrer Karl , Sager Martin , Janssen Stefan
Published: March 2024

Background

The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.

Results

To further dissect the influence of host genetics and maternal inheritance, we collected 2-cell stage embryos from two representative wildtypes, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.

Conclusions

Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate.

graphical abstract
Comparison of Single-cell Long-read and Short-read Transcriptome Sequencing of Patient-derived Organoid Cells of ccRCC: Quality Evaluation of the MAS-ISO-seq Approach
Authors: Zajac Natalia , Zhang Qin , Bratus-Neuschwander Anna , Qi Weihong , Bolck Hella Anna , Karakulak Tülay , Oltra Tamara Carrasco , Moch Holger , Kahraman Abdullah , Rehrauer Hubert
Published: March 2024

Single-cell RNA sequencing is used in profiling gene expression differences between cells. Short-read sequencing platforms provide high throughput and high-quality information at the gene-level, but the technique is hindered by limited read length, failing in providing an understanding of the cell heterogeneity at the isoform level. This gap has recently been addressed by the long-read sequencing platforms that provide the opportunity to preserve full-length transcript information during sequencing. To objectively evaluate the information obtained from both methods, we sequenced four samples of patient-derived organoid cells of clear cell renal cell carcinoma and one healthy sample of kidney organoid cells on Illumina Novaseq 6000 and PacBio Sequel IIe. For both methods, for each sample, the cDNA was derived from the same 10x Genomics 3’ single-cell gene expression cDNA library. Here we present the technical characteristics of both datasets and compare cell metrics and gene-level information. We show that the two methods largely overlap in the results but we also identify sources of variability which present a set of advantages and disadvantages to both methods.
Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data
Authors: Haag Julia , Jordan Alexander I. , Stamatakis Alexandros
Published: March 2024

Motivation

Genotype datasets typically contain a large number of single nucleotide polymorphisms for a comparatively small number of individuals. To identify similarities between individuals and to infer an individual’s origin or membership to a population, dimensionality reduction techniques are routinely deployed. However, inherent (technical) difficulties such as missing or noisy data need to be accounted for when analyzing a lower dimensional representation of genotype data, and the intrinsic uncertainty of such analyses should be reported in all studies. However, to date, there exists no stability assessment technique for genotype data that can estimate this uncertainty.

Result

Here, we present Pandora, a stability estimation framework for genotype data based on bootstrapping. Pandora computes an overall score to quantify the stability of the entire embedding, infers per-individual support values, and also deploys ak-means clustering approach to assess the uncertainty of assignments to potential cultural groups. Using published empirical and simulated datasets, we demonstrate the usage and utility of Pandora for studies that rely on dimensionality reduction techniques.

Availability and Implementation

Pandora is available on GitHubhttps://github.com/tschuelia/Pandora.

Contact

julia.haag@h-its.org

Supplementary information

Supplementary data are available online.
Phylogeny-aware modeling uncovers molecular functional convergences associated with complex multicellularity in Eukarya
Authors: Pereira Lobo Francisco , Benjamim da Costa Dalbert , Martins da Silva Thieres Tayroni , de Oliveira Maycon Douglas
Published: March 2024

A major trait of Eukarya is the independent evolution of complex multicellular lineages of animals and plants with specialized cell types organized in tissues, organs and systems. The number of cell types (NCT) has been commonly adopted as a proxy in comparative studies investigating the genomic evolution of biological complexity. Although expansions of homologous genes playing roles in extracellular processes, signal transduction pathways, and the immune system have been reported as associated with NCT variation in metazoans, the evolutionary patterns coordinating the genomic evolution of multicellularity throughout Eukarya remain poorly understood. We used Gene Ontology (GO) as a genome annotation scaffold to represent biological functions shared by genes regardless of their homology relationships to search for molecular functional convergences associated with NCT. For that we integrated phenotypic, genomic, annotation and phylogenetic data to build phylogeny-aware models and searched for expansions of homologous regions and of GO terms associated with NCT values across 49 eukaryotic species, including complex multicellular plants and metazoans. Virtually all homologous regions associated with NCT are metazoan- and vertebrate-specific expansions of paralogs with key roles in developmental pathways. The functional annotation, in contrast, detected previously unknown biological themes coded by non-homologous genes independently expanded in multicellular plants and metazoans, such as system and anatomical development, immunity, regulatory mechanisms of embryogenesis, response to external stimuli and detection of natural rhythmic processes. Our findings unveil functional molecular convergences shared by these contrasting groups due to common selective pressures in the lifestyle of complex multicellular lineages.
Lysine-Cysteine-Serine-Tryptophan Inserted into the DNA-Binding Domain of Human Mineralocorticoid Receptor Increases Transcriptional Activation by Aldosterone
Authors: Katsu Yoshinao , Zhang Jiawen , Baker Michael E.
Published: March 2024

Due to alternative splicing in an ancestral DNA-binding domain (DBD) of the mineralocorticoid receptor (MR), humans contain two almost identical MR transcripts with either 984 amino acids (MR-984) or 988 amino acids (MR-988), in which their DBDs differ by only four amino acids, Lys,Cys,Ser,Trp (KCSW). Human MRs also contain mutations at two sites, codons 180 and 241, in the amino terminal domain (NTD). Together, there are five distinct full-length human MR genes in GenBank. Human MR-984, which was cloned in 1987, has been extensively studied. Human MR-988, cloned in 1995, contains KCSW in its DBD. Neither this human MR-988 nor the other human MR-988 genes have been studied for their response to aldosterone and other corticosteroids. Here, we report that transcriptional activation of human MR-988 by aldosterone is increased by about 50% compared to activation of human MR-984 in HEK293 cells transfected with the TAT3 promoter, while the half-maximal response (EC50) is similar for aldosterone activation of MR-984 and MR-988. Transcriptional activation of human MR also depends on the amino acids at codons 180 and 241. Interestingly, in HEK293 cells transfected with the MMTV promoter, transcriptional activation by aldosterone of human MR-988 is similar to activation of human MR-984, indicating that the promoter has a role in the regulation of the response of human MR-988 to aldosterone. The physiological responses to aldosterone and other corticosteroids in humans with MR genes containing KCSW and with differences at codons 180 and 241 in the NTD warrant investigation.
Transcription factor prediction using protein 3D secondary structures
Authors: Liebold Jeanine , Neuhaus Fabian , Geiser Janina , Kurtz Stefan , Baumbach Jan , Newaz Khalique
Published: March 2024

Motivation

Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs. Recently proposed TF prediction methods do not rely on DBDs. Such methods use features of protein sequences to train a machine learning model, and then use the trained model to predict whether a protein is a TF or not. Because the 3-dimensional (3D) structure of a protein captures more information than its sequence, using 3D protein structures will likely allow for more accurate prediction of novel TFs.

Results

We propose a deep learning-based TF prediction method(StrucTFactor), which is the first method to utilize 3D secondary structural information of proteins. We compare StrucTFactor with recent state-of-the-art TF prediction methods based on∼525 000 proteins across 12 datasets, capturing different aspects of data bias (including sequence redundancy) possibly influencing a method’s performance. We find that StrucTFactor significantly (p-value<0.001) outperforms the existing TF prediction methods, improving the performance over its closest competitor by up to 17% based on Matthews correlation coefficient.

Availability

Data and source code are available athttps://github.com/lieboldj/StrucTFactorand on our website athttps://apps.cosy.bio/StrucTFactor/

Contact

khalique.newaz@uni-hamburg.de

Supplementary information

Included
Optimizing Design of Genomics Studies for Clonal Evolution Analysis
Authors: Srivatsa Arjun , Schwartz Russell
Published: March 2024

Genomic biotechnologies have seen rapid development over the past two decades, allowing for both the inference and modification of genetic and epigenetic information at the single cell level. While these tools present enormous potential for basic research, diagnostics, and treatment, they also raise difficult issues of how to design research studies to deploy these tools most effectively. In designing a study at the population or individual level, a researcher might combine several different sequencing modalities and sampling protocols, each with different utility, costs, and other tradeoffs. The central problem this paper attempts to address is then how one might create an optimal study design for a genomic analysis, with particular focus on studies involving somatic variation, typically for applications in cancer genomics. We pose the study design problem as a stochastic constrained nonlinear optimization problem and introduce a simulation-centered optimization procedure that iteratively optimizes the objective function using surrogate modeling combined with pattern and gradient search. Finally, we demonstrate the use of our procedure on diverse test cases to derive resource and study design allocations optimized for various objectives for the study of somatic cell populations.
Epidemiological, Serological, and Virological Analysis of an Outbreak of Elephant Hemorrhagic Disease in Switzerland
Authors: Ackermann Mathias , Kubacki Jakub , Heaggans-Ebbeson Sarah , Hayward Gary S. , Lechmann Julia
Published: March 2024

Elephant hemorrhagic disease (EHD), caused by several Elephant endotheliotropic herpesviruses (EEHV), represents a frequently lethal syndrome, affecting both captive and free-living elephants. In summer 2022, three young Asian elephants (Elephas maximus) succumbed to EHD in a zoo in Switzerland, despite of considerable preventive efforts and early detection of EEHV1A viremia. In this communication, we describe the extent of preventive measures in terms of prior virus detection, active survey of viremia, and antibody status. In the course of the outbreak, the causative virus was concomitantly analyzed and eventually fully sequenced and compared to other EEHV types and strains.

The conclusions from these analyses may be summarized in three points: (1) A previously undetected EEHV1A strain had remained unrecognized among these elephants. Probably, the new virus re-emerged after almost 40 years of latency from one of the oldest elephants in the zoo. (2) While two of the three affected animals had prior immune responses against EEHV1, their strain-specific immunity proved insufficient to prevent EHD. (3) There is an urgent need to develop efficient antiviral drugs and protective vaccines. In particular, ways need to be found to circumvent the present unavailability of appropriate cell cultures and animal models.