bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing magnetic orbitals and Berry curvature with circular dichroism in resonant inelastic X-ray scattering
Authors: Schüler Michael , Schmitt Thorsten , Werner Philipp 
Published: January 2023

AbstractResonant inelastic X-ray scattering (RIXS) can probe localized excitations at selected atoms in materials, including particle-hole transitions between the valence and conduction bands. These transitions are governed by fundamental properties of the corresponding Bloch wave functions, including orbital and magnetic degrees of freedom, and quantum geometric properties such as the Berry curvature. In particular, orbital angular momentum (OAM), which is closely linked to the Berry curvature, can exhibit a nontrivial momentum dependence. We demonstrate how information on such OAM textures can be extracted from the circular dichroism in RIXS. Based on accurate modeling with a first-principles treatment of the key ingredient—the light–matter interaction—we simulate dichroic RIXS spectra for the prototypical transition-metal dichalcogenide MoSe2 and the two-dimensional topological insulator 1T$${}^{{\prime}}$$

′

-MoS2. Guided by an intuitive picture of the optical selection rules, we discuss how the momentum-dependent OAM manifests itself in the dichroic RIXS signal if one controls the momentum transfer. Our calculations are performed for typical experimental geometries and parameter regimes, and demonstrate the possibility of observing the predicted circular dichroism in forthcoming experiments. Thus, our work establishes a new avenue for observing Berry curvature and topological states in quantum materials.
Mitochondria regulate intracellular coenzyme Q transport and ferroptotic resistance via STARD7
Authors: Deshwal Soni , Onishi Mashun , Tatsuta Takashi , Bartsch Tim , Cors Eileen , Ried Katharina , Lemke Kathrin , Nolte Hendrik , Giavalisco Patrick , Langer Thomas 
Published: January 2023

AbstractCoenzyme Q (or ubiquinone) is a redox-active lipid that serves as universal electron carrier in the mitochondrial respiratory chain and antioxidant in the plasma membrane limiting lipid peroxidation and ferroptosis. Mechanisms allowing cellular coenzyme Q distribution after synthesis within mitochondria are not understood. Here we identify the cytosolic lipid transfer protein STARD7 as a critical factor of intracellular coenzyme Q transport and suppressor of ferroptosis. Dual localization of STARD7 to the intermembrane space of mitochondria and the cytosol upon cleavage by the rhomboid protease PARL ensures the synthesis of coenzyme Q in mitochondria and its transport to the plasma membrane. While mitochondrial STARD7 preserves coenzyme Q synthesis, oxidative phosphorylation function and cristae morphogenesis, cytosolic STARD7 is required for the transport of coenzyme Q to the plasma membrane and protects against ferroptosis. A coenzyme Q variant competes with phosphatidylcholine for binding to purified STARD7 in vitro. Overexpression of cytosolic STARD7 increases ferroptotic resistance of the cells, but limits coenzyme Q abundance in mitochondria and respiratory cell growth. Our findings thus demonstrate the need to coordinate coenzyme Q synthesis and cellular distribution by PARL-mediated STARD7 processing and identify PARL and STARD7 as promising targets to interfere with ferroptosis.
Widespread spring phenology effects on drought recovery of Northern Hemisphere ecosystems
Authors: Li Yang , Zhang Wen , Schwalm Christopher R. , Gentine Pierre , Smith William K. , Ciais Philippe , Kimball John S. , Gazol Antonio , Kannenberg Steven A. , Chen Anping , Piao Shilong , Liu Hongyan , Chen Deliang , Wu Xiuchen 
Published: January 2023

AbstractThe time required for an ecosystem to recover from severe drought is a key component of ecological resilience. The phenology effects on drought recovery are, however, poorly understood. These effects centre on how phenology variations impact biophysical feedbacks, vegetation growth and, ultimately, recovery itself. Using multiple remotely sensed datasets, we found that more than half of ecosystems in mid- and high-latitudinal Northern Hemisphere failed to recover from extreme droughts within a single growing season. Earlier spring phenology in the drought year slowed drought recovery when extreme droughts occurred in mid-growing season. Delayed spring phenology in the subsequent year slowed drought recovery for all vegetation types (with importance of spring phenology ranging from 46% to 58%). The phenology effects on drought recovery were comparable to or larger than other well-known postdrought climatic factors. These results strongly suggest that the interactions between vegetation phenology and drought must be incorporated into Earth system models to accurately quantify ecosystem resilience.
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome
Authors: Laso-Pérez Rafael , Wu Fabai , Crémière Antoine , Speth Daan R. , Magyar John S. , Zhao Kehan , Krupovic Mart , Orphan Victoria J. 
Published: January 2023

Abstract‘CandidatusMethanophagales’ (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, ‘CandidatusMethanospirareceae’, closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.
A wearable motion capture suit and machine learning predict disease progression in Friedreich’s ataxia
Authors: Kadirvelu Balasundaram , Gavriel Constantinos , Nageshwaran Sathiji , Chan Jackson Ping Kei , Nethisinghe Suran , Athanasopoulos Stavros , Ricotti Valeria , Voit Thomas , Giunti Paola , Festenstein Richard , Faisal A. Aldo 
Published: January 2023

AbstractFriedreichʼs ataxia (FA) is caused by a variant of the Frataxin (FXN) gene, leading to its downregulation and progressively impaired cardiac and neurological function. Current gold-standard clinical scales use simplistic behavioral assessments, which require 18- to 24-month-long trials to determine if therapies are beneficial. Here we captured full-body movement kinematics from patients with wearable sensors, enabling us to define digital behavioral features based on the data from nine FA patients (six females and three males) and nine age- and sex-matched controls, who performed the 8-m walk (8-MW) test and 9-hole peg test (9 HPT). We used machine learning to combine these features to longitudinally predict the clinical scores of the FA patients, and compared these with two standard clinical assessments, Spinocerebellar Ataxia Functional Index (SCAFI) and Scale for the Assessment and Rating of Ataxia (SARA). The digital behavioral features enabled longitudinal predictions of personal SARA and SCAFI scores 9 months into the future and were 1.7 and 4 times more precise than longitudinal predictions using only SARA and SCAFI scores, respectively. Unlike the two clinical scales, the digital behavioral features accurately predicted FXN gene expression levels for each FA patient in a cross-sectional manner. Our work demonstrates how data-derived wearable biomarkers can track personal disease trajectories and indicates the potential of such biomarkers for substantially reducing the duration or size of clinical trials testing disease-modifying therapies and for enabling behavioral transcriptomics.
Different clinical characteristics of current smokers and former smokers with asthma: a cross-sectional study of adult asthma patients in China
Authors: Chen Zhifeng , Wasti Binaya , Shang Yulin , Ouyang Ruoyun , Yuan Yu , He Yi , Duan Wentao , Jia Jingsi , Xiao Bing , Zhang Dongshan , Liu Shaokun , Song Qing , Zeng Yuqin , Zeng Qingping , Zhang Xiufeng , Li Jianmin , Ji Xiaoying , Chen Ping , Ma Libing , Xiang Xudong 
Published: January 2023

AbstractSmoking is a trigger for asthma, which has led to an increase in asthma incidence in China. In smokers, asthma management starts with smoking cessation. Data on predictors of smoking cessation in Chinese patients with asthma are scarce. The objective of this study was to find the differences in clinical characteristics between current smokers and former smokers with asthma in order to identify factors associated with smoking cessation. Eligible adults with diagnosed asthma and smoking from the hospital outpatient clinics (n = 2312) were enrolled and underwent a clinical evaluation, asthma control test (ACT), and pulmonary function test. Information on demographic and sociological data, lung function, laboratory tests, ACT and asthma control questionnaire (ACQ) scores was recorded. Patients were divided into a current smokers group and a former smokers group based on whether they had quit smoking. Logistic regression analysis was used to analyze the factors associated with smoking cessation. Of all patients with asthma, 34.6% were smokers and 65.4% were former smokers, and the mean age was 54.5 ± 11.5 years. Compared with current smokers, the former smokers were older, had longer duration of asthma, had higher ICS dose, had more partially controlled and uncontrolled asthma, had more pack-years, had smoked for longer, and had worse asthma control. The logistic regression model showed that smoking cessation was positively correlated with age, female sex, pack-years, years of smoking, partially controlled asthma, uncontrolled asthma, and body mass index (BMI), but was negatively correlated with ACT, FEV1, FEV1%predicted, and widowed status. More than 30% of asthma patients in the study were still smoking. Among those who quit smoking, many quit late, often not realizing they need to quit until they have significant breathing difficulties. The related factors of smoking cessation identified in this study indicate that there are still differences between continuing smokers and former smokers, and these factors should be focused on in asthma smoking cessation interventions to improve the prognosis of patients with asthma.
Properties of non-coding mutation hotspots as urinary biomarkers for bladder cancer detection
Authors: Baxter L. , Gordon N. S. , Ott S. , Wang J. , Patel P. , Goel A. , Piechocki K. , Silcock L. , Sale C. , Zeegers M. P. , Cheng K. K. , James N. D. ,   The BladderPath trial management group, Knight A. , Gallagher J. , Magwaro S. , Hughes A. , Pope A. , Tunariu N. , Doyle H. , Liu W. , Mintz H. , Nanton V. , James K. , Hafeez S. , Catto J. W. F. , Jefferson K. , Pirrie S. J. , Bryan R. T. , Ward D. G. 
Published: January 2023

AbstractMutations at specific hotspots in non-coding regions of ADGRG6, PLEKHS1, WDR74, TBC1D12 and LEPROTL1 frequently occur in bladder cancer (BC). These mutations could function as biomarkers for the non-invasive detection of BC but this remains largely unexplored. Massively-parallel sequencing of non-coding hotspots was applied to 884 urine cell pellet DNAs: 591 from haematuria clinic patients (165 BCs, 426 non-BCs) and 293 from non-muscle invasive BC surveillance patients (29 with recurrence). Urine samples from 142 non-BC haematuria clinic patients were used to optimise variant calling. Non-coding mutations are readily detectable in the urine of BC patients and undetectable, or present at much lower frequencies, in the absence of BC. The mutations can be used to detect incident BC with 66% sensitivity (95% CI 58–75) at 92% specificity (95% CI 88–95) and recurrent disease with 55% sensitivity (95% CI 36–74) at 85% specificity (95% CI 80–89%) using a 2% variant allele frequency threshold. In the NMIBC surveillance setting, the detection of non-coding mutations in urine in the absence of clinically detectable disease was associated with an increased relative risk of future recurrence (RR = 4.62 (95% CI 3.75–5.48)). As urinary biomarkers, non-coding hotspot mutations behave similarly to driver mutations in BC-associated genes and could be included in biomarker panels for BC detection.
Thyroglobulin expression, Ki-67 index, and lymph node ratio in the prognostic assessment of papillary thyroid cancer
Authors: Lindfors Helene , Karlsen Marie , Karlton Ellinor , Zedenius Jan , Larsson Catharina , Ihre Lundgren Catharina , Juhlin C. Christofer , Shabo Ivan 
Published: January 2023

AbstractThe clinical significance of thyroglobulin (Tg) expression in papillary thyroid cancer (PTC) has not been systematically explored in relation to the Ki-67 index, lymph node ratio (LNR), or other conventional prognostic predictors. In this retrospective study of 327 patients with PTC, we investigated the immunohistochemical expression of Tg in both primary tumors and their matching lymph node metastases in relation to the Ki-67 index, LNR, and clinical data. Tumoral Tg immunoreactivity was inversely correlated to the Ki-67 index and tumor recurrence. The Ki-67 index was higher in lymph node metastases (mean 4%) than in the primary tumors (mean 3%). Reduced Tg expression, estimated as 0–25% Tg positive tumor cells, was more common in lymph node metastases compared to primary tumors. In addition to advanced metastatic burden (defined as N1b stage and LNR ≥ 21%), low Tg expression (0–25% positive tumor cells) in lymph node metastases had a significant prognostic impact with shorter recurrence-free survival. These findings support the potential value of histopathological assessment of Tg expression and Ki-67 index in lymph node metastases as complementary predictors to anticipate the prognosis of PTC patients better.
Elastic solution of surface loaded layer with couple and surface stress effects
Authors: Lawongkerd Jintara , Le Toan Minh , Wongviboonsin Wipavee , Keawsawasvong Suraparb , Limkatanyu Suchart , Van Chung Nguyen , Rungamornrat Jaroon 
Published: January 2023

AbstractIn this study, an elastic solution of an axisymmetrically surface-loaded thin layer resting on a rigid substrate is established by taking the surface stress and material microstructural effects into account. Derived solutions provide not only a means to investigate the size effects on the mechanical response but also a set of fundamental solutions essential for tackling contact problems in a micro/nano scale. In the formulation, the couple stress and surface elasticity theories are adopted to simulate the microstructured bulk layer and the surface material, respectively. A general solution of an elastic field within the bulk layer is obtained first by Hankel transform method and subsequently used together with the surface equations and boundary conditions to form a set of conditions essential for determining all unknown constants. After being fully tested with available benchmark solutions, results are used to study the role of surface and couple stresses on the load transferring mechanism to the substrate and its size-dependent characteristic for a wide range of external length scales relative to the internal length scales.
Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum
Authors: Ma Bing , Gavzy Samuel J. , Saxena Vikas , Song Yang , Piao Wenji , Lwin Hnin Wai , Lakhan Ram , Iyyathurai Jegan , Li Lushen , France Michael , Paluskievicz Christina , Shirkey Marina W. , Hittle Lauren , Munawwar Arshi , Mongodin Emmanuel F. , Bromberg Jonathan S. 
Published: January 2023

AbstractThe beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate strain, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to a porcine tropic strain B. pseudolongum ATCC25526 using a combination of cell culture and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to immune modulatory host responses. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.
An earphone fit deviation analysis algorithm
Authors: Yan Yan , Liu Yonghong , Wang Haining 
Published: January 2023

AbstractThis study provides an accurate method for evaluating the fit of earphones, which could be used for establishing a linkage between interference/gap values with human perception. Seven commercial CAD software tools stood out and were explored for the analysis of the deviation between earphone and ear. However, the current deviation analysis method remains to be improved for earphone fit evaluation due to excessive points in the calculation (Geomagic Wrap and Siemens NX), lack of value on interference (Geomagic Control X), computation boundary required (Rapidform XOR/Redesign), repetitive computation with same points and inclined calculation line segment or even invalid calculation (Solidworks, Creo). Therefore, an accurate deviation analysis algorithm was promoted, which calculated the deviation between earphone and ear exactly and classified the interference set and gap set precisely. There are five main procedures of this algorithm, which are point cloud model pre-processing, the generation of distance vectors, the discrimination of interference set and gap set, the discrimination of validity, and statistical analysis and visualization. Furthermore, the usability and validity of the deviation analysis algorithm were verified through statistical analysis and comparing visual effects based on the earphone-wearing experiment. It is certified that the deviation analysis algorithm is appropriate for earphone fit evaluation and the eight indexes of this algorithm were proved to be related to subjective comfort scores. It is meaningful for ear-worn product fit analysis, design, and development phases.
Stabilization through self-coupling in networks of small-world and scale-free topology
Authors: Luboeinski Jannik , Claro Luis , Pomi Andrés , Mizraji Eduardo 
Published: January 2023

AbstractMechanisms that ensure the stability of dynamical systems are of vital importance, in particular in our globalized and increasingly interconnected world. The so-called connectivity-stability dilemma denotes the theoretical finding that increased connectivity between the components of a large dynamical system drastically reduces its stability. This result has promoted controversies within ecology and other fields of biology, especially, because organisms as well as ecosystems constitute systems that are both highly connected and stable. Hence, it has been a major challenge to find ways to stabilize complex systems while preserving high connectivity at the same time. Investigating the stability of networks that exhibit small-world or scale-free topology is of particular interest, since these topologies have been found in many different types of real-world networks. Here, we use an approach to stabilize recurrent networks of small-world and scale-free topology by increasing the average self-coupling strength of the units of a network. For both topologies, we find that there is a sharp transition from instability to asymptotic stability. Then, most importantly, we find that the average self-coupling strength needed to stabilize a system increases much slower than its size. It appears that the qualitative shape of this relationship is the same for small-world and scale-free networks, while scale-free networks can require higher magnitudes of self-coupling. We further explore the stabilization of networks with Kronecker-Leskovec topology. Finally, we argue that our findings, in particular the stabilization of large recurrent networks through small increases in the unit self-regulation, are of practical importance for the stabilization of diverse types of complex systems.
Rapid photonic curing effects of xenon flash lamp on ITO–Ag–ITO multilayer electrodes for high throughput transparent electronics
Authors: Zhao Zhenqian , Rose Alex , Kwon Sang Jik , Jeon Yongmin , Cho Eou-Sik 
Published: January 2023

AbstractHigh-throughput transparent and flexible electronics are essential technologies for next-generation displays, semiconductors, and wearable bio-medical applications. However, to manufacture a high-quality transparent and flexible electrode, conventional annealing processes generally require 5 min or more at a high temperature condition of 300 °C or higher. This high thermal budget condition is not only difficult to apply to general polymer-based flexible substrates, but also results in low-throughput. Here, we report a high-quality transparent electrode produced with an extremely low thermal budget using Xe-flash lamp rapid photonic curing. Photonic curing is an extremely short time (~ μs) process, making it possible to induce an annealing effect of over 800 °C. The photonic curing effect was optimized by selecting the appropriate power density, the irradiation energy of the Xe-flash lamp, and Ag layer thickness. Rapid photonic curing produced an ITO–Ag–ITO electrode with a low sheet resistance of 6.5 ohm/sq, with a high luminous transmittance of 92.34%. The low thermal budget characteristics of the rapid photonic curing technology make it suitable for high-quality transparent electronics and high-throughput processes such as roll-to-roll.