bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Insights into the DNA-Binding Mechanism of BCL11A: The Integral Role of ZnF6
Authors: Viennet Thibault , Yin Maolu , Jayaraj Abhilash , Kim Woojin , Sun Zhen-Yu J. , Fujiwara Yuko , Zhang Kevin , Seruggia Davide , Seo Hyuk-Soo , Dhe-Paganon Sirano , Orkin Stuart H. , Arthanari Haribabu
Published: January 2024

The transcription factor BCL11A is a critical regulator of the switch from fetal hemoglobin (HbF: α2γ2) to adult hemoglobin (HbA: α2β2) during development. BCL11A binds at a cognate recognition site (TGACCA) in the γ-globin gene promoter and represses its expression. DNA-binding is mediated by a triple zinc finger domain, designated ZnF456. Here, we report comprehensive investigation of ZnF456, leveraging X-ray crystallography and NMR to determine the structures in both the presence and absence of DNA. We delve into the dynamics and mode of interaction with DNA. Moreover, we discovered that the last zinc finger of BCL11A (ZnF6) plays a special role in DNA binding and γ-globin gene repression. Our findings help account for some rare γ-globin gene promoter mutations that perturb BCL11A binding and lead to increased HbF in adults (hereditary persistence of fetal hemoglobin). Comprehending the DNA binding mechanism of BCL11A opens avenues for the strategic, structure-based design of novel therapeutics targeting sickle cell disease and β-thalassemia.
Deep Learning Based Identification of Tissue of Origin for Carcinomas of Unknown Primary utilizing micro-RNA expression
Authors: Raghu Ananya , Raghu Anisha , Wise Jillian F.
Published: January 2024

Carcinoma of Unknown Primary (CUP) is a subset of metastatic cancers in which the primary tissue source, or origin, remains unidentified. CUP accounts for three to five percent of all malignancies [2]. Representing an exceptionally aggressive category of metastatic cancers, the median survival of those diagnosed with CUP is approximately three to six months [1]. The tissue in which a cancer arises plays a key role in our understanding of altered gene expression, altered cellular pathways, and sensitivities to various forms of cell death in cancer cells [3]. Thus, the lack of knowledge on tissue of origin makes it difficult to devise tailored treatments for patients with CUP [4]. Developing clinically implementable methods to identify the tissue of origin of the primary site is crucial in treating CUP patients [4]. In particular, the expression profiles of non-coding RNAs can provide insight into the tissue of origin for CUP. Non-coding RNAs provide a robust route to clinical implementation due to their resistance against chemical degradation [5].

In this work, we investigate the potential of microRNAs as highly accurate biomarkers for detecting the tissue of origin for metastatic cancers. We further hypothesize that data driven approaches can identify specific microRNA biomarker targets. We used microRNA expression data from the Cancer Genome Atlas (TCGA) dataset [6] and assessed various machine learning approaches. Our results show that it is possible to design robust classifiers to detect the tissue of origin for metastatic samples on the TCGA dataset with an accuracy of up to 96%, which may be utilized in situations of CUP. As a validation of our classifiers, we evaluated the accuracy on a separate set of 194 primary tumor samples from the Sequence Read Archive (SRA) [7]. Our findings demonstrate that deep learning techniques enhance prediction accuracy. We progressed from an initial accuracy prediction of 62.5% with decision trees to 93.2% with logistic regression, finally achieving 96.1% accuracy using deep learning on metastatic samples. On the SRA validation set, a lower accuracy of 41.2% was achieved by decision tree, while deep learning achieved a higher accuracy of 81.2%. Notably, our feature importance analysis showed the top three important biomarkers for predicting tissue of origin to be mir-10b, mir-205, and mir-196b, which aligns with previous work [10]. Our findings highlight the potential of using machine learning techniques to devise tests for detecting tissue of origin for CUP. Since microRNAs are carried throughout the body via vesicles secreted from cells, they may serve as key biomarkers for liquid biopsy due to their presence in blood plasma [11]. Our work serves as a foundation towards developing blood-based cancer detection tests based on microRNA presence.
Differential Short-Term Facilitation Of Synaptic Inputs And Spike Transmission At The Retinocollicular SynapseIn Vivo
Authors: Teh Kai Lun , Dossi Elena , Rouach Nathalie , Sibille Jérémie , Kremkow Jens
Published: January 2024

Short-term plasticity (STP) is important for understanding how neuronal circuits can perform different computations. The STP of a neuron pair can be measured directly using paired whole-cell recordings. Besides, the cross-correlation between the presynaptic and postsynaptic neuronal firing is usually used as a proxy for estimating the synaptic properties. However, the relationships between the synaptic inputs and the spiking properties of the postsynaptic neurons during the STPin vivostill remain unclear. Here, we characterized the STP of both synaptic input, measured by the postsynaptic field potential (PFP), and spike transmission at the retinocollicular pathway of mice. We found that the STP of the retinocollicular pathway is mainly facilitating, where the second presynaptic spike induces a larger PFP and higher postsynaptic firing rate than the first presynaptic spike. The facilitation in the postsynaptic firing rate is generally larger than the PFP facilitation. Interestingly, the last postsynaptic spike timing also has a large facilitating effect on the postsynaptic spiking upon receiving a presynaptic input spike. However, the PFP does not depend on the last postsynaptic spike timing, suggesting that there is an input-independent component of spike transmission in STP. Overall, our results indicate that the STP of the retinocollicular pathway is likely a two-stage process, where the spiking plasticity of the postsynaptic neuron could be independent of its inputs.

Highlights

Measure the short-term plasticity of the postsynaptic dendritic response and the spike transmission simultaneously

The retinocollicular pathway exhibits paired-spike facilitation

Spike transmission facilitates more than postsynaptic dendritic response

Short last postsynaptic spike time facilitates spike transmission independent of the next presynaptic input
Genetic architecture of heritable leaf microbes
Authors: Boyle Julia A. , Frederickson Megan E. , Stinchcombe John R.
Published: January 2024

Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown, yet fundamental to the community assembly of host-associated microbiomes, and with implications for the eco-evolutionary dynamics of microbes and hosts. UsingIpomoea hederacea, Ivy-leaved morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome, and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability, and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.

Importance

We investigated how host genetic variation affected the assembly ofIpomoea hederacea’s natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance, and community composition.
RAN translation of C9orf72-related dipeptide repeat proteins in zebrafish recapitulates hallmarks of amyotrophic lateral sclerosis and identifies hypothermia as a therapeutic strategy
Authors: Burrows David J. , McGown Alexander , Abduljabbar Olfat , Castelli Lydia M. , Shaw Pamela J. , Hautbergue Guillaume M. , Ramesh Tennore M.
Published: January 2024

Objective

Hexanucleotide repeat expansions in theC9orf72gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). A large body of evidence implicates DPRs as one of the main drivers of neuronal injury in cell and animal models.

Methods

A pure repeat-associated non-AUG (RAN) translation zebrafish model of C9orf72-ALS/FTD was generated. Embryonic and adult transgenic zebrafish lysates were investigated for the presence of RAN-translated DPR species and adult-onset motor deficits. Using C9orf72 cell models as well as embryonic C9orf72-ALS/FTD zebrafish, hypothermic-therapeutic temperature management (TTM) was explored as a potential therapeutic option for C9orf72-ALS/FTD.

Results

Here we describe a pure RAN translation zebrafish model of C9orf72-ALS/FTD that exhibits significant RAN-translated DPR pathology and progressive motor decline. We further demonstrate that hypothermic-TTM results in a profound reduction in DPR species in C9orf72-ALS/FTD cell models as well as embryonic C9orf72-ALS/FTD zebrafish.

Interpretation

The transgenic model detailed in this paper provides a medium throughputin vivoresearch tool to further investigate the role of RAN-translation in C9orf72-ALS/FTD and further understand the mechanisms that underpin neuroprotective strategies. Hypothermic-TTM presents a viable therapeutic avenue to explore in the context of C9orf72-ALS/FTD.
Optical Fiber-Assisted Printing: A Platform Technology for Straightforward Photopolymer Resins Patterning and Freeform 3D Printing
Authors: Cianciosi Alessandro , Pfeiffle Maximilian , Wohlfahrt Philipp , Nürnberger Severin , Jungst Tomasz
Published: January 2024

Light-based 3D printing techniques represent powerful tools, enabling the precise fabrication of intricate objects with high resolution and control. An innovative addition to this set of printing techniques is Optical Fiber-Assisted Printing (OFAP) introduced in this manuscript. OFAP is a platform utilizing a LED-coupled optical fiber (LOF) which selectively crosslinks photopolymer resins. It allows on-the-fly change of parameters like light intensity and LOF velocity during fabrication, facilitating the creation of structures with progressive features and multi-material constructs layer-by-layer. An optimized formulation based on allyl-modified gelatin (gelAGE) with food dyes as photoabsorbers is introduced. Additionally, a novel gelatin-based biomaterial, alkyne-modified gelatin (gelGPE), featuring alkyne moieties, demonstrates near-visible light absorption thus fitting OFAP needs, paving the way for multifunctional hydrogels through thiol-yne click chemistry. Besides 2D patterning, OFAP is transferred to embedded 3D printing within a resin bath demonstrating the proof-of-concept as novel printing technology with potential applications in tissue engineering and biomimetic scaffold fabrication, offering rapid and precise freeform printing capabilities.
PbrSYP71regulates pollen tube growth by maintaining uneven distribution of the ERin Pyrus
Authors: Zhang Mingliang , Tang Chao , Lan Chi , Zhang Ningyi , Yue Dong , Xie Zhihua , Qian Ming , Sun Mengjun , Liu Zongqi , Xie Zhu , Zhang Hao , Liu Zhuqin , Zhang Shaoling , Wang Peng , Wu Juyou
Published: January 2024

The uneven distribution of endoplasmic reticulum (ER) underlies the rapid polar growth of pollen tubes. However, the mechanism governing ER distribution remains elusive. In this study, we have identified a pollen tube-specific syntaxin protein, PbrSYP71. Our findings reveal that both overexpression and knocking down ofPbrSYP71inhibited pollen tube growth. Subcellular localization analysis demonstrates that PbrSYP71 anchors to the ER via its transmembrane structure. Overexpression ofPbrSYP71leads to clustered ER distribution in the pollen tube, while knocking down ofPbrSYP71abolishes the uneven ER distribution. Remarkably, transient overexpression ofPbrSYP71ΔABD, lacking the actin binding domain (ABD) of PbrSYP71, has no impact on ER distribution or pollen tube growth. Further investigation indicates that ABD is positioned on F-actin in the pollen tube and has a direct interaction with F-actin. PbrSYP71 assists the ER in moving towards the apex of pollen tube, with ABD displaying autonomous mobility. Our study elucidates that PbrSYP71 maintains uneven distribution of the ER by tethering ER to F-actin, facilitating ER movement towards the pollen tube apex for pear pollen tube elongation. These insights shed light on the mechanisms governing ER distribution in polarized cell growth.
Geometric changes in the nucleoids of Deinococcus radiodurans reveal involvement of new proteins in recovery from ionizing radiation
Authors: Cordova Antonio , Niese Brandon , Sweet Philip , Kamat Pratik , Phillip Jude M , Gordon Vernita , Contreras Lydia M.
Published: January 2024

The extremophileDeinococcus radioduransmaintains a highly-organized and condensed nucleoid as its default state, possibly contributing to high tolerance of ionizing radiation (IR). Previous studies of theD. radioduransnucleoid were limited by reliance on manual image annotation and qualitative metrics. Here, we introduce a high-throughput approach to quantify the geometric properties of cells and nucleoids, using confocal microscopy, digital reconstructions of cells, and computational modeling. We utilize this novel approach to investigate the dynamic process of nucleoid condensation in response to IR stress. Our quantitative analysis reveals that at the population level, exposure to IR induced nucleoid compaction and decreased size ofD. radioduranscells. Morphological analysis and clustering identified six distinct sub-populations across all tested experimental conditions. Results indicate that exposure to IR induces fractional redistributions of cells across sub-populations to exhibit morphologies that associate with greater nucleoid condensation, and decreased abundance of sub-populations associated with cell division. Nucleoid associated proteins (NAPs) may link nucleoid compaction and stress tolerance, but their roles in regulating compaction inD. radioduransis unknown. Imaging of genomic mutants of known and suspected NAPs that contribute to nucleoid condensation found that deletion of nucleic acid binding proteins, not previously described as NAPs, can remodel the nucleoid by driving condensation or decondensation in the absence of stress and that IR increases the abundance of these morphological states. Thus, our integrated analysis introduces a new methodology for studying environmental influences on bacterial nucleoids and provides an opportunity to further investigate potential regulators of nucleoid condensation.

Importance

D. radiodurans, an extremophile known for its stress tolerance, constitutively maintains a highly-condensed nucleoid. Qualitative studies have described nucleoid behavior under a variety of conditions. However, a lack of quantitative data regarding nucleoid organization and dynamics have limited our understanding of regulatory mechanisms controlling nucleoid organization inD. radiodurans. Here, we introduce a quantitative approach that enables high-throughput quantitative measurements of subcellular spatial characteristics in bacterial cells. Applying this to wild-type or single-protein-deficient populations ofD. radioduranssubjected to ionizing radiation, we identified significant stress-responsive changes in cell shape, nucleoid organization, and morphology. These findings highlight this methodology’s adaptability and capacity for quantitatively analyzing the cellular response to stressors for screening cellular proteins involved in bacterial nucleoid organization.
Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the GastrotrichLepidodermella squamata(Dujardin, 1841)
Authors: Roberts Nickellaus G. , Gilmore Michael J. , Struck Torsten H. , Kocot Kevin M.
Published: January 2024

Background

Obtaining adequate DNA for long-read genome sequencing remains a roadblock to producing contiguous genomes from small-bodied organisms. Multiple displacement amplification (MDA) leverages Phi29 DNA polymerase to produce micrograms of DNA from picograms of input. Few genomes have been generated using this approach, due to concerns over biases in amplification related to GC and repeat content and chimera production. Here, we explored the utility of MDA for generating template DNA for PacBio HiFi sequencing usingCaenorhabditis elegans(Nematoda) andLepidodermella squamata(Gastrotricha).

Results

HiFi sequencing of libraries prepared from MDA DNA produced highly contiguous and complete genomes for bothC. elegans(102 Mbp assembly; 336 contigs; N50 = 868 Kbp; L50 = 39; BUSCO_nematoda: S:92.2%, D:2.7%) andL. squamata(122 Mbp assembly; 157 contigs; N50 = 3.9 Mb; L50 = 13; BUSCO_metazoa: S: 78.0%, D: 2.8%). AmplifiedC. elegansreads mapped to the reference genome with a rate of 99.92% and coverage of 99.75% with just one read (of 708,811) inferred to be chimeric. Coverage uniformity was nearly identical for reads from MDA DNA and reads from pooled worm DNA when mapped to the reference genome. The genome ofLepidodermella squamata, the first of its phylum, was leveraged to infer the phylogenetic position of Gastrotricha, which has long been debated, as the sister taxon of Platyhelminthes.

Conclusions

This methodology will help generate contiguous genomes of microscopic taxa whose body size precludes standard long-read sequencing.L. squamatais an emerging model in evolutionary developmental biology and this genome will facilitate further work on this species.
Constitutive Plasma Membrane Turnover in T-REx293 cells via Ordered Membrane Domain Endocytosis under Mitochondrial Control
Authors: Deisl Christine , Moe Orson W. , Hilgemann Donald W.
Published: January 2024

Clathrin/dynamin-independent endocytosis of ordered plasma membrane domains (orderedmembranedomainendocytosis, OMDE) can become massive in response to cytoplasmic Ca elevations, G protein activation by non-hydrolyzable GTP analogs, and enhanced oxidative metabolism. In patch-clamped murine bone marrow macrophages (BMMs), cytoplasmic succinate and pyruvate, but not β-hydroxybutyrate, induce OMDE of 75% of the plasma membrane within 2 min. The responses require palmitoylation of membrane proteins, being decreased by 70% in BMMs lacking the acyltransferase, DHHC5, by treatment with carnitine to shift long-chain acyl groups from cytoplasmic to mitochondrial acyl-CoAs, by bromopalmitate/albumin complexes to block DHHCs, and by the mitochondria-specific cyclosporin, NIM811, to block permeability transition pores that may release mitochondrial coenzyme A into the cytoplasm. Using T-REx293 cells, OMDE amounts to 40% with succinate, pyruvate, or GTPγS, and it is inhibited by actin cytoskeleton disruption. Pyruvate-induced OMDE is blocked by the hydrophobic antioxidant, edaravone, which prevents permeability transition pore openings. Using fluorescent 3kD dextrans to monitor endocytosis, OMDE appears to be constitutively active in T-REx293 cells but not in BMMs. After 1 h without substrates or bicarbonate, pyruvate and hydroxybutyrate inhibit constitutive OMDE, as expected for a shift of CoA from long-chain acyl-CoAs to other CoA metabolites. In the presence of bicarbonate, pyruvate strongly enhances OMDE, which is then blocked by β-hydroxybutyrate, bromopalmitate/albumin complexes, cyclosporines, or edaravone. After pyruvate responses, T-REx293 cells grow normally with no evidence for apoptosis. Fatty acid-free albumin (15 μM) inhibits basal OMDE in T-REx293 cells, as do cyclosporines, carnitine, and RhoA blockade. Surprisingly, OMDE in the absence of substrates and bicarbonate is not inhibited by siRNA knockdown of the acyltransferases, DHHC5 or DHHC2, which are required for activated OMDE in patch clamp experiments. We verify biochemically that small CoA metabolites decrease long-chain acyl-CoAs. We verify also that palmitoylations of many PM-associated proteins decrease and increase when OMDE is inhibited and stimulated, respectively, by different metabolites. STED microscopy reveals that vesicles formed during constitutive OMDE in T-REX293 cells have 90 to 130 nm diameters. In summary, OMDE is likely a major G-protein-dependent endocytic mechanism that can be constitutively active in some cell types, albeit not BMMs. OMDE depends on different DHHC acyltransferases in different circumstances and can be limited by local supplies of fatty acids, CoA, and long-chain acyl-CoAs.
Retinal neuroanatomy of two emerging model organisms, the spiny mouse (Acomys dimidiatus) and the Mongolian gerbil (Meriones unguiculatus)
Authors: Bills Jessica D. , Seifert Ashley W. , Morris Ann C.
Published: January 2024

Purpose

Degenerative eye diseases such as macular degeneration and retinitis pigmentosa slowly deteriorate vision, ultimately leading to blindness. Current research with laboratory animal models largely utilizes small mammals that are nocturnal and lack the ability to restore lost vision. In contrast, the Mongolian gerbil is a diurnal rodent with good photopic vision, and the eastern spiny mouse is a small desert-dwelling rodent with remarkable regenerative capabilities. The goal of this study was to identify several antibodies that detect retinal cell classes inMerionesandAcomys, and to describe the retinal anatomy of these two species in comparison to outbred laboratory mice (Mus musculus).

Methods

Retinal sections were obtained from adult eyes and subjected to histological or immuno-staining with antibodies for various retinal cell types. Sections were imaged by light, fluorescence, and confocal microscopy, assessing cell number and morphology. Cell density, morphology, and placement were compared between species qualitatively and quantitatively.

Results

Immunohistochemical visualization and analysis of all general classes of retinal neurons and Müller glia revealed a classic assembly of retinal cells with a few deviations compared toMus.Merionesdisplayed the highest density of cone photoreceptors andAcomysthe lowest. A higher density of bipolar cell bodies in the proximal portion of the inner nuclear layer was observed in bothAcomysandMerionescompared toMus, and both species exhibited an increase in amacrine cell density compared toMus.

Conclusion

We have characterized similarities and differences in the retinal anatomy and cellular density betweenMeriones,Acomys, andMus. We identified several commercially available antibodies that reliably detect retinal cell types in theAcomysandMerionesretina. Our results provide a foundation for future research into the visual system adaptations of both of these interesting rodent species.
Infant vocal category exploration as a foundation for speech development
Authors: Yoo Hyunjoo , Su Pumpki Lei , Ramsay Gordon , Long Helen L. , Bene Edina R. , Kimbrough Oller D.
Published: January 2024

Non-random exploration of infant speech-like vocalizations (e.g., squeals, growls, and vowel- like sounds or “vocants”) is pivotal in speech development. This type of vocal exploration, often noticed when infants produce particular vocal types in clusters, serves two crucial purposes: it establishes a foundation for speech because speech requires formation of new vocal categories, and it serves as a basis for vocal signaling of wellness and interaction with caregivers. Despite the significance of clustering, existing research has largely relied on subjective descriptions and anecdotal observations regarding early vocal category formation. In this study, we aim to address this gap by presenting the first large-scale empirical evidence of vocal category exploration and clustering throughout the first year of life. We observed infant vocalizations longitudinally using all-day home recordings from 130 typically developing infants across the entire first year of life. To identify clustering patterns, we conducted Fisher’s exact tests to compare the occurrence of squeals versus vocants, as well as growls versus vocants. We found that across the first year, infants demonstrated clear clustering patterns of squeals and growls, indicating that these categories were not randomly produced, but rather, it seemed, infants actively engaged in practice of these specific categories. The findings lend support to the concept of infants as manifesting active vocal exploration and category formation, a key foundation for vocal language.
Bitter taste receptor T2R14 and autophagy flux in gingival epithelial cells
Authors: Singh Nisha , Ulmer Ben , Medapati Manoj , Schroth Robert , Ghavami Saeid , Chelikani Prashen
Published: January 2024

Macroautophagy (hereafterautophagy) is a lysosomal degradation pathway that functions in nutrient recycling and as a mechanism of innate immunity. Previously we reported, a novel host-bacteria interaction between cariogenicS. mutansand bitter taste receptor (T2R14) in gingival epithelial cells (GEC) leading to an innate immune response. Further,S. mutansmight be using the host immune system to inhibit other Gram-positive bacteria, such asS. aureus. To determine whether these bacteria exploit the autophagic machinery of GEC, it is first necessary to evaluate the role of T2R14 in modulating autophagic flux. So far, the the role of T2R14 in the regulation of autophagy is not well charcterized. Therefore, in this study, for the first time, we report that T2R14 downregulates autophagy flux in GECs and T2R14 knockout increases acidic vacuoles. Transmission electron microscopy morphometric results also suggested increased number of autophagic vesicles in T2R14 knockout GEC. Further, our results suggest thatS. mutanscompetence stimulating peptide CSP-1 showed robust intracellular calcium release and this effect is both T2R14 and autophagy protein 7 dependent. In this study we provide the first evidence that T2R14 modulates autophagy flux in GEC. The results of current study culd have benefitial impact on the identifying the impact of T2R in regulation of immuno microenviroment of GEC and its impact in oral health.
Identification of a novel mosaicMTORvariant in purified neuronal DNA from depth electrodes in a patient with focal cortical dysplasia
Authors: Klein Karl Martin , Mascarenhas Rumika , Merrikh Daria , Khanbabaei Maryam , Maroilley Tatiana , Kaur Navprabhjot , Liu Yiping , Soule Tyler , Manalo Minette , Tamura Goichiro , Jacobs Julia , Hader Walter , Pfeffer Gerald , Tarailo-Graovac Maja
Published: January 2024

Background

Recent studies have identified brain somatic variants as a cause of focal epilepsy. These studies relied on resected tissue from epilepsy surgery which is not available in most patients. The use of trace tissue adherent to depth electrodes used for stereo electroencephalography (stereo EEG) has been proposed as an alternative but is hampered by the low cell quality and contamination by non-brain cells. Here, we use our improved depth electrode harvesting technique that purifies neuronal nuclei to achieve molecular diagnosis in a patient with focal cortical dysplasia (FCD).

Methods

Depth electrode tips were collected, pooled by brain region and seizure onset zone, nuclei isolated and sorted using fluorescence-activated nuclei sorting (FANS). Somatic DNA was amplified from neuronal and astrocyte nuclei using primary template amplification followed by exome sequencing of neuronal DNA from the affected pool, unaffected pool, and saliva. The identified variant was validated using droplet digital PCR.

Results

An adolescent male with drug-resistant genetic-structural epilepsy due to left anterior insula FCD had daily focal aware seizures. Stereo EEG confirmed seizure onset in the left anterior insula. The two anterior insula electrodes were combined as the affected pool and three frontal electrodes as the unaffected pool. FANS isolated 140 neuronal nuclei from the affected and 245 neuronal nuclei from the unaffected pool. A novel somatic missenseMTORvariant (p.Leu489Met, CADD score 23.7) was identified in the affected neuronal sample. Droplet digital PCR confirmed a mosaic gradient (VAF 0.78% in affected neuronal sample, variant was absent in all other samples).

Conclusions

Our finding confirms that harvesting neuronal DNA from depth electrodes followed by molecular analysis to identify brain somatic variants is feasible. Our novel method represents a significant improvement compared to the previous method by focusing the analysis on high quality cells of the cell type of interest.
Evaluation of four interventions using behavioural economics insights to increase demand for voluntary medical male circumcision in South Africa through the MoyaApp: A quasi-experimental study
Authors: Mistri Preethi , Tomescu Silviu , Bokolo Simamkele , De Nooy Alexandra , Pisa Pedro T. , Grove Skye , Schmucker Laura , Chetty-Makkan Candice , Long Lawrence , Buttenheim Alison , Maughan-Brown Brendan
Published: January 2024

Background

While voluntary medical male circumcision (VMMC) reduces the risk of HIV transmission by 60%, circumcision coverage falls short of the UNAIDS 90% target. We investigated whether behaviourally informed message framing increased demand for VMMC.

Setting

Adult users of the MoyaApp, a data free application in South Africa, who viewed a form designed to generate interest in VMMC during August-November 2022.

Methods

A quasi-experimental study was conducted to evaluate four MoyaApp VMMC intervention forms against the Standard of Care (SOC) form. All forms enabled users to provide contact details for follow-up engagement by a call centre. The primary outcome was the proportion of forms submitted. Secondary outcomes included successful contact with the user, VMMC bookings/referrals and confirmed circumcision. Multivariable ordinary least-squares regression was used for the analysis.

Results

MoyaApp VMMC form viewers totalled 118,337 of which 6% submitted a form. Foot-in-the-Door form viewers were more likely (+1.3 percentage points, p<0.01) to submit a form compared to the SOC group (6.3%). Active Choice (-1.1 percentage points, p<0.01) and Reserved for You (-0.05 percentage points, p<0.05) form viewers were less likely to submit a form compared to SOC. Users submitting on Foot-in-the-Door were less likely to be booked/referred compared to SOC (-5 percentage points, p<0.05). There were no differences between the intervention and SOC forms for successful contact and circumcisions.

Conclusions

Message framing using behavioural insights was able to nudge men to engage with VMMC services. However, more work is needed to understand how to convert initial interest into bookings and circumcisions.

Trial registration

South African Clinical Trials Registry DOH-27-062022-7811

Pan-African Clinical Trials Registry PACTR202112699416418
Early detection of malignant and pre-malignant peripheral nerve tumors using cell-free DNA fragmentomics
Authors: Sundby R. Taylor , Szymanski Jeffrey J. , Pan Alexander , Jones Paul A. , Mahmood Sana Z. , Reid Olivia H. , Srihari Divya , Armstrong Amy E , Chamberlain Stacey , Burgic Sanita , Weekley Kara , Murray Béga , Patel Sneh , Qaium Faridi , Lucas Andrea N. , Fagan Margaret , Dufek Anne , Meyer Christian F. , Collins Natalie B. , Pratilas Christine A. , Dombi Eva , Gross Andrea M. , Kim AeRang , Chrisinger John S.A. , Dehner Carina A. , Widemann Brigitte C. , Hirbe Angela C. , Chaudhuri Aadel A. , Shern Jack F.
Published: January 2024

Early detection of neurofibromatosis type 1 (NF1) associated peripheral nerve sheath tumors (PNST) informs clinical decision-making, potentially averting deadly outcomes. Here, we describe a cell-free DNA (cfDNA) fragmentomic approach which distinguishes non-malignant, pre-malignant and malignant forms of NF1 PNST. Using plasma samples from a novel cohort of 101 NF1 patients and 21 healthy controls, we validated that our previous cfDNA copy number alteration (CNA)-based approach identifies malignant peripheral nerve sheath tumor (MPNST) but cannot distinguish among benign and premalignant states. We therefore investigated the ability of fragment-based cfDNA features to differentiate NF1-associated tumors including binned genome-wide fragment length ratios, end motif analysis, and non-negative matrix factorization deconvolution of fragment lengths. Fragmentomic methods were able to differentiate pre-malignant states including atypical neurofibromas (AN). Fragmentomics also adjudicated AN cases suspicious for MPNST, correctly diagnosing samples noninvasively, which could have informed clinical management. Overall, this study pioneers the early detection of malignant and premalignant peripheral nerve sheath tumors in NF1 patients using plasma cfDNA fragmentomics. In addition to screening applications, this novel approach distinguishes atypical neurofibromas from benign plexiform neurofibromas and malignant peripheral nerve sheath tumors, enabling more precise clinical diagnosis and management.
Identification of disease-specific TCRs maintaining pathogenic T helper cell responses in postinfectious Lyme Arthritis
Authors: Dirks Johannes , Fischer Jonas , Klaussner Julia , Hofmann Christine , Holl-Wieden Annette , Buck Viktoria , Klemann Christian , Girschick Hermann , Caruana Ignazio , Erhard Florian , Morbach Henner
Published: January 2024

Background

Antibiotic-Refractory Lyme Arthritis(ARLA) involves a complex interplay of T cell responses targetingBorrelia burgdorferiantigens succeeding towards autoantigens by epitope spreading. However, the precise molecular mechanisms driving the pathogenic T cell response in ARLA remain unclear. Our aim was to elucidate the molecular program of disease-specific Th cells.

Methods

Using flow cytometry, high-throughput T cell receptor (TCR) sequencing and scRNA-seq of CD4+Th cells isolated from the joints of European ARLA patients, we aimed at inferring antigen specificity through unbiased analysis of TCR repertoire patterns, identifying surrogate markers for disease-specific TCRs and connecting TCR specificity to transcriptional patterns.

Results

PD-1hiHLA-DR+CD4+effector T cells were clonally expanded within the inflamed joints and persisted throughout disease course. Among these cells, we identified a distinct TCRβ motive restricted to HLA-DRB1*11 or *13 alleles. These alleles, being underrepresented in North American ARLA patients, were unexpectedly prevalent in our European cohort. The identified TCRβ motive served as surrogate marker for a convergent TCR response specific to ARLA, distinguishing it from other rheumatic diseases. In the scRNA-seq dataset, the TCRβ motive particularly mapped to peripheral T helper (TPH) cells displaying signs of sustained proliferation, continuous TCR signaling, and expressing CXCL13 and IFN-γ.

Conclusion

By inferring disease-specific TCRs from synovial T cells we identified a convergent TCR response in the joints of ARLA patients that continuously fueled the expansion of TPHcells expressing a pathogenic cytokine effector program. The identified TCRs will aid in uncovering the major antigen targets of the maladaptive immune response.

Funding

Supported by the German Research Foundation (DFG) MO 2160/4-1; the Federal Ministry of Education and Research (BMBF; Advanced Clinician Scientist-Program INTERACT; 01EO2108) embedded in the Interdisciplinary Center for Clinical Research (IZKF) of the University Hospital Würzburg; the German Center for Infection Research (DZIF; Clinical Leave Program; TI07.001_007) and the Interdisciplinary Center for Clinical Research (IZKF) Würzburg (Clinician Scientist Program, Z-2/CSP-30).
Deep Survival Analysis for Interpretable Time-Varying Prediction of Preeclampsia Risk
Authors: Eberhard Braden W , Gray Kathryn J , Bates David W , Kovacheva Vesela P
Published: January 2024

Objective

Survival analysis is widely utilized in healthcare to predict the timing of disease onset. Traditional methods of survival analysis are usually based on Cox Proportional Hazards model and assume proportional risk for all subjects. However, this assumption is rarely true for most diseases, as the underlying factors have complex, non-linear, and time-varying relationships. This concern is especially relevant for pregnancy, where the risk for pregnancy-related complications, such as preeclampsia, varies across gestation. Recently, deep learning survival models have shown promise in addressing the limitations of classical models, as the novel models allow for non-proportional risk handling, capturing nonlinear relationships, and navigating complex temporal dynamics.

Methods

We present a methodology to model the temporal risk of preeclampsia during pregnancy and investigate the associated clinical risk factors. We utilized a retrospective dataset including 66,425 pregnant individuals who delivered in two tertiary care centers from 2015-2023. We modeled the preeclampsia risk by modifying DeepHit, a deep survival model, which leverages neural network architecture to capture time-varying relationships between covariates in pregnancy. We applied time series k-means clustering to DeepHit’s normalized output and investigated interpretability using Shapley values.

Results

We demonstrate that DeepHit can effectively handle high-dimensional data and evolving risk hazards over time with performance similar to the Cox Proportional Hazards model, achieving an area under the curve (AUC) of 0.78 for both models. The deep survival model outperformed traditional methodology by identifying time-varied risk trajectories for preeclampsia, providing insights for early and individualized intervention. K-means clustering resulted in patients delineating into low-risk, early-onset, and late-onset preeclampsia groups— notably, each of those has distinct risk factors.

Conclusion

This work demonstrates a novel application of deep survival analysis in time-varying prediction of preeclampsia risk. Our results highlight the advantage of deep survival models compared to Cox Proportional Hazards models in providing personalized risk trajectory and demonstrating the potential of deep survival models to generate interpretable and meaningful clinical applications in medicine.
Prevalence and National Patterns of Commonly Prescribed Antidepressants and other Psychotropic Medications to patients with treatment-resistant depression in France
Authors: Alexandre Vimont , Margot Biscond , Henri Leleu , Sanchez-Rico² Marina , Nicolas Hoertel , Pierre-Michel Llorca
Published: January 2024

Background

Prevalence of Treatment-Resistant Depression (TRD) varied widely across studies due to heterogeneous definitions. Several treatment strategies exist to manage patients with TRD but evidence from real-world data is scarce. Investigating their use in real-life settings is important to understand national prescribing practices and to refine prevalence estimation.

Method

All adult patients (≥ 18 years) with a TRD episode for the year 2019 were identified in a sample of four French regions accounting for 27% of national individuals. After exclusion of patients with psychotic or bipolar disorders, Parkinson’s disease, and dementia, TRD was defined by i/ 3 successive sequences of different antidepressants (AD), or ii/ the dispensing of several different AD together, or iii/ an AD with a potentiator (lithium, antiepileptic drugs, or antipsychotic drugs) over the same treatment period. The prevalence rate was estimated for the year 2019 and treatment patterns were described by treatment class and molecule.

Results

For the year 2019, 66,810 patients were identified with TRD, accounting for 23.9% of all patients treated for depression. The mean age was 56 years (±15.9) with 63.7% of women. Standardized prevalence of TRD was estimated at 35.1 per 10 000 patients, and 25.8 per 10,000 patients when excluding patients probably treated for another primary diagnosis than depression. Association of an AD with an antipsychotic was the most frequently used strategy, with SSRIs and second-generation antipsychotics being the most often prescribed.

Conclusion

This study provides robust population-based estimates of the prevalence of TRD in the French population. Description of treatment patterns highlight the widespread use of second-generation antipsychotics as potentiator of antidepressants.
OpenMAP-T1: A Rapid Deep Learning Approach to Parcellate 280 Anatomical Regions to Cover the Whole Brain
Authors: Nishimaki Kei , Onda Kengo , Ikuta Kumpei , Uchida Yuto , Mori Susumu , Iyatomi Hitoshi , Oishi Kenichi ,   the Alzheimer’s Disease Neuroimaging Initiative,   the Australian Imaging Biomarkers and Lifestyle flagship study of aging
Published: January 2024

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This study introduces OpenMAP-T1, a deep-learning-based method for rapid and accurate whole-brain parcellation in T1-weighted brain MRI, which aims to overcome the limitations of conventional normalization-to-atlas-based approaches and multi-atlas label-fusion (MALF) techniques. Brain image parcellation is a fundamental process in neuroscientific and clinical research, enabling a detailed analysis of specific cerebral regions. Normalization-to-atlas-based methods have been employed for this task, but they face limitations due to variations in brain morphology, especially in pathological conditions. The MALF teqhniques improved the accuracy of the image parcellation and robustness to variations in brain morphology, but at the cost of high computational demand that requires a lengthy processing time. OpenMAP-T1 integrates several convolutional neural network models across six phases: preprocessing; cropping; skull-stripping; parcellation; hemisphere segmentation; and final merging. This process involves standardizing MRI images, isolating the brain tissue, and parcellating it into 280 anatomical structures that cover the whole brain, including detailed gray and white matter structures, while simplifying the parcellation processes and incorporating robust training to handle various scan types and conditions. The OpenMAP-T1 was tested on eight available open resources, including real-world clinical images, demonstrating robustness across different datasets with variations in scanner types, magnetic field strengths, and image processing techniques, such as defacing. Compared to existing methods, OpenMAP-T1 significantly reduced the processing time per image from several hours to less than 90 seconds without compromising accuracy. It was particularly effective in handling images with intensity inhomogeneity and varying head positions, conditions commonly seen in clinical settings. The adaptability of OpenMAP-T1 to a wide range of MRI datasets and its robustness to various scan conditions highlight its potential as a versatile tool in neuroimaging.
A Comparative Study: Diagnostic Performance of ChatGPT 3.5, Google Bard, Microsoft Bing, and Radiologists in Thoracic Radiology Cases
Authors: Gunes Yasin Celal , Cesur Turay
Published: January 2024

Purpose

To investigate and compare the diagnostic performance of ChatGPT 3.5, Google Bard, Microsoft Bing, and two board-certified radiologists in thoracic radiology cases published by The Society of Thoracic Radiology.

Materials and Methods

We collected 124 “Case of the Month” from the Society of Thoracic Radiology website between March 2012 and December 2023. Medical history and imaging findings were input into ChatGPT 3.5, Google Bard, and Microsoft Bing for diagnosis and differential diagnosis. Two board-certified radiologists provided their diagnoses. Cases were categorized anatomically (parenchyma, airways, mediastinum-pleura-chest wall, and vascular) and further classified as specific or non-specific for radiological diagnosis. Diagnostic accuracy and differential diagnosis scores were analyzed using chi-square, Kruskal-Wallis and Mann-Whitney U tests.

Results

Among 124 cases, ChatGPT demonstrated the highest diagnostic accuracy (53.2%), outperforming radiologists (52.4% and 41.1%), Bard (33.1%), and Bing (29.8%). Specific cases revealed varying diagnostic accuracies, with Radiologist I achieving (65.6%), surpassing ChatGPT (63.5%), Radiologist II (52.0%), Bard (39.5%), and Bing (35.4%). ChatGPT 3.5 and Bing had higher differential scores in specific cases (P<0.05), whereas Bard did not (P=0.114). All three had a higher diagnostic accuracy in specific cases (P<0.05). No differences were found in the diagnostic accuracy or differential diagnosis scores of the four anatomical location (P>0.05).

Conclusion

ChatGPT 3.5 demonstrated higher diagnostic accuracy than Bing, Bard and radiologists in text-based thoracic radiology cases. Large language models hold great promise in this field under proper medical supervision.
Intravenous iron therapy with ferric carboxymaltose results in a rapid and sustained rise in myocardial iron content through a non-canonical pathway: a translational study
Authors: Vera-Aviles M , Kabir S , Shah A , Polzella P , Lim Y , Buckley P , Ball C , Swinkels D , Matlung H , Blans C , Holdship P , Nugent J , Andreson E , Desborough M , Piechnik S , Ferreira V , Lakhal-Littleton S
Published: January 2024

Background and Aims

Intravenous iron therapies contain iron-carbohydrate complexes, designed to ensure iron becomes bioavailable via the intermediary of spleen and liver reticuloendothelial macrophages. How other tissues obtain and handle this iron remains unknown. This study addresses this question in the context of the heart.

Methods

A prospective observational study was conducted in 12 patients receiving ferric carboxymaltose (FCM) for iron deficiency. Myocardial, spleen and liver magnetic resonance relaxation times, and plasma iron markers were collected longitudinally. To examine the handling of iron taken up by the myocardium, intracellular labile iron pool (LIP) was imaged in FCM-treated mice and cells.

Results

In patients, myocardial relaxation time T1 dropped maximally 3hrs post FCM, remaining low 42 days later, while splenic T1 dropped maximally at 14 days, recovering by 42 days. In plasma, non-transferrin bound iron (NTBI) peaked at 3hrs, while ferritin peaked at 14 days. Changes in liver T1 diverged amongst patients. In mice, myocardial LIP rose 1h and remained elevated 42 days after FCM. In cardiomyocytes, FCM exposure raised LIP rapidly. This was prevented by inhibitors of NTBI transporters T-type and L-Type calcium channels and divalent metal transporter 1.

Conclusions

Intravenous iron therapy with FCM delivers iron to the myocardium rapidly through NTBI transporters, independently of reticuloendothelial macrophages. This iron remains labile for weeks, reflecting the myocardium’s limited iron storage capacity. These findings challenge current notions of how the heart obtains iron from these therapies and highlight the potential for long-term dosing to cause cumulative iron build-up in the heart.

TRANSLATIONAL PERSPECTIVE

Many patients now receive long-term IV iron therapy. The finding that a single standard dose of IV iron causes a sustained rise in myocardial iron underscores the risk for cumulative build-up to occur with multiple doses. Magnetic resonance monitoring of myocardial iron may be required to safeguard against progression towards pathological myocardial iron overload in these patients.

Plasma ferritin levels reflect the iron content of reticuloendothelial macrophages. The finding that myocardial iron elevation following IV iron therapy is independent from reticuloendothelial macrophages highlights the limitations of using plasma ferritin cut-offs to safeguard against the risk of tissue iron overload.

GRAPHICAL ABSTRACT