bluuebunny/crossref_metadata_2025 huggingface dataset:
Bipolar androgen therapy plus nivolumab for patients with metastatic castration-resistant prostate cancer: the COMBAT phase II trial
Authors: Markowski Mark C. , Taplin Mary-Ellen , Aggarwal Rahul , Sena Laura A. , Wang Hao , Qi Hanfei , Lalji Aliya , Sinibaldi Victoria , Carducci Michael A. , Paller Channing J. , Marshall Catherine H. , Eisenberger Mario A. , Sanin David E. , Yegnasubramanian Srinivasan , Gomes-Alexandre Carolina , Ozbek Busra , Jones Tracy , De Marzo Angelo M. , Denmeade Samuel R. , Antonarakis Emmanuel S.
Published: January 2024

Cyclic high-dose testosterone administration, known as bipolar androgen therapy (BAT), is a treatment strategy for patients with metastatic castration-resistant prostate cancer (mCRPC). Here, we report the results of a multicenter, single arm Phase 2 study (NCT03554317) enrolling 45 patients with heavily pretreated mCRPC who received BAT (testosterone cypionate, 400 mg intramuscularly every 28 days) with the addition of nivolumab (480 mg intravenously every 28 days) following three cycles of BAT monotherapy. The primary endpoint of a confirmed PSA50 response rate was met and estimated at 40% (N = 18/45, 95% CI: 25.7–55.7%, P = 0.02 one-sided against the 25% null hypothesis). Sixteen of the PSA50 responses were achieved before the addition of nivolumab. Secondary endpoints included objective response rate (ORR), median PSA progression-free survival, radiographic progression-free survival (rPFS), overall survival (OS), and safety/tolerability. The ORR was 24% (N = 10/42). Three of the objective responses occurred following the addition of nivolumab. After a median follow-up of 17.9 months, the median rPFS was 5.6 (95% CI: 5.4–6.8) months, and median OS was 24.4 (95% CI: 17.6–31.1) months. BAT/nivolumab was well tolerated, resulting in only five (11%) drug related, grade-3 adverse events. In a predefined exploratory analysis, clinical response rates correlated with increased baseline levels of intratumoral PD-1 + T cells. In paired metastatic tumor biopsies, BAT induced pro-inflammatory gene expression changes that were restricted to patients achieving a clinical response. These data suggest that BAT may augment antitumor immune responses that are further potentiated by immune checkpoint blockade.
Behavioral consequences of second-person pronouns in written communications between authors and reviewers of scientific papers
Authors: Sun Zhuanlan , Cao C. Clark , Liu Sheng , Li Yiwei , Ma Chao
Published: January 2024

Pronoun usage’s psychological underpinning and behavioral consequence have fascinated researchers, with much research attention paid to second-person pronouns like “you,” “your,” and “yours.” While these pronouns’ effects are understood in many contexts, their role in bilateral, dynamic conversations (especially those outside of close relationships) remains less explored. This research attempts to bridge this gap by examining 25,679 instances of peer review correspondence with Nature Communications using the difference-in-differences method. Here we show that authors addressing reviewers using second-person pronouns receive fewer questions, shorter responses, and more positive feedback. Further analyses suggest that this shift in the review process occurs because “you” (vs. non-“you”) usage creates a more personal and engaging conversation. Employing the peer review process of scientific papers as a backdrop, this research reveals the behavioral and psychological effects that second-person pronouns have in interactive written communications.
Ultrashort vertical-channel MoS2 transistor using a self-aligned contact
Authors: Liu Liting , Chen Yang , Chen Long , Xie Biao , Li Guoli , Kong Lingan , Tao Quanyang , Li Zhiwei , Yang Xiaokun , Lu Zheyi , Ma Likuan , Lu Donglin , Yang Xiangdong , Liu Yuan
Published: January 2024

Two-dimensional (2D) semiconductors hold great promises for ultra-scaled transistors. In particular, the gate length of MoS2 transistor has been scaled to 1 nm and 0.3 nm using single wall carbon nanotube and graphene, respectively. However, simultaneously scaling the channel length of these short-gate transistor is still challenging, and could be largely attributed to the processing difficulties to precisely align source-drain contact with gate electrode. Here, we report a self-alignment process for realizing ultra-scaled 2D transistors. By mechanically folding a graphene/BN/MoS2 heterostructure, source-drain metals could be precisely aligned around the folded edge, and the channel length is only dictated by heterostructure thickness. Together, we could realize sub-1 nm gate length and sub-50 nm channel length for vertical MoS2 transistor simultaneously. The self-aligned device exhibits on-off ratio over 105 and on-state current of 250 μA/μm at 4 V bias, which is over 40 times higher compared to control sample without self-alignment process.
Membrane transformations of fusion and budding
Authors: Wu Ling-Gang , Chan Chung Yu
Published: January 2024

Membrane fusion and budding mediate fundamental processes like intracellular trafficking, exocytosis, and endocytosis. Fusion is thought to open a nanometer-range pore that may subsequently close or dilate irreversibly, whereas budding transforms flat membranes into vesicles. Reviewing recent breakthroughs in real-time visualization of membrane transformations well exceeding this classical view, we synthesize a new model and describe its underlying mechanistic principles and functions. Fusion involves hemi-to-full fusion, pore expansion, constriction and/or closure while fusing vesicles may shrink, enlarge, or receive another vesicle fusion; endocytosis follows exocytosis primarily by closing Ω-shaped profiles pre-formed through the flat-to-Λ-to-Ω-shape transition or formed via fusion. Calcium/SNARE-dependent fusion machinery, cytoskeleton-dependent membrane tension, osmotic pressure, calcium/dynamin-dependent fission machinery, and actin/dynamin-dependent force machinery work together to generate fusion and budding modes differing in pore status, vesicle size, speed and quantity, controls release probability, synchronization and content release rates/amounts, and underlies exo-endocytosis coupling to maintain membrane homeostasis. These transformations, underlying mechanisms, and functions may be conserved for fusion and budding in general.
Innate immune and proinflammatory signals activate the Hippo pathway via a Tak1-STRIPAK-Tao axis
Authors: Yang Yinan , Zhou Huijing , Huang Xiawei , Wu Chengfang , Zheng Kewei , Deng Jingrong , Zheng Yonggang , Wang Jiahui , Chi Xiaofeng , Ma Xianjue , Pan Huimin , Shen Rui , Pan Duojia , Liu Bo
Published: January 2024

The Hippo pathway controls developmental, homeostatic and regenerative tissue growth, and is frequently dysregulated in various diseases. Although this pathway can be activated by innate immune/inflammatory stimuli, the underlying mechanism is not fully understood. Here, we identify a conserved signaling cascade that leads to Hippo pathway activation by innate immune/inflammatory signals. We show that Tak1, a key kinase in innate immune/inflammatory signaling, activates the Hippo pathway by inducing the lysosomal degradation of Cka, an essential subunit of the STRIPAK PP2A complex that suppresses Hippo signaling. Suppression of STRIPAK results in the activation of Hippo pathway through Tao-Hpo signaling. We further show that Tak1-mediated Hippo signaling is involved in processes ranging from cell death to phagocytosis and innate immune memory. Our findings thus reveal a molecular connection between innate immune/inflammatory signaling and the evolutionally conserved Hippo pathway, thus contributing to our understanding of infectious, inflammatory and malignant diseases.
ApoL6 associates with lipid droplets and disrupts Perilipin1-HSL interaction to inhibit lipolysis
Authors: Wang Yuhui , Nguyen Hai P. , Xue Pengya , Xie Ying , Yi Danielle , Lin Frances , Dinh Jennie , Viscarra Jose A. , Ibe Nnejiuwa U. , Duncan Robin E. , Sul Hei S.
Published: January 2024

Adipose tissue stores triacylglycerol (TAG) in lipid droplets (LD) and release fatty acids upon lipolysis during energy shortage. We identify ApoL6 as a LD-associated protein mainly found in adipose tissue, specifically in adipocytes. ApoL6 expression is low during fasting but induced upon feeding. ApoL6 knockdown results in smaller LD with lower TAG content in adipocytes, while ApoL6 overexpression causes larger LD with higher TAG content. We show that the ApoL6 affects adipocytes through inhibition of lipolysis. While ApoL6, Perilipin 1 (Plin1), and HSL can form a complex on LD, C-terminal ApoL6 directly interacts with N-terminal Plin1 to prevent Plin1 binding to HSL, to inhibit lipolysis. Thus, ApoL6 ablation decreases white adipose tissue mass, protecting mice from diet-induced obesity, while ApoL6 overexpression in adipose brings obesity and insulin resistance, making ApoL6 a potential future target against obesity and diabetes.
A stabilization rule for metal carbido cluster bearing μ3-carbido single-atom-ligand encapsulated in carbon cage
Authors: Guan Runnan , Huang Jing , Xin Jinpeng , Chen Muqing , Du Pingwu , Li Qunxiang , Tan Yuan-Zhi , Yang Shangfeng , Xie Su-Yuan
Published: January 2024

Metal carbido complexes bearing single-carbon-atom ligand such as nitrogenase provide ideal models of adsorbed carbon atoms in heterogeneous catalysis. Trimetallic μ3-carbido clusterfullerenes found recently represent the simplest metal carbido complexes with the ligands being only carbon atoms, but only few are crystallographically characterized, and its formation prerequisite is unclear. Herein, we synthesize and isolate three vanadium-based μ3-CCFs featuring V = C double bonds and high valence state of V (+4), including VSc2C@Ih(7)-C80, VSc2C@D5h(6)-C80 and VSc2C@D3h(5)-C78. Based on a systematic theoretical study of all reported μ3-carbido clusterfullerenes, we further propose a supplemental Octet Rule, i.e., an eight-electron configuration of the μ3-carbido ligand is needed for stabilization of metal carbido clusters within μ3-carbido clusterfullerenes. Distinct from the classic Effective Atomic Number rule based on valence electron count of metal proposed in the 1920s, this rule counts the valence electrons of the single-carbon-atom ligand, and offers a general rule governing the stabilities of μ3-carbido clusterfullerenes.
Overcoming therapeutic resistance in oncolytic herpes virotherapy by targeting IGF2BP3-induced NETosis in malignant glioma
Authors: Dai Weiwei , Tian Ruotong , Yu Liubing , Bian Shasha , Chen Yuling , Yin Bowen , Luan Yuxuan , Chen Siqi , Fan Zhuoyang , Yan Rucheng , Pan Xin , Hou Yingyong , Li Rong , Chen Juxiang , Shu Minfeng
Published: January 2024

Oncolytic virotherapy holds promise for cancer treatment, but the factors determining its oncolytic activity remain unclear. Neutrophil extracellular traps (NETs) are associated with cancer progression, yet their formation mechanism and role in oncolytic virotherapy remain elusive. In this study, we demonstrate that, in glioma, upregulation of IGF2BP3 enhances the expression of E3 ubiquitin protein ligase MIB1, promoting FTO degradation via the ubiquitin-proteasome pathway. This results in increased m6A-mediated CSF3 release and NET formation. Oncolytic herpes simplex virus (oHSV) stimulates IGF2BP3-induced NET formation in malignant glioma. In glioma models in female mice, a BET inhibitor enhances the oncolytic activity of oHSV by impeding IGF2BP3-induced NETosis, reinforcing virus replication through BRD4 recruitment with the CDK9/RPB-1 complex to HSV gene promoters. Our findings unveil the regulation of m6A-mediated NET formation, highlight oncolytic virus-induced NETosis as a critical checkpoint hindering oncolytic potential, and propose targeting NETosis as a strategy to overcome resistance in oncolytic virotherapy.
Vitamin C-induced CO2 capture enables high-rate ethylene production in CO2 electroreduction
Authors: Kim Jongyoun , Lee Taemin , Jung Hyun Dong , Kim Minkyoung , Eo Jungsu , Kang Byeongjae , Jung Hyeonwoo , Park Jaehyoung , Bae Daewon , Lee Yujin , Park Sojung , Kim Wooyul , Back Seoin , Lee Youngu , Nam Dae-Hyun
Published: January 2024

High-rate production of multicarbon chemicals via the electrochemical CO2 reduction can be achieved by efficient CO2 mass transport. A key challenge for C−C coupling in high-current-density CO2 reduction is how to promote *CO formation and dimerization. Here, we report molecularly enhanced CO2-to-*CO conversion and *CO dimerization for high-rate ethylene production. Nanoconfinement of ascorbic acid by graphene quantum dots enables immobilization and redox reversibility of ascorbic acid in heterogeneous electrocatalysts. Cu nanowire with ascorbic acid nanoconfined by graphene quantum dots (cAA-CuNW) demonstrates high-rate ethylene production with a Faradaic efficiency of 60.7% and a partial current density of 539 mA/cm2, a 2.9-fold improvement over that of pristine CuNW. Furthermore, under low CO2 ratio of 33%, cAA-CuNW still exhibits efficient ethylene production with a Faradaic efficiency of 41.8%. We find that cAA-CuNW increases *CO coverage and optimizes the *CO binding mode ensemble between atop and bridge for efficient C−C coupling. A mechanistic study reveals that ascorbic acid can facilitate *CO formation and dimerization by favorable electron and proton transfer with strong hydrogen bonding.
Increased Asian aerosols drive a slowdown of Atlantic Meridional Overturning Circulation
Authors: Liu Fukai , Li Xun , Luo Yiyong , Cai Wenju , Lu Jian , Zheng Xiao-Tong , Kang Sarah M. , Wang Hai , Zhou Lei
Published: January 2024

Observational evidence and climate model experiments suggest a slowdown of the Atlantic Meridional Overturning Circulation (AMOC) since the mid-1990s. Increased greenhouse gases and the declined anthropogenic aerosols (AAs) over North America and Europe are believed to contribute to the AMOC slowdown. Asian AAs continue to increase but the associated impact has been unclear. Using ensembles of climate simulations, here we show that the radiative cooling resulting from increased Asian AAs drives an AMOC reduction. The increased AAs over Asia generate circumglobal stationary Rossby waves in the northern midlatitudes, which shift the westerly jet stream southward and weaken the subpolar North Atlantic westerlies. Consequently, reduced transport of cold air from North America hinders water mass transformation in the Labrador Sea and thus contributes to the AMOC slowdown. The link between increased Asian AAs and an AMOC slowdown is supported by different models with different configurations. Thus, reducing emissions of Asian AAs will not only lower local air pollution, but also help stabilize the AMOC.
Role of UPF1-LIN28A interaction during early differentiation of pluripotent stem cells
Authors: Jung Seungwon , Ko Seung Hwan , Ahn Narae , Lee Jinsam , Park Chang-Hwan , Hwang Jungwook
Published: January 2024

UPF1 and LIN28A are RNA-binding proteins involved in post-transcriptional regulation and stem cell differentiation. Most studies on UPF1 and LIN28A have focused on the molecular mechanisms of differentiated cells and stem cell differentiation, respectively. We reveal that LIN28A directly interacts with UPF1 before UPF1-UPF2 complexing, thereby reducing UPF1 phosphorylation and inhibiting nonsense-mediated mRNA decay (NMD). We identify the interacting domains of UPF1 and LIN28A; moreover, we develop a peptide that impairs UPF1-LIN28A interaction and augments NMD efficiency. Transcriptome analysis of human pluripotent stem cells (hPSCs) confirms that the levels of NMD targets are significantly regulated by both UPF1 and LIN28A. Inhibiting the UPF1-LIN28A interaction using a CPP-conjugated peptide promotes spontaneous differentiation by repressing the pluripotency of hPSCs during proliferation. Furthermore, the UPF1-LIN28A interaction specifically regulates transcripts involved in ectodermal differentiation. Our study reveals that transcriptome regulation via the UPF1-LIN28A interaction in hPSCs determines cell fate.
Understanding the light induced hydrophilicity of metal-oxide thin films
Authors: Deshpande Rucha Anil , Navne Jesper , Adelmark Mathias Vadmand , Shkondin Evgeniy , Crovetto Andrea , Hansen Ole , Bachmann Julien , Taboryski Rafael
Published: January 2024

Photocatalytic effects resulting in water splitting, reduction of carbon dioxide to fuels using solar energy, decomposition of organic compounds, and light-induced hydrophilicity observed on surfaces of various metal oxides (MOx), all rely on the same basic physical mechanisms, and have attracted considerable interest over the past decades. TiO2 and ZnO, two natively n-type doped wide bandgap semiconductors exhibit the effects mentioned above. In this study we propose a model for the photo-induced hydrophilicity in MOx films, and we test the model for TiO2/Si and ZnO/Si heterojunctions. Experimentally, we employ a wet exposure technique whereby the MOx surface is exposed to UV light while a water droplet is sitting on the surface, which allows for a continuous recording of contact angles during illumination. The proposed model and the experimental techniques allow a determination of minority carrier diffusion lengths by contact angle measurements and suggest design rules for materials exhibiting photocatalytic hydrophilicity. We expect that this methodology can be extended to improve our physical understanding of other photocatalytic surface effects.
Prefrontal signals precede striatal signals for biased credit assignment in motivational learning biases
Authors: Algermissen Johannes , Swart Jennifer C. , Scheeringa René , Cools Roshan , den Ouden Hanneke E. M.
Published: January 2024

Actions are biased by the outcomes they can produce: Humans are more likely to show action under reward prospect, but hold back under punishment prospect. Such motivational biases derive not only from biased response selection, but also from biased learning: humans tend to attribute rewards to their own actions, but are reluctant to attribute punishments to having held back. The neural origin of these biases is unclear. Specifically, it remains open whether motivational biases arise primarily from the architecture of subcortical regions or also reflect cortical influences, the latter being typically associated with increased behavioral flexibility and control beyond stereotyped behaviors. Simultaneous EEG-fMRI allowed us to track which regions encoded biased prediction errors in which order. Biased prediction errors occurred in cortical regions (dorsal anterior and posterior cingulate cortices) before subcortical regions (striatum). These results highlight that biased learning is not a mere feature of the basal ganglia, but arises through prefrontal cortical contributions, revealing motivational biases to be a potentially flexible, sophisticated mechanism.
Intrinsically stretchable light-emitting drawing displays
Authors: Zhang Jiaxue , Lu Qianying , Wu Ming , Sun Yuping , Wang Shaolei , Wang Xiaoliang , Lu Ming-Hui , Kong Desheng
Published: January 2024

Stretchable displays that combine light-emitting capabilities with mechanical compliance are essential building blocks of next-generation wearable electronics. However, their widespread applications are currently limited by complex device architecture, limited pixel density, and immature fabrication processes. In this study, we present the device design and material developments of intrinsically stretchable light-emitting drawing displays that can show arbitrary hand-drawing features. The alternating-current electroluminescent display uses a simplified architecture comprising coplanar interdigitated liquid metal electrodes, an electroluminescent layer, and a dielectric encapsulation layer. Ink patterns on the device are coupled with the interdigitated electrodes under alternating voltage stimulations, generating localized electric fields for bright emissions. Various inks are prepared for painting, stamping, and stencil printing. Arbitrary luminous features on the devices can be either long-lasting or transient in characteristics. These skin-like devices are made entirely of compliant materials that can withstand bending, twisting, and stretching manipulations. Due to the excellent mechanical deformability, the drawing displays can be conformally laminated on the skin as body-integrated optoelectronic communication devices for graphic information.
Quantifying quantum coherence of multiple-charge states in tunable Josephson junctions
Authors: He Jiangbo , Pan Dong , Liu Mingli , Lyu Zhaozheng , Jia Zhongmou , Yang Guang , Zhu Shang , Liu Guangtong , Shen Jie , Shevchenko Sergey N. , Nori Franco , Zhao Jianhua , Lu Li , Qu Fanming
Published: January 2024

Coherence and tunneling play central roles in quantum phenomena. In a tunneling event, the time that a particle spends inside the barrier has been fiercely debated. This problem becomes more complex when tunneling repeatedly occurs back and forth, and when involving many particles. Here we report the measurement of the coherence time of various charge states tunneling in a nanowire-based tunable Josephson junction; including single charges, multiple charges, and Cooper pairs. We studied all the charge tunneling processes using Landau-Zener-Stückelberg-Majorana (LZSM) interferometry, and observed high-quality interference patterns under a microwave drive. In particular, the coherence time of the charge states tunneling back and forth was extracted from the interference fringes in Fourier space. In addition, our measurements show the break-up of Cooper pairs, from a macroscopic quantum coherent state to individual particle states. Besides the fundamental research interest, our results also establish LZSM interferometry as a powerful technique to explore the coherence time of charges in hybrid devices.
Choroid plexus volume enlargement in first-episode antipsychotic-naïve schizophrenia
Authors: Zeng Jiaxin , Zhang Tianwei , Tang Biqiu , Li Siyi , Yao Li , Bishop Jeffrey R. , Sweeney John A. , Li Zhenlin , Qiu Changjian , Gu Shi , Gong Qiyong , Zhang Wenjing , Lui Su
Published: January 2024

Investigation of the choroid plexus in schizophrenia has seen growing interest due to its role in the interaction between neuroinflammation and brain dysfunction. Most previous studies included treated and long-term ill patients, while antipsychotics and illness course might both affect the choroid plexus. Here, we recruited first-episode antipsychotic-naïve schizophrenia patients, performed high-resolution structural brain scan and manually extracted choroid plexus volume. Choroid plexus volume was compared between patients and healthy controls after controlling for age, sex and intracranial volume. Age and sex effects were examined on choroid plexus volume in patient and healthy control groups respectively. In patients, we also examined the correlation of choroid plexus volume with volume measures of cortical and subcortical gray matter, white matter, lateral ventricular as well as symptom severity and cognitive function. Schizophrenia patients showed significantly enlarged choroid plexus volume compared with healthy controls. Choroid plexus volume was positively correlated with age in only patient group and we found significantly larger choroid plexus volumes in males than females in both patient and healthy control groups, while the sex effects did not differ between groups. Choroid plexus volume was only found correlated with lateral ventricular volume among the brain volume measures. No significant correlation between choroid plexus volume and clinical ratings or cognitive performance was observed. Without potential confounding effects of pharmacotherapy or illness course, our findings indicated the enlargement of choroid plexus in schizophrenia might be an enduring trait for schizophrenia.
Space charge governs the kinetics of metal exsolution
Authors: Weber Moritz L. , Šmíd Břetislav , Breuer Uwe , Rose Marc-André , Menzler Norbert H. , Dittmann Regina , Waser Rainer , Guillon Olivier , Gunkel Felix , Lenser Christian
Published: January 2024

Nanostructured composite electrode materials play a major role in the fields of catalysis and electrochemistry. The self-assembly of metallic nanoparticles on oxide supports via metal exsolution relies on the transport of reducible dopants towards the perovskite surface to provide accessible catalytic centres at the solid–gas interface. At surfaces and interfaces, however, strong electrostatic gradients and space charges typically control the properties of oxides. Here we reveal that the nature of the surface–dopant interaction is the main determining factor for the exsolution kinetics of nickel in SrTi0.9Nb0.05Ni0.05O3–δ. The electrostatic interaction of dopants with surface space charge regions forming upon thermal oxidation results in strong surface passivation, which manifests in a retarded exsolution response. We furthermore demonstrate the controllability of the exsolution response via engineering of the perovskite surface chemistry. Our findings indicate that tailoring the electrostatic gradients at the perovskite surface is an essential step to improve exsolution-type materials in catalytic converters.
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data
Authors: Zheng Wei , Wuyun Qiqige , Li Yang , Zhang Chengxin , Freddolino Lydia , Zhang Yang
Published: January 2024

Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single- and multichain multiple-sequence alignment (MSA) construction. Large-scale benchmarks show that DeepMSA2 MSAs can remarkably increase the accuracy of protein tertiary and quaternary structure predictions compared with current state-of-the-art methods. An integrated pipeline with DeepMSA2 participated in the most recent CASP15 experiment and created complex structural models with considerably higher quality than the AlphaFold2-Multimer server (v.2.2.0). Detailed data analyses show that the major advantage of DeepMSA2 lies in its balanced alignment search and effective model selection, and in the power of integrating huge metagenomics databases. These results demonstrate a new avenue to improve deep learning protein structure prediction through advanced MSA construction and provide additional evidence that optimization of input information to deep learning-based structure prediction methods must be considered with as much care as the design of the predictor itself.
Labeled temperate hardwood tree stomatal image datasets from seven taxa of Populus and 17 hardwood species
Authors: Wang Jiaxin , Renninger Heidi J. , Ma Qin
Published: January 2024

Machine learning (ML) algorithms have shown potential in automatically detecting and measuring stomata. However, ML algorithms require substantial data to efficiently train and optimize models, but their potential is restricted by the limited availability and quality of stomatal images. To overcome this obstacle, we have compiled a collection of around 11,000 unique images of temperate broadleaf angiosperm tree leaf stomata from various projects conducted between 2015 and 2022. The dataset includes over 7,000 images of 17 commonly encountered hardwood species, such as oak, maple, ash, elm, and hickory, and over 3,000 images of 55 genotypes from seven Populus taxa. Inner_guard_cell_walls and whole_stomata (stomatal aperture and guard cells) were labeled and had a corresponding YOLO label file that can be converted into other annotation formats. With the use of our dataset, users can (1) employ state-of-the-art machine learning models to identify, count, and quantify leaf stomata; (2) explore the diverse range of stomatal characteristics across different types of hardwood trees; and (3) develop new indices for measuring stomata.
A dataset of digital holograms of normal and thalassemic cells
Authors: Abbasian Vahid , Darafsheh Arash
Published: January 2024

Digital holographic microscopy (DHM) is an intriguing medical diagnostic tool due to its label-free and quantitative nature, providing high-contrast images of phase samples. By capturing both intensity and phase information, DHM enables the numerical reconstruction of quantitative phase images. However, the lateral resolution is limited by the diffraction limit, which prompted the recent suggestion of microsphere-assisted DHM to enhance the DHM resolution straightforwardly. The use of such a technique as a medical diagnostic tool requires testing and validation of the proposed assays to prove their feasibility and viability. This paper publishes 760 and 609 microsphere-assisted DHM images of normal and thalassemic red blood cells obtained from a normal and thalassemic male individual, respectively.
PatagoniaMet: A multi-source hydrometeorological dataset for Western Patagonia
Authors: Aguayo Rodrigo , León-Muñoz Jorge , Aguayo Mauricio , Baez-Villanueva Oscar Manuel , Zambrano-Bigiarini Mauricio , Fernández Alfonso , Jacques-Coper Martin
Published: January 2024

Western Patagonia (40–56°S) is a clear example of how the systematic lack of publicly available data and poor quality control protocols have hindered further hydrometeorological studies. To address these limitations, we present PatagoniaMet (PMET), a compilation of ground-based hydrometeorological data (PMET-obs; 1950–2020), and a daily gridded product of precipitation and temperature (PMET-sim; 1980–2020). PMET-obs was developed considering a 4-step quality control process applied to 523 hydrometeorological time series obtained from eight institutions in Chile and Argentina. Following current guidelines for hydrological datasets, several climatic and geographic attributes were derived for each catchment. PMET-sim was developed using statistical bias correction procedures, spatial regression models and hydrological methods, and was compared against other bias-corrected alternatives using hydrological modelling. PMET-sim was able to achieve Kling-Gupta efficiencies greater than 0.7 in 72% of the catchments, while other alternatives exceeded this threshold in only 50% of the catchments. PatagoniaMet represents an important milestone in the availability of hydro-meteorological data that will facilitate new studies in one of the largest freshwater ecosystems in the world.
A publicly available newborn ear shape dataset for medical diagnosis of auricular deformities
Authors: Ren Liu-Jie , Luo Fei , Yang Zhi-Wei , Chen Li-Li , Wang Xin-Yue , Li Chen-Long , Xie You-Zhou , Wang Ji-Mei , Zhang Tian-Yu , Wang Shuo , Fu Yao-Yao
Published: January 2024

Early and accurate diagnosis of ear deformities in newborns is crucial for an effective non-surgical correction treatment, since this commonly seen ear anomalies would affect aesthetics and cause mental problems if untreated. It is not easy even for experienced physicians to diagnose the auricular deformities of newborns and the classification of the sub-types, because of the rich bio-metric features embedded in the ear shape. Machine learning has already been introduced to analyze the auricular shape. However, there is little publicly available datasets of ear images from newborns. We released a dataset that contains quality-controlled photos of 3,852 ears from 1,926 newborns. The dataset also contains medical diagnosis of the ear shape, and the health data of each newborn and its mother. Our aim is to provide a freely accessible dataset, which would facilitate researches related with ear anatomies, such as the AI-aided detection and classification of auricular deformities and medical risk analysis.
An annotated wing interferential pattern dataset of dipteran insects of medical interest for deep learning
Authors: Cannet Arnaud , Simon-chane Camille , Histace Aymeric , Akhoundi Mohammad , Romain Olivier , Souchaud Marc , Jacob Pierre , Sereno Darian , Bousses Philippe , Sereno Denis
Published: January 2024

Several Diptera species are known to transmit pathogens of medical and veterinary interest. However, identifying these species using conventional methods can be time-consuming, labor-intensive, or expensive. A computer vision-based system that uses Wing interferential patterns (WIPs) to identify these insects could solve this problem. This study introduces a dataset for training and evaluating a recognition system for dipteran insects of medical and veterinary importance using WIPs. The dataset includes pictures of Culicidae, Calliphoridae, Muscidae, Tabanidae, Ceratopogonidae, and Psychodidae. The dataset is complemented by previously published datasets of Glossinidae and some Culicidae members. The new dataset contains 2,399 pictures of 18 genera, with each genus documented by a variable number of species and annotated as a class. The dataset covers species variation, with some genera having up to 300 samples.
Open source and reproducible and inexpensive infrastructure for data challenges and education
Authors: DeWitt Peter E. , Rebull Margaret A. , Bennett Tellen D.
Published: January 2024

Data sharing is necessary to maximize the actionable knowledge generated from research data. Data challenges can encourage secondary analyses of datasets. Data challenges in biomedicine often rely on advanced cloud-based computing infrastructure and expensive industry partnerships. Examples include challenges that use Google Cloud virtual machines and the Sage Bionetworks Dream Challenges platform. Such robust infrastructures can be financially prohibitive for investigators without substantial resources. Given the potential to develop scientific and clinical knowledge and the NIH emphasis on data sharing and reuse, there is a need for inexpensive and computationally lightweight methods for data sharing and hosting data challenges. To fill that gap, we developed a workflow that allows for reproducible model training, testing, and evaluation. We leveraged public GitHub repositories, open-source computational languages, and Docker technology. In addition, we conducted a data challenge using the infrastructure we developed. In this manuscript, we report on the infrastructure, workflow, and data challenge results. The infrastructure and workflow are likely to be useful for data challenges and education.
East Australian Current velocity, temperature and salinity data products
Authors: Sloyan Bernadette M. , Cowley Rebecca , Chapman Christopher C.
Published: January 2024

The East Australian Current (EAC) is the complex, highly energetic western boundary current that flows along the east coast of Australia. The EAC and its associated turbulent eddies dominate the marine climate of the Coral and Tasman Seas and the eastern Australian continental shelf. Here we present a series of consistent EAC data products that combines in situ temperature, salinity and velocity observations from the Australian Integrated Marine Observing System (IMOS) and Commonwealth Scientific and Industrial Research Organisation (CSIRO) EAC mooring array and North Stradbroke Island reference site. The EAC data products are produced from over 1000 individual instrument files collected during six 18-month deployments in the East Australian Current (EAC) off Brisbane, Australia at 27 °S between 2012–2022. The mooring individual instrument files are combined, interpolated onto a common vertical, temporal (hourly and daily) and spatial grid. The ITCOMPSOM method is used to fill missing data in the time series. These data product can be used to investigate intra- and interannual EAC variability and boundary current dynamics.
Faunal remains data from Paleolithic-early Iron Age archaeological sites in the Qinghai-Tibet Plateau in China
Authors: Ren Kaidi , Ren Lele
Published: January 2024

According to published archaeological sources, zooarchaeological data collection on the Qinghai-Tibet Plateau and its marginal and transitional areas is inadequate, and relevant datasets have not been published. For this reason, we collected and collated relevant information. Our database provides the geographical location, elevation, cultural type and faunal assemblage of each site on the Qinghai-Tibet Plateau and its periphery for which zooarchaeological data have been published from the Paleolithic to the Early Iron Age. The patterns of human faunal resource use, habitat patterns, and animal abundance and spatial distribution on the Qinghai-Tibet Plateau and its surrounding areas during the Prehistoric-Early Iron Age are represented in this dataset. The data provide a reference for further understanding prehistoric-early Iron Age human behavior, subsistence patterns and material and cultural exchanges between East and West on the Qinghai-Tibet Plateau and its environs.
Prediction model of spontaneous combustion risk of extraction borehole based on PSO-BPNN and its application
Authors: Wang Wei , Liang Ran , Qi Yun , Cui Xinchao , Liu Jiao
Published: January 2024

The feasibility and accuracy of the risk prediction of gas extraction borehole spontaneous combustion is improved to avoid the occurrence of spontaneous combustion in the gas extraction borehole. A gas extraction borehole spontaneous combustion risk prediction model (PSO-BPNN model) coupling the PSO algorithm with BP neural network is established through improving the connection weight and threshold values of BP neural network by the particle swarm optimization (PSO) algorithm. The prediction results of the PSO-BPNN model are compared and analyzed with that of the BP neural network model (BPNN model), GA-BPNN model, SSA-BPNN model and MPA-BPNN model. The results showed as follows: the average relative error of the PSO-BPNN model was 4.38%; the average absolute error was 0.0678; the root mean square error was 0.0934; and the determination coefficient was 0.9874. Compared with the BPNN model, the average relative error, average absolute error and root mean square error decreased by 9.35%, 0.1707 and 0.2056 respectively; and the determination coefficient increased by 0.1169. Compared with the GA-BPNN model, the average relative error, average absolute error and root mean square error decreased by 3.19%, 0.0602 and 0.0821 respectively; and the determination coefficient increased by 0.0320. Compared with the SSA-BPNN model, the average relative error, average absolute error and root mean square error decreased by 5.70%, 0.0820 and 0.1100 respectively; and the determination coefficient increased by 0.0474. Compared with the MPA-BPNN model, the average relative error, average absolute error and root mean square error decreased by 3.50%, 0.0861 and 0.1125 respectively; and the determination coefficient increased by 0.0488, proving that the PSO-BPNN model is more accurate than the BPNN model, GA-BPNN model, SSA-BPNN model and MPA-BPNN model as for prediction. When the PSO-BPNN model was applied to three extraction boreholes A, B, and C in a coal mine of Shanxi, the prediction results were better than the BPNN model, GA-BPNN model, SSA-BPNN model and MPA-BPNN model, proving the accuracy and stability of the PSO-BPNN model in predicting risk of borehole spontaneous combustion in other mine.
Diversity, habitat endemicity and trophic ecology of the fauna of Loki’s Castle vent field on the Arctic Mid-Ocean Ridge
Authors: Eilertsen Mari Heggernes , Kongsrud Jon Anders , Tandberg Anne Helene Solberg , Alvestad Tom , Budaeva Nataliya , Martell Luis , Ramalho Sofia P. , Falkenhaug Tone , Huys Rony , Oug Eivind , Bakken Torkild , Høisæter Tore , Rauch Cessa , Carvalho Francisca C. , Savchenko Alexandra S. , Ulvatn Tone , Kongshavn Katrine , Berntsen Cassandra Mari , Olsen Bernt Rydland , Pedersen Rolf Birger
Published: January 2024

Loki’s Castle Vent Field (LCVF, 2300 m) was discovered in 2008 and represents the first black-smoker vent field discovered on the Arctic Mid-Ocean Ridge (AMOR). However, a comprehensive faunal inventory of the LCVF has not yet been published, hindering the inclusion of the Arctic in biogeographic analyses of vent fauna. There is an urgent need to understand the diversity, spatial distribution and ecosystem function of the biological communities along the AMOR, which will inform environmental impact assesments of future deep-sea mining activities in the region. Therefore, our aim with this paper is to provide a comprehensive inventory of the fauna at LCVF and present a first insight into the food web of the vent community. The fauna of LCVF has a high degree of novelty, with five new species previously described and another ten new species awaiting formal description. Most of the new species from LCVF are either hydrothermal vent specialists or have been reported from other chemosynthesis-based ecosystems. The highest taxon richness is found in the diffuse venting areas and may be promoted by the biogenic habitat generated by the foundation species Sclerolinum contortum. The isotopic signatures of the vent community of LCVF show a clear influence of chemosynthetic primary production on the foodweb. Considering the novel and specialised fauna documented in this paper, hydrothermal vents on the AMOR should be regarded as vulnerable marine ecosystems and protective measures must therefore be implemented, especially considering the potential threat from resource exploration and exploitation activities in the near future.
Thermal and optical properties of P3HT:PC70BM:ZnO nanoparticles composite films
Authors: Hajduk B. , Jarka P. , Bednarski H. , Godzierz M. , Tański T. , Staszuk M. , Nitschke P. , Jarząbek B. , Fijalkowski M. , Mazik K.
Published: January 2024

The results of studies on the influence of zinc oxide nanoparticles (ZnO-NPs) on the structural, thermal and optical properties of thin films of mixtures of phenyl-C71-butyric acid methyl ester (PCBM) with poly[3-hexylthiophene] (P3HT) of various molecular weights are described in this article. The structural properties of the layers of: polymers, mixtures of polymers with fullerenes and their composites with ZnO-NPs were investigated using X-ray diffraction. Whereas their glass transition temperature and optical parameters have been determined by temperature-dependent spectroscopic ellipsometry. The presence of ZnO-NPs was also visible in the images of the surface of the composite layers obtained using scanning electron microscopy. These blends and composite films have also been used as the active layer in bulk heterojunction photovoltaic structures. The molecular weight of P3HT (Mw = 65.2; 54.2 and 34.1 kDa) and the addition of nanoparticles affected the power conversion efficiency (PCE) of the obtained solar cells. The determined PCE was the highest for the device prepared from the blend of P3HT:PCBM with the polymer of the lowest molecular weight. However, solar cells with ZnO-NPs present in their active layer had lower efficiency, although the open-circuit voltage and fill factor of almost all devices had the same values whether they contained ZnO-NPs or not. It is worth noting that thermal studies carried out using temperature-dependent ellipsometry showed a significant effect of the presence of ZnO-NPs on the value of the glass transition temperature, which was higher for composite films than for films made of a polymer-fullerene blend alone.
Analysis on determinants of carbon emissions from plaza ground paving during the construction stage based on life cycle assessment
Authors: Nie Huayue , Wang Lizhong , Tian Meirong
Published: January 2024

The carbon emissions of paving projects are the focus of urban managers and researchers. By introducing the life cycle assessment (LCA) method and drawing up the study time and boundary, this study analyzed the carbon emissions activities of the plaza ground paving project and established a computational model of the cast-in-place architectural concrete (CAC) and natural stone pavement’s life cycle during the construction stage by comprehensively utilizing the carbon emission coefficient method and the direct source consumption statistics method of the production line. Based on the model, this study employed the ground paving of a top-notch Theme Park Plaza in Beijing as a sample to calculate the carbon emissions of two different types of building materials at various phases of their life cycle and made a comparative evaluation. It is concluded that the carbon emissions (expressed in CO2) produced by the CAC ground in the sample area is 75.46 kg CO2/m2, while that of the natural stone pavement is 110.81 kg CO2/m2. Our results demonstrate significantly linear relationship between the overall emissions of carbon and the material carbon factor. This study adds to the body of knowledge by calculating the carbon emissions and determining the trend of carbon footprint for ground paving. Furthermore, the study's findings can be used to enhance construction management options and choose green materials. The findings can also be used to provide supporting theories for the development of regulations and carbon reduction policies based on constructing energy conservation and greenhouse gas reduction.
Morphological and vascular evidence of glaucomatous damage in myopic guinea pigs with scleral crosslinking
Authors: Guo Lei , Tao Jun , Guo Ziqi , Tong Yang , Chen Shichao , Zhao Xin , Hua Rui
Published: January 2024

Guinea pigs are often used as models for myopia studies. However, the imaging structure and vasculature of the optic nerve head (ONH) in guinea pigs are tentative. This study investigated morphological parameters and vascular characteristics of the ONH in guinea pigs with form deprivation (FD) myopia before and after scleral crosslinking (CXL), using optical coherence tomography (OCT) and OCT angiography (OCTA). Refractive error, axial length (AL), intraocular pressure (IOP), and OCT-based structural parameters of the ONH were measured at baseline and 3 weeks after the FD + CXL procedure in guinea pigs. The 88 guinea pigs analysed in this study were aged 3 (n = 29), 4 (n = 51), and 5 (n = 8) weeks. The IOP, AL, average and vertical cup-to-disc ratio (C/D), circumpapillary retinal nerve fibre layer, disc area, and cup volume increased at 3 weeks compared to baseline values (all p < 0.001). The refractive error and rim area decreased at 3 weeks compared to baseline values (all p < 0.001). After adjustment for age, IOP was correlated positively with average C/D (p = 0.039) and negatively with rim area (p = 0.009). The severity of blood signal defects was positively associated with the average C/D at 3 weeks (p = 0.027). These findings may facilitate further research on myopia using guinea pigs.
miR-199a/b-3p inhibits HCC cell proliferation and invasion through a novel compensatory signaling pathway DJ-1\Ras\PI3K/AKT
Authors: Ma Li-Na , Wu Li-Na , Liu Shuai wei , Zhang Xu , Luo Xia , Nawaz Shah , Ma Zi min , Ding Xiang-Chun
Published: January 2024

Several studies have reported the effects of DJ-1 gene and miR-199a/b-3p on HCC development. However, whether miR-199a/b-3p regulates HCC progression through a novel compensatory signaling pathway involving DJ-1, Ras, and PI3K/AKT remains unknown. We used (TCGA, HPA, miRWalk and Target scan) databases, cancer and para-tissue HCC patients, dual-luciferase reporter gene analysis, proteomic imprinting, qPCR, cell proliferation, scratch, transport, and flow cytometry to detect the molecular mechanism of DJ-1 and miR-199a/b-3p co-expression in HCC cell lines. Bioinformatics analysis showed that DJ-1 was highly expressed in HCC ((P < 0.001) were closely associated with tumor stage (T), portal vein vascular invasion, OS, DSS, and PFI (P < 0.05); miR-199a/b-3p was lowly expressed in HCC (P < 0.001), which was the upstream regulator of DJ-1. Spearman coefficient r = −0.113, P = 0.031; Dual luciferase gene report verified the negative targeting relationship between them P< 0.001; Western blotting demonstrated that miR-199a/b-3p could inhibit the protein expression of DJ-1, Ras and AKT(P < 0.05); The results of CCK8, cell scratch, Transwell migration and flow cytometry showed that OE + DJ-1 increased the proliferation, migration and invasion ability of HepG2 cells, and decreased the apoptosis process, and the differences were statistically significant (P < 0.05), while miR-199a/b-3p had the opposite effect (P < 0.05).