Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan

Sulfur-oxidizing bacteria play a crucial role in various processes, including mine bioleaching, biodesulfurization, and treatment of sulfur-containing wastewater. Nevertheless, the pathway involved in sulfur oxidation is highly intricate, making it complete comprehension a formidable and protracted undertaking. The mechanisms of sulfur oxidation within the Acidithiobacillus genus, along with the process of energy production, remain areas that necessitate further research and elucidation. In this study, a novel strain of sulfur-oxidizing bacterium, Acidithiobacillus Ameehan, was isolated. Several physiological characteristics of the strain Ameehan were verified and its complete genome sequence was presented in the study. Besides, the first genome-scale metabolic network model (AMEE_WP1377) was reconstructed for Acidithiobacillus Ameehan to gain a comprehensive understanding of the metabolic capacity of the strain.The characteristics of Acidithiobacillus Ameehan included morphological size and an optimal growth temperature range of 37-45°C, as well as an optimal growth pH range of pH 2.0-8.0. The microbe was found to be capable of growth when sulfur and K2O6S4 were supplied as the energy source and electron donor for CO2 fixation. Conversely, it could not utilize Na2S2O3, FeS2, and FeSO4·7H2O as the energy source or electron donor for CO2 fixation, nor could it grow using glucose or yeast extract as a carbon source. Genome annotation revealed that the strain Ameehan possessed a series of sulfur oxidizing genes that enabled it to oxidize elemental sulfur or various reduced inorganic sulfur compounds (RISCs). In addition, the bacterium also possessed carbon fixing genes involved in the incomplete Calvin-Benson-Bassham (CBB) cycle. However, the bacterium lacked the ability to oxidize iron and fix nitrogen. By implementing a constraint-based flux analysis to predict cellular growth in the presence of 71 carbon sources, 88.7% agreement with experimental Biolog data was observed. Five sulfur oxidation pathways were discovered through model simulations. The optimal sulfur oxidation pathway had the highest ATP production rate of 14.81 mmol/gDW/h, NADH/NADPH production rate of 5.76 mmol/gDW/h, consumed 1.575 mmol/gDW/h of CO2, and 1.5 mmol/gDW/h of sulfur. Our findings provide a comprehensive outlook on the most effective cellular metabolic pathways implicated in sulfur oxidation within Acidithiobacillus Ameehan. It suggests that the OMP (outer-membrane proteins) and SQR enzymes (sulfide: quinone oxidoreductase) have a significant impact on the energy production efficiency of sulfur oxidation, which could have potential biotechnological applications.
Comparison of MPPT based on Deep Reinforcement Learning by DQN, DDPG and TD3

The renewable energy, especially photovoltaic (PV), is growing exponentially for being able to harvest solar power, which is abundant, especially in tropical countries, like Indonesia. There is the limit of the power harvested, first is PV efficiency and also how the generated power is transferred to the load. The power generated by PV (PPV ) should be able to be transferred to the load close to its maximum generated power. This task is done by an MPPT (Maximum Power Point Tracking) module in the PV System. MPPT has been widely implemented especially the conventional methods like Perturb and Observe (P&O). The review of conventional and even AI-based MPPT elucidates problems when MPPT transfers the power during the partial shading condition (PSC) and also at low generated power. The power fluctuates and is significantly inefficient in both conditions respectively. The latest studies showed that MPPT by Deep Reinforcement Learning (DRL) has provided a stable and more efficient PVP compared to P&O and other conventional methods. The study in this research continues the previous one on DRL by reproducing MPPT using DQN (Deep Q-Network) and DDPG (Deep Deterministic Policy Gradient) and introducing TD3 (Twin Delayed Deep Deterministic Policy Gradient). The study shows that at irradiation 1000W/m2 condition, TD3 produced output power 8.37% higher than DDPG and 1.61% higher than DQN. Then at low irradiation, 250W/m2 TD3 is higher 13.93% than DDPG but lower 29.27% than DQN. On both conditions TD3 is the least fluctuated, the standard deviation is 0.02, while DQN is 4.04 at clear day and DDPG is 5.8 at cloudy day. This is a promising outcome for renewable energy harvesting, especially on a large scale.
The unfolding water drama in the Anthropocene: towards a resilience‐based perspective on water for global sustainability

The human influence on the global hydrological cycle is now the dominant force behind changes in water resources across the world and in regulating the resilience of the Earth system. The rise in human pressures on global freshwater resources is in par with other anthropogenic changes in the Earth system (from climate to ecosystem change), which has prompted science to suggest that humanity has entered a new geological epoch, the Anthropocene. This paper focuses on the critical role of water for resilience of social‐ecological systems across scales, by avoiding major regime shifts away from stable environmental conditions, and in safeguarding life‐support systems for human wellbeing. It highlights the dramatic increase of water crowding: near‐future challenges for global water security and expansion of food production in competition with carbon sequestration and biofuel production. It addresses the human alterations of rainfall stability, due to both land‐use changes and climate change, the ongoing overuse of blue water, reflected in river depletion, expanding river basin closure, groundwater overexploitation and water pollution risks. The rising water turbulence in the Anthropocene changes the water research and policy agenda, from a water‐resource efficiency to a water resilience focus. This includes integrated land and water stewardship to sustain wetness‐dependent ecological functions at the landscape scale and a stronger emphasis on green water management for ecosystem services. A new paradigm of water governance emerges, encouraging land‐use practices that explicitly take account of the multifunctional roles of water, with adequate attention to planetary freshwater boundaries and cross‐scale interactions. © 2014 The Authors. Ecohydrology published by John Wiley & Sons, Ltd.
Evolution Mechanism of Sputtered Film Uniformity with the Erosion Groove Size: Integrated Simulation and Experiment

In this work, Cu thin films were experimentally fabricated at different target–substrate distances by 2-inch and 4-inch circular planar magnetron targets. Meanwhile, the sputtering deposition of Cu thin films was investigated via an integrated multiscale simulation, where the magnetron sputtering discharge was modeled using the Monte Carlo (MC) method, and the sputtered particle transport was simulated using a coupled Monte Carlo (MC) and molecular dynamics (MD) method. Experimental results indicated that, as the target–substrate distance increased from 30 to 120 mm, the film thickness distribution of the 2-inch target sputtering changed from a bell-shaped curve to a line-shaped curve, while that of the 4-inch target sputtering varied from a saddle-shaped curve to a line-shaped curve. The simulation results were accordant with the experimental results. The simulation results revealed that, at a target–substrate distance of 30 mm, the sputtering particle flow from the 2-inch target overlapped strongly near the substrate center, leading to a bell-shaped film thickness distribution, while the increased diameter of the erosion groove on the 4-inch target reduced the superposition effect of the sputtering particle flow near the substrate center, resulting in a saddle-shaped film thickness distribution. In addition, when the target–substrate distance ranged from 30 to 120 mm, the film thickness uniformity of 4-inch target sputtering was superior to that of 2-inch target sputtering, and the underlying mechanism was discussed in detail.
Oceanographic patterns and carbonate chemistry in the vicinity of cold‐water coral reefs in the Gulf of Mexico: Implications for resilience in a changing ocean

To accurately assess the threat that global climate change poses to marine systems, a detailed baseline of the current carbonate chemistry and other oceanographic conditions is required. Despite the heightened vulnerability of deep‐sea communities to ocean acidification, there have been relatively few studies investigating the carbonate chemistry immediately above cold‐water coral reefs. Here, we present data collected during five cruises from 2010 to 2014 in the northern Gulf of Mexico and quantify the carbonate system and other oceanographic parameters in offshore surface‐waters, the water column, and at deep benthic sites. Benthic sites containing the scleractinian cold‐water coral L. pertusa occurred in waters with a relatively wide temperature range (6.8–13.6°C), low potential density (σθ = 26.9 ± 0.3 kg m−3), low dissolved oxygen concentration (111.3 ± 2.0 μmol kg−1), low pHT (7.87 ± 0.04), low ΩARAG (1.31 ± 0.14), and a low availability of carbonate ions (94.4 ± 9.2 μmol kg−1) compared with L. pertusa habitats in other regions. Based on previous modelling and experimental results, these values place L. pertusa at the edge of its viable niche in the deep Gulf of Mexico. However, significantly elevated total alkalinity (+39–44 μmol kg−1) was detected above large L. pertusa mounds, suggesting that carbonate dissolution within the mounds may be partially ameliorating the direct effects of ocean acidification. Together, these results provide an important baseline for assessing future oceanographic changes in the Gulf of Mexico and for predicting the resilience of cold‐water coral reefs to global climate and ocean change.
INFLUÊNCIA DOS COMBUSTÍVEIS AUTOMOTIVOS NO MATERIAL PARTICULADO ATMOSFÉRICO DE SÃO PAULO E RIO DE JANEIRO

São apresentados os resultados de um estudo realizado pela Petrobras, USP e PUC-RJ para determinar a influência das principais fontes na formação do material particulado (MP) nas regiões metropolitanas de São Paulo e Rio de Janeiro, em especial o MP 2,5. Um dos objetivos foi a caracterização completa do MP presente no gás de escapamento de veículos típicos da frota brasileira. Utilizando técnicas de amostragem e medição inovadoras, foram testados combustíveis com diversos teores de enxofre em veículos leves (ciclo Otto e ciclo Diesel), ciclomotores e motores pesados a diesel. Durante um ano fez-se a coleta de MP ambiental em oito estações de monitoramento, quatro em cada metrópole. Técnicas avançadas de análise foram empregadas para caracterizar o material particulado coletado. Na sequência, foram utilizadas técnicas de estatística multivariada para quantificar a participação de certas tipologias de fontes de poluentes. Os resultados obtidos mostraram que, nos últimos anos, a qualidade do ar não sofreu alteração importante nas metrópoles estudadas, o que pode ser creditado à evolução nas tecnologias veiculares e nos combustíveis, além da renovação da frota. Com relação à contribuição dos combustíveis automotivos na formação do MP 2,5 atmosférico, verificou-se que esta é de cerca de 60% nos dois centros, considerando as emissões diretas e os aerossóis secundários, a maior parte dos quais pode ser atribuída a reações em que participam compostos orgânicos de origem veicular.
The late glacial Federmesser site of Borneck-Ost, Germany : a technological re-analysis of the lithic assemblage using a chaîne opératoire approach

The present study is a technological re-analysis of the late-glacial extant collection from Borneck-Ost, Ahrensburgian tunnel valley, Germany. The site is attributed to the Federmesser culture (12 000 – 10 800 cal BC), and has figured in the Late Glacial research canon because remains of a "spectacle-shaped" tent were identified there (Rust 1958). The focus of this study is to determine if the previous interpretation of Borneck-Ost is reliable according to modern archaeological practice. Using a chaîne opératoire as the methodological framework, the lithic material from the site has been technologically reanalysed. Refitting has supplied additional information. A source-critical perspective on the re-analysis of extant collections is imperative, since these were studied according to a different analytical paradigm. In addition to the procedural aspect of the re-analysis, new information on knapping techniques is discussed. New and revised results and interpretations for the Federmesser site Borneck-Ost will be presented.
Huber SVR-Based Hybrid Models for Significant Wave Height Forecasting Using Buoy Sensors

Ocean buoy sensors stand out as the most reliable means of recording significant wave height (SWH). However, accurate forecasting of SWH is still challenging in energy production. To circumvent such a challenge, this letter introduces a Huber support vector regression (SVR)-based wave hybrid model for short-term SWH forecasting using data collected from the buoy sensors. The model employs three distinct signal techniques, including wavelet decomposition, empirical mode decomposition, and variational mode decomposition, along with particle swarm optimization to fine-tune the parameters of the Huber SVR model. Our extensive experimental analysis encompassed six cases from buoys located at four different geographical regions. We compared the Huber SVR-based wave hybrid models with 12 alternative models incorporating $\epsilon$-SVR, LS-SVR, or long short-term memory network (LSTM) models with different decomposition methods. The results of our numerical experiments demonstrate that the Huber SVR-based wave hybrid models yield superior SWH predictions compared to the other existing models.
Research on quantitative identification of infrared characteristics of progressive failure of bolted roadway surrounding rock

By means of uniaxial loading and thermal infrared imaging technology, this paper makes physical model test on progressive failure of bolted roadway surrounding rock. The results indicate that: (I) before stress peak, the infrared radiation temperature (IRT) on surface of roadway surrounding rock rise non-synchronously, and the IRT on stress concentration and shear fracture areas is higher and intensive than that on stress relaxation and tensile fracture areas; (II) the IRT on various parts of model such as roof, walls, floor and angles, changes nonsynchronously, which can be reflected through the change rate of IRT to identify the progressive failure of roadway surrounding rock; (Ⅲ) two kinds of infrared precursors can be obtained corresponding to the progressive failure areas of roadway surrounding rock respectively. The bolted areas are determined from the change ratios of TIR temperature of the various areas of the bolted surrounding rocks, which provides a theoretical basis for designing parameter of bolt supporting. It is also verified that the thermal infrared imaging technology can be used to study the mechanism of bolt supporting and supervise the stability of roadway surrounding rock.
Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts

Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.
Microtransit in Latin America and the Caribbean: Governance, operations, and regulation for socially inclusive and sustainable urban mobility

This document provides an overview of the current landscape of app-based collective transportation in Latin America and the Caribbean from the perspective of its contributions to social inclusion and environmental sustainability. The research builds on a review of the recent academic literature and a review of available secondary evidence from technical reports and policy documents. The analysis of secondary evidence is expanded upon through primary evidence from a stakeholder survey and semi-structured interviews with a select group of stakeholders in the transportation sector in the region. The manuscript shows the current situation in what remains an emerging industry in Latin America and the Caribbean, spanning from the terminology used by practitioners in different sectors to refer to app-based collective transportation, such as vanpooling, microtransit or micro transport, to the overview of different business approaches and regulatory responses in various contexts. The paper finalizes by presenting an evidence-based reflection of the prospects and expectations from different perspectives about the contribution of technology-enabled collective transportation to social and environmental challenges for transport in the region.
The development of solid food intake in calves. 4. The effect of the addition of material to the rumen, or its removal from the rumen, on voluntary food intake

1. Eight British Friesian male calves were fitted with rumen cannulae at 4 weeks of age, and were given either chopped or pelleted dried grass to appetite. After weaning at 6 weeks the animals were allowed to eat to appetite, or the appropriate food material was added via the cannula, or digesta removed, at the rate of 20 % (dry-matter basis) of voluntary food intake, in alternating periods of 7 days. 2. The addition of food material resulted in a depression in drymatter intake (DMI) which was greater than the increase in DMI following the removal of digesta, and the difference approached significance in the small number of comparisons possible. 3. The response in voluntary food intake increased significantly with age, and reached or exceeded ‘adult’ levels within 6 weeks from weaning. It is postulated that oropharyngeal factors associated with the development of eating behaviour control the initial development of solid food intake; the influences of physical or metabolic limitations upon food intake increase with time.
A mechanism for swarming in the tunicate Salpa thompsoni (Foxton, 1961)

Two populations of Salpa thompsoni, collected from the Weddell–Scotia confluence area at the end of two summers (1994 and 1995) with contrasting densities, are compared. The present study was aimed at corroborating whether fluctuations in abundance could be related to some life history parameters considered as indicators of growth rate in salp populations, such as the body size of solitary reproductive individuals, number of buds per block or chain in the stolon, and the offspring to parent ratio. No differences were observed in the sizes reached by aggregate individuals, or in the size at which oocyte maturity was attained (moment at which the development of the embryo can be detected). There were no differences in the size reached by the embryos during their residence inside the mother's blastozooid. In 1995, the percentage of non-fecundated blastozooids (which included even the largest individuals) was higher than in 1994. The mean size of the solitary individuals was significantly higher in 1994 than in 1995. The number of buds per block was also significantly higher in most of the stages, confirming that this is the mechanism used by these organisms to produce swarms. This species eventually attains high population densities under favorable environmental conditions such as poor sea-ice cover in winter. Under optimal conditions, the number of potential descendants produced by a single solitary individual would exceed 800.
Use of the Subcutaneous Triptorelin Stimulation Test for Diagnosis of Central Precocious Puberty

Background: The gold standard gonadotropin-releasing hormone (GnRH) stimulation test uses the response to intravenously injected gonadorelin to diagnose central precocious puberty (CPP). However, gonadorelin is not always readily available. Objective: This study investigated the diagnostic efficacy of the subcutaneous triptorelin test and the optimal blood sampling time for diagnosis of CPP. Methods: This study retrospectively examined the medical records of 220 girls who had undergone either the triptorelin or gonadorelin test and compared their clinical characteristics. We retrospectively compared clinical parameters between girls diagnosed with CPP (n = 111) and idiopathic premature thelarche (IPT) (n = 109) using three different diagnostic methods: the gonadorelin, triptorelin 120 min, and triptorelin 180 min tests. The diagnostic ability of the stimulated luteinizing hormone (LH) concentration in the triptorelin test for CPP was evaluated using receiver operating characteristic (ROC) analysis. Results: The CPP group exhibited higher basal and peak gonadotropin levels, more advanced bone age, and a lower body mass index standard deviation score than the IPT group. In the gonadorelin test group, all girls with CPP exhibited a peak LH response 30–60 min after intravenous gonadorelin injection. In the triptorelin test group, most girls with CPP exhibited a peak LH response 60–180 min after subcutaneous triptorelin injection (n = 68). On the ROC curve, a peak LH concentration of ≥ 4.52 IU/L at 120 min had the highest CPP diagnostic accuracy, with sensitivity and specificity of 100% and 95.83%, respectively.
Exploring Internet Use, Problematic Behavior, and Their Impact on Mental Health: A Comprehensive Review

This literature review examines the relationship between internet usage, problematic online behaviors, and their impact on the mental health of young adults and adolescents. As the internet and digital technologies become integral to daily life, concerns have grown regarding the consequences of excessive internet use, particularly problematic internet use (PIU). The review starts by systematically assessing the increasing prevalence of internet use among young individuals, emphasizing the need to differentiate regular usage from PIU. It also explores problematic smartphone use and its connection to psychopathology, especially anxiety and depression, which share characteristics with behavioral addiction. Furthermore, the review investigates longitudinal trends in internet use and trust levels among American adults and late adolescents from 1972 to 2012. It reveals a significant decline in trust and confidence, potentially associated with increased internet use. The review also examines the prevalence of Internet Gaming Disorder (IGD) and its co-occurrence with depression, offering insights into the diagnostic criteria for IGD. In summary, this comprehensive literature review underscores the need for further research to understand the evolving dynamics and develop effective interventions related to internet use. It emphasizes the bidirectional relationship between internet use and mental health and highlights the relevance of diminishing trust and confidence. These considerations are vital for shaping strategies to promote mental well-being in the digital age.