bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping nanoscale carrier confinement in polycrystalline graphene by terahertz spectroscopy
Authors: Whelan Patrick R. , De Fazio Domenico , Pasternak Iwona , Thomsen Joachim D. , Zelzer Steffen , Mikkelsen Martin O. , Booth Timothy J. , Diekhöner Lars , Sassi Ugo , Johnstone Duncan , Midgley Paul A. , Strupinski Wlodek , Jepsen Peter U. , Ferrari Andrea C. , Bøggild Peter 
Published: February 2024

AbstractTerahertz time-domain spectroscopy (THz-TDS) can be used to map spatial variations in electrical properties such as sheet conductivity, carrier density, and carrier mobility in graphene. Here, we consider wafer-scale graphene grown on germanium by chemical vapor deposition with non-uniformities and small domains due to reconstructions of the substrate during growth. The THz conductivity spectrum matches the predictions of the phenomenological Drude–Smith model for conductors with non-isotropic scattering caused by backscattering from boundaries and line defects. We compare the charge carrier mean free path determined by THz-TDS with the average defect distance assessed by Raman spectroscopy, and the grain boundary dimensions as determined by transmission electron microscopy. The results indicate that even small angle orientation variations below 5° within graphene grains influence the scattering behavior, consistent with significant backscattering contributions from grain boundaries.
Poverty prediction using E-commerce dataset and filter-based feature selection approach
Authors: Wijaya Dedy Rahman , Ibadurrohman Raden Ilham Fadhilah , Hernawati Elis , Wikusna Wawa 
Published: February 2024

AbstractPoverty is a problem that occurs in many countries, notably in Indonesia. The common methods used to obtain poverty information are surveys and censuses. However, this process takes a long time and uses a lot of human resources. On the other hand, governments and policymakers need a faster approach to know social-economic conditions for area development plans. Hence, in this paper, we develop e-commerce data and machine learning algorithms as a proxy for poverty levels that can provide faster information than surveys or censuses. The e-commerce dataset is used and this high-dimensional data becomes a challenge. Hence, feature selection algorithms are employed to determine the best features before building a machine learning model. Furthermore, three machine learning algorithms such as support vector regression, linear regression, and k-nearest neighbor are compared to predict the poverty rate. Hence, the contribution of this paper is to propose the combination of statistical-based feature selection and machine learning algorithms to predict the poverty rate based on e-commerce data. According to the experimental results, the combination of f-score feature selection and support vector regression surpasses other methods. It shows that e-commerce data and machine learning algorithms can be potentially used as a proxy for predicting poverty.
Unsupervised analysis of whole transcriptome data from human pluripotent stem cells cardiac differentiation
Authors: P. Agostinho Sofia , A. Branco Mariana , E. S. Nogueira Diogo , Diogo Maria Margarida , S. Cabral Joaquim M. , N. Fred Ana L. , V. Rodrigues Carlos A. 
Published: February 2024

AbstractThe main objective of the present work was to highlight differences and similarities in gene expression patterns between different pluripotent stem cell cardiac differentiation protocols, using a workflow based on unsupervised machine learning algorithms to analyse the transcriptome of cells cultured as a 2D monolayer or as 3D aggregates. This unsupervised approach effectively allowed to portray the transcriptomic changes that occurred throughout the differentiation processes, with a visual representation of the entire transcriptome. The results allowed to corroborate previously reported data and also to unveil new gene expression patterns. In particular, it was possible to identify a correlation between low cardiomyocyte differentiation efficiencies and the early expression of a set of non-mesodermal genes, which can be further explored as predictive markers of differentiation efficiency. The workflow here developed can also be applied to analyse other stem cell differentiation transcriptomic datasets, envisaging future clinical implementation of cellular therapies.
Electric field modulation of ERK dynamics shows dependency on waveform and timing
Authors: Hu Minxi , Li Houpu , Zhu Kan , Guo Liang , Zhao Min , Zhan Huiwang , Devreotes Peter N. , Qing Quan 
Published: February 2024

AbstractDifferent exogenous electric fields (EF) can guide cell migration, disrupt proliferation, and program cell development. Studies have shown that many of these processes were initiated at the cell membrane, but the mechanism has been unclear, especially for conventionally non-excitable cells. In this study, we focus on the electrostatic aspects of EF coupling with the cell membrane by eliminating Faradaic processes using dielectric-coated microelectrodes. Our data unveil a distinctive biphasic response of the ERK signaling pathway of epithelial cells (MCF10A) to alternate current (AC) EF. The ERK signal exhibits both inhibition and activation phases, with the former triggered by a lower threshold of AC EF, featuring a swifter peaking time and briefer refractory periods than the later-occurring activation phase, induced at a higher threshold. Interestingly, the biphasic ERK responses are sensitive to the waveform and timing of EF stimulation pulses, depicting the characteristics of electrostatic and dissipative interactions. Blocker tests and correlated changes of active Ras on the cell membrane with ERK signals indicated that both EGFR and Ras were involved in the rich ERK dynamics induced by EF. We propose that the frequency-dependent dielectric relaxation process could be an important mechanism to couple EF energy to the cell membrane region and modulate membrane protein-initiated signaling pathways, which can be further explored to precisely control cell behavior and fate with high temporal and spatial resolution.
Cognitive control adjustments are dependent on the level of conflict
Authors: Bognar Miklos , Szekely Zsuzsa , Varga Marton A. , Nagy Kinga , Spinelli Giacomo , Hartanto Andree , Majeed Nadyanna M. , Chen Nicole Rui Ying , Gyurkovics Mate , Aczel Balazs 
Published: February 2024

AbstractThe congruency sequence effect (CSE) is one of the most investigated effects in the cognitive control literature. The conflict monitoring theory suggests that the CSE is the result of adjustments in cognitive control based on perceived conflict. A recent paper by Zhang and colleagues, has investigated whether the manipulation of conflict level by changing distractor incompatibility in a flanker task affects the amount of adjustments in cognitive control. Their study produced mixed findings, somewhat supporting the original conflict monitoring theory, but also suggesting other explanations, such as the repetition expectancy account. We replicated the experimental design in a multisite online study (N = 347), with Hungarian, Italian, and Singaporean participants. Our results supported the prediction that changes in the level of conflict trigger conflict adaptation, revealing that increasing conflict levels induced stronger adaptive control. Bayesian hypothesis testing indicated a monotonic reduction in congruency effects as a function of previous conflict strength. This finding is in line with the extension of the traditional conflict monitoring theory, as well as other theories like affective signaling and expected value of control, implying that the relationship between conflict and interference effects is gradual, rather than a binary function.
Growth control of Marchantia polymorpha gemmae using nonthermal plasma irradiation
Authors: Tsuboyama Shoko , Okumura Takamasa , Attri Pankaj , Koga Kazunori , Shiratani Masaharu , Kuchitsu Kazuyuki 
Published: February 2024

AbstractSeveral studies have documented that treatment by cold atmospheric pressure plasma (CAPP) on plants foster seed germination and growth in recent years. However, the molecular processes that underlie the action of CAPP on the seeds and plants remain mostly enigmatic. We here introduce gemmae of Marchantia polymorpha, a basal liverwort, as a novel model plant material suitable for CAPP research. Treating the gemmae with CAPP for a constant time interval at low power resulted in consistent growth enhancement, while growth inhibition at higher power in a dose-dependent manner. These results distinctly demonstrate that CAPP irradiation can positively and negatively regulate plant growth depending on the plasma intensity of irradiation, offering a suitable experimental system for understanding the molecular mechanisms underlying the action of CAPP in plants.
Prospective study of predictors for anxiety, depression, and somatization in a sample of 1807 cancer patients
Authors: Velasco-Durantez Veronica , Cruz-Castellanos Patricia , Hernandez Raquel , Rodriguez-Gonzalez Adan , Fernandez Montes Ana , Gallego Alejandro , Manzano-Fernandez Aranzazu , Sorribes Elena , Zafra Marta , Carmona-Bayonas Alberto , Calderon Caterina , Jiménez-Fonseca Paula 
Published: February 2024

AbstractIn cancer patients, psychological distress, which encompasses anxiety, depression, and somatization, arises from the complex interplay of emotional and behavioral reactions to the diagnosis and treatment, significantly influencing their functionality and quality of life. The aim was to investigate factors associated with psychological distress in cancer patients. This prospective and multicenter study, conducted by the Spanish Society of Medical Oncology (SEOM), included two cohorts of patients with cancer (localized resected or advanced unresectable). They completed surveys assessing psychological distress (BSI-18) before and after cancer treatment and coping (MINI-MAC) and spirituality (FACIT-sp) prior to therapy. A multivariable logistic regression analysis and a Structural Equation Modeling (SEM) were conducted. Between 2019 and 2022, 1807 patients were evaluated, mostly women (54%), average age 64 years. The most frequent cancers were colorectal (30%), breast (25%) and lung (18%). Men had lower levels of anxiety and depression (OR 0.66, 95% CI 0.52–0.84; OR 0.72, 95% CI 0.56–0.93). Colorectal cancer patients experienced less anxiety (OR 0.63, 95% CI 0.43–0.92), depression (OR 0.55, 95% CI 0.37–0.81), and somatization (OR 0.59, 95% CI 0.42–0.83). Patients with localized cancer and spiritual beliefs had reduced psychological distress, whereas those with anxious preoccupation had higher level. SEM revealed a relationship between psychological distress and coping strategies, emphasizing how baseline anxious preoccupation exacerbates post-treatment distress. This study suggests that age, sex, extension and location of cancer, coping and spirituality influence psychological distress in cancer patients.
Zeocin-induced DNA damage response in barley and its dependence on ATR
Authors: Vladejić Jovanka , Kovacik Martin , Zwyrtková Jana , Szurman-Zubrzycka Miriam , Doležel Jaroslav , Pecinka Ales 
Published: February 2024

AbstractDNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.
Optimal feedback improves behavioral focus during self-regulated computer-based work
Authors: Wirzberger Maria , Lado Anastasia , Prentice Mike , Oreshnikov Ivan , Passy Jean-Claude , Stock Adrian , Lieder Falk 
Published: February 2024

AbstractDistractions are omnipresent and can derail our attention, which is a precious and very limited resource. To achieve their goals in the face of distractions, people need to regulate their attention, thoughts, and behavior; this is known asself-regulation. How can self-regulation be supported or strengthened in ways that are relevant for everyday work and learning activities? To address this question, we introduce and evaluate a desktop application that helps people stay focused on their work and train self-regulation at the same time. Our application lets the user set a goal for what they want to do during a defined period of focused work at their computer, then gives negative feedback when they get distracted, and positive feedback when they reorient their attention towards their goal. After this so-called focus session, the user receives overall feedback on how well they focused on their goal relative to previous sessions. While existing approaches to attention training often use artificial tasks, our approach transforms real-life challenges into opportunities for building strong attention control skills. Our results indicate that optimal attentional feedback can generate large increases in behavioral focus, task motivation, and self-control—benefitting users to successfully achieve their long-term goals.
Clinical and molecular study of radiation-induced gliomas
Authors: Trkova Katerina , Sumerauer David , Bubenikova Adela , Krskova Lenka , Vicha Ales , Koblizek Miroslav , Zamecnik Josef , Jurasek Bruno , Kyncl Martin , Malinova Bela , Ondrova Barbora , Jones David T. W. , Sill Martin , Strnadova Martina , Stolova Lucie , Misove Adela , Benes Vladimir , Zapotocky Michal 
Published: February 2024

AbstractIn this study, we provide a comprehensive clinical and molecular biological characterization of radiation-induced gliomas (RIG), including a risk assessment for developing gliomas. A cohort of 12 patients who developed RIG 9.5 years (3–31 years) after previous cranial radiotherapy for brain tumors or T-cell acute lymphoblastic leukemia was established. The derived risk of RIG development based on our consecutive cohort of 371 irradiated patients was 1.6% at 10 years and 3.02% at 15 years. Patients with RIG glioma had a dismal prognosis with a median survival of 7.3 months. We described radiology features that might indicate the suspicion of RIG rather than the primary tumor recurrence. Typical molecular features identified by molecular biology examination included the absence of Histon3 mutation, methylation profile of pedHGG-RTK1 and the presence of recurrent PDGFRA amplification and CDKN2A/B deletion. Of the two long-term surviving patients, one had gliomatosis cerebri, and the other had pleomorphic xanthoastrocytoma with BRAF V600E mutation. In summary, our experience highlights the need for tissue diagnostics to allow detailed molecular biological characterization of the tumor, differentiation of the secondary tumor from the recurrence of the primary disease and potentially finding a therapeutic target.
Hypothermia increases adenosine monophosphate and xanthosine monophosphate levels in the mouse hippocampus, preventing their reduction by global cerebral ischemia
Authors: Doshi Masaru , Natori Yujin , Ishii Akira , Saigusa Daisuke , Watanabe Shiro , Hosoyamada Makoto , Hirashima-Akae Yutaka 
Published: February 2024

AbstractGlobal cerebral ischemia (GCI) caused by clinical conditions such as cardiac arrest leads to delayed neuronal death in the hippocampus, resulting in physical and mental disability. However, the mechanism of delayed neuronal death following GCI remains unclear. To elucidate the mechanism, we performed a metabolome analysis using a mouse model in which hypothermia (HT) during GCI, which was induced by the transient occlusion of the bilateral common carotid arteries, markedly suppressed the development of delayed neuronal death in the hippocampus after reperfusion. Fifteen metabolites whose levels were significantly changed by GCI and 12 metabolites whose levels were significantly changed by HT were identified. Furthermore, the metabolites common for both changes were narrowed down to two, adenosine monophosphate (AMP) and xanthosine monophosphate (XMP). The levels of both AMP and XMP were found to be decreased by GCI, but increased by HT, thereby preventing their decrease. In contrast, the levels of adenosine, inosine, hypoxanthine, xanthine, and guanosine, the downstream metabolites of AMP and XMP, were increased by GCI, but were not affected by HT. Our results may provide a clue to understanding the mechanism by which HT during GCI suppresses the development of delayed neuronal death in the hippocampus.
HPAIV outbreak triggers short-term colony connectivity in a seabird metapopulation
Authors: Jeglinski Jana W. E. , Lane Jude V. , Votier Steven C. , Furness Robert W. , Hamer Keith C. , McCafferty Dominic J. , Nager Ruedi G. , Sheddan Maggie , Wanless Sarah , Matthiopoulos Jason 
Published: February 2024

AbstractDisease outbreaks can drastically disturb the environment of surviving animals, but the behavioural, ecological, and epidemiological consequences of disease-driven disturbance are poorly understood. Here, we show that an outbreak of High Pathogenicity Avian Influenza Virus (HPAIV) coincided with unprecedented short-term behavioural changes in Northern gannets (Morus bassanus). Breeding gannets show characteristically strong fidelity to their nest sites and foraging areas (2015–2019; n = 120), but during the 2022 HPAIV outbreak, GPS-tagged gannets instigated long-distance movements beyond well-documented previous ranges and the first ever recorded visits of GPS-tagged adults to other gannet breeding colonies. Our findings suggest that the HPAIV outbreak triggered changes in space use patterns of exposed individuals that amplified the epidemiological connectivity among colonies and may generate super-spreader events that accelerate disease transmission across the metapopulation. Such self-propagating transmission from and towards high density animal aggregations may explain the unexpectedly rapid pan-European spread of HPAIV in the gannet.
Embryo-endometrial interaction associated with the location of the embryo during the mobility phase in mares
Authors: de Castro Thadeu , van Heule Machteld , Domingues Rafael R. , Jacob Julio C. F. , Daels Peter F. , Meyers Stuart A. , Conley Alan J. , Dini Pouya 
Published: February 2024

AbstractEmbryo-maternal crosstalk is essential to establish pregnancy, with the equine embryo moving throughout the uterus on days 9–15 (ovulation = day 0) as part of this interaction. We hypothesized that the presence of a mobile embryo induces local changes in the gene expression of the endometrium. On Day 12, the endometrial transcripts were compared among three groups: uterine horn with an embryo (P+, n = 7), without an embryo (P−, n = 7) in pregnant mares, and both uterine horns of nonbred mares (NB, n = 6). We identified 1,101 differentially expressed genes (DEGs) between P+ vs. NB and 1,229 DEGs between P− vs. NB. The genes upregulated in both P+ and P− relative to NB were involved in growth factor pathway and fatty acid activation, while downregulated genes were associated with oxytocin signaling pathway and estrogen receptor signaling. Comparing the transcriptome of P+ to that of P−, we found 59 DEGs, of which 30 genes had a higher expression in P+. These genes are associated with regulating vascular growth factors and the immune system, all known to be essential in early pregnancy. Overall, this study suggests that the mobile embryo influences the endometrial gene expression locally.
Into the Holocene, anatomy of the Younger Dryas cold reversal and preboreal oscillation
Authors: Velay-Vitow Jesse , Chandan Deepak , Peltier W. Richard 
Published: February 2024

AbstractDuring the most recent deglaciation, the upwards trend of warmer Northern Hemisphere (NH) temperatures was punctuated by a rapid and intense return to glacial conditions: the Younger Dryas (YD). The end of this event marks the beginning of the Holocene. Using the University of Toronto version of CCSM4, a model of the climate prior to the YD was created with correct boundary conditions. Various amounts of freshwater forcing were then applied to the Beaufort Gyre for forcing intervals ranging from 1 to 125 years. In several cases, this was sufficient to collapse the Atlantic Meridional Overturning Circulation (AMOC) and cause significant cooling over the NH. Crucially, after the forcing was ceased, the AMOC stayed in an off state for approximately a millennium before mounting a rapid recover to pre-YD levels. This recovery, which permanently reduced the extent of NH sea ice, occurred through the mechanism of a Polynya opening in the Irminger Sea during winter and led to a pronounced “overshoot” of the AMOC, during which NH temperatures were higher than before the YD.
Anti-aquaporin-4 immune complex stimulates complement-dependent Th17 cytokine release in neuromyelitis optica spectrum disorders
Authors: Nishiyama Shuhei , Seok Jin Myong , Wright Amy E. , Lotan Itay , Mikami Takahisa , Drosu Natalia C. , Bobrowski-Khoury Natasha , Anderson Monique R. , Bilodeau Philippe A. , Schindler Patrick , Paul Friedemann , Aoki Masashi , Yeaman Michael R. , Levy Michael ,   The Guthy-Jackson Charitable Foundation CIRCLES Study Group, Behne Jacinta M. , Behne Megan K. , Bennett Jeffrey L. , Blaschke Terrence F. , Chitnis Tanuja , Cook Lawrence J. , Levy Michael , Planchon Sarah M. , Repovic Pavle , Riley Claire S. , Smith Terry J. , Traboulsee Anthony , R. Yeaman Michael 
Published: February 2024

AbstractProinflammatory cytokines, such as (IL: interleukin) IL-6 and IL-17A, and complement fixation are critical in the immunopathogenesis of neuromyelitis optica spectrum disorders (NMOSD). Blocking the IL-6 receptor or the C5 complement pathway reduces relapse risk. However, the role of interleukin (IL)-6 and complement in aquaporin-4 (AQP4) autoimmunity remains unclear. To investigate the role of the anti-AQP4 immunoglobulin (AQP4-IgG)/AQP4 immunocomplex on the induction and profile of ex vivo cytokine and surface marker expression in peripheral blood mononuclear cells (PBMC) culture. Isolated PBMCs obtained from 18 patients with AQP4-IgG-seropositive-NMOSD (8 treatment-naive, 10 rituximab-treated) or ten healthy controls were cultured with AQP4-immunocomplex with or without complement. Changes in PBMC surface markers and cytokine expression were profiled using flow cytometry and ELISA. PBMCs derived from treatment-naive NMOSD patients stimulated with a complex mixture of serum complement proteins produced significant elevations of IL-17A and IL-6. Rituximab-treated patients also exhibited higher IL-6 but not IL-17A release. IL-6 and IL-17A elevations are not observed without complement. Co-stimulation of PBMCs with AQP4-IgG/AQP4 immunocomplex and complement prompts a Th17-biased response consistent with the inflammatory paradigm observed in NMOSD. A possible inflammation model is proposed via antigen-specific autoreactive peripheral blood cells, including NK/NKT cells.