Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome

Sugarcane contributes 80% of global sugar production and to bioethanol generation for the bioenergy industry. Its productivity is threatened by drought that can cause up to 60% yield loss. This study used RNA-Seq to gain a better understanding of the underlying mechanism by which drought-tolerant sugarcane copes with water stress. We compared gene expression in KPS01-12 (drought-tolerant genotype) and UT12 (drought-sensitive genotype) that have significantly different yield loss rates under drought conditions. We treated KPS01-12 and UT12 with mild and moderate water stress and found differentially expressed genes in various biological processes. KPS01-12 had higher expression of genes that were involved in water retention, antioxidant secondary metabolite biosynthesis, and oxidative and osmotic stress response than UT12. In contrast, the sensitive genotype had more down-regulated genes that were involved in photosynthesis, carbon fixation and Calvin cycle than the tolerant genotype. Our obtained expression profiles suggest that the tolerant sugarcane has a more effective genetic response than the sensitive genotype at the initiation of drought stress. The knowledge gained from this study may be applied in breeding programs to improve sugarcane production in drought conditions.
Impact of Protein Intake on Protein Metabolism and Exercise Performance in Endurance-Trained Males

Background: Current recommendations for athletes consider dietary protein requirements that maintain nitrogen (i.e. protein) balance rather than an optimal dosage to enhance metabolism and exercise performance. Purpose: The primary objective of this study was to determine how differing protein intakes alter protein metabolism and exercise performance. Methods: Using a double blind randomized crossover design, 10 male runners completed 3 trials involving 4 days of controlled training and ingestion of either 0.94 (LOW), 1.20 (MOD) or 1.83 g protein/kg body weight/d (HIGH). Whole body protein metabolism and exercise performance were assessed. Results: Whole body net protein balance displayed a relative dose-response (HIGH > MOD > LOW, P < 0.05). Inferential statistics revealed that 1.83 g protein/kg provides notable benefits in exercise performance compared to intakes of 0.94 g/kg or 1.2 g/kg. Conclusion: These data suggest that consuming protein towards the high end of recommendations (1.2-2g/kg) better maintains metabolism and exercise performance.
Isfahan as a destination for promoting historical nostalgia tourism with an emphasis on World War II memories

ABSTRACT World War II lasted from 1939 to1945 and affected most of the world, creating memories for places and people everywhere. This research focuses on Isfahan, Iran, as a case study comprising World War II memories with an emphasis on Polish children. This research has three major purposes: (1) to ascertain the attraction of historical nostalgia tourism with an emphasis on the footprint of Polish children; (2) to consider the activities and strategies which can promote nostalgia tourism in Isfahan and (3) to measure tourists’ tendency towards visiting attractions based around Polish refugees in the study area. The results demonstrate that Isfahan has some monuments and trails which include Polish children’s memories and can be regarded as tourist attractions for this niche tourism. Moreover, the results recommend organizing thematic tours regarding Poland and Isfahan and training tour leaders in this regard. Integrating historical nostalgia tourism with other niche tourism, organizing events and scientific meetings, boosting marketing and advertising regarding historical nostalgia tourism and policymaking for promoting historical nostalgia tourism in Isfahan are strategies and activities which can promote this type of tourism in Isfahan. Furthermore, our results illustrate that tourists are interested in attractions based around Polish refugees.
Age of the Sääksjärvi impact structure, Finland: reconciling the timing of small impacts in crystalline basement with regional basin development

We report a new age for the Sääksjärvi impact structure, Finland, a 6 km diameter feature that formed in crystalline rocks of the Precambrian Baltic Shield. Two previous studies reported 40Ar/39Ar data for Sääksjärvi and suggested conflicting formation ages of ≤330 Ma or c. 560 Ma. The former age represents a possible complication for models which indicate that the region was covered by sediments of the Caledonian foreland basin throughout much of the Phanerozoic. We conducted a study combining imaging, microstructural analysis and U–Pb dating of shocked zircon from Sääksjärvi. The U–Pb dataset indicates a c. 600 Ma impact into predominantly c. 1850 Ma target rocks. A concordia age of 608 ± 8 Ma (2σ) confirms Sääksjärvi as the first known Ediacaran impact structure in the Baltic Shield and only the second worldwide. Our data indicate that the Sääksjärvi impact structure formed in exposed crystalline basement rocks of the Baltic Shield prior to the development of the Caledonian foreland basin. Given that most impact structures on Earth are relatively small features, radiometric dating of small impact structures in crystalline basement may place boundaries on the timing and spatial extent of palaeobasins that might otherwise be difficult to constrain. Supplementary material: Additional imaging and microstructural analysis of zircon, additional concordia plots, and U–Pb data tables are available at https://doi.org/10.6084/m9.figshare. c.5043462
Can alternating temperature, moist chilling and gibberellin interchangeably promote the completion of germination of Clematis vitalba seeds?

Each plant species has particular requirements for seed germination, and some of them respond differently to constant or alternating temperature regimes. In this study, the interchangeable effects of different treatments and temperatures on the completion of seed germination of Clematis vitalba L. were investigated. The seeds were tested with a constant (from 5 °C to 25 °C) or a fluctuating (25/10 °C) temperature regime, and the effect of gibberellic acid (GA3), incubation at warm (W) or cold (C) temperatures while being imbibed, and drying after ripening (DAR) were evaluated. The final germination percentages and the time in days required to reach 50% of germination (T50) were calculated. GA3 and C significantly enhanced completion of seed germination at all of the temperatures tested. A strong positive effect of alternating temperature was observed, which triggered completion of seed germination regardless of treatment. Under the fluctuating temperature, the chilled seeds had the most rapid germination.
Comprehensive analysis of mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method called Split Read Insertion Detection (SRID) that enables the identification of the exact mobilizable unit of MGEs. Leveraging the SRID method, we curated a database of 5600 putative MGEs encompassing seven MGE classes called ImmeDB (Intestinal microbiome mobile element database) (https://immedb.mit.edu/). We observed that many MGEs carry genes that confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Additionally, we observed that horizontal transfer of MGEs is extensive within phyla but rare across phyla. Taken together, our findings support a phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future fundamental and translational studies on the gut microbiome and MGE communities.
3D Reverse Geometrical Modeling and Building Information Modeling of Historic Buildings

Historic buildings combining functional, historic, scientific, art and social values, deserve scientific conservation. Thus, it is of significance to establish the information archiving. This paper mainly focuses on 3D reverse modeling and building information modeling of historic buildings, laying a foundation for digital archiving and life-cycle maintenance management. According to the conservation requirements and data characteristics for different parts of historic buildings, three-dimensional laser scanning, UAV aerial photography and close-range photography are selected to acquire point cloud model. And then, the 3D geometric model of a historical building can be created by 3DS Max and Geomagic, and integrated in 3DS Max. In order to solve the problem of poor generality and large amount of data of geometric model created by reverse modeling technology, an efficient way to transform geometric model to BIM is proposed. Components are automatically identified and classified according to their characteristics with Maxscript language, and the geometric information of components is imported into text files according to the syntax of component's creation in Revit API. Then, a program called Revit API was developed to read the text files and to fulfill data com-pression through parameter analysis of components in historical buildings, and the 3D geometrical model of the historical building was automatically trans-formed into a building information model, which can integrate many types of information such as history, structure and materials. Finally, taking Shanghai Jade Buddha Temple as an example to verify the validity of the above procedure. Its BIM model is successfully generated and has been developed into a 4D model by integrating the past repair and rehabilitation information.
Earthquake-Resistant Design Principles of the Traditional House in Lombok Island

Indonesia lies above one of the active three tectonic plates on earth, which causes earthquake disasters frequently. In 2018 the island of Lombok was hit by a 7.0 Richter Scale earthquake creating major destruction of buildings. While most of the modern building construction damaged when hit the waves, some of the traditional houses in the Segenter region remained steady and safe from the disaster. This study examines the structural and construction system of some traditional houses safe from the waves in Lombok. It focuses on the views of the geometry of building, joint of structure-construction system, as well as building materials applied. Field observation was held to understand the details of constructions. Collected data were analyzed based on earthquake resistance design principles. The outcomes of this study would be beneficial for modern house designs in the future.
Characterization of bioactive compounds from monascus purpureus fermented different cereal substrates

Solid-state fermenting of cereals by Monascus is interesting strategy to produce cereals with more beneficial components. The objective of this study was to determine selected primary and secondary metabolites in cereals (rice, wheat, barley, sorghum, corn, buckwheat) fermented by Monascus purpreus and subsequently compare amount of these compounds with control sample (cereals without Monascus ). In fermented cereals was determined higher protein, fat, reducing sugars, crude fiber and ash content with compare to non-fermented cereals. The antioxidant activity measured by DPPH assay, ABTS assay as well as reducing power assay was also higher in fermented Monascus cereals with the best results in rice (3.09 ±0.02; 62.9 ±2.24; 43.19 ±2.07 mg TEAC per g of dry weight). Sample of fermented rice contained the highest level of total polyphenols (15.31 ±3.62 mg GAE per g of dry weight), total flavonoids (1.65 mg QE per g of dry weight) and total phenolic acids (9.47 ±0.56 mg CAE per g of dry weight). In fermented cereals was also determined higher contact of reducing sugars (highest value in rice 246.97 ±7.96 mg GE per g), proteins (highest value in buckwheat 28.47 ±1.24%), ash (highest value in sorghum 2.74 ±0.08%) and fat (highest value in corn 4.89 ±0.03%) with compare to non-fermented samples. Results of crude fiber content of both - fermented and non-fermented cereals were balanced with similar values. Results of this study shown that Monascus purpureus fermented cereal substrates might be a potential sources of several bioactive compounds in food products.
Synthetic Regulation of Eukaryotic Gene Expression by Noncoding RNA

Synthetic biological systems promise to combine the spectacular diversity of biological functionality with engineering principles to design new life to address many pressing needs. As these engineered systems advance in sophistication, there is ever-greater need for customizable, situation-specific expression of desired genes. However, existing gene control platforms are generally not modular, or do not display performance requirements required for robust phenotypic responses to input signals. This work expands the capabilities of eukaryotic gene control in two important directions. For development of greater modularity, we extend the use of synthetic self-cleaving ribozyme switches to detect changes in input protein levels and convey that information into programmed gene expression in eukaryotic cells. We demonstrate both up- and down-regulation of levels of an output transgene by more than 4-fold in response to rising input protein levels, with maximal output gene expression approaching the highest levels observed in yeast. In vitro experiments demonstrate protein-dependent ribozyme activity modulation. We further demonstrate the platform in mammalian cells. Our switch devices do not depend on special input protein activity, and can be tailored to respond to any input protein to which a suitable RNA aptamer can be developed. This platform can potentially be employed to regulate the expression of any transgene or any endogenous gene by 3’ UTR replacement, allowing for more complex cell state-specific reprogramming. We also address an important concern with ribozyme switches, and riboswitch performance in general, their dynamic range. While riboswitches have generally allowed for versatile and modular regulation, so far their dynamic ranges of output gene modulation have been modest, generally at most 10-fold. We address this shortcoming by developing a modular genetic amplifier for near-digital control of eukaryotic gene expression. We combine ribozyme switch-mediated regulation of a synthetic TF with TF-mediated regulation of an output gene. The amplifier platform allows for as much as 20-fold regulation of output gene expression in response to input signal, with maximal expression approaching the highest levels observed in yeast, yet being tunable to intermediate and lower expression levels. EC50 values are more than 4 times lower than in previously best-performing non-amplifier ribozyme switches. The system design retains the modular-input architecture of the ribozyme switch platform, and the near-digital dynamic ranges of TF-based gene control. Together, these developments suggest great potential for the wide applicability of these platforms for better-performing eukaryotic gene regulation, and more sophisticated, customizable reprogramming of cellular activity.
In-GPU Cache for Acceleration of Anomaly Detection in Blockchain

SUMMARY Blockchain is a distributed ledger system composed of a P2P network and is used for a wide range of applications, such as international remittance, inter-individual transactions, and asset conservation. In Blockchain systems, tamper resistance is enhanced by the property of transaction that cannot be changed or deleted by everyone including the creator of the transaction. However, this property also becomes a problem that unintended transaction created by miss operation or secret key theft cannot be corrected later. Due to this problem, once an illegal transaction such as theft occurs, the damage will expand. To suppress the damage, we need countermeasures, such as detecting illegal transaction at high speed and correcting the transaction before approval. However, anomaly detection in the Blockchain at high speed is computationally heavy, because we need to repeat the detection process using various feature quantities and the feature extractions become overhead. In this paper, to accelerate anomaly detection, we propose to cache transaction information necessary for extracting feature in GPU device memory and perform both feature extraction and anomaly detection in the GPU. We also propose a conditional feature extraction method to reduce computation cost of anomaly detection. We employ anomaly detection using K-means algorithm based on the conditional features. When the number of users is one million and the number of transactions is 100 millions, our proposed method achieves 8.6 times faster than CPU processing method and 2.6 times faster than GPU processing method that does not perform feature extraction on the GPU. In addition, the conditional feature extraction method achieves 1.7 times faster than the unconditional method when the number of users satisfying a given condition is 200 thousands out of one million.
Investigation and Assessment of the Management of Natural Resources in the State of California Using the Conceptual Framework of Water–Energy–Food Nexus

The current analysis attempts to quantify the interlinkages between the water, energy and food sectors of California covering the period 2002–2015. The results reveal that 25% (60,696 GWh) of the annual energy consumption is attributed to agriculture, while 75% (174,709 GWh) is used for water supply purposes. The agricultural sector consumes 77% (32,629 m3) of the irrigation water, and the energy sector is vulnerable to water availability fluctuations, because many hydroelectric facilities are connected to its grid. Considering the water scarcity and the uneven geographical distribution of water in the state, its central role in California’s water–energy–food (WEF) Nexus becomes apparent.
Empirical and conditional likelihoods for two‐phase studies

Two‐phase, response‐dependent sampling is often used in regression settings that involve expensive covariate measurements. Conditional maximum likelihood (CML) is an attractive approach in many cases as it avoids modelling of the covariate distribution, unlike full maximum likelihood. Scott & Wild (2011) introduced an augmented CML approach which is semi‐parametric efficient in certain settings with a discrete response variable. We consider general regression models and show the Scott–Wild estimator of covariate effects has the same asymptotic efficiency as two empirical likelihood estimators, and that these estimators dominate the CML estimator. We compare the efficiencies of various estimators in simulation studies and illustrate the methodology in a two‐phase genetics study.
Innovative Energy Clusters' Infrastructure

Purpose: The purpose of the study is to develop recommendations for the creation of systemic, open, interactive data on innovative energy clusters, allowing cluster managers to build inter-cluster relationships, to assess the impact of clusters on economic development. Design/Methodology/Approach: The methodology is based on the conceptual provisions of the works of foreign and Russian scientists on the research topic. Using the methods of grouping and comparative analysis of statistical data, we analyzed the volume of electricity production and production of alternative energy in calculation on one inhabitant of the leading energy powers in the world. We also conducted a comparative analysis of databases Clustered Russia map, Cluster map of the US and European cluster maps, were studied the dynamics of the development of innovative energy clusters. Data are from the Global Energy Statistical Yearbook, government statistics, data of the Russian Cluster Observatory, the US Cluster Mapping and the European Cluster Observatory. Findings: Innovative energy clusters are mainly created on the basis of large generating and transmission energy companies. These clusters specialize in the production of bioenergy, introduce energy-saving technologies, increase energy efficiency, diversify the national energy system, and ensure the economic growth of the territories. The development of innovative energy clusters depends on the solution of a number of problems. In the study it has formulated the following ways of solving problems. Creation of an interactive cluster map that accumulates a complete database of cluster entities. Clarification of specialization groups of Russian clusters used in the course of cluster mapping, taking into account comparable groups of specializations of American and European clusters. Development of recommendations for the creation of an interactive resource of systemic, open, data on cluster formations. Practical Implications: The results and recommendations are addressed to developers of regional cluster policy, strategic planning documents, and cluster managers, and can also be used in the process of creating an interactive cluster map of Russia. Originality/Value: Recommendations were developed for the development of innovative energy clusters that ensure an increase in bioenergy production and economic growth.
Biochemical Effects of Dichlorvos Pesticide on the Liver of Poultry Birds ( Gallus domestica )

Continuous use of pesticides can pose severe health hazards to humans and animals. Dichlorvos (DDVP) is widely used as an insecticide to control household pests, in public health, protecting stored product from insects and control of parasites in livestock. The objective of this study is to determine the effect of dichlorvos on biochemical parameters of the liver of poultry birds. Seven weeks old poultry birds (pullets) were fed on commercial poultry feed contaminated with 0.01, 0.02 and 0.04% dichlorvos (w/v). The control group has no pesticide added to their feed. The birds were sacrificed after 10 weeks of exposure and the liver removed. Analysis of the liver homogenates revealed a significant (p 0.05) in the levels of triglyceride in the cytoplasm of the liver between the control and the birds exposed to pesticide. However, there was a significant reduction (p < 0.05) in the concentration of membrane bound triglyceride from 4.65 ± 0.023 mg/g tissue to 2.81 ± 0.015 mg/g tissue in the birds exposed to 0.04% pesticide. There was a significant increase in serum protein and lipid peroxidation; significant reduction (p<0.05) in serum glutathione and glutathione s-transferase activity at 0.04% pesticide contamination as against the control. The above results show that biochemical parameters can be used as indicators of pesticide exposure in poultry birds.
Calculation of Any M+ Value in Mass Spectrometry

This paper discusses our “Dry Lab” experiment where students are shown the procedure for calculating the nominal and precise M+ values of a compound. However, our main focus deals with the detailed step-by-step process for calculating the precise M+1 and M+2 values of a compound, as well as any of its higher order M+ values, when its molecular formula is known.