Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular insight into thymoquinone mechanism of action against Mycobacterium tuberculosis

Natural products are promising antimicrobials, usually having multiple and different cellular targets than synthetic antibiotics. Their influence on bacteria at various metabolic and functional levels contributes to higher efficacy even against drug-resistant strains. One such compound is a naturally occurring p-benzoquinone – thymoquinone. It is effective against different bacteria, including multidrug-resistant and extremely drug-resistant Mycobacterium tuberculosis. Its antibacterial mechanism of action was studied in several bacterial species except mycobacteria. To get an insight into the antimycobacterial activity of thymoquinone at the molecular level, we performed metabolomic and transcriptomic analyzes of bacteria exposed to this compound. The expression of genes coding stress-responsive sigma factors revealed that thymoquinone rapidly induces the production of sigE transcripts. At the same time, prolonged influence results in the overexpression of all sigma factor genes and significantly upregulates sigF. The metabolomic analysis confirmed that the antimycobacterial activity of thymoquinone was related to the depletion of NAD and ATP pools and the downregulation of plasma membrane lipids. This state was observed after 24 h and was persistent the next day, suggesting that bacteria could not activate catabolic mechanisms and produce energy. Additionally, the presence of a thymoquinone nitrogen derivative in the bacterial broth and the culture was reported.
Quantification of the Uncertainties in Soil and Vegetation Parameterizations for Regional Climate Simulations in Europe

AbstractThe deterministic description of the subgrid-scale land–atmosphere interaction in regional climate model (RCM) simulations is changed by using stochastic soil and vegetation parameterizations. For this, the land–atmosphere interaction parameterized in a land surface model (LSM) is perturbed stochastically by adding a random value to the input parameters using a random number generator. In this way, a stochastic ensemble is created that represents the impact of the uncertainties in these subgrid-scale processes on the resolved scale circulation. In a first step, stochastic stand-alone simulations with the VEG3D LSM are performed to identify sensitive model parameters. Afterward, VEG3D is coupled to the Consortium for Small-Scale Modeling–Climate Limited-Area Modeling (COSMO-CLM) RCM and stochastically perturbed simulations driven by ERA-Interim (2001–10) are performed for the Coordinated Downscaling Experiment–European Domain (EURO-CORDEX) at a horizontal resolution of 0.22°. The simulation results.
Inpatient Admissions and Re-Admissions in Medicare Beneficiaries Initiating Umeclidinium/Vilanterol or Tiotropium Therapy

Purpose Patients with chronic obstructive pulmonary disease (COPD) who are hospitalized are more likely to die from their illness and have increased likelihood of re-admission than those who are not. Subsequent re-admissions further increase the burden on healthcare systems. This study compared inpatient admission rates and time-to-first COPD-related inpatient admission among Medicare beneficiaries with COPD indexed on umeclidinium/vilanterol (UMEC/VI) versus tiotropium (TIO). Patients and Methods This retrospective study used the All-Payer Claims Database to investigate hospital admission and re-admission outcomes in Medicare beneficiaries with COPD with an initial pharmacy claim for UMEC/VI or TIO from 1 January 2015 to 28 February 2020. Inpatient admissions, baseline, and follow-up variables were assessed in patients indexed on UMEC/VI and TIO after propensity score matching (PSM), with time-to-first on-treatment COPD-related inpatient admission as the primary endpoint. Re-admissions were assessed among patients with a COPD-related inpatient admission in the 30- and 90-days post-discharge. Results Post-PSM, 7152 patients indexed on UMEC/VI and 7069 on TIO were eligible for admissions analysis. The mean (standard deviation [SD]) time-to-first COPD-related inpatient admission was 46.71 (87.99) days for patients indexed on UMEC/VI and 44.96 (85.90) days for those on TIO (p=0.06). The mean (SD) number of inpatient admissions per patient was 1.24 (2.92) for patients indexed on UMEC/VI and 1.26 (3.05) for those on TIO (p=0.49). Proportion of patients undergoing re-admissions was similar between treatments over both 30 and 90 days, excluding a significantly lower proportion of patients indexed on UMEC/VI than those indexed on TIO for COPD-related re-admissions for hospital stays of 4–7 days and 7–14 days, and all-cause re-admissions for stays of 4–7 days. Conclusion Patients with COPD using Medicare in the US and receiving UMEC/VI or TIO reported similar time-to-first inpatient admission and similar proportion of re-admissions.
The Emergence of Inequality in a Former Hunter-Gatherer Society: A Baka Case Study

The Baka people of the western Congo Basin are associated with an immediate-return hunter-gatherer lifeway. During the twentieth century they began to sedentarize and to adopt agriculture due to external pressures. The Baka community of Asoumondele are a group of 200 people, today pursuing a mixed subsistence strategy. They live on the border of Cameroon and the Republic of the Congo in a permanent village alongside Njem farmers, with whom the Baka have patron-client styled relationships often characterized by discrimination. The Baka are also politically marginalized as an ethnic group within the Cameroonian state. In 2006 an Australian mining company began establishing an iron ore mine near Asoumondele. By 2008 a rudimentary dirt road was built in order to facilitate mining activities. The advent of the mine and road has precipitated rapid transformation in this Baka society, which had already transitioned some way from the immediate-return form of egalitarianism. This thesis shows that there have been three main factors in this process, namely 1) adoption of bride wealth practices due to involvement in the ivory trade which may date back as far as the precolonial period; 2) sedentarization and the concomitant switch to delayed-return subsistence practices since the 1980s; and 3) exposure to the monetarized global economy due to the arrival of the mine. As a result of the third step, an ethnic identity crisis has caused experimental and risk-seeking attempts to level up to those higher up the social hierarchy on the part of the Baka. Examples of this are their experiments with individualistic economic activities, changes in kinship organization, agitated ritual performances, addiction to alcohol and frequent outbreaks of intra-group and domestic violence. These new patterns amount to a failure of levelling mechanisms and hence the emergence of inequality, in particular an already entrenched power difference between gender groups. The thesis supports the hypothesis that the foundations of inequality are inextricably linked with gender inequality, where the proximate mechanism of its emergence is the creation of private property (aided by storage) and the ultimate mechanism is the reproductive advantage bestowed on those men who are able to accumulate wealth. Paradoxically, an innate psychological aversion to inequity may accelerate the breakdown of egalitarian society in situations where inequalities already exist.
Explainable Artificial Intelligence Model for Predictive Maintenance in Smart Agricultural Facilities

Artificial Intelligence (AI) in Smart Agricultural Facilities (SAF) often lacks explainability, hindering farmers from taking full advantage of their capabilities. This study tackles this gap by introducing a model that combines eXplainable Artificial Intelligence (XAI), with Predictive Maintenance (PdM). The model aims to provide both predictive insights and explanations across four key dimensions, namely data, model, outcome, and end-user. This approach marks a shift in agricultural AI, reshaping how these technologies are understood and applied. The model outperforms related studies, showing quantifiable improvements. Specifically, the Long-Short-Term Memory (LSTM) classifier shows a 5.81% rise in accuracy. The eXtreme Gradient Boosting (XGBoost) classifier exhibits a 7.09% higher F1 score, 10.66% increased accuracy, and a 4.29% increase in Receiver Operating Characteristic-Area Under the Curve (ROC-AUC). These results could lead to more precise maintenance predictions in real-world settings. This study also provides insights into data purity, global and local explanations, and counterfactual scenarios for PdM in SAF. It advances AI by emphasising the importance of explainability beyond traditional accuracy metrics. The results confirm the superiority of the proposed model, marking a significant contribution to PdM in SAF. Moreover, this study promotes the understanding of AI in agriculture, emphasising explainability dimensions. Future research directions are advocated, including multi-modal data integration and implementing Human-in-the-Loop (HITL) systems aimed at improving the effectiveness of AI and addressing ethical concerns such as Fairness, Accountability, and Transparency (FAT) in agricultural AI applications.
Characteristics and impact of mesoscale eddies in the eastern tropical North Atlantic = Charakteristik und Einfluss mesoscaliger Wirbel im östlichen tropischen Nord Atlantik

A combination of multiple ocean observing system elements is used to assess the mesoscale eddy activity in the tropical Atlantic off northwestern Africa (12-22°N and 15-26°W). Considering just the rotation direction of the surface flow field, eddies are categorized into cyclonic (CEs) and anticyclonic eddies. If vertical stratification is considered additionally, a refinement can be made by distinguishing between anticyclonic (AEs) and anticyclonic modewater eddies (ACMEs). ACMEs are characterized by a subsurface mode of rather homogenous water located between upward and downward displaced isopycnals. Eddies can be identified and classified from space by investigating the sea surface parameters: Sea level anomaly (SLA), sea surface temperature (SST) and sea surface salinity (SSS). AEs/CEs are associated with an elevation/depression of SLA and enhanced/reduced SST and SSS in their cores. However, 20% of all anticyclonic eddies are associated with reduced SST and SSS instead and are identified as ACMEs. In the area of interest, about 146±4 eddies per year with a minimum lifetime of 7 days are identified (52% CEs, 39% AEs, 9% ACMEs). All observed eddies are isolated and serve as transport agents, exporting water from the coast into the open ocean. In CEs and ACMEs low oxygen cores are identified and related to enhanced primary production at the surface and an associated elevated respiration rates within the isolated eddy cores. It could be observed that the phase speed of NIWs and the speed of the mean eddy flow are of similar magnitude. Therefore, critical layer formation is expected and mixing is likely to occur close to the euphotic zone at the eddy periphery. These processes describe one mechanism that support an upward nutrient flux towards the euphotic zone and the coexistence with a highly isolated eddy core. The analysis shows that anomalous environments associated with eddy cores occur more frequently than previously expected.
Disrupted properties of functional brain networks in major depressive disorder during emotional face recognition: an EEG study via graph theory analysis

Previous neuroimaging studies have revealed abnormal brain networks in patients with major depressive disorder (MDD) in emotional processing. While any cognitive task consists of a series of stages, little is yet known about the topology of functional brain networks in MDD for these stages during emotional face recognition. To address this problem, electroencephalography (EEG)-based functional brain networks of MDD patients at different stages of facial information processing were investigated in this study. First, EEG signals were collected from 16 patients with MDD and 18 age-, gender-, and education-matched normal subjects when performing an emotional face recognition task. Second, the global field power (GFP) method was employed to divide group-averaged event-related potentials into different stages. Third, using the phase transfer entropy (PTE) approach, the brain networks of MDD patients and normal individuals were constructed for each stage in negative and positive face processing, respectively. Finally, we compared the topological properties of brain networks of each stage between the two groups using graph theory approaches. The results showed that the analyzed three stages of emotional face processing corresponded to specific neurophysiological phases, namely, visual perception, face recognition, and emotional decision-making. It was also demonstrated that depressed patients showed abnormally decreased characteristic path length at the visual perception stage of negative face recognition and normalized characteristic path length in the stage of emotional decision-making during positive face processing compared to healthy subjects. Furthermore, while both the MDD and normal groups’ brain networks were found to exhibit small-world network characteristics, the brain network of patients with depression tended to be randomized. Moreover, for patients with MDD, the centro-parietal region may lose its status as a hub in the process of facial expression identification. Together, our findings suggested that altered emotional function in MDD patients might be associated with disruptions in the topological organization of functional brain networks during emotional face recognition, which further deepened our understanding of the emotion processing dysfunction underlying MDD.
Microstructural preservation and the effects of diagenesis on the carbon and oxygen isotope composition of Late Cretaceous aragonitic mollusks from the Gulf Coastal Plain and the Western Interior Seaway

The carbon and oxygen isotope compositions of calcium carbonate shells are widely accepted and applied proxies for tracking changes in paleoenvironmental conditions such as temperature, salinity and productivity. In order to accurately interpret isotopic measurements, diagenetic alteration must first be assessed. The occurrence of aragonitic shells is often taken as a first order sign of unaltered material because aragonite at the Earth's surface is metastable and converts to calcite. However, even specimens that retain an aragonitic composition and are macroscopically well preserved often exhibit subtle to considerable signs of alteration when shell microstructure is examined using scanning electron microscopy (SEM). To determine the textural and isotopic effects of progressive alteration on differing types of shell microstructure, we undertook a comparative study of aragonitic shells from two regions frequently used in paleoenvironmental reconstructions and diagenetic studies – the Upper Cretaceous of the Gulf Coastal Plain (GCP) and the Western Interior Seaway (WIS). Because the GCP is within a passive margin setting and the WIS has experienced tectonic processes, we also evaluate how diagenetic history affects isotopic composition. Visually well-preserved ammonite, bivalve, and gastropod shells were collected from one locality in the GCP and examined using SEM. To evaluate microstructural preservation, we used a previously published scale based on WIS specimens for nacreous shell material and a complementary scale we developed for crossed lamellar microstructure. The stable carbon and oxygen isotope compositions of specimens across the preservational scale from both regions were analyzed. Isotopic composition does not change systematically with degrading preservation in the GCP specimens, a result that contrasts strongly with patterns in WIS specimens where isotopic composition systematically decreases with decreasing microstructural preservation. Dissimilar tectonic regimes that led to unique post-depositional conditions for each region are invoked to explain this difference. The WIS was a foreland basin subjected to significant meteoritic groundwater flow driven by active uplift, while the GCP was a passive margin that has remained close to sea level, with low hydraulic potential, since the time of deposition. Thus, during diagenesis the WIS shells were exposed to fluids that differed greatly from the seawater in which the organisms grew, whereas diagenetic fluids in GCP settings likely were similar to marine waters. As expected, shells with the best-preserved microstructure provide the most consistently reliable isotopic data for paleoenvironmental reconstructions, but our comparisons show that similar degrees of microstructural alteration can express very different diagenetic shifts in isotopic values.
From Hunter-Gathering to the Roman Conquest: An archaeobotanical resource assessment and research agenda for prehistoric Wales (c.8000 BC – AD 100)

This thesis highlights the significance and potential of archaeobotanical research undertaken on prehistoric sites in Wales (c. 8000 cal BC – 100 cal AD), providing insights into agricultural practices, food, diet, woodland exploitation and environments. It represents the first comprehensive review of archaeobotanical evidence for prehistoric Wales in over two decades. A total of over 300 archaeobotanical records were collated and the focus of this research lies in providing an assessment of the quantity and quality of the current dataset to develop a resource assessment and research agenda. A critical review of the dataset is first provided focusing on its chronological and geographical coverage and the quality of the available evidence. Following this, a detailed chronological review of the evidence is provided from the Mesolithic to the Iron Age and for each major period the dataset is discussed in a wider context. A number of methodological issues with the dataset are outlined and major gaps in the current state of knowledge identified. On this basis, research priorities are recommended. Ultimately, it aims to stimulate further discussion and to highlight the significance and potential of archaeobotanical research to a wider archaeological audience.
Accounting for model uncertainty in individualized designs for discrete choice experiments

Abstract We develop a method for finding optimal designs in discrete choice experiments (DCEs). More specifically, we deal with individualized designs, which are sequentially generated for each person undertaking a survey, using, at each stage, responses from previous choice sets in order to select the next best set. Currently, the optimal design for a DCE is predicated on a specific mixed logit model that represents the probability of choosing a specific alternative in a choice set through a linear predictor combining several attributes or factors deemed to be relevant in each choice. Using a unique model represents a major limitation, which we overcome by allowing for a collection of different models characterized by distinct linear predictors. Our approach is fully Bayesian and incorporates a prior distribution on the model space as well as a prior on the parameter space specific to each respondent. To perform our optimal design strategy for DCEs, we specify two distinct utility functions, one being targeted to model discrimination while the other aims at the dual purpose of model discrimination and parameter estimation. We implement our methodology using a sequential Monte Carlo algorithm suitably tailored to account for model uncertainty and individual-specific parameters. To evaluate our methodology, several simulation settings are considered in detail. Comparisons with alternative methods are also investigated.
Daptomycin and Ceftaroline Combination Therapy in Complicated Endovascular Infections Caused by Methicillin-Resistant Staphylococcus epidermidis

Background In complicated endovascular infections by methicillin-resistant Staphylococcus aureus (MRSA) or Staphylococcus epidermidis (MRSE), when first-line therapy with vancomycin (VAN) or daptomycin (DAP) fails, combination therapy with ceftaroline (CFT) and DAP has been shown to be a useful approach as salvage therapy for persistent MRSA bacteremia. Objectives This study aimed to describe experience with daptomycin and ceftaroline combination therapy in MRSE-complicated endovascular infections. Methods A single-center retrospective review of consecutive patients with MRSE-complicated endovascular infections treated with ≥72 hours of DAP+CFT at any time during the course of treatment, from January 1, 2016 to December 31, 2020, at Centro Hospitalar Universitário São João (CHUSJ), Porto, Portugal, was conducted. The exclusion criteria were known resistance to daptomycin or ceftaroline, total time of combination therapy <72 hours and loss to follow-up. Results We identified seven cases that matched our criteria: five endocarditis and two central venous catheter infections. Six patients switched to combination therapy due to treatment failure with first-line agents - three due to persistent bacteremia and three due to progression of infection despite negative blood cultures. Effective surgical source control took one to four weeks to occur. Three patients died during the treatment, one from progression of the disease and two due to another infection. Conclusions We consider the DAP+CFT combination therapy to be a valid and safe therapeutic choice in complicated patients, such as those with severe infection, poor functional status, and impossibility or delay of surgical source control. However, conclusions on the role of combination therapy should be careful due to the low number of patients and the several confounding factors.
Anodal transcranial direct current stimulation (atDCS) and functional transcranial Doppler sonography (fTCD) in healthy elderly and patients with MCI: modulation of age-related changes in word fluency and language lateralization

Introduction: In addition to age-related changes in language, hemispheric lateralization of language functions steadily declines with age. Also, performance on word fluency tasks declines and is sensitive to the expression of dementia-related changes. The aim of this study is to evaluate the effect of anodal tDCS combined with a word fluency training on language lateralization and word fluency performance in healthy elderly subjects and in persons with mild cognitive impairment (MCI). Methods: The effect of anodal tDCS over the left inferio frontal gyrus (IFG) was measured in a group of healthy elderly up to the age of 67 years (YG, Ø = 63.9 ± 3.02), a group of healthy elderly aged 68 years and older (OG, Ø = 78.1, ± 4.85), and a group of patients with MCI (Ø = 81.18, ± 7.35) by comparing performance in phonological and semantic word fluency tasks before and after 3 days of tDCS. Half of the experimental participants received sham stimulation. In addition, language lateralization was determined using a lateralization index (LI) measured with functional transcranial Doppler sonography (fTCD) before and after the stimulation period. Results: Anodal tDCS was associated with significantly higher scores in phonological but not semantic word fluency in both YG and OG. In MCI patients, no difference was measured between the tDCS and sham groups in either word fluency task. fTCD showed significantly increased left lateralization in all three groups after the training phase. However, this effect was independent of tDCS and the degree of lateralization could not be predicted by word fluency performance in any of the groups. Discussion: Phonological word fluency can be increased with atDCS in healthy elderly people by stimulating the IFG in a 3-day training. When cognitive decline has reached a certain stage, as is the case with MCI, this paradigm does not seem to be effective enough.