bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuroendocrine Prostate Cancer Drivers SOX2 and BRN2 Confer Differential Responses to Imipridones ONC201, ONC206, and ONC212 in Prostate Cancer Cell Lines
Authors: Purcell Connor , Srinivasan Praveen R. , Pinho-Schwermann Maximilian , MacDonald William J. , Ding Elizabeth , El-Deiry Wafik S.
Published: August 2024

Prostate cancer (PCa) is the leading cause death from cancer in men worldwide. Approximately 30% of castrate-resistant PCa’s become refractory to therapy due to neuroendocrine differentiation (NED) that is present in <1% of androgen-sensitive tumors. First-in-class imipridone ONC201/TIC10 has shown clinical activity against midline gliomas, neuroendocrine tumors and PCa. We explored the question of whether NED promotes sensitivity to imipridones ONC201 and ONC206 by inducible overexpression of SOX2 and BRN2, well-known neuroendocrine drivers, in human PCa cell lines DU145 or LNCaP. Slight protection from ONC201 or ONC206 with SOX2 and BRN2 overexpression was observed in the inducible LNCaP cells but not in the DU145 cells. At 2 months, there was an apparent increase in CLpP expression in LNCaP SOX2-overexpressing cells but this did not confer enhanced sensitivity to ONC201. DU145 SOX2-overexpressing cells had a significantly reduced ONC201 sensitivity than DU145 control cells. The results support the idea that treatment of castrate-resistant prostate cancer by imipridones may not be significantly impacted by neuroendocrine differentiation as a therapy-resistance mechanism. The results support further testing of imipridones across subtypes of androgen-sensitive and castrate-resistant prostate cancer.
3D-Aligner: An advanced computational tool designed to correct image distortion in expansion microscopy for precise 3D reconstitution and quantitative analysis
Authors: Loi Jonathan , Ghone Dhaval , Qu Xiaofei , Suzuki Aussie
Published: August 2024

Expansion Microscopy (ExM) is an innovative and cost-effective super-resolution microscopy technique that has become popular in cell biology research. It achieves super-resolution by physically expanding specimens. Since its introduction, ExM has undergone continuous methodological developments to enhance its resolution and labeling capabilities. However, ExM imaging often encounters sample drift during image acquisition due to the physical movement of the expanded hydrogel, posing a significant challenge for accurate image reconstruction. Despite many proposed experimental solutions to mitigate sample drift, a universal solution has yet to be established. In response to this challenge, we developed 3D-Aligner, an advanced and user-friendly image analysis tool designed to computationally correct drift in ExM images for precise three-dimensional image reconstruction and downstream quantification. We demonstrate that 3D-Aligner effectively determines and corrects drift in ExM images with different expansion rates and various fluorescently labeled biological targets, showcasing its capabilities and robustness in drift correction. Additionally, we validate the precision of 3D-Aligner by comparing drift values across different labeled targets and highlight the importance of drift correction in quantification of biological structures.
Prediction and principle discovery of drug combination based on multimodal friendship features
Authors: Chen He-Gang , Zhou Xionghui
Published: August 2024

Combination therapy, which can improve therapeutic efficacy and reduce side effects, plays an important role in the treatment of multiple complex diseases. Yet, the design principles of molecular combinations remain unclear. In addition, the huge search space of candidate drug combinations and the numerous heterogeneous data has brought us a big challenge. Here, we proposed a Friendship based Method (FSM), which integrates diverse drug-to-drug information to predict drug combinations for specific diseases. By quantifying the friendship-based relationship between drugs, we found that there is a moderate similarity between the drugs of effective drug combinations in a high-dimensional, heterogeneous feature space. Following this discovery, FSM applied a two-step strategy to predict clinically efficacious drug combinations for specific diseases. First, our method employs the friendship features to evaluate whether each drug is combinable. Then, the synergistic potential of combinable drugs was further evaluated. FSM was validated on two types of disease. The results show that FSM achieves substantial performance improvement over other state-of-the-art methods and tends to have low toxicity. These results indicate that our model could potentially offer a generic, powerful strategy to identify efficacious combination therapies in the vast search space.
Caveolin assemblies displace one bilayer leaflet to organize and bend membranes
Authors: Doktorova Milka , Daum Sebastian , Ebenhan Jan , Neudorf Sarah , Han Bing , Sharma Satyan , Kasson Peter , Levental Kandice R. , Bacia Kirsten , Kenworthy Anne K. , Levental Ilya
Published: August 2024

Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim of this disc are highly hydrophobic, suggesting that the complex incorporates into membranes by displacing hundreds of lipids from one leaflet. The feasibility of this unique molecular architecture and its biophysical and functional consequences are currently unknown. Using Langmuir film balance measurements, we find that CAV1-8S is highly surface active and intercalates into lipid monolayers. Molecular simulations of biomimetic bilayers support this ‘leaflet replacement’ model and reveal that while CAV1-8S effectively displaces phospholipids from one bilayer leaflet, it accumulates 40−70 cholesterol molecules into a disordered monolayer between the complex and its distal lipid leaflet. We find that CAV1-8S preferentially associates with positively curved membrane surfaces due to its influence on the conformations of distal leaflet lipids, and that these effects laterally sort lipids of the distal leaflet. Large-scale simulations of multiple caveolin assemblies confirmed their association with large, positively curved membrane morphologies, consistent with the shape of caveolae. Further, association with curved membranes regulates the exposure of caveolin residues implicated in protein-protein interactions. Altogether, the unique structure of CAV1-8S imparts unusual modes of membrane interaction with implications for membrane organization, morphology, and physiology.

STATEMENT OF SIGNIFICANCE

Caveolae are membrane invaginations heavily implicated in cellular physiology and disease; however, how their unique shape and function are produced remains enigmatic. Here, following on recent characterization of the unusual structure of the CAV1-8S oligomer, we examine the molecular details of its interactions with its solvating lipid membrane. We describe a novel mode of membrane interaction—which we term ‘leaflet replacement’—for the CAV1-8S complex that has not previously been observed for any other protein. The biophysical consequences of this unique molecular organization provide mechanistic insights into the functions and organization of caveolae in cells.
Genetic ancestry proportion influences risk of adverse events from tuberculosis treatment in Brazil
Authors: Piekos Jacqueline A. , Amorim Gustavo , Ridolfi Felipe , Cordeiro-Santos Marcelo , Kritski Afrânio L. , Figueiredo Marina C. , Andrade Bruno B. , Santos Adalberto R. , Haas David W. , Sterling Timothy R. , Rolla Valeria C. , Edwards Digna R. Velez ,   the Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil consortium
Published: August 2024

Tuberculosis (TB) treatment is highly effective, but response to therapy can vary by geography, race, and ethnicity. We assessed for differences in TB treatment response in a representative and heterogeneous Brazilian population. We estimated genetic ancestry proportion according to major ancestry groups (African, European, and Amerindian ancestry) in the Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil cohort. RePORT-Brazil is an observational prospective cohort study of individuals with newly-diagnosed, culture-confirmed, pulmonary TB. TB treatment outcomes that were attributed to TB treatment included Grade 2 or higher adverse drug reaction (ADR), Grade 3 or higher ADR, hepatic ADR, and failure/recurrence. Ancestry proportion was the main predictor in logistic regression for each outcome, with adjustments for candidate confounders. There were 941 pulmonary TB patients included in this study. We observed a decreased risk of Grade 2+ ADR when African ancestry proportion increased by 10% (Odds Ratio [OR] 0.41, 95% Confidence Interval [CI] 0.20 -0.85) and an increased risk for Grade 2+ ADR with increasing European ancestry (OR 2.84, 95% CI 1.47 - 5.48). We then performed the same analysis adding HIV status as an interaction term. The decreased risk for Grade 2+ ADR seen for African ancestry proportion did not hold for persons living with HIV; we observed increased risk for Grade 2+ ADR with increasing African ancestry proportion. There were no associations with Amerindian ancestry or for other treatment outcomes. In this Brazilian TB cohort, toxicity risk was associated with African and European ancestry, divergent, and affected by HIV.

#RePORT-Brazil Consortium members include:

Aline Benjamin and Flavia M. Sant’Anna

Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil

Jamile Garcia de Oliveira and João Marine

Clínica de Saúde Rinaldo Delmare, Rio de Janeiro, Brazil

Adriana Rezende and Anna Cristina Carvalho

Secretaria de Saúde de Duque de Caxias, Rio de Janeiro, Brazil

Michael Rocha and Betânia Nogueira

Instituto Brasileiro para Investigação da Tuberculose, Fundação José Silveira, Salvador, Brazil

Alexandra Brito and Renata Spener

Fundação Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil

Megan Turner

Vanderbilt University Medical Center, Nashville, USA
The effect of pre-existing coronavirus antibodies on SARS-CoV-2 infection outcomes in exposed household members
Authors: Westerhof Ilse , Sikkema Reina , Rozhnova Ganna , van Beek Janko , Koopmans Marion , Bruijning-Verhagen Patricia
Published: August 2024

Background/Rationale

We investigated the effect of pre-existing antibodies against SARS-CoV-2 and seasonal human coronaviruses on infection outcomes in Omicron BA1/2 exposed household members from January to March 2022.

Methods

Data from a prospective household study in the Netherlands were used including 63 households with 195 household members exposed to a SARS-CoV-2 Omicron BA1/2 index case. The protocol included repeated nose-throat swab and saliva RT-PCR testing, paired serology, and self-reported daily symptom scoring by household members. Infection outcomes included the occurrence of secondary infections, symptom severity, and CT-value trajectories. We studied the effect of baseline binding antibody levels for SARS-CoVs and seasonal coronaviruses (hCoV) NL63, 229E, HKU1 and OC43 spike protein, on SARS-CoV-2 infection outcomes.

Results

132 of 195 (68%) exposed household members developed a SARS-CoV-2 infection. Among exposed household members, higher levels of SARS-CoV-2 and beta hCoV antibodies (HKU1 and OC43) at baseline, were associated with a reduced risk of secondary infection (adjusted Odds ratio 0.61; 95% Confidence interval 0.44-0.84 and aOR 0.72; 95%CI 0.56-0.92, respectively). No significant differences between antibody levels and symptom burden or CT-value trajectories were observed.

Conclusions

Our study suggests that prior SARS-CoV-2 and beta hCoV antibodies provide some protection against Omicron BA.1/BA.2 infection, while effects on symptom burden or CT-value could not be demonstrated. The results highlight the relatively limited, but not negligible role of cross-protective antibodies, especially when facing immune escape variants of SARS-CoV-2.
Gene expression-based identification of prognostic markers in lung adenocarcinoma
Authors: Salomonsson Annette , Ehinger Daniel , Jönsson Mats , Botling Johan , Micke Patrick , Brunnström Hans , Staaf Johan , Planck Maria
Published: August 2024

Introduction

Many studies have aimed at identifying additional prognostic tools to guide treatment choices and patient surveillance in lung cancer by assessing the expression of individual proteins through immunohistochemistry (IHC) or, more recently, through gene expression-based signatures. As a proof-of-concept, we used a multi-cohort, gene expression-based discovery and validation strategy to identify genes with prognostic potential in lung adenocarcinoma. The clinical applicability of this strategy was further assessed by evaluating a selection of the markers by IHC.

Materials and Methods

Publicly available gene expression data sets from six microarray-based studies were divided into four discovery and two validation data sets. First, genes associated with overall survival (OS) in all four discovery data sets were identified. The prognostic potential of each identified gene was then assessed in the two validation data sets, and genes associated with OS in both data sets were considered as potential prognostic markers. Finally, IHC for selected potential prognostic markers was performed in two independent and clinically well-characterized lung cancer cohorts.

Results and Conclusions

The gene expression-based strategy identified 19 genes with correlation to OS in all six data sets. Out of these genes, we selected Ki67, MCM4 and TYMS for further assessment with IHC. Although an independent prognostic ability of the selected markers could not be confirmed by IHC, this proof-of-concept study demonstrates that by employing a gene expression-based discovery and validation strategy, potential prognostic markers can be identified and further assessed by a technique universally applicable in the clinical practice. The concept of studying potential prognostic markers through gene expression-based strategies, with a subsequent evaluation of the clinical utility, warrants further exploration.
Genetic analysis of asymptomatic antinuclear antibody production
Authors: Hocaoglu Mehmet , Casares-Marfil Desiré , Sawalha Amr H.
Published: August 2024

Objective

Antinuclear antibodies (ANA) are detected in up to 14% of the population and the majority of individuals with ANA are asymptomatic. The literature on the genetic contribution to asymptomatic ANA positivity in the population is limited. In this study, we aimed to perform a multi-ancestry genome-wide association study (GWAS) of asymptomatic ANA positivity.

Methods

Asymptomatic ANA positive and negative individuals from the All of Us Research Program were included in this study, selecting those with an ANA test by immunofluorescence and no evidence of autoimmune disease. Imputation was performed and a multi-ancestry meta-analysis including approximately 6 million single-nucleotide polymorphisms (SNPs) was conducted. Genome-wide SNP based heritability was estimated using the GCTA software. A cumulative genetic risk score for lupus was constructed using previously reported genome-wide significant loci.

Results

1,955 asymptomatic ANA positive and 3,634 asymptomatic ANA negative individuals were included across three genetic ancestries. The multi-ancestry meta-analysis revealed SNPs with a suggestive association (p-value < 1×10−5) across 8 different loci, but no genome-wide significant loci were identified. A gene variant upstream ofHLA-DQB1(rs17211748,P= 1.4×10-6, OR = 0.82, 95% CI 0.76-0.89) showed the most significant association. The heritability of asymptomatic ANA positivity was estimated to be 24.9%. Asymptomatic ANA positive individuals did not exhibit increased cumulative genetic risk for lupus compared to ANA negative individuals.

Conclusion

ANA production is not associated with significant genetic risk and is primarily determined by non-genetic, likely environmental, factors.
Empathy in psychotherapy: subjective ratings versus remote biosensing of interpersonal heart rate synchrony as outcome predictors
Authors: Gernert Clara C. , Falkai Peter , Falter-Wagner Christine M.
Published: August 2024

In addition to understanding empathy in an affective and cognitive dimension, the physiological domain plays a crucial role, especially in the emotional dynamics of interpersonal interactions during psychotherapy. Within the complex bio-psycho-social system of cognitive behavioural therapy language, cognition, emotion and physiological states of both, client and therapist, intertwine through interaction dynamics. The current study aimed to explore interpersonal physiological dynamics during psychotherapy sessions as an objective biomarker for predicting therapy outcome. In a follow-up assessment design, involving 25 client-psychotherapist dyads, wearable sensors monitored individual’s heart rate, while video cameras recorded movement behaviour during regular cognitive behavioural therapy sessions. Post-session reports and symptom questionnaires were collected from both, clients and therapists, after each session. Results showed that synchrony in head movement and heart rate emerged during psychotherapy sessions. Notably, heart rate synchrony from the initial session predicted changes in patients’ self-rated global severity index over time. The objective predictor, heart rate synchrony, emerged as particularly robust, surpassing patients’ subjective ratings of affiliation in explaining a higher variance of the therapy outcome variable. These findings highlight the potential shown by remote biomarker sensing of interpersonal dynamics for the prediction of psychotherapeutic effectiveness.
Fat burning capacity in a mixed macronutrient meal protocol does not reflect metabolic flexibility in women who are overweight or obese
Authors: Ahern Mary M. , Artegoitia Virginia M. , Bosviel Rémy , Newman John W. , Keim Nancy L. , Krishnan Sridevi
Published: August 2024

Introduction

Metabolic flexibility, the ability to switch from glucose to fat as a fuel source, is considered a marker of metabolic health. Higher fat oxidation is often associated with greater flexibility and insulin sensitivity, while lower fat oxidation is linked to metabolic inflexibility and insulin resistance. However, our study challenges the universal validity of this relationship, uncovering a more nuanced understanding of the complex interplay between fuel source switching and fat oxidation, especially in the presence of insulin resistance.

Methods

In an 8-week controlled feeding intervention, overweight to obese women with insulin resistance (as defined by McAuley’s index) were randomized to consume either a diet based on the Dietary Guidelines for Americans 2010 (DGA) or a ‘Typical’ American Diet (TAD), n = 22 each. Participants were given a high-fat mixed macronutrient challenge test (MMCT) (60% fat, 28% carbohydrates, and 12% protein) at weeks 0, 2, and 8. Plasma lipids, metabolome, and lipidome were measured at 0, 0.5, 3, and 6h postprandial (PP); substrate oxidation measures were also recorded at 0,1 3, and 6h PP. Metabolic flexibility was evaluated as the change in fat oxidation from fasting to PP. Mixed model and multivariate analyses were used to evaluate the effect of diet on these outcomes, and to identify variables of interest to metabolic flexibility.

Results

Intervention diets (DGA and TAD) did not differentially affect substrate oxidation or metabolic flexibility, and equivalence tests indicated that groups could be combined for subsequent analyses. Participants were classified into three groups based on the % of consumed MMCT fat was oxidized in the 6h post meal period at weeks 0, 2 and 8. Low fat burners (LB, n = 6, burned <30% of fat in MMCT) and high fat burners (HB, n = 7, burned > 40% of fat in MMCT) at all weeks. Compared to LB, HB group had higher fat mass, total mass, lean mass, BMI, lower HDLc and lower RER (p < 0.05), but not different % body fat or % lean mass. During week 0, at 1h PP, LB had an increase in % fat oxidation change from 0h compared to HB (p<0.05), suggesting higher metabolic flexibility. This difference disappeared later in the PP phase, and we did not detect this beyond week 0. Partial least squares discriminant analysis (PLSDA (regular and repeated measures (sPLSDA)) models identified that LB group, in the late PP phase, was associated with higher rates of disappearance of acylcarnitines (AC) and lysophosphatidylcholines (LPC) from plasma (Q2: 0.20, R2X: 0.177, R2Y: 0.716).

Conclusion

In women with insulin resistance, a high fat burning capacity does not imply high metabolic flexibility, and not all women with insulin resistance are metabolically inflexible. LPCs and ACs are promising biomarkers of metabolic flexibility.
SAHVAI-3D and 4D: A New, Automated Subarachnoid Hemorrhage Volumetric Artificial Intelligence (SAHVAI) Measurement Approach Using Non-Contrast Head CT Scans
Authors: Wirtz Melina , Salman Saif , Wei Yujia , Patel Vishal , Sharma Rohan , Gupta Vikash , Gu Qiangqiang , Dherin Benoit , Reddy Sanjana , Tawk Rabih , Erickson Bradley J , Freeman William David
Published: August 2024

Objectives

To automate subarachnoid hemorrhage volume (SAHV) calculation (SAHVAI-SAHV ArtificialIntelligence)and create 3D volumetric images (SAHVAI-3D) using non-contrast head CT (NCCT) imaging data in aneurysmal subarachnoid hemorrhage (SAH) patients. We also defined SAHVAI-4D, representing SAHV over time. The aim was to compare automated SAHVAI volumes to manual SAHV methods and computation times, explore these imaging biomarkers’ potential in identifying at-risk brain regions for delayed cerebral ischemia (DCI), and explore potential insights in future neurotherapeutic interventions for SAH patient recovery.

Methods

A training set of 10 consecutive aneurysmal SAH cases was used to manually compute SAHV, SAHVAI-3D, and SAHVAI-4D, involving 92 non-contrast CT scans (182 slices each). The SAHVAI deep learning (DL) algorithm generated automated SAHV values in cubic centimeters (cc). For both SAHVAI and manual evaluations, a 3D SAH brain map was created for each patient. Blood volumetric outputs were analyzed and compared to neurological outcomes at discharge, including DCI events, symptomatic vasospasm (sVSP), and areas with the thickest SAH blood concentration.

Results

SAHVAI quantified SAH blood volume (SAHV) in average of 6.7 seconds per scan, significantly faster than the manual method, which took over 60 minutes per scan (Fisher’s exact test, P value <0.001). SAHVAI demonstrated an accuracy of 99.8%, a Dice score of 0.701, a false positive rate of 0.0005, and a negative predictive value of 0.999. The mean absolute error between SAHVAI and manual methods was 5.67 ml. The SAHVAI-3D brain map and total SAHV at admission were strongly associated with neurological outcomes, inversely with Glasgow coma scale (R2=0.23, p=0.017) and directly with length of hospital stay (R2=0.175, p=0.004), especially in regions with dense blood concentration.

Conclusion

SAHVAI-3D and SAHVAI-4D brain mapping techniques represent innovative imaging biomarkers for SAH. These advancements enable rapid evaluation and targeted interventions, potentially improving patient care in SAH management.
Exploring associations between estrogen and gene candidates identified by coronary artery disease genome-wide association studies
Authors: Aminbakhsh Ava P. , Théberge Emilie T. , Burden Elizabeth , Kalenga Adejumo Cindy , Lehman Anna , Sedlak Tara L.
Published: August 2024

Introduction

Coronary artery disease (CAD) is the leading cause of death around the world, with well-described epidemiological sex and gender differences in prevalence, pathophysiology and management outcomes. It has been hypothesized that sex steroids, like estrogen, may contribute to these sex differences. There is a relatively large genetic component to developing CAD, with heritability estimates ranging between 40-60%. In the last two decades, the computational methods, capabilities and scalability of genome-wide association studies (GWAS) have contributed substantially to advancing the understanding of which genetic candidates contribute to CAD. The aim of this study was to determine if genes discovered in CAD GWASs are affected by estrogen by means of direct modulation or indirect down-stream targets.

Methods

A scoping review of the literature was conducted using MEDLINE and EMBASE through to April 24, 2024, for studies synonymous to an atherosclerotic coronary artery disease phenotype, and a genome-wide association study (GWAS) design. Analysis was limited to candidate genes with corresponding single nucleotide polymorphisms (SNPs) surpassing genome-wide significance and had been mapped to genes by study authors. The number of studies that conducted sex-stratified analyses with significant genes were quantified. A literature search of the final gene lists was done to examine any evidence suggesting estrogen may modulate the genes and/or gene products.

Results

There were 60 eligible CAD GWAS studies meeting inclusion criteria for data extraction. Of these 60, only 36 had genome-wide significant SNPs reported, and only 3 of these had significant SNPs from sex-stratified analyses mapped to genes. From these 36 studies, a total of 61 genes were curated, of which 26 genes (43%) were found to have modulation by estrogen. All 26 were discovered in studies that adjusted for sex. 12/26 genes were also discovered in studies that conducted sex-stratified analyses. 12/26 genes were classified as having a role in lipid synthesis, metabolism and/or lipoprotein mechanisms, while 11/26 were classified as having a role in vascular integrity, and 3/26 were classified as having a role in thrombosis.

Discussion

This study provides further evidence of the relationship between estrogen, genetic risk and the development of CAD. More sex-stratified research will need to be conducted to further characterize estrogen’s relation to sex differences in the pathology and progression of CAD.
Questionable practices in data and code sharing policy in high-profile medical journal and research
Authors: Li Wei , Liu Xuerong , Zhang Qianyu , Shi Liping , Zhang Jing-Xuan , Zhang Xiaolin , Luan Jia , Li Yue , Xu Ting , Zhang Rong , Han Xiaodi , Lei Jingyu , Wang Xueqian , Wang Yaozhi , Lan Hai , Chen Xiaohan , Wu Yi , Wu Yan , Xia Lei , Liao Haiping , Shen Chang , Yu Yang , Xu Xinyu , Deng Chao , Liu Pei , Feng Zhengzhi , Huang Chun-Ji , Chen Zhiyi
Published: August 2024

Background

The spurious and unavailable data/code sharing actions are crashing open medical sciences. In this study, we aimed to illustrate how high-profile medical journals are practically carried out their sharing policies and what questionable practices regarding data/code sharing are conducted by authors.

Methods

In this study, we appraised the policy on data/code availability of high-profile medical journals ranked at Q1 according to Clarivate Journal Citation Report (JCR 2021). Furthermore, we recruited post-publications published by four leading medical journals (i.e., The BMJ, JAMA, NEJM and The Lancet) from the issuing of data/code availability policy to December 2022 for the questionable practices in data/code sharing. The appraisal of papers was conducted by the Data/code Availability Statement Practice Evaluation Tool (DANCE), developed by systematically integrating mainstreaming open data/code guidelines.

Findings

We found that less than one-tenth journals (9.1%) mandated authors to share data/code, with an available statement. Among these journals, 70.6% (61.2%) did not consider censoring (restricting) spurious/invalid data/code sharing in publications. Furthermore, though journal impact factor could predict policy stringency on “offering availability statements” (p< .001), it failed to predict ones in “sharing data/code” (p= .73). For publications, even in leading medical journals (i.e., The BMJ, JAMA, NEJM and The Lancet), only 0.5% of the papers (16/3,191) fully complied with their public sharing statements for reaching reproducibility. Lack of availability statement, declining data/code sharing without reasons, and invalid repositories were leading questionable practices conducted by authors.

Interpretation

We clarified specific questionable actions of implementing and practicing the sharing policy both in journal and papers, which should be addressed not only by the supportive publication ecosystem but also by crediting authors for taking responsibility and maintaining scientific integrity in data/code sharing.

Funding

No funding.
Single-Molecule Studies of Cognate and Near-Cognate Elongation in anin vitroEukaryotic Translation System
Authors: Fritsch Clark , Bhattacharya Arpan , Ng Martin Y. , Li Hong , Nelson Philip C. , Cooperman Barry S. , Goldman Yale E.
Published: August 2024

The ribosome plays a central role in translation of the genetic code into amino acid sequences during synthesis of polypeptides. During each cycle of peptide elongation, the ribosome must discriminate between correct and incorrect aminoacyl-tRNAs according to the codon present in its A-site. Ribosomes rely on a complex sequence of proofreading mechanisms to minimize erroneous selection of incorrect aminoacyl-tRNAs that would lead to mistakes in translation. These mechanisms have been studied extensively in prokaryotic organisms, but eukaryotic elongation is less well understood. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) with anin vitroeukaryotic translation system to investigate tRNA selection and subsequent steps during peptide elongation. We compared accommodation of a tryptophan-aminoacyl-tRNA into the ribosomal A-site containing either a cognate or near-cognate codon and unexpectedly found that, following an initial slow sampling event, subsequent near-cognate sampling events proceeded more rapidly than the initial event. Further, we found a strong negative correlation between the concentration of near-cognate aminoacyl-tRNA and the efficiency of tRNA accommodation. These novel characteristics of near-cognate interaction with the eukaryotic ribosome suggest that rejection of a near-cognate tRNAs leads to formation of an altered ribosomal conformation that assists in rejecting subsequent incorrect tRNA interactions.
Expression of IL-1R2 by T follicular regulatory cells prevents the exacerbation of allergy by blocking their IL-1-dependent proliferation
Authors: Engeroff Paul , Belbezier Aude , Vaineau Romain , Fourcade Gwladys , Lujan Hugo D , Bellier Bertrand , Graff-Dubois Stephanie , Klatzmann David
Published: August 2024

The antibody response is regulated by follicular T helper (Tfh) and regulatory (Tfr) cells that control the germinal center (GC) reaction. Recent research has shown that Tfh/Tfr have a unique pattern of IL-1 receptor expression. We investigated the mechanisms by which this IL-1 axis in GCs could regulate the allergic response.

To study this, we generated CD4creIL-1R1loxmice, specifically lacking IL-1R1 expression in T cells and FoxP3creIL-1R2loxmice, specifically lacking IL-1R2 expression in Tfr cells. The conditional knockout mice were compared to their respective control mice in a model of ovalbumin (OVA) sensitization and anaphylaxis, and a phenotypic and functional characterization of humoral and cellular responses was performed.

While CD4creIL-1R1loxmice showed little phenotypic changes, FoxP3creIL-1R2loxmice were highly susceptible to allergic anaphylaxis and generated an increase in IgE responses that promoted basophil degranulation. Additionally, FoxP3creIL-1R2loxmice displayed significantly reduced OVA-specific IgG responses, limiting their ability to control allergy via the inhibitory IgG receptor FcγRIIb. Although FoxP3creIL-1R2loxmice showed an overall increase in splenic T and B cell numbers, they were unable to efficiently generate proliferating GC B cells. Uponex vivoIL-1β and/or OVA re-stimulation, we observed a striking IL-1R1-dependent activation and proliferation of Tfr cells in FoxP3creIL-1R2loxsplenocytes, that was neither observed in Tregs nor in Tfh. At the same time, B cell proliferation upon re-stimulation was suppressed.

These findings suggest that IL-1R2 expression on Tfr cells prevents allergy by limiting excessive Tfr activation and suppressing the IgG/IgE ratio.
Phase separation promotes Atg8 lipidation for autophagy progression
Authors: Fujioka Yuko , Tsuji Takuma , Kotani Tetsuya , Kumeta Hiroyuki , Kakuta Chika , Fujimoto Toyoshi , Nakatogawa Hitoshi , Noda Nobuo N.
Published: August 2024

Upon starvation, the autophagy-initiating Atg1 complex undergoes phase separation to organize the pre-autophagosomal structure (PAS) in yeast, from which autophagosome formation is considered to proceed. However, the physiological roles of the PAS as a liquid droplet remain unclear. Here we show that core Atg proteins are recruited into early PAS droplets that are formed by phase separation of the Atg1 complex with different efficiencies in vitro. The Atg12–Atg5–Atg16 E3 ligase complex for Atg8 lipidation is the most efficiently condensed in the droplets via specific Atg12–Atg17 interaction, which is also important for the PAS targeting of the E3 complex in vivo. In vitro reconstitution experiments reveal that E3-enriched early PAS droplets promote Atg8 lipidation and incorporate Atg8-coated vesicles to the interior, thereby protecting them from Atg4-mediated delipidation. These data suggest that the PAS utilizes its liquid-like property to function as an efficient production site for lipidated Atg8 and pool membrane seeds to drive autophagosome formation.
Trait-space disparity in fish communities spanning 380 million years from the Late Devonian to present
Authors: Llewelyn John S , Long John A , Cloutier Richard , Clement Alice M , Strona Giovanni , Saltre Frederik , Lee Michael S. Y. , Choo Brian , Trinajstic Kate , Vanhaesebroucke Olivia , Bradshaw Corey J. A.
Published: August 2024

Aim: The diversity and distribution of traits in an ecological community determine how it functions. Modern fish communities conserve trait space across similar habitats. However, little is known about trait-space variation through deep time (or across vastly different habitats). In this paper, we sought to identify how trait diversity varies through space and time. Location: Global Devonian and modern fish communities. Methods: We examined two Devonian fish communities - a tropical reef (Gogo, Australia) and a tropical estuary (Miguasha, Canada) - and compared their trait space with that of six modern communities from diverse habitats. Results: Trait-space metrics reflecting the amount of diversity found in each community (functional richness: FRic) and the similarity among species in each community (functional nearest-neighbour distance: FNND) indicated Devonian communities had similar scores to modern communities, but were less functionally rich than their closest modern analogues. Metrics describing location in trait space (centroid distances and hypervolume overlap) also showed distinctions between Devonian and modern communities. Indeed, location in trait space of Devonian and modern communities differed on several axes associated with a range of traits. Functional richness and nearest-neighbour distance also varied with habitat type and climate zone: estuarine communities had the highest nearest-neighbour distances followed by reef communities; reefs were the most functionally rich communities followed by estuaries; and functional richness was highest in tropical communities. Main Conclusions: Fish community trait space varies with time, habitat and climate, suggesting (i) lability in fish trait space and (ii) evolutionary history, environmental filtering, and stochasticity influence community assembly. Furthermore, the large changes in community trait space that have occurred over deep time indicate changes in community structure and function.
Genome-wide methylation profiling of cell-free DNA in maternal plasma using Methylated DNA Sequencing (MeD-seq)
Authors: van Vliet Marjolein M. , Boers Ruben G. , Boers Joachim B. , Schäffers Olivier J.M. , van der Meeren Lotte E. , Steegers-Theunissen Régine P.M. , Gribnau Joost , Schoenmakers Sam
Published: August 2024

Background

Placental-originated cell-free DNA (cfDNA) provides unique opportunities to study (epi)genetic placental programming remotely, but studies investigating the cfDNA methylome are scarce and usually technologically challenging. Methylated DNA sequencing (MeD-seq) is well-compatible with low cfDNA concentrations and has a high genome-wide coverage. We therefore aim to investigate the feasibility of genome-wide methylation profiling of first trimester maternal cfDNA using MeD-seq, by identifying placental-specific methylation marks in cfDNA.

Methods

We collected cfDNA from non-pregnant controls (female n=6, male n=12) and pregnant women (n=10), first trimester placentas (n=10), and paired preconceptional and first trimester buffy coats (total n=20). Differentially methylated regions (DMRs) were identified between pregnant and non-pregnant women. We investigated placental-specific markers in maternal cfDNA, includingRASSF1promoter and Y-chromosomal methylation, and studied overlap with placental and buffy coat DNA methylation.

Results

We identified 436 DMRs between cfDNA from pregnant and non-pregnant women which were validated using male cfDNA.RASSF1promoter methylation was higher in maternal cfDNA (fold change 2.87, unpaired t-test p<0.0001). Differential methylation of Y-chromosomal sequences could determine fetal sex. DMRs in maternal cfDNA showed large overlap with DNA methylation of these regions in placentas and buffy coats, indicating a placental and immune-cell contribution to the pregnancy-specific cfDNA methylation signature. Sixteen DMRs in maternal cfDNA were specifically found only in placentas. These novel potential placental-specific DMRs were more prominent thanRASSF1.

Conclusions

MeD-seq can detect (novel) genome-wide placental DNA methylation marks and determine fetal sex in maternal cfDNA. This study supports future research into maternal cfDNA methylation using MeD-seq.

Graphical abstract

Studies investigating the maternal cell-free DNA (cfDNA) methylome are scarce and generally technologically challenging. We identified 436 autosomal differentially methylated regions (DMRs) between cfDNA from pregnant and non-pregnant women, using the innovative methylated DNA sequencing (MeD-seq) technique. Y-chromosomal methylation could determine fetal sex, we show hypermethylation of the placental-markerRASSF1, and identify 16 novel placental-specific markers in maternal cfDNA including DMRs related toTMEM240, DHRS3, andPCMTD2. This pilot study supports future research into the maternal cfDNA methylome using MeD-seq.
An affordable solution for investigating zebra finch intracranial electroencephalography (iEEG) signals
Authors: Abolghasemi Mohammad-Mahdi , Shirsavar Shahriar Rezghi , Bahramani Amirreza , Yekani Milad
Published: August 2024

The zebra finch is a well-studied animal model for investigating the neural mechanisms of vocal learning, and electrophysiology is the primary technique for understanding their song system. Most of the studies on zebra finches have focused on intracerebral recordings. However, these methods are only affordable for limited laboratories. Recently, different open-source hardware for acquiring electroencephalography (EEG) signals has been developed. It’s unclear whether these solutions suit zebra finch studies as they have not been evaluated. Electrocorticography signals can provide a preliminary guide for more in-depth inquiries and also aid in understanding the global behavior of the bird’s brain, as opposed to the more common localized approach. We present a detailed protocol for acquiring intracranial electroencephalography (iEEG) data from zebra finches using the OpenBCI Cyton board, an open-source device. We implemented stainless steel electrodes on the brain’s surface and recorded the brain signals from two recording sites above two auditory-responsive nuclei. To validate our method, we ran two different experiments. In the first experiment, we recorded neural activity under various concentrations of isoflurane and extracted the suppression duration to measure anesthesia depth. In the second experiment, we head-fixed the birds and, under light anesthesia, presented them with various auditory stimuli to evaluate event-related potentials (ERP) and generate spectrograms. The results showed a significant increase in suppression duration with deeper anesthesia, and the ERP and spectrogram responses to auditory stimuli differed accordingly. These findings indicate that using our methodology, one can successfully collect iEEG signals from zebra finches. These findings pave the way for future studies to use iEEG to investigate bird cognition in a more affordable way.
Evaluation of a Deep Learning Based Approach to Computational Label Free Cell Viability Quantification
Authors: Reno Allison , Tang Jianan , Sudbeck Madeline , Fe Custodio Precious , Baldus Brandi , McLaughlin Elizabeth , Peng Fei , Xiao Hai
Published: August 2024

One of the most common techniques found in a cell biology or tissue engineering lab is the cytotoxicity assay. This can be performed using a variety of different dyes and stains and various protocols to result in a clear indication of dead and live cells within a culture to quantify the viability of a culture and monitor for sudden drops or increases in viability by a drug, material, viral vector, etc introduced into the culture. This assay helps cell biologists determine the health of their culture and what toxicity added substances may add to the culture and whether they are appropriate and safe to use with human cells. However, many of the dyes and stains used for this process are eventually toxic to cells, rendering the cells useless after testing and preventing real time monitoring of the same culture over a period of hours or days. Computation biology is moving cell biology towards novel and innovative techniques such as in silico labeling and dye free labeling using deep learning algorithms. In this work, we investigate whether it is feasible to train a Resnet CNN model to detect morphological changes in human cells that indicate cell death in order to classify cells as live or dead without utilizing a stain or dye. This work also aims to train one CNN model to count all cells regardless of viability status to get a total cell count, and then one CNN model that specifically identifies and counts all of the dead cells for an accurate dead and live cell total by utilizing both pieces of data to determine a general viability percentage for the culture. Additionally, this work explores the use of various image enhancements to understand if this process helps or impedes the deep learning models in their detection of total cells and dead cells.
Bisphenol A Disrupts Mitochondrial Functionality Leading to Senescence and Apoptosis in Human Amniotic Mesenchymal Stromal Cells
Authors: Ficai Sara , Papait Andrea , Magatti Marta , Masserdotti Alice , Gasik Michael , Silini Antonietta Rosa , Parolini Ornella
Published: August 2024

In today’s context, microplastics pollution has become an increasingly pressing issue not only for the environmental fallout but also for the assumed negative effects on human health. It is now well-established that microplastics (>1 mm in size) can enter the human body through ingestion, inhalation, dermal contact and also maternal-fetal transmission. Alarming was the recent findings of microplastics within the human term placenta. Among the degradation by-products of microplastics, Bisphenol A (BPA) has emerged as a hazardous chemical, with potential toxicity at multisystemic level, particularly on the earliest stages of human development. Based on these findings, our study focuses on assessing the impact of BPA on properties and functions of mesenchymal stromal cells isolated from the amniotic membrane (hAMSC) of the human term placenta. The amniotic membrane surrounds the fetus, playing a fundamental protective role toward toxic chemicals and pollutants that the mother may encounter. Our research revealed how exposure to increasing concentrations of BPA compromise mitochondrial functionality in hAMSC, resulting in enhanced production of reactive oxygen species at mitochondrial level (mtROS). This, in turn, leads to the stabilization of p53, which triggers an increased expression of p21 and p27 encoding genes and an imbalance in the genetic expression of Bax and Bcl-2. Additionally, we observed upregulated expression of cytokines and chemokines associated with the senescence-associated secretory phenotype (SASP). The increased oxidative stress, which plays a central role in BPA-mediated toxicity, can trigger the activation of the senescence pathways, or culminate in cell death, due to the overwhelming stress conditions. Therefore, our results provide novel insights into the mechanism of action of BPA and elucidates its impact on the functionality of hAMSC. This underscores the pressing need to reconsider the use of BPA as a plastic additive, mitigating the potential adverse effects on babies.
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon
Authors: Hartley Gabrielle A. , Okhovat Mariam , Hoyt Savannah J. , Fuller Emily , Pauloski Nicole , Alexandre Nicolas , Alexandrov Ivan , Drennan Ryan , Dubocanin Danilo , Gilbert David M. , Mao Yizi , McCann Christine , Neph Shane , Ryabov Fedor , Sasaki Takayo , Storer Jessica M. , Svendsen Derek , Troy William , Wells Jackson , Core Leighton , Stergachis Andrew , Carbone Lucia , O’Neill Rachel J.
Published: August 2024

Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon,Hoolock leuconedys(HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a “perfect storm” of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.