bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thin Clouds Control the Cloud Radiative Effect Along the Sc‐Cu Transition
Authors: Choudhury Goutam , Goren Tom 
Published: May 2024

AbstractIn situ and spaceborne studies reveal the prevalence of thin clouds in the major Stratocumulus‐to‐Cumulus Transition (SCT) regions. Using instantaneous satellite and reanalysis data, this study investigates the properties of thin clouds in the Southeast Pacific Ocean and their impact on the cloud radiative effect (CRE). Our findings demonstrate that thin clouds are intrinsic to the SCT. The overcast stratocumulus‐dominated regime exhibits a minimal presence of thin clouds, which become notably prominent after the clouds breakup into the cumulus‐dominated regime. The regime dependence of the occurrence of thin clouds is also observed in terms of the marine cold‐air outbreak parameter and the sea surface temperature. Thin clouds at a given cloud cover significantly modulate the shortwave (SW) and longwave (LW) components of CRE. SW CRE decreases by 46 %–65 % with increasing thin cloud cover. They account for a larger variance in cloud albedo than the combined influence of the liquid water path and effective radius. Furthermore, LW CRE decreases by about 12 %–52 % with thin cloud cover. An increase in the fraction of thin clouds also leads to a larger fraction of negative SW CRE offset by positive LW CRE at a given cloud cover. This LW compensation ranges from approximately 8 % at overcast cloud cover to as much as 19 % at about 50 % cloud cover. These findings elucidate the crucial role of thin clouds, and thus cloud morphology, in modulating CRE and underscore the necessity of their accurate representation in climate models.
Spectral Study of Rare Upward Developing, Circling, and Branching Cloud‐To‐Ground Lightning
Authors: Xu Liwen , Gou Xueqiang , Yuan Ping , An Tingting , Jiang Rubin , Deng Hong 
Published: May 2024

AbstractThe development of cloud‐to‐ground (CG) lightning channel is one of the main bases reflecting the discharge characteristics. Time‐resolved spectra of CG lightning with eight return strokes were recorded by a slit‐less high‐speed spectroscope. We found an unusual phenomenon in which a branch developed upward from a node following a circling structure into the cloud after the first return stroke. To investigate the propagation properties of this lightning, characteristic parameters such as the two‐dimensional speed of the leader, node temperature, and electron density are analyzed. The physical mechanism of the branch is discussed. Spectral analysis reveals that the main channel temperature and electron density are approximately 2.72–3.07 × 104 K and 0.23–2.03 × 1018 cm−3, respectively. The temperature and electron density increase as the branch approaches the cloud base, similar to the feature of the main channel approaching the ground. The temperature and electron density of the node are higher than at other locations in the circular channel, indicating that massive charge accumulated around the node. Lightning occurred in the Qilian Mountains in a complex landscape, which easily yielded an uneven distribution in the local electric field of the air, resulting in channel bending, kinking, and even circle development. The phenomenon of the branch developed from the node to the cloud may be due to the fact that the branch is formed during the return stroke process.
Enhancing Nitrate Removal With Industrial Wine Residue: Insights From Laboratory Batch and Column Experiments Using Chemical, Isotopic and Numerical Modeling Tools
Authors: Abu Alex , Carrey Raúl , Navarro‐Ciurana Dídac , Margalef‐Marti Rosanna , Soler Albert , Otero Neus , Causapé Jesús , Domènech Cristina 
Published: May 2024

AbstractAgricultural run‐off exposes recipient water bodies to nitrate (NO3−) pollution. Biological denitrification is a suitable method for removing NO3− in water resources that can be induced by the use of industrial organic liquid waste as an electron donor source. In light of this, batch and column laboratory experiments were performed to assess the potential of two industrial wine residues (lías and vínico) to induce biological denitrification of NO3− contaminated water from a constructed wetland and to evaluate the efficiency of these treatments using chemical and isotopic tools. In batch experiments (performed at a C/N ratio of 1.25), vínico was not efficient enough in removing N species, attenuating only 35% NO3− and was not used in column experiments. In similar experimental conditions, lías completely removed N species from water in both batch and column experiments. The calculated isotope fractionation (ε15NNO3 and ε18ONO3) was the same in both batch and column experiments biostimulated with lías and differed from those for vínico. The isotopic data confirmed that denitrification was the principal NO3− attenuation pathway in all the experiments. The isotopic fractionation can be later applied to field studies to quantify the efficiency of biologically enhanced denitrification. A numerical geochemical model that accounts for the changes in nitrate, nitrite concentration and isotopic composition due to the degradation of lías and vínico, including transport in the case of the column experiment, was performed to simulate the experimental results and can be up‐scaled in field treatments.
Molecular subgroups of T-cell acute lymphoblastic leukemia in adults treated according to pediatric-based GMALL protocols
Authors: Neumann Martin , Beder Thomas , Bastian Lorenz , Hänzelmann Sonja , Bultmann Miriam , Wolgast Nadine , Hartmann Alina , Trautmann Heiko , Ortiz-Tanchez Jutta , Schlee Cornelia , Schroeder Michael , Fransecky Lars , Vosberg Sebastian , Fiedler Walter , Alakel Nael , Heberling Lisa , Kondakci Mustafa , Starck Michael , Schwartz Stefan , Raffel Simon , Müller-Tidow Carsten , Schneller Folker , Reichle Albrecht , Burmeister Thomas , Greif Philipp A. , Brüggemann Monika , Gökbuget Nicola , Baldus Claudia D. 
Published: May 2024

AbstractIn contrast to B-cell precursor acute lymphoblastic leukemia (ALL), molecular subgroups are less well defined in T-lineage ALL. Comprehensive studies on molecular T-ALL subgroups have been predominantly performed in pediatric ALL patients. Currently, molecular characteristics are rarely considered for risk stratification. Herein, we present a homogenously treated cohort of 230 adult T-ALL patients characterized on transcriptome, and partly on DNA methylation and gene mutation level in correlation with clinical outcome. We identified nine molecular subgroups based on aberrant oncogene expression correlating to four distinct DNA methylation patterns. The subgroup distribution differed from reported pediatric T-ALL cohorts with higher frequencies of prognostic unfavorable subgroups like HOXA or LYL1/LMO2. A small subset (3%) of HOXA adult T-ALL patients revealed restricted expression of posterior HOX genes with aberrant activation of lncRNA HOTTIP. With respect to outcome, TLX1 (n = 44) and NKX2-1 (n = 4) had an exceptionally favorable 3-year overall survival (3y-OS) of 94%. Within thymic T-ALL, the non TLX1 patients had an inferior but still good prognosis. To our knowledge this is the largest cohort of adult T-ALL patients characterized by transcriptome sequencing with meaningful clinical follow-up. Risk classification based on molecular subgroups might emerge and contribute to improvements in outcome.
Investigating heart rate variability measures during pregnancy as predictors of postpartum depression and anxiety: an exploratory study
Authors: Eriksson Allison , Kimmel Mary Claire , Furmark Tomas , Wikman Anna , Grueschow Marcus , Skalkidou Alkistis , Frick Andreas , Fransson Emma 
Published: May 2024

AbstractPerinatal affective disorders are common, but standard screening measures reliant on subjective self-reports might not be sufficient to identify pregnant women at-risk for developing postpartum depression and anxiety. Lower heart rate variability (HRV) has been shown to be associated with affective disorders. The current exploratory study aimed to evaluate the predictive utility of late pregnancy HRV measurements of postpartum affective symptoms. A subset of participants from the BASIC study (Uppsala, Sweden) took part in a sub-study at pregnancy week 38 where HRV was measured before and after a mild stressor (n = 122). Outcome measures were 6-week postpartum depression and anxiety symptoms as quantified by the Edinburgh Postnatal Depression Scale (EPDS) and the Beck Anxiety Inventory (BAI). In total, 112 women were included in a depression outcome analysis and 106 women were included in an anxiety outcome analysis. Group comparisons indicated that lower pregnancy HRV was associated with depressive or anxious symptomatology at 6 weeks postpartum. Elastic net logistic regression analyses indicated that HRV indices alone were not predictive of postpartum depression or anxiety outcomes, but HRV indices were selected as predictors in a combined model with background and pregnancy variables. ROC curves for the combined models gave an area under the curve (AUC) of 0.93 for the depression outcome and an AUC of 0.83 for the anxiety outcome. HRV indices predictive of postpartum depression generally differed from those predictive of postpartum anxiety. HRV indices did not significantly improve prediction models comprised of psychological measures only in women with pregnancy depression or anxiety.
Bax Inhibitor-1 preserves pancreatic β-cell proteostasis by limiting proinsulin misfolding and programmed cell death
Authors: Blanc Marina , Habbouche Lama , Xiao Peng , Lebeaupin Cynthia , Janona Marion , Vaillant Nathalie , Irondelle Marie , Gilleron Jérôme , Murcy Florent , Rousseau Déborah , Luci Carmelo , Barouillet Thibault , Marchetti Sandrine , Lacas-Gervais Sandra , Yvan-Charvet Laurent , Gual Philippe , Cardozo Alessandra K. , Bailly-Maitre Béatrice 
Published: May 2024

AbstractThe prevalence of diabetes steadily increases worldwide mirroring the prevalence of obesity. Endoplasmic reticulum (ER) stress is activated in diabetes and contributes to β-cell dysfunction and apoptosis through the activation of a terminal unfolded protein response (UPR). Our results uncover a new role for Bax Inhibitor-One (BI-1), a negative regulator of inositol-requiring enzyme 1 (IRE1α) in preserving β-cell health against terminal UPR-induced apoptosis and pyroptosis in the context of supraphysiological loads of insulin production. BI-1-deficient mice experience a decline in endocrine pancreatic function in physiological and pathophysiological conditions, namely obesity induced by high-fat diet (HFD). We observed early-onset diabetes characterized by hyperglycemia, reduced serum insulin levels, β-cell loss, increased pancreatic lipases and pro-inflammatory cytokines, and the progression of metabolic dysfunction. Pancreatic section analysis revealed that BI-1 deletion overburdens unfolded proinsulin in the ER of β-cells, confirmed by ultrastructural signs of ER stress with overwhelmed IRE1α endoribonuclease (RNase) activity in freshly isolated islets. ER stress led to β-cell dysfunction and islet loss, due to an increase in immature proinsulin granules and defects in insulin crystallization with the presence of Rod-like granules. These results correlated with the induction of autophagy, ER phagy, and crinophagy quality control mechanisms, likely to alleviate the atypical accumulation of misfolded proinsulin in the ER. In fine, BI-1 in β-cells limited IRE1α RNase activity from triggering programmed β-cell death through apoptosis and pyroptosis (caspase-1, IL-1β) via NLRP3 inflammasome activation and metabolic dysfunction. Pharmaceutical IRE1α inhibition with STF-083010 reversed β-cell failure and normalized the metabolic phenotype. These results uncover a new protective role for BI-1 in pancreatic β-cell physiology as a stress integrator to modulate the UPR triggered by accumulating unfolded proinsulin in the ER, as well as autophagy and programmed cell death, with consequences on β-cell function and insulin secretion.
The NTE domain of PTENα/β promotes cancer progression by interacting with WDR5 via its SSSRRSS motif
Authors: Huang Xiaolei , Zhang Cheng , Shang Xinci , Chen Yichang , Xiao Qin , Wei Zhengguo , Wang Guanghui , Zhen Xuechu , Xu Guoqiang , Min Jinrong , Shen Shaoming , Liu Yanli 
Published: May 2024

AbstractPTENα/β, two variants of PTEN, play a key role in promoting tumor growth by interacting with WDR5 through their N-terminal extensions (NTEs). This interaction facilitates the recruitment of the SET1/MLL methyltransferase complex, resulting in histone H3K4 trimethylation and upregulation of oncogenes such as NOTCH3, which in turn promotes tumor growth. However, the molecular mechanism underlying this interaction has remained elusive. In this study, we determined the first crystal structure of PTENα-NTE in complex with WDR5, which reveals that PTENα utilizes a unique binding motif of a sequence SSSRRSS found in the NTE domain of PTENα/β to specifically bind to the WIN site of WDR5. Disruption of this interaction significantly impedes cell proliferation and tumor growth, highlighting the potential of the WIN site inhibitors of WDR5 as a way of therapeutic intervention of the PTENα/β associated cancers. These findings not only shed light on the important role of the PTENα/β-WDR5 interaction in carcinogenesis, but also present a promising avenue for developing cancer treatments that target this pathway.
Disentangling oncogenic amplicons in esophageal adenocarcinoma
Authors: Ng Alvin Wei Tian , McClurg Dylan Peter , Wesley Ben , Zamani Shahriar A. , Black Emily , Miremadi Ahmad , Giger Olivier , Hoopen Rogier ten , Devonshire Ginny , Redmond Aisling M. , Grehan Nicola , Jammula Sriganesh , Blasko Adrienn , Li Xiaodun , Aparicio Samuel , Tavaré Simon ,   Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Edwards Paul A. W. , Grehan Nicola , Nutzinger Barbara , Loreno Christine , Abbas Sujath , Freeman Adam , Smyth Elizabeth C. , O’Donovan Maria , Miremadi Ahmad , Malhotra Shalini , Tripathi Monika , Cheah Calvin , Coles Hannah , Millington Curtis , Eldridge Matthew , Secrier Maria , Jammula Sriganesh , Davies Jim , Crichton Charles , Carroll Nick , Hardwick Richard H. , Safranek Peter , Hindmarsh Andrew , Sujendran Vijayendran , Hayes Stephen J. , Ang Yeng , Sharrocks Andrew , Preston Shaun R. , Bagwan Izhar , Save Vicki , Skipworth Richard J. E. , Hupp Ted R. , O’Neill J. Robert , Tucker Olga , Beggs Andrew , Taniere Philippe , Puig Sonia , Contino Gianmarco , Underwood Timothy J. , Walker Robert C. , Grace Ben L. , Lagergren Jesper , Gossage James , Davies Andrew , Chang Fuju , Mahadeva Ula , Goh Vicky , Ciccarelli Francesca D. , Sanders Grant , Berrisford Richard , Chan David , Cheong Ed , Kumar Bhaskar , Sreedharan L. , Parsons Simon L. , Soomro Irshad , Kaye Philip , Saunders John , Lovat Laurence , Haidry Rehan , Scott Michael , Sothi Sharmila , Lishman Suzy , Hanna George B. , Peters Christopher J. , Moorthy Krishna , Grabowska Anna , Turkington Richard , McManus Damian , Coleman Helen , Petty Russell D. , Bartlet Freddie , Nowicki-Osuch Karol , Fitzgerald Rebecca C. 
Published: May 2024

AbstractEsophageal adenocarcinoma is a prominent example of cancer characterized by frequent amplifications in oncogenes. However, the mechanisms leading to amplicons that involve breakage-fusion-bridge cycles and extrachromosomal DNA are poorly understood. Here, we use 710 esophageal adenocarcinoma cases with matched samples and patient-derived organoids to disentangle complex amplicons and their associated mechanisms. Short-read sequencing identifies ERBB2, MYC, MDM2, and HMGA2 as the most frequent oncogenes amplified in extrachromosomal DNAs. We resolve complex extrachromosomal DNA and breakage-fusion-bridge cycles amplicons by integrating of de-novo assemblies and DNA methylation in nine long-read sequenced cases. Complex amplicons shared between precancerous biopsy and late-stage tumor, an enrichment of putative enhancer elements and mobile element insertions are potential drivers of complex amplicons’ origin. We find that patient-derived organoids recapitulate extrachromosomal DNA observed in the primary tumors and single-cell DNA sequencing capture extrachromosomal DNA-driven clonal dynamics across passages. Prospectively, long-read and single-cell DNA sequencing technologies can lead to better prediction of clonal evolution in esophageal adenocarcinoma.
Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters
Authors: Jiang Anmin , Kudo Kye , Gormal Rachel S. , Ellis Sevannah , Guo Sikao , Wallis Tristan P. , Longfield Shanley F. , Robinson Phillip J. , Johnson Margaret E. , Joensuu Merja , Meunier Frédéric A. 
Published: May 2024

AbstractEndocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endocytic structures. How cytosolic proteins such as dynamin concentrate at discrete sites that are sparsely distributed across the plasma membrane remains poorly understood. Two dynamin-1 major splice variants differ by the length of their C-terminal proline-rich region (short-tail and long-tail). Using sptPALM in PC12 cells, neurons and MEF cells, we demonstrate that short-tail dynamin-1 isoforms ab and bb display an activity-dependent recruitment to the membrane, promptly followed by their concentration into nanoclusters. These nanoclusters are sensitive to both Calcineurin and dynamin GTPase inhibitors, and are larger, denser, and more numerous than that of long-tail isoform aa. Spatiotemporal modelling confirms that dynamin-1 isoforms perform distinct search patterns and undergo dimensional reduction to generate endocytic nanoclusters, with short-tail isoforms more robustly exploiting lateral trapping in the generation of nanoclusters compared to the long-tail isoform.
Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants
Authors: Dzanibe Sonwabile , Wilk Aaron J. , Canny Susan , Ranganath Thanmayi , Alinde Berenice , Rubelt Florian , Huang Huang , Davis Mark M. , Holmes Susan P. , Jaspan Heather B. , Blish Catherine A. , Gray Clive M. 
Published: May 2024

AbstractWhile preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations in T cell memory differentiation between iHEU and iHUU being significant from week 15 of life. The altered memory T cell differentiation in iHEU was preceded by lower TCR Vβ clonotypic diversity and linked to TCR clonal depletion within the naïve T cell compartment. Compared to iHUU, iHEU had elevated CD56loCD16loPerforin+CD38+CD45RA+FcεRIγ+ NK cells at 1 month postpartum and whose abundance pre-vaccination were predictive of vaccine-induced pertussis and rotavirus antibody responses post 3 months of life. Collectively, HIV/ARV exposure disrupted the trajectory of innate and adaptive immunity from birth which may underlie relative vulnerability to infections in iHEU.
Dynamics of growing carbon nanotube interfaces probed by machine learning-enabled molecular simulations
Authors: Hedman Daniel , McLean Ben , Bichara Christophe , Maruyama Shigeo , Larsson J. Andreas , Ding Feng 
Published: May 2024

AbstractCarbon nanotubes (CNTs), hollow cylinders of carbon, hold great promise for advanced technologies, provided their structure remains uniform throughout their length. Their growth takes place at high temperatures across a tube-catalyst interface. Structural defects formed during growth alter CNT properties. These defects are believed to form and heal at the tube-catalyst interface but an understanding of these mechanisms at the atomic-level is lacking. Here we present DeepCNT-22, a machine learning force field (MLFF) to drive molecular dynamics simulations through which we unveil the mechanisms of CNT formation, from nucleation to growth including defect formation and healing. We find the tube-catalyst interface to be highly dynamic, with large fluctuations in the chiral structure of the CNT-edge. This does not support continuous spiral growth as a general mechanism, instead, at these growth conditions, the growing tube edge exhibits significant configurational entropy. We demonstrate that defects form stochastically at the tube-catalyst interface, but under low growth rates and high temperatures, these heal before becoming incorporated in the tube wall, allowing CNTs to grow defect-free to seemingly unlimited lengths. These insights, not readily available through experiments, demonstrate the remarkable power of MLFF-driven simulations and fill long-standing gaps in our understanding of CNT growth mechanisms.
De novo motor learning creates structure in neural activity that shapes adaptation
Authors: Chang Joanna C. , Perich Matthew G. , Miller Lee E. , Gallego Juan A. , Clopath Claudia 
Published: May 2024

AbstractAnimals can quickly adapt learned movements to external perturbations, and their existing motor repertoire likely influences their ease of adaptation. Long-term learning causes lasting changes in neural connectivity, which shapes the activity patterns that can be produced during adaptation. Here, we examined how a neural population’s existing activity patterns, acquired through de novo learning, affect subsequent adaptation by modeling motor cortical neural population dynamics with recurrent neural networks. We trained networks on different motor repertoires comprising varying numbers of movements, which they acquired following various learning experiences. Networks with multiple movements had more constrained and robust dynamics, which were associated with more defined neural ‘structure’—organization in the available population activity patterns. This structure facilitated adaptation, but only when the changes imposed by the perturbation were congruent with the organization of the inputs and the structure in neural activity acquired during de novo learning. These results highlight trade-offs in skill acquisition and demonstrate how different learning experiences can shape the geometrical properties of neural population activity and subsequent adaptation.
Sustainable upcycling of mixed spent cathodes to a high-voltage polyanionic cathode material
Authors: Ji Guanjun , Tang Di , Wang Junxiong , Liang Zheng , Ji Haocheng , Ma Jun , Zhuang Zhaofeng , Liu Song , Zhou Guangmin , Cheng Hui-Ming 
Published: May 2024

AbstractSustainable battery recycling is essential for achieving resource conservation and alleviating environmental issues. Many open/closed-loop strategies for critical metal recycling or direct recovery aim at a single component, and the reuse of mixed cathode materials is a significant challenge. To address this barrier, here we propose an upcycling strategy for spent LiFePO4 and Mn-rich cathodes by structural design and transition metal replacement, for which uses a green deep eutectic solvent to regenerate a high-voltage polyanionic cathode material. This process ensures the complete recycling of all the elements in mixed cathodes and the deep eutectic solvent can be reused. The regenerated LiFe0.5Mn0.5PO4 has an increased mean voltage (3.68 V versus Li/Li+) and energy density (559 Wh kg–1) compared with a commercial LiFePO4 (3.38 V and 524 Wh kg–1). The proposed upcycling strategy can expand at a gram-grade scale and was also applicable for LiFe0.5Mn0.5PO4 recovery, thus achieving a closed-loop recycling between the mixed spent cathodes and the next generation cathode materials. Techno-economic analysis shows that this strategy has potentially high environmental and economic benefits, while providing a sustainable approach for the value-added utilization of waste battery materials.