bluuebunny/crossref_metadata_2025 huggingface dataset:
Mediators and moderators of the effects of a school-based intervention on adolescents’ fruit and vegetable consumption: the HEIA study
Authors: Daas Merel Celine , Gebremariam Mekdes Kebede , Poelman Maartje P , Andersen Lene Frost , Klepp Knut-Inge , Bjelland Mona , Lien Nanna
Published: January 2024

Objective:

To examine whether targeted determinants mediated the effects of the HEalth In Adolescents (HEIA) intervention on fruit and vegetable (FV) consumption and explore if these mediating effects were moderated by sex, parental education or weight status.

Design:

Cluster-randomised controlled trial.

Setting:

The HEIA study (2007–2009) was a Norwegian 20-month multi-component school-based intervention to promote healthy weight development. FV consumption and targeted determinants were self-reported at baseline, mid-way (8 months) and post-intervention (20 months).

Participants:

Adolescents (11–13-year-old) in twenty-five control schools (n 746) and twelve intervention schools (n 375).

Results:

At post-intervention, more adolescents in the intervention group compared with the control group had knowledge of the FV recommendations (OR: 1·4, 95 % CI 1·1, 1·9) and reported a decreased availability of vegetables at home (β: –0·1, 95 % CI –0·2, 0·0). Availability/accessibility of FV at home, availability of vegetables at dinner, taste preferences for different types of FV and knowledge of the FV recommendations were positively associated with the consumption of FV. However, none of the post-intervention determinants significantly mediated the intervention effects on FV consumption. Although no moderating influences by sex, parental education or weights status were observed on the mediating effects, exploratory analyses revealed significant moderations in the b-paths.

Conclusions:

Since none of the targeted determinants could explain the increase in FV consumption, it remains unclear why the intervention was effective. Reporting on a wide range of mediators and moderators in school-based interventions is needed to reveal the pathways through which intervention effects are achieved.
The Nature of the Critique of Pure Reason and the Architectonic Unity of Metaphysics: A Response to my Critics
Authors: Gava Gabriele
Published: January 2024

I respond to Karin de Boer, Thomas Land, and Claudio La Rocca’s comments on Kant’s Critique of Pure Reason and the Method of Metaphysics (CUP 2023). I first provide a quick outline of some of the main claims I make in the book.  I then directly address their criticisms, which I group into three categories. The first group of comments raises doubts concerning my characterization of the central tasks of the critique of pure reason. The second targets the fact that I downplay faculty analysis as an essential characteristic of the critique. The third has to do with my claim that the Critique of Pure Reason aims to show that metaphysics is capable of architectonic unity, where this unity is only achievable when we construe metaphysics according to the worldly concept of philosophy.
Time‐Dependent Deformation in the Damage Zone of the Chelungpu Fault System and Potential Stress Relaxation
Authors: Talukdar Mayukh , Sone Hiroki
Published: January 2024

High fracture density in fault damage zones not only reduces the elastic stiffness of rocks but may also promote time‐dependent bulk deformation through the sliding of fracture and thus alter the stress in fault zones. On comparing the damage zones of the three faults in the Chelungpu fault system encountered in the Taiwan Chelungpu fault Drilling Project (TCDP), the youngest damage zone showed pronounced sonic velocity reduction even though fracture density is the same for all three fault zones, consistent with the shorter time for velocity recovery in the youngest fault. Caliper log data showed a time‐dependent enlargement of the borehole wall at the damage zone. These damage zones record lower differential stress than the surrounding host rock, which cannot be explained by the reduced elastic stiffness in the damage zone. Stress relaxation caused by time‐dependent bulk deformation in the damage zone may be responsible for the observed low differential stress.
Dynamical control of nanoscale light-matter interactions in low-dimensional quantum materials
Authors: Koo Yeonjeong , Moon Taeyoung , Kang Mingu , Joo Huitae , Lee Changjoo , Lee Hyeongwoo , Kravtsov Vasily , Park Kyoung-Duck
Published: January 2024

Tip-enhanced nano-spectroscopy and -imaging have significantly advanced our understanding of low-dimensional quantum materials and their interactions with light, providing a rich insight into the underlying physics at their natural length scale. Recently, various functionalities of the plasmonic tip expand the capabilities of the nanoscopy, enabling dynamic manipulation of light-matter interactions at the nanoscale. In this review, we focus on a new paradigm of the nanoscopy, shifting from the conventional role of imaging and spectroscopy to the dynamical control approach of the tip-induced light-matter interactions. We present three different approaches of tip-induced control of light-matter interactions, such as cavity-gap control, pressure control, and near-field polarization control. Specifically, we discuss the nanoscale modifications of radiative emissions for various emitters from weak to strong coupling regime, achieved by the precise engineering of the cavity-gap. Furthermore, we introduce recent works on light-matter interactions controlled by tip-pressure and near-field polarization, especially tunability of the bandgap, crystal structure, photoluminescence quantum yield, exciton density, and energy transfer in a wide range of quantum materials. We envision that this comprehensive review not only contributes to a deeper understanding of the physics of nanoscale light-matter interactions but also offers a valuable resource to nanophotonics, plasmonics, and materials science for future technological advancements.
LUBAC promotes angiogenesis and lung tumorigenesis by ubiquitinating and antagonizing autophagic degradation of HIF1α
Authors: Jin Ying , Peng Yazhi , Xu Jie , Yuan Ye , Yang Nan , Zhang Zemei , Xu Lei , Li Lin , Xiong Yulian , Sun Dejiao , Pan Yamu , Wu Ruiqing , Fu Jian
Published: January 2024

Hypoxia-inducible factor 1 (HIF1) is critically important for driving angiogenesis and tumorigenesis. Linear ubiquitin chain assembly complex (LUBAC), the only known ubiquitin ligase capable of catalyzing protein linear ubiquitination to date, is implicated in cell signaling and associated with cancers. However, the role and mechanism of LUBAC in regulating the expression and function of HIF1α, the labile subunit of HIF1, remain to be elucidated. Herein we showed that LUBAC increases HIF1α protein expression in cultured cells and tissues of human lung cancer and enhances HIF1α DNA-binding and transcriptional activities, which are dependent upon LUBAC enzymatic activity. Mechanistically, LUBAC increases HIF1α stability through antagonizing HIF1α decay by the chaperone-mediated autophagy (CMA)-lysosome pathway, thereby potentiating HIF1α activity. We further demonstrated that HIF1α selectively interacts with HOIP (the catalytic subunit of LUBAC) primarily in the cytoplasm. LUBAC catalyzes linear ubiquitination of HIF1α at lysine 362. Linear ubiquitination shields HIF1α from interacting with heat-shock cognate protein of 70 kDa and lysosome-associated membrane protein type 2 A, two components of CMA. Consequently, linear ubiquitination confers protection against CMA-mediated destruction of HIF1α, increasing HIF1α stability and activity. We found that prolyl hydroxylation is not a perquisite for LUBAC’s effects on HIF1α. Functionally, LUBAC facilitates proliferation, clonogenic formation, invasion and migration of lung cancer cells. LUBAC also boosts angiogenesis and exacerbates lung cancer growth in mice, which are greatly compromised by inhibition of HIF1α. This work provides novel mechanistic insights into the role of LUBAC in regulating HIF1α homeostasis, tumor angiogenesis and tumorigenesis of lung cancer, making LUBAC an attractive therapeutic target for cancers.
Development and multi-site external validation of a generalizable risk prediction model for bipolar disorder
Authors: Walsh Colin G. , Ripperger Michael A. , Hu Yirui , Sheu Yi-han , Lee Hyunjoon , Wilimitis Drew , Zheutlin Amanda B. , Rocha Daniel , Choi Karmel W. , Castro Victor M. , Kirchner H. Lester , Chabris Christopher F. , Davis Lea K. , Smoller Jordan W.
Published: January 2024

Bipolar disorder is a leading contributor to disability, premature mortality, and suicide. Early identification of risk for bipolar disorder using generalizable predictive models trained on diverse cohorts around the United States could improve targeted assessment of high risk individuals, reduce misdiagnosis, and improve the allocation of limited mental health resources. This observational case-control study intended to develop and validate generalizable predictive models of bipolar disorder as part of the multisite, multinational PsycheMERGE Network across diverse and large biobanks with linked electronic health records (EHRs) from three academic medical centers: in the Northeast (Massachusetts General Brigham), the Mid-Atlantic (Geisinger) and the Mid-South (Vanderbilt University Medical Center). Predictive models were developed and valid with multiple algorithms at each study site: random forests, gradient boosting machines, penalized regression, including stacked ensemble learning algorithms combining them. Predictors were limited to widely available EHR-based features agnostic to a common data model including demographics, diagnostic codes, and medications. The main study outcome was bipolar disorder diagnosis as defined by the International Cohort Collection for Bipolar Disorder, 2015. In total, the study included records for 3,529,569 patients including 12,533 cases (0.3%) of bipolar disorder. After internal and external validation, algorithms demonstrated optimal performance in their respective development sites. The stacked ensemble achieved the best combination of overall discrimination (AUC = 0.82–0.87) and calibration performance with positive predictive values above 5% in the highest risk quantiles at all three study sites. In conclusion, generalizable predictive models of risk for bipolar disorder can be feasibly developed across diverse sites to enable precision medicine. Comparison of a range of machine learning methods indicated that an ensemble approach provides the best performance overall but required local retraining. These models will be disseminated via the PsycheMERGE Network website.
Major depressive disorder associated alterations in the effective connectivity of the face processing network: a systematic review
Authors: Jamieson Alec J. , Leonards Christine A. , Davey Christopher G. , Harrison Ben J.
Published: January 2024

Major depressive disorder (MDD) is marked by altered processing of emotional stimuli, including facial expressions. Recent neuroimaging research has attempted to investigate how these stimuli alter the directional interactions between brain regions in those with MDD; however, methodological heterogeneity has made identifying consistent effects difficult. To address this, we systematically examined studies investigating MDD-associated differences present in effective connectivity during the processing of emotional facial expressions. We searched five databases: PsycINFO, EMBASE, PubMed, Scopus, and Web of Science, using a preregistered protocol (registration number: CRD42021271586). Of the 510 unique studies screened, 17 met our inclusion criteria. These studies identified that compared with healthy controls, participants with MDD demonstrated (1) reduced connectivity from the dorsolateral prefrontal cortex to the amygdala during the processing of negatively valenced expressions, and (2) increased inhibitory connectivity from the ventromedial prefrontal cortex to amygdala during the processing of happy facial expressions. Most studies investigating the amygdala and anterior cingulate cortex noted differences in their connectivity; however, the precise nature of these differences was inconsistent between studies. As such, commonalities observed across neuroimaging modalities warrant careful investigation to determine the specificity of these effects to particular subregions and emotional expressions. Future research examining longitudinal connectivity changes associated with treatment response may provide important insights into mechanisms underpinning therapeutic interventions, thus enabling more targeted treatment strategies.
Prediction models for postoperative delirium in elderly patients with machine-learning algorithms and SHapley Additive exPlanations
Authors: Song Yuxiang , Zhang Di , Wang Qian , Liu Yuqing , Chen Kunsha , Sun Jingjia , Shi Likai , Li Baowei , Yang Xiaodong , Mi Weidong , Cao Jiangbei
Published: January 2024

Postoperative delirium (POD) is a common and severe complication in elderly patients with hip fractures. Identifying high-risk patients with POD can help improve the outcome of patients with hip fractures. We conducted a retrospective study on elderly patients (≥65 years of age) who underwent orthopedic surgery with hip fracture between January 2014 and August 2019. Conventional logistic regression and five machine-learning algorithms were used to construct prediction models of POD. A nomogram for POD prediction was built with the logistic regression method. The area under the receiver operating characteristic curve (AUC-ROC), accuracy, sensitivity, and precision were calculated to evaluate different models. Feature importance of individuals was interpreted using Shapley Additive Explanations (SHAP). About 797 patients were enrolled in the study, with the incidence of POD at 9.28% (74/797). The age, renal insufficiency, chronic obstructive pulmonary disease (COPD), use of antipsychotics, lactate dehydrogenase (LDH), and C-reactive protein are used to build a nomogram for POD with an AUC of 0.71. The AUCs of five machine-learning models are 0.81 (Random Forest), 0.80 (GBM), 0.68 (AdaBoost), 0.77 (XGBoost), and 0.70 (SVM). The sensitivities of the six models range from 68.8% (logistic regression and SVM) to 91.9% (Random Forest). The precisions of the six machine-learning models range from 18.3% (logistic regression) to 67.8% (SVM). Six prediction models of POD in patients with hip fractures were constructed using logistic regression and five machine-learning algorithms. The application of machine-learning algorithms could provide convenient POD risk stratification to benefit elderly hip fracture patients.
Identification of a novel perifornical-hypothalamic-area-projecting serotonergic system that inhibits innate panic and conditioned fear responses
Authors: Bernabe Cristian S. , Caliman Izabela F. , de Abreu Aline R. R. , Molosh Andrei I. , Truitt William A. , Shekhar Anantha , Johnson Philip L.
Published: January 2024

The serotonin (5-HT) system is heavily implicated in the regulation of anxiety and trauma-related disorders such as panic disorder and post-traumatic stress disorder, respectively. However, the neural mechanisms of how serotonergic neurotransmission regulates innate panic and fear brain networks are poorly understood. Our earlier studies have identified that orexin (OX)/glutamate neurons within the perifornical hypothalamic area (PFA) play a critical role in adaptive and pathological panic and fear. While site-specific and electrophysiological studies have shown that intracranial injection and bath application of 5-HT inhibits PFA neurons via 5-HT1a receptors, they largely ignore circuit-specific neurotransmission and its physiological properties that occur in vivo. Here, we investigate the role of raphe nuclei 5-HT inputs into the PFA in panic and fear behaviors. We initially confirmed that photostimulation of glutamatergic neurons in the PFA of rats produces robust cardioexcitation and flight/aversive behaviors resembling panic-like responses. Using the retrograde tracer cholera toxin B, we determined that the PFA receives discrete innervation of serotonergic neurons clustered in the lateral wings of the dorsal (lwDRN) and in the median (MRN) raphe nuclei. Selective lesions of these serotonergic projections with saporin toxin resulted in similar panic-like responses during the suffocation-related CO2 challenge and increased freezing to fear-conditioning paradigm. Conversely, selective stimulation of serotonergic fibers in the PFA attenuated both flight/escape behaviors and cardioexcitation responses elicited by the CO2 challenge and induced conditioned place preference. The data here support the hypothesis that PFA projecting 5-HT neurons in the lwDRN/MRN represents a panic/fear-off circuit and may also play a role in reward behavior.
The effect of continuous theta burst stimulation on antipsychotic-induced weight gain in first-episode drug-naive individuals with schizophrenia: a double-blind, randomized, sham-controlled feasibility trial
Authors: Kang Dongyu , Song Chuhan , Peng Xingjie , Yu Guo , Yang Ye , Chen Chuwei , Long Yujun , Shao Ping , Wu Renrong
Published: January 2024

Antipsychotic intake may induce weight gain in drug-naive individuals with schizophrenia, leading to poor compliance in clinical management. However, there is still a lack of effective approaches to treat or prevent this side-effect. Therefore, we conducted this pilot study to investigate the effect of continuous theta burst stimulation (cTBS), a non-invasive magnetic stimulation technique, on preventing olanzapine-induced weight gain. Thirty-nine first-episode drug-naive individuals with schizophrenia were randomly assigned to receive either the active or sham cTBS intervention for 25 sessions (5 times per day for 5 consecutive days). The primary outcomes were changes in body weight and body mass index (BMI). Secondary outcomes included psychiatric symptoms, eating behavior scales, behavior tasks, and metabolic measures. For the result, the body weight and BMI increased significantly in the sham group but not in the active group, with a significant group effect. The active group exhibited a selective increase in the cognitive restraint domain in the Three-Factor Eating Questionnaire (TFEQ-CR) and a decrease in stop-signal reaction time compared to the sham group. The effect of cTBS on body weight was mediated by TFEQ-CR. Our findings demonstrated the feasibility that cTBS intervention could be a potential method for preventing olanzapine-induced weight gain in drug-naive first-episode schizophrenia patients through enhancing cognitive restraint to food. Trial registration: clinical trial registered with clinicaltrials.gov (NCT05086133).
A zinc finger transcription factor enables social behaviors while controlling transposable elements and immune response in prefrontal cortex
Authors: Truby Natalie L. , Kim R. Kijoon , Silva Gabriella M. , Qu Xufeng , Picone Joseph A. , Alemu Rebecca , Atiyeh Claire N. , Neve Rachael L. , Liu Jinze , Cui Xiaohong , Hamilton Peter J.
Published: January 2024

The neurobiological origins of social behaviors are incompletely understood. Here we utilized synthetic biology approaches to reprogram the function of ZFP189, a transcription factor whose expression and function in rodent prefrontal cortex was previously demonstrated to be protective against stress-induced social deficits. We created novel synthetic ZFP189 transcription factors including ZFP189VPR, which activates the transcription of target genes and therefore exerts opposite functional control from the endogenous, transcriptionally repressive ZFP189WT. Following viral delivery of these synthetic ZFP189 transcription factors to mouse prefrontal cortex, we observe that ZFP189-mediated transcriptional control promotes mature dendritic spine morphology on transduced pyramidal neurons. Interestingly, inversion of ZFP189-mediated transcription in this brain area, achieved by viral delivery of synthetic ZFP189VPR, precipitates social behavioral deficits in terms of social interaction, motivation, and the cognition necessary for the maintenance of social hierarchy, without other observable behavioral deficits. RNA sequencing of virally manipulated prefrontal cortex tissues reveals that ZFP189 transcription factors of opposing regulatory function (ZFP189WT versus ZFP189VPR) have opposite influence on the expression of genetic transposable elements as well as genes that participate in adaptive immune functions. Collectively, this work reveals that ZFP189 function in the prefrontal cortex coordinates structural and transcriptional neuroadaptations necessary for complex social behaviors while regulating transposable element-rich regions of DNA and the expression of immune-related genes. Given the evidence for a co-evolution of social behavior and the brain immune response, we posit that ZFP189 may have evolved to augment brain transposon-associated immune function as a way of enhancing an animal’s capacity for functioning in social groups.
The quest for a biological phenotype of adolescent non-suicidal self-injury: a machine-learning approach
Authors: Mürner-Lavanchy Ines , Koenig Julian , Reichl Corinna , Josi Johannes , Cavelti Marialuisa , Kaess Michael
Published: January 2024

Non-suicidal self-injury (NSSI) is a transdiagnostic psychiatric symptom with high prevalence and relevance in child and adolescent psychiatry. Therefore, it is of great interest to identify a biological phenotype associated with NSSI. The aim of the present study was to cross-sectionally investigate patterns of biological markers underlying NSSI and associated psychopathology in a sample of female patients and healthy controls. Comprehensive clinical data, saliva and blood samples, heart rate variability and pain sensitivity, were collected in n = 149 patients with NSSI and n = 40 healthy participants. Using machine-based learning, we tested the extent to which oxytocin, dehydroepiandrosterone (DHEA), beta-endorphin, free triiodothyronine (fT3), leukocytes, heart rate variability and pain sensitivity were able to classify participants regarding their clinical outcomes in NSSI, depression and borderline personality disorder symptomatology. We evaluated the predictive performance of several models (linear and logistic regression, elastic net regression, random forests, gradient boosted trees) using repeated cross-validation. With NSSI as an outcome variable, both logistic regression and machine learning models showed moderate predictive performance (Area under the Receiver Operating Characteristic Curve between 0.67 and 0.69). Predictors with the highest predictive power were low oxytocin (OR = 0.55; p = 0.002), low pain sensitivity (OR = 1.15; p = 0.021), and high leukocytes (OR = 1.67; p = 0.015). For the psychopathological outcome variables, i.e., depression and borderline personality disorder symptomatology, models including the biological variables performed not better than the null model. A combination of hormonal and inflammatory markers, as well as pain sensitivity, were able to discriminate between participants with and without NSSI disorder. Based on this dataset, however, complex machine learning models were not able to detect non-linear patterns of associations between the biological markers. These findings need replication and future research will reveal the extent to which the respective biomarkers are useful for longitudinal prediction of clinical outcomes or treatment response.
Alterations in chromosome 1q in multiple myeloma randomized clinical trials: a systematic review
Authors: Neupane Karun , Fortuna Gliceida Galarza , Dahal Riyasha , Schmidt Timothy , Fonseca Rafael , Chakraborty Rajshekhar , Koehn Kelly Ann , Mohan Meera , Mian Hira , Costa Luciano J. , Sborov Douglas , Mohyuddin Ghulam Rehman
Published: January 2024

Extra copies of chromosome 1q21 (+1q: gain = 3 copies, amp >= 4 copies) are associated with worse outcomes in multiple myeloma (MM). This systematic review assesses the current reporting trends of +1q, the efficacy of existing regimens on +1q, and its prognostic implications in MM randomized controlled trials (RCTs). Pubmed, Embase and Cochrane Registry of RCTs were searched from January 2012 to December 2022. Only MM RCTs were included. A total of 124 RCTs were included, of which 29 (23%) studies reported on +1q. Among them, 10% defined thresholds for +1q, 14% reported survival data separately for gain and amp, and 79% considered +1q a high-risk cytogenetic abnormality. Amongst RCTs that met the primary endpoint showing improvement in progression free survival (PFS), lenalidomide maintenance (Myeloma XI), selinexor (BOSTON), and isatuximab (IKEMA and ICARIA) were shown to improve PFS for patients with evidence of +1q. Some additional RCT’s such as Myeloma XI+ (carfilzomib), ELOQUENT-3 (elotuzumab), and HOVON-65/GMMG-HD4 (bortezomib) met their endpoint showing improvement in PFS and also showed improvement in PFS in the +1q cohort, although the confidence interval crossed 1. All six studies that reported HR for +1q patients vs. without (across both arms) showed worse OS and PFS for +1q. There is considerable heterogeneity in the reporting of +1q. All interventions that have shown to be successful in RCTs and have clearly reported on the +1q subgroup have shown concordant direction of results and benefit of the applied intervention. A more standardized approach to reporting this abnormality is needed.
The implications of FASN in immune cell biology and related diseases
Authors: Xiao Yucai , Yang Yonghong , Xiong Huabao , Dong Guanjun
Published: January 2024

Fatty acid metabolism, particularly fatty acid synthesis, is a very important cellular physiological process in which nutrients are used for energy storage and biofilm synthesis. As a key enzyme in the fatty acid metabolism, fatty acid synthase (FASN) is receiving increasing attention. Although previous studies on FASN have mainly focused on various malignancies, many studies have recently reported that FASN regulates the survival, differentiation, and function of various immune cells, and subsequently participates in the occurrence and development of immune-related diseases. However, few studies to date systematically summarized the function and molecular mechanisms of FASN in immune cell biology and related diseases. In this review, we discuss the regulatory effect of FASN on immune cells, and the progress in research on the implications of FASN in immune-related diseases. Understanding the function of FASN in immune cell biology and related diseases can offer insights into novel treatment strategies for clinical diseases.
SHMT2 promotes papillary thyroid cancer metastasis through epigenetic activation of AKT signaling
Authors: Sun Min , Zhao Mingjian , Li Ruowen , Zhang Yankun , Shi Xiaojia , Ding Changyuan , Ma Chunhong , Lu Jinghui , Yue Xuetian
Published: January 2024

Cancer cells alter their metabolism and epigenetics to support cancer progression. However, very few modulators connecting metabolism and epigenetics have been uncovered. Here, we reveal that serine hydroxymethyltransferase-2 (SHMT2) generates S-adenosylmethionine (SAM) to epigenetically repress phosphatase and tensin homolog (PTEN), leading to papillary thyroid cancer (PTC) metastasis depending on activation of AKT signaling. SHMT2 is elevated in PTC, and is associated with poor prognosis. Overexpressed SHMT2 promotes PTC metastasis both in vitro and in vivo. Proteomic enrichment analysis shows that AKT signaling is activated, and is positively associated with SHMT2 in PTC specimens. Blocking AKT activation eliminates the effects of SHMT2 on promoting PTC metastasis. Furthermore, SHMT2 expression is negatively associated with PTEN, a negative AKT regulator, in PTC specimens. Mechanistically, SHMT2 catalyzes serine metabolism and produces activated one-carbon units that can generate SAM for the methylation of CpG islands in PTEN promoter for PTEN suppression and following AKT activation. Importantly, interference with PTEN expression affects SHMT2 function by promoting AKT signaling activation and PTC metastasis. Collectively, our research demonstrates that SHMT2 connects metabolic reprogramming and epigenetics, contributing to the poor progression of PTC.
Uveitic glaucoma-like features in Yap conditional knockout mice
Authors: Bitard Juliette , Grellier Elodie-Kim , Lourdel Sophie , Filipe Helena Prior , Hamon Annaïg , Fenaille François , Castelli Florence Anne , Chu-Van Emeline , Roger Jérôme E. , Locker Morgane , Perron Muriel
Published: January 2024

Glaucoma is a multifactorial neurodegenerative disease characterized by the progressive and irreversible degeneration of the optic nerve and retinal ganglion cells. Despite medical advances aiming at slowing degeneration, around 40% of treated glaucomatous patients will undergo vision loss. It is thus of utmost importance to have a better understanding of the disease and to investigate more deeply its early causes. The transcriptional coactivator YAP, an important regulator of eye homeostasis, has recently drawn attention in the glaucoma research field. Here we show that Yap conditional knockout mice (Yap cKO), in which the deletion of Yap is induced in both Müller glia (i.e. the only retinal YAP-expressing cells) and the non-pigmented epithelial cells of the ciliary body, exhibit a breakdown of the aqueous-blood barrier, accompanied by a progressive collapse of the ciliary body. A similar phenotype is observed in human samples that we obtained from patients presenting with uveitis. In addition, aged Yap cKO mice harbor glaucoma-like features, including deregulation of key homeostatic Müller-derived proteins, retinal vascular defects, optic nerve degeneration and retinal ganglion cell death. Finally, transcriptomic analysis of Yap cKO retinas pointed to early-deregulated genes involved in extracellular matrix organization potentially underlying the onset and/or progression of the observed phenotype. Together, our findings reveal the essential role of YAP in preserving the integrity of the ciliary body and retinal ganglion cells, thereby preventing the onset of uveitic glaucoma-like features.
Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer
Authors: Lykoskoufis Nikolaos M. R. , Planet Evarist , Ongen Halit , Trono Didier , Dermitzakis Emmanouil T.
Published: January 2024

Transposable elements (TEs) are prevalent repeats in the human genome, play a significant role in the regulome, and their disruption can contribute to tumorigenesis. However, TE influence on gene expression in cancer remains unclear. Here, we analyze 275 normal colon and 276 colorectal cancer samples from the SYSCOL cohort, discovering 10,231 and 5,199 TE-expression quantitative trait loci (eQTLs) in normal and tumor tissues, respectively, of which 376 are colorectal cancer specific eQTLs, likely due to methylation changes. Tumor-specific TE-eQTLs show greater enrichment of transcription factors, compared to shared TE-eQTLs suggesting specific regulation of their expression in tumor. Bayesian networks reveal 1,766 TEs as mediators of genetic effects, altering the expression of 1,558 genes, including 55 known cancer driver genes and show that tumor-specific TE-eQTLs trigger the driver capability of TEs. These insights expand our knowledge of cancer drivers, deepening our understanding of tumorigenesis and presenting potential avenues for therapeutic interventions.
Noise learning of instruments for high-contrast, high-resolution and fast hyperspectral microscopy and nanoscopy
Authors: He Hao , Cao Maofeng , Gao Yun , Zheng Peng , Yan Sen , Zhong Jin-Hui , Wang Lei , Jin Dayong , Ren Bin
Published: January 2024

The low scattering efficiency of Raman scattering makes it challenging to simultaneously achieve good signal-to-noise ratio (SNR), high imaging speed, and adequate spatial and spectral resolutions. Here, we report a noise learning (NL) approach that estimates the intrinsic noise distribution of each instrument by statistically learning the noise in the pixel-spatial frequency domain. The estimated noise is then removed from the noisy spectra. This enhances the SNR by ca. 10 folds, and suppresses the mean-square error by almost 150 folds. NL allows us to improve the positioning accuracy and spatial resolution and largely eliminates the impact of thermal drift on tip-enhanced Raman spectroscopic nanoimaging. NL is also applicable to enhance SNR in fluorescence and photoluminescence imaging. Our method manages the ground truth spectra and the instrumental noise simultaneously within the training dataset, which bypasses the tedious labelling of huge dataset required in conventional deep learning, potentially shifting deep learning from sample-dependent to instrument-dependent.
Unraveling radiation damage and healing mechanisms in halide perovskites using energy-tuned dual irradiation dosing
Authors: Kirmani Ahmad R. , Byers Todd A. , Ni Zhenyi , VanSant Kaitlyn , Saini Darshpreet K. , Scheidt Rebecca , Zheng Xiaopeng , Kum Tatchen Buh , Sellers Ian R. , McMillon-Brown Lyndsey , Huang Jinsong , Rout Bibhudutta , Luther Joseph M.
Published: January 2024

Perovskite photovoltaics have been shown to recover, or heal, after radiation damage. Here, we deconvolve the effects of radiation based on different energy loss mechanisms from incident protons which induce defects or can promote efficiency recovery. We design a dual dose experiment first exposing devices to low-energy protons efficient in creating atomic displacements. Devices are then irradiated with high-energy protons that interact differently. Correlated with modeling, high-energy protons (with increased ionizing energy loss component) effectively anneal the initial radiation damage, and recover the device efficiency, thus directly detailing the different interactions of irradiation. We relate these differences to the energy loss (ionization or non-ionization) using simulation. Dual dose experiments provide insight into understanding the radiation response of perovskite solar cells and highlight that radiation-matter interactions in soft lattice materials are distinct from conventional semiconductors. These results present electronic ionization as a unique handle to remedying defects and trap states in perovskites.
WNT-dependent interaction between inflammatory fibroblasts and FOLR2+ macrophages promotes fibrosis in chronic kidney disease
Authors: Cohen Camille , Mhaidly Rana , Croizer Hugo , Kieffer Yann , Leclere Renaud , Vincent-Salomon Anne , Robley Catherine , Anglicheau Dany , Rabant Marion , Sannier Aurélie , Timsit Marc-Olivier , Eddy Sean , Kretzler Matthias , Ju Wenjun , Mechta-Grigoriou Fatima
Published: January 2024

Chronic kidney disease (CKD) is a public health problem driven by myofibroblast accumulation, leading to interstitial fibrosis. Heterogeneity is a recently recognized characteristic in kidney fibroblasts in CKD, but the role of different populations is still unclear. Here, we characterize a proinflammatory fibroblast population (named CXCL-iFibro), which corresponds to an early state of myofibroblast differentiation in CKD. We demonstrate that CXCL-iFibro co-localize with macrophages in the kidney and participate in their attraction, accumulation, and switch into FOLR2+ macrophages from early CKD stages on. In vitro, macrophages promote the switch of CXCL-iFibro into ECM-secreting myofibroblasts through a WNT/β-catenin-dependent pathway, thereby suggesting a reciprocal crosstalk between these populations of fibroblasts and macrophages. Finally, the detection of CXCL-iFibro at early stages of CKD is predictive of poor patient prognosis, which shows that the CXCL-iFibro population is an early player in CKD progression and demonstrates the clinical relevance of our findings.
Structure and elasticity of CaC2O5 suggests carbonate contribution to the seismic anomalies of Earth’s mantle
Authors: Wang Hanyu , Liu Lei , Gao Zihan , Yang Longxing , Naren Gerile , Mao Shide
Published: January 2024

Knowledge of carbonate compounds under high pressure inside Earth is key to understanding the internal structure of the Earth, the deep carbon cycle and major geological events. Here we use first-principles simulations to calculate the structure and elasticity of CaC2O5-minerals with different symmetries under high pressure. Our calculations show that CaC2O5-minerals represent a group of low-density low-seismic-wave velocity mantle minerals. Changes in seismic wave velocity caused by the phase transformation of CaC2O5-Cc to CaC2O5-I$$\bar{4}$$

4

¯

2d (CaC2O5-C2-l) agree with wave velocity discontinuity at a depth of 660 km in the mantle transition zone. Moreover, when CaC2O5-Fdd2 transforms into CaC2O5-C2 under 70 GPa, its shear wave velocity decreases by 7.4%, and its density increases by 5.8%, which is consistent with the characteristics of large low-shear-velocity provinces (LLSVPs). Furthermore, the shear wave velocity of CaC2O5-I$$\bar{4}$$

4

¯

2d is very similar to that of cubic Ca-perovskite, which is one of the main constituents of the previously detected LLSVPs. Therefore, we propose that CaC2O5 and its high-pressure polymorphs may be a main component of LLSVPs.
Revisiting the Plasmodium sporozoite inoculum and elucidating the efficiency with which malaria parasites progress through the mosquito
Authors: Kanatani Sachie , Stiffler Deborah , Bousema Teun , Yenokyan Gayane , Sinnis Photini
Published: January 2024

Malaria is initiated when infected anopheline mosquitoes inoculate sporozoites as they probe for blood. It is thought that all infected mosquitoes are equivalent in terms of their infectious potential, with parasite burden having no role in transmission success. In this study, using mosquitoes harboring the entire range of salivary gland sporozoite loads observed in the field, we demonstrate a strong and highly significant correlation between mosquito parasite burden and inoculum size. We then link the inoculum data to oocyst counts, the most commonly-used metric to assess mosquito infection in the field, and determine the efficiency with which oocyst sporozoites enter mosquito salivary glands. Taken together our data support the conclusion that mosquitoes with higher parasite burdens are more likely to initiate infection and contribute to onward transmission. Overall these data may account for some of the unexplained heterogeneity in transmission and enable more precise benchmarks for transmission-blocking interventions.
Efficient, narrow-band, and stable electroluminescence from organoboron-nitrogen-carbonyl emitter
Authors: Cheng Ying-Chun , Tang Xun , Wang Kai , Xiong Xin , Fan Xiao-Chun , Luo Shulin , Walia Rajat , Xie Yue , Zhang Tao , Zhang Dandan , Yu Jia , Chen Xian-Kai , Adachi Chihaya , Zhang Xiao-Hong
Published: January 2024

Organic light-emitting diodes (OLEDs) exploiting simple binary emissive layers (EMLs) blending only emitters and hosts have natural advantages in low-cost commercialization. However, previously reported OLEDs based on binary EMLs hardly simultaneously achieved desired comprehensive performances, e.g., high efficiency, low efficiency roll-off, narrow emission bands, and high operation stability. Here, we report a molecular-design strategy. Such a strategy leads to a fast reverse intersystem crossing rate in our designed emitter h-BNCO-1 of 1.79×105 s−1. An OLED exploiting a binary EML with h-BNCO-1 achieves ultrapure emission, a maximum external quantum efficiency of over 40% and a mild roll-off of 14% at 1000 cd·m−2. Moreover, h-BNCO-1 also exhibits promising operational stability in an alternative OLED exploiting a compact binary EML (the lifetime reaching 95% of the initial luminance at 1000 cd m−2 is ~ 137 h). Here, our work has thus provided a molecular-design strategy for OLEDs with promising comprehensive performance.
A developmental increase of inhibition promotes the emergence of hippocampal ripples
Authors: Pochinok Irina , Stöber Tristan M. , Triesch Jochen , Chini Mattia , Hanganu-Opatz Ileana L.
Published: January 2024

Sharp wave-ripples (SPW-Rs) are a hippocampal network phenomenon critical for memory consolidation and planning. SPW-Rs have been extensively studied in the adult brain, yet their developmental trajectory is poorly understood. While SPWs have been recorded in rodents shortly after birth, the time point and mechanisms of ripple emergence are still unclear. Here, we combine in vivo electrophysiology with optogenetics and chemogenetics in 4 to 12-day-old mice to address this knowledge gap. We show that ripples are robustly detected and induced by light stimulation of channelrhodopsin-2-transfected CA1 pyramidal neurons only from postnatal day 10 onwards. Leveraging a spiking neural network model, we mechanistically link the maturation of inhibition and ripple emergence. We corroborate these findings by reducing ripple rate upon chemogenetic silencing of CA1 interneurons. Finally, we show that early SPW-Rs elicit a more robust prefrontal cortex response than SPWs lacking ripples. Thus, development of inhibition promotes ripples emergence.
2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein
Authors: Ghanim George E. , Sekne Zala , Balch Sebastian , van Roon Anne-Marie M. , Nguyen Thi Hoang Duong
Published: January 2024

Telomerase is a ribonucleoprotein (RNP) enzyme that extends telomeric repeats at eukaryotic chromosome ends to counterbalance telomere loss caused by incomplete genome replication. Human telomerase is comprised of two distinct functional lobes tethered by telomerase RNA (hTR): a catalytic core, responsible for DNA extension; and a Hinge and ACA (H/ACA) box RNP, responsible for telomerase biogenesis. H/ACA RNPs also have a general role in pseudouridylation of spliceosomal and ribosomal RNAs, which is critical for the biogenesis of the spliceosome and ribosome. Much of our structural understanding of eukaryotic H/ACA RNPs comes from structures of the human telomerase H/ACA RNP. Here we report a 2.7 Å cryo-electron microscopy structure of the telomerase H/ACA RNP. The significant improvement in resolution over previous 3.3 Å to 8.2 Å structures allows us to uncover new molecular interactions within the H/ACA RNP. Many disease mutations are mapped to these interaction sites. The structure also reveals unprecedented insights into a region critical for pseudouridylation in canonical H/ACA RNPs. Together, our work advances understanding of telomerase-related disease mutations and the mechanism of pseudouridylation by eukaryotic H/ACA RNPs.
Engineering metal-carbide hydrogen traps in steels
Authors: Liu Pang-Yu , Zhang Boning , Niu Ranming , Lu Shao-Lun , Huang Chao , Wang Maoqiu , Tian Fuyang , Mao Yong , Li Tong , Burr Patrick A. , Lu Hongzhou , Guo Aimin , Yen Hung-Wei , Cairney Julie M. , Chen Hao , Chen Yi-Sheng
Published: January 2024

Hydrogen embrittlement reduces the durability of the structural steels required for the hydrogen economy. Understanding how hydrogen interacts with the materials plays a crucial role in managing the embrittlement problems. Theoretical models have indicated that carbon vacancies in metal carbide precipitates are effective hydrogen traps in steels. Increasing the number of carbon vacancies in individual metal carbides is important since the overall hydrogen trapping capacity can be leveraged by introducing abundant metal carbides in steels. To verify this concept, we compare a reference steel containing titanium carbides (TiCs), which lack carbon vacancies, with an experimental steel added with molybdenum (Mo), which form Ti-Mo carbides comprising more carbon vacancies than TiCs. We employ theoretical and experimental techniques to examine the hydrogen trapping behavior of the carbides, demonstrating adding Mo alters the hydrogen trapping mechanism, enabling hydrogen to access carbon vacancy traps within the carbides, leading to an increase in trapping capacity.
MHC-I upregulation safeguards neoplastic T cells in the skin against NK cell-mediated eradication in mycosis fungoides
Authors: Chang Yun-Tsan , Prompsy Pacôme , Kimeswenger Susanne , Tsai Yi-Chien , Ignatova Desislava , Pavlova Olesya , Iselin Christoph , French Lars E. , Levesque Mitchell P. , Kuonen François , Bobrowicz Malgorzata , Brunner Patrick M. , Pascolo Steve , Hoetzenecker Wolfram , Guenova Emmanuella
Published: January 2024

Cancer-associated immune dysfunction is a major challenge for effective therapies. The emergence of antibodies targeting tumor cell-surface antigens led to advancements in the treatment of hematopoietic malignancies, particularly blood cancers. Yet their impact is constrained against tumors of hematopoietic origin manifesting in the skin. In this study, we employ a clonality-supervised deep learning methodology to dissect key pathological features implicated in mycosis fungoides, the most common cutaneous T-cell lymphoma. Our investigations unveil the prominence of the IL-32β–major histocompatibility complex (MHC)-I axis as a critical determinant in tumor T-cell immune evasion within the skin microenvironment. In patients’ skin, we find MHC-I to detrimentally impact the functionality of natural killer (NK) cells, diminishing antibody-dependent cellular cytotoxicity and promoting resistance of tumor skin T-cells to cell-surface targeting therapies. Through murine experiments in female mice, we demonstrate that disruption of the MHC-I interaction with NK cell inhibitory Ly49 receptors restores NK cell anti-tumor activity and targeted T-cell lymphoma elimination in vivo. These findings underscore the significance of attenuating the MHC-I-dependent immunosuppressive networks within skin tumors. Overall, our study introduces a strategy to reinvigorate NK cell-mediated anti-tumor responses to overcome treatment resistance to existing cell-surface targeted therapies for skin lymphoma.
Chromosome-level genome assembly of Hippophae gyantsensis
Authors: Chen Mingyue , Yang Danni , Yang Shihai , Yang Xingyu , Chen Zhiyu , Yang Tianyu , Yang Yunqiang , Yang Yongping
Published: January 2024

Hippophae gyantsensis, which is a native tree species in China, is ideal for windbreak and sand-fixing forests. It is an economically and ecologically valuable tree species distributed exclusively in the Qinghai-Tibet Plateau in China. In our study, we assembled a chromosome-level genome of H. gyantsensis using Illumina sequencing, Nanopore sequencing and chromosome structure capture technique. The genome was 716.32 Mb in size with scaffold N50 length of 64.84 Mb. A total of 716.25 Mb genome data was anchored and orientated onto 12 chromosomes with a mounting rate of up to 99.99%. Additionally, the genome was found to comprise approximately 56.84% repeat sequences, of which long terminal repeats(LTRs) that accounted for 33.19% of the entire genome. Meanwhile, a total of 32,316 protein-coding genes were predicted, and 91.07% of these genes were functionally annotated. We also completed a series of comparative genomic analyses to provide researchers with useful reference material for future studies on seabuckthorn.