bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia
Authors: Zhao Meixi , Shi Yanyan , Zhang Congcong , Lu Meiqin , Shen Meili , Xie Lijian , Wang Libo , Lu Aizhen
Published: February 2025

Pneumonia is the leading cause of morbidity and mortality in children and needs rapid and accurate pathogenic diagnosis. The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMTs) for pathogen detection in children with severe or refractory pneumonia. In this retrospective study, the clinical data of 127 children with severe or refractory pneumonia admitted to the respiratory department from June 2021 to March 2022 were analyzed. BALF mNGS and CMTs were utilized for pathogen diagnosis and comparison of their detection performance for different pathogens. The pathogenic diagnosis rate was 95.28% (121/127) by combining mNGS and CMTs. mNGS had significantly higher overall (96.06% vs 72.44%,
P
< 0.001), bacterial (69.29% vs 12.60%,
P
< 0.001), and fungal (11.81% vs 3.15%,
P
= 0.009) detection rates than CMTs. However, there was no significant difference of detection rates between them for respiratory viruses (33.86% vs 33.75%,
P
= 0.99) and
Mycoplasma pneumoniae
(48.03% vs 45.67%,
P
= 0.71). The sensitivities of mNGS for total pathogens, bacteria, and fungi were 99.17%, 100%, and 87.50%, respectively, which were higher than those of CMTs. CMTs for
M. pneumoniae
had the highest sensitivity (91.23%) compared with mNGS (89.47%) and multiplex PCR (88.57%). For respiratory viruses, mNGS and mPCR had similar sensitivities (97.67% vs 96.43%). mNGS was superior to CMTs in bacterial and fungal detection, while it was comparable to multiplex PCR for the detection of
M. pneumoniae
and respiratory viruses. Different detection methods should be rationalized for different pathogens.

IMPORTANCE

This study on 127 patients with severe and refractory pneumonia showed that mNGS was significantly superior to CMTs in terms of bacterial and fungal detection. We also found that multiplex PCR assay was comparable to mNGS for the detection of
Mycoplasma pneumoniae
and respiratory viruses and may have greater application advantages in combination with CMTs, such as
M. pneumoniae
IgM. For severe and refractory pneumonia, or when empiric treatment is not effective, collecting BALF for mNGS can help to quickly identify the causative organisms at an early stage. It is also important to choose more appropriate methods or combinations for different pathogens.
Children who develop celiac disease are predicted to exhibit distinct metabolic pathways among their gut microbiota years before diagnosis
Authors: Kelley Kristina , Dogru Dogus , Huang Qian , Yang Yi , Palm Noah W. , Altindis Emrah , Ludvigsson Johnny
Published: February 2025

Celiac disease (CD) is an autoimmune disease caused by a loss of gluten tolerance in genetically predisposed individuals. While 30%–40% of people possess the predisposing alleles, only 1%–2% are diagnosed with CD, suggesting that environmental factors are involved in disease pathogenesis. To determine an association between pediatric CD and the gut microbiome, we analyzed fecal samples from a prospective cohort study (ABIS). These samples were collected from children who later developed CD (CD progressors) and age-matched healthy children (at ages 1, 2.5, and 5) with similar HLA genotypes, breastfeeding durations, and gluten exposure times. We previously reported gut microbiome differences at ages 2.5 and 5 in this cohort; here, we present findings from samples collected at age 1 (
n
= 5). We identified 14 ASVs differing significantly between CD progressors and controls, including taxa linked to CD pathogenesis. CD progressors had increased Firmicutes and higher alpha diversity in IgA− bacteria. Using PICRUSt, we analyzed metabolic pathways enriched in CD progressors compared to controls at ages 1, 2.5, and 5 (
n
= 5–16), revealing enriched inflammatory and pathogenic pathways potentially contributing to CD-related immune dysregulation. While results are based on the primary EdgeR analysis, we also applied a non-parametric method of statistical analysis, reporting those results with supplementary figures. In conclusion, our findings suggest distinct metabolic pathways enriched in the gut microbiome of CD progressors years before diagnosis, which could inform targeted therapeutics for CD. As discussed in the limitations section, this small pilot study should be replicated with larger sample sizes for broader generalization.

IMPORTANCE

We analyzed gut microbiome data from children who later developed celiac disease (CD progressors) compared to healthy children in the first 5 years of life. Using fecal samples corresponding to the three phases of gut microbiome development, we uncovered enriched functional microbial pathways in CD progressors at age 1. Some of these pathways, implicated in bacterial pathogenesis, microbiota modulation, and inflammation, have been correlated with CD. We also identified taxa in CD progressors at age 1 including
Lachnospiraceae
,
Alistipes
, and
Bifidobacterium dentium
that were previously associated with CD. These findings suggest a potential role for these taxa and enriched pathways in pediatric CD onset years before diagnosis, highlighting potential for early interventions. While the findings of this exploratory study should be validated with larger sample sizes, our study suggests microbial metabolic pathways related to CD onset, enhancing our understanding of CD pathogenesis and the role of gut microbiome-mediated early alterations.
Microbial players in autoimmunity: multicentric analysis of the association between
Mycoplasma hominis
serostatus and rheumatoid arthritis
Authors: Erre G. L. , Phan Ngoc Dan Thanh , Diaz N. , Congiargiu A. , Mundula N. , Mangoni A. A. , Phan Thi Minh Phuong , Margarita V. , Fiori P. L. , Rappelli P. , Cacciotto C. , Alberti A. , Dessì D.
Published: February 2025

Resident mucosal pathogens may induce immune tolerance breach, specific autoimmune response, and the development of rheumatoid arthritis (RA) in susceptible individuals. Despite a number of studies linking infections by
Mollicutes
bacteria to autoimmune disorders’ onset and progression, the role of
Mycoplasma hominis
, a common urogenital mucosa colonizing bacterium, in inducing a specific humoral response in RA has been seldom addressed. This study reports
M. hominis
seroprevalence in RA patients compared to healthy controls (HC) by testing two separate cohorts sampled in two distinct geographical settings (Italy and Vietnam). The amount of circulating anti-lipid-associated membrane proteins (LAMPs) antibodies was significantly higher in RA patients than HC in both cohorts. Also, a significantly higher seroprevalence of anti-
M
.
hominis
antibodies in RA patients compared to HC in both cohorts was observed. Notably, neither ELISA OD values nor positivity of anti-LAMPs were significantly associated with RA-specific variables. Further studies are essential to elucidate the underlying mechanisms by which
Mycoplasma
species may contribute to the pathogenesis of RA, thereby advancing our understanding of the potential causal links between
Mollicutes
and autoimmune disorders.

IMPORTANCE

Mycoplasmas may cause persistent asymptomatic mucosal infections and elicit chronic host immune responses. In this study, we evaluated the prevalence of serological response to the sexually transmitted bacterium
Mycoplasma hominis
in patients with rheumatoid arthritis. We show that sera of patients with rheumatoid arthritis are enriched with antibodies specifically recognizing microbial surface antigens compared with the general population. This suggests that
M. hominis
genital infection, with its peculiar host immunity subversion mechanisms, might play a role in predisposing to the development and progression of chronic arthritis in susceptible individuals. Thus, the range of microbes with a role as triggers of autoimmune disease (
P. gingivalis
, A.
actinomycetemcomitans
,
Streptococcus
spp., and
F. nucleatum
, among others) might have a new member in
M. hominis
. The potential role of the interactions taking place at the host–pathogen interface during persistent
M. hominis
infections in inducing autoimmunity should be further explored and characterized.
Development and characterization of a double-fluorescent HIV-1 reporter cellular model to tackle the Rev-dependent export pathway
Authors: Wadas Jakub , Ali Haider , Osiecka Aleksandra , Dorman Agnieszka , Pyrc Krzysztof , Kula-Pacurar Anna
Published: February 2025

The Rev-dependent nuclear export of unspliced and singly-spliced transcripts of human immunodeficiency virus type 1 (HIV-1) constitutes a critical yet poorly characterized post-transcriptional event essential for effective viral replication. In this study, we engineered a dual-fluorescent HIV-1-based cellular reporter system to elucidate the mechanisms underpinning Rev-dependent export. By generating multiple stably integrated inducible cellular clones, we ensured the expression of two distinct fluorescent proteins, mKO2, and ECFP, from unspliced (Rev dependent) and multiply spliced (Rev independent) HIV-1 transcripts, respectively. Utilizing flow cytometry, we performed quantitative analyses of dual-fluorescent cell populations. The developed tool enables precise assessment of the Rev-dependent export, and we validated it using known inhibitors of this pathway (leptomycin D), as well as targeted depletion of MATR3, an essential cofactor of Rev, and CRNKL1, a repressor of unspliced HIV-1 RNA export.

IMPORTANCE

The developed dual-fluorescent reporter system represents a powerful and handy tool for the identification and characterization of novel molecular players involved in the Rev-dependent export pathway. This system not only holds promise for advancing our understanding of human immunodeficiency virus type 1 (HIV-1) biology but also serves as an invaluable platform for high-throughput drug screening aimed at targeting post-transcriptional HIV-1 RNA processes, particularly nuclear export. Consequently, this study offers significant implications for the development of novel therapeutic strategies to eradicate the virus.
Partially purified
Strongyloides ratti
antigen improved the diagnostic performance of strongyloidiasis by enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test (ICT)
Authors: Wongphutorn Phattharaphon , Worasith Chanika , Kopolrat Kulthida Y. , Eamudomkarn Chatanun , Pitaksakulrat Opal , Hongsrichan Nuttanan , Tippayawat Patcharaporn , Techasen Anchalee , Sithithaworn Jiraporn , Homsombut Teeranat , Odermatt Peter , Noordin Rahmah , Sithithaworn Paiboon
Published: February 2025

Strongyloides stercoralis
infection is a neglected tropical disease with a global distribution. Serodiagnosis is a sensitive method, but improving its performance and simplifying into a point-of-care test (POCT) are needed. This study aimed to improve the diagnostic performance of serological tests using partially purified
Strongyloides ratti
antigen in an enzyme-linked immunosorbent assay (ELISA) and an immunochromatographic test (ICT). Crude
S. ratti
antigen was purified by an IgG affinity column to partition the antigen into flow-through, washing fraction (WF), and elution fractions. Optimized ELISA and ICT using crude and antigen fractions were used to analyze sera from three groups of subjects. Group 1 comprised subjects with proven strongyloidiasis, Group 2 were subjects with other parasitic infections, and Group 3 were negative parasitic infections. The diagnostic performance and Kappa agreement of the serological tests were analyzed and compared, using larvae detection as the reference test (fecal examination). The results showed that the WF was the most efficient antigen in terms of sensitivity and specificity, as determined by the ELISA and ICT. Kappa’s agreement between fecal examination and WF-ELISA was moderate (Kappa = 0.52), and WF-ICT was almost perfect (Kappa = 0.94). The WF antigen reduced cross-reactivity to other parasitic infections, that is,
Opisthorchis viverrini
,
Taenia
spp., and hookworms, compared to crude
S. ratti
antigen when assessed by ELISA and ICT. We concluded that the WF of purified
S. ratti
improved the ELISA and ICT diagnostic performance, and the latter assay format could be used as a POCT for screening and controlling strongyloidiasis.

IMPORTANCE

This study aimed to improve the serological diagnosis of strongyloidiasis, a disease caused by infection with the intestinal nematode
Strongyloides stercoralis
, by evaluating the impact of
Strongyloides ratti
antigen purification using an IgG affinity column for detecting parasite-specific IgG in serum via enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test (ICT) formats. Compared to crude
S. ratti
antigen, the washing fraction (WF) of the purified antigen demonstrated significantly improved sensitivity and specificity in both ELISA and ICT, achieving strong diagnostic concordance with the gold-standard fecal examination. Furthermore, the WF antigen fraction exhibited reduced cross-reactivity with coinfections caused by the liver fluke (
Opisthorchis viverrini
), tapeworms (
Taenia
spp.), and hookworms. These findings underscore antigen purification as a promising strategy to enhance the accuracy of strongyloidiasis serodiagnosis.
Exploring the effect of sequential antibiotic exposure in resistant
Escherichia coli
causing urinary tract infections: a proof of principle study
Authors: Göpel Lisa , Kirchhoff Laura , Gopleac Olivia , Tüeffers Leif , Hauswaldt Susanne , Boutin Sébastien , Rupp Jan , Nurjadi Dennis
Published: February 2025

Antimicrobial resistance development, particularly in infections such as urinary tract infections (UTIs), is a global clinical concern. The objective of this study was to determine if sequential antibiotic exposure with ciprofloxacin and mecillinam can reduce the growth of resistant clinical
Escherichia coli
strains, thus improving the effectiveness of antibiotic therapy. Six
E. coli
isolates with heterogeneous resistance to ciprofloxacin and/or mecillinam obtained from patients with UTIs were exposed to one of the antibiotics (0.75 × minimum inhibitory concentration, MIC) for 1 h. This was followed by treatment with the second antibiotic at different concentrations (0.0375/0.075/0.375/0.75 × MIC). Continuous growth measurements were conducted in order to assess the impact of sequential exposure. One representative strain was selected for intact cell counting. In addition, a checkerboard assay was conducted to investigate the synergistic impact of ciprofloxacin and mecillinam, and genetic analyses were performed to identify the mechanisms of resistance for all isolates. The six
E. coli
strains were phylogenetically different, and none exhibited a synergistic effect for ciprofloxacin and mecillinam. Our data suggest that sequential exposure to mecillinam and ciprofloxacin appears to reduce the growth capacity of clinical
E. coli
isolates with phenotypic resistance to either or both agents. Sequential antibiotic exposure may be an interesting strategy to improve the antibiotic efficacy of current agents to overcome phenotypic resistance in
E. coli
.

IMPORTANCE

As global rates of antibiotic resistance increase and the development of new antibiotics become more difficult and costly, it is important to explore alternative strategies to improve the effectiveness of existing antibiotics. Previous studies have shown that sequential exposure of
Pseudomonas aeruginosa
to two antibiotics can effectively kill the bacteria and reduce the likelihood of resistance developing. However, the potential of this sequential approach for the treatment of
Escherichia coli
infections has not been thoroughly investigated. In our study, we conducted a proof-of-principle study to determine whether sequential exposure to mecillinam and ciprofloxacin can overcome phenotypic resistance to one or both drugs. We found that when
E. coli
were treated with subinhibitory doses of mecillinam followed by ciprofloxacin, their growth was significantly inhibited compared to treatment with ciprofloxacin alone, suggesting that sequential antibiotic exposure may be a viable strategy for treating infections caused by resistant
E. coli
.
Human milk and bronchopulmonary dysplasia have a dose-dependent effect: a cohort study
Authors: Yang Jiaming , Li Jiaxin , Wang Huiyan , Chen Xueyu , Yang Chuanzhong , ChaoMu Liga , Cao Aifen , Xiong Xiaoyun
Published: February 2025

Background

Human milk (HM) is considered a potential protective factor against bronchopulmonary dysplasia (BPD), but the specific volume needed for its protective effect in mixed feeding is unclear. This study aimed to investigate the impact of different HM volumes on BPD risk.

Methods

A retrospective cohort study examined the association between HM volume and BPD risk in very low birthweight (VLBW) infants. Dose-dependent analysis with spline smoothing curve and univariate, multivariate analyses and sensitivity analyses were conducted.

Result

The study included 339 VLBW infants. BPD incidence was 4.7% (6 infants) in the high HM group (HM volume≥1190 mL), 27.0% (48 infants) in the low HM group (HM volume<1190 mL) and 9.1% (3 infants) in the exclusive formula group, and the difference is statistically significant. Both univariate and multivariate logistic regression analyses showed significantly higher BPD incidence in the low HM group (OR 3.237, 95% CI 0.81 to 12.89) compared with the exclusive formula group. The sensitivity analysis showed that low HM remained a risk factor for BPD (model I OR 3.26, 95% CI 0.92 to 11.53; model II OR 3.28, 95% CI 0.81 to 13.1).

Conclusion

Higher HM volumes (≥1190 mL) were associated with decreased BPD risk compared with low HM and formula feeding. Although not statistically significant, the low HM group exhibited increased BPD incidence compared with the exclusive formula group. These findings emphasise the importance of considering HM quantity in mixed feeding practices.
ESPGHAN and NASPGHAN 2024 protocol for paediatric functional constipation treatment guidelines (standard operating procedure)
Authors: Gordon Morris , de Geus Anna , Banasiuk Marcin , Benninga Marc A , Borrelli Osvaldo , Boruta Mary , Darbari Anil , Dore-Stites Dawn , Gould Michelle , Hawa Juliette , Jones Kirsten Brooke , Khlevner Julie , Kilgore Alexandra , Mousa Hayat , Nurko Samuel , Sinopoulou Vassiliki , Tabbers Merit , Thapar Nikhil
Published: February 2025

Introduction

Functional constipation is common in childhood, with chronicity leading to a significant impact on patients and their families. There is a significant range of therapies available to healthcare professionals for this condition, with many novel or recently studied. There is a need for an update to the joint European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN)/North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) guidelines last released in 2014. We present the prospectively agreed operating procedure and technical review protocol in this manuscript.

Methods

‘Grading of Recommendations Assessment, Development and Evaluation’ (GRADE) will be used for all phases of this guideline development. The Guideline Development Group is formed by paediatric gastroenterologists from both the ESPGHAN as well as the NASPGHAN. A prospective exercise will agree on key outcomes, thresholds of magnitude that are significant at small, moderate and large levels. Systematic evidence searches, selection, extraction, appraisal and analysis will be performed following Cochrane guidance and GRADE guidance for objectively agreeing the certainty of findings. Additional use of network meta-analysis will identify areas of broad triangulation in the evidence. Summary of findings tables will be produced and inform evidence to decision frameworks. These will guide GRADE recommendations with voting to reach a consensus.
Neurodevelopmental delay, musculoskeletal disorders and dysmorphia associated with a novel pathogenic interstitial deletion of chromosome 10q21.1q21.3
Authors: Dutta Dibyendu , Black Jennifer , Montoya Emily A , Burrow Thomas Andrew , Shieh Joseph , McGivern Bobbi , Raymond Michelle , Sheedy Christina B , Smith Scott C. , Garg Ria
Published: February 2025

Background

Previous reports of distal deletions in chromosome 10q in patients have described distinct facial features combined with other neurodevelopmental abnormalities, including intellectual disability. However, the association of interstitial deletions in chromosome 10q with global developmental delay, musculoskeletal abnormalities, and dysmorphic features has not been previously reported.

Methods

Genetic testing using whole exome sequencing (WES) was performed on three patients with neurodevelopmental delay, musculoskeletal abnormalities and dysmorphic features. Sequencing reads were aligned to the human genome build GRCh37/UCSC hg19 and analysed for both sequence and copy number variants.

Results

WES identified similar interstitial deletions in the 10q21.1q21.3 locus in all three patients. The deleted region includes online Mendelian inheritance in man (OMIM)-annotated genes with clinical significance, such asANK3(*600465),JMJD1C(*604503),EGR2(*129010),BICC1(*614295),ZNF365(*607818) andTFAM(*600438). Deletion of this region is considered pathogenic and is implicated in the aetiology of the clinical phenotypes observed in these patients.

Conclusions

This is the first report associating interstitial deletions in the 10q21.1q21.3 locus with neurodevelopmental delay, musculoskeletal abnormalities and dysmorphic features. Our findings highlight the clinical significance of this deleted region and suggest possible mechanisms underlying the observed pathological phenotypes.
The Role of Drone’s Digital Facial Emotions and Gaze in Shaping Individuals’ Social Proxemics and Interpretation
Authors: Bretin Robin , Khamis Mohamed , Cross Emily , Obaid Mohammad
Published: February 2025

The potential for drones to engage with people and find applications in social contexts is often constrained by their mechanical design, leading to concerns and negative associations that significantly affect people’s acceptance of drones in their personal space. In this study, we explore how social cues can impact the spatial dynamic of Human–Drone Interaction (HDI). Within a fully immersive virtual environment, 25 participants engaged with and navigated around a drone that communicated several facial emotions on a digital display such as Joy, Sadness and Anger, and enacted distinct ”gaze” behaviors (i.e., following participants or averting its gaze). Our results indicate that participants responded to the drone’s gaze in a manner akin to what is reported during human interaction: maintaining a greater distance when the drone established eye contact and instinctively getting closer when it averted its gaze. A more granular analysis revealed that participants who lacked prior familiarity with drones or possessed neutral to positive attitudes toward them demonstrated a higher sensitivity to the drone’s digital facial emotions. This finding highlights the potential for leveraging social cues to facilitate the integration of drones into various human-centric environments and tailor their design and behavior to suit specific individuals and situations.
Modal Crash Types for WAR-Aware Intermittent Computing
Authors: Dotzel Myra , Derakhshan Farzaneh , Surbatovich Milijana , Jia Limin
Published: February 2025

Programs are executed intermittently on devices that experience arbitrary power failures such as Energy Harvesting Devices (EHDs). To ensure progress, intermittent systems need runtime support to checkpoint state and re-execute after power failure by restoring the last saved state. Such re-execution should be
correct
, i.e., simulated by a continuously-powered execution. We study the logical underpinning of intermittent computing and model checkpoint, crash, restore, and re-execution operations as computation on crash types. We draw inspiration from adjoint logic and define crash types by introducing two adjoint modality operators to model persistent and transient memory values of partial (re-)executions and the transitions between them caused by checkpoints and restoration. Our formalism is general enough to accommodate a variety of checkpointing policies. We define a crash type system for a core calculus. To prove the correctness of intermittent systems, we define a novel logical relation for crash types.
Navigating Uncertainty: A User-Perspective Survey of Trustworthiness of AI in Healthcare
Authors: Ojha Jaya , Presacan Oriana , Goncalves Lind Pedro , Monteiro Eric , Yazidi Anis
Published: February 2025

This paper offers an extensive survey of one of the fundamental aspects of the trustworthiness of Artificial Intelligence (AI) in healthcare, namely uncertainty, focusing on the large panoply of recent studies addressing the connection between uncertainty, AI, and healthcare. The concept of uncertainty is a recurring theme across multiple disciplines, with varying focuses and approaches. Here, we focus on the diverse nature of uncertainty in medical applications, emphasizing the importance of quantifying uncertainty in model predictions and its advantages in specific clinical settings. Questions that emerge in this context range from the guidelines for AI integration in the healthcare domain to the ethical deliberations and their compatibility with cutting-edge AI research. Together with a description of the main specific works in this context, we also discuss that, as medicine evolves and introduces novel sources of uncertainty, there is a need for more versatile uncertainty quantification methods to be developed collaboratively by researchers and healthcare professionals. Finally, we acknowledge the limitations of current uncertainty quantification methods in addressing the different facets of uncertainty within the medical domain. In particular, we identify from this survey a relative paucity of approaches that focus on the user’s perception of uncertainty and accordingly of trustworthiness.
The Linguistics of Urban Youth Languages in Africa
Authors: Hurst Harosh Ellen
Published: February 2025

This article provides an overview of research on African Urban Youth Languages focusing on common linguistic features identified in existing studies. It outlines a distinction between urban vernaculars that form the base languages of youth styles, and youth styles themselves, that draw on strategies of play or manipulation. It describes morphosyntactic, phonological, and lexical features that may be specific to youth language practices and that support deeper pragmatic analysis. The article also discusses the theoretical developments that led to expanded interest in this field—namely, the third wave of variation studies, the sociolinguistics of mobility, and the decolonial turn—and discusses the field's implications for variation studies and sociolinguistics.
Leveraging Large Language Models to Generate Clinical Histories for Oncologic Imaging Requisitions
Authors: Bhayana Rajesh , Alwahbi Omar , Ladak Aly Muhammad , Deng Yangqing , Basso Dias Adriano , Elbanna Khaled , Abreu Gomez Jorge , Jajodia Ankush , Jhaveri Kartik , Johnson Sarah , Kajal Dilkash , Wang David , Soong Christine , Kielar Ania , Krishna Satheesh
Published: February 2025

Large language models enabled accurate automated clinical histories for oncologic imaging that were markedly more complete than original requisition histories and preferred by radiologists for image interpretation and safety.
The Newman Model for Phase-Change Electrodes: Physics-Based Hysteresis
Authors: Foster Jamie M. , Grudeva Yoana , Korotkin Ivan , Dickinson Edmund J.F. , Offer Gregory J , Richardson Giles
Published: February 2025

Many modern, commercially relevant Li-ion batteries use insertion materials that exhibit lithiation-induced phase change (e.g. lithium iron phosphate). However, the standard physics-based model---the Newman model---uses a microscopic description of particle lithiation (based on diffusion) that is incapable of describing phase-change behaviour and the physical origins of the voltage hysteresis exhibited by such phase-change electrodes. In this work a simple and rational model of hysteretic lithiation (in an electrode comprised of an ensemble of phase-change nanoparticles) is derived using an approach based on minimisation of the Gibbs energy. Voltage hysteresis arises naturally as a prediction of the model. Initially, equations that model the phase-change dynamics in a single particle of active material are considered. These are generalised to a model, termed the composite phase-change model, of a coupled ensemble of particles in a thin electrode. The composite phase-change model is then incorporated into the framework of a classical Newman model, allowing for the inclusion of transport effects in the electrolyte and electrode conductivity. The resulting modified Newman model is used to predict voltage hysteresis in a graphite/LFP cell. A simulation tool that allows readers to replicate, and extend, the results presented here is provided via the DandeLiion simulator at www.dandeliion.com.
Effects of maternal edible THC consumption on offspring lung growth and function in a rhesus macaque model
Authors: Shorey-Kendrick Lyndsey E. , Crosland B. Adam , Schabel Matthias C. , Messaoudi Ilhem , Guo Minzhe , Drake Matthew G. , Nie Zhenying , Edenfield R. Clayton , Cinco Isaac , Davies Michael , Graham Jason A. , Hagen Olivia L. , McCarty Owen J.T. , McEvoy Cindy T. , Spindel Eliot R. , Lo Jamie O.
Published: February 2025

Prenatal cannabis use is rising, in part due to legalization and perceptions of safety. The impact of prenatal cannabis exposure on offspring development, especially respiratory health, remains largely unknown. The objective of this study was to determine whether in utero exposure to delta-9-tetrahydrocannabinol (THC), the main psychoactive component of cannabis, is deleterious to offspring lung development and function using a rhesus macaque model. Female rhesus macaques received a daily edible containing either THC (2.5mg/7kg/day, equivalent to a heavy medical cannabis dose) or placebo during gestation and postnatally. Serial in utero magnetic resonance imaging (MRI) was performed during pregnancy at approximately G110 and G150. At 6 months of age infants underwent pulmonary function testing, followed by tissue collection for molecular analysis (bulk-RNAseq, whole genome bisulfite sequencing, and spatial-RNAseq). THC exposed infants displayed significantly reduced forced residual capacity (FRC) which correlated with non-significant decreases in total lung capacity (TLC), lung diffusion capacity (DLCO) and lower fetal lung perfusion, oxygen availability, and lung volume measured by MRI. Consistent with these decreases in volume indices, levels of pulmonary growth factors were decreased in bronchial alveolar lavage at 6 months. Molecular analysis of infant lungs revealed altered epigenetic regulation of gene expression, including at genes involved in extracellular matrix organization and lung development, and activation of immune signaling. Our study suggests that exposure to edible prenatal THC alters epigenetic regulation of lung gene expression and may negatively affect offspring lung development and function. Data from this study will help guide healthcare provider counseling on cannabis use in pregnancy.
Figure S4 from Harnessing the Potential of FAP-IL12mut TMEkine for Targeted and Enhanced Antitumor Responses
Authors: Lee Dahea , Kim Dongsu , Kim Donggeon , Kang Jisu , Lee Kiram , Lee Hyunji , Yoon Yujin , Lee Youngin , Kim Nahmju , Cho Byoung Chul , Chang Jihoon , Lee Byoung Chul
Published: February 2025

Supplementary Figure 4. Systemic depletion of CD8+ T cells. The graph demonstrates the efficient depletion of CD8+ T cells (CD45+CD3+CD8+) from lymph nodes, spleen, and peripheral blood after six injections of CD8-depleting antibody. Data are presented as mean ± SEM: VC, vehicle control; LNs, lymph nodes.
Supplementary Table S3 from Characteristics of a CCL21 Gene–Modified Dendritic Cell Vaccine Utilized for a Clinical Trial in Non–Small Cell Lung Cancer
Authors: Oh Michael S. , Dumitras Camelia , Salehi-Rad Ramin , Tran Linh M. , Krysan Kostyantyn , Lim Raymond J. , Jing Zhe , Tappuni Shahed , Lisberg Aaron , Garon Edward B. , Dubinett Steven M. , Liu Bin
Published: February 2025

Supplementary Table S3. Regulon specificity score (RSS) of transcription factor regulons for DC clusters.
Supplementary Table S2 from Characteristics of a CCL21 Gene–Modified Dendritic Cell Vaccine Utilized for a Clinical Trial in Non–Small Cell Lung Cancer
Authors: Oh Michael S. , Dumitras Camelia , Salehi-Rad Ramin , Tran Linh M. , Krysan Kostyantyn , Lim Raymond J. , Jing Zhe , Tappuni Shahed , Lisberg Aaron , Garon Edward B. , Dubinett Steven M. , Liu Bin
Published: February 2025

Supplementary Table S2. Mean area under the curve (AUC) enrichment of transcription factor regulons across DC clusters.
Supplementary Table S1 from Targeting NAD+ Metabolism Vulnerability in FH-Deficient Hereditary Leiomyomatosis and Renal Cell Carcinoma with the Novel NAMPT Inhibitor OT-82
Authors: Najera Susana S. , Ricketts Christopher J. , Schmidt Laura S. , Medina Julia I. , Saito Keita , Ileva Lilia , Brender Jeffrey R. , James Amy M. , Peer Cody J. , Gouker Brad , Karim Baktiar O. , Chernova Olga , Wells Catherine , Wei Ming-Hui , Yang Youfeng , Zhang Xiaohu , Klumpp-Thomas Carleen , Travers Jameson , Chen Lu , Wilson Kelli M. , Issaq Sameer H. , Figg William D. , Difilippantonio Simone , Kalen Joseph D. , Krishna Murali C. , Thomas Craig J. , Ceribelli Michele , Heske Christine M. , Crooks Daniel R. , Meier Jordan L.
Published: February 2025

Validation of MIPE hits in 96-well cytotoxicity screens and comparison of NAMPT inhibitor efficacy across a panel of HLRCC cell lines.
Supplementary Figure S4 from Characteristics of a CCL21 Gene–Modified Dendritic Cell Vaccine Utilized for a Clinical Trial in Non–Small Cell Lung Cancer
Authors: Oh Michael S. , Dumitras Camelia , Salehi-Rad Ramin , Tran Linh M. , Krysan Kostyantyn , Lim Raymond J. , Jing Zhe , Tappuni Shahed , Lisberg Aaron , Garon Edward B. , Dubinett Steven M. , Liu Bin
Published: February 2025

Supplementary Figure S4. Quality control measures of single cell RNA-sequencing analysis.
Supplementary Figure S2 from Characteristics of a CCL21 Gene–Modified Dendritic Cell Vaccine Utilized for a Clinical Trial in Non–Small Cell Lung Cancer
Authors: Oh Michael S. , Dumitras Camelia , Salehi-Rad Ramin , Tran Linh M. , Krysan Kostyantyn , Lim Raymond J. , Jing Zhe , Tappuni Shahed , Lisberg Aaron , Garon Edward B. , Dubinett Steven M. , Liu Bin
Published: February 2025

Supplementary Figure S2. Comparison of CCL21-DC vaccine batches from the same patient.
Supplementary Figure S5. from Targeting NAD+ Metabolism Vulnerability in FH-Deficient Hereditary Leiomyomatosis and Renal Cell Carcinoma with the Novel NAMPT Inhibitor OT-82
Authors: Najera Susana S. , Ricketts Christopher J. , Schmidt Laura S. , Medina Julia I. , Saito Keita , Ileva Lilia , Brender Jeffrey R. , James Amy M. , Peer Cody J. , Gouker Brad , Karim Baktiar O. , Chernova Olga , Wells Catherine , Wei Ming-Hui , Yang Youfeng , Zhang Xiaohu , Klumpp-Thomas Carleen , Travers Jameson , Chen Lu , Wilson Kelli M. , Issaq Sameer H. , Figg William D. , Difilippantonio Simone , Kalen Joseph D. , Krishna Murali C. , Thomas Craig J. , Ceribelli Michele , Heske Christine M. , Crooks Daniel R. , Meier Jordan L.
Published: February 2025

HLRCC spheroid characterization and OT-82 effect on 3D culture. A) UOK262 and (B) UOK365 spheroids plated at different cell densities (8000, 4000, and 2000 cells/well in triplicate) after 24h, showing different degrees of cell aggregation. Cell viability of UOK262 (C) and UOK365 (D) spheroids treated with GNE-618 (1 nM-500 nM) or OT-82 (0.2 nM-100 nM) assessed with Cell-Titer Glo 3D assay decreases in a dose dependent manner.
Supplementary Figure S3. from Targeting NAD+ Metabolism Vulnerability in FH-Deficient Hereditary Leiomyomatosis and Renal Cell Carcinoma with the Novel NAMPT Inhibitor OT-82
Authors: Najera Susana S. , Ricketts Christopher J. , Schmidt Laura S. , Medina Julia I. , Saito Keita , Ileva Lilia , Brender Jeffrey R. , James Amy M. , Peer Cody J. , Gouker Brad , Karim Baktiar O. , Chernova Olga , Wells Catherine , Wei Ming-Hui , Yang Youfeng , Zhang Xiaohu , Klumpp-Thomas Carleen , Travers Jameson , Chen Lu , Wilson Kelli M. , Issaq Sameer H. , Figg William D. , Difilippantonio Simone , Kalen Joseph D. , Krishna Murali C. , Thomas Craig J. , Ceribelli Michele , Heske Christine M. , Crooks Daniel R. , Meier Jordan L.
Published: February 2025

Cell proliferation rates of HLRCC cell lines treated with low and high concentrations of NAMPT inhibitors. A) Effect of OT-82 at 0.8nM or 100nM (left) and GNE-618 at 8nM or 200nM (right) on cell proliferation of UOK262 after 96 hours. B) Effect of OT-82 at 0.8nM or 100nM (left) and GNE-618 at 8nM or 200nM (right) on cell proliferation of UOK268 after 96 hours. C) Effect of OT-82 at 0.8nM or 100nM (left) and GNE-618 at 8nM or 200nM (right) on cell proliferation of UOK365 after 96 hours.
Supplementary Figure S13 from Targeting NAD+ Metabolism Vulnerability in FH-Deficient Hereditary Leiomyomatosis and Renal Cell Carcinoma with the Novel NAMPT Inhibitor OT-82
Authors: Najera Susana S. , Ricketts Christopher J. , Schmidt Laura S. , Medina Julia I. , Saito Keita , Ileva Lilia , Brender Jeffrey R. , James Amy M. , Peer Cody J. , Gouker Brad , Karim Baktiar O. , Chernova Olga , Wells Catherine , Wei Ming-Hui , Yang Youfeng , Zhang Xiaohu , Klumpp-Thomas Carleen , Travers Jameson , Chen Lu , Wilson Kelli M. , Issaq Sameer H. , Figg William D. , Difilippantonio Simone , Kalen Joseph D. , Krishna Murali C. , Thomas Craig J. , Ceribelli Michele , Heske Christine M. , Crooks Daniel R. , Meier Jordan L.
Published: February 2025

Time course study design for imaging and OT-82 treatment for hyperpolarized pyruvate 13C-MRSI. Post treatment MRSI was performed 5 hours post OT-82 dose #2.
Supplementary Figure S1 from Targeting NAD+ Metabolism Vulnerability in FH-Deficient Hereditary Leiomyomatosis and Renal Cell Carcinoma with the Novel NAMPT Inhibitor OT-82
Authors: Najera Susana S. , Ricketts Christopher J. , Schmidt Laura S. , Medina Julia I. , Saito Keita , Ileva Lilia , Brender Jeffrey R. , James Amy M. , Peer Cody J. , Gouker Brad , Karim Baktiar O. , Chernova Olga , Wells Catherine , Wei Ming-Hui , Yang Youfeng , Zhang Xiaohu , Klumpp-Thomas Carleen , Travers Jameson , Chen Lu , Wilson Kelli M. , Issaq Sameer H. , Figg William D. , Difilippantonio Simone , Kalen Joseph D. , Krishna Murali C. , Thomas Craig J. , Ceribelli Michele , Heske Christine M. , Crooks Daniel R. , Meier Jordan L.
Published: February 2025

Structural figures of NAMPT inhibitors.
Figure S3 from HPV and p53 Status as Precision Determinants of Head and Neck Cancer Response to DNA-PKcs Inhibition in Combination with Irradiation
Authors: Hayrapetyan Liana , Roth Selina M. , Quintin Aurélie , Hovhannisyan Lusine , Medo Matúš , Riedo Rahel , Ott Julien G. , Albers Joachim , Aebersold Daniel M. , Zimmer Yitzhak , Medová Michaela
Published: February 2025

Live-dead assays and apoptosis: (A) Live/Dead assay performed 5 days after the indicated treatments. Right panels: Representative pictures of dead (red; Ethidium homodimer-1) and living (green; calcein-AM) cells. Left panels: Quantification of living (green) and dead (red) cells. (B) Mean percentage of both early and late apoptotic (Annexin V+) cells 48 hours post-treatment. Data is represented as mean ± SEM; *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001).
Figure S2 from Potential Mechanisms of Interstitial Lung Disease Induced by Antibody–Drug Conjugates Based on Quantitative Analysis of Drug Distribution
Authors: Koganemaru Shigehiro , Fuchigami Hirobumi , Morizono Chihiro , Shinohara Hiroko , Kuboki Yasutoshi , Furuuchi Keiji , Uenaka Toshimitsu , Doi Toshihiko , Yasunaga Masahiro
Published: February 2025

Concentration of TNF-α in the supernatants in THP-1 cells.
Supplementary Methods from Preclinical Characterization of XB002, an Anti–Tissue Factor Antibody–Drug Conjugate for the Treatment of Solid Tumors
Authors: Kantak Seema , Faggioni Raffaella , Cai Allen G. , Bhatti Maryam M. , Li Jing , Vainshtein Inna , Cheng Jackie , Mendelsohn Brian A. , Gaudreault Jacques , Migone Thi-Sau , Theunissen Jan-Willem
Published: February 2025

Analysis of Released Payload
Figure S9 from Preclinical Characterization of XB002, an Anti–Tissue Factor Antibody–Drug Conjugate for the Treatment of Solid Tumors
Authors: Kantak Seema , Faggioni Raffaella , Cai Allen G. , Bhatti Maryam M. , Li Jing , Vainshtein Inna , Cheng Jackie , Mendelsohn Brian A. , Gaudreault Jacques , Migone Thi-Sau , Theunissen Jan-Willem
Published: February 2025

Intact XB002 and total antibody measurements
Supplementary Methods from Development and Characterization of a Lysosome-Targeting SLC3A2/PD-L1 Bispecific Antibody–Drug Conjugate for Enhanced Antitumor Efficacy in Solid Tumors
Authors: Wang Zeng , Zheng Meijun , Li Mengyao , Lu Huaqing , Liu Nanxi , Chen Yongdong , Yang Nian , Zeng Wanqin , Dong Yijun , Li Jia , Zhu Zhixiong , Yang Chen , Zhang Zongliang , Lu Qizhong , Li Hexian , Zhou Liangxue , Yang Hui , Tong Aiping
Published: February 2025

Preparation and characterization of the antibody-drug conjugates
Figure S5 from Preclinical Characterization of XB002, an Anti–Tissue Factor Antibody–Drug Conjugate for the Treatment of Solid Tumors
Authors: Kantak Seema , Faggioni Raffaella , Cai Allen G. , Bhatti Maryam M. , Li Jing , Vainshtein Inna , Cheng Jackie , Mendelsohn Brian A. , Gaudreault Jacques , Migone Thi-Sau , Theunissen Jan-Willem
Published: February 2025

Elution profiles of zovodotin and vedotin by high-performance liquid chromatography
Figure S3 from Preclinical Characterization of XB002, an Anti–Tissue Factor Antibody–Drug Conjugate for the Treatment of Solid Tumors
Authors: Kantak Seema , Faggioni Raffaella , Cai Allen G. , Bhatti Maryam M. , Li Jing , Vainshtein Inna , Cheng Jackie , Mendelsohn Brian A. , Gaudreault Jacques , Migone Thi-Sau , Theunissen Jan-Willem
Published: February 2025

XB002 analytical profile
Figure S2 from Development and Characterization of a Lysosome-Targeting SLC3A2/PD-L1 Bispecific Antibody–Drug Conjugate for Enhanced Antitumor Efficacy in Solid Tumors
Authors: Wang Zeng , Zheng Meijun , Li Mengyao , Lu Huaqing , Liu Nanxi , Chen Yongdong , Yang Nian , Zeng Wanqin , Dong Yijun , Li Jia , Zhu Zhixiong , Yang Chen , Zhang Zongliang , Lu Qizhong , Li Hexian , Zhou Liangxue , Yang Hui , Tong Aiping
Published: February 2025

Supplementary Figure 2. Specific targeting of anti-SLC3A2 19G4 mAb and anti-PD-L1 mAb. A, Sequencing results for HeLa SLC3A2KO cells using CRISPR/Cas9 technology. B, Flow cytometry analysis of 19G4 mAb specific binding to SLC3A2 in HeLa-WT and HeLa-SLC3A2KO cell lines. C, Flow cytometry analysis of 2217B3 mAb specific binding to PD-L1 in HeLa-WT and HeLa-PD-L1 cell lines. D, Flow cytometry analysis of 19G4 mAb binding to SLC7A5 and mouse SLC3A2. E, Flow cytometry analysis of 2217B3 mAb binding to PD-1 and mouse PD-L1.
Figure S1 from Preclinical Characterization of XB002, an Anti–Tissue Factor Antibody–Drug Conjugate for the Treatment of Solid Tumors
Authors: Kantak Seema , Faggioni Raffaella , Cai Allen G. , Bhatti Maryam M. , Li Jing , Vainshtein Inna , Cheng Jackie , Mendelsohn Brian A. , Gaudreault Jacques , Migone Thi-Sau , Theunissen Jan-Willem
Published: February 2025

Sensorgrams of 25A3 binding to TF antigen
Figure S1 from Development and Characterization of a Lysosome-Targeting SLC3A2/PD-L1 Bispecific Antibody–Drug Conjugate for Enhanced Antitumor Efficacy in Solid Tumors
Authors: Wang Zeng , Zheng Meijun , Li Mengyao , Lu Huaqing , Liu Nanxi , Chen Yongdong , Yang Nian , Zeng Wanqin , Dong Yijun , Li Jia , Zhu Zhixiong , Yang Chen , Zhang Zongliang , Lu Qizhong , Li Hexian , Zhou Liangxue , Yang Hui , Tong Aiping
Published: February 2025

Supplementary Figure 1. DepMap database of Expression Public 23Q2 identify co-expression of SLC3A2 and PD-L1 in numerous cell lines.
Supplementary Figure S2 from Modeling the Acute Mucosal Toxicity of Fractionated Radiotherapy Combined with the ATM Inhibitor WSD0628
Authors: Garcia Darwin A. , Rathi Sneha , Connors Margaret A. , Grams Michael , Vaubel Rachael A. , Bakken Katrina K. , Ott Lauren L. , Carlson Brett L. , Hu Zeng , Decker Paul A. , Eckel-Passow Jeanette E. , Burgenske Danielle M. , Zhong Wei , Trzasko Joshua D. , Herman Michael G. , Elmquist William F. , Remmes Nicholas B. , Sarkaria Jann N.
Published: February 2025

Supplementary Figure S2 demonstrates agreement between AUC computed from simulated and measured profiles.
Supplementary Data S2 from Modeling the Acute Mucosal Toxicity of Fractionated Radiotherapy Combined with the ATM Inhibitor WSD0628
Authors: Garcia Darwin A. , Rathi Sneha , Connors Margaret A. , Grams Michael , Vaubel Rachael A. , Bakken Katrina K. , Ott Lauren L. , Carlson Brett L. , Hu Zeng , Decker Paul A. , Eckel-Passow Jeanette E. , Burgenske Danielle M. , Zhong Wei , Trzasko Joshua D. , Herman Michael G. , Elmquist William F. , Remmes Nicholas B. , Sarkaria Jann N.
Published: February 2025

Supplementary Data S2: derivation of modified biologically effective dose model.
Suppl Figure 7 from Soluble CD146 Cooperates with VEGFa to Generate an Immunosuppressive Microenvironment in CD146-Positive Tumors: Interest of a Combined Antibody-Based Therapy
Authors: Joshkon Ahmad , Traboulsi Wael , Terme Magali , Bachelier Richard , Fayyad-Kazan Hussein , Dignat-George Françoise , Foucault-Bertaud Alexandrine , Leroyer Aurelie S. , Bardin Nathalie , Blot-Chabaud Marcel
Published: February 2025

Suppl Figure 7
Supplementary Methods from Pancreatic CAF-Derived Autotaxin Drives Autocrine CTGF Expression to Modulate Protumorigenic Signaling
Authors: Volat Fanny , Medhi Ragini , Maggs Lauren Z. , Deken Marcel A. , Price Alice , Andrews Lauren , Clark Jonathan , Taylor Diane , Carruthers Alan , Taylor-Smith Ewan , Pacheco Natalia , Rudge Simon A. , Fraser Amy , Lopez-Clavijo Andrea F. , Sousa Bebiana C. , Johnson Zoë , Di Conza Giusy , van der Veen Lars , Shah Pritom , Sandig Hilary , Sharpe Hayley J. , Farrow Stuart
Published: February 2025

Supplementary Methods
Suppl Figure 10 from Soluble CD146 Cooperates with VEGFa to Generate an Immunosuppressive Microenvironment in CD146-Positive Tumors: Interest of a Combined Antibody-Based Therapy
Authors: Joshkon Ahmad , Traboulsi Wael , Terme Magali , Bachelier Richard , Fayyad-Kazan Hussein , Dignat-George Françoise , Foucault-Bertaud Alexandrine , Leroyer Aurelie S. , Bardin Nathalie , Blot-Chabaud Marcel
Published: February 2025

Suppl Figure 10