Miracle-dz/UniFAR-FTUs huggingface dataset:
Association study of CLDN14 variations in patients with kidney stones

Abstract Claudin-14 protein plays an essential role in regulating calcium ions in the kidney and ear. Two phenotypes, hearing loss and kidney stones, were reportedly associated with variations in the CLDN14 gene. This study aimed to understand CLDN14 mutations’ contribution to hearing loss and renal stone formation in a Pakistani cohort. We analyzed CLDN14 sequence variations in 100 patients, along with healthy individuals, to assess whether specific polymorphisms were associated with the disease. Also, we performed an in silico analysis using a mutation database and protein annotation. The rs219779’s genotype CT (p = 0.0020) and rs219780’s genotype AG (p = 0.0012) were significantly associated with kidney stones. We also found that a novel haplotype, “TA” associated with kidney stone formation, has moderate linkage disequilibrium. The TA haplotype was significantly correlated with a kidney stone risk formation of 3.76-fold (OR (CI 95%) = 3.76 (1.83–7.72)) and p = 0.0016 compared to other haplotypes. In silico analysis revealed that mutations associated with hearing loss were not correlated with renal stone formation but affected claudin-14 protein stability. We structurally mapped a novel TA haplotype of CLDN14 that, based on our analysis, likely contributes to the pathogenesis of renal stones.
Deciphering the developmental order and microstructural patterns of 1 early white matter pathways in a diffusion MRI based fetal brain atlas 2 Altered WM microstructures in the brains of fetuses with CHD the fetal brain

14 White matter of the fetal brain undergoes rapid development to form the early structural connections. 15 Diffusion MRI has shown to be a useful tool to depict the fetal brain white matter in utero , and many 16 studies have observed increasing fractional anisotropy and decreasing mean diffusivity in the fetal brain 17 during the second-to-third trimester, whereas others reported non-monotonic changes. Unbiased 18 diffusion MRI atlases of the fetal brain are important for characterizing developmental trajectories of 19 white matter and providing normative references for in-utero diagnosis of prenatal abnormalities. To 20 date, the sole fetal brain diffusion MRI atlas was collected from a Caucasian/mixed population, and was 21 constructed based on the diffusion tensor model with limited spatial resolution. 22 In this work, we proposed a fiber orientation distribution (FOD) based pipeline for the generation of 23 fetal brain diffusion MRI atlases, which showed better registration accuracy than diffusion tensor-based 24 pipeline. Based on the FOD pipeline, we constructed the first Chinese fetal brain diffusion MRI atlas 25 using 89 normal fetal diffusion MRI scans at GA between 24 and 38 weeks. Complex non-monotonic 26 trends of tensor- and FOD-derived microstructural parameters in eight white matter tracts were 27 observed, which jointly pointed to different phases of microstructural development. Specifically, we speculated that the turning point of the diffusivity trajectory may correspond to the starting point of pre- myelination, based on which, the developmental order of white matter tracts can be mapped and the 30 order was in agreement with order of myelination from histological studies. The normative atlas also provided a reference for detection of abnormal white matter development, such as that in congenital heart disease. Therefore, the high-order fetal brain diffusion MRI atlas established in this study depicted 33 the spatiotemporal pattern of early white matter development, and findings may help decipher the 34 distinct microstructural events in utero . subjects SCC P and group in GCC
Activation of the actin/MRTF-A/SRF signalling pathway in pre-malignant mammary epithelial cells by P-cadherin is essential for transformation

Alterations in the expression or function of cell adhesion molecules have been implicated in all steps of tumour progression. Among those, P-cadherin expression is highly enriched in basal-like breast cancer, a molecular subset of triple-negative breast carcinomas, playing a central role in inducing cancer cell self-renewal, as well as collective cell migration and invasion capacity. To decipher the P-cadherin-dependent signalling network, we generated a humanised P-cadherin fly model, establishing a clinically relevant platform for functional exploration of P-cadherin effectors in vivo. We report that actin nucleators, MRTF and SRF are main effectors of P-cadherin functional effects. In addition, we validated these findings in a human mammary epithelial cell line with conditional activation of the Src oncogene, which recapitulates molecular events taking place during cellular transformation. We show that prior to triggering the gain of malignant phenotypes, Src induces a transient increase in P-cadherin expression levels, which correlates with MRTF-A accumulation, its nuclear translocation and the upregulation of SRF target genes. Moreover, knocking down P-cadherin, or preventing Factin polymerization with Latrunculin A, impairs SRF transcriptional activity. Furthermore, blocking MRTF-A nuclear translocation with CCG-203971 hampers proliferation, selfrenewal and invasion. Thus, in addition to sustaining malignant phenotypes, P-cadherin can also play a major role in the very early stages of breast carcinogenesis by promoting a transient boost of MRTF-A/SRF signalling through actin regulation.
iPSC‐based modeling of THD recapitulates disease phenotypes and reveals neuronal malformation

Tyrosine hydroxylase deficiency (THD) is a rare genetic disorder leading to dopaminergic depletion and early-onset parkinsonism. Affected children present with either a severe form that does not respond to L-Dopa treatment (THD-B), or a milder L-Dopa responsive form (THD-A). We generated induced pluripotent stem cells (iPSCs) from THD patients that were differentiated into dopaminergic neurons (DAn) and compared with control-DAn from healthy individuals and gene-corrected isogenic controls. Consistent with patients, THD iPSC-DAn displayed lower levels of DA metabolites and reduced TH expression, when compared to controls. Moreover, THD iPSC-DAn showed abnormal morphology, including reduced total neurite length and either an abnormal TH proximodistal gradient (THDA), or neurite arborization defects (THDB). Treatment of THD-iPSC-DAn with L-Dopa rescued the neuronal defects and disease phenotype only in THDA-DAn. Interestingly, L-Dopa treatment at the stage of neuronal precursors could prevent the alterations in THDB-iPSC-DAn, thus suggesting the existence of a critical developmental window in THD. Our iPSC-based model recapitulates THD disease phenotypes and response to treatment, representing a promising tool for investigating pathogenic mechanisms, drug screening, and personalized management.
FtsH Protease Inactivation Allows Accumulation of Aberrant Photosystem II in a Chlamydomonas Rubredoxin Mutant

The assembly of photosystem II (PSII) requires the participation of assembly proteins that facilitate the step-wise association of its protein and pigment components into a functional complex capable of oxidizing water and reducing plastoquinone. We previously identified one such factor, the membrane-bound rubredoxin RBD1, but its precise role remains unknown in part due to the inability of the 2pac mutant strain of Chlamydomonas reinhardtii, which lacks RBD1, to accumulate PSII. Here, we show that decreased PSII accumulation in 2pac is due to increased proteolytic degradation. Inactivating the thylakoid membrane FtsH protease in the 2pac mutant background led to an increase in the abundance of PSII subunits and their integration into higher molecular weight complexes, including PSII dimers, capable of sustaining photoautotrophic growth. Dark- and low light-grown 2pac ftsh1-1 both accumulated a 23-kD fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage or photoinhibition. We introduced a HIS-tagged version of the PsbH protein into the 2pac ftsh1-1 background to purify and examine PSII. We found no detectable changes with respect to cofactor composition relative to the wild-type, leading to us to propose a model in which RBD1 promotes the proper folding of D1, possibly via delivery or reduction of the non-heme iron during PSII assembly. Our results demonstrate that introduction of the ftsh1-1 mutation into mutants defective in the biogenesis of thylakoid membrane complexes can allow for the accumulation and study of aberrant complexes that would otherwise be degraded due to their high protease sensitivity.
Using predictive validity to compare associations between brain damage and behavior

Lesion-behavior mapping (LBM) provides a statistical map of the association between voxel-wise brain damage and individual differences in behavior. To understand whether two behaviors are mediated by damage to distinct regions, researchers often compare LBM weight outputs by either the Overlap method or the Correlation method. However, these methods lack statistical criteria to determine whether two LBM are distinct vs. the same and are disconnected from a major goal of LBMs: predicting behavior from brain damage. Without such criteria, researchers may draw conclusions from numeric differences between LBMs that are irrelevant to predicting behavior. We developed and validated a Predictive Validity Comparison method (PVC) that establishes a statistical criterion for comparing two LBMs using predictive accuracy: two LBMs are distinct if and only if they provide unique predictive power for the behaviors being assessed. We applied PVC to two lesion-behavior stroke data sets, demonstrating its utility for determining when behaviors arise from the same vs. different lesion patterns. Using region-of-interest based simulations derived from proportion damage from a large data set (n = 131), PVC accurately detected when behaviors were mediated by different regions (high sensitivity) vs. the same region (high specificity). Both the Overlap method and Correlation method performed poorly on the simulated data. By objectively determining whether two behavioral deficits can be explained by a single vs. distinct patterns of brain damage, PVC provides a critical advance in establishing the brain bases of behavior. We have developed and released a GUI-driven web app to encourage widespread adoption.
Zebrafish her3 knockout impacts developmental and cancer-related gene signatures

HES3 is a basic helix-loop-helix transcription factor that regulates neural stem cell renewal during development. HES3 overexpression is predictive of reduced overall survival in patients with fusion-positive rhabdomyosarcoma, a pediatric cancer that resembles immature and undifferentiated skeletal muscle. However, the mechanisms of HES3 cooperation in fusion-positive rhabdomyosarcoma are unclear and are likely related to her3/HES3’s role in neurogenesis. To investigate HES3’s function during development, we generated a zebrafish CRISPR/Cas9 knockout of her3, the zebrafish ortholog of HES3. Loss of her3 is not embryonic lethal and adults exhibit expected Mendelian ratios. Embryonic her3 zebrafish mutants are significantly smaller than wildtype and a subset present with lens defects as adults. Transcriptomic analysis of her3 mutant embryos indicates that genes involved in organ development, such as pctp and grinab, are significantly downregulated. Further, differentially expressed genes in her3 knockout embryos are enriched for HOX and SOX10 motifs. Several cancer-related gene pathways are impacted, including the inhibition of matrix metalloproteinases. Altogether, this new model is a powerful system to study her3/HES3-mediated neural development and its misappropriation in cancer contexts. Summary Statement Here, we generate and characterize a zebrafish her3/HES3 knockout to elucidate the functional role of her3/HES3, a transcriptional repressor, in neural development and tumorigenic processes.
Long-term culture of patient-derived cardiac organoids recapitulated Duchenne muscular dystrophy cardiomyopathy and disease progression

Duchenne Muscular Dystrophy (DMD) is an X-linked neuromuscular disease which to-date incurable. The major cause of death is dilated cardiomyopathy, however the pathogenesis is unclear as existing cellular and animal models do not fully recapitulate the human disease phenotypes. In this study, we generated cardiac organoids from patient-derived pluripotent stem cells (DMD-CO) and isogenic-corrected controls (DMD-Iso-CO) and studied if DMD-related cardiomyopathy and disease progression occur in the organoids upon long-term culture (up to 93 days). Histological analysis showed that DMD-CO lacks initial proliferative capacity, displayed a progressive loss of α-sarcoglycan localization and high stress in endoplasmic reticulum. Additionally, the cardiomyocyte deteriorated over time, and fibrosis and adipogenesis were observed in DMD-CO. RNA sequencing analysis confirmed a distinct transcriptomic profile in DMD-CO which were associated with functional enrichment in hypertrophy/dilated cardiomyopathy, arrhythmia, adipogenesis and fibrosis pathways. Moreover, five miRNAs were identified to be crucial in this dysregulated gene network. In conclusion, we generated patient-derived cardiac organoid model that displayed DMD-related cardiomyopathy and disease progression phenotypes in long-term culture. We envision the feasibility to develop a more complex, realistic and reliable in vitro 3D human cardiac-mimics to study DMD-related cardiomyopathies.
IgG1 responses following SARS-CoV-2 infection are polyclonal and highly personalized, whereby each donor and each clone displays a distinct pattern of cross-reactivity against SARS-CoV-2 variants

Using a recently introduced efficient mass spectrometry-based approach we monitored in molecular detail the IgG1 clonal responses in individual donorsindividual donors’ IgG1 clonal responses in molecular detail, examining SARS-CoV-2 spike-protein-specific IgG1 repertoires. We monitored the plasma clonal IgG1 profiles of 8 donors (4 male and 4 female) who had recently experienced an infection by either the wild type Wuhan Hu-1 virus or one of 3 VOCs (Alpha, Beta and Gamma). In these donors we charted the full plasma IgG1 repertoires as well as the IgG1 repertoires targeting the SARS-CoV-2 spike protein trimer as antigen. We observed that shortly after infection in between <0.1% to almost 10% of all IgG1 antibody molecules present in plasma did bind to the spike protein. Each donor displayed a unique plasma IgG1 repertoire, but also each donor displayed a unique and polyclonal antibody response against the SARS-CoV-2 spike-protein variants. Our analyses revealed that certain clones exhibit (alike) binding affinity towards all four tested spike-protein variants, whereas other clones displayed strong unique mutant-specific affinity. We conclude that each infected person generates a unique polyclonal response following infection, whereby some of these clones can bind multiple viral variants, whereas other clones do not display such cross-reactivity. In general, by assessing IgG1 repertoires following infection it becomes possible to identify and select fully matured human plasma antibodies that target specific antigens, and display either high specificity or cross-reactivity versus mutated versions of the antigen, which will aid in selecting antibodies that may be developed into biotherapeutics.
Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein

Respiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. Because no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus may lead to antibody resistance are greatly needed. ABSTRACT Monoclonal antibodies are increasingly used for the prevention and/or treatment of viral infections. One caveat of their use is the ability of viruses to evolve resistance to antibody binding and neutralization. Computational strategies to identify viral mutations that may disrupt antibody binding would leverage the wealth of viral genomic sequence data to monitor for potential antibody-resistant mutations. The respiratory syncytial virus is an important pathogen for which monoclonal antibodies against the fusion (F) protein are used to prevent severe disease in high-risk infants. In this study, we used an approach that combines molecular dynamics simulations with FoldX to estimate changes in free energy in F protein folding and binding to the motavizumab antibody upon each possible amino acid change. We systematically selected 8 predicted escape mutations and tested them in an infectious clone. Consistent with our F protein stability predictions, replication-effective viruses were observed for each selected mutation. Six of the eight variants showed increased resistance to neutralization by motavizumab. Flow cytometry was used to validate the estimated (model-predicted) effects on antibody binding to F. Using surface plasmon resonance, we determined that changes in the on-rate of motavizumab binding were associated with the reduced affinity for two novel escape mutations. Our study empirically validated the accuracy of our molecular modeling approach and emphasized the role of biophysical protein modeling in predicting viral resistance to antibody-based therapeutics that can be used to monitor the emergence of resistant viruses and to design improved therapeutic antibodies. IMPORTANCE Respiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. Because no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus may lead to antibody resistance are greatly needed.
Pyroptosis-Related LncRNA Signatures Correlate With Lung Adenocarcinoma Prognosis

Background Pyroptosis is a new type of programmed cell death, accompanied by an intense inflammatory response. Previous studies have shown that pyroptosis can modify long-chain non-coding RNA (lncRNA), thereby affecting the occurrence and progression of tumors. However, the underlying role of pyroptosis-related lncRNA in lung adenocarcinoma (LUAD) remains to be elucidated. Therefore, the purpose of our study was to evaluate the prognostic value of pyrolysis-related lncRNA in patients with LUAD. Methods A total of 454 LUAD samples were downloaded from The Cancer Genome Atlas (TCGA) database. Pearson’s correlation coefficient was used to identify the pyroptosis-related lncRNAs. Unsupervised consensus clustering was used to identify the various LUAD molecular subtypes. A least absolute shrinkage and selection operator (LASSO) analysis was conducted to construct a prognostic signature. Results An 11-lncRNA prognostic signature out of 19 identified pyroptosis-related prognostic lncRNAs was constructed. The patients with LUAD were divided into low-risk and high-risk groups. Patients in the high-risk group had higher score values and mortality. The immune score, stromal score, and estimate score were lower in the high-risk group. The risk score was an independent predictor for OS in multivariate Cox regression analyses (HR > 1, p < 0.01). BTLA, PD-1, PD-L1, CTLA, and CD47 were lower expressed in the high-risk group. Conclusions Our study identified an 11-pyroptosis-related lncRNA signature. These findings could further clarify the role of pyroptosis in LUAD and guide the prognosis and individualized treatment of patients.
Uncertainties Associated With Simulating Regional Sea Surface Height and Tides: A Case Study of the East China Seas

Modeling sea surface height (SSH) and tides is important but challenging in shelf seas. The Eastern China Seas (ECSs) is such a shelf sea with large inter-model deviations in prior studies. In order to assess and compare the possible uncertainty sources, numerical scenarios of varying the open boundary forcing, bottom roughness length scale, atmospheric forcing, grid resolution, and regional bathymetry were conducted in a hydrodynamic model of the ECSs. Results indicate that bathymetry data and open boundary forcing with inadequate accuracy generate uncertainties in SSH and tides locally and throughout the basin. An increase in bottom roughness enhances tidal dissipation and shifts amphidromes to the left relative to the incoming Kelvin waves, causing SSH variations in the ECSs. Refining the model resolution from 4 to 2 km mainly affects nearshore SSH and tides due to minor changes in depicted coastlines. Using different reanalysis meteorological data appears more important on the episodic than annual scale. It is highlighted that some uncertainty sources have opposing effects on SSH or tides and counteract their individual biases, making it difficult to achieve a realistic simulation. For example, increasing bottom roughness can not only compensate effects of overestimated tidal amplitude at open boundaries, but also balance out the overestimated M2 phase along the West Coast of Korea in a coarser-resolution model. Based on findings in this study, suggestions are provided for further reducing uncertainties in SSH and tide modeling in the ECSs and other shelf seas.
Efficacy and Safety of Veno-Arterial Extracorporeal Membrane Oxygenation in the Treatment of High-Risk Pulmonary Embolism: A Retrospective Cohort Study

Objectives Veno-arterial extracorporeal membrane oxygenation (ECMO) is increasingly used to treat high-risk pulmonary embolism (PE). However, its efficacy and safety remain uncertain. This retrospective cohort study aimed to determine whether ECMO could improve the clinical outcomes of patients with high-risk PE. Methods Forty patients with high-risk PE, who were admitted to Kaohsiung Chang Gung Memorial Hospital between January 2012 and December 2019, were included in this study. Demographic data and clinical outcomes were compared between patients treated without ECMO (non-ECMO group) and those treated with ECMO (ECMO group). Appropriate statistical tools were used to compare variables between groups and the survival was analyzed using the Kaplan–Meier method. Results The overall in-hospital mortality rate was 55%, in which 65% (26/40) of patients presented with cardiac arrest with a mortality rate of 77%, which was higher than that of patients without cardiac arrest (14%). There was no significant difference in major complications and in-hospital mortality between the non-ECMO and ECMO groups. However, in subgroup analysis, compared with patients treated without ECMO, earlier ECMO treatment was associated with a reduced risk of cardiac arrest (P = 0.023) and lower in-hospital mortality (P = 0.036). A log-rank test showed a significantly higher cumulative overall survival in the earlier ECMO treatment group (P = 0.033). Conclusions In this retrospective cohort study, earlier ECMO treatment was associated with lower in-hospital mortality among unstable patients without cardiac arrest. Our findings suggest that ECMO can be considered as an initial treatment option for patients with high-risk PE in higher-volume hospitals.