bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spin-filtered measurements of Andreev bound states in semiconductor-superconductor nanowire devices
Authors: van Driel David , Wang Guanzhong , Bordin Alberto , van Loo Nick , Zatelli Francesco , Mazur Grzegorz P. , Xu Di , Gazibegovic Sasa , Badawy Ghada , Bakkers Erik P. A. M. , Kouwenhoven Leo P. , Dvir Tom 
Published: October 2023

AbstractSemiconductor nanowires coupled to superconductors can host Andreev bound states with distinct spin and parity, including a spin-zero state with an even number of electrons and a spin-1/2 state with odd-parity. Considering the difference in spin of the even and odd states, spin-filtered measurements can reveal the underlying ground state. To directly measure the spin of single-electron excitations, we probe an Andreev bound state using a spin-polarized quantum dot that acts as a bipolar spin filter, in combination with a non-polarized tunnel junction in a three-terminal circuit. We observe a spin-polarized excitation spectrum of the Andreev bound state, which can be fully spin-polarized, despite strong spin-orbit interaction in the InSb nanowires. Decoupling the hybrid from the normal lead causes a current blockade, by trapping the Andreev bound state in an excited state. Spin-polarized spectroscopy of hybrid nanowire devices, as demonstrated here, is proposed as an experimental tool to support the observation of topological superconductivity.
Tracing multiple scattering trajectories for deep optical imaging in scattering media
Authors: Kang Sungsam , Kwon Yongwoo , Lee Hojun , Kim Seho , Hong Jin Hee , Yoon Seokchan , Choi Wonshik 
Published: October 2023

AbstractMultiple light scattering hampers imaging objects in complex scattering media. Approaches used in real practices mainly aim to filter out multiple scattering obscuring the ballistic waves that travel straight through the scattering medium. Here, we propose a method that makes the deterministic use of multiple scattering for microscopic imaging of an object embedded deep within scattering media. The proposed method finds a stack of multiple complex phase plates that generate similar light trajectories as the original scattering medium. By implementing the inverse scattering using the identified phase plates, our method rectifies multiple scattering and amplifies ballistic waves by almost 600 times. This leads to a significant increase in imaging depth—more than three times the scattering mean free path—as well as the correction of image distortions. Our study marks an important milestone in solving the long-standing high-order inverse scattering problems.
Ambient noise differential adjoint tomography reveals fluid-bearing rocks near active faults in Los Angeles
Authors: Liu Xin , Beroza Gregory C. , Li Hongyi 
Published: October 2023

AbstractWater scarcity is a pressing issue in California. We develop ambient noise differential adjoint tomography that improves the sensitivity to fluid-bearing rocks by canceling bias caused by noise sources. Here we image the shallow S-wave velocity structure using this method beneath a linear seismic array (LASSIE) in Los Angeles Basin, which shows significant velocity reduction marking a major regional water producer, the Silverado aquifer, along with other fluid-bearing structures. Based on the S-wave tomography and previous P-wave studies, we derive the porosity in Long Beach and discover that the rock from 1-2 km depth surrounding the Newport-Inglewood Fault contains abundant fluids with pore-fluid fraction ~0.33. The high-porosity rock around the fault coincides with previously observed week-long shallow seismicity south of LASSIE array in Long Beach. The imaged S-wave velocity in the top layer shows a similar trend in the geotechnical layer Vs 30, suggesting additional applications to ground motion prediction.
Emergence of cortical network motifs for short-term memory during learning
Authors: Chia Xin Wei , Tan Jian Kwang , Ang Lee Fang , Kamigaki Tsukasa , Makino Hiroshi 
Published: October 2023

AbstractLearning of adaptive behaviors requires the refinement of coordinated activity across multiple brain regions. However, how neural communications develop during learning remains poorly understood. Here, using two-photon calcium imaging, we simultaneously recorded the activity of layer 2/3 excitatory neurons in eight regions of the mouse dorsal cortex during learning of a delayed-response task. Across learning, while global functional connectivity became sparser, there emerged a subnetwork comprising of neurons in the anterior lateral motor cortex (ALM) and posterior parietal cortex (PPC). Neurons in this subnetwork shared a similar choice code during action preparation and formed recurrent functional connectivity across learning. Suppression of PPC activity disrupted choice selectivity in ALM and impaired task performance. Recurrent neural networks reconstructed from ALM activity revealed that PPC-ALM interactions rendered choice-related attractor dynamics more stable. Thus, learning constructs cortical network motifs by recruiting specific inter-areal communication channels to promote efficient and robust sensorimotor transformation.
Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection
Authors: Hashimi Marziah , Sebrell T. Andrew , Hedges Jodi F. , Snyder Deann , Lyon Katrina N. , Byrum Stephanie D. , Mackintosh Samuel G. , Crowley Dan , Cherne Michelle D. , Skwarchuk David , Robison Amanda , Sidar Barkan , Kunze Anja , Loveday Emma K. , Taylor Matthew P. , Chang Connie B. , Wilking James N. , Walk Seth T. , Schountz Tony , Jutila Mark A. , Bimczok Diane 
Published: October 2023

AbstractBats are natural reservoirs for several zoonotic viruses, potentially due to an enhanced capacity to control viral infection. However, the mechanisms of antiviral responses in bats are poorly defined. Here we established a Jamaican fruit bat (JFB, Artibeus jamaicensis) intestinal organoid model of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Upon infection with SARS-CoV-2, increased viral RNA and subgenomic RNA was detected, but no infectious virus was released, indicating that JFB organoids support only limited viral replication but not viral reproduction. SARS-CoV-2 replication was associated with significantly increased gene expression of type I interferons and inflammatory cytokines. Interestingly, SARS-CoV-2 also caused enhanced formation and growth of JFB organoids. Proteomics revealed an increase in inflammatory signaling, cell turnover, cell repair, and SARS-CoV-2 infection pathways. Collectively, our findings suggest that primary JFB intestinal epithelial cells mount successful antiviral interferon responses and that SARS-CoV-2 infection in JFB cells induces protective regenerative pathways.
Ventral striatal islands of Calleja neurons bidirectionally mediate depression-like behaviors in mice
Authors: Zhang Yun-Feng , Wu Jialiang , Wang Yingqi , Johnson Natalie L. , Bhattarai Janardhan P. , Li Guanqing , Wang Wenqiang , Guevara Camilo , Shoenhard Hannah , Fuccillo Marc V. , Wesson Daniel W. , Ma Minghong 
Published: October 2023

AbstractThe ventral striatum is a reward center implicated in the pathophysiology of depression. It contains islands of Calleja, clusters of dopamine D3 receptor-expressing granule cells, predominantly in the olfactory tubercle (OT). These OT D3 neurons regulate self-grooming, a repetitive behavior manifested in affective disorders. Here we show that chronic restraint stress (CRS) induces robust depression-like behaviors in mice and decreases excitability of OT D3 neurons. Ablation or inhibition of these neurons leads to depression-like behaviors, whereas their activation ameliorates CRS-induced depression-like behaviors. Moreover, activation of OT D3 neurons has a rewarding effect, which diminishes when grooming is blocked. Finally, we propose a model that explains how OT D3 neurons may influence dopamine release via synaptic connections with OT spiny projection neurons (SPNs) that project to midbrain dopamine neurons. Our study reveals a crucial role of OT D3 neurons in bidirectionally mediating depression-like behaviors, suggesting a potential therapeutic target.
The therapeutic value of bifidobacteria in cardiovascular disease
Authors: Tang Jia , Wei Yumeng , Pi Chao , Zheng Wenwu , Zuo Ying , Shi Peng , Chen Jinglin , Xiong Linjin , Chen Tao , Liu Huiyang , Zhao Qianjiao , Yin Suyu , Ren Wei , Cao Peng , Zeng Nan , Zhao Ling 
Published: October 2023

AbstractThere has been an increase in cardiovascular morbidity and mortality over the past few decades, making cardiovascular disease (CVD) the leading cause of death worldwide. However, the pathogenesis of CVD is multi-factorial, complex, and not fully understood. The gut microbiome has long been recognized to play a critical role in maintaining the physiological and metabolic health of the host. Recent scientific advances have provided evidence that alterations in the gut microbiome and its metabolites have a profound influence on the development and progression of CVD. Among the trillions of microorganisms in the gut, bifidobacteria, which, interestingly, were found through the literature to play a key role not only in regulating gut microbiota function and metabolism, but also in reducing classical risk factors for CVD (e.g., obesity, hyperlipidemia, diabetes) by suppressing oxidative stress, improving immunomodulation, and correcting lipid, glucose, and cholesterol metabolism. This review explores the direct and indirect effects of bifidobacteria on the development of CVD and highlights its potential therapeutic value in hypertension, atherosclerosis, myocardial infarction, and heart failure. By describing the key role of Bifidobacterium in the link between gut microbiology and CVD, we aim to provide a theoretical basis for improving the subsequent clinical applications of Bifidobacterium and for the development of Bifidobacterium nutritional products.
Trajectory sampling and finite-size effects in first-principles stopping power calculations
Authors: Kononov Alina , Hentschel Thomas W. , Hansen Stephanie B. , Baczewski Andrew D. 
Published: October 2023

AbstractReal-time time-dependent density functional theory (TDDFT) is presently the most accurate available method for computing electronic stopping powers from first principles. However, obtaining application-relevant results often involves either costly averages over multiple calculations or ad hoc selection of a representative ion trajectory. We consider a broadly applicable, quantitative metric for evaluating and optimizing trajectories in this context. This methodology enables rigorous analysis of the failure modes of various common trajectory choices in crystalline materials. Although randomly selecting trajectories is common practice in stopping power calculations in solids, we show that nearly 30% of random trajectories in an FCC aluminum crystal will not representatively sample the material over the time and length scales feasibly simulated with TDDFT, and unrepresentative choices incur errors of up to 60%. We also show that finite-size effects depend on ion trajectory via “ouroboros” effects beyond the prevailing plasmon-based interpretation, and we propose a cost-reducing scheme to obtain converged results even when expensive core-electron contributions preclude large supercells. This work helps to mitigate poorly controlled approximations in first-principles stopping power calculations, allowing 1–2 order of magnitude cost reductions for obtaining representatively averaged and converged results.
A mechanosensitive caveolae–invadosome interplay drives matrix remodelling for cancer cell invasion
Authors: Monteiro Pedro , Remy David , Lemerle Eline , Routet Fiona , Macé Anne-Sophie , Guedj Chloé , Ladoux Benoit , Vassilopoulos Stéphane , Lamaze Christophe , Chavrier Philippe 
Published: October 2023

AbstractInvadosomes and caveolae are mechanosensitive structures that are implicated in metastasis. Here, we describe a unique juxtaposition of caveola clusters and matrix degradative invadosomes at contact sites between the plasma membrane of cancer cells and constricting fibrils both in 2D and 3D type I collagen matrix environments. Preferential association between caveolae and straight segments of the fibrils, and between invadosomes and bent segments of the fibrils, was observed along with matrix remodelling. Caveola recruitment precedes and is required for invadosome formation and activity. Reciprocally, invadosome disruption results in the accumulation of fibril-associated caveolae. Moreover, caveolae and the collagen receptor β1 integrin co-localize at contact sites with the fibrils, and integrins control caveola recruitment to fibrils. In turn, caveolae mediate the clearance of β1 integrin and collagen uptake in an invadosome-dependent and collagen-cleavage-dependent mechanism. Our data reveal a reciprocal interplay between caveolae and invadosomes that coordinates adhesion to and proteolytic remodelling of confining fibrils to support tumour cell dissemination.
Association between pathologic response and survival after neoadjuvant therapy in lung cancer
Authors: Deutsch Julie Stein , Cimino-Mathews Ashley , Thompson Elizabeth , Provencio Mariano , Forde Patrick M. , Spicer Jonathan , Girard Nicolas , Wang Daphne , Anders Robert A. , Gabrielson Edward , Illei Peter , Jedrych Jaroslaw , Danilova Ludmila , Sunshine Joel , Kerr Keith M. , Tran Mia , Bushong Judith , Cai Junliang , Devas Vipul , Neely Jaclyn , Balli David , Cottrell Tricia R. , Baras Alex S. , Taube Janis M. 
Published: October 2023

AbstractNeoadjuvant immunotherapy plus chemotherapy improves event-free survival (EFS) and pathologic complete response (0% residual viable tumor (RVT) in primary tumor (PT) and lymph nodes (LNs)), and is approved for treatment of resectable lung cancer. Pathologic response assessment after neoadjuvant therapy is the potential analog to radiographic response for advanced disease. However, %RVT thresholds beyond pathologic complete response and major pathologic response (≤10% RVT) have not been explored. Pathologic response was prospectively assessed in the randomized, phase 3 CheckMate 816 trial (NCT02998528), which evaluated neoadjuvant nivolumab (anti-programmed death protein 1) plus chemotherapy in patients with resectable lung cancer. RVT, regression and necrosis were quantified (0–100%) in PT and LNs using a pan-tumor scoring system and tested for association with EFS in a prespecified exploratory analysis. Regardless of LN involvement, EFS improved with 0% versus >0% RVT-PT (hazard ratio = 0.18). RVT-PT predicted EFS for nivolumab plus chemotherapy (area under the curve = 0.74); 2-year EFS rates were 90%, 60%, 57% and 39% for patients with 0–5%, >5–30%, >30–80% and >80% RVT, respectively. Each 1% RVT associated with a 0.017 hazard ratio increase for EFS. Combining pathologic response from PT and LNs helped differentiate outcomes. When compared with radiographic response and circulating tumor DNA clearance, %RVT best approximated EFS. These findings support pathologic response as an emerging survival surrogate. Further assessment of the full spectrum of %RVT in lung cancer and other tumor types is warranted. ClinicalTrials.gov registration: NCT02998528.
Dissecting neural computations in the human auditory pathway using deep neural networks for speech
Authors: Li Yuanning , Anumanchipalli Gopala K. , Mohamed Abdelrahman , Chen Peili , Carney Laurel H. , Lu Junfeng , Wu Jinsong , Chang Edward F. 
Published: October 2023

AbstractThe human auditory system extracts rich linguistic abstractions from speech signals. Traditional approaches to understanding this complex process have used linear feature-encoding models, with limited success. Artificial neural networks excel in speech recognition tasks and offer promising computational models of speech processing. We used speech representations in state-of-the-art deep neural network (DNN) models to investigate neural coding from the auditory nerve to the speech cortex. Representations in hierarchical layers of the DNN correlated well with the neural activity throughout the ascending auditory system. Unsupervised speech models performed at least as well as other purely supervised or fine-tuned models. Deeper DNN layers were better correlated with the neural activity in the higher-order auditory cortex, with computations aligned with phonemic and syllabic structures in speech. Accordingly, DNN models trained on either English or Mandarin predicted cortical responses in native speakers of each language. These results reveal convergence between DNN model representations and the biological auditory pathway, offering new approaches for modeling neural coding in the auditory cortex.
Assessment of the eye surface and subjective symptoms after using 0.1% dexamethasone drops with and without preservatives in patients after cataract surgery
Authors: Muzyka-Woźniak Maria , Stróżecki Łukasz , Przeździecka-Dołyk Joanna 
Published: October 2023

AbstractCataract surgery can cause dry eye symptoms. One of the many factors compromising the ocular surface is the use of benzalkonium chloride (BAC)-preserved topical eye drops administered during the postoperative period. In this open-label, prospective, randomized, comparative clinical trial, 40 patients not previously affected by dry eye disease were assigned to receive either preservative-free (PFD) or preserved (PD) dexamethasone 0.1% eye drops for two weeks after a standard phacoemulsification procedure. Fluorescein break-up time, ocular surface staining score, Schirmer test, Ocular Surface Disease Index and anterior chamber (AC) cells were evaluated at baseline prior to the surgery and 2 weeks after surgery. No statistically significant differences in baseline assessments were observed between groups. At week 2, a significant increase in corneal staining scores (p = 0.003) and foreign body sensation (p = 0.04) was observed for the PD group only. The conjunctival staining score was significantly higher in both groups. The mean AC cell grading was higher in the PFD group than in the PD group (0.28 ± 0.30 and 0.07 ± 0.18, respectively; p = 0.013). Preservative-free dexamethasone eye drops after cataract surgery caused milder dry eye symptoms as compared with preserved dexamethasone. The AC inflammation control comparison may require a larger study group. Trial registration: ClinicalTrials.gov identifier NCT05753787, 03/03/2023.
Features of architectural landscape fragmentation in traditional villages in Western Hunan, China
Authors: Zeng Can , Liu Peilin , Huang Liuqian , Feng Shun , Li Yu 
Published: October 2023

AbstractWith rapid industrialization and urbanization in China, inadequate preservation of traditional architecture coupled with natural deterioration have led to the fragmentation of architectural landscapes. Drawing from ecological fragmentation research in landscape ecology, we consider the cultural landscape as our research object, viewing buildings as landscape patches, and determine a system for measuring architectural landscape fragmentation in traditional villages. The study shows the degree of landscape fragmentation can reveal the characteristics of traditional villages and the process of regional modernization. The results are as follows: (1) From the perspective of landscape diversity, the study area was rich in landscape types in all dimensions, and the relative evenness index was high, signifying evident or severe fragmentation. (2) The index of landscape heterogeneity in the dimensions of building quality, height, and landscape appearance is low in the study area, with mild levels of landscape fragmentation caused by heterogeneity in the aforementioned dimensions. (3) Mild fragmentation suggests the integrity and homogeneity of architectural landscape types, reflecting a lagging level of economic development, whereas high fragmentation signifies rapid economic development, leading to a substantial deterioration in the integrity and homogeneity of architectural landscape types. Therefore, efforts to preserve and develop traditional villages should not solely aim for low fragmentation as it could potentially constrain sustainable development.
Exploring intrinsic variability between cultured nasal and bronchial epithelia in cystic fibrosis
Authors: Rodenburg Lisa W. , Metzemaekers Mieke , van der Windt Isabelle S. , Smits Shannon M. A. , den Hertog-Oosterhoff Loes A. , Kruisselbrink Evelien , Brunsveld Jesse E. , Michel Sabine , de Winter-de Groot Karin M. , van der Ent Cornelis K. , Stadhouders Ralph , Beekman Jeffrey M. , Amatngalim Gimano D. 
Published: October 2023

AbstractThe nasal and bronchial epithelium are unified parts of the respiratory tract that are affected in the monogenic disorder cystic fibrosis (CF). Recent studies have uncovered that nasal and bronchial tissues exhibit intrinsic variability, including differences in mucociliary cell composition and expression of unique transcriptional regulatory proteins which relate to germ layer origin. In the present study, we explored whether intrinsic differences between nasal and bronchial epithelial cells persist in cell cultures and affect epithelial cell functioning in CF. Comparison of air–liquid interface (ALI) differentiated epithelial cells from subjects with CF revealed distinct mucociliary differentiation states of nasal and bronchial cultures. Moreover, using RNA sequencing we identified cell type-specific signature transcription factors in differentiated nasal and bronchial epithelial cells, some of which were already poised for expression in basal progenitor cells as evidenced by ATAC sequencing. Analysis of differentiated nasal and bronchial epithelial 3D organoids revealed distinct capacities for fluid secretion, which was linked to differences in ciliated cell differentiation. In conclusion, we show that unique phenotypical and functional features of nasal and bronchial epithelial cells persist in cell culture models, which can be further used to investigate the effects of tissue-specific features on upper and lower respiratory disease development in CF.