Miracle-dz/UniFAR-FTUs huggingface dataset:
Rosmarinic Acid Protects Skin Keratinocytes from Particulate Matter 2.5-Induced Apoptosis

Background: The exposure of the human skin to particulate matter 2.5 (PM2.5) results in adverse health outcomes, such as skin aging, wrinkle formation, pigment spots, and atopic dermatitis. It has previously been shown that rosmarinic acid (RA) can protect keratinocytes from ultraviolet B radiation by enhancing cellular antioxidant systems and reducing oxidative damage; however, its protective action against the adverse effects of PM2.5 on skin cells remains unclear. Therefore, in this study, we explored the mechanism underlying the protective effects of RA against PM2.5-mediated oxidative stress in HaCaT keratinocytes. Methods: HaCaT keratinocytes were pretreated with RA and exposed to PM2.5. Thereafter, reactive oxygen species (ROS) production, protein carbonylation, lipid peroxidation, DNA damage, and cellular apoptosis were investigated using various methods, including confocal microscopy, western blot analysis, and flow cytometry. Results: RA significantly inhibited PM2.5-induced lipid peroxidation, protein carbonylation, DNA damage, increases in intracellular Ca2+ level, and mitochondrial depolarization. It also significantly attenuated PM2.5-induced apoptosis by downregulating Bcl-2-associated X, cleaved caspase-9, and cleaved caspase-3 protein levels, while upregulating B-cell lymphoma 2 protein level. Further, our results indicated that PM2.5-induced apoptosis was associated with the activation of the mitogen-activated protein kinase (MAPK) signaling pathway and that MAPK inhibitors as well as RA exhibited protective effects against PM2.5-induced apoptosis. Conclusion: RA protected HaCaT cells from PM2.5-induced apoptosis by lowering oxidative stress.
Validity and Reliability Study of Online Cognitive Tracking Software (BEYNEX)

Background: Detecting cognitive impairment such as Alzheimer’s disease early and tracking it over time is essential for individuals at risk of cognitive decline. Objective: This research aimed to validate the Beynex app’s gamified assessment tests and the Beynex Performance Index (BPI) score, which monitor cognitive performance across seven categories, considering age and education data. Methods: Beynex test cut-off scores of participants (n = 91) were derived from the optimization function and compared to the Montreal Cognitive Assessment (MoCA) test. Validation and reliability analyses were carried out with data collected from an additional 214 participants. Results: Beynex categorization scores showed a moderate agreement with MoCA ratings (weighted Cohen’s Kappa = 0.48; 95% CI: 0.38–0.60). Calculated Cronbach’s Alpha indicates good internal consistency. Test-retest reliability analysis using a linear regression line fitted to results yielded R∧2 of 0.65 with a 95% CI: 0.58, 0.71. Discussion: Beynex’s ability to reliably detect and track cognitive impairment could significantly impact public health, early intervention strategies and improve patient outcomes.
Recent trends in modeling spatio-temporal data

This articles provides a review of recent advances in modeling spatio-temporal data. In an attempt to unify the modeling strategies we describe the primary spatio-temporal data types. We then discuss general models for point reference data only. Spatial-temporal modeling has largely been developed through applications in environmental, geostatistics, hydrology and meteorology. We review current methods for many such application areas.
Method of Solving Moist Thermodynamic Equations in NTU-Purdue Non-Hydrostatic Model and Tests on 2D Moist Mountain Waves

A moving frame of reference technique is proposed so that the retrievalof cross-beam wind components is feasible from observations by singleDoppler Radar without sacrificing data resolution.In this algorithm,thereflectivity fields observed by consecutive radar scans are used to find amoving Lagrangian coordinate on which the reflectivity measurements areas stationary as possible.After interpolating all the observational data tothis optimal moving frame,and assuming the wind field is steady state withinseveral radar scans,one can formulate a cost function which contains thefollowing weak constraints:(1)reflectivity is preserved;(2)a geometricrelationship between radial velocity Vr and the Cartesian components u,v,w;(3)mass conservation;and(4)weak vertical vorticity.By minimizingthis cost function,the unobserved cross-beam wind component can be recovered.Applying this algorithm to a simulated,idealized Rankine vortex circulation,it is found that with an appropriate scan strategy,that is,a sufficientnumber of radar scans(＞2),separated by a short enough period oftime(～3 minutes),low level circulation can be successfully retrieved usingdata detected by single Doppler radar.This technique is robust in compensatingfor observational errors,and,in a qualitative sense,works well whenonly reflectivity measurements are available.
Impedance Spectroscopy Modeling of Solution-Processed Amorphous Indium-Gallium-Zinc-Oxide Metal-Semiconductor-Metal Diode

In this study, we analyze the impedance spectroscopic characteristics of solution-processed amorphous indium-gallium-zinc-oxide (a-IGZO) metal-semiconductor-metal diodes adopting aluminum and heavily doped Si electrodes. The Cole–Cole plots extracted from the capacitance-voltage (<inline-formula> <tex-math notation="LaTeX">${C}$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">${V}$ </tex-math></inline-formula>) measurements exhibited variations depending on the voltage bias polarity and were simplified using two types of equivalent circuits. These circuits include the effects of oxidation near the aluminum electrode, tunneling at the metal/a-IGZO layer interface from the tunneling diode model, and the presence of native oxide. The thickness dependence of the <inline-formula> <tex-math notation="LaTeX">${C}$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">${V}$ </tex-math></inline-formula> measurements indicates that oxidation of the Al electrodes and the quantum mechanical distribution of the electron density dominantly affected the <inline-formula> <tex-math notation="LaTeX">${C}$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">${V}$ </tex-math></inline-formula> results at the Al/IGZO interface.
Overview of Footprints and Relations Between Carbon and Nitrogen Footprints

This contribution provides an overview of the variety of footprints. The distinction is assessed between indicators of environmental impacts and footprints. Definitions and reviews of generally accepted as well as new footprints are provided. Emphasis is given towards an adversarial relationship between carbon and nitrogen footprints. Biomass energy production is an example where carbon footprint can be significantly reduced, however this is closely linked to an enlarged nitrogen cycle. A case study of domestic wood combustion is used to demonstrate the relation between those footprints where different energy sources (natural gas, coal and fuel oil) are supplemented by biomass combustion. The results prove that the carbon footprint from domestic wood combustion is almost carbon neutral, whilst the nitrogen footprint is ~ 50 % higher compared with coal burning.
Untargeted Plasma Metabolomic Profiling in Patients with Depressive Disorders: A Preliminary Study

Depressive disorder is a multifactorial disease that is based on dysfunctions in mental and biological processes. The search for biomarkers can improve its diagnosis, personalize therapy, and lead to a deep understanding of the biochemical processes underlying depression. The purpose of this work was a metabolomic analysis of blood serum to classify patients with depressive disorders and healthy individuals using Compound Discoverer software. Using high-resolution mass spectrometry, blood plasma samples from 60 people were analyzed, of which 30 were included in a comparison group (healthy donors), and 30 were patients with a depressive episode (F32.11) and recurrent depressive disorder (F33.11). Differences between patient and control groups were identified using the built-in utilities in Compound Discoverer software. Compounds were identified by their accurate mass and fragment patterns using the mzCloud database and tentatively identified by their exact mass using the ChemSpider search engine and the KEGG, ChEBI, FDA UNII-NLM, Human Metabolome and LipidMAPS databases. We identified 18 metabolites that could divide patients with depressive disorders from healthy donors. Of these, only two compounds were tentatively identified using the mzCloud database (betaine and piperine) based on their fragmentation spectra. For three compounds ((4S,5S,8S,10R)-4,5,8-trihydroxy-10-methyl-3,4,5,8,9,10-hexahydro-2H-oxecin-2-one, (2E,4E)-N-(2-hydroxy-2-methylpropyl)-2,4-tetradecadienamide and 17α-methyl-androstan-3-hydroxyimine-17β-ol), matches were found in the mzCloud database but with low score, which could not serve as reliable evidence of their structure. Another 13 compounds were identified by their exact mass in the ChemSpider database, 9 (g-butyrobetaine, 6-diazonio-5-oxo-L-norleucine, 11-aminoundecanoic acid, methyl N-acetyl-2-diazonionorleucinate, glycyl-glycyl-argininal, dilaurylmethylamine, 12-ketodeoxycholic acid, dicetylamine, 1-linoleoyl-2-hydroxy-sn-glycero-3-PC) had only molecular formulas proposed, and 4 were unidentified. Thus, the use of Compound Discoverer software alone was not sufficient to identify all revealed metabolites. Nevertheless, the combination of the found metabolites made it possible to divide patients with depressive disorders from healthy donors.
Activity of Potassium Channels in CD8+ T Lymphocytes: Diagnostic and Prognostic Biomarker in Ovarian Cancer?

CD8+ T cells play a role in the suppression of tumor growth and immunotherapy. Ion channels control the Ca2+-dependent function of CD8+ lymphocytes such as cytokine/granzyme production and tumor killing. Kv1.3 and KCa3.1 K+ channels stabilize the negative membrane potential of T cells to maintain Ca2+ influx through CRAC channels. We assessed the expression of Kv1.3, KCa3.1 and CRAC in CD8+ cells from ovarian cancer (OC) patients (n = 7). We found that the expression level of Kv1.3 was higher in patients with malignant tumors than in control or benign tumor groups while the KCa3.1 activity was lower in the malignant tumor group as compared to the others. We demonstrated that the Ca2+ response in malignant tumor patients is higher compared to control groups. We propose that altered Kv1.3 and KCa3.1 expression in CD8+ cells in OC could be a reporter and may serve as a biomarker in diagnostics and that increased Ca2+ response through CRAC may contribute to the impaired CD8+ function.
A bridge over troubled water: A contextual analysis of social vulnerability to climate change in a riverine landscape in south-east Norway

ABSTRACT Local communities in the Gudbrandsdalen region in Norway are increasingly exposed to climate-induced hazards such as floods and landslides. A core question is how community members respond to climate change and what factors contribute to more resilient communities. The authors used a contextual approach to analyze data from semi-structured interviews along five dimensions. In Gaustad Muncipality they found that individuals’ motivation to adapt to climate change depended largely on subjective values such as identity, place attachment, cultural values, and social networks among individuals, which means it is crucial that strategic plans for adaptation to climate change at different policy levels are experienced as relevant by community members. While the studied community has experienced heavy floods in river systems and streams, little evidence of adaptation was observed. Instead, they appeared to adopt coping strategies. Landowners may have limited incentives to adapt to climate change due to contraproductive policy measures such as economic compensation for direct losses without requiring improved practices. Effective adaptation to climate change on the local level is likely to require making compensation mechanisms contingent upon landowners showing willingness to change from coping to adaptive practices, as well as a contextualized approach integrating local and scientific forms of knowledge.
A Global study of intended instructional time and official school curricula, 1980-2000. Paper commissioned for the EFA Global Monitoring Report 2005, The Quality Imperative

The report is organized into five parts: Following this introduction, Section II briefly reviews relevant background literature and previous research. Section III describes the methodology of the study, including the compilation of curricular data, and the coding and construction of the study’s main variables. Section IV presents empirical findings regarding intended instructional time, the organization of the official curriculum, with special attention to language education, mathematics and several additional subject areas, and lastly the ‘overloading’ of school timetables. Section V briefly discusses the report’s main findings in the context of emergent scholarly debates. A special methodological appendix is included, which details the data sources used for instructional time estimates and measures of the official curriculum.
Endothelial Senescence: From Macro- to Micro-Vasculature and Its Implications on Cardiovascular Health

Endothelial cells line at the most inner layer of blood vessels. They act to control hemostasis, arterial tone/reactivity, wound healing, tissue oxygen, and nutrient supply. With age, endothelial cells become senescent, characterized by reduced regeneration capacity, inflammation, and abnormal secretory profile. Endothelial senescence represents one of the earliest features of arterial ageing and contributes to many age-related diseases. Compared to those in arteries and veins, endothelial cells of the microcirculation exhibit a greater extent of heterogeneity. Microcirculatory endothelial senescence leads to a declined capillary density, reduced angiogenic potentials, decreased blood flow, impaired barrier properties, and hypoperfusion in a tissue or organ-dependent manner. The heterogeneous phenotypes of microvascular endothelial cells in a particular vascular bed and across different tissues remain largely unknown. Accordingly, the mechanisms underlying macro- and micro-vascular endothelial senescence vary in different pathophysiological conditions, thus offering specific target(s) for therapeutic development of senolytic drugs.
Neuropsychology of chronic back pain managed with long-term opioid use

Chronic pain is commonly treated with long-term opioids, but the neuropsychological outcomes associated with stable long-duration opioid use remain unclear. Here, we contrasted the psychological profiles, brain activity, and brain structure of 70 chronic back pain patients on opioids (CBP+O, average opioid exposure 6.2 years) with 70 patients managing their pain without opioids. CBP+O exhibited moderately worse psychological profiles and small differences in brain morphology. However, CBP+O had starkly different spontaneous brain activity, dominated by increased mesocorticolimbic and decreased dorsolateral-prefrontal activity, even after controlling for pain intensity and duration. These differences strongly reflected cortical opioid and serotonin receptor densities and mapped to two antagonistic resting-state circuits. The circuits' dynamics were explained by mesocorticolimbic activity and reflected negative affect. We reassessed a sub-group of CBP+O after they briefly abstained from taking opioids. Network dynamics, but not spontaneous activity, reflected exacerbated signs of withdrawal. Our results have implications for the management and tapering of opioids in chronic pain.
The association of lifestyle with cardiovascular and all-cause mortality based on machine learning: A Prospective Study from the NHANES

Objective: To develop a machine learning (ML) risk stratification model for predicting all-cause mortality and cardiovascular mortality while estimating the influence of lifestyle behavioral factors on the model's efficacy. Method: A prospective cohort study was conducted using a nationally representative sample of adults aged 40 years or older, drawn from the US National Health and Nutrition Examination Survey from 2007 to 2010. The participants underwent a comprehensive in-person interview and medical laboratory examinations, and subsequently, their records were linked with the National Death Index for further analysis. Result: Within a cohort comprising 7921 participants, spanning an average follow-up duration of 9.75 years, a total of 1911 deaths, including 585 cardiovascular-related deaths, were recorded. The model predicted mortality with an area under the receiver operating characteristic curve (AUC) of 0.848 and 0.829. Stratifying participants into distinct risk groups based on ML scores proved effective. All lifestyle behaviors exhibited an inverse association with all-cause and cardiovascular mortality. As age increases, the discernible impacts of dietary scores and sedentary time become increasingly apparent, whereas an opposite trend was observed for physical activity. Conclusion: We develop a ML model based on lifestyle behaviors to predict all-cause and cardiovascular mortality. The developed model offers valuable insights for the assessment of individual lifestyle-related risks. It applies to individuals, healthcare professionals, and policymakers to make informed decisions.
ChEC-seq2: an improved chromatin endogenous cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein–DNA interactions

Abstract Defining the in vivo DNA binding specificity of transcription factors (TFs) has relied nearly exclusively on chromatin immunoprecipitation (ChIP). While ChIP reveals TF binding patterns, its resolution is low. Higher resolution methods employing nucleases such as ChIP-exo, chromatin endogenous cleavage (ChEC-seq) and CUT&RUN resolve both TF occupancy and binding site protection. ChEC-seq, in which an endogenous TF is fused to micrococcal nuclease, requires neither fixation nor antibodies. However, the specificity of DNA cleavage during ChEC has been suggested to be lower than the specificity of the peaks identified by ChIP or ChIP-exo, perhaps reflecting non-specific binding of transcription factors to DNA. We have simplified the ChEC-seq protocol to minimize nuclease digestion while increasing the yield of cleaved DNA. ChEC-seq2 cleavage patterns were highly reproducible between replicates and with published ChEC-seq data. Combined with DoubleChEC, a new bioinformatic pipeline that removes non-specific cleavage sites, ChEC-seq2 identified high-confidence cleavage sites for three different yeast TFs that are strongly enriched for their known binding sites and adjacent to known target genes.
Exploring Alzheimer's disease: a comprehensive brain connectome-based survey

Abstract Dementia is an escalating global health challenge, with Alzheimer's disease (AD) at its forefront. Substantial evidence highlights the accumulation of AD-related pathological proteins in specific brain regions and their subsequent dissemination throughout the broader area along the brain network, leading to disruptions in both individual brain regions and their interconnections. Although a comprehensive understanding of the neurodegeneration-brain network link is lacking, it is undeniable that brain networks play a pivotal role in the development and progression of AD. To thoroughly elucidate the intricate network of elements and connections constituting the human brain, the concept of the brain connectome was introduced. Research based on the connectome holds immense potential for revealing the mechanisms underlying disease development, and it has become a prominent topic that has attracted the attention of numerous researchers. In this review, we aim to systematically summarize studies on brain networks within the context of AD, critically analyze the strengths and weaknesses of existing methodologies, and offer novel perspectives and insights, intending to serve as inspiration for future research.
Tetramethylpyrazine protects mitochondrial function by up-regulation of TFAM and inhibition of neuronal apoptosis in a rat model of surgical brain injury

Objective(s): Mitochondrial dysfunction caused by mitochondrial DNA (mtDNA) damage and mutation is widely accepted as one of the pathological processes of neurodegenerative diseases. As an mtDNA binding protein, mitochondrial transcription factor A (TFAM) maintains the integrity of mtDNA through transcription, replication, nucleoid formation, damage perception, and DNA repair. In recent works, the overexpression of TFAM increased the mtDNA copy count, promoted mitochondrial function, and improved the neurological dysfunction of neurodegenerative diseases. The role of TFAM in neurodegenerative diseases has been well explained. However, the role of TFAM after surgical brain injury (SBI) has not been studied. In this work, we aimed to study the role of TFAM in the brain after SBI and its mechanism of action. Materials and Methods: One hour after the occurrence of SBI, tetramethylpyrazine (TMP) was injected into the abdominal cavity of rats, and the brain was collected 48 hr later for testing. The evaluation included neurobehavioral function test, brain water content measurement, immunofluorescence, western blot, TUNEL staining, FJC staining, ROS test, and ATP test. Results: After SBI, the content of TFAM on the ipsilateral side increased and reached a peak at about 48 hr. After intraperitoneal injection of TMP in rats, 48 hr after SBI, the concentration of TFAM, Bcl-2, and adenosine triphosphate (ATP) increased; the content of caspase-3, reactive oxygen species (ROS), and cerebral edema decreased; and the nerve function significantly improved. Conclusion: TMP inhibited cell apoptosis after SBI in rats by up-regulating TFAM and protecting brain tissues.
Climate change and the biodiversity of alpine ponds: Challenges and perspectives

Abstract Inland waters are among the most threatened biodiversity hotspots. Ponds located in alpine areas are experiencing more rapid and dramatic water temperature increases than any other biome. Despite their prevalence, alpine ponds and their biodiversity responses to climate change have been poorly explored, reflecting their small size and difficult access. To understand the effects of climate change on alpine pond biodiversity, we performed a comprehensive literature review for papers published since 1955. Through analysis of their geographic distribution, environmental features, and biodiversity values, we identified which environmental factors related to climate change would have direct or indirect effects on alpine pond biodiversity. We then synthesized this information to produce a conceptual model of the effects of climate change on alpine pond biodiversity. Increased water temperature, reduced hydroperiod, and loss of connectivity between alpine ponds were the main drivers of biodiversity geographic distribution, leading to predictable changes in spatial patterns of biodiversity. We identified three major research gaps that, if addressed, can guide conservation and restoration strategies for alpine ponds biodiversity in an uncertain future.