bluuebunny/crossref_metadata_2025 huggingface dataset:
Sperm chromatin accessibility’s involvement in the intergenerational effects of stress hormone receptor activation
Authors: Fischer Vincent , Kretschmer Miriam , Germain Pierre-Luc , Kaur Jasmine , Mompart-Barrenechea Sergio , Pelczar Pawel , Schürmann David , Schär Primo , Gapp Katharina
Published: December 2023

Dexamethasone is a stress hormone receptor agonist used widely in clinics. We and others previously showed that paternal administration of dexamethasone in mice affects the phenotype of their offspring. The substrate of intergenerational transmission of environmentally induced effects often involves changes in sperm RNA, yet other epigenetic modifications in the germline can be affected and are also plausible candidates. First, we tested the involvement of altered sperm RNAs in the transmission of dexamethasone induced phenotypes across generations. We did this by injecting sperm RNA into naïve fertilized oocytes, before performing metabolic and behavioral phenotyping of the offspring. We observed phenotypic changes in discordance with those found in offspring generated by in vitro fertilization using sperm from dexamethasone exposed males. Second, we investigated the effect of dexamethasone on chromatin accessibility using ATAC sequencing and found significant changes at specific genomic features and gene regulatory loci. Employing q-RT-PCR, we show altered expression of a gene in the tissue of offspring affected by accessibility changes in sperm. Third, we establish a correlation between specific DNA modifications and stress hormone receptor activity as a likely contributing factor influencing sperm accessibility. Finally, we independently investigated this dependency by genetically reducing thymine-DNA glycosylase levels and observing concomitant changes at the level of chromatin accessibility and stress hormone receptor activity.
Real world data on outcomes of anti-CD38 antibody treated, including triple class refractory, patients with multiple myeloma: a multi-institutional report from the Canadian Myeloma Research Group (CMRG) Database
Authors: Visram A. , De La Torre A. , White D. , Su J. , Masih-Khan E. , Chu M. , Jimenez-Zepeda V. , McCurdy A. , LeBlanc R. , Song K. , Mian H. , Louzada M. , Sebag M. , Bergstrom D. , Stakiw J. , Reiman A. , Kotb R. , Aslam M. , Venner C. , Kaedbey R. , Gul E. , Reece D.
Published: December 2023

Multiple myeloma (MM) remains incurable despite the availability of novel agents. This multi-center retrospective cohort study used the Canadian Myeloma Research Group Database to describe real-world outcomes of patients withanti-CD38 monoclonal antibody (mAb) refractory MM subsequently treated with standard of care (SoC) regimens. Patients with triple class refractory (TCR) disease (refractory to a proteasome inhibitor, immunomodulatory drug, and anti-CD38 mAb) were examined as a distinct cohort. Overall, 663 patients had disease progression on anti-CD38 mAb therapy, 466 received further treatment (346 with SoC regimens were included, 120 with investigational agents on clinical trial and were excluded). The median age at initiation of subsequent SoC therapy of 67.9 (range 39.6–89.6) years with a median of 3 prior lines (range 1–9). The median PFS and OS from the start of subsequent therapy was 4.6 (95% CI 4.1–5.6) months and 13.3 (95% CI 10.6–16.6) months, respectively. The median PFS and OS of patients with TCR disease (n = 199) was 4.4 (95% CI 3.6–5.3) months and 10.5 (95% CI 8.5–13.8) months. Our results reinforce that real-world patients with relapsed MM, particularly those with TCR disease, have dismal outcomes. There remains an urgent unmet need for the development of and access to effective therapeutics for these patients.
Local production of reactive oxygen species drives vincristine-induced axon degeneration
Authors: Gomez-Deza Jorge , Slavutsky Anastasia L. , Nebiyou Matthew , Le Pichon Claire E.
Published: December 2023

Neurological side effects arising from chemotherapy, such as severe pain and cognitive impairment, are a major concern for cancer patients. These major side effects can lead to reduction or termination of chemotherapy medication in patients, negatively impacting their prognoses. With cancer survival rates improving dramatically, addressing side effects of cancer treatment has become pressing. Here, we use iPSC-derived human neurons to investigate the molecular mechanisms that lead to neurotoxicity induced by vincristine, a common chemotherapeutic used to treat solid tumors. Our results uncover a novel mechanism by which vincristine causes a local increase in mitochondrial proteins that produce reactive oxygen species (ROS) in the axon. Vincristine triggers a cascade of axon pathology, causing mitochondrial dysfunction that leads to elevated axonal ROS levels and SARM1-dependent axon degeneration. Importantly, we show that the neurotoxic effect of increased axonal ROS can be mitigated by the small molecule mitochondrial division inhibitor 1 (mdivi-1) and antioxidants glutathione and mitoquinone, identifying a novel therapeutic avenue to treat the neurological effects of chemotherapy.
Human frataxin, the Friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain
Authors: Doni Davide , Cavion Federica , Bortolus Marco , Baschiera Elisa , Muccioli Silvia , Tombesi Giulia , d’Ettorre Federica , Ottaviani Daniele , Marchesan Elena , Leanza Luigi , Greggio Elisa , Ziviani Elena , Russo Antonella , Bellin Milena , Sartori Geppo , Carbonera Donatella , Salviati Leonardo , Costantini Paola
Published: December 2023

Friedreich ataxia (FRDA) is a rare, inherited neurodegenerative disease caused by an expanded GAA repeat in the first intron of the FXN gene, leading to transcriptional silencing and reduced expression of frataxin. Frataxin participates in the mitochondrial assembly of FeS clusters, redox cofactors of the respiratory complexes I, II and III. To date it is still unclear how frataxin deficiency culminates in the decrease of bioenergetics efficiency in FRDA patients’ cells. We previously demonstrated that in healthy cells frataxin is closely attached to the mitochondrial cristae, which contain both the FeS cluster assembly machinery and the respiratory chain complexes, whereas in FRDA patients’ cells with impaired respiration the residual frataxin is largely displaced in the matrix. To gain novel insights into the function of frataxin in the mitochondrial pathophysiology, and in the upstream metabolic defects leading to FRDA disease onset and progression, here we explored the potential interaction of frataxin with the FeS cluster-containing respiratory complexes I, II and III. Using healthy cells and different FRDA cellular models we found that frataxin interacts with these three respiratory complexes. Furthermore, by EPR spectroscopy, we observed that in mitochondria from FRDA patients’ cells the decreased level of frataxin specifically affects the FeS cluster content of complex I. Remarkably, we also found that the frataxin-like protein Nqo15 from T. thermophilus complex I ameliorates the mitochondrial respiratory phenotype when expressed in FRDA patient’s cells. Our data point to a structural and functional interaction of frataxin with complex I and open a perspective to explore therapeutic rationales for FRDA targeted to this respiratory complex.
YY1 modulates the radiosensitivity of esophageal squamous cell carcinoma through KIF3B-mediated Hippo signaling pathway
Authors: Zheng Chunyan , Li Zhe , Zhao Chuanxi , Yin Xiaoyang , Feng Lei , Wang Zhongtang , Liu Chengxin , Li Baosheng
Published: December 2023

Radiotherapy is an important strategy in the comprehensive treatment of esophageal squamous cell carcinoma (ESCC). However, effectiveness of radiotherapy is still restricted by radioresistance. Herein, we aimed to understand the mechanisms underlying ESCC radioresistance, for which we looked into the potential role of YY1. YY1 was upregulated in radioresistant tissues and correlated with poor prognosis of patients with ESCC. YY1 depletion enhanced the radiosensitivity of ESCC in vitro and in vivo. Multi-group sequencing showed that downregulation of YY1 inhibited the transcriptional activity of Kinesin Family Member 3B (KIF3B), which further activated the Hippo signaling pathway by interacting with Integrin-beta1 (ITGB1). Once the Hippo pathway was activated, its main effector, Yes-associated protein 1 (YAP1), was phosphorylated in the cytoplasm and its expression reduced in the nucleus, thus enhancing the radiosensitivity by regulating its targeted genes. Our study provides new insights into the mechanisms underlying ESCC radioresistance and highlights the potential role of YY1 as a therapeutic target for ESCC.
Heat shock protein HSPA13 promotes hepatocellular carcinoma progression by stabilizing TANK
Authors: Cen Xuesong , Lu Yuyan , Lu Jing , Luo Changhong , Zhan Ping , Cheng Yizhe , Yang Fan , Xie Chengrong , Yin Zhenyu , Wang Fuqiang
Published: December 2023

HSPA13, an important member of the heat shock protein family, plays an essential role in the oncogenesis of many organs, but the mechanism and function in hepatocellular carcinoma (HCC) is still unclear. In the present study, we found that HSPA13 was highly expressed in HCC and predicted poor clinical prognosis. Upregulation of HSPA13 was significantly associated with vascular invasion in HCC patients. Functionally, knockdown experiments demonstrated that HSPA13 promoted HCC proliferation, migration, and invasion. Mechanistic investigation showed that HSPA13 could interact with TANK to inhibit its ubiquitination and degradation. In addition, the expression of HSPA13 and TANK were positively correlated in HCC tissues. To conclude, the present study uncovers the oncogenic function of HSPA13 in the progression of HCC by regulating the stability of TANK. These findings suggest that HSPA13 and TANK may serve as promising targets for the diagnosis and treatment of HCC.
Light-enhanced osmotic energy generation with an aramid nanofiber membrane
Authors: Chen Cheng , Lin Yunxiao , Lei Weiwei , Yang Guoliang , Liu Yuchen , Xu Mao , Li Xinhao , Liu Dan
Published: December 2023

Osmotic energy generation with reverse electrodialysis through membranes provides a worldwide free energy resource. Photo-driven proton transport in photosynthesis supplies basal energy for plants and living organisms on the planet. Here, we utilized aramid nanofiber (ANF) semiconductor-based membranes to enable light-driven proton transport for osmotic energy generation. Under unilateral illumination, the light-driven proton transport system converted light energy into electrical energy and showed wavelength- and intensity-dependent transmembrane potentials and currents. Interestingly, the synergistic effects of simultaneous illumination and pressure provided a five-fold increase in the voltage and a three-fold increase in the current relative to pressure alone. Density functional theory calculations and spectroscopic measurements demonstrated that the ANF and photoinduced electrons enabled proton transport during illumination and generated a transmembrane potential and current. The light-driven proton transport system supports the development of devices with flexible and stable ANF membranes.
Plasmonic metasurfaces of cellulose nanocrystal matrices with quadrants of aligned gold nanorods for photothermal anti-icing
Authors: Pyeon Jeongsu , Park Soon Mo , Kim Juri , Kim Jeong-Hwan , Yoon Yong-Jin , Yoon Dong Ki , Kim Hyoungsoo
Published: December 2023

Cellulose nanocrystals (CNCs) are intriguing as a matrix for plasmonic metasurfaces made of gold nanorods (GNRs) because of their distinctive properties, including renewability, biodegradability, non-toxicity, and low cost. Nevertheless, it is very difficult to precisely regulate the positioning and orientation of CNCs on the substrate in a consistent pattern. In this study, CNCs and GNRs, which exhibit tunable optical and anti-icing capabilities, are employed to manufacture a uniform plasmonic metasurface using a drop-casting technique. Two physical phenomena—(i) spontaneous and rapid self-dewetting and (ii) evaporation-induced self-assembly—are used to accomplish this. Additionally, we improve the CNC-GNR ink composition and determine the crucial coating parameters necessary to balance the two physical mechanisms in order to produce thin films without coffee rings. The final homogeneous CNC-GNR film has consistent annular ring patterns with plasmonic quadrant hues that are properly aligned, which enhances plasmonic photothermal effects. The CNC-GNR multi-array platform offers above-zero temperatures on a substrate that is subcooled below the freezing point. The current study presents a physicochemical approach for functional nanomaterial-based CNC control.
A naturally occurring polyacetylene isolated from carrots promotes health and delays signatures of aging
Authors: Thomas Carolin , Erni Reto , Wu Jia Yee , Fischer Fabian , Lamers Greta , Grigolon Giovanna , Mitchell Sarah J. , Zarse Kim , Carreira Erick M. , Ristow Michael
Published: December 2023

To ameliorate or even prevent signatures of aging in ultimately humans, we here report the identification of a previously undescribed polyacetylene contained in the root of carrots (Daucus carota), hereafter named isofalcarintriol, which we reveal as potent promoter of longevity in the nematode C. elegans. We assign the absolute configuration of the compound as (3 S,8 R,9 R,E)-heptadeca-10-en-4,6-diyne-3,8,9-triol, and develop a modular asymmetric synthesis route for all E-isofalcarintriol stereoisomers. At the molecular level, isofalcarintriol affects cellular respiration in mammalian cells, C. elegans, and mice, and interacts with the α-subunit of the mitochondrial ATP synthase to promote mitochondrial biogenesis. Phenotypically, this also results in decreased mammalian cancer cell growth, as well as improved motility and stress resistance in C. elegans, paralleled by reduced protein accumulation in nematodal models of neurodegeneration. In addition, isofalcarintriol supplementation to both wild-type C57BL/6NRj mice on high-fat diet, and aged mice on chow diet results in improved glucose metabolism, increased exercise endurance, and attenuated parameters of frailty at an advanced age. Given these diverse effects on health parameters in both nematodes and mice, isofalcarintriol might become a promising mitohormesis-inducing compound to delay, ameliorate, or prevent aging-associated diseases in humans.
Characterization of nucleolar SUMO isopeptidases unveils a general p53-independent checkpoint of impaired ribosome biogenesis
Authors: Dönig Judith , Mende Hannah , Davila Gallesio Jimena , Wagner Kristina , Hotz Paul , Schunck Kathrin , Piller Tanja , Hölper Soraya , Uhan Sara , Kaulich Manuel , Wirth Matthias , Keller Ulrich , Tascher Georg , Bohnsack Katherine E. , Müller Stefan
Published: December 2023

Ribosome biogenesis is a multi-step process, in which a network of trans-acting factors ensures the coordinated assembly of pre-ribosomal particles in order to generate functional ribosomes. Ribosome biogenesis is tightly coordinated with cell proliferation and its perturbation activates a p53-dependent cell-cycle checkpoint. How p53-independent signalling networks connect impaired ribosome biogenesis to the cell-cycle machinery has remained largely enigmatic. We demonstrate that inactivation of the nucleolar SUMO isopeptidases SENP3 and SENP5 disturbs distinct steps of 40S and 60S ribosomal subunit assembly pathways, thereby triggering the canonical p53-dependent impaired ribosome biogenesis checkpoint. However, inactivation of SENP3 or SENP5 also induces a p53-independent checkpoint that converges on the specific downregulation of the key cell-cycle regulator CDK6. We further reveal that impaired ribosome biogenesis generally triggers the downregulation of CDK6, independent of the cellular p53 status. Altogether, these data define the role of SUMO signalling in ribosome biogenesis and unveil a p53-independent checkpoint of impaired ribosome biogenesis.
A highly proton conductive perfluorinated covalent triazine framework via low-temperature synthesis
Authors: Guan Lijiang , Guo Zhaoqi , Zhou Qi , Zhang Jin , Cheng Cheng , Wang Shengyao , Zhu Xiang , Dai Sheng , Jin Shangbin
Published: December 2023

Proton-conducting materials are essential to the emerging hydrogen economy. Covalent triazine frameworks (CTFs) are promising proton-conducting materials at high temperatures but need more effective sites to strengthen interaction for proton carriers. However, their construction and design in a concise condition are still challenges. Herein, we show a low temperature approach to synthesize CTFs via a direct cyclotrimerization of aromatic aldehyde using ammonium iodide as facile nitrogen source. Among the CTFs, the perfluorinated CTF (CTF-TF) was successfully synthesized with much lower temperature ( ≤ 160 °C) and open-air atmosphere. Due to the additional hydrogen-bonding interaction between fluorine atoms and proton carriers (H3PO4), the CTF-TF achieves a proton conductivity of 1.82 × 10−1 S cm−1 at 150 °C after H3PO4 loading. Moreover, the CTF-TF can be readily integrated into mixed matrix membranes, displaying high proton conduction abilities and good mechanical strength. This work provides an alternative strategy for rational design of proton conducting media.
A class of secreted mammalian peptides with potential to expand cell-cell communication
Authors: Wiggenhorn Amanda L. , Abuzaid Hind Z. , Coassolo Laetitia , Li Veronica L. , Tanzo Julia T. , Wei Wei , Lyu Xuchao , Svensson Katrin J. , Long Jonathan Z.
Published: December 2023

Peptide hormones and neuropeptides are signaling molecules that control diverse aspects of mammalian homeostasis and physiology. Here we provide evidence for the endogenous presence of a sequence diverse class of blood-borne peptides that we call “capped peptides.” Capped peptides are fragments of secreted proteins and defined by the presence of two post-translational modifications – N-terminal pyroglutamylation and C-terminal amidation – which function as chemical “caps” of the intervening sequence. Capped peptides share many regulatory characteristics in common with that of other signaling peptides, including dynamic physiologic regulation. One capped peptide, CAP-TAC1, is a tachykinin neuropeptide-like molecule and a nanomolar agonist of mammalian tachykinin receptors. A second capped peptide, CAP-GDF15, is a 12-mer peptide cleaved from the prepropeptide region of full-length GDF15 that, like the canonical GDF15 hormone, also reduces food intake and body weight. Capped peptides are a potentially large class of signaling molecules with potential to broadly regulate cell-cell communication in mammalian physiology.
Norepinephrine regulates calcium signals and fate of oligodendrocyte precursor cells in the mouse cerebral cortex
Authors: Fiore Frederic , Alhalaseh Khaleel , Dereddi Ram R. , Bodaleo Torres Felipe , Çoban Ilknur , Harb Ali , Agarwal Amit
Published: December 2023

Oligodendrocyte precursor cells (OPCs) generate oligodendrocytes, contributing to myelination and myelin repair. OPCs contact axons and respond to neuronal activity, but how the information relayed by the neuronal activity translates into OPC Ca2+ signals, which in turn influence their fate, remains unknown. We generated transgenic mice for concomitant monitoring of OPCs Ca2+ signals and cell fate using 2-photon microscopy in the somatosensory cortex of awake-behaving mice. Ca2+ signals in OPCs mainly occur within processes and confine to Ca2+ microdomains. A subpopulation of OPCs enhances Ca2+ transients while mice engaged in exploratory locomotion. We found that OPCs responsive to locomotion preferentially differentiate into oligodendrocytes, and locomotion-non-responsive OPCs divide. Norepinephrine mediates locomotion-evoked Ca2+ increases in OPCs by activating α1 adrenergic receptors, and chemogenetic activation of OPCs or noradrenergic neurons promotes OPC differentiation. Hence, we uncovered that for fate decisions OPCs integrate Ca2+ signals, and norepinephrine is a potent regulator of OPC fate.
Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease
Authors: Zhou Yanyan , Yang Zhen , Liu Jinguang , Li Xudong , Wang Xingxiang , Dai Chuanchao , Zhang Taolin , Carrión Víctor J. , Wei Zhong , Cao Fuliang , Delgado-Baquerizo Manuel , Li Xiaogang
Published: December 2023

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.
Electrical performance of a fully reconfigurable series-parallel photovoltaic module
Authors: Calcabrini Andres , Muttillo Mirco , Zeman Miro , Manganiello Patrizio , Isabella Olindo
Published: December 2023

Reconfigurable photovoltaic modules are a promising approach to improve the energy yield of partially shaded systems. So far, the feasibility of this concept has been evaluated through simulations or simplified experiments. In this work, we analyse the outdoor performance of a full-scale prototype of a series-parallel photovoltaic module with six reconfigurable blocks. Over a 4-month-long period, its performance was compared to a reference photovoltaic module with static interconnections and six bypass diodes. The results show that under partial shading, the reconfigurable module produced 10.2% more energy than the reference module. In contrast, under uniform illumination the energy yield of the reconfigurable PV module was 1.9% lower due to the additional losses introduced by its switching matrix. Finally, a modification in the reconfiguration algorithm is proposed to reduce the output current–voltage range of the module and simplify the design of module-level power converters while limiting the shading tolerance loss.
LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation
Authors: Zhu Yixiao , Huang Chengmei , Zhang Chao , Zhou Yi , Zhao Enen , Zhang Yaxin , Pan Xingyan , Huang Huilin , Liao Wenting , Wang Xin
Published: December 2023

Gastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subtype associated with a poor prognosis. Here, we apply integrated network analysis to uncover lncRNA heterogeneity between GC subtypes, and identify MIR200CHG as a master regulator mediating EMT specifically in MSS/EMT GC. The expression of MIR200CHG is silenced in MSS/EMT GC by promoter hypermethylation, associated with poor prognosis. MIR200CHG reverses the mesenchymal identity of GC cells in vitro and inhibits metastasis in vivo. Mechanistically, MIR200CHG not only facilitates the biogenesis of its intronic miRNAs miR-200c and miR-141, but also protects miR-200c from target-directed miRNA degradation (TDMD) through direct binding to miR-200c. Our studies reveal a landscape of a subtype-specific lncRNA regulatory network, providing clinically relevant biological insights towards MSS/EMT GC.
Nutrient deprivation alters the rate of COPII subunit recruitment at ER subdomains to tune secretory protein transport
Authors: Kasberg William , Luong Peter , Swift Kevin A. , Audhya Anjon
Published: December 2023

Co-assembly of the multilayered coat protein complex II (COPII) with the Sar1 GTPase at subdomains of the endoplasmic reticulum (ER) enables secretory cargoes to be concentrated efficiently within nascent transport intermediates, which subsequently deliver their contents to ER-Golgi intermediate compartments. Here, we define the spatiotemporal accumulation of native COPII subunits and secretory cargoes at ER subdomains under differing nutrient availability conditions using a combination of CRISPR/Cas9-mediated genome editing and live cell imaging. Our findings demonstrate that the rate of inner COPII coat recruitment serves as a determinant for the pace of cargo export, irrespective of COPII subunit expression levels. Moreover, increasing inner COPII coat recruitment kinetics is sufficient to rescue cargo trafficking deficits caused by acute nutrient limitation. Our findings are consistent with a model in which the rate of inner COPII coat addition acts as an important control point to regulate cargo export from the ER.
BACH1 promotes tissue necrosis and Mycobacterium tuberculosis susceptibility
Authors: Amaral Eduardo P. , Namasivayam Sivaranjani , Queiroz Artur T. L. , Fukutani Eduardo , Hilligan Kerry L. , Aberman Kate , Fisher Logan , Bomfim Caio Cesar B. , Kauffman Keith , Buchanan Jay , Santuo Leslie , Gazzinelli-Guimaraes Pedro Henrique , Costa Diego L. , Teixeira Mariane Araujo , Barreto-Duarte Beatriz , Rocha Clarissa Gurgel , Santana Monique Freire , Cordeiro-Santos Marcelo , Barber Daniel L. , Wilkinson Robert J. , Kramnik Igor , Igarashi Kazuhiko , Scriba Thomas , Mayer-Barber Katrin D. , Andrade Bruno B. , Sher Alan
Published: December 2023

Oxidative stress triggers ferroptosis, a form of cellular necrosis characterized by iron-dependent lipid peroxidation, and has been implicated in Mycobacterium tuberculosis (Mtb) pathogenesis. We investigated whether Bach1, a transcription factor that represses multiple antioxidant genes, regulates host resistance to Mtb. We found that BACH1 expression is associated clinically with active pulmonary tuberculosis. Bach1 deletion in Mtb-infected mice increased glutathione levels and Gpx4 expression that inhibit lipid peroxidation. Bach1−/− macrophages exhibited increased resistance to Mtb-induced cell death, while Mtb-infected Bach1-deficient mice displayed reduced bacterial loads, pulmonary necrosis and lipid peroxidation concurrent with increased survival. Single-cell RNA-seq analysis of lungs from Mtb-infected Bach1−/− mice revealed an enrichment of genes associated with ferroptosis suppression. Bach1 depletion in Mtb-infected B6.Sst1S mice that display human-like necrotic lung pathology also markedly reduced necrosis and increased host resistance. These findings identify Bach1 as a key regulator of cellular and tissue necrosis and host resistance in Mtb infection.
RNAseq of diverse spring wheat cultivars released during last 110 years
Authors: Maqbool Saman , Naseer Samar , Zahra Nageen , Rasool Fatima , Qayyum Humaira , Majeed Khawar , Jahanzaib Muhammad , Sajjad Muhammad , Fayyaz Muhammad , Naeem Muhammad Kashif , Khan Muhammad Ramzan , Zhang Hao , Rasheed Awais , Li Huihui
Published: December 2023

Here, we performed RNA-seq based expression analysis of root and leaf tissues of a set of 24 historical spring wheat cultivars representing 110 years of temporal genetic variations. This huge 130 tissues RNAseq dataset was initially used to study expression pattern of 97 genes regulating root growth and development in wheat. Root system architecture (RSA) is an important target for breeding stress-resilient and high-yielding wheat cultivars under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research due to their below ground presence. We also validated the dataset by performing correlation analysis between expression of RSA related genes in roots and leaves with 25 root traits analyzed under varying moisture conditions and 10 yield-related traits. The Pearson’s correlation coefficients between root phenotypes and expression of root-specific genes varied from −0.72 to 0.78, and strong correlations with genes such as DRO1, TaMOR, ARF4, PIN1 was observed. The presented datasets have multiple uses such as a) studying the change in expression pattern of genes during time, b) differential expression of genes in two very important tissues of wheat i.e., leaf and roots, and c) studying customized expression of genes associated with important phenotypes in diverse wheat cultivars. The initial findings presented here provided key insights into understanding the transcriptomic basis of phenotypic variability of RSA in wheat cultivars.
Selective digestive tract decontamination to prevent healthcare associated infections in critically ill children: the PICNIC multicentre randomised pilot clinical trial
Authors: Pathan Nazima , Woolfall Kerry , Popa Mariana , de la Fuente Gema Milla , Ferrando-Vivas Paloma , Brown Alanna , Gouliouris Theodore , Tume Lyvonne N. , Shulman Robert , Cuthbertson Brian H. , Sale Isobel , Feltbower Richard G. , Myburgh John , Pappachan John , Harrison David , Mouncey Paul , Rowan Kathryn ,   the PICNIC study investigators, Fulham Charlotte , James Melanie , Beadon Kirsten , Postlethwaite Cat , Pond Jenny , Hargadon-Lowe Antonia , Cassidy Jane , Robbins Ceri , Milner Phil , Dwarakanathan Buvana , De Queiroz Joana Gomes , Daubney Esther , White Deborah , Davis Peter , Dodge Laura , Moody Francesca
Published: December 2023

Healthcare-associated infections (HCAIs) are a major cause of morbidity and mortality in critically ill children. Data from adult studies suggest Selective Decontamination of the Digestive tract (SDD) may reduce the incidence of HCAIs and improve survival. There are no data from randomised clinical trials in the paediatric setting. An open label, parallel group pilot cRCT and mixed-methods perspectives study was conducted in six paediatric intensive care units (PICUs) in England. Participants were children (> 37 weeks corrected gestational age, up to 16 years) requiring mechanical ventilation expected to last for at least 48 h. Sites undertook standard care for a period of 9 weeks and were randomised into 3 sites which continued standard care and 3 where SDD was incorporated into infection control practice for eligible children. Interviews and focus groups were conducted for parents and staff working in PICU. 434 children fulfilled eligibility criteria, of whom 368 (85%) were enrolled. This included 207 in the baseline phase (Period One) and 161 in the intervention period (Period Two). In sites delivering SDD, the majority (98%) of children received at least one dose of SDD and of these, 68% commenced within the first 6 h. Whilst admission swabs were collected in 91% of enrolled children, consent for the collection of additional swabs was low (44%). Recruited children were representative of the wider PICU population. Overall, 3.6 children/site/week were recruited compared with the potential recruitment rate for a definitive cRCT of 3 children/site/week, based on data from all UK PICUs. Parents (n = 65) and staff (n = 44) were supportive of the aims of the study, suggesting adaptations for a larger definitive trial including formulation and administration of SDD paste, approaches to consent and ecology monitoring. Stakeholders identified preferred clinical outcomes, focusing on complications of critical illness and quality-of-life. A definitive cRCT in SDD to prevent HCAIs in critically ill children is feasible but should include adaptations to ecology monitoring along with the dosing schedule and packaging into a paediatric specific format. A definitive study is supported by the findings with adaptations to ecology monitoring and SDD administration.

Trial Registration: ISRCTN40310490 Registered 30/10/2020.
Phenotyping EMT and MET cellular states in lung cancer patient liquid biopsies at a personalized level using mass cytometry
Authors: Karacosta Loukia G. , Pancirer Danny , Preiss Jordan S. , Benson Jalen A. , Trope Winston , Shrager Joseph B. , Sung Arthur Wai , Neal Joel W. , Bendall Sean C. , Wakelee Heather , Plevritis Sylvia K.
Published: December 2023

Malignant pleural effusions (MPEs) can be utilized as liquid biopsy for phenotyping malignant cells and for precision immunotherapy, yet MPEs are inadequately studied at the single-cell proteomic level. Here we leverage mass cytometry to interrogate immune and epithelial cellular profiles of primary tumors and pleural effusions (PEs) from early and late-stage non-small cell lung cancer (NSCLC) patients, with the goal of assessing epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) states in patient specimens. By using the EMT–MET reference map PHENOSTAMP, we observe a variety of EMT states in cytokeratin positive (CK+) cells, and report for the first time MET-enriched CK+ cells in MPEs. We show that these states may be relevant to disease stage and therapy response. Furthermore, we found that the fraction of CD33+ myeloid cells in PEs was positively correlated to the fraction of CK+ cells. Longitudinal analysis of MPEs drawn 2 months apart from a patient undergoing therapy, revealed that CK+ cells acquired heterogeneous EMT features during treatment. We present this work as a feasibility study that justifies deeper characterization of EMT and MET states in malignant cells found in PEs as a promising clinical platform to better evaluate disease progression and treatment response at a personalized level.
Influenza activity and regional mortality for non-small cell lung cancer
Authors: Kinslow Connor J. , Wang Yuankun , Liu Yi , Zuev Konstantin M. , Chaudhary Kunal R. , Wang Tony J. C. , Donalek Ciro , Amori Michael , Cheng Simon K.
Published: December 2023

Lung cancer is the leading cause of cancer deaths in the United States and worldwide. While influenza illness is known to be particularly dangerous for frail and elderly patients, the relationship between influenza illness and outcomes in patients with cancer remains largely unknown. The Surveillance, Epidemiology, and End Results (SEER) database was queried to identify patients with non-small cell lung cancer (NSCLC) diagnosed between 2009 and 2015. Influenza-like illness (ILI) activity, provided by the Outpatient Influenza-like Illness Surveillance Network of the Center of Disease for Control and Prevention, was merged with the SEER dataset on the state-month level. Regional monthly mortality rates were compared during low versus high flu months in this ecological cohort study. 202,485 patients with NSCLC from 13 SEER-reporting states were included in the analysis. 53 of 1049 state-months (5.1%) had high flu activity. Monthly mortality rates during low and high flu months were 0.041 (95% CI 0.041–0.042) and 0.051 (95% CI 0.050–0.053), respectively (RR 1.24 [95% CI 1.21–1.27]). The association between ILI activity and mortality was observed at the individual state level and in all clinical and regional subgroups. Increased regional influenza activity is associated with higher mortality rates for patients with NSCLC. Vaccine-directed initiatives and increased awareness amongst providers will be necessary to address the growing but potentially preventable burden of influenza-related lung cancer deaths in the U.S.
Complexity and 1/f slope jointly reflect brain states
Authors: Medel Vicente , Irani Martín , Crossley Nicolás , Ossandón Tomás , Boncompte Gonzalo
Published: December 2023

Characterization of brain states is essential for understanding its functioning in the absence of external stimuli. Brain states differ on their balance between excitation and inhibition, and on the diversity of their activity patterns. These can be respectively indexed by 1/f slope and Lempel–Ziv complexity (LZc). However, whether and how these two brain state properties relate remain elusive. Here we analyzed the relation between 1/f slope and LZc with two in-silico approaches and in both rat EEG and monkey ECoG data. We contrasted resting state with propofol anesthesia, which directly modulates the excitation-inhibition balance. We found convergent results among simulated and empirical data, showing a strong, inverse and non trivial monotonic relation between 1/f slope and complexity, consistent at both ECoG and EEG scales. We hypothesize that differentially entropic regimes could underlie the link between the excitation-inhibition balance and the vastness of the repertoire of brain systems.
Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets
Authors: Fyles Martyn , Vihta Karina-Doris , Sudre Carole H , Long Harry , Das Rajenki , Jay Caroline , Wingfield Tom , Cumming Fergus , Green William , Hadjipantelis Pantelis , Kirk Joni , Steves Claire J , Ourselin Sebastien , Medley Graham F , Fearon Elizabeth , House Thomas
Published: December 2023

Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt upon which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance, in balancing the sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in isolation and across age bands, before using methods that allow us to compare multiple datasets. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design. This is expected to have implications for the identification and management of community SARS-CoV-2 cases and could be further applied to symptom-based management of other diseases and syndromes.
Model-based deep learning framework for accelerated optical projection tomography
Authors: Obando Marcos , Bassi Andrea , Ducros Nicolas , Mato Germán , Correia Teresa M.
Published: December 2023

In this work, we propose a model-based deep learning reconstruction algorithm for optical projection tomography (ToMoDL), to greatly reduce acquisition and reconstruction times. The proposed method iterates over a data consistency step and an image domain artefact removal step achieved by a convolutional neural network. A preprocessing stage is also included to avoid potential misalignments between the sample center of rotation and the detector. The algorithm is trained using a database of wild-type zebrafish (Danio rerio) at different stages of development to minimise the mean square error for a fixed number of iterations. Using a cross-validation scheme, we compare the results to other reconstruction methods, such as filtered backprojection, compressed sensing and a direct deep learning method where the pseudo-inverse solution is corrected by a U-Net. The proposed method performs equally well or better than the alternatives. For a highly reduced number of projections, only the U-Net method provides images comparable to those obtained with ToMoDL. However, ToMoDL has a much better performance if the amount of data available for training is limited, given that the number of network trainable parameters is smaller.
Sex-specific effects of a high fat diet on aortic inflammation and dysfunction
Authors: Tran Vivian , Brettle Holly , Diep Henry , Dinh Quynh Nhu , O’Keeffe Maeve , Fanson Kerry V. , Sobey Christopher G. , Lim Kyungjoon , Drummond Grant R. , Vinh Antony , Jelinic Maria
Published: December 2023

Obesity and vascular dysfunction are independent and sexually dimorphic risk factors for cardiovascular disease. A high fat diet (HFD) is often used to model obesity in mice, but the sex-specific effects of this diet on aortic inflammation and function are unclear. Therefore, we characterized the aortic immune cell profile and function in 6-week-old male and female C57BL/6 mice fed a normal chow diet (NCD) or HFD for 10 weeks. Metabolic parameters were measured weekly and fortnightly. At end point, aortic immune cell populations and endothelial function were characterized using flow cytometry and wire myography. HFD-male mice had higher bodyweight, blood cholesterol, fasting blood glucose and plasma insulin levels than NCD mice (P < 0.05). HFD did not alter systolic blood pressure (SBP), glycated hemoglobin or blood triglycerides in either sex. HFD-females had delayed increases in bodyweight with a transient increase in fasting blood glucose at week 8 (P < 0.05). Flow cytometry revealed fewer proinflammatory aortic monocytes in females fed a HFD compared to NCD. HFD did not affect aortic leukocyte populations in males. Conversely, HFD impaired endothelium-dependent vasorelaxation, but only in males. Overall, this highlights biological sex as a key factor determining vascular disease severity in HFD-fed mice.
Multidisciplinary optimization of automotive mega-castings merging classical structural optimization with response-surface-based optimization enhanced by machine learning
Authors: Triller Jens , Lopez Marta L. , Nossek Matthias , Frenzel Moritz A.
Published: December 2023

Large high pressure die castings (HPDC), recently referred to as mega-castings, can replace plenty of steel metal sheets usually employed for body-in-white (BIW) structures. They can save manufacturing expense and unleash additional lightweight potential thanks to additional design freedom and material properties. The BIW plays a major role in automotive design since it must fulfill numerous structural targets ranging from stiffness for vehicle dynamics, dynamic responses for NVH (noise, vibration, harshness), driving comfort standards and several passive safety requirements. The use of mega-casting structures leads to additional requirements with respect to castability and material quality. Achieving a lightweight design considering requirements related to crash or castability is a challenge on its own, due to the high computational cost of related simulation techniques. Considering multiple requirements simultaneously, therefore often leads to non-weight-optimal structures. To exploit the full lightweight potential, we present a generative multidisciplinary optimization pipeline for the structural design of automotive mega-casting parts in this paper. The approach combines established methods in automotive industry such as topology optimization and response-surface-based (RSM) optimization and enhances the latter by machine learning (ML) based clustering and classification. In a first step topology optimization is employed to derive optimal load-paths for multidisciplinary loading conditions. For this purpose, casting manufacturing constraints as well as more than hundred linearized loads are used to incorporate NVH and passive safety requirements. In a next step the optimal thickness distribution and rib orientation of the structure is achieved using RSM optimization algorithms for the computationally expensive nonlinear crash and casting simulations. Performance indicators are treated by unsupervised learning based on clustering. This enables classification constraints based on simulation field results from hundreds of samples to be included into RSM optimization. It resolves a typical risk of pure scalar, regression-type targets, where supposed optimal results fail when domain experts examine the full field result of the corresponding simulation. It is shown how this approach is superior in achieving a weight-optimal design and turnaround time compared to a design workflow classically used for BIW structures.
A realistic computational model for the formation of a Place Cell
Authors: Mazzara Camille , Migliore Michele
Published: December 2023

Hippocampal Place Cells (PCs) are pyramidal neurons showing spatially localized firing when an animal gets into a specific area within an environment. Because of their obvious and clear relation with specific cognitive functions, Place Cells operations and modulations are intensely studied experimentally. However, although a lot of data have been gathered since their discovery, the cellular processes that interplay to turn a hippocampal pyramidal neuron into a Place Cell are still not completely understood. Here, we used a morphologically and biophysically detailed computational model of a CA1 pyramidal neuron to show how, and under which conditions, it can turn into a neuron coding for a specific cue location, through the self-organization of its synaptic inputs in response to external signals targeting different dendritic layers. Our results show that the model is consistent with experimental findings demonstrating PCs stability within the same spatial context over different trajectories, environment rotations, and place field remapping to adapt to changes in the environment. To date, this is the only biophysically and morphologically accurate cellular model of PCs formation, which can be directly used in physiologically accurate microcircuits and large-scale model networks to study cognitive functions and dysfunctions at cellular level.
DNA metabarcoding focusing on the plankton community: an effective approach to reconstruct the paleo-environment
Authors: Nakamura Yasuhide , Ogiso-Tanaka Eri , Seto Koji , Ando Takuto , Katsuki Kota , Saito Yoshiki
Published: December 2023

DNA metabarcoding (DNA-MB) targeting the whole plankton community is a promising approach in studies of sediment samples from water bodies, but its effectiveness in ancient material is not well demonstrated. We applied DNA-MB of plankton in a sediment core to reconstruct the paleo-environment of Lake Shinji, Japan, through a marine lagoon/freshwater lake transition during the past 2300 years. We interpreted core-sample plankton taxonomy and habitat by reference to the modern plankton community in water samples. OTUs (operational taxonomic units) belonging to Dictyochophyceae were 81.05% of the total reads in sediments. However, Ciliophora, Copepoda and Labyrinthulea formed the majority of plankton taxa in the water samples, suggesting that they are under-represented in sediment. A drastic change in plankton composition correlated with a large decrease in sediment sulfur concentration, implying the change of aquatic environment from marine lagoon to freshwater lake. This event took place ca. 1200 CE in Lake Shinji. A 250 year-long transitional period followed, during which the total DNA sequence reads were very low. This suggests that salinity fluctuations created a hostile environment for both marine and freshwater plankton species. Our results show that DNA-MB of the whole plankton community is effective in reconstructing paleo-environments.