bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nerve cells in gastrointestinal cancers: from molecular mechanisms to clinical intervention
Authors: Lyu Yang , Xie Fuda , Chen Bonan , Shin Wing Sum , Chen Wei , He Yulong , Leung Kam Tong , Tse Gary M. K. , Yu Jun , To Ka Fai , Kang Wei 
Published: December 2023

AbstractGastrointestinal (GI) cancer is a formidable malignancy with significant morbidity and mortality rates. Recent studies have shed light on the complex interplay between the nervous system and the GI system, influencing various aspects of GI tumorigenesis, such as the malignance of cancer cells, the conformation of tumor microenvironment (TME), and the resistance to chemotherapies. The discussion in this review first focused on exploring the intricate details of the biological function of the nervous system in the development of the GI tract and the progression of tumors within it. Meanwhile, the cancer cell-originated feedback regulation on the nervous system is revealed to play a crucial role in the growth and development of nerve cells within tumor tissues. This interaction is vital for understanding the complex relationship between the nervous system and GI oncogenesis. Additionally, the study identified various components within the TME that possess a significant influence on the occurrence and progression of GI cancer, including microbiota, immune cells, and fibroblasts. Moreover, we highlighted the transformation relationship between non-neuronal cells and neuronal cells during GI cancer progression, inspiring the development of strategies for nervous system-guided anti-tumor drugs. By further elucidating the deep mechanism of various neuroregulatory signals and neuronal intervention, we underlined the potential of these targeted drugs translating into effective therapies for GI cancer treatment. In summary, this review provides an overview of the mechanisms of neuromodulation and explores potential therapeutic opportunities, providing insights into the understanding and management of GI cancers.
Examining the relationship of acetaminophen use during pregnancy with early language development in children
Authors: Woodbury Megan L. , Cintora Patricia , Ng Shukhan , Hadley Pamela A. , Schantz Susan L. 
Published: December 2023

Abstract
Background
Acetaminophen is the only analgesic considered safe for use throughout pregnancy. Recent studies suggest that use during pregnancy may be associated with poorer neurodevelopmental outcomes in children, but few have examined language development.

Methods
The Illinois Kids Development Study is a prospective birth cohort in east-central Illinois. Between December 2013 and March 2020, 532 newborns were enrolled and had exposure data available. Participants reported the number of times they took acetaminophen six times across pregnancy. Language data were collected at 26.5–28.5 months using the MacArthur-Bates Communicative Development Inventories (CDI; n = 298), and 36–38 months using the Speech and Language Assessment Scale (SLAS; n = 254).

Results
Taking more acetaminophen during the second or third trimester was associated with marginally smaller vocabularies and shorter utterance length (M3L) at 26.5–28.5 months. More acetaminophen use during the third trimester was also associated with increased odds of M3L scores ≤25th percentile in male children. More use during the second or third trimester was associated with lower SLAS scores at 36–38 months. Third trimester use was specifically related to lower SLAS scores in male children.

Conclusions
Higher prenatal acetaminophen use during pregnancy may be associated with poorer early language development.

Impact

Taking more acetaminophen during pregnancy, particularly during the second and third trimesters, was associated with poorer scores on measures of language development when children were 26.5–28.5 and 36–38 months of age.

Only male children had lower scores in analyses stratified by child sex.

To our knowledge, this is the first study that has used a standardized measure of language development to assess the potential impact of prenatal exposure to acetaminophen on language development.

This study adds to the growing body of literature suggesting that the potential impact of acetaminophen use during pregnancy on fetal neurodevelopment should be carefully evaluated.
The effects of glycemic index on prostate cancer progression in a xenograft mouse model
Authors: Galván Gloria Cecilia , Macias Everardo , Sanders Sergio , Ramirez-Torres Adela , Stock Shannon , You Sungyong , Riera Celine E. , Tamukong Patrick , Smith-Warner Stephanie A. , Genkinger Jeanine M. , Luthringer Daniel J. , Freeman Michael R. , Freedland Stephen J. 
Published: December 2023

Abstract
Background
Previously, we found low-carbohydrate diets slowed prostate cancer (PC) growth and increased survival vs. a Western diet in mice, by inhibiting the insulin/IGF-1 axis. Thus, we tested whether modifying carbohydrate quality to lower glycemic index (GI) without changing quantity results in similar benefits as with reduced quantity.

Methods
Male SCID mice injected with LAPC-4 cells were single-housed and randomized when their tumors reached 200 mm3 on average to a LoGI (48% carbohydrate kcal, from Hylon-VII) or HiGI Western diet (48% carbohydrate kcal, from sucrose). Body weight and tumor volume were measured weekly. Body composition was assessed 35 days after randomization. Blood glucose and serum insulin, IGF-1 and IGFBP3 were measured at study end when tumor volumes reached 800 mm3. We analyzed gene expression of mice tumors by RNA-sequencing and human tumors using the Prostate Cancer Transcriptome Atlas.

Results
There were no significant differences in tumor volume (P > 0.05), tumor proliferation (P = 0.29), and overall survival (P = 0.15) between groups. At 35 days after randomization, the LoGI group had 30% lower body fat (P = 0.007) despite similar body weight (P = 0.58). At sacrifice, LoGI mice had smaller livers (P < 0.001) and lower glucose (P = 0.15), insulin (P = 0.11), IGF-1 (P = 0.07) and IGF-1:IGFBP3 ratio (P = 0.05), and higher IGFBP3 (P = 0.09) vs. HiGI, although none of these metabolic differences reached statistical significance. We observed differential gene expression and pathway enrichment in mice tumors by diet. The most upregulated and downregulated gene in the LoGI group showed expression patterns more closely resembling expression in human benign prostate tissue vs. PC.

Conclusions
In this single mouse xenograft model, consuming a low GI diet did not delay PC growth or survival vs. a high GI diet despite suggestions of decreased activation of the insulin/IGF-1 pathway. These data suggest that improving carbohydrate quality alone while consuming a high carbohydrate diet may not effectively slow PC growth.
Higher intraocular pressure is associated with slower axial growth in children with non-pathological high myopia
Authors: Yii Fabian SL , He Mingguang , Chappell Francesca , Bernabeu Miguel O. , MacGillivray Tom , Dhillon Baljean , Tatham Andrew , Strang Niall 
Published: December 2023

Abstract
Objectives
To investigate the association between intraocular pressure (IOP) and axial elongation rate in highly myopic children from the ZOC-BHVI High Myopia Cohort Study.

Methods
162 eyes of 81 healthy children (baseline spherical equivalent: −6.25 D to −15.50 D) aged 7–12 years with non-pathological high myopia were studied over five biennial visits. The mean (SD) follow-up duration was 5.2 (3.3) years. A linear mixed-effects model (LMM) was used to assess the association between IOP (at time point t−1) and axial elongation rate (annual rate of change in AL from t−1 to t), controlling for a pre-defined set of covariates including sex, age, central corneal thickness, anterior chamber depth and lens thickness (at t−1). LMM was also used to assess the contemporaneous association between IOP and axial length (AL) at t, controlling for the same set of covariates (at t) as before.

Results
Higher IOP was associated with slower axial growth (β = −0.01, 95% CI −0.02 to −0.005, p = 0.001). There was a positive contemporaneous association between IOP and AL (β = 0.03, 95% CI 0.01–0.05, p = 0.004), but this association became progressively less positive with increasing age, as indicated by a negative interaction effect between IOP and age on AL (β = −0.01, 95% CI −0.01 to −0.003, p = 0.001).

Conclusions
Higher IOP is associated with slower rather than faster axial growth in children with non-pathological high myopia, an association plausibly confounded by the increased influence of ocular compliance on IOP.
Seismic arrival-time picking on distributed acoustic sensing data using semi-supervised learning
Authors: Zhu Weiqiang , Biondi Ettore , Li Jiaxuan , Yin Jiuxun , Ross Zachary E. , Zhan Zhongwen 
Published: December 2023

AbstractDistributed Acoustic Sensing (DAS) is an emerging technology for earthquake monitoring and subsurface imaging. However, its distinct characteristics, such as unknown ground coupling and high noise level, pose challenges to signal processing. Existing machine learning models optimized for conventional seismic data struggle with DAS data due to its ultra-dense spatial sampling and limited manual labels. We introduce a semi-supervised learning approach to address the phase-picking task of DAS data. We use the pre-trained PhaseNet model to generate noisy labels of P/S arrivals in DAS data and apply the Gaussian mixture model phase association (GaMMA) method to refine these noisy labels and build training datasets. We develop PhaseNet-DAS, a deep learning model designed to process 2D spatio-temporal DAS data to achieve accurate phase picking and efficient earthquake detection. Our study demonstrates a method to develop deep learning models for DAS data, unlocking the potential of integrating DAS in enhancing earthquake monitoring.
Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition
Authors: McShan Andrew C. , Flores-Solis David , Sun Yi , Garfinkle Samuel E. , Toor Jugmohit S. , Young Michael C. , Sgourakis Nikolaos G. 
Published: December 2023

AbstractThe conformational landscapes of peptide/human leucocyte antigen (pHLA) protein complexes encompassing tumor neoantigens provide a rationale for target selection towards autologous T cell, vaccine, and antibody-based therapeutic modalities. Here, using complementary biophysical and computational methods, we characterize recurrent RAS55-64Q61 neoepitopes presented by the common HLA-A*01:01 allotype. We integrate sparse NMR restraints with Rosetta docking to determine the solution structure of NRASQ61K/HLA-A*01:01, which enables modeling of other common RAS55-64neoepitopes. Hydrogen/deuterium exchange mass spectrometry experiments alongside molecular dynamics simulations reveal differences in solvent accessibility and conformational plasticity across a panel of common Q61 neoepitopes that are relevant for recognition by immunoreceptors. Finally, we predict binding and provide structural models of NRASQ61Kantigens spanning the entire HLA allelic landscape, together with in vitro validation for HLA-A*01:191, HLA-B*15:01, and HLA-C*08:02. Our work provides a basis to delineate the solution surface features and immunogenicity of clinically relevant neoepitope/HLA targets for cancer therapy.
ComplexEye: a multi-lens array microscope for high-throughput embedded immune cell migration analysis
Authors: Cibir Zülal , Hassel Jacqueline , Sonneck Justin , Kowitz Lennart , Beer Alexander , Kraus Andreas , Hallekamp Gabriel , Rosenkranz Martin , Raffelberg Pascal , Olfen Sven , Smilowski Kamil , Burkard Roman , Helfrich Iris , Tuz Ali Ata , Singh Vikramjeet , Ghosh Susmita , Sickmann Albert , Klebl Anne-Kathrin , Eickhoff Jan Eike , Klebl Bert , Seidl Karsten , Chen Jianxu , Grabmaier Anton , Viga Reinhard , Gunzer Matthias 
Published: December 2023

AbstractAutonomous migration is essential for the function of immune cells such as neutrophils and plays an important role in numerous diseases. The ability to routinely measure or target it would offer a wealth of clinical applications. Video microscopy of live cells is ideal for migration analysis, but cannot be performed at sufficiently high-throughput (HT). Here we introduce ComplexEye, an array microscope with 16 independent aberration-corrected glass lenses spaced at the pitch of a 96-well plate to produce high-resolution movies of migrating cells. With the system, we enable HT migration analysis of immune cells in 96- and 384-well plates with very energy-efficient performance. We demonstrate that the system can measure multiple clinical samples simultaneously. Furthermore, we screen 1000 compounds and identify 17 modifiers of migration in human neutrophils in just 4 days, a task that requires 60-times longer with a conventional video microscope. ComplexEye thus opens the field of phenotypic HT migration screens and enables routine migration analysis for the clinical setting.
Manipulation of fractionalized charge in the metastable topologically entangled state of a doped Wigner crystal
Authors: Mraz Anze , Diego Michele , Kranjec Andrej , Vodeb Jaka , Karpov Peter , Gerasimenko Yaroslav , Ravnik Jan , Vaskivskyi Yevhenii , Venturini Rok , Kabanov Viktor , Lipovšek Benjamin , Topič Marko , Vaskivskyi Igor , Mihailovic Dragan 
Published: December 2023

AbstractMetastability of many-body quantum states is rare and still poorly understood. An exceptional example is the low-temperature metallic state of the layered dichalcogenide 1T-TaS2 in which electronic order is frozen after external excitation. Here we visualize the microscopic dynamics of injected charges in the metastable state using a multiple-tip scanning tunnelling microscope. We observe non-thermal formation of a metastable network of dislocations interconnected by domain walls, that leads to macroscopic robustness of the state to external thermal perturbations, such as small applied currents. With higher currents, we observe annihilation of dislocations following topological rules, accompanied with a change of macroscopic electrical resistance. Modelling carrier injection into a Wigner crystal reveals the origin of formation of fractionalized, topologically entangled networks, which defines the spatial fabric through which single particle excitations propagate. The possibility of manipulating topological entanglement of such networks suggests the way forward in the search for elusive metastable states in quantum many body systems.
Nonintrusive thermal-wave sensor for operando quantification of degradation in commercial batteries
Authors: Zeng Yuqiang , Shen Fengyu , Zhang Buyi , Lee Jaeheon , Chalise Divya , Zheng Qiye , Fu Yanbao , Kaur Sumanjeet , Lubner Sean D. , Battaglia Vincent S. , McCloskey Bryan D. , Tucker Michael C. , Prasher Ravi S. 
Published: December 2023

AbstractMonitoring real-world battery degradation is crucial for the widespread application of batteries in different scenarios. However, acquiring quantitative degradation information in operating commercial cells is challenging due to the complex, embedded, and/or qualitative nature of most existing sensing techniques. This process is essentially limited by the type of signals used for detection. Here, we report the use of effective battery thermal conductivity (keff) as a quantitative indicator of battery degradation by leveraging the strong dependence of keff on battery-structure changes. A measurement scheme based on attachable thermal-wave sensors is developed for non-embedded detection and quantitative assessment. A proof-of-concept study of battery degradation during fast charging demonstrates that the amount of lithium plating and electrolyte consumption associated with the side reactions on the graphite anode and deposited lithium can be quantitatively distinguished using our method. Therefore, this work opens the door to the quantitative evaluation of battery degradation using simple non-embedded thermal-wave sensors.
Hydrogen-bonding and π-π interaction promoted solution-processable covalent organic frameworks
Authors: Zhang Lei , Zhu Qiu-Hong , Zhou Yue-Ru , Wang Shuang-Long , Fu Jie , Liu Jia-Ying , Zhang Guo-Hao , Ma Lijian , Tao Guohua , Tao Guo-Hong , He Ling 
Published: December 2023

AbstractCovalent organic frameworks show great potential in gas adsorption/separation, biomedicine, device, sensing, and printing arenas. However, covalent organic frameworks are generally not dispersible in common solvents resulting in the poor processability, which severely obstruct their application in practice. In this study, we develop a convenient top-down process for fabricating solution-processable covalent organic frameworks by introducing intermolecular hydrogen bonding and π-π interactions from ionic liquids. The bulk powders of imine-linked, azine-linked, and β-ketoenamine linked covalent organic frameworks can be dispersed homogeneously in optimal ionic liquid 1-methyl-3-octylimidazolium bromide after heat treatment. The resulting high-concentration colloids are utilized to create the covalent organic framework inks that can be directly printed onto the surface. Molecular dynamics simulations and the quantum mechanical calculations suggest that C‒H···π and π-π interaction between ionic liquid cations and covalent organic frameworks may promote the formation of colloidal solution. These findings offer a roadmap for preparing solution-processable covalent organic frameworks, enabling their practical applications.
Non-identical moiré twins in bilayer graphene
Authors: Arrighi Everton , Nguyen Viet-Hung , Di Luca Mario , Maffione Gaia , Hong Yuanzhuo , Farrar Liam , Watanabe Kenji , Taniguchi Takashi , Mailly Dominique , Charlier Jean-Christophe , Ribeiro-Palau Rebeca 
Published: December 2023

AbstractThe superlattice obtained by aligning a monolayer graphene and boron nitride (BN) inherits from the hexagonal lattice a sixty degrees periodicity with the layer alignment. It implies that, in principle, the properties of the heterostructure must be identical for 0° and 60° of layer alignment. Here, we demonstrate, using dynamically rotatable van der Waals heterostructures, that the moiré superlattice formed in a bilayer graphene/BN has different electronic properties at 0° and 60° of alignment. Although the existence of these non-identical moiré twins is explained by different relaxation of the atomic structures for each alignment, the origin of the observed valley Hall effect remains to be explained. A simple Berry curvature argument is not sufficient to explain the 120° periodicity of this observation. Our results highlight the complexity of the interplay between mechanical and electronic properties in moiré structures and the importance of taking into account atomic structure relaxation to understand their electronic properties.
Evidence for increased parallel information transmission in human brain networks compared to macaques and male mice
Authors: Griffa Alessandra , Mach Mathieu , Dedelley Julien , Gutierrez-Barragan Daniel , Gozzi Alessandro , Allali Gilles , Grandjean Joanes , Van De Ville Dimitri , Amico Enrico 
Published: December 2023

AbstractBrain communication, defined as information transmission through white-matter connections, is at the foundation of the brain’s computational capacities that subtend almost all aspects of behavior: from sensory perception shared across mammalian species, to complex cognitive functions in humans. How did communication strategies in macroscale brain networks adapt across evolution to accomplish increasingly complex functions? By applying a graph- and information-theory approach to assess information-related pathways in male mouse, macaque and human brains, we show a brain communication gap between selective information transmission in non-human mammals, where brain regions share information through single polysynaptic pathways, and parallel information transmission in humans, where regions share information through multiple parallel pathways. In humans, parallel transmission acts as a major connector between unimodal and transmodal systems. The layout of information-related pathways is unique to individuals across different mammalian species, pointing at the individual-level specificity of information routing architecture. Our work provides evidence that different communication patterns are tied to the evolution of mammalian brain networks.
Debiased inference for heterogeneous subpopulations in a high-dimensional logistic regression model
Authors: Kim Hyunjin , Lee Eun Ryung , Park Seyoung 
Published: December 2023

AbstractDue to the prevalence of complex data, data heterogeneity is often observed in contemporary scientific studies and various applications. Motivated by studies on cancer cell lines, we consider the analysis of heterogeneous subpopulations with binary responses and high-dimensional covariates. In many practical scenarios, it is common to use a single regression model for the entire data set. To do this effectively, it is critical to quantify the heterogeneity of the effect of covariates across subpopulations through appropriate statistical inference. However, the high dimensionality and discrete nature of the data can lead to challenges in inference. Therefore, we propose a novel statistical inference method for a high-dimensional logistic regression model that accounts for heterogeneous subpopulations. Our primary goal is to investigate heterogeneity across subpopulations by testing the equivalence of the effect of a covariate and the significance of the overall effects of a covariate. To achieve overall sparsity of the coefficients and their fusions across subpopulations, we employ a fused group Lasso penalization method. In addition, we develop a statistical inference method that incorporates bias correction of the proposed penalized method. To address computational issues due to the nonlinear log-likelihood and the fused Lasso penalty, we propose a computationally efficient and fast algorithm by adapting the ideas of the proximal gradient method and the alternating direction method of multipliers (ADMM) to our settings. Furthermore, we develop non-asymptotic analyses for the proposed fused group Lasso and prove that the debiased test statistics admit chi-squared approximations even in the presence of high-dimensional variables. In simulations, the proposed test outperforms existing methods. The practical effectiveness of the proposed method is demonstrated by analyzing data from the Cancer Cell Line Encyclopedia (CCLE).