bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning enhanced evaluation of semiconductor quantum dots
Authors: Corcione Emilio , Jakob Fabian , Wagner Lukas , Joos Raphael , Bisquerra Andre , Schmidt Marcel , Wieck Andreas D. , Ludwig Arne , Jetter Michael , Portalupi Simone L. , Michler Peter , Tarín Cristina 
Published: February 2024

AbstractA key challenge in quantum photonics today is the efficient and on-demand generation of high-quality single photons and entangled photon pairs. In this regard, one of the most promising types of emitters are semiconductor quantum dots, fluorescent nanostructures also described as artificial atoms. The main technological challenge in upscaling to an industrial level is the typically random spatial and spectral distribution in their growth. Furthermore, depending on the intended application, different requirements are imposed on a quantum dot, which are reflected in its spectral properties. Given that an in-depth suitability analysis is lengthy and costly, it is common practice to pre-select promising candidate quantum dots using their emission spectrum. Currently, this is done by hand. Therefore, to automate and expedite this process, in this paper, we propose a data-driven machine-learning-based method of evaluating the applicability of a semiconductor quantum dot as single photon source. For this, first, a minimally redundant, but maximally relevant feature representation for quantum dot emission spectra is derived by combining conventional spectral analysis with an autoencoding convolutional neural network. The obtained feature vector is subsequently used as input to a neural network regression model, which is specifically designed to not only return a rating score, gauging the technical suitability of a quantum dot, but also a measure of confidence for its evaluation. For training and testing, a large dataset of self-assembled InAs/GaAs semiconductor quantum dot emission spectra is used, partially labelled by a team of experts in the field. Overall, highly convincing results are achieved, as quantum dots are reliably evaluated correctly. Note, that the presented methodology can account for different spectral requirements and is applicable regardless of the underlying photonic structure, fabrication method and material composition. We therefore consider it the first step towards a fully integrated evaluation framework for quantum dots, proving the use of machine learning beneficial in the advancement of future quantum technologies.
Tropical decadal variability in nutrient supply and phytoplankton community in the Central Equatorial Pacific during the late Holocene
Authors: Guilderson T. P. , Glynn D. S. , McCarthy M. D. 
Published: February 2024

AbstractWe have reconstructed baseline δ15N and δ13C of export production at Kingman Reef in the Central Equatorial Pacific (CEP) at sub-decadal resolution, nearly continuously over the last 2000 years. The changes in δ15N reflects the strength of the North Equatorial Counter Current (NECC) relative to the South Equatorial Current (SEC), and to a lesser extent, the North Equatorial Current (NEC). Seasonal to multi-decadal variation in the strength of these currents, through the redistribution of heat, have global climate impacts and influence marine and terrestrial ecosystems. We use modern El Niño-La Nina dynamics and the Tropical Pacific Decadal Variability (TPDV) pattern, which is defined in the CEP, as a framework for analyzing the isotopic data. The CEP δ15N and δ13C records exhibit multi-decadal (50–60 year) variability consistent with TPDV. A large multi-centennial feature in the CEP δ15N data, within age-model uncertainties, is consistent with one of the prolonged dry-pluvial sequences in the American west at the end of the Medieval Climate Anomaly, where low TPDV is correlated with drier conditions. This unique record shows that the strength of the NECC, as reflected in baseline δ15N and δ13C, has at quasi-predictable intervals throughout the late Holocene, toggled the phytoplankton community between prokaryotes and picoplankton versus eukaryotes.
Machine learning-based investigation of regulated cell death for predicting prognosis and immunotherapy response in glioma patients
Authors: Zhang Wei , Dang Ruiyue , Liu Hongyi , Dai Luohuan , Liu Hongwei , Adegboro Abraham Ayodeji , Zhang Yihao , Li Wang , Peng Kang , Hong Jidong , Li Xuejun 
Published: February 2024

AbstractGlioblastoma is a highly aggressive and malignant type of brain cancer that originates from glial cells in the brain, with a median survival time of 15 months and a 5-year survival rate of less than 5%. Regulated cell death (RCD) is the autonomous and orderly cell death under genetic control, controlled by precise signaling pathways and molecularly defined effector mechanisms, modulated by pharmacological or genetic interventions, and plays a key role in maintaining homeostasis of the internal environment. The comprehensive and systemic landscape of the RCD in glioma is not fully investigated and explored. After collecting 18 RCD-related signatures from the opening literature, we comprehensively explored the RCD landscape, integrating the multi-omics data, including large-scale bulk data, single-cell level data, glioma cell lines, and proteome level data. We also provided a machine learning framework for screening the potentially therapeutic candidates. Here, based on bulk and single-cell sequencing samples, we explored RCD-related phenotypes, investigated the profile of the RCD, and developed an RCD gene pair scoring system, named RCD.GP signature, showing a reliable and robust performance in predicting the prognosis of glioblastoma. Using the machine learning framework consisting of Lasso, RSF, XgBoost, Enet, CoxBoost and Boruta, we identified seven RCD genes as potential therapeutic targets in glioma and verified that the SLC43A3 highly expressed in glioma grades and glioma cell lines through qRT-PCR. Our study provided comprehensive insights into the RCD roles in glioma, developed a robust RCD gene pair signature for predicting the prognosis of glioma patients, constructed a machine learning framework for screening the core candidates and identified the SLC43A3 as an oncogenic role and a prediction biomarker in glioblastoma.
Microcirculatory changes in the skin after postmastectomy radiotherapy in women with breast cancer
Authors: Elawa Sherif , Mirdell Robin , Stefanis Aristotelis , Tesselaar Erik , Farnebo Simon 
Published: February 2024

AbstractPostmastectomy radiotherapy (PMRT) increases the risk for complications after breast reconstruction. The pathophysiological mechanism underlying this increased risk is not completely understood. The aim of this study was to examine if there is a relationship between PMRT and microvascular perfusion in the skin directly after, and at 2 and 6 months after PMRT and to assess if there is impaired responsiveness to a topically applied vasodilator (Methyl nicotinate—MN) after PMRT. Skin microvascular responses after PMRT were measured on two sites in the irradiated chest wall of 22 women before, immediately after, and at 2 and 6 months after unilateral PMRT with the contralateral breast as a control. A significant increase in basal skin perfusion was observed in the irradiated chest wall immediately after RT (p < 0.0001). At 2 and 6 months after RT, there was no longer a difference in basal skin perfusion compared to the contralateral breast and compared to baseline. Similarly, the blood flow response in the skin after application of MN was stronger immediately after RT compared to before RT (p < 0.0001), but there was no difference at later time points. These results indicate that the increased risk for complications after surgical procedures are not directly related to changes in skin perfusion and microvascular responsiveness observed after postmastectomy RT.
Anticipatory postural control in adaptation of goal-directed lower extremity movements
Authors: Moriyama Mai , Kouzaki Motoki , Hagio Shota 
Published: February 2024

AbstractSkilled football players can adapt their kicking movements depending on external environments. Predictive postural control movements, known as anticipatory postural adjustments (APAs), are needed preceding kicking movements to precisely control them while maintaining a standing posture only with the support leg. We aimed to clarify APAs of the support leg in the process of adaptation of goal-directed movements with the lower limb. Participants replicated ball-kicking movements such that they reached a cursor, representing a kicking-foot position towards a forward target while standing with the support leg. APAs were observed as the centre of pressure of the support leg shifted approximately 300 ms in advance of the onset of movement of the kicking foot. When the cursor trajectory of the kicking foot was visually rotated during the task, the kicking-foot movement was gradually modified to reach the target, indicating adaptation to the novel visuomotor environment. Interestingly, APAs in the mediolateral direction were also altered following the change in kicking-foot movements. Additionally, the APAs modified more slowly than the kicking-foot movements. These results suggest that flexible changes in predictive postural control might support the adaptation of goal-directed movements of the lower limb.
Global prevalence of functional dyspepsia according to Rome criteria, 1990–2020: a systematic review and meta-analysis
Authors: Lee Kwanjoo , Kwon Chang-il , Yeniova Abdullah Özgür , Koyanagi Ai , Jacob Louis , Smith Lee , Lee Seung Won , Rahmati Masoud , Shin Ju-Young , Shin Jae Il , Cho Wonyoung , Yon Dong Keon 
Published: February 2024

AbstractAlthough functional dyspepsia (FD) is a common functional gastroduodenal disorder with a high socioeconomic burden, little is known about its global prevalence. Thus, we performed a comprehensive study to estimate long-term trends in the prevalence of FD. We searched PubMed/MEDLINE, Embase, and Google Scholar from 1990 to 2022 for population-based studies that reported the prevalence of FD in adults (≥ 18 years old) according to Rome I, II, III, or IV criteria. The prevalence of FD was extracted from included studies to obtain pooled prevalence with 95% confidence intervals (CI) and 95% prediction intervals. Subgroup analysis was performed according to certain characteristics, including geographic region. A total of 44 studies met the eligibility criteria, including 256,915 participants from 40 countries across six continents. The overall global pooled prevalence of FD was 8.4% (95% CI 7.4–.9.5). The prevalence was the highest in Rome I (11.9%; 95% CI 5.1–25.4) and lowest in Rome IV (6.8%; 95% CI 5.8–7.9). Developing countries showed a higher prevalence than developed countries (9.1% versus 8.0%), and prevalence was higher in women, irrespective of the definition used (9.0% versus 7.0%). The pooled prevalence gradually decreased from 1990 to 2020 (12.4% [8.2–18.3] in 1990–2002 versus 7.3% [6.1–8.7] in 2013–2020). The prevalence of FD differs by country, economic status, geographical region, and sex, and the global prevalence has been gradually declining. Despite the heterogeneity of sample population, our study estimates the current global burden of FD and provides information to heath care policy decisions.
The gephyrin scaffold modulates cortical layer 2/3 pyramidal neuron responsiveness to single whisker stimulation
Authors: Tsai Yuan-Chen , Hleihil Mohammad , Otomo Kanako , Abegg Andrin , Cavaccini Anna , Panzanelli Patrizia , Cramer Teresa , Ferrari Kim David , Barrett Matthew J. P. , Bosshard Giovanna , Karayannis Theofanis , Weber Bruno , Tyagarajan Shiva K. , Stobart Jillian L. 
Published: February 2024

AbstractGephyrin is the main scaffolding protein at inhibitory postsynaptic sites, and its clusters are the signaling hubs where several molecular pathways converge. Post-translational modifications (PTMs) of gephyrin alter GABAA receptor clustering at the synapse, but it is unclear how this affects neuronal activity at the circuit level. We assessed the contribution of gephyrin PTMs to microcircuit activity in the mouse barrel cortex by slice electrophysiology and in vivo two-photon calcium imaging of layer 2/3 (L2/3) pyramidal cells during single-whisker stimulation. Our results suggest that, depending on the type of gephyrin PTM, the neuronal activities of L2/3 pyramidal neurons can be differentially modulated, leading to changes in the size of the neuronal population responding to the single-whisker stimulation. Furthermore, we show that gephyrin PTMs have their preference for selecting synaptic GABAA receptor subunits. Our results identify an important role of gephyrin and GABAergic postsynaptic sites for cortical microcircuit function during sensory stimulation.
Modeling dry eye with an air–liquid interface in corneal epithelium-on-a-chip
Authors: Kado Abdalkader Rodi , Chaleckis Romanas , Fujita Takuya , Kamei Ken-ichiro 
Published: February 2024

AbstractDry eye syndrome (DES) is a complex ocular condition characterized by an unstable tear film and inadequate tear production, leading to tissue damage. Despite its common occurrence, there is currently no comprehensive in vitro model that accurately reproduce the cellular characteristics of DES. Here we modified a corneal epithelium-on-a-chip (CEpOC) model to recapitulate DES by subjecting HCE-T human corneal epithelial cells to an air–liquid (AL) interface stimulus. We then assessed the effects of AL stimulation both in the presence and absence of diclofenac (DCF), non-steroidal anti-inflammatory drug. Transcriptomic analysis revealed distinct gene expression changes in response to AL and AL_DCF, affecting pathways related to development, epithelial structure, inflammation, and extracellular matrix remodeling. Both treatments upregulated PIEZO2, linked to corneal damage signaling, while downregulating OCLN, involved in cell–cell junctions. They increased the expression of inflammatory genes (e.g., IL-6) and reduced mucin production genes (e.g., MUC16), reflecting dry eye characteristics. Metabolomic analysis showed increased secretion of metabolites associated with cell damage and inflammation (e.g., methyl-2-oxovaleric acid, 3-methyl-2-oxobutanoic acid, lauroyl-carnitine) in response to AL and even more with AL_DCF, indicating a shift in cellular metabolism. This study showcases the potential use of AL stimulus within the CEpOC to induce cellular characteristics relevant to DES.
Stress-induced stenotic vascular remodeling via reduction of plasma omega-3 fatty acid metabolite 4-oxoDHA by noradrenaline
Authors: Nishimori Makoto , Hayasaka Naomi , Otsui Kazunori , Inoue Nobutaka , Asakura Junko , Nagao Manabu , Toh Ryuji , Ishida Tatsuro , Hirata Ken-ichi , Furuyashiki Tomoyuki , Shinohara Masakazu 
Published: February 2024

AbstractStress has garnered significant attention as a prominent risk factor for inflammation-related diseases, particularly cardiovascular diseases (CVDs). However, the precise mechanisms underlying stress-driven CVDs remain elusive, thereby impeding the development of preventive and therapeutic strategies. To explore the correlation between plasma lipid metabolites and human depressive states, liquid chromatography–mass spectrometry (LC/MS) based analysis of plasma and the self-rating depression (SDS) scale questionnaire were employed. We also used a mouse model with restraint stress to study its effects on plasma lipid metabolites and stenotic vascular remodeling following carotid ligation. In vitro functional and mechanistic studies were performed using macrophages, endothelial cells, and neutrophil cells. We revealed a significant association between depressive state and reduced plasma levels of 4-oxoDHA, a specific omega-3 fatty acid metabolite biosynthesized by 5-lipoxygenase (LO), mainly in neutrophils. In mice, restraint stress decreased plasma 4-oxoDHA levels and exacerbated stenotic vascular remodeling, ameliorated by 4-oxoDHA supplementation. 4-oxoDHA enhanced Nrf2-HO-1 pathways, exerting anti-inflammatory effects on endothelial cells and macrophages. One of the stress hormones, noradrenaline, reduced 4-oxoDHA and the degraded 5-LO in neutrophils through the proteasome system, facilitated by dopamine D2-like receptor activation. Our study proposed circulating 4-oxoDHA levels as a stress biomarker and supplementation of 4-oxoDHA as a novel therapeutic approach for controlling stress-related vascular inflammation.
Acoustic emission characteristics and damage evolution of different rocks under uniaxial compression conditions
Authors: Ou Jianchun , Wang Enyuan , Wang Xinyu , Wang Bican , Zhu Guoqing 
Published: February 2024

AbstractDue to the complexity of the strata, it is difficult to monitor and identify the disasters induced by rock fractures in the process of mining deep coal resources. This will seriously affect the safety and sustainable mining of coal. Therefore, it is necessary to understand the failure mechanisms and acoustic emission (AE) characteristics of different rocks. In this paper, uniaxial compression tests as well as simultaneous AE monitoring were carried out on four different rocks. The four rocks include yellow sandstone, white sandstone, marble and limestone. The mechanical properties, energy evolution and AE characteristics of different rocks were analysed. It is found that the AE response of rocks is closely related to the damage and fracture process. The more brittle the rock is, the less energy is dissipated before failure, and the less obvious the AE precursor is, and the RA-AF values can effectively characterise the failure modes of different rocks. Finally, the damage models were developed from the perspectives of AE energy and dissipated energy, respectively. The damage model based on dissipated energy can better reflect the stress and damage state of the rock, and the theoretical curves of stress–strain are in good agreement with the measured curves.
Selpercatinib combination with the mitochondria-targeted antioxidant MitoQ effectively suppresses RET–mutant thyroid cancer
Authors: Chen Wenjing , Dream Sophie , Leung Pui-Yin , Wu Pui-Kei , Wong Stuart , Park Jong-In 
Published: February 2024

AbstractGenetic alternation of REarranged during Transfection (RET) that leads to constitutive RET activation is a crucial etiological factor for thyroid cancer. RET is known to regulate mitochondrial processes, although the underlying molecular mechanisms remain unclear. We previously showed that the multi-kinase inhibitors vandetanib and cabozantinib increase the mitochondrial membrane potential (Δψm) in RET-mutated thyroid tumor cells and that this effect can be exploited to increase mitochondrial enrichment of Δψm-sensitive agents in the tumor cells. In this study, we hypothesized that the RET-selective inhibitor, selpercatinib, can increase Δψm and, subsequently, tumor cell uptake of the mitochondria-targeted ubiquinone (MitoQ) to the level to break the mitochondrial homeostasis and induce lethal responses in RET-mutated thyroid tumor cells. We show that selpercatinib significantly increased Δψm, and its combination with MitoQ synergistically suppressed RET-mutated human thyroid tumor cells, which we validated using RET-targeted genetic approaches. Selpercatinib and MitoQ, in combination, also suppressed CCDC6-RET fusion cell line xenografts in mice and prolonged animal survival more effectively than single treatments of each agent. Moreover, we treated two patients with CCDC6-RET or RETM918T thyroid cancer, who could not take selpercatinib at regular doses due to adverse effects, with a dose-reduced selpercatinib and MitoQ combination. In response to this combination therapy, both patients showed tumor reduction. The quality of life of one patient significantly improved over a year until the tumor relapsed. This combination of selpercatinib with MitoQ may have therapeutic potential for patients with RET-mutated tumors and intolerant to regular selpercatinib doses.
Antidepressant use during pregnancy and the risk of preterm birth – a cohort study
Authors: Amit Guy , Yanover Chen , Bivas-Benita Maytal , Girshovitz Irena , Helbitz Tal , Sudry Tamar , Bar Vered , Tang Alice S. , Le Brian L. , Roger Jacquelyn , Woldemariam Sarah , Kosti Idit , Oskotsky Tomiko T. , Akiva Pinchas , Sirota Marina 
Published: February 2024

AbstractMajor depressive disorder and exposure to antidepressants during pregnancy have been previously associated with preterm birth (PTB). However, the reported results are inconsistent. In this study, we aimed to estimate the effects of antidepressants and maternal depression on the risk of PTB using data from electronic health records (EHRs). This is a population-based retrospective cohort study, utilizing data from primary care EHRs. The cohort included 216,070 deliveries of 176,866 patients from the UK between January 1996 and February 2019. We analyzed the effects of antidepressant exposure during pregnancy on the risk of PTB and additional control outcomes in subgroups of patients with a history of depression, and with recent pre-pregnancy treatment. We also assessed the effect of depression alone, in untreated patients. The analysis utilized large-scale propensity score matching that included all demographic and clinical covariates, and effect estimation using a Cox model. The main cohort included 17,615 (8.2%) PTBs. Among patients who were not exposed to antidepressants during pregnancy, a history of depression was associated with an increased risk of PTB (HR 1.10, CI [1.04,1.15], P < 0.01]. Patients exposed to SSRIs during the first 22 weeks of gestation were not at a significantly higher risk of PTB compared to unexposed patients (HR 1.08 CI [0.98,1.18], P = 0.11). Moreover, treatment continuation during pregnancy did not affect the risk of PTB among patients with pre-pregnancy treatment (HR 1.03 CI [0.92,1.15], P = 0.61), and among patients with a history of depression (HR 1.00 CI [0.90,1.11], P = 0.98). Additionally, exposure to antidepressants was associated with a reduced risk of some common medical conditions during the outcome follow-up period. Our findings indicate that the concern of PTB should not affect the clinical decision of medical treatment for pregnant women suffering from depression, since antidepressant treatment by itself does not increase the risk of PTB.