bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ptycho-endoscopy on a lensless ultrathin fiber bundle tip
Authors: Song Pengming , Wang Ruihai , Loetgering Lars , Liu Jia , Vouras Peter , Lee Yujin , Jiang Shaowei , Feng Bin , Maiden Andrew , Yang Changhuei , Zheng Guoan 
Published: July 2024

AbstractSynthetic aperture radar (SAR) utilizes an aircraft-carried antenna to emit electromagnetic pulses and detect the returning echoes. As the aircraft travels across a designated area, it synthesizes a large virtual aperture to improve image resolution. Inspired by SAR, we introduce synthetic aperture ptycho-endoscopy (SAPE) for micro-endoscopic imaging beyond the diffraction limit. SAPE operates by hand-holding a lensless fiber bundle tip to record coherent diffraction patterns from specimens. The fiber cores at the distal tip modulate the diffracted wavefield within a confined area, emulating the role of the ‘airborne antenna’ in SAR. The handheld operation introduces positional shifts to the tip, analogous to the aircraft’s movement. These shifts facilitate the acquisition of a ptychogram and synthesize a large virtual aperture extending beyond the bundle’s physical limit. We mitigate the influences of hand motion and fiber bending through a low-rank spatiotemporal decomposition of the bundle’s modulation profile. Our tests demonstrate the ability to resolve a 548-nm linewidth on a resolution target. The achieved space-bandwidth product is ~1.1 million effective pixels, representing a 36-fold increase compared to that of the original fiber bundle. Furthermore, SAPE’s refocusing capability enables imaging over an extended depth of field exceeding 2 cm. The aperture synthesizing process in SAPE surpasses the diffraction limit set by the probe’s maximum collection angle, opening new opportunities for both fiber-based and distal-chip endoscopy in applications such as medical diagnostics and industrial inspection.
Phenomena of hypo- and hyperconnectivity in basal ganglia-thalamo-cortical circuits linked to major depression: a 7T fMRI study
Authors: Hagen Jana , Ramkiran Shukti , Schnellbächer Gereon J. , Rajkumar Ravichandran , Collee Maria , Khudeish Nibal , Veselinović Tanja , Shah N. Jon , Neuner Irene 
Published: July 2024

Abstract
Major depressive disorder (MDD) typically manifests itself in depressed affect, anhedonia, low energy, and additional symptoms. Despite its high global prevalence, its pathophysiology still gives rise to questions. Current research places alterations in functional connectivity among MDD’s most promising biomarkers. However, given the heterogeneity of previous findings, the use of higher-resolution imaging techniques, like ultra-high field (UHF) fMRI (≥7 Tesla, 7T), may offer greater specificity in delineating fundamental impairments. In this study, 7T UHF fMRI scans were conducted on 31 MDD patients and 27 age-gender matched healthy controls to exploratorily contrast cerebral resting-state functional connectivity patterns between both groups. The CONN toolbox was used to generate functional network connectivity (FNC) analysis based on the region of interest (ROI)-to-ROI correlations in order to enable the identification of clusters of significantly different connections. Correction for multiple comparisons was implemented at the cluster level using a false discovery rate (FDR). The analysis revealed three significant clusters differentiating MDD patients and healthy controls. In Clusters 1 and 2, MDD patients exhibited between-network hypoconnectivity in basal ganglia-cortical pathways as well as hyperconnectivity in thalamo-cortical pathways, including several individual ROI-to-ROI connections. In Cluster 3, they showed increased occipital interhemispheric within-network connectivity. These findings suggest that alterations in basal ganglia-thalamo-cortical circuits play a substantial role in the pathophysiology of MDD. Furthermore, they indicate potential MDD-related deficits relating to a combination of perception (vision, audition, and somatosensation) as well as more complex functions, especially social-emotional processing, modulation, and regulation. It is anticipated that these findings might further inform more accurate clinical procedures for addressing MDD.
Exploring treatment options in cancer: tumor treatment strategies
Authors: Liu Beilei , Zhou Hongyu , Tan Licheng , Siu Kin To Hugo , Guan Xin-Yuan 
Published: July 2024

AbstractTraditional therapeutic approaches such as chemotherapy and radiation therapy have burdened cancer patients with onerous physical and psychological challenges. Encouragingly, the landscape of tumor treatment has undergone a comprehensive and remarkable transformation. Emerging as fervently pursued modalities are small molecule targeted agents, antibody-drug conjugates (ADCs), cell-based therapies, and gene therapy. These cutting-edge treatment modalities not only afford personalized and precise tumor targeting, but also provide patients with enhanced therapeutic comfort and the potential to impede disease progression. Nonetheless, it is acknowledged that these therapeutic strategies still harbour untapped potential for further advancement. Gaining a comprehensive understanding of the merits and limitations of these treatment modalities holds the promise of offering novel perspectives for clinical practice and foundational research endeavours. In this review, we discussed the different treatment modalities, including small molecule targeted drugs, peptide drugs, antibody drugs, cell therapy, and gene therapy. It will provide a detailed explanation of each method, addressing their status of development, clinical challenges, and potential solutions. The aim is to assist clinicians and researchers in gaining a deeper understanding of these diverse treatment options, enabling them to carry out effective treatment and advance their research more efficiently.
A rare case of spinal involvement in hereditary hemorrhagic telangiectasia
Authors: Hvingelby V. , Mikkelsen Ronni , Gudmundsdottir Gudrun , Andersen Marlene , Hagen Ellen Merete 
Published: July 2024

Abstract
Introduction
Here, we describe a rare case of a spinal arteriovenous fistula in a patient with known hereditary hemorrhagic telangiectasia (HHT) and spontaneous intraspinal hemorrhage. Furthermore, we provide a brief review of the literature on the formation of spinal arteriovenous malformations (AVM) in relation to this disease.

Case presentation
The case involves a 54-year-old male with known HHT. At the age of 49, the patient experienced recurrent cystitis. Urological evaluation ruled the cause to be neurological and subsequent imaging revealed a thoracic AVM. Four years later, the patient was admitted to A&E with chest pain and loss of function of the lower extremities and right arm, suspicious for ruptured aortic dissection. Trauma-CT excluded this and a final diagnosis of ruptured spinal AVM was made. Seven months post-injury, a spinal angiography was performed confirming the AVM. The remaining AVM was embolized under general anesthesia with acceptable results.

Discussion
Spinal involvement in HHT is exceedingly rare but remains an important differential diagnosis, especially when patients present autonomic symptoms as these could potentially progress to life-threatening complications. The literature and the presented case indicate the prudence of closing spinal AVMs in HHT in case of symptoms, including autonomic, such as bladder dysfunction.
Altered insular functional activity among electronic cigarettes users with nicotine dependence
Authors: Sun Yunkai , Xie An , Fang Yehong , Chen Haobo , Li Ling , Tang Jinsong , Liao Yanhui 
Published: July 2024

AbstractElectronic cigarettes (e-cigs) use, especially among youngsters, has been on the rise in recent years. However, little is known about the long-term effects of the use of e-cigs on brain functional activity. We acquired the resting-state functional magnetic resonance imaging (rs-fMRI) data from 93 e-cigs users with nicotine dependence and 103 health controls (HC). The local synchronization was analyzed via the regional homogeneity (ReHo) method at voxel-wise level. The functional connectivity (FC) between the nucleus accumbens (NAcc), the ventral tegmental area (VTA), and the insula was calculated at ROI-wise level. The support vector machining classification model based on rs-fMRI measures was used to identify e-cigs users from HC. Compared with HC, nicotine-dependent e-cigs users showed increased ReHo in the right rolandic operculum and the right insula (p < 0.05, FDR corrected). At the ROI-wise level, abnormal FCs between the NAcc, the VTA, and the insula were found in e-cigs users compared to HC (p < 0.05, FDR corrected). Correlation analysis found a significant negative correlation between ReHo in the left NAcc and duration of e-cigs use (r = −0.273, p = 0.008, FDR corrected). The following support vector machine model based on significant results of rs-fMRI successfully differentiates chronic e-cigs users from HC with an accuracy of 73.47%, an AUC of 0.781, a sensitivity of 67.74%, and a specificity of 78.64%. Dysregulated spontaneous activity and FC of addiction-related regions were found in e-cigs users with nicotine dependence, which provides crucial insights into the prevention of its initial use and intervention for quitting e-cigs.
Differential effects of desvenlafaxine on hot flashes in women with breast cancer taking tamoxifen: a randomized controlled trial
Authors: Kim Yongjoo , Yeom Chan-Woo , Lee Hyun Jeong , Kim Jeong-Hyun , Lee Kwang-Min , Kim Tae-Yong , Lee Han-Byoel , Kim Hoon , Im Seock-Ah , Lee Kyung-Hun , Kim Miso , Han Wonsik , Moon Hyeong-Gon , Spiegel David , Hahm Bong-Jin , Son Kyung-Lak 
Published: July 2024

AbstractHot flashes (HF) are a common adverse event of prolonged tamoxifen use in women with estrogen receptor-positive breast cancer, impacting psychiatric health and quality of life. While desvenlafaxine does not interact with tamoxifen, its efficacy and safety in breast cancer patients remain unstudied. This phase 3, four-week, multi-center, three-arm, parallel-group, randomized, double-blind, placebo-controlled trial investigated the efficacy and safety of desvenlafaxine for treating HF in women with breast cancer taking tamoxifen, assessing potential differential effects in patients with psychiatric and inflammatory conditions. Between December 2017 and February 2019, 57 women aged 19 or older, regularly taking tamoxifen as adjuvant therapy, experiencing moderate-to-severe HFs for more than a month, were randomized to receive desvenlafaxine 50 mg/day (D-50), desvenlafaxine 100 mg/day (D-100), or placebo for four weeks. The primary endpoint was the change rate in HF scores over four weeks, with adverse events as a secondary endpoint. Both desvenlafaxine arms demonstrated greater HF score reductions compared to placebo: D-50 (2.20 points/week, 95% CI: 0.71, 3.68) and D-100 (2.34 points/week, 95% CI: 0.92, 3.76). Notably, D-50 arm showed significantly greater efficacy in patients with depression or elevated inflammation. Desvenlafaxine offers an effective and safe treatment regimen for HF in women with breast cancer taking tamoxifen. The presence of depression and inflammation may guide optimal desvenlafaxine dosing. (Trial Registration: ClinicalTrials.gov Identifier: NCT02819921)
Learning together: Towards foundation models for machine learning interatomic potentials with meta-learning
Authors: Allen Alice E. A. , Lubbers Nicholas , Matin Sakib , Smith Justin , Messerly Richard , Tretiak Sergei , Barros Kipton 
Published: July 2024

AbstractThe development of machine learning models has led to an abundance of datasets containing quantum mechanical (QM) calculations for molecular and material systems. However, traditional training methods for machine learning models are unable to leverage the plethora of data available as they require that each dataset be generated using the same QM method. Taking machine learning interatomic potentials (MLIPs) as an example, we show that meta-learning techniques, a recent advancement from the machine learning community, can be used to fit multiple levels of QM theory in the same training process. Meta-learning changes the training procedure to learn a representation that can be easily re-trained to new tasks with small amounts of data. We then demonstrate that meta-learning enables simultaneously training to multiple large organic molecule datasets. As a proof of concept, we examine the performance of a MLIP refit to a small drug-like molecule and show that pre-training potentials to multiple levels of theory with meta-learning improves performance. This difference in performance can be seen both in the reduced error and in the improved smoothness of the potential energy surface produced. We therefore show that meta-learning can utilize existing datasets with inconsistent QM levels of theory to produce models that are better at specializing to new datasets. This opens new routes for creating pre-trained, foundation models for interatomic potentials.
A deep position-encoding model for predicting olfactory perception from molecular structures and electrostatics
Authors: Zhang Mengji , Hiki Yusuke , Funahashi Akira , Kobayashi Tetsuya J. 
Published: July 2024

AbstractPredicting olfactory perceptions from odorant molecules is challenging due to the complex and potentially discontinuous nature of the perceptual space for smells. In this study, we introduce a deep learning model, Mol-PECO (Molecular Representation by Positional Encoding of Coulomb Matrix), designed to predict olfactory perceptions based on molecular structures and electrostatics. Mol-PECO learns the efficient embedding of molecules by utilizing the Coulomb matrix, which encodes atomic coordinates and charges, as an alternative of the adjacency matrix and its Laplacian eigenfunctions as positional encoding of atoms. With a comprehensive dataset of odor molecules and descriptors, Mol-PECO outperforms traditional machine learning methods using molecular fingerprints and graph neural networks based on adjacency matrices. The learned embeddings by Mol-PECO effectively capture the odor space, enabling global clustering of descriptors and local retrieval of similar odorants. This work contributes to a deeper understanding of the olfactory sense and its mechanisms.
Position-dependent function of human sequence-specific transcription factors
Authors: Duttke Sascha H. , Guzman Carlos , Chang Max , Delos Santos Nathaniel P. , McDonald Bayley R. , Xie Jialei , Carlin Aaron F. , Heinz Sven , Benner Christopher 
Published: July 2024

AbstractPatterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, contain similar assortments of sequence-specific transcription factor (TF) binding sites1–3. Knowledge of how these sequence motifs encode multiple, often overlapping, gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease4,5. Here, by studying gene regulation from the perspective of individual transcription start sites (TSSs), using natural genetic variation, perturbation of endogenous TF protein levels and massively parallel analysis of natural and synthetic regulatory elements, we show that the effect of TF binding on transcription initiation is position dependent. Analysing TF-binding-site occurrences relative to the TSS, we identified several motifs with highly preferential positioning. We show that these patterns are a combination of a TF’s distinct functional profiles—many TFs, including canonical activators such as NRF1, NFY and Sp1, activate or repress transcription initiation depending on their precise position relative to the TSS. As such, TFs and their spacing collectively guide the site and frequency of transcription initiation. More broadly, these findings reveal how similar assortments of TF binding sites can generate distinct gene regulatory outcomes depending on their spatial configuration and how DNA sequence polymorphisms may contribute to transcription variation and disease and underscore a critical role for TSS data in decoding the regulatory information of our genome.
In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution
Authors: Renz Peter F. , Ghoshdastider Umesh , Baghai Sain Simona , Valdivia-Francia Fabiola , Khandekar Ameya , Ormiston Mark , Bernasconi Martino , Duré Clara , Kretz Jonas A. , Lee Minkyoung , Hyams Katie , Forny Merima , Pohly Marcel , Ficht Xenia , Ellis Stephanie J. , Moor Andreas E. , Sendoel Ataman 
Published: July 2024

AbstractThe tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues1–3, the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial–mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.
Giant chiral magnetoelectric oscillations in a van der Waals multiferroic
Authors: Gao Frank Y. , Peng Xinyue , Cheng Xinle , Viñas Boström Emil , Kim Dong Seob , Jain Ravish K. , Vishnu Deepak , Raju Kalaivanan , Sankar Raman , Lee Shang-Fan , Sentef Michael A. , Kurumaji Takashi , Li Xiaoqin , Tang Peizhe , Rubio Angel , Baldini Edoardo 
Published: July 2024

AbstractHelical spin structures are expressions of magnetically induced chirality, entangling the dipolar and magnetic orders in materials1–4. The recent discovery of helical van der Waals multiferroics down to the ultrathin limit raises prospects of large chiral magnetoelectric correlations in two dimensions5,6. However, the exact nature and magnitude of these couplings have remained unknown so far. Here we perform a precision measurement of the dynamical magnetoelectric coupling for an enantiopure domain in an exfoliated van der Waals multiferroic. We evaluate this interaction in resonance with a collective electromagnon mode, capturing the impact of its oscillations on the dipolar and magnetic orders of the material with a suite of ultrafast optical probes. Our data show a giant natural optical activity at terahertz frequencies, characterized by quadrature modulations between the electric polarization and magnetization components. First-principles calculations further show that these chiral couplings originate from the synergy between the non-collinear spin texture and relativistic spin–orbit interactions, resulting in substantial enhancements over lattice-mediated effects. Our findings highlight the potential for intertwined orders to enable unique functionalities in the two-dimensional limit and pave the way for the development of van der Waals magnetoelectric devices operating at terahertz speeds.
A hot-Jupiter progenitor on a super-eccentric retrograde orbit
Authors: Gupta Arvind F. , Millholland Sarah C. , Im Haedam , Dong Jiayin , Jackson Jonathan M. , Carleo Ilaria , Libby-Roberts Jessica , Delamer Megan , Giovinazzi Mark R. , Lin Andrea S. J. , Kanodia Shubham , Wang Xian-Yu , Stassun Keivan , Masseron Thomas , Dragomir Diana , Mahadevan Suvrath , Wright Jason , Alvarado-Montes Jaime A. , Bender Chad , Blake Cullen H. , Caldwell Douglas , Cañas Caleb I. , Cochran William D. , Dalba Paul , Everett Mark E. , Fernandez Pipa , Golub Eli , Guillet Bruno , Halverson Samuel , Hebb Leslie , Higuera Jesus , Huang Chelsea X. , Klusmeyer Jessica , Knight Rachel , Leroux Liouba , Logsdon Sarah E. , Loose Margaret , McElwain Michael W. , Monson Andrew , Ninan Joe P. , Nowak Grzegorz , Palle Enric , Patel Yatrik , Pepper Joshua , Primm Michael , Rajagopal Jayadev , Robertson Paul , Roy Arpita , Schneider Donald P. , Schwab Christian , Schweiker Heidi , Sgro Lauren , Shimizu Masao , Simard Georges , Stefánsson Guðmundur , Stevens Daniel J. , Villanueva Steven , Wisniewski John , Will Stefan , Ziegler Carl 
Published: July 2024

AbstractGiant exoplanets orbiting close to their host stars are unlikely to have formed in their present configurations1. These ‘hot Jupiter’ planets are instead thought to have migrated inward from beyond the ice line and several viable migration channels have been proposed, including eccentricity excitation through angular-momentum exchange with a third body followed by tidally driven orbital circularization2,3. The discovery of the extremely eccentric (e = 0.93) giant exoplanet HD 80606 b (ref. 4) provided observational evidence that hot Jupiters may have formed through this high-eccentricity tidal-migration pathway5. However, no similar hot-Jupiter progenitors have been found and simulations predict that one factor affecting the efficacy of this mechanism is exoplanet mass, as low-mass planets are more likely to be tidally disrupted during periastron passage6–8. Here we present spectroscopic and photometric observations of TIC 241249530 b, a high-mass, transiting warm Jupiter with an extreme orbital eccentricity of e = 0.94. The orbit of TIC 241249530 b is consistent with a history of eccentricity oscillations and a future tidal circularization trajectory. Our analysis of the mass and eccentricity distributions of the transiting-warm-Jupiter population further reveals a correlation between high mass and high eccentricity.