bluuebunny/crossref_metadata_2025 huggingface dataset:
Divergent immune microenvironments in two tumor nodules from a patient with mismatch repair-deficient prostate cancer
Authors: Bergom Hannah E. , Sena Laura A. , Day Abderrahman , Miller Benjamin , Miller Carly D. , Lozada John R. , Zorko Nicholas , Wang Jinhua , Shenderov Eugene , Lobo Francisco Pereira , Caramella-Pereira Fernanda , Marchionni Luigi , Drake Charles G. , Lotan Tamara , De Marzo Angelo M. , Hwang Justin , Antonarakis Emmanuel S.
Published: January 2024

Patients with prostate cancer (PC) generally do not respond favorably to immune checkpoint inhibitors, which may be due to a low abundance of tumor-infiltrating lymphocytes even when mutational load is high. Here, we identified a patient who presented with high-grade primary prostate cancer with two adjacent tumor nodules. While both nodules were mismatch repair-deficient (MMRd), exhibited pathogenicMSH2andMSH6alterations, had a high tumor mutational burden (TMB), and demonstrated high microsatellite instability (MSI), they had markedly distinct immune phenotypes. The first displayed a dense infiltrate of lymphocytes (“hot nodule”), while the second displayed significantly fewer infiltrating lymphocytes (“cold nodule”). Whole-exome DNA analysis found that both nodules shared many identical mutations, indicating that they were derived from a single clone. However, the cold nodule appeared to be sub-clonal relative to the hot nodule, suggesting divergent evolution of the cold nodule from the hot nodule. Whole-transcriptome RNA analysis found that the cold nodule demonstrated lower expression of genes related to antigen presentation (HLA) and, paradoxically, classical tumor immune tolerance markers such as PD-L1 (CD274) and CTLA-4. Immune cell deconvolution suggested that the hot nodule was enriched not only in CD8+ and CD4 + T lymphocytes, but also in M1 macrophages, activated NK cells, and γδ T cells compared to the cold nodule. This case highlights that MMRd/TMB-high PC can evolve to minimize an anti-tumor immune response, and nominates downregulation of antigen presentation machinery (HLA loss) as a potential mechanism of adaptive immune evasion in PC.
Theoretical guarantees for permutation-equivariant quantum neural networks
Authors: Schatzki Louis , Larocca Martín , Nguyen Quynh T. , Sauvage Frédéric , Cerezo M.
Published: January 2024

Despite the great promise of quantum machine learning models, there are several challenges one must overcome before unlocking their full potential. For instance, models based on quantum neural networks (QNNs) can suffer from excessive local minima and barren plateaus in their training landscapes. Recently, the nascent field of geometric quantum machine learning (GQML) has emerged as a potential solution to some of those issues. The key insight of GQML is that one should design architectures, such as equivariant QNNs, encoding the symmetries of the problem at hand. Here, we focus on problems with permutation symmetry (i.e., symmetry group Sn), and show how to build Sn-equivariant QNNs We provide an analytical study of their performance, proving that they do not suffer from barren plateaus, quickly reach overparametrization, and generalize well from small amounts of data. To verify our results, we perform numerical simulations for a graph state classification task. Our work provides theoretical guarantees for equivariant QNNs, thus indicating the power and potential of GQML.
Quantum LOSR networks cannot generate graph states with high fidelity
Authors: Wang Yi-Xuan , Xu Zhen-Peng , Gühne Otfried
Published: January 2024

Quantum networks lead to novel notions of locality and correlations and an important problem concerns the question of which quantum states can be experimentally prepared with a given network structure and devices and which not. We prove that all multi-qubit graph states arising from a connected graph cannot originate from any quantum network with bipartite sources, as long as feed-forward and quantum memories are not available. Moreover, the fidelity of a multi-qubit graph state and any network state cannot exceed 9/10. Similar results can also be established for a large class of multi-qudit graph states.
Inferring chemical disequilibrium biosignatures for Proterozoic Earth-like exoplanets
Authors: Young Amber V. , Robinson Tyler D. , Krissansen-Totton Joshua , Schwieterman Edward W. , Wogan Nicholas F. , Way Michael J. , Sohl Linda E. , Arney Giada N. , Reinhard Christopher T. , Line Michael R. , Catling David C. , Windsor James D.
Published: January 2024

Chemical disequilibrium quantified using the available free energy has previously been proposed as a potential biosignature. However, researchers remotely sensing exoplanet biosignatures have not yet investigated how observational uncertainties impact the ability to infer a life-generated available free energy. We pair an atmospheric retrieval tool to a thermodynamics model to assess the detectability of chemical disequilibrium signatures of Earth-like exoplanets, focusing on the Proterozoic eon when the atmospheric abundances of oxygen–methane disequilibrium pairs may have been relatively high. Retrieval model studies applied across a range of gas abundances revealed that order-of-magnitude constraints on the disequilibrium energy are achieved with simulated reflected-light observations for the high-abundance scenario and high signal-to-noise ratios (50), whereas weak constraints are found for moderate signal-to-noise ratios (20–30) and medium- to low-abundance cases. Furthermore, the disequilibrium-energy constraints are improved by using the modest thermal information encoded in water vapour opacities at optical and near-infrared wavelengths. These results highlight how remotely detecting chemical disequilibrium biosignatures can be a useful and metabolism-agnostic approach to biosignature detection.
Transnational conservation to anticipate future plant shifts in Europe
Authors: Chauvier-Mendes Yohann , Pollock Laura J. , Verburg Peter H. , Karger Dirk N. , Pellissier Loïc , Lavergne Sébastien , Zimmermann Niklaus E. , Thuiller Wilfried
Published: January 2024

To meet the COP15 biodiversity framework in the European Union (EU), one target is to protect 30% of its land by 2030 through a resilient transnational conservation network. The European Alps are a key hub of this network hosting some of the most extensive natural areas and biodiversity hotspots in Europe. Here we assess the robustness of the current European reserve network to safeguard the European Alps’ flora by 2080 using semi-mechanistic simulations. We first highlight that the current network needs strong readjustments as it does not capture biodiversity patterns as well as our conservation simulations. Overall, we predict a strong shift in conservation need through time along latitudes, and from lower to higher elevations as plants migrate upslope and shrink their distribution. While increasing species, trait and evolutionary diversity, migration could also threaten 70% of the resident flora. In the face of global changes, the future European reserve network will need to ensure strong elevation and latitudinal connections to complementarily protect multifaceted biodiversity beyond national borders.
Shoreline classification maps and ground truth data for the Neuse River Estuary, North Carolina
Authors: Sirianni Hannah , Richter Jessica , Sirianni Matthew J. , Pettyjohn Sarah
Published: January 2024

Estuaries provide essential ecosystem services and economic value but are facing widespread degradation due to changing anthropogenic and climatic factors. In North Carolina, coastal structures, like bulkheads and riprap, are widely used by property owners throughout the Albemarle-Pamlico estuary to stop erosion and reclaim lost land following storm events. While coastal development is tightly governed, limited historical and no up-to-date data report on the spatial distribution of coastal structures throughout the Albemarle-Pamlico estuary. Here we describe the development of a dataset that classifies and catalogues 67 km of shoreline type along the Neuse River Estuary (NRE), a large tributary of the Albemarle-Pamlico. We used available LiDAR digital elevation models (DEMs), aerial imagery, and a ground truthing field campaign to determine shoreline type present along the NRE as of 2020. We validated these results using an intensive manual editing procedure that comparatively examines DEMs, LiDAR derived slope, aerial imagery, and ground truth photography of the shoreline. This dataset is available for public download.
Molecular dynamics simulations of displacement cascades in LiAlO2 and LiAl5O8 ceramics
Authors: Roy Ankit , Casella Andrew M. , Senor David J. , Jiang Weilin , Devanathan Ram
Published: January 2024

Molecular dynamics was employed to investigate the radiation damage due to collision cascades in LiAlO2 and LiAl5O8, the latter being a secondary phase formed in the former during irradiation. Atomic displacement cascades were simulated by initiating primary knock-on atoms (PKA) with energy values = 5, 10 and 15 keV and the damage was quantified by the number of Frenkel pairs formed for each species: Li, Al and O. The primary challenges of modeling an ionic system with and without a core–shell model for oxygen atoms were addressed and new findings on the radiation resistance of these ceramics are presented. The working of a variable timestep function and the kinetics in the background of the simulations have been elaborated to highlight the novelty of the simulation approach. More importantly, the key results indicated that LiAlO2 experiences much more radiation damage than LiAl5O8, where the number of Li Frenkel pairs in LiAlO2 was 3–5 times higher than in LiAl5O8 while the number of Frenkel pairs for Al and O in LiAlO2 are ~ 2 times higher than in LiAl5O8. The primary reason is high displacement threshold energies (Ed) in LiAl5O8 for Li cations. The greater Ed for Li imparts higher resistance to damage during the collision cascade and thus inhibits amorphization in LiAl5O8. The presented results suggest that LiAl5O8 is likely to maintain structural integrity better than LiAlO2 in the irradiation conditions studied in this work.
A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison
Authors: Wehrenberg Gerrit , Tokarska Małgorzata , Cocchiararo Berardino , Nowak Carsten
Published: January 2024

The European bison was saved from the brink of extinction due to considerable conservation efforts since the early twentieth century. The current global population of > 9500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world’s first studbook of a threatened species.
Interaction of designed cationic antimicrobial peptides with the outer membrane of gram-negative bacteria
Authors: He Shelley , Deber Charles M.
Published: January 2024

The outer membrane (OM) is a hallmark feature of gram-negative bacteria that provides the species with heightened resistance against antibiotic threats while cationic antimicrobial peptides (CAPs) are natural antibiotics broadly recognized for their ability to disrupt bacterial membranes. It has been well-established that lipopolysaccharides present on the OM are among major targets of CAP activity against gram-negative species. Here we investigate how the relative distribution of charged residues along the primary peptide sequence, in conjunction with its overall hydrophobicity, affects such peptide-OM interactions in the natural CAP Ponericin W1. Using a designed peptide library derived from Ponericin W1, we determined that the consecutive placement of Lys residues at the peptide N- or C-terminus (ex. “PonN”: KKKKKKWLGSALIGALLPSVVGLFQ) enhances peptide binding affinity to OM lipopolysaccharides compared to constructs where Lys residues are interspersed throughout the primary sequence (ex. “PonAmp”: WLKKALKIGAKLLPSVVKLFKGSGQ). Antimicrobial activity against multidrug resistant strains of Pseudomonas aeruginosa was similarly found to be highest among Lys-clustered sequences. Our findings suggest that while native Ponericin W1 exerts its initial activity at the OM, Lys-clustering may be a promising means to enhance potency towards this interface, thereby augmenting peptide entry and activity at the IM, with apparent advantage against multidrug-resistant species.
Pneumonia detection based on RSNA dataset and anchor-free deep learning detector
Authors: Wu Linghua , Zhang Jing , Wang Yilin , Ding Rong , Cao Yueqin , Liu Guiqin , Liufu Changsheng , Xie Baowei , Kang Shanping , Liu Rui , Li Wenle , Guan Furen
Published: January 2024

Pneumonia is a highly lethal disease, and research on its treatment and early screening tools has received extensive attention from researchers. Due to the maturity and cost reduction of chest X-ray technology, and with the development of artificial intelligence technology, pneumonia identification based on deep learning and chest X-ray has attracted attention from all over the world. Although the feature extraction capability of deep learning is strong, existing deep learning object detection frameworks are based on pre-defined anchors, which require a lot of tuning and experience to guarantee their excellent results in the face of new applications or data. To avoid the influence of anchor settings in pneumonia detection, this paper proposes an anchor-free object detection framework and RSNA dataset based on pneumonia detection. First, a data enhancement scheme is used to preprocess the chest X-ray images; second, an anchor-free object detection framework is used for pneumonia detection, which contains a feature pyramid, two-branch detection head, and focal loss. The average precision of 51.5 obtained by Intersection over Union (IoU) calculation shows that the pneumonia detection results obtained in this paper can surpass the existing classical object detection framework, providing an idea for future research and exploration.
Open data for energy networks: introducing DAVE—a data fusion tool for automated network generation
Authors: Banze Tobias , Kneiske Tanja M.
Published: January 2024

Developing a sustainable energy system for the future requires new ways of planning and operating energy infrastructure. A large part of this involves suitable network models. Real network data is not available for research without restrictions since energy networks are part of the critical infrastructure. Using open datasets and expert rules to generate non-restricted models is one solution to this. This paper introduces open data for energy networks generated by the open-source software “DAVE”. The Python-based data fusion tool DAVE can automatically generate customized energy network models quickly and on demand. The software collects data from various databases and uses appropriate methods to fuse them. The current version of the tool can create GIS-based power networks and gas transportation networks, with output that is compatible with common network simulation software. Further developments are planned for creating thermal and gas distribution networks, as these are important for local heat power transition. Implementing a quality description for fused datasets will also be included in future development.
H∞ state estimation of continuous-time neural networks with uncertainties
Authors: Li Aiting , Chen Yanhui , Hu Yun , Liu Dazhi , Liu Jinhui
Published: January 2024

$$H_{\infty }$$

H
∞

state estimation is addressed for continuous-time neural networks in the paper. The norm-bounded uncertainties are considered in communication neural networks. For the considered neural networks with uncertainties, a reduced-order $$H_{\infty }$$

H
∞

state estimator is designed, which makes that the error dynamics is exponentially stable and has weighted $$H_{\infty }$$

H
∞

performance index by Lyapunov function method. Moreover, it is also given the devised method of the reduced-order $$H_{\infty }$$

H
∞

state estimator. Then, considering that sampling the output y(t) of the neural network at every moment will result in waste of excess resources, the event-triggered sampling strategy is used to solve the oversampling problem. In addition, a devised method is also given for the event-triggered reduced-order $$H_{\infty }$$

H
∞

state estimator. Finally, by the well-known Tunnel Diode Circuit example, it shows that a lower order state estimator can be designed under the premise of maintaining the same weighted $$H_{\infty }$$

H
∞

performance index, and using the event-triggered sampling method can reduce the computational and time costs and save communication resources.
Human amnion epithelial cell therapy reduces hypertension-induced vascular stiffening and cognitive impairment
Authors: Dinh Quynh Nhu , Lo Cecilia , Zhang David Wong , Tran Vivian , Gibson-Hughes Tayla , Sheriff Ashleigh , Diep Henry , Kim Hyun Ah , Zhang Shenpeng R. , Barreto-Arce Liz J. , Jelinic Maria , Vinh Antony , Arumugam Thiruma V. , Chan Siow Teng , Lim Rebecca , Drummond Grant R. , Sobey Christopher G. , De Silva T. Michael
Published: January 2024

Vascular inflammation and fibrosis are hallmarks of hypertension and contribute to the development of cardiovascular disease and cognitive impairment. However, current anti-hypertensive drugs do not treat the underlying tissue damage, such as inflammation-associated fibrosis. Human amnion epithelial cells have several properties amenable for treating vascular pathology. This study tested the effect of amnion epithelial cells on vascular pathology and cognitive impairment during hypertension. Male C57Bl6 mice (8–12 weeks) were administered vehicle (saline; n = 58) or angiotensin II (0.7 mg/kg/d, n = 56) subcutaneously for 14 d. After surgery, a subset of mice were injected with 106 amnion epithelial cells intravenously. Angiotensin II infusion increased systolic blood pressure, aortic pulse wave velocity, accumulation of aortic leukocytes, and aortic mRNA expression of collagen subtypes compared to vehicle-infused mice (n = 9–11, P < 0.05). Administration of amnion epithelial cells attenuated these effects of angiotensin II (P < 0.05). Angiotensin II-induced cognitive impairment was prevented by amnion epithelial cell therapy (n = 7–9, P < 0.05). In the brain, amnion epithelial cells modulated some of the inflammatory genes that angiotensin II promoted differential expression of (n = 6, p-adjusted < 0.05). These findings suggest that amnion epithelial cells could be explored as a potential therapy to inhibit vascular pathology and cognitive impairment during hypertension.
Drivers’ behavior confronting fixed and point-to-point speed enforcement camera: agent-based simulation and translation to crash relative risk change
Authors: Safavi-Naini Seyed Amir Ahmad , Sobhani Shayan , Malekpour Mohammad-Reza , Bhalla Kavi , Shahraz Saeid , Haghshenas Rosa , Ghamari Seyyed-Hadi , Abbasi-Kangevari Mohsen , Rezaei Nazila , Heydari Seyed Taghi , Rezaei Negar , Lankarani Kamran B. , Farzadfar Farshad
Published: January 2024

Utilizing a novel microsimulation approach, this study evaluates the impact of fixed and average point-to-point Speed Enforcement Cameras (SEC) on driving safety. Using the SUMO software, agent-based models for a 6-km highway without exits or obstacles were created. Telematics data from 93,160 trips were used to determine the desired free-flow speed. A total of 13,860 scenarios were simulated with 30 random seeds. The ratio of unsafe driving (RUD) is the spatial division of the total distance travelled at an unsafe speed by the total travel distance. The study compared different SEC implementations under different road traffic and community behaviours using the Power Model and calculated crash risk changes. Results showed that adding one or two fixed SECs reduced RUD by 0.20% (0.18–0.23) and 0.57% (0.54–0.59), respectively. However, average SECs significantly lowered RUD by 10.97% (10.95–10.99). Furthermore, a 1% increase in telematics enforcement decreased RUD by 0.22% (0.21–0.22). Point-to-point cameras effectively reduced crash risk in all implementation scenarios, with reductions ranging from − 3.44 to − 11.27%, pointing to their superiority as speed enforcement across various scenarios. Our cost-conscious and replicable approach can provide interim assessments of SEC effectiveness, even in low-income countries.
Role of membrane vesicles in the transmission of vancomycin resistance in Enterococcus faecium
Authors: Lehmkuhl Johanna , Schneider Julia Sophie , Werth Kari Lavinia vom , Scherff Natalie , Mellmann Alexander , Kampmeier Stefanie
Published: January 2024

Clonal transmission and horizontal gene transfer (HGT) contribute to the spread of vancomycin-resistant enterococci (VRE) in global healthcare. Our study investigated vesiduction, a HGT mechanism via membrane vesicles (MVs), for vanA and vanB genes that determine vancomycin resistance. We isolated MVs for VRE of different sequence types (STs) and analysed them by nanoparticle tracking analysis. Selected MV samples were subjected to DNA sequence analysis. In resistance transfer experiments, vancomycin-susceptible enterococci were exposed to MVs and bacterial supernatants of VRE. Compared to bacteria grown in lysogeny broth (MVs/LB), cultivation under vancomycin stress (MVs/VAN) resulted in increased particle concentrations of up to 139-fold (ST80). As a key finding, we could show that VRE isolates of ST80 and ST117 produced remarkably more vesicles at subinhibitory antibiotic concentrations (approx. 9.2 × 1011 particles/ml for ST80 and 2.4 × 1011 particles/ml for ST117) than enterococci of other STs (range between 1.8 × 1010 and 5.3 × 1010 particles/ml). In those MV samples, the respective resistance genes vanA and vanB were completely verifiable using sequence analysis. Nevertheless, no vancomycin resistance transfer via MVs to vancomycin-susceptible Enterococcus faecium was phenotypically detectable. However, our results outline the potential of future research on ST-specific MV properties, promising new insights into VRE mechanisms.
Investigating the importance of left atrial compliance on fluid dynamics in a novel mock circulatory loop
Authors: Meskin Masoud , Starkey Philip Alexander , Kaspersen Alexander Emil , Ringgaard Steffen , Sand Signe Gram , Nygaard Jens Vinge , Jensen Jørgen Arendt , Traberg Marie Sand , Johansen Peter
Published: January 2024

The left atrium (LA) hemodynamic indices hold prognostic value in various cardiac diseases and disorders. To understand the mechanisms of these conditions and to assess the performance of cardiac devices and interventions, in vitro models can be used to replicate the complex physiological interplay between the pulmonary veins, LA, and left ventricle. In this study, a comprehensive and adaptable in vitro model was created. The model includes a flexible LA made from silicone and allows distinct control over the systolic and diastolic functions of both the LA and left ventricle. The LA was mechanically matched with porcine LAs through expansion tests. Fluid dynamic measures were validated against the literature and pulmonary venous flows recorded on five healthy individuals using magnetic resonance flow imaging. Furthermore, the fluid dynamic measures were also used to construct LA pressure–volume loops. The in vitro pressure and flow recordings expressed a high resemblance to physiological waveforms. By decreasing the compliance of the LA, the model behaved realistically, elevating the a- and v-wave peaks of the LA pressure from 12 to 19 mmHg and 22 to 26 mmHg, respectively, while reducing the S/D ratio of the pulmonary venous flowrate from 1.5 to 0.3. This model provides a realistic platform and framework for developing and evaluating left heart procedures and interventions.
Impact of homeostatic body hydration status, evaluated by hemodynamic measures, on different pain sensitization paths to a chronic pain syndrome
Authors: Davydov Dmitry M. , de la Coba Pablo , Contreras-Merino Ana M. , Reyes del Paso Gustavo A.
Published: January 2024

Contrasting findings on the mechanisms of chronic pain and hypertension development render the current conventional evidence of a negative relationship between blood pressure (BP) and pain severity insufficient for developing personalized treatments. In this interdisciplinary study, patients with fibromyalgia (FM) exhibiting clinically normal or elevated BP, alongside healthy participants were assessed. Different pain sensitization responses were evaluated using a dynamic 'slowly repeated evoked pain' (SREP) measure, as well as static pain pressure threshold and tolerance measures. Cardiovascular responses to clino-orthostatic (lying-standing) challenges were also examined as acute re- and de-hydration events, challenging cardiovascular and cerebrovascular homeostasis. These challenges involve compensating effects from various cardiac preload or afterload mechanisms associated with different homeostatic body hydration statuses. Additionally, hair cortisol concentration was considered as a factor with an impact on chronic hydration statuses. Pain windup (SREP) and lower pain threshold in FM patients were found to be related to BP rise during clinostatic (lying) rehydration or orthostatic (standing) dehydration events, respectively. These events were determined by acute systemic vasoconstriction (i.e., cardiac afterload response) overcompensating for clinostatic or orthostatic cardiac preload under-responses (low cardiac output or stroke volume). Lower pain tolerance was associated with tonic blood pressure reduction, determined by permanent hypovolemia (low stroke volume) decompensated by permanent systemic vasodilation. In conclusion, the body hydration status profiles assessed by (re)activity of systemic vascular resistance and effective blood volume-related measures can help predict the risk and intensity of different pain sensitization components in chronic pain syndrome, facilitating a more personalized management approach.
Application of a long short-term memory neural network algorithm fused with Kalman filter in UWB indoor positioning
Authors: Tian Yalin , Lian Zengzeng , Wang Penghui , Wang Mengqi , Yue Zhe , Chai Huabin
Published: January 2024

Ultra-wideband technology has good anti-interference capabilities and development prospects in indoor positioning. Since ultra-wideband will be affected by random errors in indoor positioning, to exploit the advantages of the Kalman filter (KF) and the long short-term memory (LSTM) network, this paper proposes a long short-term memory neural network algorithm fused with the Kalman filter (KF–LSTM) to improve UWB positioning. First, the ultra-wideband data is processed through KF to weaken the noise in the data, and then the data is fed into the LSTM network for training, and the capability of the LSTM network to process time series features is employed to obtain more accurate label positions. Finally, simulation and measurement results show that the KF–LSTM algorithm achieves 71.31%, 37.28%, and 49.31% higher average positioning accuracy than the back propagation (BP) network, (back propagation network fused with the Kalman filter (KF-BP), and LSTM network algorithms, respectively, and the KF–LSTM algorithm performs more stably. Meanwhile, the more noise the data contains, the more obvious the stability contrast between the four algorithms.
An automated deep learning pipeline for EMVI classification and response prediction of rectal cancer using baseline MRI: a multi-centre study
Authors: Cai Lishan , Lambregts Doenja M. J. , Beets Geerard L. , Maas Monique , Pooch Eduardo H. P. , Guérendel Corentin , Beets-Tan Regina G. H. , Benson Sean
Published: January 2024

The classification of extramural vascular invasion status using baseline magnetic resonance imaging in rectal cancer has gained significant attention as it is an important prognostic marker. Also, the accurate prediction of patients achieving complete response with primary staging MRI assists clinicians in determining subsequent treatment plans. Most studies utilised radiomics-based methods, requiring manually annotated segmentation and handcrafted features, which tend to generalise poorly. We retrospectively collected 509 patients from 9 centres, and proposed a fully automated pipeline for EMVI status classification and CR prediction with diffusion weighted imaging and T2-weighted imaging. We applied nnUNet, a self-configuring deep learning model, for tumour segmentation and employed learned multiple-level image features to train classification models, named MLNet. This ensures a more comprehensive representation of the tumour features, in terms of both fine-grained detail and global context. On external validation, MLNet, yielding similar AUCs as internal validation, outperformed 3D ResNet10, a deep neural network with ten layers designed for analysing spatiotemporal data, in both CR and EMVI tasks. For CR prediction, MLNet showed better results than the current state-of-the-art model using imaging and clinical features in the same external cohort. Our study demonstrated that incorporating multi-level image representations learned by a deep learning based tumour segmentation model on primary MRI improves the results of EMVI classification and CR prediction with good generalisation to external data. We observed variations in the contributions of individual feature maps to different classification tasks. This pipeline has the potential to be applied in clinical settings, particularly for EMVI classification.
DRG-LLaMA : tuning LLaMA model to predict diagnosis-related group for hospitalized patients
Authors: Wang Hanyin , Gao Chufan , Dantona Christopher , Hull Bryan , Sun Jimeng
Published: January 2024

In the U.S. inpatient payment system, the Diagnosis-Related Group (DRG) is pivotal, but its assignment process is inefficient. The study introduces , an advanced large language model (LLM) fine-tuned on clinical notes to enhance DRGs assignment. Utilizing LLaMA as the foundational model and optimizing it through Low-Rank Adaptation (LoRA) on 236,192 MIMIC-IV discharge summaries, our -7B model exhibited a noteworthy macro-averaged F1 score of 0.327, a top-1 prediction accuracy of 52.0%, and a macro-averaged Area Under the Curve (AUC) of 0.986, with a maximum input token length of 512. This model surpassed the performance of prior leading models in DRG prediction, showing a relative improvement of 40.3% and 35.7% in macro-averaged F1 score compared to ClinicalBERT and CAML, respectively. Applied to base DRG and complication or comorbidity (CC)/major complication or comorbidity (MCC) prediction, achieved a top-1 prediction accuracy of 67.8% and 67.5%, respectively. Additionally, our findings indicate that ’s performance correlates with increased model parameters and input context lengths.
Diagnostic performance of artificial intelligence-assisted PET imaging for Parkinson’s disease: a systematic review and meta-analysis
Authors: Wang Jing , Xue Le , Jiang Jiehui , Liu Fengtao , Wu Ping , Lu Jiaying , Zhang Huiwei , Bao Weiqi , Xu Qian , Ju Zizhao , Chen Li , Jiao Fangyang , Lin Huamei , Ge Jingjie , Zuo Chuantao , Tian Mei
Published: January 2024

Artificial intelligence (AI)-assisted PET imaging is emerging as a promising tool for the diagnosis of Parkinson’s disease (PD). We aim to systematically review the diagnostic accuracy of AI-assisted PET in detecting PD. The Ovid MEDLINE, Ovid Embase, Web of Science, and IEEE Xplore databases were systematically searched for related studies that developed an AI algorithm in PET imaging for diagnostic performance from PD and were published by August 17, 2023. Binary diagnostic accuracy data were extracted for meta-analysis to derive outcomes of interest: area under the curve (AUC). 23 eligible studies provided sufficient data to construct contingency tables that allowed the calculation of diagnostic accuracy. Specifically, 11 studies were identified that distinguished PD from normal control, with a pooled AUC of 0.96 (95% CI: 0.94–0.97) for presynaptic dopamine (DA) and 0.90 (95% CI: 0.87–0.93) for glucose metabolism (18F-FDG). 13 studies were identified that distinguished PD from the atypical parkinsonism (AP), with a pooled AUC of 0.93 (95% CI: 0.91 − 0.95) for presynaptic DA, 0.79 (95% CI: 0.75–0.82) for postsynaptic DA, and 0.97 (95% CI: 0.96–0.99) for 18F-FDG. Acceptable diagnostic performance of PD with AI algorithms-assisted PET imaging was highlighted across the subgroups. More rigorous reporting standards that take into account the unique challenges of AI research could improve future studies.
Synthesis of the land carbon fluxes of the Amazon region between 2010 and 2020
Authors: Rosan Thais M. , Sitch Stephen , O’Sullivan Michael , Basso Luana S. , Wilson Chris , Silva Camila , Gloor Emanuel , Fawcett Dominic , Heinrich Viola , Souza Jefferson G. , Bezerra Francisco Gilney Silva , von Randow Celso , Mercado Lina M. , Gatti Luciana , Wiltshire Andy , Friedlingstein Pierre , Pongratz Julia , Schwingshackl Clemens , Williams Mathew , Smallman Luke , Knauer Jürgen , Arora Vivek , Kennedy Daniel , Tian Hanqin , Yuan Wenping , Jain Atul K. , Falk Stefanie , Poulter Benjamin , Arneth Almut , Sun Qing , Zaehle Sönke , Walker Anthony P. , Kato Etsushi , Yue Xu , Bastos Ana , Ciais Philippe , Wigneron Jean-Pierre , Albergel Clement , Aragão Luiz E. O. C.
Published: January 2024

The Amazon is the largest continuous tropical forest in the world and plays a key role in the global carbon cycle. Human-induced disturbances and climate change have impacted the Amazon carbon balance. Here we conduct a comprehensive synthesis of existing state-of-the-art estimates of the contemporary land carbon fluxes in the Amazon using a set of bottom-up methods (i.e., dynamic vegetation models and bookkeeping models) and a top-down inversion (atmospheric inversion model) over the Brazilian Amazon and the whole Biogeographical Amazon domain. Over the whole biogeographical Amazon region bottom-up methodologies suggest a small average carbon sink over 2010-2020, in contrast to a small carbon source simulated by top-down inversion (2010-2018). However, these estimates are not significantly different from one another when accounting for their large individual uncertainties, highlighting remaining knowledge gaps, and the urgent need to reduce such uncertainties. Nevertheless, both methodologies agreed that the Brazilian Amazon has been a net carbon source during recent climate extremes and that the south-eastern Amazon was a net land carbon source over the whole study period (2010-2020). Overall, our results point to increasing human-induced disturbances (deforestation and forest degradation by wildfires) and reduction in the old-growth forest sink during drought.
Nomo1 deficiency causes autism-like behavior in zebrafish
Authors: Zhang Qi , Li Fei , Li Tingting , Lin Jia , Jian Jing , Zhang Yinglan , Chen Xudong , Liu Ting , Gou Shenglan , Zhang Yawen , Liu Xiuyun , Ji Yongxia , Wang Xu , Li Qiang
Published: January 2024

Patients with neuropsychiatric disorders often exhibit a combination of clinical symptoms such as autism, epilepsy, or schizophrenia, complicating diagnosis and development of therapeutic strategies. Functional studies of novel genes associated with co-morbidities can provide clues to understand the pathogenic mechanisms and interventions. NOMO1 is one of the candidate genes located at 16p13.11, a hotspot of neuropsychiatric diseases. Here, we generate nomo1−/− zebrafish to get further insight into the function of NOMO1. Nomo1 mutants show abnormal brain and neuronal development and activation of apoptosis and inflammation-related pathways in the brain. Adult Nomo1-deficient zebrafish exhibit multiple neuropsychiatric behaviors such as hyperactive locomotor activity, social deficits, and repetitive stereotypic behaviors. The Habenular nucleus and the pineal gland in the telencephalon are affected, and the melatonin level of nomo1−/− is reduced. Melatonin treatment restores locomotor activity, reduces repetitive stereotypic behaviors, and rescues the noninfectious brain inflammatory responses caused by nomo1 deficiency. These results suggest melatonin supplementation as a potential therapeutic regimen for neuropsychiatric disorders caused by NOMO1 deficiency.
Multi-band perfect absorber based on an elliptical cavity coupled with an elliptical metal nanorod
Authors: Pan Yizhao , Li Yuchang , Chen Fang , Cheng Shubo , Yang Wenxing , Wang Boyun , Yi Zao
Published: January 2024

The proposed structure possessed a multi-narrowband, and all peaks had absorption rates >99.41%.
Martinoid: the peptoid martini force field
Authors: Swanson Hamish W. A. , van Teijlingen Alexander , Lau King Hang Aaron , Tuttle Tell
Published: January 2024

Martinoid is an expansive forcefield for coarse grained simulation of peptoids. It successfully reproduces various peptoid assembly results. A python tool to generate CG input files is also made available.
Three water-soluble copper(ii) N-heterocyclic carbene complexes: toward copper-catalyzed ketone reduction under sustainable conditions
Authors: Sharma Mitu , Perkins Amanda M. , Awoyemi Raymond Femi , Schmittou Allison N. , Raju Selvam , Pierce Brad S. , Donnadieu Bruno , Wipf David O. , Stokes Sean L. , Emerson Joseph P.
Published: January 2024

A series of tridentate copper(ii) N-heterocyclic carbene (NHC) complexes with imidazole, benzimidazole, and 5,6-dimethylbenzimidazole azole rings were synthesized and comprehensively characterized via X-ray crystallography, ESI-MS, CV, and UV-Vis and EPR spectroscopic studies.
Enhancing the reliability of dyes for color filters through TiO2 adsorption: comprehensive identification of factors affecting photocatalysis
Authors: Kim Wan Soo , Park So Jeong , Hwang Tae Gyu , Kim Hong Mo , Lee Hyun Kyu , Kim Suhyeon , Choi Woo Jin , Yoon Jun Ho , Kim Yoo Sang , Lee Dong Jun , Jang Seong Hyun , Kim Jin Young , Kim Jae Pil
Published: January 2024

Increased ICT increase charge transfer from the dye to TiO2 resulting in increased radical generation, leading to a reduced photo stability of the dye. The study elucidated the factors and mechanism affecting photocatalysis.
Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors
Authors: Governa Paolo , Biagi Marco , Manetti Fabrizio , Forli Stefano
Published: January 2024

We identified natural compounds with P-glycoprotein inhibitory activity using a consensus virtual screening approach able to differentiate between inhibitors, substrates, and non-binders.
Synthesis of 6,8-diaminopurines via acid-induced cascade cyclization of 5-aminoimidazole precursors and preliminary anticancer evaluation
Authors: Senhorães Nádia R. , Silva Bruna F. , Sousa Raquel , Leite Bruna P. , Gonçalves Jorge M. , Almeida Paz Filipe A. , Pereira-Wilson Cristina , Dias Alice M.
Published: January 2024

Novel 6,8-diaminopurines were synthesized using a fast cascade reaction from easily accessible 5-aminoimidazole precursors. Preliminary assessments suggest that the new entities are excellent candidates for further development as anticancer agents.
Ligand based pharmacophore modelling and integrated computational approaches in the quest for small molecule inhibitors against hCA IX
Authors: Saravanan Venkatesan , Chagaleti Bharath Kumar , Packiapalavesam Shakthi Devi , Kathiravan Muthukumaradoss
Published: January 2024

An integrated computational approach in search of potent hCA IX inhibitors.
The permeability of diamond and other microphase-separated morphologies in copolymer films
Authors: Erukhimovich Igor Ya. , Kriksin Yury A. , Kudryavtsev Yaroslav V.
Published: January 2024

A method is proposed for the theoretical assessment of potential membrane properties in materials based on microphase-separated block copolymer films subjected to the etching of one of the components.
Conductivity of cold sintered diphasic composites containing a ceramic active material and a solid-state electrolyte or carbon for all solid-state batteries
Authors: Grady Zane M. , Fan Zhongming , Fanghanel Julian , Randall Clive A.
Published: January 2024

Low temperature sintering enables dense composites of ceramic active materials and conductive agents. Conductivity and microstructure of composites is characterized.
Selective reactivity-assisted sacrificial additive coating for surface passivation of wide bandgap perovskite solar cells with cesium tetrafluoroborate
Authors: Koh Jaehyuk , Kim Daehan , Park Sang Woo , Kim Hyungjun , Hong Ki-Ha , Shin Byungha
Published: January 2024

A novel method, named “selective reactivity-assisted sacrificial additive coating”, allowed the BF4− from the sacrificial additive to react selectively with the Cs+ from the perovskite, forming CsBF4 to passivate the A-site vacancy on the surface.
Nanostructured (oxy)nitrides controllably synthesized by flux-assisted nitridation for promoted photocatalytic water splitting
Authors: Yuan Zhongxu , Liu Chunjiang , Chen Shanshan , Zhang Fuxiang
Published: January 2024

Flux-assisted nitridation is an effective method to develop (oxy)nitride photocatalysts with enhanced charge separation. Herein, the systematic illustration of (oxy)nitride photocatalysts for water splitting in such preparation approach is reviewed.
Fluorometric and colorimetric dual-mode sensing of α-glucosidase based on aggregation-induced emission enhancement of AuNCs
Authors: Li Songrui , Zhang Huifeng , Huang Zhenzhen , Jia Qiong
Published: January 2024

This work firstly developed a fluorometric and colorimetric dual-mode assay platform for α-glucosidase sensing based on aggregation-induced emission enhancement of AuNCs.
pH-Responsive nanoplatform synergistic gas/photothermal therapy to eliminate biofilms in poly(l-lactic acid) scaffolds
Authors: Qian Guowen , Mao Yuqian , Zhao Huihui , Zhang Lemin , Xiong Long , Long Zhisheng
Published: January 2024

The constructed ZnS–Ti3C2/PLLA scaffolds were able to release H2S gas to disrupt biofilm and further remove bacteria through photothermal. In addition, the Zn2+ released from the composite scaffolds could promote osteogenic differentiation of BMSCs.
Electrospun nanofibers applications in caries lesions: prevention, treatment and regeneration
Authors: Chen Xiangshu , Liu Zhenqi , Ma Rui , Lu Junzhuo , Zhang Linglin
Published: January 2024

Dental caries caused mineral loss and degradation of organic matrix in dental hard tissues. In this review, we highlighted recent advances concerning electrospun nanofibers for caries lesions' treatment.
Construction of a logic gate computation and visual test paper for methyl paraoxon assay based on a fluorescent europium–organic framework
Authors: Li Nan , Yu Yanyan , Zhou Yuanyuan , Xu Kexin , Zhou Yunshan , Zhang Lijuan , Zhong Yuxu
Published: January 2024

A fluorescent Eu-MOF showed high selectivity and sensitivity for the assay of DMNP, which was further extended to fabricate logic gates and a fibrous strip for the in situ visual detection of DMNP.
Improved energy storage properties of polypropylene-based composite dielectrics by introducing surface-charged BaTiO3@chitisan ultrafine constructions
Authors: Wu Yujie , Zhao Hang , Zhang Na , Wang Huiqin , Zhang Chuying , Yin Lei , Bai Jinbo
Published: January 2024

Surface-charged BaTiO3@chitisan ultrafine constructions can effectively improve the energy storage properties of PP-based composite dielectrics through interfacial-regulation and trap introduction.
Correction: Revisiting lignin: a tour through its structural features, characterization methods and applications
Authors: Melro Elodie , Filipe Alexandra , Sousa Dora , Medronho Bruno , Romano Anabela
Published: January 2024

Correction for ‘Revisiting lignin: a tour through its structural features, characterization methods and applications’ by Elodie Melro et al., New J. Chem., 2021, 45, 6986–7013, https://doi.org/10.1039/D0NJ06234K.
Correction: Multi-layer 3D printed dipeptide-based low molecular weight gels
Authors: Hill Max J. S. , Adams Dave J.
Published: January 2024

Correction for ‘Multi-layer 3D printed dipeptide-based low molecular weight gels’ by Max J. S. Hill et al., Soft Matter, 2022, 18, 5960–5965, https://doi.org/10.1039/D2SM00663D.
What Do Adults Who Stutter Think About the Nature of Stuttering Treatment?
Authors: Vanryckeghem Martine , Van Eerdenbrugh Sabine
Published: January 2024

Purpose:

Worldwide, there is an abundance of different treatment strategies, mechanisms, and constituents for individuals who stutter. This study explored what adults who stutter (AWS) think about the nature of stuttering treatment and its components and whether they feel stigmatized.

Method:

A survey containing nine statements about components of stuttering treatment and one question related to stigmatization was sent to AWS around the world. In total, 213 respondents were included in the study, spread out over North America, South America, Asia, Europe, and Australia/Oceania. Finally, three open-ended questions explored their opinion about important treatment aspects, the qualities of a speech-language pathologist (SLP), and what an ideal treatment looks like.

Results:

The nine statements referring to stuttering treatment were all seen as key components by more than half of the respondents. Nearly 80% found it very or extremely important that an SLP helps them with stuttering-related anxiety and thoughts, feeling more comfortable in different speaking situations, introducing them to speech strategies, and providing assistance in accepting themselves as a speaker. Three of these four statements were found more important by men than women. Especially respondents from North America and Europe found that (self) acceptance is important. About 50% think they are stigmatized.

Conclusions:

The survey unveiled that AWS particularly found treatment components focusing on speech and underlying thoughts important. However, it is also clear that AWS' individual opinions vary relative to what they think are important treatment components. Translating these findings to daily practice entails that SLPs should be trained in different treatment programs or approaches to meet the individual needs of each AWS. One size does not fit all. It seems crucial that researchers who conduct clinical trials for stuttering treatments employ more than stuttering reduction as an outcome measure.