bluuebunny/crossref_metadata_2025_split huggingface dataset:
Programmable integrated photonics for topological Hamiltonians
Authors: On Mehmet Berkay , Ashtiani Farshid , Sanchez-Jacome David , Perez-Lopez Daniel , Yoo S. J. Ben , Blanco-Redondo Andrea 
Published: January 2024

AbstractA variety of topological Hamiltonians have been demonstrated in photonic platforms, leading to fundamental discoveries and enhanced robustness in applications such as lasing, sensing, and quantum technologies. To date, each topological photonic platform implements a specific type of Hamiltonian with inexistent or limited reconfigurability. Here, we propose and demonstrate different topological models by using the same reprogrammable integrated photonics platform, consisting of a hexagonal mesh of silicon Mach-Zehnder interferometers with phase shifters. We specifically demonstrate a one-dimensional Su-Schrieffer-Heeger Hamiltonian supporting a localized topological edge mode and a higher-order topological insulator based on a two-dimensional breathing Kagome Hamiltonian with three corner states. These results highlight a nearly universal platform for topological models that may fast-track research progress toward applications of topological photonics and other coupled systems.
ATG14 targets lipid droplets and acts as an autophagic receptor for syntaxin18-regulated lipid droplet turnover
Authors: Yuan Zhen , Cai Kun , Li Jiajia , Chen Ruifeng , Zhang Fuhai , Tan Xuan , Jiu Yaming , Chang Haishuang , Hu Bing , Zhang Weiyi , Ding Binbin 
Published: January 2024

AbstractLipid droplets (LDs) are dynamic lipid storage organelles that can be degraded by autophagy machinery to release neutral lipids, a process called lipophagy. However, specific receptors and regulation mechanisms for lipophagy remain largely unknown. Here, we identify that ATG14, the core unit of the PI3KC3-C1 complex, also targets LD and acts as an autophagic receptor that facilitates LD degradation. A negative regulator, Syntaxin18 (STX18) binds ATG14, disrupting the ATG14-ATG8 family members interactions and subverting the PI3KC3-C1 complex formation. Knockdown of STX18 activates lipophagy dependent on ATG14 not only as the core unit of PI3KC3-C1 complex but also as the autophagic receptor, resulting in the degradation of LD-associated anti-viral protein Viperin. Furthermore, coronavirus M protein binds STX18 and subverts the STX18-ATG14 interaction to induce lipophagy and degrade Viperin, facilitating virus production. Altogether, our data provide a previously undescribed mechanism for additional roles of ATG14 in lipid metabolism and virus production.
Interaction-selective molecular sieving adsorbent for direct separation of ethylene from senary C2-C4 olefin/paraffin mixture
Authors: Peng Yong , Xiong Hanting , Zhang Peixin , Zhao Zhiwei , Liu Xing , Tang Shihui , Liu Yuan , Zhu Zhenliang , Zhou Weizhen , Deng Zhenning , Liu Junhui , Zhong Yao , Wu Zeliang , Chen Jingwen , Zhou Zhenyu , Chen Shixia , Deng Shuguang , Wang Jun 
Published: January 2024

AbstractOlefin/paraffin separations are among the most energy-intensive processes in the petrochemical industry, with ethylene being the most widely consumed chemical feedstock. Adsorptive separation utilizing molecular sieving adsorbents can optimize energy efficiency, whereas the size-exclusive mechanism alone cannot achieve multiple olefin/paraffin sieving in a single adsorbent. Herein, an unprecedented sieving adsorbent, BFFOUR-Cu-dpds (BFFOUR = BF4-, dpds = 4,4’-bipyridinedisulfide), is reported for simultaneous sieving of C2-C4 olefins from their corresponding paraffins. The interlayer spaces can be selectively opened through stronger guest-host interactions induced by unsaturated C = C bonds in olefins, as opposed to saturated paraffins. In equimolar six-component breakthrough experiments (C2H4/C2H6/C3H6/C3H8/n-C4H8/n-C4H10), BFFOUR-Cu-dpds can simultaneously divide olefins from paraffins in the first column, while high-purity ethylene ( > 99.99%) can be directly obtained through the subsequent column using granular porous carbons. Moreover, gas-loaded single-crystal analysis, in-situ infrared spectroscopy measurements, and computational simulations demonstrate the accommodation patterns, interaction bonds, and energy pathways for olefin/paraffin separations.
Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis
Authors: Tang Qiulin , Huang Huixi , Xu Huanji , Xia Hongwei , Zhang Chenliang , Ye Di , Bi Feng 
Published: January 2024

AbstractA high-fat diet (HFD) may be linked to an increased colorectal cancer (CRC) risk. Stem cell proliferation and adipokine release under inflammatory and obese conditions are the main factors regulating CRC progression. Furthermore, alterations in intestinal flora have been linked to tumorigenesis and tumour progression. However, whether a HFD can promote CRC occurrence by altering intestinal flora remains unclear. The objective of this study was to identify bacterial strains enriched by a HFD and investigate the association and mechanism by which a HFD and bacterial enrichment promote CRC occurrence and development. In this study, the intestinal microbiota of mice was assessed using 16S rRNA and metagenomic sequencing. Serum metabolites of HFD-fed mice were assessed using tandem liquid chromatography-mass spectrometry. CRC cell lines and organoids were co-cultured with Coriobacteriaceae to evaluate the effect of these bacteria on the CPT1A-ERK signalling pathway. We found that Coriobacteriaceae were enriched in the colons of HFD-fed mice. An endogenous Coriobacteriaceae strain, designated as Cori.ST1911, was successfully isolated and cultured from the stools of HFD-fed mice, and the tumorigenic potential of Cori.ST1911 in CRC was validated in several CRC mouse models. Furthermore, Cori.ST1911 increased acylcarnitine levels by activating CPT1A, demonstrating the involvement of the CPT1A-ERK axis. We also found that the endogenous Lactobacillus strain La.mu730 can interfere with Cori.ST1911 colonisation and restore gut barrier function. In conclusion, we identified a novel endogenous intestinal Coriobacteriaceae, Cori.ST1911, which might lead to a new gut microbiota intervention strategy for the prevention and treatment of CRC.
Predicting response to neoadjuvant chemotherapy with liquid biopsies and multiparametric MRI in patients with breast cancer
Authors: Janssen L. M. , Janse M. H. A. , Penning de Vries B. B. L. , van der Velden B. H. M. , Wolters-van der Ben E. J. M. , van den Bosch S. M. , Sartori A. , Jovelet C. , Agterof M. J. , Ten Bokkel Huinink D. , Bouman-Wammes E. W. , van Diest P. J. , van der Wall E. , Elias S. G. , Gilhuijs K. G. A. 
Published: January 2024

AbstractAccurate prediction of response to neoadjuvant chemotherapy (NAC) can help tailor treatment to individual patients’ needs. Little is known about the combination of liquid biopsies and computer extracted features from multiparametric magnetic resonance imaging (MRI) for the prediction of NAC response in breast cancer. Here, we report on a prospective study with the aim to explore the predictive potential of this combination in adjunct to standard clinical and pathological information before, during and after NAC. The study was performed in four Dutch hospitals. Patients without metastases treated with NAC underwent 3 T multiparametric MRI scans before, during and after NAC. Liquid biopsies were obtained before every chemotherapy cycle and before surgery. Prediction models were developed using penalized linear regression to forecast residual cancer burden after NAC and evaluated for pathologic complete response (pCR) using leave-one-out-cross-validation (LOOCV). Sixty-one patients were included. Twenty-three patients (38%) achieved pCR. Most prediction models yielded the highest estimated LOOCV area under the curve (AUC) at the post-treatment timepoint. A clinical-only model including tumor grade, nodal status and receptor subtype yielded an estimated LOOCV AUC for pCR of 0.76, which increased to 0.82 by incorporating post-treatment radiological MRI assessment (i.e., the “clinical-radiological” model). The estimated LOOCV AUC was 0.84 after incorporation of computer-extracted MRI features, and 0.85 when liquid biopsy information was added instead of the radiological MRI assessment. Adding liquid biopsy information to the clinical-radiological resulted in an estimated LOOCV AUC of 0.86. In conclusion, inclusion of liquid biopsy-derived markers in clinical-radiological prediction models may have potential to improve prediction of pCR after NAC in breast cancer.
A polygenic score associated with fracture risk in breast cancer patients treated with aromatase inhibitors
Authors: Hook Christine , Chatterjee Udit , Sheng Haiyang , Zhu Qianqian , Robinson Timothy , Roh Janise M. , Laurent Cecile A. , Lee Catherine , Delmerico Jennifer , Lo Joan C. , Ambrosone Christine B. , Kushi Lawrence H. , Kwan Marilyn L. , Yao Song 
Published: January 2024

AbstractIdentifying women at high risk of osteoporotic fracture from aromatase inhibitor (AI) therapy for breast cancer is largely based on known risk factors for healthy postmenopausal women, which might not accurately reflect the risk in breast cancer patients post-AI therapy. To determine whether a polygenic score associated with fracture in healthy women is also significant in women treated with AIs for breast cancer, we used data from a prospective observational cohort of 2152 women diagnosed with hormonal receptor positive breast cancer treated with AIs as the initial endocrine therapy and examined a polygenic score of heel quantitative ultrasound speed of sound (gSOS) in relation to incident osteoporotic fracture after AI therapy during a median 6.1 years of follow up after AI initiation. In multivariable models, patients with the second and third highest tertiles (T) versus the lowest tertile of gSOS had significantly lower risk of fracture (T2: adjusted HR = 0.61, 95% CI: 0.46-0.80; T3: adjusted HR = 0.53, 95% CI: 0.40-0.70). The lower risk of fracture in patients with the highest tertile of gSOS remained significant after further adjustment for BMD at the hip (T3: adjusted HR = 0.62, 95% CI: 0.42-0.91). In conclusion, our analysis showed gSOS as a novel genetic predictor for fracture risk independent of BMD among breast cancer patients treated with AIs. Future studies are warranted to evaluate the performance of incorporating gSOS in prediction models for the risk of AI-related fracture in breast cancer patients.
Machine learned force-fields for an Ab-initio quality description of metal-organic frameworks
Authors: Wieser Sandro , Zojer Egbert 
Published: January 2024

AbstractMetal-organic frameworks (MOFs) are an incredibly diverse group of highly porous hybrid materials, which are interesting for a wide range of possible applications. For a meaningful theoretical description of many of their properties accurate and computationally highly efficient methods are in high demand. These would avoid compromises regarding either the quality of modelling results or the level of complexity of the calculated properties. With the advent of machine learning approaches, it is now possible to generate such approaches with relatively little human effort. Here, we build on existing types of machine-learned force fields belonging to the moment-tensor and kernel-based potential families to develop a recipe for their efficient parametrization. This yields exceptionally accurate and computationally highly efficient force fields. The parametrization relies on reference configurations generated during molecular dynamics based, active learning runs. The performance of the potentials is benchmarked for a representative selection of commonly studied MOFs revealing a close to DFT accuracy in predicting forces and structural parameters for a set of validation structures. The same applies to elastic constants and phonon band structures. Additionally, for MOF-5 the thermal conductivity is obtained with full quantitative agreement to single-crystal experiments. All this is possible while maintaining a very high degree of computational efficiency. The exceptional accuracy of the parameterized force field potentials combined with their computational efficiency has the potential of lifting the computational modelling of MOFs to the next level.
Whole genome sequencing enables new genetic diagnosis for inherited retinal diseases by identifying pathogenic variants
Authors: Liu Xubing , Hu Fangyuan , Zhang Daowei , Li Zhe , He Jianquan , Zhang Shenghai , Wang Zhenguo , Zhao Yingke , Wu Jiawen , Liu Chen , Li Chenchen , Li Xin , Wu Jihong 
Published: January 2024

AbstractInherited retinal diseases (IRDs) are a group of common primary retinal degenerative disorders. Conventional genetic testing strategies, such as panel-based sequencing and whole exome sequencing (WES), can only elucidate the genetic etiology in approximately 60% of IRD patients. Studies have suggested that unsolved IRD cases could be attributed to previously undetected structural variants (SVs) and intronic variants in IRD-related genes. The aim of our study was to obtain a definitive genetic diagnosis by employing whole genome sequencing (WGS) in IRD cases where the causative genes were inconclusive following an initial screening by panel sequencing. A total of 271 unresolved IRD patients and their available family members (n = 646) were screened using WGS to identify pathogenic SVs and intronic variants in 792 known ocular disease genes. Overall, 13% (34/271) of IRD patients received a confirmed genetic diagnosis, among which 7% were exclusively attributed to SVs, 4% to a combination of single nucleotide variants (SNVs) and SVs while another 2% were linked to intronic variants. 22 SVs, 3 deep-intronic variants, and 2 non-canonical splice-site variants across 14 IRD genes were identified in the entire cohort. Notably, all of these detected SVs and intronic variants were novel pathogenic variants. Among those, 74% (20/27) of variants were found in genes causally linked to Retinitis Pigmentosa (RP), with the gene EYS being the most frequently affected by SVs. The identification of SVs and intronic variants through WGS enhances the genetic diagnostic yield of IRDs and broadens the mutational spectrum of known IRD-associated genes.
Early-stage idiopathic Parkinson’s disease is associated with reduced circular RNA expression
Authors: Whittle Benjamin J. , Izuogu Osagie G. , Lowes Hannah , Deen Dasha , Pyle Angela , Coxhead Jon , Lawson Rachael A. , Yarnall Alison J. , Jackson Michael S. , Santibanez-Koref Mauro , Hudson Gavin 
Published: January 2024

AbstractNeurodegeneration in Parkinson’s disease (PD) precedes diagnosis by years. Early neurodegeneration may be reflected in RNA levels and measurable as a biomarker. Here, we present the largest quantification of whole blood linear and circular RNAs (circRNA) in early-stage idiopathic PD, using RNA sequencing data from two cohorts (PPMI = 259 PD, 161 Controls; ICICLE-PD = 48 PD, 48 Controls). We identified a replicable increase inTMEM252andLMNB1gene expression in PD. We identified novel differences in the expression of circRNAs fromESYT2,BMS1P1andCCDC9, and replicated trends of previously reported circRNAs. Overall, using circRNA as a diagnostic biomarker in PD did not show any clear improvement over linear RNA, minimising its potential clinical utility. More interestingly, we observed a general reduction in circRNA expression in both PD cohorts, accompanied by an increase inRNASELexpression. This imbalance implicates the activation of an innate antiviral immune response and suggests a previously unknown aspect of circRNA regulation in PD.
High-field immiscibility of electrons belonging to adjacent twinned bismuth crystals
Authors: Ye Yuhao , Yamada Akiyoshi , Kinoshita Yuto , Wang Jinhua , Nie Pan , Xu Liangcai , Zuo Huakun , Tokunaga Masashi , Harrison Neil , McDonald Ross D. , Suslov Alexey V. , Ardavan Arzhang , Nam Moon-Sun , LeBoeuf David , Proust Cyril , Fauqué Benoît , Fuseya Yuki , Zhu Zengwei , Behnia Kamran 
Published: January 2024

AbstractBulk bismuth has a complex Landau spectrum. The small effective masses and the large g-factors are anisotropic. The chemical potential drifts at high magnetic fields. Moreover, twin boundaries further complexify the interpretation of the data by producing extra anomalies in the extreme quantum limit. Here, we present a study of angle dependence of magnetoresistance up to 65 T in bismuth complemented with Nernst, ultrasound, and magneto-optic data. All observed anomalies can be explained in a single-particle picture of a sample consisting of two twinned crystals tilted by 108° and with two adjacent crystals keeping their own chemical potentials despite a shift between chemical potentials as large as 68 meV at 65 T. This implies an energy barrier between adjacent twinned crystals reminiscent of a metal- semiconductor Schottky barrier or a p-n junction. We argue that this barrier is built by accumulating charge carriers of opposite signs across a twin boundary.
MSCs mediate long-term efficacy in a Crohn’s disease model by sustained anti-inflammatory macrophage programming via efferocytosis
Authors: Dave Maneesh , Dev Atul , Somoza Rodrigo A. , Zhao Nan , Viswanath Satish , Mina Pooja Rani , Chirra Prathyush , Obmann Verena Carola , Mahabeleshwar Ganapati H. , Menghini Paola , Durbin-Johnson Blythe , Nolta Jan , Soto Christopher , Osme Abdullah , Khuat Lam T. , Murphy William J. , Caplan Arnold I. , Cominelli Fabio 
Published: January 2024

AbstractMesenchymal stem cells (MSCs) are novel therapeutics for the treatment of Crohn’s disease. However, their mechanism of action is unclear, especially in disease-relevant chronic models of inflammation. Thus, we used SAMP-1/YitFc (SAMP), a chronic and spontaneous murine model of small intestinal inflammation, to study the therapeutic effects and mechanism of action of human bone marrow-derived MSCs (hMSC). hMSC dose-dependently inhibited naïve T lymphocyte proliferation via prostaglandin E2 (PGE2) secretion and reprogrammed macrophages to an anti-inflammatory phenotype. We found that the hMSCs promoted mucosal healing and immunologic response early after administration in SAMP when live hMSCs are present (until day 9) and resulted in a complete response characterized by mucosal, histological, immunologic, and radiological healing by day 28 when no live hMSCs are present. hMSCs mediate their effect via modulation of T cells and macrophages in the mesentery and mesenteric lymph nodes (mLN). Sc-RNAseq confirmed the anti-inflammatory phenotype of macrophages and identified macrophage efferocytosis of apoptotic hMSCs as a mechanism that explains their long-term efficacy. Taken together, our findings show that hMSCs result in healing and tissue regeneration in a chronic model of small intestinal inflammation and despite being short-lived, exert long-term effects via sustained anti-inflammatory programming of macrophages via efferocytosis.
An analysis of emerging food safety and fraud risks of novel insect proteins within complex supply chains
Authors: Traynor A. , Burns D. Thorburn , Wu D. , Karoonuthaisiri N. , Petchkongkaew A. , Elliott C. T. 
Published: January 2024

AbstractFood consumption play a crucial role in human life, yet conventional food production and consumption patterns can be detrimental to the environment. Thus, research and development has been directed towards alternative proteins, with edible insects being promising sources. Edible insects have been recognised for their sustainable benefits providing protein, with less emission of greenhouse gas, land and water usage compared to sources, such as beef, chicken, and dairy products. Among the over 2000 known edible insect species, only four, namely yellow mealworm (Tenebrio molitor), migratory locust/grasshopper (Locusta migratoria), grain mould beetle, also known as lesser mealworm which is a larval form of Alphitobius diaperinus (from the family of Tenebrionidae of darkling beetles) and house cricket (Acheta domesticus), are currently authorised in specific products through specific producers in the EU. The expansion of such foods into Western diets face challenges such as consumer barriers, gaps in microbiological and chemical safety hazard data during production and processing, and the potential for fraudulent supply chain activity. The main aim of this study was to map the supply chain, through interviews with personnel along the supply chain, coupled with searches for relevant publications and governmental documents. Thus, the main potential points of food safety and fraud along the edible insect supply chain were identified. Feed substrate was identified as the main area of concern regarding microbiological and chemical food safety and novel processing techniques were forecast to be of most concern for future fraudulent activity. Despite the on-going authorisation of insect species in many countries there are substantial food safety and authenticity information gaps in this industry that need to be addressed before edible insects can be viewed as a safe and sustainable protein sources by Western consumers.
Development of performance and learning rate evaluation models in robot-assisted surgery using electroencephalography and eye-tracking
Authors: Shafiei Somayeh B. , Shadpour Saeed , Sasangohar Farzan , Mohler James L. , Attwood Kristopher , Jing Zhe 
Published: January 2024

AbstractThe existing performance evaluation methods in robot-assisted surgery (RAS) are mainly subjective, costly, and affected by shortcomings such as the inconsistency of results and dependency on the raters’ opinions. The aim of this study was to develop models for an objective evaluation of performance and rate of learning RAS skills while practicing surgical simulator tasks. The electroencephalogram (EEG) and eye-tracking data were recorded from 26 subjects while performing Tubes, Suture Sponge, and Dots and Needles tasks. Performance scores were generated by the simulator program. The functional brain networks were extracted using EEG data and coherence analysis. Then these networks, along with community detection analysis, facilitated the extraction of average search information and average temporal flexibility features at 21 Brodmann areas (BA) and four band frequencies. Twelve eye-tracking features were extracted and used to develop linear random intercept models for performance evaluation and multivariate linear regression models for the evaluation of the learning rate. Results showed that subject-wise standardization of features improved the R2 of the models. Average pupil diameter and rate of saccade were associated with performance in the Tubes task (multivariate analysis; p-value = 0.01 and p-value = 0.04, respectively). Entropy of pupil diameter was associated with performance in Dots and Needles task (multivariate analysis; p-value = 0.01). Average temporal flexibility and search information in several BAs and band frequencies were associated with performance and rate of learning. The models may be used to objectify performance and learning rate evaluation in RAS once validated with a broader sample size and tasks.
Bio-inspired design of next-generation ultrapermeable membrane systems
Authors: Luo Jiu , Li Mingheng , Heng Yi 
Published: January 2024

AbstractUltrapermeable membranes (UPMs) have the potential of improving water production efficiency. However, operating at high water fluxes will intensify concentration polarization and membrane fouling. Inspired by the V-formation of birds in nature we propose a transformative membrane module that enables a doubled mass transfer coefficient with a moderately increased friction loss coefficient. Moreover, we present a practical technological pathway for the UPM systems to achieve 338% improvement of average water flux and 18% energy savings relative to state-of-the-art seawater desalination plants. The work makes it practical to operate at a high average water flux of 84 L m−2 h−1 with a controlled concentration polarization for the UPM systems. It breaks through the module development bottlenecks for the next-generation UPM systems and has enormous potential application for alleviating water scarcity crisis in the coming decades.