bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brain and blood transcriptome profiles delineate common genetic pathways across suicidal ideation and suicide
Authors: Sun Shengnan , Liu Qingkun , Wang Zhaoyu , Huang Yung-yu , Sublette M. Elizabeth , Dwork Andrew J. , Rosoklija Gorazd , Ge Yongchao , Galfalvy Hanga , Mann J. John , Haghighi Fatemeh 
Published: January 2024

AbstractHuman genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to the severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with the presence of suicidal ideation were found within 18 co-expressed modules (p < 0.05), as well as in 3 co-expressed modules associated with suicidal ideation severity (p < 0.05, not explained by severity of depression). Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified and investigated using RNA-seq data from postmortem brain that revealed gene expression differences with moderate effect sizes in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity are associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.
Persistence of amygdala hyperactivity to subliminal negative emotion processing in the long-term course of depression
Authors: Klug Melissa , Enneking Verena , Borgers Tiana , Jacobs Charlotte M. , Dohm Katharina , Kraus Anna , Grotegerd Dominik , Opel Nils , Repple Jonathan , Suslow Thomas , Meinert Susanne , Lemke Hannah , Leehr Elisabeth J. , Bauer Jochen , Dannlowski Udo , Redlich Ronny 
Published: January 2024

AbstractBiased emotion processing has been suggested to underlie the etiology and maintenance of depression. Neuroimaging studies have shown mood-congruent alterations in amygdala activity in patients with acute depression, even during early, automatic stages of emotion processing. However, due to a lack of prospective studies over periods longer than 8 weeks, it is unclear whether these neurofunctional abnormalities represent a persistent correlate of depression even in remission. In this prospective case-control study, we aimed to examine brain functional correlates of automatic emotion processing in the long-term course of depression. In a naturalistic design, n = 57 patients with acute major depressive disorder (MDD) and n = 37 healthy controls (HC) were assessed with functional magnetic resonance imaging (fMRI) at baseline and after 2 years. Patients were divided into two subgroups according to their course of illness during the study period (n = 37 relapse, n = 20 no-relapse). During fMRI, participants underwent an affective priming task that assessed emotion processing of subliminally presented sad and happy compared to neutral face stimuli. A group × time × condition (3 × 2 × 2) ANOVA was performed for the amygdala as region-of-interest (ROI). At baseline, there was a significant group × condition interaction, resulting from amygdala hyperactivity to sad primes in patients with MDD compared to HC, whereas no difference between groups emerged for happy primes. In both patient subgroups, amygdala hyperactivity to sad primes persisted after 2 years, regardless of relapse or remission at follow-up. The results suggest that amygdala hyperactivity during automatic processing of negative stimuli persists during remission and represents a trait rather than a state marker of depression. Enduring neurofunctional abnormalities may reflect a consequence of or a vulnerability to depression.
The regulations of telomerase reverse transcriptase (TERT) in cancer
Authors: Liu Mingdi , Zhang Yuning , Jian Yongping , Gu Liting , Zhang Dan , Zhou Honglan , Wang Yishu , Xu Zhi-Xiang 
Published: January 2024

AbstractAbnormal activation of telomerase occurs in most cancer types, which facilitates escaping from cell senescence. As the key component of telomerase, telomerase reverse transcriptase (TERT) is regulated by various regulation pathways. TERT gene changing in its promoter and phosphorylation respectively leads to TERT ectopic expression at the transcription and protein levels. The co-interacting factors play an important role in the regulation of TERT in different cancer types. In this review, we focus on the regulators of TERT and these downstream functions in cancer regulation. Determining the specific regulatory mechanism will help to facilitate the development of a cancer treatment strategy that targets telomerase and cancer cell senescence.
Epigenetic priming targets tumor heterogeneity to shift transcriptomic phenotype of pancreatic ductal adenocarcinoma towards a Vitamin D susceptible state
Authors: He Bo , Stoffel Lauren , He Clifford Jiajun , Cho Kumsun , Li Albert M. , Jiang Haowen , Flowers Brittany M. , Nguyen Kha The , Wang Kelly Wen , Zhao Audrey Yixin , Zhou Meng-Ning , Ferreira Sofia , Attardi Laura D. , Ye Jiangbin 
Published: January 2024

AbstractAs a highly heterogeneous tumor, pancreatic ductal adenocarcinoma (PDAC) exhibits non-uniform responses to therapies across subtypes. Overcoming therapeutic resistance stemming from this heterogeneity remains a significant challenge. Here, we report that Vitamin D-resistant PDAC cells hijacked Vitamin D signaling to promote tumor progression, whereas epigenetic priming with glyceryl triacetate (GTA) and 5-Aza-2′-deoxycytidine (5-Aza) overcame Vitamin D resistance and shifted the transcriptomic phenotype of PDAC toward a Vitamin D-susceptible state. Increasing overall H3K27 acetylation with GTA and reducing overall DNA methylation with 5-Aza not only elevated the Vitamin D receptor (VDR) expression but also reprogrammed the Vitamin D-responsive genes. Consequently, Vitamin D inhibited cell viability and migration in the epigenetically primed PDAC cells by activating genes involved in apoptosis as well as genes involved in negative regulation of cell proliferation and migration, while the opposite effect of Vitamin D was observed in unprimed cells. Studies in genetically engineered mouse PDAC cells further validated the effects of epigenetic priming for enhancing the anti-tumor activity of Vitamin D. Using gain- and loss-of-function experiments, we further demonstrated that VDR expression was necessary but not sufficient for activating the favorable transcriptomic phenotype in respond to Vitamin D treatment in PDAC, highlighting that both the VDR and Vitamin D-responsive genes were prerequisites for Vitamin D response. These data reveal a previously undefined mechanism in which epigenetic state orchestrates the expression of both VDR and Vitamin D-responsive genes and determines the therapeutic response to Vitamin D in PDAC.
Short-term response to anti-VEGF as indicator of visual prognosis in refractory age-related macular degeneration
Authors: Gigon Anthony , Iskandar Antonio , Kasser Sophie , Naso Sacha , Zola Marta , Mantel Irmela 
Published: January 2024

Abstract
Background
Some patients with neovascular age-related macular degeneration (nAMD) respond insufficiently to anti-VEGF treatment despite maximal monthly intravitreal injections. Their short-term response between injections was investigated for extent and visual prognosis.

Subjects/Methods
Monocentric retrospective observational study. 45 eyes from 41 patients with refractory nAMD (who previously received at least 12 months of anti-VEGF treatment), evaluated by optical coherence tomography (OCT) in between monthly anti-VEGF injections. The fluid profile on OCT was evaluated before, 1 week after, and 1 month after an intravitreal injection, using central retinal thickness (CRT), manual measurements, and fluid specific volumetric measurements performed by an automated algorithm based on artificial intelligence.

Results
A significant improvement was found at week 1 in terms of CRT (p < 0.0001), intraretinal (IRF) (p = 0.007), subretinal fluid (SRF) (p < 0.0001), and pigment epithelium detachment (PED) volume (p < 0.0001). Volumetric fluid measures revealed a >50% reduction at week 1 for both IRF and SRF for approximately two-thirds of eyes. Poorer short-term response was associated with larger exudative fluid amounts (IRF + SRF) (p = 0.003), larger PED (p = 0.007), lower visual acuity (p = 0.004) and less anatomic changes at treatment initiation (p < 0.0001). Univariate and multivariate analysis revealed that visual outcomes 4 and 5 years later was significantly worse with weaker short-term responsiveness (p = 0.005), with the presence of atrophy (p = 0.01) and larger PED volumes (p = 0.002).

Conclusions
Incomplete responders to anti-VEGF showed a significant short-term response, identifiable at 1 week after injection, with rapid recurrence at 1 month. Weaker short-term responsiveness at 1 week was associated with poorer long term visual prognosis. These patients may need adjuvant treatment to improve their prognosis.
Preclinical dose response study shows NR2E3 can attenuate retinal degeneration in the retinitis pigmentosa mouse model RhoP23H+/−
Authors: McNamee Shannon M. , Chan Natalie P. , Akula Monica , Avola Marielle O. , Whalen Maiya , Nystuen Kaden , Singh Pushpendra , Upadhyay Arun K. , DeAngelis Margaret M. , Haider Neena B. 
Published: January 2024

AbstractRetinitis pigmentosa (RP) is a heterogeneous disease and the main cause of vision loss within the group of inherited retinal diseases (IRDs). IRDs are a group of rare disorders caused by mutations in one or more of over 280 genes which ultimately result in blindness. Modifier genes play a key role in modulating disease phenotypes, and mutations in them can affect disease outcomes, rate of progression, and severity. Our previous studies have demonstrated that the nuclear hormone receptor 2 family e, member 3 (Nr2e3) gene reduced disease progression and loss of photoreceptor cell layers in RhoP23H−/− mice. This follow up, pharmacology study evaluates a longitudinal NR2E3 dose response in the clinically relevant heterozygous RhoP23H mouse. Reduced retinal degeneration and improved retinal morphology was observed 6 months following treatment evaluating three different NR2E3 doses. Histological and immunohistochemical analysis revealed regions of photoreceptor rescue in the treated retinas of RhoP23H+/− mice. Functional assessment by electroretinogram (ERG) showed attenuated photoreceptor degeneration with all doses. This study demonstrates the effectiveness of different doses of NR2E3 at reducing retinal degeneration and informs dose selection for clinical trials of RhoP23H-associated RP.
Using deep learning to quantify neuronal activation from single-cell and spatial transcriptomic data
Authors: Bahl Ethan , Chatterjee Snehajyoti , Mukherjee Utsav , Elsadany Muhammad , Vanrobaeys Yann , Lin Li-Chun , McDonough Miriam , Resch Jon , Giese K. Peter , Abel Ted , Michaelson Jacob J. 
Published: January 2024

AbstractNeuronal activity-dependent transcription directs molecular processes that regulate synaptic plasticity, brain circuit development, behavioral adaptation, and long-term memory. Single cell RNA-sequencing technologies (scRNAseq) are rapidly developing and allow for the interrogation of activity-dependent transcription at cellular resolution. Here, we present NEUROeSTIMator, a deep learning model that integrates transcriptomic signals to estimate neuronal activation in a way that we demonstrate is associated with Patch-seq electrophysiological features and that is robust against differences in species, cell type, and brain region. We demonstrate this method’s ability to accurately detect neuronal activity in previously published studies of single cell activity-induced gene expression. Further, we applied our model in a spatial transcriptomic study to identify unique patterns of learning-induced activity across different brain regions in male mice. Altogether, our findings establish NEUROeSTIMator as a powerful and broadly applicable tool for measuring neuronal activation, whether as a critical covariate or a primary readout of interest.
Structural connectome architecture shapes the maturation of cortical morphology from childhood to adolescence
Authors: Liang Xinyuan , Sun Lianglong , Liao Xuhong , Lei Tianyuan , Xia Mingrui , Duan Dingna , Zeng Zilong , Li Qiongling , Xu Zhilei , Men Weiwei , Wang Yanpei , Tan Shuping , Gao Jia-Hong , Qin Shaozheng , Tao Sha , Dong Qi , Zhao Tengda , He Yong 
Published: January 2024

AbstractCortical thinning is an important hallmark of the maturation of brain morphology during childhood and adolescence. However, the connectome-based wiring mechanism that underlies cortical maturation remains unclear. Here, we show cortical thinning patterns primarily located in the lateral frontal and parietal heteromodal nodes during childhood and adolescence, which are structurally constrained by white matter network architecture and are particularly represented using a network-based diffusion model. Furthermore, connectome-based constraints are regionally heterogeneous, with the largest constraints residing in frontoparietal nodes, and are associated with gene expression signatures of microstructural neurodevelopmental events. These results are highly reproducible in another independent dataset. These findings advance our understanding of network-level mechanisms and the associated genetic basis that underlies the maturational process of cortical morphology during childhood and adolescence.
Mechanochemical synthesis of organoselenium compounds
Authors: Chen Shanshan , Fan Chunying , Xu Zijian , Pei Mengyao , Wang Jiemin , Zhang Jiye , Zhang Yilei , Li Jiyu , Lu Junliang , Peng Cheng , Wei Xiaofeng 
Published: January 2024

AbstractWe disclose herein a strategy for the rapid synthesis of versatile organoselenium compounds under mild conditions. In this work, magnesium-based selenium nucleophiles are formed in situ from easily available organic halides, magnesium metal, and elemental selenium via mechanical stimulation. This process occurs under liquid-assisted grinding (LAG) conditions, requires no complicated pre-activation procedures, and operates broadly across a diverse range of aryl, heteroaryl, and alkyl substrates. In this work, symmetrical diselenides are efficiently obtained after work-up in the air, while one-pot nucleophilic addition reactions with various electrophiles allow the comprehensive synthesis of unsymmetrical monoselenides with high functional group tolerance. Notably, the method is applied to regioselective selenylation reactions of diiodoarenes and polyaromatic aryl halides that are difficult to operate via solution approaches. Besides selenium, elemental sulfur and tellurium are also competent in this process, which showcases the potential of the methodology for the facile synthesis of organochalcogen compounds.
MARC-3, a membrane-associated ubiquitin ligase, is required for fast polyspermy block in Caenorhabditis elegans
Authors: Kawasaki Ichiro , Sugiura Kenta , Sasaki Taeko , Matsuda Noriyuki , Sato Miyuki , Sato Ken 
Published: January 2024

AbstractIn many sexually reproducing organisms, oocytes are fundamentally fertilized with one sperm. In Caenorhabditis elegans, chitin layer formation after fertilization by the EGG complex is one of the mechanisms of polyspermy block, but other mechanisms remain unknown. Here, we demonstrate that MARC-3, a membrane-associated RING-CH-type ubiquitin ligase that localizes to the plasma membrane and cortical puncta in oocytes, is involved in fast polyspermy block. During polyspermy, the second sperm entry occurs within approximately 10 s after fertilization in MARC-3-deficient zygotes, whereas it occurs approximately 200 s after fertilization in egg-3 mutant zygotes defective in the chitin layer formation. MARC-3 also functions in the selective degradation of maternal plasma membrane proteins and the transient accumulation of endosomal lysine 63-linked polyubiquitin after fertilization. The RING-finger domain of MARC-3 is required for its in vitro ubiquitination activity and polyspermy block, suggesting that a ubiquitination-mediated mechanism sequentially regulates fast polyspermy block and maternal membrane protein degradation during the oocyte-to-embryo transition.
The transcription factor AP2XI-2 is a key negative regulator of Toxoplasma gondii merogony
Authors: Wang Jin-Lei , Li Ting-Ting , Zhang Nian-Zhang , Wang Meng , Sun Li-Xiu , Zhang Zhi-Wei , Fu Bao-Quan , Elsheikha Hany M. , Zhu Xing-Quan 
Published: January 2024

AbstractSexual development inToxoplasma gondiiis a multistep process that culminates in the production of oocysts, constituting approximately 50% of human infections. However, the molecular mechanisms governing sexual commitment in this parasite remain poorly understood. Here, we demonstrate that the transcription factors AP2XI-2 and AP2XII-1 act as negative regulators, suppressing merozoite-primed pre-sexual commitment during asexual development. Depletion of AP2XI-2 in type II Pru strain induces merogony and production of mature merozoites in an alkaline medium but not in a neutral medium. In contrast, AP2XII-1-depleted Pru strain undergoes several rounds of merogony and produces merozoites in a neutral medium, with more pronounced effects observed under alkaline conditions. Additionally, we identified two additional AP2XI-2-interacting proteins involved in repressing merozoite programming. These findings underscore the intricate regulation of pre-sexual commitment by a network of factors and suggest that AP2XI-2 or AP2XII-1-depleted Pru parasites can serve as a model for studying merogony in vitro.
Chirality manipulation of ultrafast phase switches in a correlated CDW-Weyl semimetal
Authors: Cheng Bing , Cheng Di , Jiang Tao , Xia Wei , Song Boqun , Mootz Martin , Luo Liang , Perakis Ilias E. , Yao Yongxin , Guo Yanfeng , Wang Jigang 
Published: January 2024

AbstractLight engineering of correlated states in topological materials provides a new avenue of achieving exotic topological phases inaccessible by conventional tuning methods. Here we demonstrate a light control of correlation gaps in a model charge-density-wave (CDW) and polaron insulator (TaSe4)2I recently predicted to be an axion insulator. Our ultrafast terahertz photocurrent spectroscopy reveals a two-step, non-thermal melting of polarons and electronic CDW gap via the fluence dependence of a longitudinal circular photogalvanic current. This helicity-dependent photocurrent reveals continuous ultrafast phase switches from the polaronic state to the CDW (axion) phase, and finally to a hidden Weyl phase as the pump fluence increases. Additional distinctive attributes aligning with the light-induced switches include: the mode-selective coupling of coherent phonons to the polaron and CDW modulation, and the emergence of a non-thermal chiral photocurrent above the pump threshold of CDW-related phonons. The demonstrated ultrafast chirality control of correlated topological states here holds large potentials for realizing axion electrodynamics and advancing quantum-computing applications.
High-spatial resolution functional chemistry of nitrogen compounds in the observed UK meteorite fall Winchcombe
Authors: Vollmer Christian , Kepaptsoglou Demie , Leitner Jan , Mosberg Aleksander B. , El Hajraoui Khalil , King Ashley J. , Bays Charlotte L. , Schofield Paul F. , Araki Tohru , Ramasse Quentin M. 
Published: January 2024

AbstractOrganic matter in extraterrestrial samples is a complex material that might have played an important role in the delivery of prebiotic molecules to the early Earth. We report here on the identification of nitrogen-containing compounds such as amino acids and N-heterocycles within the recent observed meteorite fall Winchcombe by high-spatial resolution spectroscopy techniques. Although nitrogen contents of Winchcombe organic matter are low (N/C ~ 1–3%), we were able to detect the presence of these compounds using a low-noise direct electron detector. These biologically relevant molecules have therefore been tentatively found within a fresh, minimally processed meteorite sample by high spatial resolution techniques conserving the overall petrographic context. Carbon functional chemistry investigations show that sizes of aromatic domains are small and that abundances of carboxylic functional groups are low. Our observations demonstrate that Winchcombe represents an important addition to the collection of carbonaceous chondrites and still preserves pristine extraterrestrial organic matter.
A wearable electrostimulation-augmented ionic-gel photothermal patch doped with MXene for skin tumor treatment
Authors: Ju Xingkai , Kong Jiao , Qi Guohua , Hou Shuping , Diao Xingkang , Dong Shaojun , Jin Yongdong 
Published: January 2024

AbstractA wearable biological patch capable of producing multiple responses to light and electricity without interfering with daily activities is highly desired for skin cancer treatment, but remains a key challenge. Herein, the skin-mountable electrostimulation-augmented photothermal patch (eT-patch) comprising transparent ionic gel with MXene (Ti3C2Tx) doping is developed and applied for the treatment of melanoma under photostimulation at 0.5 W/cm2. The eT-patch designed has superior photothermal and electrical characteristics owing to ionic gels doped with MXene which provides high photothermal conversion efficiency and electrical conductivity as a medium. Simultaneously, the ionic gel-based eT-patch having excellent optical transparency actualizes real-time observation of skin response and melanoma treatment process under photothermal and electrical stimulation (PES) co-therapy. Systematical cellular study on anti-tumor mechanism of the eT-patch under PES treatment revealed that eT-patch under PES treatment can synergically trigger cancer cell apoptosis and pyroptosis, which together lead to the death of melanoma cells. Due to the obvious advantages of relatively safe and less side effects in healthy organs, the developed eT-patch provides a promising cost-effective therapeutic strategy for skin tumors and will open a new avenue for biomedical applications of ionic gels.
A cytomegalovirus inflammasome inhibitor reduces proinflammatory cytokine release and pyroptosis
Authors: Deng Yingqi , Ostermann Eleonore , Brune Wolfram 
Published: January 2024

AbstractIn response to viral infection, cells can initiate programmed cell death (PCD), leading to a reduction in the release of viral progeny. Viruses have therefore evolved specific mechanisms to curb PCD. Cytomegaloviruses (CMVs) are sophisticated manipulators of cellular defenses and encode potent inhibitors of apoptosis and necroptosis. However, a CMV inhibitor of pyroptosis has not been clearly identified and characterized. Here we identify the mouse cytomegalovirus M84 protein as an inhibitor of pyroptosis and proinflammatory cytokine release. M84 interacts with the pyrin domain of AIM2 and ASC to inhibit inflammasome assembly. It thereby prevents Caspase-1-mediated activation of interleukin 1β (IL-1β), IL-18, and Gasdermin D. Growth attenuation of an M84-deficient MCMV in macrophages is rescued by knockout of either Aim2 or Asc or by treatment with a Caspase-1 inhibitor, and its attenuation in infected mice is partially rescued in Asc knockout mice. Thus, viral inhibition of the inflammasome-pyroptosis pathway is important to promote viral replication in vivo.