bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma
Authors: Calderaro Julien , Ghaffari Laleh Narmin , Zeng Qinghe , Maille Pascale , Favre Loetitia , Pujals Anaïs , Klein Christophe , Bazille Céline , Heij Lara R. , Uguen Arnaud , Luedde Tom , Di Tommaso Luca , Beaufrère Aurélie , Chatain Augustin , Gastineau Delphine , Nguyen Cong Trung , Nguyen-Canh Hiep , Thi Khuyen Nguyen , Gnemmi Viviane , Graham Rondell P. , Charlotte Frédéric , Wendum Dominique , Vij Mukul , Allende Daniela S. , Aucejo Federico , Diaz Alba , Rivière Benjamin , Herrero Astrid , Evert Katja , Calvisi Diego Francesco , Augustin Jérémy , Leow Wei Qiang , Leung Howard Ho Wai , Boleslawski Emmanuel , Rela Mohamed , François Arnaud , Cha Anthony Wing-Hung , Forner Alejandro , Reig Maria , Allaire Manon , Scatton Olivier , Chatelain Denis , Boulagnon-Rombi Camille , Sturm Nathalie , Menahem Benjamin , Frouin Eric , Tougeron David , Tournigand Christophe , Kempf Emmanuelle , Kim Haeryoung , Ningarhari Massih , Michalak-Provost Sophie , Gopal Purva , Brustia Raffaele , Vibert Eric , Schulze Kornelius , Rüther Darius F. , Weidemann Sören A. , Rhaiem Rami , Pawlotsky Jean-Michel , Zhang Xuchen , Luciani Alain , Mulé Sébastien , Laurent Alexis , Amaddeo Giuliana , Regnault Hélène , De Martin Eleonora , Sempoux Christine , Navale Pooja , Westerhoff Maria , Lo Regina Cheuk-Lam , Bednarsch Jan , Gouw Annette , Guettier Catherine , Lequoy Marie , Harada Kenichi , Sripongpun Pimsiri , Wetwittayaklang Poowadon , Loménie Nicolas , Tantipisit Jarukit , Kaewdech Apichat , Shen Jeanne , Paradis Valérie , Caruso Stefano , Kather Jakob Nikolas 
Published: December 2023

AbstractPrimary liver cancer arises either from hepatocytic or biliary lineage cells, giving rise to hepatocellular carcinoma (HCC) or intrahepatic cholangiocarcinoma (ICCA). Combined hepatocellular- cholangiocarcinomas (cHCC-CCA) exhibit equivocal or mixed features of both, causing diagnostic uncertainty and difficulty in determining proper management. Here, we perform a comprehensive deep learning-based phenotyping of multiple cohorts of patients. We show that deep learning can reproduce the diagnosis of HCC vs. CCA with a high performance. We analyze a series of 405 cHCC-CCA patients and demonstrate that the model can reclassify the tumors as HCC or ICCA, and that the predictions are consistent with clinical outcomes, genetic alterations and in situ spatial gene expression profiling. This type of approach could improve treatment decisions and ultimately clinical outcome for patients with rare and biphenotypic cancers such as cHCC-CCA.
Hydrogels with tunable mechanical plasticity regulate endothelial cell outgrowth in vasculogenesis and angiogenesis
Authors: Wei Zhao , Lei Meng , Wang Yaohui , Xie Yizhou , Xie Xueyong , Lan Dongwei , Jia Yuanbo , Liu Jingyi , Ma Yufei , Cheng Bo , Gerecht Sharon , Xu Feng 
Published: December 2023

AbstractThe endothelial cell (EC) outgrowth in both vasculogenesis and angiogenesis starts with remodeling surrounding matrix and proceeds with the crosstalk between cells for the multicellular vasculature formation. The mechanical plasticity of matrix, defined as the ability to permanently deform by external traction, is pivotal in modulating cell behaviors. Nevertheless, the implications of matrix plasticity on cell-to-cell interactions during EC outgrowth, along with the molecular pathways involved, remain elusive. Here we develop a collagen-hyaluronic acid based hydrogel platform with tunable plasticity by using compositing strategy of dynamic and covalent networks. We show that although the increasing plasticity of the hydrogel facilitates the matrix remodeling by ECs, the largest tubular lumens and the longest invading distance unexpectedly appear in hydrogels with medium plasticity instead of the highest ones. We unravel that the high plasticity of the hydrogels promotes stable integrin cluster of ECs and recruitment of focal adhesion kinase with an overenhanced contractility which downregulates the vascular endothelial cadherin expression and destabilizes the adherens junctions between individual ECs. Our results, further validated with mathematical simulations and in vivo angiogenic tests, demonstrate that a balance of matrix plasticity facilitates both cell-matrix binding and cell-to-cell adherens, for promoting vascular assembly and invasion.
Evolutionary modelling indicates that mosquito metabolism shapes the life-history strategies of Plasmodium parasites
Authors: Carrillo-Bustamante Paola , Costa Giulia , Lampe Lena , Levashina Elena A. 
Published: December 2023

AbstractWithin-host survival and between-host transmission are key life-history traits of single-celled malaria parasites. Understanding the evolutionary forces that shape these traits is crucial to predict malaria epidemiology, drug resistance, and virulence. However, very little is known about how Plasmodium parasites adapt to their mosquito vectors. Here, we examine the evolution of the time Plasmodium parasites require to develop within the vector (extrinsic incubation period) with an individual-based model of malaria transmission that includes mosquito metabolism. Specifically, we model the metabolic cascade of resource allocation induced by blood-feeding, as well as the influence of multiple blood meals on parasite development. Our model predicts that successful vector-to-human transmission events are rare, and are caused by long-lived mosquitoes. Importantly, our results show that the life-history strategies of malaria parasites depend on the mosquito’s metabolic status. In our model, additional resources provided by multiple blood meals lead to selection for parasites with slow or intermediate developmental time. These results challenge the current assumption that evolution favors fast developing parasites to maximize their chances to complete their within-mosquito life cycle. We propose that the long sporogonic cycle observed for Plasmodium is not a constraint but rather an adaptation to increase transmission potential.
Edge effects on tree architecture exacerbate biomass loss of fragmented Amazonian forests
Authors: Nunes Matheus Henrique , Vaz Marcel Caritá , Camargo José Luís Campana , Laurance William F. , de Andrade Ana , Vicentini Alberto , Laurance Susan , Raumonen Pasi , Jackson Toby , Zuquim Gabriela , Wu Jin , Peñuelas Josep , Chave Jérôme , Maeda Eduardo Eiji 
Published: December 2023

AbstractHabitat fragmentation could potentially affect tree architecture and allometry. Here, we use ground surveys of terrestrial LiDAR in Central Amazonia to explore the influence of forest edge effects on tree architecture and allometry, as well as forest biomass, 40 years after fragmentation. We find that young trees colonising the forest fragments have thicker branches and architectural traits that optimise for light capture, which result in 50% more woody volume than their counterparts of similar stem size and height in the forest interior. However, we observe a disproportionately lower height in some large trees, leading to a 30% decline in their woody volume. Despite the substantial wood production of colonising trees, the lower height of some large trees has resulted in a net loss of 6.0 Mg ha−1 of aboveground biomass – representing 2.3% of the aboveground biomass of edge forests. Our findings indicate a strong influence of edge effects on tree architecture and allometry, and uncover an overlooked factor that likely exacerbates carbon losses in fragmented forests.
PolyMOF nanoparticles constructed from intrinsically microporous polymer ligand towards scalable composite membranes for CO2 separation
Authors: Lee Tae Hoon , Lee Byung Kwan , Yoo Seung Yeon , Lee Hyunhee , Wu Wan-Ni , Smith Zachary P. , Park Ho Bum 
Published: December 2023

AbstractIntegrating different modification strategies into a single step to achieve the desired properties of metal–organic frameworks (MOFs) has been very synthetically challenging, especially in developing advanced MOF/polymer mixed matrix membranes (MMMs). Herein, we report a polymer–MOF (polyMOF) system constructed from a carboxylated polymer with intrinsic microporosity (cPIM-1) ligand. This intrinsically microporous ligand could coordinate with metals, leading to ~100 nm-sized polyMOF nanoparticles. Compared to control MOFs, these polyMOFs exhibit enhanced ultramicroporosity for efficient molecular sieving, and they have better dispersion properties in casting solutions to prepare MMMs. Ultimately, integrating coordination chemistries through the cPIM-1 and polymer-based functionality into porous materials results in polyMOF/PIM-1 MMMs that display excellent CO2 separation performance (surpassing the CO2/N2 and CO2/CH4 upper bounds). In addition to exploring the physicochemical and transport properties of this polyMOF system, scalability has been demonstrated by converting the developed MMM material into large-area (400 cm2) thin-film nanocomposite (TFN) membranes.
Prediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors
Authors: He Yixuan , Qian David C. , Diao James A. , Cho Michael H. , Silverman Edwin K. , Gusev Alexander , Manrai Arjun K. , Martin Alicia R. , Patel Chirag J. 
Published: December 2023

AbstractSmoking is the leading risk factor for chronic obstructive pulmonary disease (COPD) worldwide, yet many people who never smoke develop COPD. We perform a longitudinal analysis of COPD in the UK Biobank to derive and validate the Socioeconomic and Environmental Risk Score which captures additive and cumulative environmental, behavioral, and socioeconomic exposure risks beyond tobacco smoking. The Socioeconomic and Environmental Risk Score is more predictive of COPD than smoking status and pack-years. Individuals in the highest decile of the risk score have a greater risk for incident COPD compared to the remaining population. Never smokers in the highest decile of exposure risk are more likely to develop COPD than previous and current smokers in the lowest decile. In general, the prediction accuracy of the Social and Environmental Risk Score is lower in non-European populations. While smoking status is often considered in screening COPD, our finding highlights the importance of other non-smoking environmental and socioeconomic variables.
Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors
Authors: Hsu Hao-Chi , Li Daqiang , Zhan Wenhu , Ye Jianxiang , Liu Yi Jing , Leung Annie , Qin Junling , Crespo Benigno , Gamo Francisco-Javier , Zhang Hao , Cui Liwang , Roth Alison , Kirkman Laura A. , Li Huilin , Lin Gang 
Published: December 2023

AbstractThe proteasome of the malaria parasite Plasmodium falciparum (Pf20S) is an advantageous drug target because its inhibition kills P. falciparum in multiple stages of its life cycle and synergizes with artemisinins. We recently developed a macrocyclic peptide, TDI-8304, that is highly selective for Pf20S over human proteasomes and is potent in vitro and in vivo against P. falciparum. A mutation in the Pf20S β6 subunit, A117D, confers resistance to TDI-8304, yet enhances both enzyme inhibition and anti-parasite activity of a tripeptide vinyl sulfone β2 inhibitor, WLW-vs. Here we present the high-resolution cryo-EM structures of Pf20S with TDI-8304, of human constitutive proteasome with TDI-8304, and of Pf20Sβ6A117D with WLW-vs that give insights into the species selectivity of TDI-8304, resistance to it, and the collateral sensitivity associated with resistance, including that TDI-8304 binds β2 and β5 in wild type Pf20S as well as WLW-vs binds β2 and β5 in Pf20Sβ6A117D. We further show that TDI-8304 kills P. falciparum as quickly as chloroquine and artemisinin and is active against P. cynomolgi at the liver stage. This increases interest in using these structures to facilitate the development of Pf20S inhibitors that target multiple proteasome subunits and limit the emergence of resistance.
How frictional slip evolves
Authors: Shi Songlin , Wang Meng , Poles Yonatan , Fineberg Jay 
Published: December 2023

AbstractEarthquake-like ruptures break the contacts that form the frictional interface separating contacting bodies and mediate the onset of frictional motion (stick-slip). The slip (motion) of the interface immediately resulting from the rupture that initiates each stick-slip event is generally much smaller than the total slip logged over the duration of the event. Slip after the onset of friction is generally attributed to continuous motion globally attributed to ‘dynamic friction’. Here we show, by means of direct measurements of real contact area and slip at the frictional interface, that sequences of myriad hitherto invisible, secondary ruptures are triggered immediately in the wake of each initial rupture. Each secondary rupture generates incremental slip that, when not resolved, may appear as steady sliding of the interface. Each slip increment is linked, via fracture mechanics, to corresponding variations of contact area and local strain. Only by accounting for the contributions of these secondary ruptures can the accumulated interface slip be described. These results have important ramifications both to our fundamental understanding of frictional motion as well as to the essential role of aftershocks within natural faults in generating earthquake-mediated slip.
Site-selective chemical reactions by on-water surface sequential assembly
Authors: Prasoon Anupam , Yu Xiaoqing , Hambsch Mike , Bodesheim David , Liu Kejun , Zacarias Angelica , Nguyen Nguyen Ngan , Seki Takakazu , Dianat Aerzoo , Croy Alexander , Cuniberti Gianaurelio , Fontaine Philippe , Nagata Yuki , Mannsfeld Stefan C. B. , Dong Renhao , Bonn Mischa , Feng Xinliang 
Published: December 2023

AbstractControlling site-selectivity and reactivity in chemical reactions continues to be a key challenge in modern synthetic chemistry. Here, we demonstrate the discovery of site-selective chemical reactions on the water surface via a sequential assembly approach. A negatively charged surfactant monolayer on the water surface guides the electrostatically driven, epitaxial, and aligned assembly of reagent amino-substituted porphyrin molecules, resulting in a well-defined J-aggregated structure. This constrained geometry of the porphyrin molecules prompts the subsequent directional alignment of the perylenetetracarboxylic dianhydride reagent, enabling the selective formation of a one-sided imide bond between porphyrin and reagent. Surface-specific in-situ spectroscopies reveal the underlying mechanism of the dynamic interface that promotes multilayer growth of the site-selective imide product. The site-selective reaction on the water surface is further demonstrated by three reversible and irreversible chemical reactions, such as imide-, imine-, and 1, 3-diazole (imidazole)- bonds involving porphyrin molecules. This unique sequential assembly approach enables site-selective chemical reactions that can bring on-water surface synthesis to the forefront of modern organic chemistry.
Pyrotinib plus docetaxel as first-line treatment for HER2-positive metastatic breast cancer: the PANDORA phase II trial
Authors: Zheng Yabing , Cao Wen-Ming , Shao Xiying , Shi Yanxia , Cai Li , Chen Wenyan , Liu Jian , Shen Peng , Chen Yiding , Wang Xian , Li Huiping , Li Man , Chen Zhanhong , Wang Xiaojia 
Published: December 2023

AbstractThe role of pyrotinib in the treatment of HER2-positive metastatic breast cancer (MBC) has been well-established. This multicenter, single-arm phase II trial (NCT03876587) aimed to assess the benefit of pyrotinib plus docetaxel as a first-line treatment for HER2-positive MBC. Women with HER2-positive MBC who had not undergone HER2 blockade or chemotherapy for metastatic disease were enrolled in the study and received daily oral pyrotinib 400 mg plus intravenous docetaxel 75 mg/m2 every 3 weeks. The primary endpoint was the objective response rate (ORR), secondary endpoints included progression-free survival (PFS), duration of response (DoR), clinical benefit rate (CBR), overall survival (OS) and safety. From June 2019 to June 2021, 79 patients were enrolled. The confirmed ORR was 79.7% (95% confidence interval [CI], 70.8-88.6), and the CBR was 87.3% (95%CI, 80.0-94.6) in the intention-to-treat population. The pre-specified primary endpoint was met. The median DoR was 15.9 months (interquartile range, 8.3-19.5); the median PFS was 16.0 months (95% CI, 11.2-20.8), and the median OS was not reached. The most common grade ≥3 treatment-related adverse events observed were leukopenia (29.1%), neutropenia (27.8%), and diarrhea (21.5%). This study demonstrates that pyrotinib plus docetaxel show an acceptable safety profile and promising antitumor activity as a first-line treatment option for patients with HER2-positive MBC.
Elemental partitioning and corrosion resistance of Ni–Cr alloys revealed by accurate ab-initio thermodynamic and electrochemical calculations
Authors: Huang Liang-Feng , Xie Yusi , Sieradzki Karl , Rondinelli James M. 
Published: December 2023

AbstractElemental partitioning during thermal processing can significantly affect the corrosion resistance of bulk alloys operating in aggressive electrochemical environments, for which, despite decades of experimental and theoretical studies, the thermodynamic and electrochemical mechanisms still lack accurate quantitative descriptions. Here, we formulate an ab initio thermodynamic model to obtain the composition- and temperature-dependent free energies of formation (ΔfG) for Ni–Cr alloys, a prototypical group of corrosion-resistant metals, and discover two equilibrium states that produce the driving forces for the elemental partitioning in Ni–Cr. The results are in quantitative agreement with the experimental studies on the thermodynamic stability of Ni–Cr. We further construct electrochemical (potential–pH) diagrams by obtaining the required ΔfG values of native oxides and (oxy)hydroxides using high-fidelity ab-initio calculations that include exact electronic exchange and phononic contributions. We then analyze the passivation and electrochemical trends of Ni–Cr alloys, which closely explain various oxide-film growth and corrosion behaviors observed on alloy surfaces. We finally determine the optimal Cr content range of 14–34 at%, which provides the Ni–Cr alloys with both the preferred heat-treatment stability and superior corrosion resistance. We conclude by discussing the consequences of these findings on other Ni–Cr alloys with more complex additives, which can guide the further optimization of industrial Ni–Cr-based alloys.
Temporal patterns of fucoxanthin in four species of European marine brown macroalgae
Authors: Cunningham Eoghan M. , O’Kane Aaron P. , Ford Lauren , Sheldrake Gary N. , Cuthbert Ross N. , Dick Jaimie T. A. , Maggs Christine A. , Walsh Pamela J. 
Published: December 2023

AbstractBrown seaweeds are a rich source of carotenoids, particularly fucoxanthin, which has a wide range of potential health applications. Fucoxanthin fluctuates within and among seaweeds over time, frustrating efforts to utilise this resource. Thus, we require comprehensive analyses of long- and short-term concentrations across species in field conditions. Here, we used High Performance Liquid Chromatography to compare fucoxanthin content in four brown macroalgae, Ascophyllum nodosum, Fucus serratus, Fucus vesiculosus and Saccharina latissima, monthly for 1 year. F. serratus and F. vesiculosus had significantly higher fucoxanthin content (mg/g), which was highest in Spring (0.39 ± 0.04) and Autumn (0.45 ± 0.04) [mean (± SE)]. Two species, A. nodosum and F. serratus, were collected monthly at the same location for a further two non-consecutive years. For both A. nodosum and F. serratus, a significant interaction effect of seasons and years was identified, highlighting that there is variation in fucoxanthin content among and within species over time. We also show that fucoxanthin content differs significantly among months even within seasons. Therefore, it is not sufficient to assess fucoxanthin in single months to represent seasonality. We discuss how weather, nutrients and reproduction may have driven the seasonal variation, and reveal patterns of fucoxanthin concentration that can provide information concerning its availability for many important medical functions.
Altitude measurement method of VHF radar based on spatial smoothing of correlation matrix
Authors: Wang Xianchao , Wei Yanping , Li Shaoyi , Hou Changhui , Zhang Guoming 
Published: December 2023

AbstractFor very high frequency (VHF) phased array radar, the key problem to be solved in altitude measurement is the super-resolution spatial spectrum estimation under the condition of coherent sources. The spatial smoothing algorithm is a kind of decorrelation algorithm with excellent properties, but the decorrelation process is at the expense of the effective array aperture. Because it only uses the autocorrelation information of the subspace, its performance is significantly reduced, when the positions of the coherent sources are very close. In order to solve the above problems, this paper proposes an altitude measurement method of VHF radar based on the space smoothing of autocorrelation and cross-correlation matrix, which is used to realize the correlation and super-resolution processing of echo signals and multipath signals. The proposed method does not need to construct a weighting matrix, and can make full use of the received data, enhance the signal components in the equivalent spatial smoothing matrix, reduce the impact of noise, and improve the resolution of coherent sources. The simulation results show that the weighted spatial smoothing method proposed in this paper is correct and effective.
First discovery of charcoal-based prehistoric cave art in Dordogne
Authors: Reiche Ina , Coquinot Yvan , Trosseau Antoine , Maigret Anne 
Published: December 2023

AbstractArchaeologists have long been puzzled by the exact age of Paleolithic cave art in Europe especially in the Franco-Cantabrian region with hundreds of decorated caves because the creation of this parietal art (paintings, drawings and engravings) is closely tied to the appearance of first modern humans in Europe and their ways of life. The Dordogne region, one of the richest regions in terms of Paleolithic cave art in the world with more than 200 cave sites, is currently known to provide figures of cave art solely made with mineral coloring matters that cannot be dated directly. Using in-situ non-invasive Raman spectroscopy combined with portable X-ray fluorescence analysis as well as visible and infrared imaging of the decor of the Font-de-Gaume cave, we show the presence of a large number of charcoal-based Paleolithic figures besides others made of iron and manganese oxides in the main galleries for the first time. The creation periods of the cave art at Font-de-Gaume are mainly attributed to the Magdalenian period and probably more complicated constituted of at least two creation phases than commonly established as shown by the direct or partial superimposition of carbon-based and iron- and/or manganese-based figures. Our new results contribute to a better understanding of the organisation of the ornamentation and thus of the imaginary language of our Prehistoric ancestors. The discovery opens new research possibilities for re-reading of the complex panels and absolute radiocarbon dating.